diff options
| author | Andrej Shadura <andrewsh@debian.org> | 2019-03-09 22:30:46 +0000 |
|---|---|---|
| committer | Andrej Shadura <andrewsh@debian.org> | 2019-03-09 22:30:46 +0000 |
| commit | 0a055548ae9f9d5c639bb29ca32e0fd88de37c1d (patch) | |
| tree | 3bd93fd4bb0ae6025a6fcfadeb7844669fea457c | |
| parent | 38212b3127e90751fb39cda34250bc11be62b76c (diff) | |
Import Upstream version 0.7.1
2117 files changed, 11828 insertions, 2122 deletions
diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 00000000..1f121057 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,5 @@ +language: java +install: mvn -Psvg,tutorial,svm -DskipTests=true -Dmaven.javadoc.skip=true -B -V clean install +script: mvn -Pcodecov -DskipTests=false -Dmaven.javadoc.skip=true -B -V test +before_install: pip install --user codecov +after_success: codecov @@ -1,5 +1,8 @@ # ELKI ##### Environment for Developing KDD-Applications Supported by Index-Structures +[](http://dblp.uni-trier.de/rec/bibtex/journals/pvldb/SchubertKEZSZ15) +[](http://elki.dbs.ifi.lmu.de/wiki/License) +[](https://travis-ci.org/elki-project/elki) ## Quick Summary ELKI is an open source (AGPLv3) data mining software written in Java. The focus of ELKI is research in algorithms, with an emphasis on unsupervised methods in cluster analysis and outlier detection. diff --git a/addons/3dpc/pom.xml b/addons/3dpc/pom.xml index 609e2fe8..db42809c 100644 --- a/addons/3dpc/pom.xml +++ b/addons/3dpc/pom.xml @@ -1,10 +1,11 @@ +<?xml version='1.0' encoding='UTF-8'?> <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> <modelVersion>4.0.0</modelVersion> <parent> <groupId>de.lmu.ifi.dbs.elki</groupId> - <version>0.7.0</version> + <version>0.7.1</version> <artifactId>elki-project</artifactId> <relativePath>../../</relativePath> </parent> @@ -25,27 +26,6 @@ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> </properties> - <build> - <plugins> - <!-- javadoc --> - <plugin> - <groupId>org.apache.maven.plugins</groupId> - <artifactId>maven-javadoc-plugin</artifactId> - <version>2.9.1</version> - <configuration> - </configuration> - </plugin> - <!-- jar packaging --> - <plugin> - <groupId>org.apache.maven.plugins</groupId> - <artifactId>maven-jar-plugin</artifactId> - <version>2.3.1</version> - <configuration> - </configuration> - </plugin> - </plugins> - </build> - <dependencies> <dependency> <groupId>de.lmu.ifi.dbs.elki</groupId> diff --git a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/OpenGL3DParallelCoordinates.java b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/OpenGL3DParallelCoordinates.java index 966ead1c..410f1dbb 100644 --- a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/OpenGL3DParallelCoordinates.java +++ b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/OpenGL3DParallelCoordinates.java @@ -106,6 +106,7 @@ import de.lmu.ifi.dbs.elki.visualization.style.StylingPolicy; * FIXME: proper depth-sorting of edges. It's not that simple, unfortunately. * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Object type */ diff --git a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/Parallel3DRenderer.java b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/Parallel3DRenderer.java index d313dc57..fe0e4796 100644 --- a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/Parallel3DRenderer.java +++ b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/Parallel3DRenderer.java @@ -77,6 +77,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; * TODO: generalize to non-numeric features and scales. * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Object type */ diff --git a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/AbstractLayout3DPC.java b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/AbstractLayout3DPC.java index a5190091..b5c5ffa5 100644 --- a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/AbstractLayout3DPC.java +++ b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/AbstractLayout3DPC.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.visualization.parallel3d.layout.Layout.Edge; * Abstract class for dimension similarity based layouters. * * @author Erich Schubert + * @since 0.6.0 */ public abstract class AbstractLayout3DPC<N extends Layout.Node> implements SimilarityBasedLayouter3DPC<NumberVector> { /** diff --git a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/CompactCircularMSTLayout3DPC.java b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/CompactCircularMSTLayout3DPC.java index bb85b152..d2377e7f 100644 --- a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/CompactCircularMSTLayout3DPC.java +++ b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/CompactCircularMSTLayout3DPC.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "Elke Achtert, Hans-Peter Kriegel, Erich Schubert, Arthur Zimek", title = "Interactive Data Mining with 3D-Parallel-Coordinate-Trees", booktitle = "Proc. of the 2013 ACM International Conference on Management of Data (SIGMOD)", url = "http://dx.doi.org/10.1145/2463676.2463696") public class CompactCircularMSTLayout3DPC extends AbstractLayout3DPC<CompactCircularMSTLayout3DPC.Node> { diff --git a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/Layout.java b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/Layout.java index 152f028b..42b16ee5 100644 --- a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/Layout.java +++ b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/Layout.java @@ -29,6 +29,7 @@ import java.util.List; * Layout class. * * @author Erich Schubert + * @since 0.6.0 */ public class Layout { /** diff --git a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/Layouter3DPC.java b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/Layouter3DPC.java index 7fe50320..5516d01a 100644 --- a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/Layouter3DPC.java +++ b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/Layouter3DPC.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * Arrange parallel coordinates on a 2D plane, for 3D parallel coordinates. * * @author Erich Schubert + * @since 0.6.0 * * @param <V> Object type */ diff --git a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/MultidimensionalScalingMSTLayout3DPC.java b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/MultidimensionalScalingMSTLayout3DPC.java index 95aaa99e..825fc3ac 100644 --- a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/MultidimensionalScalingMSTLayout3DPC.java +++ b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/MultidimensionalScalingMSTLayout3DPC.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "Elke Achtert, Hans-Peter Kriegel, Erich Schubert, Arthur Zimek", title = "Interactive Data Mining with 3D-Parallel-Coordinate-Trees", booktitle = "Proc. of the 2013 ACM International Conference on Management of Data (SIGMOD)", url = "http://dx.doi.org/10.1145/2463676.2463696") public class MultidimensionalScalingMSTLayout3DPC extends AbstractLayout3DPC<MultidimensionalScalingMSTLayout3DPC.Node> { diff --git a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/SimilarityBasedLayouter3DPC.java b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/SimilarityBasedLayouter3DPC.java index c69a4837..d6620dd9 100644 --- a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/SimilarityBasedLayouter3DPC.java +++ b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/SimilarityBasedLayouter3DPC.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; * Similarity based layouting algorithms. * * @author Erich Schubert + * @since 0.6.0 * * @param <V> Data type */ diff --git a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/SimpleCircularMSTLayout3DPC.java b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/SimpleCircularMSTLayout3DPC.java index accf9547..e293ad0d 100644 --- a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/SimpleCircularMSTLayout3DPC.java +++ b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/SimpleCircularMSTLayout3DPC.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "Elke Achtert, Hans-Peter Kriegel, Erich Schubert, Arthur Zimek", title = "Interactive Data Mining with 3D-Parallel-Coordinate-Trees", booktitle = "Proc. of the 2013 ACM International Conference on Management of Data (SIGMOD)", url = "http://dx.doi.org/10.1145/2463676.2463696") public class SimpleCircularMSTLayout3DPC extends AbstractLayout3DPC<SimpleCircularMSTLayout3DPC.Node> { diff --git a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/AbstractSimpleOverlay.java b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/AbstractSimpleOverlay.java index 43e43f31..d747851a 100644 --- a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/AbstractSimpleOverlay.java +++ b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/AbstractSimpleOverlay.java @@ -31,6 +31,7 @@ import javax.media.opengl.GL2; * TODO: make color configurable? * * @author Erich Schubert + * @since 0.6.0 */ public abstract class AbstractSimpleOverlay { /** diff --git a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/Arcball1DOFAdapter.java b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/Arcball1DOFAdapter.java index a24e63c7..862eab04 100644 --- a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/Arcball1DOFAdapter.java +++ b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/Arcball1DOFAdapter.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.VMath; * Arcball style helper. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses Simple1DOFCamera */ diff --git a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/Simple1DOFCamera.java b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/Simple1DOFCamera.java index c0d33be1..c4b538cd 100644 --- a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/Simple1DOFCamera.java +++ b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/Simple1DOFCamera.java @@ -38,6 +38,7 @@ import javax.media.opengl.glu.GLU; * view will have the usual X/Y plane on the ground. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses CameraListener */ diff --git a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/SimpleMenuOverlay.java b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/SimpleMenuOverlay.java index 9cd55198..8f136606 100644 --- a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/SimpleMenuOverlay.java +++ b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/SimpleMenuOverlay.java @@ -39,6 +39,7 @@ import com.jogamp.opengl.util.awt.TextRenderer; * TODO: Hover effects? * * @author Erich Schubert + * @since 0.6.0 */ public abstract class SimpleMenuOverlay extends AbstractSimpleOverlay implements MouseListener { /** diff --git a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/SimpleMessageOverlay.java b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/SimpleMessageOverlay.java index fc8f916d..5e808f51 100644 --- a/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/SimpleMessageOverlay.java +++ b/addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/util/SimpleMessageOverlay.java @@ -34,6 +34,7 @@ import com.jogamp.opengl.util.awt.TextRenderer; * Simple menu overlay. * * @author Erich Schubert + * @since 0.6.0 */ public class SimpleMessageOverlay extends AbstractSimpleOverlay { /** diff --git a/addons/batikvis/pom.xml b/addons/batikvis/pom.xml index 4b892ab0..53c298fb 100644 --- a/addons/batikvis/pom.xml +++ b/addons/batikvis/pom.xml @@ -1,10 +1,11 @@ +<?xml version='1.0' encoding='UTF-8'?> <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> <modelVersion>4.0.0</modelVersion> <parent> <groupId>de.lmu.ifi.dbs.elki</groupId> - <version>0.7.0</version> + <version>0.7.1</version> <artifactId>elki-project</artifactId> <relativePath>../../</relativePath> </parent> @@ -29,9 +30,7 @@ <plugins> <!-- jar packaging --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-jar-plugin</artifactId> - <version>2.3.1</version> <configuration> <archive> <manifestFile>${elki.projdir}/elki/src/main/resources/META-INF/MANIFEST.MF</manifestFile> @@ -45,7 +44,6 @@ </plugin> <!-- Ensure the directory exists, for code below. --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-antrun-plugin</artifactId> <executions> <execution> @@ -66,7 +64,6 @@ <plugin> <groupId>org.codehaus.mojo</groupId> <artifactId>exec-maven-plugin</artifactId> - <version>1.3.2</version> <executions> <execution> <id>generate-javadoc-parameters</id> @@ -130,6 +127,11 @@ <dependency> <groupId>org.apache.xmlgraphics</groupId> + <artifactId>batik-codec</artifactId> + </dependency> + + <dependency> + <groupId>org.apache.xmlgraphics</groupId> <artifactId>xmlgraphics-commons</artifactId> </dependency> diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/VisualizePairwiseGainMatrix.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/VisualizePairwiseGainMatrix.java index 28435915..dce3eef1 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/VisualizePairwiseGainMatrix.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/VisualizePairwiseGainMatrix.java @@ -86,6 +86,7 @@ import de.lmu.ifi.dbs.elki.workflow.InputStep; * </p> * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.composedOf VisualizerParameterizer * @apiviz.composedOf SimilarityMatrixVisualizer diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/ResultVisualizer.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/result/AutomaticVisualization.java index 64ddfaa3..2c9ec8ef 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/ResultVisualizer.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/result/AutomaticVisualization.java @@ -1,10 +1,10 @@ -package de.lmu.ifi.dbs.elki.visualization.gui; +package de.lmu.ifi.dbs.elki.result; /* This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures - Copyright (C) 2015 + Copyright (C) 2016 Ludwig-Maximilians-Universität München Lehr- und Forschungseinheit für Datenbanksysteme ELKI Development Team @@ -39,22 +39,24 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.StringParameter; import de.lmu.ifi.dbs.elki.visualization.VisualizerContext; import de.lmu.ifi.dbs.elki.visualization.VisualizerParameterizer; +import de.lmu.ifi.dbs.elki.visualization.gui.ResultWindow; /** * Handler to process and visualize a Result. * * @author Erich Schubert * @author Remigius Wojdanowski + * @since 0.3 * * @apiviz.composedOf VisualizerParameterizer * @apiviz.uses ResultWindow oneway */ -@Alias({ "visualizer", "vis", "ResultVisualizer" }) -public class ResultVisualizer implements ResultHandler { +@Alias({ "visualizer", "vis", "ResultVisualizer", "de.lmu.ifi.dbs.elki.visualization.gui.ResultVisualizer" }) +public class AutomaticVisualization implements ResultHandler { /** * Get a logger for this class. */ - private static final Logging LOG = Logging.getLogger(ResultVisualizer.class); + private static final Logging LOG = Logging.getLogger(AutomaticVisualization.class); /** * Stores the set title. @@ -88,7 +90,7 @@ public class ResultVisualizer implements ResultHandler { * @param manager Parameterization manager for visualizers * @param single Flag to indicat single-view mode. */ - public ResultVisualizer(String title, VisualizerParameterizer manager, boolean single) { + public AutomaticVisualization(String title, VisualizerParameterizer manager, boolean single) { super(); this.title = title; this.manager = manager; @@ -183,8 +185,8 @@ public class ResultVisualizer implements ResultHandler { } @Override - protected ResultVisualizer makeInstance() { - return new ResultVisualizer(title, manager, single); + protected AutomaticVisualization makeInstance() { + return new AutomaticVisualization(title, manager, single); } } } diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/ExportVisualizations.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/result/ExportVisualizations.java index bf552880..150d384f 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/ExportVisualizations.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/result/ExportVisualizations.java @@ -1,4 +1,4 @@ -package de.lmu.ifi.dbs.elki.visualization; +package de.lmu.ifi.dbs.elki.result; /* This file is part of ELKI: @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.result.Result; import de.lmu.ifi.dbs.elki.result.ResultHandler; import de.lmu.ifi.dbs.elki.result.ResultHierarchy; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.datastructures.hierarchy.Hierarchy; import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; @@ -44,6 +45,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter.FileType; +import de.lmu.ifi.dbs.elki.visualization.VisualizationTask; +import de.lmu.ifi.dbs.elki.visualization.VisualizerContext; +import de.lmu.ifi.dbs.elki.visualization.VisualizerParameterizer; import de.lmu.ifi.dbs.elki.visualization.gui.VisualizationPlot; import de.lmu.ifi.dbs.elki.visualization.gui.overview.PlotItem; import de.lmu.ifi.dbs.elki.visualization.projector.Projector; @@ -56,9 +60,11 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * visualizers to run. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.composedOf VisualizerParameterizer */ +@Alias("de.lmu.ifi.dbs.elki.visualization.ExportVisualizations") public class ExportVisualizations implements ResultHandler { /** * Get a logger for this class. @@ -212,7 +218,7 @@ public class ExportVisualizations implements ResultHandler { String prefix = null; prefix = (prefix == null && item.proj != null) ? item.proj.getMenuName() : prefix; - prefix = (prefix == null && item.tasks.size() > 0) ? item.tasks.get(0).name : prefix; + prefix = (prefix == null && item.tasks.size() > 0) ? item.tasks.get(0).getMenuName() : prefix; prefix = (prefix != null ? prefix : "plot"); // TODO: generate names... Integer count = counter.get(prefix); diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationItem.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationItem.java index 3f6c6f19..d1606839 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationItem.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationItem.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.visualization; * of improving type safety. * * @author Erich Schubert + * @since 0.6.0 */ public interface VisualizationItem { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationListener.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationListener.java index 4a8b3f03..5dec07ad 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationListener.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationListener.java @@ -29,6 +29,7 @@ import java.util.EventListener; * Listener for visualization events. * * @author Erich Schubert + * @since 0.4.0 */ public interface VisualizationListener extends EventListener { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationMenuAction.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationMenuAction.java index f16a208e..b0f8b777 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationMenuAction.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationMenuAction.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.visualization; * Visualizer actions. * * @author Erich Schubert + * @since 0.6.0 */ public interface VisualizationMenuAction extends VisualizationItem { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationMenuToggle.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationMenuToggle.java index ad0ec9b3..ade01e26 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationMenuToggle.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationMenuToggle.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.visualization; * Toggle action. * * @author Erich Schubert + * @since 0.4.0 */ public interface VisualizationMenuToggle extends VisualizationItem { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationProcessor.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationProcessor.java index 70271c1a..e1f7a9bc 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationProcessor.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationProcessor.java @@ -26,6 +26,7 @@ package de.lmu.ifi.dbs.elki.visualization; * Visualization processor * * @author Erich Schubert + * @since 0.4.0 */ public interface VisualizationProcessor { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationTask.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationTask.java index 7be18864..a90a9765 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationTask.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationTask.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.VisFactory; * Container class, with ugly casts to reduce generics crazyness. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.has VisualizerContext diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationTree.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationTree.java index 8e76716c..ed45e397 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationTree.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizationTree.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.hierarchy.StackedIter; * Tree - actually a forest - to manage visualizations. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has Handler1 * @apiviz.has Handler2 diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizerContext.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizerContext.java index 8d288ce6..98f77e89 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizerContext.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizerContext.java @@ -55,6 +55,7 @@ import de.lmu.ifi.dbs.elki.visualization.style.StylingPolicy; * that should to be shared among plots, such as line colors, styles etc. * * @author Erich Schubert + * @since 0.3 * * @apiviz.landmark * @apiviz.composedOf StyleLibrary diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizerParameterizer.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizerParameterizer.java index df3d99de..f3242059 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizerParameterizer.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizerParameterizer.java @@ -69,6 +69,7 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * * @author Erich Schubert * @author Remigius Wojdanowski + * @since 0.3 * * @apiviz.landmark * @apiviz.has VisualizerContext oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/AddCSSClass.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/AddCSSClass.java index e32d84a3..b1d4c103 100755 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/AddCSSClass.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/AddCSSClass.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; * Add a CSS class to the event target. * * @author Erich Schubert + * @since 0.2 * */ public class AddCSSClass implements EventListener { diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/AttributeModifier.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/AttributeModifier.java index 21409018..30afdf7e 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/AttributeModifier.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/AttributeModifier.java @@ -29,6 +29,7 @@ import org.w3c.dom.Element; * Runnable wrapper for modifying XML-Attributes. * * @author Remigius Wojdanowski + * @since 0.3 * */ // FIXME: Unused? Remove? diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/BatikUtil.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/BatikUtil.java index 44eb38d6..de1857a2 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/BatikUtil.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/BatikUtil.java @@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.visualization.batikutil; This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures - Copyright (C) 2015 + Copyright (C) 2016 Ludwig-Maximilians-Universität München Lehr- und Forschungseinheit für Datenbanksysteme ELKI Development Team @@ -33,14 +33,15 @@ import org.w3c.dom.svg.SVGPoint; /** * Batik helper class with static methods. - * + * * @author Erich Schubert + * @since 0.3 */ public final class BatikUtil { /** * Get the relative coordinates of a point within the coordinate system of a * particular SVG Element. - * + * * @param evt Event, needs to be a DOMMouseEvent * @param reference SVG Element the coordinate system is used of * @return Array containing the X and Y values @@ -62,4 +63,21 @@ public final class BatikUtil { } return null; } + + /** + * Test whether FOP were installed (for PDF, PS and EPS output support). + * + * @return {@code true} when FOP is available. + */ + public static boolean hasFOPInstalled() { + try { + Class<?> c1 = Class.forName("org.apache.fop.svg.PDFTranscoder"); + Class<?> c2 = Class.forName("org.apache.fop.render.ps.PSTranscoder"); + Class<?> c3 = Class.forName("org.apache.fop.render.ps.EPSTranscoder"); + return (c1 != null) && (c2 != null) && (c3 != null); + } + catch(ClassNotFoundException e) { + return false; + } + } } diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/CSSHoverClass.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/CSSHoverClass.java index 7140b73f..bdf9bae9 100755 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/CSSHoverClass.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/CSSHoverClass.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; * Do a hover effect using a CSS class. * * @author Erich Schubert + * @since 0.2 * */ public class CSSHoverClass implements EventListener { diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/CloneInlineImages.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/CloneInlineImages.java index 93033f01..154713f9 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/CloneInlineImages.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/CloneInlineImages.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGCloneVisible; * Clone an SVG document, inlining temporary and in-memory linked images. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has ThumbnailRegistryEntry */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/DragableArea.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/DragableArea.java index dc5dd388..b9bb1c4c 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/DragableArea.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/DragableArea.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; * A simple dragable area for Batik. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has DragListener * @apiviz.has Element diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/JSVGSynchronizedCanvas.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/JSVGSynchronizedCanvas.java index 2f9ac431..07a1d157 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/JSVGSynchronizedCanvas.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/JSVGSynchronizedCanvas.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGPlot; * objects. * * @author Erich Schubert + * @since 0.3 * * @apiviz.composedOf JSVGUpdateSynchronizer * @apiviz.has SVGPlot oneway - - displays diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/JSVGUpdateSynchronizer.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/JSVGUpdateSynchronizer.java index 6fe43df1..b043fddd 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/JSVGUpdateSynchronizer.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/JSVGUpdateSynchronizer.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.UpdateSynchronizer; * This class is used to synchronize SVG updates with an JSVG canvas. * * @author Erich Schubert + * @since 0.3 * * @apiviz.uses UpdateRunner */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/LazyCanvasResizer.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/LazyCanvasResizer.java index c180d329..98c7192c 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/LazyCanvasResizer.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/LazyCanvasResizer.java @@ -31,6 +31,7 @@ import java.awt.event.ComponentEvent; * Class to lazily process canvas resize events by applying a threshold. * * @author Erich Schubert + * @since 0.2 */ public abstract class LazyCanvasResizer extends ComponentAdapter { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeAppendChild.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeAppendChild.java index 79bdab54..16fa54cf 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeAppendChild.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeAppendChild.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGPlot; * Runnable wrapper for appending XML-Elements to existing Elements. * * @author Remigius Wojdanowski + * @since 0.3 */ public class NodeAppendChild implements Runnable { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeReplaceAllChildren.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeReplaceAllChildren.java index 45f2b25d..c69e7c66 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeReplaceAllChildren.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeReplaceAllChildren.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGPlot; * Runnable wrapper to replace all children of a given node. * * @author Erich Schubert + * @since 0.3 */ public class NodeReplaceAllChildren extends NodeAppendChild { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeReplaceByID.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeReplaceByID.java index 27ac9672..40683760 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeReplaceByID.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeReplaceByID.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGPlot; * be put on the update queue. * * @author Erich Schubert + * @since 0.2 */ public class NodeReplaceByID implements Runnable { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeSubstitute.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeSubstitute.java index bef276dc..3e3e652c 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeSubstitute.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/NodeSubstitute.java @@ -30,6 +30,7 @@ import org.w3c.dom.Element; * be put on the update queue. * * @author Erich Schubert + * @since 0.2 */ public class NodeSubstitute implements Runnable { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/RemoveCSSClass.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/RemoveCSSClass.java index c7d48690..39a699f9 100755 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/RemoveCSSClass.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/RemoveCSSClass.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; * Remove a CSS class to the event target. * * @author Erich Schubert + * @since 0.2 * */ public class RemoveCSSClass implements EventListener { diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/ThumbnailRegistryEntry.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/ThumbnailRegistryEntry.java index 3f1c5cda..ebb464f4 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/ThumbnailRegistryEntry.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/ThumbnailRegistryEntry.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * Access images via an internal image registry. * * @author Erich Schubert + * @since 0.5.0 */ public class ThumbnailRegistryEntry extends AbstractRegistryEntry implements URLRegistryEntry, ParsedURLProtocolHandler { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/ThumbnailTranscoder.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/ThumbnailTranscoder.java index b0c16ef1..1ff84d03 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/ThumbnailTranscoder.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/ThumbnailTranscoder.java @@ -33,6 +33,7 @@ import org.apache.batik.transcoder.image.ImageTranscoder; * Transcode images to in-memory thumbnails. * * @author Erich Schubert + * @since 0.2 */ public class ThumbnailTranscoder extends ImageTranscoder { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/colors/ColorLibrary.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/colors/ColorLibrary.java index dc668924..fd7b5632 100755 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/colors/ColorLibrary.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/colors/ColorLibrary.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.visualization.colors; * Color scheme interface * * @author Erich Schubert + * @since 0.2 */ public interface ColorLibrary { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/colors/ListBasedColorLibrary.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/colors/ListBasedColorLibrary.java index 60ae0a81..3892c72c 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/colors/ListBasedColorLibrary.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/colors/ListBasedColorLibrary.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.visualization.colors; * Color library using the color names from a list. * * @author Erich Schubert + * @since 0.3 */ public class ListBasedColorLibrary implements ColorLibrary { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/css/CSSClass.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/css/CSSClass.java index 56d15810..2341bb10 100755 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/css/CSSClass.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/css/CSSClass.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * Class representing a single CSS class. * * @author Erich Schubert + * @since 0.2 */ public class CSSClass { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/css/CSSClassManager.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/css/CSSClassManager.java index 003f6f74..c799dea9 100755 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/css/CSSClassManager.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/css/CSSClassManager.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; * Manager class to track CSS classes used in a particular SVG document. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has de.lmu.ifi.dbs.elki.visualization.css.CSSClass */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/ResultWindow.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/ResultWindow.java index f82a21a0..9312d1f7 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/ResultWindow.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/ResultWindow.java @@ -78,6 +78,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGPlot; * * @author Erich Schubert * @author Remigius Wojdanowski + * @since 0.3 * * @apiviz.composedOf JSVGSynchronizedCanvas * @apiviz.composedOf OverviewPlot diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/SelectionTableWindow.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/SelectionTableWindow.java index 5e9af1ed..09c43617 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/SelectionTableWindow.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/SelectionTableWindow.java @@ -63,6 +63,7 @@ import de.lmu.ifi.dbs.elki.visualization.VisualizerContext; * * @author Heidi Kolb * @author Erich Schubert + * @since 0.4.0 */ // FIXME: INCOMPLETE TRANSITION TO MULTI-REPRESENTED DATA public class SelectionTableWindow extends JFrame implements DataStoreListener, ResultListener { diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/SimpleSVGViewer.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/SimpleSVGViewer.java index cdd7758c..197014f6 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/SimpleSVGViewer.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/SimpleSVGViewer.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGPlot; * A minimalistic SVG viewer with export dialog. * * @author Erich Schubert + * @since 0.4.0 */ public class SimpleSVGViewer extends JFrame { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/VisualizationPlot.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/VisualizationPlot.java index 7360a0da..385a9b48 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/VisualizationPlot.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/VisualizationPlot.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * SVG plot that allows visualization to schedule updates. * * @author Erich Schubert + * @since 0.7.0 */ public class VisualizationPlot extends SVGPlot { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/detail/DetailView.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/detail/DetailView.java index 64359463..b6d78368 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/detail/DetailView.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/detail/DetailView.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Manages a detail view. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has Visualization * @apiviz.has PlotItem diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/DetailViewSelectedEvent.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/DetailViewSelectedEvent.java index 16c59fee..779fcdf6 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/DetailViewSelectedEvent.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/DetailViewSelectedEvent.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.visualization.gui.detail.DetailView; * by their coordinates on the screen. * * @author Erich Schubert + * @since 0.3 */ public class DetailViewSelectedEvent extends ActionEvent { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/LayerMap.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/LayerMap.java index 0cdbb29e..00e515f2 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/LayerMap.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/LayerMap.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Class to help keeping track of the materialized layers of the different visualizations. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has PlotItem * @apiviz.has VisualizationTask diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/OverviewPlot.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/OverviewPlot.java index 23ab2c21..56fecfaf 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/OverviewPlot.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/OverviewPlot.java @@ -63,6 +63,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * * @author Erich Schubert * @author Remigius Wojdanowski + * @since 0.3 * * @apiviz.landmark * @apiviz.has VisualizerContext diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/PlotItem.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/PlotItem.java index b95ef7e2..c75a520e 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/PlotItem.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/PlotItem.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.visualization.projections.Projection; * Note: this is a {@code LinkedList<VisualizationTask>}! * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf Projection * @apiviz.composedOf VisualizationTask diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/RectangleArranger.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/RectangleArranger.java index ef05b6c0..29166573 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/RectangleArranger.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/gui/overview/RectangleArranger.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.DoubleArray; * a greedy placement strategy, extending the canvas as little as possible. * * @author Erich Schubert + * @since 0.4.0 * * @param <T> Key type */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/opticsplot/OPTICSCut.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/opticsplot/OPTICSCut.java index d85a9415..60f9ce1a 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/opticsplot/OPTICSCut.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/opticsplot/OPTICSCut.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.database.ids.ModifiableDBIDs; * * @author Heidi Kolb * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses ClusterOrder */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/opticsplot/OPTICSPlot.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/opticsplot/OPTICSPlot.java index c25a7961..7114c1b6 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/opticsplot/OPTICSPlot.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/opticsplot/OPTICSPlot.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.visualization.style.StylingPolicy; * Class to produce an OPTICS plot image. * * @author Erich Schubert + * @since 0.3 * * @apiviz.composedOf LinearScale * @apiviz.has ClusterOrder oneway - - renders diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AbstractFullProjection.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AbstractFullProjection.java index 4c57a6f0..2893e7da 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AbstractFullProjection.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AbstractFullProjection.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.visualization.projector.Projector; * clear use case that cannot be done by the low level fast projections. * * @author Erich Schubert + * @since 0.4.0 */ public abstract class AbstractFullProjection extends AbstractProjection implements FullProjection { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AbstractProjection.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AbstractProjection.java index bbcd1bcd..c6d7616b 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AbstractProjection.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AbstractProjection.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.visualization.projector.Projector; * Abstract base projection class. * * @author Erich Schubert + * @since 0.4.0 */ public abstract class AbstractProjection implements Projection { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AbstractSimpleProjection.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AbstractSimpleProjection.java index 4b0715a9..6cbdf481 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AbstractSimpleProjection.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AbstractSimpleProjection.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.visualization.projector.Projector; * Simple projections use the given scaling and dimension selection only. * * @author Erich Schubert + * @since 0.4.0 */ public abstract class AbstractSimpleProjection extends AbstractFullProjection { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AffineProjection.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AffineProjection.java index a04c57fc..a3c5d846 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AffineProjection.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/AffineProjection.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.visualization.projector.Projector; * However, this comes at the cost of a matrix multiplication. * * @author Erich Schubert + * @since 0.4.0 */ public class AffineProjection extends AbstractFullProjection implements Projection2D { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/CanvasSize.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/CanvasSize.java index b915ed07..a50fabfe 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/CanvasSize.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/CanvasSize.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.visualization.projections; * Size of a canvas. A 2D bounding rectangle. * * @author Erich Schubert + * @since 0.5.0 */ public class CanvasSize { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/FullProjection.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/FullProjection.java index 553d8faa..a8b7219d 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/FullProjection.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/FullProjection.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.data.NumberVector; * case for them as opposed to always using the low-level fast projections. * * @author Erich Schubert + * @since 0.4.0 */ public interface FullProjection extends Projection { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/OPTICSProjection.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/OPTICSProjection.java index b06d0a6d..de3eb42b 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/OPTICSProjection.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/OPTICSProjection.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.visualization.projector.Projector; * consistency in the visualizer API. * * @author Erich Schubert + * @since 0.4.0 */ public class OPTICSProjection implements Projection { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Projection.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Projection.java index 1a501608..456e1ded 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Projection.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Projection.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.visualization.style.StyleLibrary; * projections in the required dimensions! * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Projection1D.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Projection1D.java index a5daf0d3..ceac1d41 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Projection1D.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Projection1D.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.data.NumberVector; * first component. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Projection2D.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Projection2D.java index 6f9f17b0..cd3d1c05 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Projection2D.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Projection2D.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.data.NumberVector; * dimensions of the projection. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/ProjectionParallel.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/ProjectionParallel.java index 435a2146..fdd88f89 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/ProjectionParallel.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/ProjectionParallel.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.math.scales.LinearScale; * * @author Robert Rödler * @author Erich Schubert + * @since 0.5.0 */ public interface ProjectionParallel extends Projection { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Simple1D.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Simple1D.java index b4560152..0df92ef3 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Simple1D.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Simple1D.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.visualization.projector.Projector; * Dimension-selecting 1D projection. * * @author Erich Schubert + * @since 0.4.0 */ public class Simple1D extends AbstractSimpleProjection implements Projection1D { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Simple2D.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Simple2D.java index 3dff7c3b..1e2b9159 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Simple2D.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/Simple2D.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.visualization.projector.Projector; * Dimension-selecting 2D projection. * * @author Erich Schubert + * @since 0.4.0 */ public class Simple2D extends AbstractSimpleProjection implements Projection2D { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/SimpleParallel.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/SimpleParallel.java index e25d4088..a5e6b832 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/SimpleParallel.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projections/SimpleParallel.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.visualization.style.StyleLibrary; * * @author Robert Rödler * @author Erich Schubert + * @since 0.5.0 */ public class SimpleParallel implements ProjectionParallel { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/HistogramFactory.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/HistogramFactory.java index c7843576..100a114e 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/HistogramFactory.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/HistogramFactory.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.visualization.VisualizerContext; * Produce one-dimensional projections. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has HistogramProjector */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/HistogramProjector.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/HistogramProjector.java index d46265e7..7ca7edd7 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/HistogramProjector.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/HistogramProjector.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.visunproj.LabelVisualizatio * visualizations. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses ScalesResult * @apiviz.uses Projection1D diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/OPTICSProjector.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/OPTICSProjector.java index 2e615c89..84b30de9 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/OPTICSProjector.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/OPTICSProjector.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.visualization.projections.OPTICSProjection; * Projection for OPTICS plots. * * @author Erich Schubert + * @since 0.4.0 */ public class OPTICSProjector implements Projector { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/OPTICSProjectorFactory.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/OPTICSProjectorFactory.java index 32a0e540..c1c6df75 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/OPTICSProjectorFactory.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/OPTICSProjectorFactory.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.visualization.VisualizerContext; * Produce OPTICS plot projections * * @author Erich Schubert + * @since 0.2 * * @apiviz.has OPTICSProjector */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ParallelPlotFactory.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ParallelPlotFactory.java index 1bf12d79..a3f39ebb 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ParallelPlotFactory.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ParallelPlotFactory.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.visualization.VisualizationTree; * Produce parallel axes projections. * * @author Robert Rödler + * @since 0.5.0 * * @apiviz.has ParallelPlotProjector */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ParallelPlotProjector.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ParallelPlotProjector.java index 28069cc4..fce0dcec 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ParallelPlotProjector.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ParallelPlotProjector.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.visualization.projections.SimpleParallel; * visualization. * * @author Robert Rödler + * @since 0.5.0 * * @param <V> Vector type */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/Projector.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/Projector.java index b726dfef..27bd7f5e 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/Projector.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/Projector.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.visualization.gui.overview.PlotItem; * A projector is responsible for adding projections to the visualization. * * @author Erich Schubert + * @since 0.4.0 */ public interface Projector extends VisualizationItem { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ProjectorFactory.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ProjectorFactory.java index 10ad8bd9..61792247 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ProjectorFactory.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ProjectorFactory.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.visualization.VisualizerContext; * detecting appropriate relations in the database. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has Projector */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ScatterPlotFactory.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ScatterPlotFactory.java index 785ea672..9e69dd83 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ScatterPlotFactory.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ScatterPlotFactory.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.visualization.VisualizerContext; * Produce scatterplot projections. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has ScatterPlotProjector */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ScatterPlotProjector.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ScatterPlotProjector.java index b8705a39..d3982f3d 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ScatterPlotProjector.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/ScatterPlotProjector.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.visunproj.LabelVisualizatio * visualizations. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses ScalesResult * @apiviz.uses Projection2D diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/savedialog/SVGSaveDialog.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/savedialog/SVGSaveDialog.java index 345e1b68..8dab2663 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/savedialog/SVGSaveDialog.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/savedialog/SVGSaveDialog.java @@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.visualization.savedialog; This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures - Copyright (C) 2015 + Copyright (C) 2016 Ludwig-Maximilians-Universität München Lehr- und Forschungseinheit für Datenbanksysteme ELKI Development Team @@ -26,33 +26,39 @@ package de.lmu.ifi.dbs.elki.visualization.savedialog; import java.awt.Component; import java.io.File; import java.io.IOException; +import java.util.ArrayList; import javax.swing.JFileChooser; import javax.swing.JOptionPane; import javax.xml.transform.TransformerException; import javax.xml.transform.TransformerFactoryConfigurationError; +import org.apache.batik.ext.awt.image.spi.ImageTagRegistry; +import org.apache.batik.ext.awt.image.spi.ImageWriterRegistry; import org.apache.batik.transcoder.TranscoderException; import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.utilities.FileUtil; +import de.lmu.ifi.dbs.elki.visualization.batikutil.BatikUtil; import de.lmu.ifi.dbs.elki.visualization.svg.SVGPlot; /** * A save dialog to save/export a SVG image to a file. - * + * * Supported formats: * <ul> - * <li>JPEG (broken) (with width and height options)</li> - * <li>PNG (with width and height options)</li> - * <li>PDF</li> - * <li>PS</li> - * <li>EPS</li> * <li>SVG</li> + * <li>PNG (with width and height options)</li> + * <li>JPEG (with width and height options, and if an ImageWrite is available) + * </li> + * <li>PDF (if FOP transcoders are available)</li> + * <li>PS (if FOP transcoders are available)</li> + * <li>EPS (if FOP transcoders are available)</li> * </ul> - * + * * @author Simon Mittermüller - * + * @since 0.2 + * * @apiviz.composedOf SaveOptionsPanel */ public class SVGSaveDialog { @@ -63,28 +69,47 @@ public class SVGSaveDialog { private static final Logging LOG = Logging.getLogger(SVGSaveDialog.class); /** Automagic file format */ - final static String automagic_format = "automatic"; + final static String AUTOMAGIC_FORMAT = "automatic"; /** Supported file format (extensions) */ - final static String[] formats; + final static String[] FORMATS; /** Visible file formats */ - final static String[] visibleformats; + final static String[] VISIBLE_FORMATS; static { + ArrayList<String> fmt = new ArrayList<>(); + fmt.add(AUTOMAGIC_FORMAT); + fmt.add("svg"); + + // Check that the image writers are available: + ImageWriterRegistry reg = ImageWriterRegistry.getInstance(); + // Detect broken Batik unable to use inlined base64 images: + ImageTagRegistry tagreg = ImageTagRegistry.getRegistry(); + // These will only work if we can decode pngs (thumbnails in overview)! + if(tagreg.getRegisteredMimeTypes().contains("image/png")) { + if(reg.getWriterFor("image/png") != null) { + fmt.add("png"); + } + if(reg.getWriterFor("image/jpeg") != null) { + fmt.add("jpeg"); + } + } + // FOP installed? - if (SVGPlot.hasFOPInstalled()) { - formats = new String[] { "svg", "png", "jpeg", "jpg", "pdf", "ps", "eps" }; - visibleformats = new String[] { automagic_format, "svg", "png", "jpeg", "pdf", "ps", "eps" }; - } else { - formats = new String[] { "svg", "png", "jpeg", "jpg" }; - visibleformats = new String[] { automagic_format, "svg", "png", "jpeg" }; + if(BatikUtil.hasFOPInstalled()) { + fmt.add("pdf"); + fmt.add("ps"); + fmt.add("eps"); } + FORMATS = fmt.toArray(new String[fmt.size()]); + fmt.remove(0); + VISIBLE_FORMATS = fmt.toArray(new String[fmt.size()]); } /** * Show a "Save as" dialog. - * + * * @param plot The plot to be exported. * @param width The width of the exported image (when export to JPEG/PNG). * @param height The height of the exported image (when export to JPEG/PNG). @@ -102,54 +127,70 @@ public class SVGSaveDialog { ret = fc.showSaveDialog(null); fc.setDialogTitle("Saving... Please wait."); - if (ret == JFileChooser.APPROVE_OPTION) { + if(ret == JFileChooser.APPROVE_OPTION) { File file = fc.getSelectedFile(); String format = optionsPanel.getSelectedFormat(); - if (format == null || automagic_format.equals(format)) { + if(format == null || AUTOMAGIC_FORMAT.equals(format)) { format = guessFormat(file.getName()); } try { - if (format == null) { + if(format == null) { showError(fc, "Error saving image.", "File format not recognized."); - } else if ("jpeg".equals(format) || "jpg".equals(format)) { + } + else if("jpeg".equals(format) || "jpg".equals(format)) { quality = optionsPanel.getJPEGQuality(); plot.saveAsJPEG(file, width, height, quality); - } else if ("png".equals(format)) { + } + else if("png".equals(format)) { plot.saveAsPNG(file, width, height); - } else if ("ps".equals(format)) { + } + else if("ps".equals(format)) { plot.saveAsPS(file); - } else if ("eps".equals(format)) { + } + else if("eps".equals(format)) { plot.saveAsEPS(file); - } else if ("pdf".equals(format)) { + } + else if("pdf".equals(format)) { plot.saveAsPDF(file); - } else if ("svg".equals(format)) { + } + else if("svg".equals(format)) { plot.saveAsSVG(file); - } else { + } + else { showError(fc, "Error saving image.", "Unsupported format: " + format); } - } catch (java.lang.IncompatibleClassChangeError e) { + } + catch(java.lang.IncompatibleClassChangeError e) { showError(fc, "Error saving image.", "It seems that your Java version is incompatible with this version of Batik and Jpeg writing. Sorry."); - } catch (ClassNotFoundException e) { + } + catch(ClassNotFoundException e) { showError(fc, "Error saving image.", "A class was not found when saving this image. Maybe installing Apache FOP will help (for PDF, PS and EPS output).\n" + e.toString()); - } catch (IOException e) { + } + catch(IOException e) { LOG.exception(e); showError(fc, "Error saving image.", e.toString()); - } catch (TranscoderException e) { + } + catch(TranscoderException e) { LOG.exception(e); showError(fc, "Error saving image.", e.toString()); - } catch (TransformerFactoryConfigurationError e) { + } + catch(TransformerFactoryConfigurationError e) { LOG.exception(e); showError(fc, "Error saving image.", e.toString()); - } catch (TransformerException e) { + } + catch(TransformerException e) { LOG.exception(e); showError(fc, "Error saving image.", e.toString()); - } catch (Exception e) { + } + catch(Exception e) { LOG.exception(e); showError(fc, "Error saving image.", e.toString()); } - } else if (ret == JFileChooser.ERROR_OPTION) { + } + else if(ret == JFileChooser.ERROR_OPTION) { showError(fc, "Error in file dialog.", "Unknown Error."); - } else if (ret == JFileChooser.CANCEL_OPTION) { + } + else if(ret == JFileChooser.CANCEL_OPTION) { // do nothing - except return result } return ret; @@ -157,14 +198,14 @@ public class SVGSaveDialog { /** * Guess a supported format from the file name. For "auto" format handling. - * + * * @param name File name * @return format or "null" */ public static String guessFormat(String name) { String ext = FileUtil.getFilenameExtension(name); - for (String format : formats) { - if (format.equals(ext)) { + for(String format : FORMATS) { + if(format.equals(ext)) { return ext; } } @@ -175,23 +216,23 @@ public class SVGSaveDialog { * @return the formats */ public static String[] getFormats() { - return formats; + return FORMATS; } /** * @return the visibleformats */ public static String[] getVisibleFormats() { - return visibleformats; + return VISIBLE_FORMATS; } /** * Helper method to show a error message as "popup". Calls * {@link JOptionPane#showMessageDialog(java.awt.Component, Object)}. - * + * * @param parent The parent component for the popup. * @param msg The message to be displayed. - * */ + */ private static void showError(Component parent, String title, String msg) { JOptionPane.showMessageDialog(parent, msg, title, JOptionPane.ERROR_MESSAGE); } diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/savedialog/SaveOptionsPanel.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/savedialog/SaveOptionsPanel.java index 6e45ac99..2ebf8523 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/savedialog/SaveOptionsPanel.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/savedialog/SaveOptionsPanel.java @@ -49,6 +49,7 @@ import javax.swing.event.ChangeListener; * additional options when saving as JPEG or PNG. * * @author Simon Mittermüller + * @since 0.2 */ public class SaveOptionsPanel extends JPanel { // TODO: externalize strings diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/ClassStylingPolicy.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/ClassStylingPolicy.java index 7bc50182..5279f2a0 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/ClassStylingPolicy.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/ClassStylingPolicy.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * is preferred when possible. * * @author Erich Schubert + * @since 0.4.0 */ public interface ClassStylingPolicy extends StylingPolicy { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/ClusterStylingPolicy.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/ClusterStylingPolicy.java index 643f4328..48b8ec06 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/ClusterStylingPolicy.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/ClusterStylingPolicy.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; * Styling policy based on cluster membership. * * @author Erich Schubert + * @since 0.4.0 * */ // TODO: fast enough? Some other kind of mapping we can use? diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/PropertiesBasedStyleLibrary.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/PropertiesBasedStyleLibrary.java index c8440067..16c0a4c2 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/PropertiesBasedStyleLibrary.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/PropertiesBasedStyleLibrary.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.visualization.style.marker.PrettyMarkers; * Style library loading the parameters from a properties file. * * @author Erich Schubert + * @since 0.3 */ // TODO: also use Caching for String values? public class PropertiesBasedStyleLibrary implements StyleLibrary { diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/SingleObjectsStylingPolicy.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/SingleObjectsStylingPolicy.java index 0e26bf80..f6c4d242 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/SingleObjectsStylingPolicy.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/SingleObjectsStylingPolicy.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.visualization.style; * Styling policy based on assigning objects individual colors. * * @author Erich Schubert + * @since 0.4.0 */ public interface SingleObjectsStylingPolicy extends StylingPolicy { // TODO: finish and use, e.g. for outliers and density visualization diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/StyleLibrary.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/StyleLibrary.java index 5ca93be6..3ddca759 100755 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/StyleLibrary.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/StyleLibrary.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.visualization.style.marker.MarkerLibrary; * having to change program code. * * @author Erich Schubert + * @since 0.3 * * @apiviz.composedOf ColorLibrary * @apiviz.composedOf LineStyleLibrary diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/StylingPolicy.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/StylingPolicy.java index 406b6aff..29b2160b 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/StylingPolicy.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/StylingPolicy.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.visualization.VisualizationItem; * support these known interfaces. * * @author Erich Schubert + * @since 0.4.0 */ public interface StylingPolicy extends VisualizationItem { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/lines/DashedLineStyleLibrary.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/lines/DashedLineStyleLibrary.java index 49b8cc91..4b525f35 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/lines/DashedLineStyleLibrary.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/lines/DashedLineStyleLibrary.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; * patterns. * * @author Erich Schubert + * @since 0.3 * * @apiviz.composedOf ColorLibrary */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/lines/LineStyleLibrary.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/lines/LineStyleLibrary.java index 48212f16..e6264798 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/lines/LineStyleLibrary.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/lines/LineStyleLibrary.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.visualization.css.CSSClass; * </dl> * * @author Erich Schubert + * @since 0.3 * * @apiviz.uses CSSClass oneway */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/lines/SolidLineStyleLibrary.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/lines/SolidLineStyleLibrary.java index 61765f1a..c94c500d 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/lines/SolidLineStyleLibrary.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/lines/SolidLineStyleLibrary.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; * {@link LineStyleLibrary#FLAG_INTERPOLATED} will result in dashed lines. * * @author Erich Schubert + * @since 0.3 * * @apiviz.composedOf ColorLibrary */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/CircleMarkers.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/CircleMarkers.java index c4078091..3e91d380 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/CircleMarkers.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/CircleMarkers.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; * coordinates. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf ColorLibrary */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/MarkerLibrary.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/MarkerLibrary.java index 522097aa..6292c6fb 100755 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/MarkerLibrary.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/MarkerLibrary.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGPlot; * screen, thumbnail, print) * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses Element oneway - - «create» */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/MinimalMarkers.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/MinimalMarkers.java index a3390a6d..82ce6fb3 100755 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/MinimalMarkers.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/MinimalMarkers.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; * coordinates. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf ColorLibrary */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/PrettyMarkers.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/PrettyMarkers.java index be99c6b1..c386179c 100755 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/PrettyMarkers.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/marker/PrettyMarkers.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; * shapes with different colors. Uses object ID management by SVGPlot. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf ColorLibrary */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGArrow.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGArrow.java index afa42afd..da7b0d5b 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGArrow.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGArrow.java @@ -30,6 +30,7 @@ import org.w3c.dom.Element; * * @author Erich Schubert * @author Robert Rödler + * @since 0.5.5 * * @apiviz.uses SVGPath */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGButton.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGButton.java index 6a542a7e..2912b88f 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGButton.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGButton.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.visualization.css.CSSClass; * Class to draw a button as SVG. * * @author Erich Schubert + * @since 0.5.0 */ public class SVGButton { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGCheckbox.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGCheckbox.java index 1cab95b9..e6bbe0d1 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGCheckbox.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGCheckbox.java @@ -37,6 +37,7 @@ import org.w3c.dom.events.EventTarget; * SVG checkbox. * * @author Sascha Goldhofer + * @since 0.5.0 */ public class SVGCheckbox { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGCloneVisible.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGCloneVisible.java index c09717f7..0f20cf73 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGCloneVisible.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGCloneVisible.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.xml.DOMCloner; * Clone visible parts of an SVG document. * * @author Erich Schubert + * @since 0.2 */ public class SVGCloneVisible extends DOMCloner { @Override diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGEffects.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGEffects.java index 4171ce51..eae1717a 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGEffects.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGEffects.java @@ -29,6 +29,7 @@ import org.w3c.dom.Element; * Class containing some popular SVG effects. * * @author Erich Schubert + * @since 0.5.0 */ public class SVGEffects { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGHyperCube.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGHyperCube.java index 9faad348..e17e97bc 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGHyperCube.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGHyperCube.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.visualization.projections.Projection2D; * Utility class to draw hypercubes, wireframe and filled. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses SVGPath * @apiviz.uses Projection2D diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGHyperSphere.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGHyperSphere.java index e3fc9386..1ed7962d 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGHyperSphere.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGHyperSphere.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.visualization.projections.Projection2D; * Utility class to draw hypercubes, wireframe and filled. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses SVGPath * @apiviz.uses Projection2D diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPath.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPath.java index 948f09a7..fe71b50b 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPath.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPath.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.ArrayListIter; * Element used for building an SVG path using a string buffer. * * @author Erich Schubert + * @since 0.3 * * @apiviz.uses Element oneway - - «create» */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java index 7eb51819..3c58ced7 100755 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java @@ -73,6 +73,7 @@ import de.lmu.ifi.dbs.elki.visualization.css.CSSClassManager.CSSNamingConflict; * creation, axis plotting, markers and number formatting for SVG. * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * @apiviz.composedOf CSSClassManager @@ -488,23 +489,6 @@ public class SVGPlot { } /** - * Test whether FOP were installed (for PDF, PS and EPS output support). - * - * @return true when FOP is available. - */ - public static boolean hasFOPInstalled() { - try { - Class<?> c1 = Class.forName("org.apache.fop.svg.PDFTranscoder"); - Class<?> c2 = Class.forName("org.apache.fop.render.ps.PSTranscoder"); - Class<?> c3 = Class.forName("org.apache.fop.render.ps.EPSTranscoder"); - return (c1 != null) && (c2 != null) && (c3 != null); - } - catch(ClassNotFoundException e) { - return false; - } - } - - /** * Transcode file to PNG. * * @param file Output filename diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGScoreBar.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGScoreBar.java index dd16070d..cd1a5274 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGScoreBar.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGScoreBar.java @@ -33,6 +33,7 @@ import org.w3c.dom.Element; * a relative score. * * @author Sascha Goldhofer + * @since 0.5.0 */ // TODO: refactor to get a progress bar? public class SVGScoreBar { diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGSimpleLinearAxis.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGSimpleLinearAxis.java index 5559e602..f80f6128 100755 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGSimpleLinearAxis.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGSimpleLinearAxis.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.visualization.style.StyleLibrary; * Class to draw a simple axis with tick marks on the plot. * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses CSSClass * @apiviz.uses CSSClassManager diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGUtil.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGUtil.java index b85af07e..08fef1be 100755 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGUtil.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGUtil.java @@ -51,6 +51,7 @@ import gnu.trove.map.hash.TObjectIntHashMap; * string) and Namespace handling * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses Element oneway - - «create» */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/UpdateRunner.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/UpdateRunner.java index 17033ef8..4e57ed09 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/UpdateRunner.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/UpdateRunner.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.logging.LoggingUtil; * Batik UI. * * @author Erich Schubert + * @since 0.3 * * @apiviz.has Runnable * @apiviz.uses UpdateSynchronizer diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/UpdateSynchronizer.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/UpdateSynchronizer.java index 30eaa304..49a8c6bc 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/UpdateSynchronizer.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/UpdateSynchronizer.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.visualization.svg; * API to synchronize updates * * @author Erich Schubert + * @since 0.3 * * @apiviz.has UpdateRunner */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/VoronoiDraw.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/VoronoiDraw.java index 434bf240..c816fbe0 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/VoronoiDraw.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/VoronoiDraw.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.visualization.projections.Projection2D; * * @author Robert Rödler * @author Erich Schubert + * @since 0.5.0 * * @apiviz.uses de.lmu.ifi.dbs.elki.math.geometry.SweepHullDelaunay2D.Triangle * @apiviz.uses Projection2D diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/AbstractVisFactory.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/AbstractVisFactory.java index 841ea83f..d8a9525d 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/AbstractVisFactory.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/AbstractVisFactory.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.thumbs.ThumbnailVisualizati * Abstract superclass for Visualizers (aka: Visualization Factories). * * @author Remigius Wojdanowski + * @since 0.4.0 * * @apiviz.uses ThumbnailVisualization oneway - - «create» * @apiviz.excludeSubtypes diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/AbstractVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/AbstractVisualization.java index 49e749c0..91cc9323 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/AbstractVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/AbstractVisualization.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.visualization.style.StylingPolicy; * Abstract base class for visualizations. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.excludeSubtypes */ @@ -197,7 +198,7 @@ public abstract class AbstractVisualization implements Visualization, ResultList @Override public void visualizationChanged(VisualizationItem item) { - if(task.getResult() == item) { + if(task == item || task.getResult() == item) { svgp.requestRedraw(this.task, this); return; } diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/StaticVisualizationInstance.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/StaticVisualizationInstance.java index b89720fe..e3b2432b 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/StaticVisualizationInstance.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/StaticVisualizationInstance.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.visualization.gui.VisualizationPlot; * Static visualization * * @author Erich Schubert + * @since 0.4.0 */ public class StaticVisualizationInstance extends AbstractVisualization { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/VisFactory.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/VisFactory.java index bf30fe8f..aca34382 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/VisFactory.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/VisFactory.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.visualization.projections.Projection; * parameters (default constructor) to be used for parameterization. * * @author Remigius Wojdanowski + * @since 0.3 * * @apiviz.landmark * @apiviz.stereotype factory diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/Visualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/Visualization.java index ee355e4a..e7ea486c 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/Visualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/Visualization.java @@ -29,6 +29,7 @@ import org.w3c.dom.Element; * Base class for a materialized Visualization. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.has Element oneway diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/actions/ClusterStyleAction.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/actions/ClusterStyleAction.java index 7923509e..a86cc3dd 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/actions/ClusterStyleAction.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/actions/ClusterStyleAction.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Actions to use clusterings for styling. * * @author Erich Schubert + * @since 0.7.0 */ public class ClusterStyleAction extends AbstractVisFactory { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/histogram/AbstractHistogramVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/histogram/AbstractHistogramVisualization.java index 34c648ba..4f1b8b50 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/histogram/AbstractHistogramVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/histogram/AbstractHistogramVisualization.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.AbstractVisualization; * One-dimensional projected visualization. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.has Projection1D diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/histogram/ColoredHistogramVisualizer.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/histogram/ColoredHistogramVisualizer.java index 80bbfeeb..27528059 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/histogram/ColoredHistogramVisualizer.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/histogram/ColoredHistogramVisualizer.java @@ -93,6 +93,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * * @author Remigius Wojdanowski * @author Erich Schubert + * @since 0.3 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/AbstractOPTICSVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/AbstractOPTICSVisualization.java index 401e05e6..21f91a99 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/AbstractOPTICSVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/AbstractOPTICSVisualization.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.AbstractVisualization; * Abstract base class for OPTICS visualizer * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses OPTICSProjection */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSClusterVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSClusterVisualization.java index e1cd5c66..10eb8b79 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSClusterVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSClusterVisualization.java @@ -53,6 +53,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Plot. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSPlotCutVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSPlotCutVisualization.java index 65e00430..a4f95e7d 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSPlotCutVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSPlotCutVisualization.java @@ -55,6 +55,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * * @author Heidi Kolb * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSPlotSelectionVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSPlotSelectionVisualization.java index 7abc5609..f723cfef 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSPlotSelectionVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSPlotSelectionVisualization.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Handle the marker in an OPTICS plot. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSPlotVisualizer.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSPlotVisualizer.java index 65d8ecf3..4110e416 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSPlotVisualizer.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSPlotVisualizer.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Visualize an OPTICS result by constructing an OPTICS plot for it. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSSteepAreaVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSSteepAreaVisualization.java index ef8f6198..88ee710d 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSSteepAreaVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/OPTICSSteepAreaVisualization.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Visualize the steep areas found in an OPTICS plot * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/pairsegments/CircleSegmentsVisualizer.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/pairsegments/CircleSegmentsVisualizer.java index 72e9ccef..4a33c504 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/pairsegments/CircleSegmentsVisualizer.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/pairsegments/CircleSegmentsVisualizer.java @@ -84,6 +84,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * * @author Sascha Goldhofer * @author Erich Schubert + * @since 0.5.0 * * @apiviz.landmark * diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/pairsegments/SegmentsStylingPolicy.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/pairsegments/SegmentsStylingPolicy.java index 7e38d951..3a95f33c 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/pairsegments/SegmentsStylingPolicy.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/pairsegments/SegmentsStylingPolicy.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; * * @author Sascha Goldhofer * @author Erich Schubert + * @since 0.5.0 */ public class SegmentsStylingPolicy implements ClassStylingPolicy { /** diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/AbstractParallelVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/AbstractParallelVisualization.java index 3ac02de2..b5398ccb 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/AbstractParallelVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/AbstractParallelVisualization.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.AbstractVisualization; * * @author Robert Rödler * @author Erich Schubert + * @since 0.5.0 * * @param <NV> Data type in relation */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/AxisReorderVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/AxisReorderVisualization.java index ce24ad2a..e7ac7193 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/AxisReorderVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/AxisReorderVisualization.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * * @author Robert Rödler * @author Erich Schubert + * @since 0.5.5 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/AxisVisibilityVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/AxisVisibilityVisualization.java index 1e12f87c..3b57dd48 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/AxisVisibilityVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/AxisVisibilityVisualization.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * * @author Robert Rödler * @author Erich Schubert + * @since 0.5.5 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/BoundingBoxVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/BoundingBoxVisualization.java index 6b3671d1..3b0fb572 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/BoundingBoxVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/BoundingBoxVisualization.java @@ -57,6 +57,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Draw spatial objects (except vectors!) * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/LineVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/LineVisualization.java index a13bdb74..3bee4b2a 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/LineVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/LineVisualization.java @@ -57,6 +57,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Generates data lines. * * @author Robert Rödler + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/ParallelAxisVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/ParallelAxisVisualization.java index 4f35faf6..70962a08 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/ParallelAxisVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/ParallelAxisVisualization.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Generates a SVG-Element containing axes, including labeling. * * @author Robert Rödler + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/cluster/ClusterOutlineVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/cluster/ClusterOutlineVisualization.java index 1a660bf9..04777614 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/cluster/ClusterOutlineVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/cluster/ClusterOutlineVisualization.java @@ -67,6 +67,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.cluster.Cluster * Generates a SVG-Element that visualizes the area covered by a cluster. * * @author Robert Rödler + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/cluster/ClusterParallelMeanVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/cluster/ClusterParallelMeanVisualization.java index 6e0dc167..bb842166 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/cluster/ClusterParallelMeanVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/cluster/ClusterParallelMeanVisualization.java @@ -60,6 +60,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.parallel.AbstractParallelVi * Generates a SVG-Element that visualizes cluster means. * * @author Robert Rödler + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/index/RTreeParallelVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/index/RTreeParallelVisualization.java index 338729f4..d8a7a476 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/index/RTreeParallelVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/index/RTreeParallelVisualization.java @@ -58,6 +58,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.index.TreeMBRVi * Visualize the of an R-Tree based index. * * @author Robert Rödler + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionAxisRangeVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionAxisRangeVisualization.java index 5f56e774..f9a3ada3 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionAxisRangeVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionAxisRangeVisualization.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.parallel.AbstractParallelVi * Visualizer for generating an SVG-Element representing the selected range. * * @author Robert Rödler + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionLineVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionLineVisualization.java index b4107147..4f80bcae 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionLineVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionLineVisualization.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.parallel.AbstractParallelVi * Visualizer for generating SVG-Elements representing the selected objects * * @author Robert Rödler + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionToolAxisRangeVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionToolAxisRangeVisualization.java index 3dd96007..cc6e1e2f 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionToolAxisRangeVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionToolAxisRangeVisualization.java @@ -58,6 +58,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.parallel.AbstractParallelVi * Tool-Visualization for the tool to select axis ranges * * @author Robert Rödler + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionToolLineVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionToolLineVisualization.java index aa22a267..1a481548 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionToolLineVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/parallel/selection/SelectionToolLineVisualization.java @@ -60,6 +60,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.parallel.AbstractParallelVi * Tool-Visualization for the tool to select objects * * @author Robert Rödler + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/AbstractScatterplotVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/AbstractScatterplotVisualization.java index 13225426..08ca1eac 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/AbstractScatterplotVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/AbstractScatterplotVisualization.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.AbstractVisualization; * Default class to handle 2D projected visualizations. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.has Projection2D diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/AbstractTooltipVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/AbstractTooltipVisualization.java index 313b2dff..ff4f14e6 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/AbstractTooltipVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/AbstractTooltipVisualization.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; * General base class for a tooltip visualizer. * * @author Erich Schubert + * @since 0.4.0 */ // TODO: can we improve performance by not adding as many hovers? public abstract class AbstractTooltipVisualization extends AbstractScatterplotVisualization implements DataStoreListener { diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/AxisVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/AxisVisualization.java index 9fa1bd96..64fcb381 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/AxisVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/AxisVisualization.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * * @author Remigius Wojdanowski * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/MarkerVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/MarkerVisualization.java index 6508d9ce..07e8cd13 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/MarkerVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/MarkerVisualization.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * kind of result we have a style source for. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/PolygonVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/PolygonVisualization.java index 796d8f5f..032a319a 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/PolygonVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/PolygonVisualization.java @@ -53,6 +53,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Renders PolygonsObject in the data set. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/ReferencePointsVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/ReferencePointsVisualization.java index 1f0246e0..b75113cc 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/ReferencePointsVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/ReferencePointsVisualization.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * * @author Remigius Wojdanowski * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/TooltipScoreVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/TooltipScoreVisualization.java index 585b5405..656bac0b 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/TooltipScoreVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/TooltipScoreVisualization.java @@ -61,6 +61,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * * @author Remigius Wojdanowski * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/TooltipStringVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/TooltipStringVisualization.java index d367306d..4f694518 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/TooltipStringVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/TooltipStringVisualization.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * * @author Remigius Wojdanowski * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterHullVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterHullVisualization.java index fb4ed69c..b1f0a78d 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterHullVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterHullVisualization.java @@ -77,6 +77,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * * @author Robert Rödler * @author Erich Schubert + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterMeanVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterMeanVisualization.java index bd597111..768d0ab6 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterMeanVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterMeanVisualization.java @@ -58,6 +58,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * Visualize the mean of a KMeans-Clustering * * @author Heidi Kolb + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterOrderVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterOrderVisualization.java index 9a029c79..a11bc1c3 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterOrderVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterOrderVisualization.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * order represents. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterStarVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterStarVisualization.java index c0bedc4a..c848f6c1 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterStarVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/ClusterStarVisualization.java @@ -58,6 +58,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * Visualize the mean of a KMeans-Clustering using stars. * * @author Heidi Kolb + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/EMClusterVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/EMClusterVisualization.java index 04a2d241..deccbfb9 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/EMClusterVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/EMClusterVisualization.java @@ -70,6 +70,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * tries to approximate the cluster extends. * * @author Robert Rödler + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/VoronoiVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/VoronoiVisualization.java index f1d9051b..cd13dde9 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/VoronoiVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/cluster/VoronoiVisualization.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.EnumParameter; +import de.lmu.ifi.dbs.elki.visualization.VisualizationMenuAction; import de.lmu.ifi.dbs.elki.visualization.VisualizationTask; import de.lmu.ifi.dbs.elki.visualization.VisualizationTree; import de.lmu.ifi.dbs.elki.visualization.VisualizerContext; @@ -68,6 +69,9 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * * See also: {@link de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansLloyd * KMeans clustering} + * + * @author Erich Schubert + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» @@ -134,6 +138,62 @@ public class VoronoiVisualization extends AbstractVisFactory { task.level = VisualizationTask.LEVEL_DATA + 3; task.addUpdateFlags(VisualizationTask.ON_STYLEPOLICY); context.addVis(p, task); + context.addVis(p, new SwitchModeAction(task, context)); + } + } + + /** + * Menu item to change visualization styles. + * + * @author Erich Schubert + */ + public class SwitchModeAction implements VisualizationMenuAction { + /** + * Task we represent. + */ + private VisualizationTask task; + + /** + * Visualizer context. + */ + private VisualizerContext context; + + /** + * Constructor. + * + * @param task Task + * @param context Visualizer context + */ + public SwitchModeAction(VisualizationTask task, VisualizerContext context) { + super(); + this.task = task; + this.context = context; + } + + @Override + public String getMenuName() { + return "Switch Voronoi Mode"; + } + + @Override + public void activate() { + switch(mode){ + case VORONOI: + mode = Mode.DELAUNAY; + break; + case DELAUNAY: + mode = Mode.V_AND_D; + break; + case V_AND_D: + mode = Mode.VORONOI; + break; + } + context.visChanged(task); + } + + @Override + public boolean enabled() { + return true; } } diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/density/DensityEstimationOverlay.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/density/DensityEstimationOverlay.java index 95239509..31049ebf 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/density/DensityEstimationOverlay.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/density/DensityEstimationOverlay.java @@ -55,6 +55,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * <em>in the projection, not the actual data!</em> * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/index/TreeMBRVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/index/TreeMBRVisualization.java index 67fd97a7..8296c697 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/index/TreeMBRVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/index/TreeMBRVisualization.java @@ -59,6 +59,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * Visualize the bounding rectangles of an R-Tree based index. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/index/TreeSphereVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/index/TreeSphereVisualization.java index f4eb6a95..1cd93017 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/index/TreeSphereVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/index/TreeSphereVisualization.java @@ -65,6 +65,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * Visualize the bounding sphere of a metric index. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/outlier/BubbleVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/outlier/BubbleVisualization.java index f99b52f4..68e4e281 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/outlier/BubbleVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/outlier/BubbleVisualization.java @@ -67,6 +67,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * * @author Remigius Wojdanowski * @author Erich Schubert + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/outlier/COPVectorVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/outlier/COPVectorVisualization.java index b2abeb9f..762b2e0a 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/outlier/COPVectorVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/outlier/COPVectorVisualization.java @@ -56,6 +56,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * Visualize error vectors as produced by COP. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/DistanceFunctionVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/DistanceFunctionVisualization.java index 4751605f..7d73400a 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/DistanceFunctionVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/DistanceFunctionVisualization.java @@ -72,6 +72,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * * @author Erich Schubert * @author Robert Rödler + * @since 0.5.5 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/MoveObjectsToolVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/MoveObjectsToolVisualization.java index c594d500..b8082301 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/MoveObjectsToolVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/MoveObjectsToolVisualization.java @@ -58,6 +58,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * * @author Heidi Kolb * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionConvexHullVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionConvexHullVisualization.java index add2ab8d..5ad2a432 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionConvexHullVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionConvexHullVisualization.java @@ -57,6 +57,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * selected points * * @author Robert Rödler + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionCubeVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionCubeVisualization.java index 7ad7b32b..d060bdce 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionCubeVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionCubeVisualization.java @@ -57,6 +57,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * representing the selected range for each dimension * * @author Heidi Kolb + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionDotVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionDotVisualization.java index c9aed72f..478fbd5b 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionDotVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionDotVisualization.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * representing the selected Database's objects. * * @author Heidi Kolb + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionToolCubeVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionToolCubeVisualization.java index 0cc56e08..cd383865 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionToolCubeVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionToolCubeVisualization.java @@ -62,6 +62,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * TODO: support non-point spatial data * * @author Heidi Kolb + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionToolDotVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionToolDotVisualization.java index 04a092b5..3b0831ff 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionToolDotVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/selection/SelectionToolDotVisualization.java @@ -56,6 +56,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * Tool-Visualization for the tool to select objects * * @author Heidi Kolb + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses Instance - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/uncertain/UncertainBoundingBoxVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/uncertain/UncertainBoundingBoxVisualization.java index 4e4cca3a..f7d27fc6 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/uncertain/UncertainBoundingBoxVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/uncertain/UncertainBoundingBoxVisualization.java @@ -58,6 +58,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * But it serves the purpose. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/uncertain/UncertainInstancesVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/uncertain/UncertainInstancesVisualization.java index c66d88e3..da2df885 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/uncertain/UncertainInstancesVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/uncertain/UncertainInstancesVisualization.java @@ -56,6 +56,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * But it serves the purpose. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/uncertain/UncertainSamplesVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/uncertain/UncertainSamplesVisualization.java index a186d881..80339e0a 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/uncertain/UncertainSamplesVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/uncertain/UncertainSamplesVisualization.java @@ -62,6 +62,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatter * But it serves the purpose. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/thumbs/ThumbnailThread.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/thumbs/ThumbnailThread.java index e43656cf..c594e3a3 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/thumbs/ThumbnailThread.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/thumbs/ThumbnailThread.java @@ -30,6 +30,7 @@ import java.util.concurrent.ConcurrentLinkedQueue; * Thread to render thumbnails in the background. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses Listener oneway - - signals */ diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/thumbs/ThumbnailVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/thumbs/ThumbnailVisualization.java index 1c0dd760..e05481d2 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/thumbs/ThumbnailVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/thumbs/ThumbnailVisualization.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Thumbnail visualization. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses ThumbnailThread */ @@ -200,7 +201,7 @@ public class ThumbnailVisualization extends AbstractVisualization implements Thu @Override public void resultChanged(Result current) { // Default is to redraw when the result we are attached to changed. - if(task.getResult() == current) { + if(task == current || task.getResult() == current) { refreshThumbnail(); return; } @@ -216,7 +217,7 @@ public class ThumbnailVisualization extends AbstractVisualization implements Thu @Override public void visualizationChanged(VisualizationItem item) { - if(task.updateOnAny(VisualizationTask.ON_STYLEPOLICY) && item instanceof StylingPolicy) { + if(task == item || (task.updateOnAny(VisualizationTask.ON_STYLEPOLICY) && item instanceof StylingPolicy)) { refreshThumbnail(); return; } diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/DendrogramVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/DendrogramVisualization.java new file mode 100644 index 00000000..1536f1a5 --- /dev/null +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/DendrogramVisualization.java @@ -0,0 +1,438 @@ +package de.lmu.ifi.dbs.elki.visualization.visualizers.visunproj; +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.apache.batik.util.SVGConstants; +import org.w3c.dom.Element; + +import de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.PointerHierarchyRepresentationResult; +import de.lmu.ifi.dbs.elki.database.datastore.DBIDDataStore; +import de.lmu.ifi.dbs.elki.database.datastore.DataStoreUtil; +import de.lmu.ifi.dbs.elki.database.datastore.DoubleDataStore; +import de.lmu.ifi.dbs.elki.database.datastore.IntegerDataStore; +import de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs; +import de.lmu.ifi.dbs.elki.database.ids.DBIDIter; +import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; +import de.lmu.ifi.dbs.elki.database.ids.DBIDVar; +import de.lmu.ifi.dbs.elki.database.ids.DBIDs; +import de.lmu.ifi.dbs.elki.logging.LoggingUtil; +import de.lmu.ifi.dbs.elki.math.scales.LinearScale; +import de.lmu.ifi.dbs.elki.utilities.datastructures.hierarchy.Hierarchy; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.EnumParameter; +import de.lmu.ifi.dbs.elki.visualization.VisualizationMenuAction; +import de.lmu.ifi.dbs.elki.visualization.VisualizationTask; +import de.lmu.ifi.dbs.elki.visualization.VisualizationTree; +import de.lmu.ifi.dbs.elki.visualization.VisualizerContext; +import de.lmu.ifi.dbs.elki.visualization.colors.ColorLibrary; +import de.lmu.ifi.dbs.elki.visualization.css.CSSClass; +import de.lmu.ifi.dbs.elki.visualization.css.CSSClassManager.CSSNamingConflict; +import de.lmu.ifi.dbs.elki.visualization.gui.VisualizationPlot; +import de.lmu.ifi.dbs.elki.visualization.projections.Projection; +import de.lmu.ifi.dbs.elki.visualization.style.ClassStylingPolicy; +import de.lmu.ifi.dbs.elki.visualization.style.StyleLibrary; +import de.lmu.ifi.dbs.elki.visualization.style.StylingPolicy; +import de.lmu.ifi.dbs.elki.visualization.svg.SVGPath; +import de.lmu.ifi.dbs.elki.visualization.svg.SVGPlot; +import de.lmu.ifi.dbs.elki.visualization.svg.SVGSimpleLinearAxis; +import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; +import de.lmu.ifi.dbs.elki.visualization.visualizers.AbstractVisFactory; +import de.lmu.ifi.dbs.elki.visualization.visualizers.AbstractVisualization; +import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; + +/** + * Dendrogram visualizer. + * + * @author Erich Schubert + * @since 0.7.1 + * + * @apiviz.stereotype factory + * @apiviz.uses Instance oneway - - «create» + */ +public class DendrogramVisualization extends AbstractVisFactory { + /** + * Visualizer name. + */ + private static final String NAME = "Dendrogram"; + + /** + * Styles for dendrograms. + * + * @author Erich Schubert + * + * @apiviz.exclude + */ + public static enum Style { + RECTANGULAR, // + TRIANGULAR, // + } + + /** + * Drawing style. + */ + private Style style = Style.RECTANGULAR; + + /** + * Constructor. + * + * @param style Visualization style. + */ + public DendrogramVisualization(Style style) { + super(); + this.style = style; + } + + @Override + public void processNewResult(VisualizerContext context, Object start) { + // Ensure there is a clustering result: + Hierarchy.Iter<PointerHierarchyRepresentationResult> it = VisualizationTree.filterResults(context, start, PointerHierarchyRepresentationResult.class); + for(; it.valid(); it.advance()) { + PointerHierarchyRepresentationResult pi = it.get(); + final VisualizationTask task = new VisualizationTask(NAME, context, pi, null, this); + task.level = VisualizationTask.LEVEL_STATIC; + task.addUpdateFlags(VisualizationTask.ON_STYLEPOLICY); + task.reqwidth = 1.; + task.reqheight = 1.; + context.addVis(context.getStylingPolicy(), task); + context.addVis(pi, new SwitchStyleAction(task, context)); + } + } + + @Override + public Visualization makeVisualization(VisualizationTask task, VisualizationPlot plot, double width, double height, Projection proj) { + return new Instance(task, plot, width, height); + } + + /** + * Menu item to change visualization styles. + * + * @author Erich Schubert + */ + public class SwitchStyleAction implements VisualizationMenuAction { + /** + * Task we represent. + */ + private VisualizationTask task; + + /** + * Visualizer context. + */ + private VisualizerContext context; + + /** + * Constructor. + * + * @param task Task + * @param context Visualizer context + */ + public SwitchStyleAction(VisualizationTask task, VisualizerContext context) { + super(); + this.task = task; + this.context = context; + } + + @Override + public String getMenuName() { + return "Switch Dendrogram Style"; + } + + @Override + public void activate() { + switch(style){ + case RECTANGULAR: + style = Style.TRIANGULAR; + break; + case TRIANGULAR: + style = Style.RECTANGULAR; + break; + } + context.visChanged(task); + } + + @Override + public boolean enabled() { + return true; + } + } + + /** + * Visualization instance. + * + * @author Erich Schubert + */ + public class Instance extends AbstractVisualization { + /** + * CSS class for key captions. + */ + private static final String KEY_CAPTION = "key-caption"; + + /** + * CSS class for hierarchy plot lines + */ + private static final String KEY_HIERLINE = "key-hierarchy"; + + /** + * Constructor. + * + * @param task Visualization task + * @param plot Plot to draw to + * @param width Embedding width + * @param height Embedding height + */ + public Instance(VisualizationTask task, VisualizationPlot plot, double width, double height) { + super(task, plot, width, height); + addListeners(); + } + + @Override + public void fullRedraw() { + layer = svgp.svgElement(SVGConstants.SVG_G_TAG); + + StyleLibrary style = context.getStyleLibrary(); + StylingPolicy spol = context.getStylingPolicy(); + + PointerHierarchyRepresentationResult p = task.getResult(); + + DBIDs ids = p.getDBIDs(); + DBIDDataStore par = p.getParentStore(); + DoubleDataStore pdi = p.getParentDistanceStore(); + IntegerDataStore pos = p.getPositions(); + DBIDVar pa = DBIDUtil.newVar(); + + final int size = ids.size(); + double linew = StyleLibrary.SCALE * .1 / Math.log1p(size); + double width = StyleLibrary.SCALE, + height = width / getWidth() * getHeight(); + double xscale = width / size, xoff = xscale * .5; + double maxh = Double.MIN_NORMAL; + for(DBIDIter it = ids.iter(); it.valid(); it.advance()) { + if(DBIDUtil.equal(it, par.assignVar(it, pa))) { + continue; // Root + } + double v = pdi.doubleValue(it); + if(v == Double.POSITIVE_INFINITY) { + continue; + } + maxh = v > maxh ? v : maxh; + } + LinearScale yscale = new LinearScale(0, maxh); + // add axes + try { + SVGSimpleLinearAxis.drawAxis(svgp, layer, yscale, 0, height, 0, 0, SVGSimpleLinearAxis.LabelStyle.LEFTHAND, style); + } + catch(CSSNamingConflict e) { + LoggingUtil.exception(e); + } + + // Initial positions: + double[] xy = new double[size << 1]; + for(DBIDIter it = ids.iter(); it.valid(); it.advance()) { + final int off = pos.intValue(it); + xy[off] = off * xscale + xoff; + xy[off + size] = height; + } + // Draw ascending by distance + ArrayModifiableDBIDs order = DBIDUtil.newArray(ids); + order.sort(new DataStoreUtil.AscendingByDoubleDataStoreAndId(pdi)); + + if(spol instanceof ClassStylingPolicy) { + ClassStylingPolicy cspol = (ClassStylingPolicy) spol; + setupCSS(svgp, cspol, linew); + int mins = cspol.getMinStyle() - 1, maxs = cspol.getMaxStyle(); + SVGPath[] paths = new SVGPath[maxs - mins + 1]; + for(int i = 0; i < paths.length; i++) { + paths[i] = new SVGPath(); + } + for(DBIDIter it = order.iter(); it.valid(); it.advance()) { + par.assignVar(it, pa); // Get parent. + double h = pdi.doubleValue(it); + final int o1 = pos.intValue(it); + final int p1 = cspol.getStyleForDBID(it); + double x1 = xy[o1], y1 = xy[o1 + size]; + if(DBIDUtil.equal(it, pa)) { + paths[p1 - mins + 1].moveTo(x1, y1).verticalLineTo(height * (1 - yscale.getScaled(h))); + continue; // Root + } + final int o2 = pos.intValue(pa); + final int p2 = cspol.getStyleForDBID(pa); + double x2 = xy[o2], y2 = xy[o2 + size]; + double x3 = (x1 + x2) * .5, y3 = height * (1 - yscale.getScaled(h)); + switch(DendrogramVisualization.this.style){ + case RECTANGULAR: + if(p1 == p2) { + paths[p1 - mins + 1].moveTo(x1, y1).verticalLineTo(y3).horizontalLineTo(x2).verticalLineTo(y2); + } + else { + paths[y1 == height ? p1 - mins + 1 : 0].moveTo(x1, y1).verticalLineTo(y3); + paths[y2 == height ? p2 - mins + 1 : 0].moveTo(x2, y2).verticalLineTo(y3); + paths[0].moveTo(x1, y3).horizontalLineTo(x2); + } + break; + case TRIANGULAR: + if(p1 == p2) { + paths[p1 - mins + 1].moveTo(x1, y1).drawTo(x3, y3).drawTo(x2, y2); + } + else { + paths[y1 == height ? p1 - mins + 1 : 0].moveTo(x1, y1).drawTo(x3, y3); + paths[y2 == height ? p2 - mins + 1 : 0].moveTo(x2, y2).drawTo(x3, y3); + } + break; + } + xy[o2] = x3; + xy[o2 + size] = y3; + } + for(int i = 0; i < paths.length; i++) { + SVGPath path = paths[i]; + if(!path.isStarted()) { + continue; + } + Element elem = path.makeElement(svgp); + SVGUtil.setCSSClass(elem, (i > 0 ? KEY_HIERLINE + "_" + (i + mins - 1) : KEY_HIERLINE)); + layer.appendChild(elem); + } + } + else { + setupCSS(svgp, linew); + SVGPath dendrogram = new SVGPath(); + + for(DBIDIter it = order.iter(); it.valid(); it.advance()) { + double h = pdi.doubleValue(it); + final int o1 = pos.intValue(it); + double x1 = xy[o1], y1 = xy[o1 + size]; + if(DBIDUtil.equal(it, par.assignVar(it, pa))) { + dendrogram.moveTo(x1, y1).verticalLineTo(height * (1 - yscale.getScaled(h))); + continue; // Root + } + final int o2 = pos.intValue(pa); + double x2 = xy[o2], y2 = xy[o2 + size]; + double x3 = (x1 + x2) * .5, y3 = height * (1 - yscale.getScaled(h)); + switch(DendrogramVisualization.this.style){ + case RECTANGULAR: + dendrogram.moveTo(x1, y1).verticalLineTo(y3).horizontalLineTo(x2).verticalLineTo(y2); + break; + case TRIANGULAR: + dendrogram.moveTo(x1, y1).drawTo(x3, y3).drawTo(x2, y2); + break; + } + xy[o2] = x3; + xy[o2 + size] = y3; + } + Element elem = dendrogram.makeElement(svgp); + SVGUtil.setCSSClass(elem, KEY_HIERLINE); + layer.appendChild(elem); + } + + final double margin = style.getSize(StyleLibrary.MARGIN); + final String transform = SVGUtil.makeMarginTransform(getWidth(), getHeight(), width, height, margin); + SVGUtil.setAtt(layer, SVGConstants.SVG_TRANSFORM_ATTRIBUTE, transform); + } + + /** + * Register the CSS classes. + * + * @param svgp the SVGPlot to register the CSS classes. + * @param linew Line width adjustment + */ + protected void setupCSS(SVGPlot svgp, double linew) { + final StyleLibrary style = context.getStyleLibrary(); + final double fontsize = style.getTextSize(StyleLibrary.KEY); + final String fontfamily = style.getFontFamily(StyleLibrary.KEY); + final String color = style.getColor(StyleLibrary.KEY); + + CSSClass keycaption = new CSSClass(svgp, KEY_CAPTION); + keycaption.setStatement(SVGConstants.CSS_FONT_SIZE_PROPERTY, fontsize); + keycaption.setStatement(SVGConstants.CSS_FONT_FAMILY_PROPERTY, fontfamily); + keycaption.setStatement(SVGConstants.CSS_FILL_PROPERTY, color); + keycaption.setStatement(SVGConstants.CSS_FONT_WEIGHT_PROPERTY, SVGConstants.CSS_BOLD_VALUE); + svgp.addCSSClassOrLogError(keycaption); + + CSSClass hierline = new CSSClass(svgp, KEY_HIERLINE); + hierline.setStatement(SVGConstants.CSS_STROKE_PROPERTY, color); + hierline.setStatement(SVGConstants.CSS_STROKE_WIDTH_PROPERTY, linew * style.getLineWidth("key.hierarchy") / StyleLibrary.SCALE); + hierline.setStatement(SVGConstants.CSS_STROKE_LINECAP_PROPERTY, SVGConstants.CSS_ROUND_VALUE); + hierline.setStatement(SVGConstants.CSS_FILL_PROPERTY, SVGConstants.CSS_NONE_VALUE); + svgp.addCSSClassOrLogError(hierline); + + svgp.updateStyleElement(); + } + + /** + * Register the CSS classes. + * + * @param svgp the SVGPlot to register the CSS classes. + * @param cspol Class styling policy + * @param linew Line width adjustment + */ + protected void setupCSS(SVGPlot svgp, ClassStylingPolicy cspol, double linew) { + setupCSS(svgp, linew); + StyleLibrary style = context.getStyleLibrary(); + ColorLibrary colors = style.getColorSet(StyleLibrary.PLOT); + + for(int i = cspol.getMinStyle(); i <= cspol.getMaxStyle(); i++) { + CSSClass hierline = new CSSClass(svgp, KEY_HIERLINE + "_" + i); + hierline.setStatement(SVGConstants.CSS_STROKE_PROPERTY, colors.getColor(i)); + hierline.setStatement(SVGConstants.CSS_STROKE_WIDTH_PROPERTY, linew * style.getLineWidth("key.hierarchy") / StyleLibrary.SCALE); + hierline.setStatement(SVGConstants.CSS_STROKE_LINECAP_PROPERTY, SVGConstants.CSS_ROUND_VALUE); + hierline.setStatement(SVGConstants.CSS_FILL_PROPERTY, SVGConstants.CSS_NONE_VALUE); + svgp.addCSSClassOrLogError(hierline); + } + + svgp.updateStyleElement(); + } + } + + /** + * Parameterization class. + * + * @author Erich Schubert + * + * @apiviz.exclude + */ + public static class Parameterizer extends AbstractParameterizer { + /** + * Dendrogram drawing style. + */ + public static final OptionID STYLE_ID = new OptionID("dendrogram.style", "Drawing style for dendrograms."); + + /** + * Drawing style. + */ + private Style style = Style.RECTANGULAR; + + @Override + protected void makeOptions(Parameterization config) { + super.makeOptions(config); + EnumParameter<Style> styleP = new EnumParameter<>(STYLE_ID, Style.class, Style.RECTANGULAR); + if(config.grab(styleP)) { + style = styleP.getValue(); + } + } + + @Override + protected DendrogramVisualization makeInstance() { + return new DendrogramVisualization(style); + } + } +}
\ No newline at end of file diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/EvaluationVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/EvaluationVisualization.java index b378c71a..12d16af2 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/EvaluationVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/EvaluationVisualization.java @@ -57,6 +57,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * * @author Erich Schubert * @author Sascha Goldhofer + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses StaticVisualizationInstance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/HistogramVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/HistogramVisualization.java index 1d3e8771..3051e365 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/HistogramVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/HistogramVisualization.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Visualizer to draw histograms. * * @author Erich Schubert + * @since 0.3 * * @apiviz.stereotype factory * @apiviz.uses StaticVisualizationInstance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/KeyVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/KeyVisualization.java index 7361bd4e..9676d943 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/KeyVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/KeyVisualization.java @@ -61,6 +61,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * TODO: also show in scatter plot detail view. * * @author Erich Schubert + * @since 0.3 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/LabelVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/LabelVisualization.java index c89d9c75..9727ace3 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/LabelVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/LabelVisualization.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * be used for dimension labels in the overview. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses StaticVisualizationInstance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/PixmapVisualizer.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/PixmapVisualizer.java index b6fcdd57..99d7cd18 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/PixmapVisualizer.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/PixmapVisualizer.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Visualize an arbitrary pixmap result. * * @author Erich Schubert + * @since 0.3 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/SettingsVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/SettingsVisualization.java index 3efa04d1..d7786699 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/SettingsVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/SettingsVisualization.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Pseudo-Visualizer, that lists the settings of the algorithm- * * @author Erich Schubert + * @since 0.3 * * @apiviz.stereotype factory * @apiviz.uses StaticVisualizationInstance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/SimilarityMatrixVisualizer.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/SimilarityMatrixVisualizer.java index 0b64d6c3..007db56b 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/SimilarityMatrixVisualizer.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/SimilarityMatrixVisualizer.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Visualize a similarity matrix with object labels * * @author Erich Schubert + * @since 0.3 * * @apiviz.stereotype factory * @apiviz.uses Instance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/XYCurveVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/XYCurveVisualization.java index 3c620a8f..0939a309 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/XYCurveVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/XYCurveVisualization.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Visualizer to render a simple 2D curve such as a ROC curve. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses StaticVisualizationInstance oneway - - «create» diff --git a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/XYPlotVisualization.java b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/XYPlotVisualization.java index 3b07860d..0158cd0f 100644 --- a/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/XYPlotVisualization.java +++ b/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/XYPlotVisualization.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; * Visualizer to render a simple 2D curve such as a ROC curve. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.stereotype factory * @apiviz.uses StaticVisualizationInstance oneway - - «create» diff --git a/addons/batikvis/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.result.ResultHandler b/addons/batikvis/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.result.ResultHandler index 00032d8f..f2e962aa 100644 --- a/addons/batikvis/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.result.ResultHandler +++ b/addons/batikvis/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.result.ResultHandler @@ -1,2 +1,2 @@ -de.lmu.ifi.dbs.elki.visualization.gui.ResultVisualizer visualizer vis ResultVisualizer -de.lmu.ifi.dbs.elki.visualization.ExportVisualizations +de.lmu.ifi.dbs.elki.result.AutomaticVisualization de.lmu.ifi.dbs.elki.visualization.gui.ResultVisualizer visualizer vis ResultVisualizer +de.lmu.ifi.dbs.elki.result.ExportVisualizations de.lmu.ifi.dbs.elki.visualization.ExportVisualizations diff --git a/addons/batikvis/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.visualization.VisualizationProcessor b/addons/batikvis/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.visualization.VisualizationProcessor index 3ba543d8..10ead960 100644 --- a/addons/batikvis/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.visualization.VisualizationProcessor +++ b/addons/batikvis/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.visualization.VisualizationProcessor @@ -52,6 +52,7 @@ de.lmu.ifi.dbs.elki.visualization.visualizers.visunproj.LabelVisualization de.lmu.ifi.dbs.elki.visualization.visualizers.visunproj.PixmapVisualizer de.lmu.ifi.dbs.elki.visualization.visualizers.visunproj.SimilarityMatrixVisualizer de.lmu.ifi.dbs.elki.visualization.visualizers.visunproj.KeyVisualization +de.lmu.ifi.dbs.elki.visualization.visualizers.visunproj.DendrogramVisualization de.lmu.ifi.dbs.elki.visualization.visualizers.visunproj.SettingsVisualization de.lmu.ifi.dbs.elki.visualization.visualizers.optics.OPTICSClusterVisualization de.lmu.ifi.dbs.elki.visualization.visualizers.optics.OPTICSPlotCutVisualization diff --git a/addons/batikvis/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.visualization.visualizers.VisFactory b/addons/batikvis/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.visualization.visualizers.VisFactory index 19c05f02..975bda67 100644 --- a/addons/batikvis/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.visualization.visualizers.VisFactory +++ b/addons/batikvis/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.visualization.visualizers.VisFactory @@ -48,6 +48,7 @@ de.lmu.ifi.dbs.elki.visualization.visualizers.visunproj.LabelVisualization de.lmu.ifi.dbs.elki.visualization.visualizers.visunproj.PixmapVisualizer de.lmu.ifi.dbs.elki.visualization.visualizers.visunproj.SimilarityMatrixVisualizer de.lmu.ifi.dbs.elki.visualization.visualizers.visunproj.KeyVisualization +de.lmu.ifi.dbs.elki.visualization.visualizers.visunproj.DendrogramVisualization de.lmu.ifi.dbs.elki.visualization.visualizers.visunproj.SettingsVisualization de.lmu.ifi.dbs.elki.visualization.visualizers.optics.OPTICSClusterVisualization de.lmu.ifi.dbs.elki.visualization.visualizers.optics.OPTICSPlotCutVisualization diff --git a/addons/batikvis/src/main/resources/META-INF/services/org.apache.batik.ext.awt.image.spi.ImageWriter b/addons/batikvis/src/main/resources/META-INF/services/org.apache.batik.ext.awt.image.spi.ImageWriter new file mode 100644 index 00000000..1ed70164 --- /dev/null +++ b/addons/batikvis/src/main/resources/META-INF/services/org.apache.batik.ext.awt.image.spi.ImageWriter @@ -0,0 +1,2 @@ +# BUG FIX for Batik 1.8 +org.apache.batik.ext.awt.image.codec.png.PNGImageWriter
\ No newline at end of file diff --git a/addons/batikvis/src/main/resources/META-INF/services/org.apache.batik.ext.awt.image.spi.RegistryEntry b/addons/batikvis/src/main/resources/META-INF/services/org.apache.batik.ext.awt.image.spi.RegistryEntry index f1252025..3529e5ce 100644 --- a/addons/batikvis/src/main/resources/META-INF/services/org.apache.batik.ext.awt.image.spi.RegistryEntry +++ b/addons/batikvis/src/main/resources/META-INF/services/org.apache.batik.ext.awt.image.spi.RegistryEntry @@ -1 +1,3 @@ -de.lmu.ifi.dbs.elki.visualization.batikutil.ThumbnailRegistryEntry
\ No newline at end of file +de.lmu.ifi.dbs.elki.visualization.batikutil.ThumbnailRegistryEntry +# BUG FIX for Batik 1.8 +org.apache.batik.ext.awt.image.codec.png.PNGRegistryEntry
\ No newline at end of file diff --git a/addons/bundle/pom.xml b/addons/bundle/pom.xml index a7785b84..211d9c1c 100644 --- a/addons/bundle/pom.xml +++ b/addons/bundle/pom.xml @@ -1,10 +1,11 @@ +<?xml version='1.0' encoding='UTF-8'?> <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> <modelVersion>4.0.0</modelVersion> <parent> <groupId>de.lmu.ifi.dbs.elki</groupId> - <version>0.7.0</version> + <version>0.7.1</version> <artifactId>elki-project</artifactId> <relativePath>../..</relativePath> </parent> @@ -53,16 +54,15 @@ <plugins> <!-- Ensure the directory exists, for code below. --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-antrun-plugin</artifactId> <executions> <execution> <id>createJavadocDir</id> - <phase>prepare-package</phase> + <phase>compile</phase><!-- abuse compile to run before prepare-package --> <configuration> - <tasks> + <target> <mkdir dir="${project.build.directory}/apidocs" /> - </tasks> + </target> </configuration> <goals> <goal>run</goal> @@ -70,11 +70,27 @@ </execution> </executions> </plugin> + <!-- Copy dependencies earlier: --> + <plugin> + <artifactId>maven-dependency-plugin</artifactId> + <executions> + <execution> + <id>copy-dependencies</id> + <phase>compile</phase> <!-- abuse compile to run before prepare-package --> + <goals> + <goal>copy-dependencies</goal> + </goals> + <configuration> + <outputDirectory>${outputDir}</outputDirectory> + <excludeArtifactIds>junit:*,org.hamcrest:*</excludeArtifactIds> + </configuration> + </execution> + </executions> + </plugin> <!-- Extract (and rename) licensing information; build additional documentation --> <plugin> <groupId>org.codehaus.mojo</groupId> <artifactId>exec-maven-plugin</artifactId> - <version>1.3.1</version> <executions> <execution> <id>build-legal</id> @@ -100,8 +116,7 @@ <configuration> <executable>java</executable> <arguments> - <!-- <argument>-cp</argument> - <classpath/> --> + <!-- <argument>-cp</argument> <classpath/> --> <!-- This is a hack, because these applications will currently ignore jars, so we need the folders on the classpath, too --> <argument>-cp</argument> @@ -122,8 +137,7 @@ <configuration> <executable>java</executable> <arguments> - <!-- <argument>-cp</argument> - <classpath/> --> + <!-- <argument>-cp</argument> <classpath/> --> <!-- This is a hack, because these applications will currently ignore jars, so we need the folders on the classpath, too --> <argument>-cp</argument> @@ -139,9 +153,7 @@ </plugin> <!-- jar plugin --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-jar-plugin</artifactId> - <version>2.4</version> <configuration> <archive> <manifestFile>${elki.projdir}/elki/src/main/resources/META-INF/MANIFEST.MF</manifestFile> @@ -154,7 +166,6 @@ </plugin> <!-- shade plugin --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-shade-plugin</artifactId> <version>2.3</version> <executions> @@ -242,7 +253,6 @@ <!-- copy additional javadoc resources --> <plugin> <artifactId>maven-resources-plugin</artifactId> - <version>2.7</version> <executions> <execution> <id>copy-resources</id> @@ -269,9 +279,7 @@ </plugin> <!-- Build JavaDoc --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-javadoc-plugin</artifactId> - <version>2.10.3</version> <executions> <execution> <id>attach-javadocs</id> @@ -293,9 +301,7 @@ </plugin> <!-- Fake source code packaging --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-source-plugin</artifactId> - <version>2.2.1</version> <executions> <execution> <id>attach-sources</id> diff --git a/addons/joglvis/pom.xml b/addons/joglvis/pom.xml index 4c9df934..a2c80ada 100644 --- a/addons/joglvis/pom.xml +++ b/addons/joglvis/pom.xml @@ -1,10 +1,11 @@ +<?xml version='1.0' encoding='UTF-8'?> <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> <modelVersion>4.0.0</modelVersion> <parent> <groupId>de.lmu.ifi.dbs.elki</groupId> - <version>0.6.5-SNAPSHOT</version> + <version>0.7.1</version> <artifactId>elki-project</artifactId> <relativePath>../../</relativePath> </parent> @@ -25,32 +26,11 @@ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> </properties> - <build> - <plugins> - <!-- javadoc --> - <plugin> - <groupId>org.apache.maven.plugins</groupId> - <artifactId>maven-javadoc-plugin</artifactId> - <version>2.9.1</version> - <configuration> - </configuration> - </plugin> - <!-- jar packaging --> - <plugin> - <groupId>org.apache.maven.plugins</groupId> - <artifactId>maven-jar-plugin</artifactId> - <version>2.3.1</version> - <configuration> - </configuration> - </plugin> - </plugins> - </build> - <dependencies> <dependency> <groupId>de.lmu.ifi.dbs.elki</groupId> <artifactId>elki</artifactId> - <version>0.6.5-SNAPSHOT</version> + <version>${project.version}</version> </dependency> <dependency> <groupId>org.jogamp.jogl</groupId> @@ -65,7 +45,7 @@ <dependency> <groupId>de.lmu.ifi.dbs.elki</groupId> <artifactId>elki-batik-visualization</artifactId> - <version>0.6.5-SNAPSHOT</version> + <version>${project.version}</version> </dependency> </dependencies> </project> diff --git a/addons/joglvis/src/main/java/de/lmu/ifi/dbs/elki/joglvis/ShaderUtil.java b/addons/joglvis/src/main/java/de/lmu/ifi/dbs/elki/joglvis/ShaderUtil.java index e9d3fbda..37e86ca3 100644 --- a/addons/joglvis/src/main/java/de/lmu/ifi/dbs/elki/joglvis/ShaderUtil.java +++ b/addons/joglvis/src/main/java/de/lmu/ifi/dbs/elki/joglvis/ShaderUtil.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.FileUtil; * Class to help dealing with shaders. * * @author Erich Schubert + * @since 0.6.0 */ public class ShaderUtil { /** diff --git a/addons/joglvis/src/main/java/de/lmu/ifi/dbs/elki/joglvis/SimpleCamera3D.java b/addons/joglvis/src/main/java/de/lmu/ifi/dbs/elki/joglvis/SimpleCamera3D.java index 9925c3a0..f4f22191 100644 --- a/addons/joglvis/src/main/java/de/lmu/ifi/dbs/elki/joglvis/SimpleCamera3D.java +++ b/addons/joglvis/src/main/java/de/lmu/ifi/dbs/elki/joglvis/SimpleCamera3D.java @@ -29,6 +29,7 @@ import javax.media.opengl.glu.GLU; * Very simple (rotating) camera. * * @author Erich Schubert + * @since 0.6.0 */ public class SimpleCamera3D { /** diff --git a/addons/joglvis/src/main/java/de/lmu/ifi/dbs/elki/joglvis/scatterplot/ScatterData.java b/addons/joglvis/src/main/java/de/lmu/ifi/dbs/elki/joglvis/scatterplot/ScatterData.java index 1182c450..47576b25 100644 --- a/addons/joglvis/src/main/java/de/lmu/ifi/dbs/elki/joglvis/scatterplot/ScatterData.java +++ b/addons/joglvis/src/main/java/de/lmu/ifi/dbs/elki/joglvis/scatterplot/ScatterData.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.FormatUtil; * Class to manage the vector data in the GPU. * * @author Erich Schubert + * @since 0.6.0 */ public class ScatterData { /** diff --git a/addons/libsvm/pom.xml b/addons/libsvm/pom.xml index 7d4686eb..53d4c174 100644 --- a/addons/libsvm/pom.xml +++ b/addons/libsvm/pom.xml @@ -1,10 +1,11 @@ +<?xml version='1.0' encoding='UTF-8'?> <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> <modelVersion>4.0.0</modelVersion> <parent> <groupId>de.lmu.ifi.dbs.elki</groupId> - <version>0.7.0</version> + <version>0.7.1</version> <artifactId>elki-project</artifactId> <relativePath>../../</relativePath> </parent> diff --git a/addons/libsvm/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/svm/LibSVMOneClassOutlierDetection.java b/addons/libsvm/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/svm/LibSVMOneClassOutlierDetection.java index 6908ade3..d282bc54 100644 --- a/addons/libsvm/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/svm/LibSVMOneClassOutlierDetection.java +++ b/addons/libsvm/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/svm/LibSVMOneClassOutlierDetection.java @@ -70,6 +70,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.EnumParameter; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @param V vector type */ diff --git a/addons/lucene/pom.xml b/addons/lucene/pom.xml index 90458e9b..c478379a 100644 --- a/addons/lucene/pom.xml +++ b/addons/lucene/pom.xml @@ -1,10 +1,11 @@ +<?xml version='1.0' encoding='UTF-8'?> <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> <modelVersion>4.0.0</modelVersion> <parent> <groupId>de.lmu.ifi.dbs.elki</groupId> - <version>0.7.0</version> + <version>0.7.1</version> <artifactId>elki-project</artifactId> <relativePath>../../</relativePath> </parent> @@ -25,27 +26,6 @@ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> </properties> - <build> - <plugins> - <!-- javadoc --> - <plugin> - <groupId>org.apache.maven.plugins</groupId> - <artifactId>maven-javadoc-plugin</artifactId> - <version>2.9.1</version> - <configuration> - </configuration> - </plugin> - <!-- jar packaging --> - <plugin> - <groupId>org.apache.maven.plugins</groupId> - <artifactId>maven-jar-plugin</artifactId> - <version>2.3.1</version> - <configuration> - </configuration> - </plugin> - </plugins> - </build> - <dependencies> <dependency> <groupId>de.lmu.ifi.dbs.elki</groupId> diff --git a/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/application/lucene/SimpleTextLoader.java b/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/application/lucene/SimpleTextLoader.java index c04812e0..c6f1e36a 100644 --- a/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/application/lucene/SimpleTextLoader.java +++ b/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/application/lucene/SimpleTextLoader.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; * Simple text loader, assuming a folder with plain text files. * * @author Erich Schubert + * @since 0.6.0 */ public class SimpleTextLoader extends AbstractApplication { /** diff --git a/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDatabase.java b/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDatabase.java index dcb1a03a..865fcde7 100644 --- a/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDatabase.java +++ b/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDatabase.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; * Database backend using Lucene 3. * * @author Erich Schubert + * @since 0.6.0 */ public class LuceneDatabase extends AbstractDatabase { /** diff --git a/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDistanceFunction.java b/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDistanceFunction.java index c1ac81a4..d3202606 100644 --- a/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDistanceFunction.java +++ b/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDistanceFunction.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * Distance function, interfacing back into Lucene. * * @author Erich Schubert + * @since 0.4.0 */ public class LuceneDistanceFunction extends AbstractDBIDRangeDistanceFunction { /** diff --git a/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDistanceKNNQuery.java b/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDistanceKNNQuery.java index 70816bbd..b49dc455 100644 --- a/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDistanceKNNQuery.java +++ b/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDistanceKNNQuery.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * Perform similarity search using lucene. * * @author Erich Schubert + * @since 0.6.0 */ public class LuceneDistanceKNNQuery extends AbstractDistanceKNNQuery<DBID> { /** diff --git a/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDistanceRangeQuery.java b/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDistanceRangeQuery.java index 03a318df..e0e3f265 100644 --- a/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDistanceRangeQuery.java +++ b/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDistanceRangeQuery.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * Perform range similarity search using lucene. * * @author Erich Schubert + * @since 0.6.0 */ public class LuceneDistanceRangeQuery extends AbstractDistanceRangeQuery<DBID> { /** diff --git a/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDocumentRelation.java b/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDocumentRelation.java index 0afbb8f0..ac329680 100644 --- a/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDocumentRelation.java +++ b/addons/lucene/src/main/java/de/lmu/ifi/dbs/elki/database/lucene/LuceneDocumentRelation.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * Relation representing the Lucene document. * * @author Erich Schubert + * @since 0.4.0 */ public class LuceneDocumentRelation extends AbstractRelation<Document> { /** diff --git a/addons/tutorial/pom.xml b/addons/tutorial/pom.xml index 5d39e6e7..2384571d 100644 --- a/addons/tutorial/pom.xml +++ b/addons/tutorial/pom.xml @@ -1,10 +1,11 @@ +<?xml version='1.0' encoding='UTF-8'?> <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> <modelVersion>4.0.0</modelVersion> <parent> <groupId>de.lmu.ifi.dbs.elki</groupId> - <version>0.7.0</version> + <version>0.7.1</version> <artifactId>elki-project</artifactId> <relativePath>../../</relativePath> </parent> @@ -29,9 +30,7 @@ <plugins> <!-- jar packaging --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-jar-plugin</artifactId> - <version>2.3.1</version> <configuration> <archive> <manifestFile>${elki.projdir}/elki/src/main/resources/META-INF/MANIFEST.MF</manifestFile> @@ -63,6 +62,7 @@ <groupId>de.lmu.ifi.dbs.elki</groupId> <artifactId>elki-batik-visualization</artifactId> <version>${project.version}</version> + <optional>true</optional> </dependency> </dependencies> </project> diff --git a/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering1.java b/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering1.java index 1535ef9c..f5aba0ec 100644 --- a/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering1.java +++ b/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering1.java @@ -65,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * algorithm (however, only for single-linkage). * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Object type */ diff --git a/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering2.java b/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering2.java index f0b1cbd9..9d6eacaa 100644 --- a/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering2.java +++ b/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering2.java @@ -65,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * algorithm (however, only for single-linkage). * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Object type */ diff --git a/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering3.java b/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering3.java index 6bf133ec..3178d366 100644 --- a/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering3.java +++ b/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering3.java @@ -76,6 +76,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Object type */ diff --git a/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering4.java b/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering4.java index 6b5b59cf..1e5a8b7e 100644 --- a/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering4.java +++ b/addons/tutorial/src/main/java/tutorial/clustering/NaiveAgglomerativeHierarchicalClustering4.java @@ -69,6 +69,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.EnumParameter; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Object type */ diff --git a/addons/tutorial/src/main/java/tutorial/clustering/SameSizeKMeansAlgorithm.java b/addons/tutorial/src/main/java/tutorial/clustering/SameSizeKMeansAlgorithm.java index 06fe1276..a7f9376b 100644 --- a/addons/tutorial/src/main/java/tutorial/clustering/SameSizeKMeansAlgorithm.java +++ b/addons/tutorial/src/main/java/tutorial/clustering/SameSizeKMeansAlgorithm.java @@ -74,6 +74,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * http://elki.dbs.ifi.lmu.de/wiki/Releases * * @author Erich Schubert + * @since 0.5.5 * * @param <V> Vector type */ diff --git a/addons/tutorial/src/main/java/tutorial/distancefunction/MultiLPNorm.java b/addons/tutorial/src/main/java/tutorial/distancefunction/MultiLPNorm.java index 64ac95e0..a3992708 100644 --- a/addons/tutorial/src/main/java/tutorial/distancefunction/MultiLPNorm.java +++ b/addons/tutorial/src/main/java/tutorial/distancefunction/MultiLPNorm.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleListParamet * function tutorial</a> * * @author Erich Schubert + * @since 0.5.0 */ public class MultiLPNorm extends AbstractNumberVectorDistanceFunction { /** diff --git a/addons/tutorial/src/main/java/tutorial/distancefunction/TutorialDistanceFunction.java b/addons/tutorial/src/main/java/tutorial/distancefunction/TutorialDistanceFunction.java index 7e1bbf9e..ebbd0d52 100644 --- a/addons/tutorial/src/main/java/tutorial/distancefunction/TutorialDistanceFunction.java +++ b/addons/tutorial/src/main/java/tutorial/distancefunction/TutorialDistanceFunction.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractNumberVectorDistanc * function tutorial</a> * * @author Erich Schubert + * @since 0.4.0 */ public class TutorialDistanceFunction extends AbstractNumberVectorDistanceFunction { @Override diff --git a/addons/tutorial/src/main/java/tutorial/javaapi/PassingDataToELKI.java b/addons/tutorial/src/main/java/tutorial/javaapi/PassingDataToELKI.java index 96d460eb..5fa3da24 100644 --- a/addons/tutorial/src/main/java/tutorial/javaapi/PassingDataToELKI.java +++ b/addons/tutorial/src/main/java/tutorial/javaapi/PassingDataToELKI.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.math.random.RandomFactory; * Example program to generate a random data set, and run k-means on it. * * @author Erich Schubert + * @since 0.7.0 */ public class PassingDataToELKI { /** diff --git a/addons/tutorial/src/main/java/tutorial/outlier/DistanceStddevOutlier.java b/addons/tutorial/src/main/java/tutorial/outlier/DistanceStddevOutlier.java index c9529113..1a022892 100644 --- a/addons/tutorial/src/main/java/tutorial/outlier/DistanceStddevOutlier.java +++ b/addons/tutorial/src/main/java/tutorial/outlier/DistanceStddevOutlier.java @@ -56,6 +56,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * the kNN distances. * * @author Erich Schubert + * @since 0.5.0 * * @param <O> Object type */ diff --git a/addons/tutorial/src/main/java/tutorial/outlier/ODIN.java b/addons/tutorial/src/main/java/tutorial/outlier/ODIN.java index b498aea4..48605102 100644 --- a/addons/tutorial/src/main/java/tutorial/outlier/ODIN.java +++ b/addons/tutorial/src/main/java/tutorial/outlier/ODIN.java @@ -64,6 +64,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Object type */ diff --git a/addons/tutorial/src/main/java/tutorial/outlier/SimpleScoreDumper.java b/addons/tutorial/src/main/java/tutorial/outlier/SimpleScoreDumper.java index f3b84eaf..2ecef2ad 100644 --- a/addons/tutorial/src/main/java/tutorial/outlier/SimpleScoreDumper.java +++ b/addons/tutorial/src/main/java/tutorial/outlier/SimpleScoreDumper.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; * Simple example output handler for processing outlier scores. * * @author Erich Schubert + * @since 0.2 */ public class SimpleScoreDumper implements ResultHandler { @Override diff --git a/elki/pom.xml b/elki/pom.xml index dfa3d273..9be1ea8d 100644 --- a/elki/pom.xml +++ b/elki/pom.xml @@ -1,10 +1,11 @@ +<?xml version='1.0' encoding='UTF-8'?> <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> <modelVersion>4.0.0</modelVersion> <parent> <groupId>de.lmu.ifi.dbs.elki</groupId> - <version>0.7.0</version> + <version>0.7.1</version> <artifactId>elki-project</artifactId> <relativePath>../</relativePath> </parent> @@ -51,9 +52,7 @@ <plugins> <!-- jar packaging --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-jar-plugin</artifactId> - <version>2.3.1</version> <configuration> <archive> <manifestFile>${elki.projdir}/elki/src/main/resources/META-INF/MANIFEST.MF</manifestFile> @@ -68,7 +67,6 @@ <!-- copy additional javadoc resources --> <plugin> <artifactId>maven-resources-plugin</artifactId> - <version>2.7</version> <executions> <execution> <id>copy-resources</id> @@ -94,7 +92,6 @@ <plugin> <groupId>org.codehaus.mojo</groupId> <artifactId>exec-maven-plugin</artifactId> - <version>1.3.2</version> <executions> <execution> <id>generate-javadoc-parameters</id> @@ -134,9 +131,7 @@ </plugin> <!-- Build JavaDoc --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-javadoc-plugin</artifactId> - <version>2.10.1</version> <executions> <execution> <id>attach-javadocs</id> diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/KDDTask.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/KDDTask.java index 307387d0..1d58b3ba 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/KDDTask.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/KDDTask.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.workflow.OutputStep; * discovery task. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.composedOf InputStep * @apiviz.composedOf AlgorithmStep diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractAlgorithm.java index 0851a898..8f721fdc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractAlgorithm.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Arthur Zimek + * @since 0.2 * * @apiviz.landmark * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractDistanceBasedAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractDistanceBasedAlgorithm.java index 5729695c..bbf76f03 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractDistanceBasedAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractDistanceBasedAlgorithm.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Abstract base class for distance-based algorithms. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.landmark * @apiviz.has DistanceFunction diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractNumberVectorDistanceBasedAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractNumberVectorDistanceBasedAlgorithm.java index 5c09d4a8..e0beaa36 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractNumberVectorDistanceBasedAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractNumberVectorDistanceBasedAlgorithm.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * synthetic numerical vectors such as <b>mean</b> vectors. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has NumberVectorDistanceFunction * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractPrimitiveDistanceBasedAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractPrimitiveDistanceBasedAlgorithm.java index 06625263..21de6b59 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractPrimitiveDistanceBasedAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/AbstractPrimitiveDistanceBasedAlgorithm.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * only database objects! * * @author Arthur Zimek + * @since 0.2 * * @apiviz.has PrimitiveDistanceFunction * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/Algorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/Algorithm.java index 1ca6ffa3..cea7f4b3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/Algorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/Algorithm.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.result.Result; * </p> * * @author Arthur Zimek + * @since 0.2 */ public interface Algorithm { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/DependencyDerivator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/DependencyDerivator.java index 3c6dbba6..b46fc6ac 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/DependencyDerivator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/DependencyDerivator.java @@ -71,6 +71,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Arthur Zimek + * @since 0.2 * @param <V> the type of FeatureVector handled by this Algorithm */ @Title("Dependency Derivator: Deriving numerical inter-dependencies on data") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/DistanceBasedAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/DistanceBasedAlgorithm.java index 5171de6d..5c4eaaf8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/DistanceBasedAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/DistanceBasedAlgorithm.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; * Very broad interface for distance based algorithms. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/DummyAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/DummyAlgorithm.java index 595de4bd..7aa28b70 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/DummyAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/DummyAlgorithm.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * NullAlgorithm} instead. * * @author Erich Schubert + * @since 0.2 * @param <O> Vector type * * @apiviz.uses KNNQuery diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/KNNDistancesSampler.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/KNNDistancesSampler.java index 3e78ba77..a81823c1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/KNNDistancesSampler.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/KNNDistancesSampler.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress; import de.lmu.ifi.dbs.elki.math.geometry.XYCurve; import de.lmu.ifi.dbs.elki.math.random.RandomFactory; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; @@ -59,11 +60,13 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * and look for a bend or knee in this plot. * * @author Arthur Zimek + * @since 0.7.0 * * @param <O> the type of objects handled by this Algorithm */ @Title("KNN-Distance-Order") @Description("Assesses the knn distances for a specified k and orders them.") +@Alias("de.lmu.ifi.dbs.elki.algorithm.KNNDistanceOrder") public class KNNDistancesSampler<O> extends AbstractDistanceBasedAlgorithm<O, KNNDistanceOrderResult> { /** * The logger for this class. @@ -115,7 +118,7 @@ public class KNNDistancesSampler<O> extends AbstractDistanceBasedAlgorithm<O, KN final int size = (int) ((sample <= 1.) ? Math.ceil(relation.size() * sample) : sample); DBIDs sample = DBIDUtil.randomSample(relation.getDBIDs(), size, rnd); - FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Sampling kNN distances.", size, LOG) : null; + FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Sampling kNN distances", size, LOG) : null; double[] knnDistances = new double[size]; int i = 0; for(DBIDIter iditer = sample.iter(); iditer.valid(); iditer.advance(), i++) { @@ -251,4 +254,4 @@ public class KNNDistancesSampler<O> extends AbstractDistanceBasedAlgorithm<O, KN return new KNNDistancesSampler<>(distanceFunction, k, percentage, rnd); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/KNNJoin.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/KNNJoin.java index 593582ed..ff1ae57f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/KNNJoin.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/KNNJoin.java @@ -71,6 +71,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * * @author Elke Achtert * @author Erich Schubert + * @since 0.2 * * @param <V> the type of FeatureVector handled by this Algorithm * @param <N> the type of node used in the spatial index structure diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/MaterializeDistances.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/MaterializeDistances.java index f9de15b0..ea061a71 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/MaterializeDistances.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/MaterializeDistances.java @@ -49,6 +49,9 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * MultipleFileInput to use cached distances. * * Symmetry is assumed. + * + * @author Erich Schubert + * @since 0.2 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/NullAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/NullAlgorithm.java index 5e7cf151..57eb6910 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/NullAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/NullAlgorithm.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * set. * * @author Erich Schubert + * @since 0.2 */ @Title("Null Algorithm") @Description("Algorithm which does nothing, just return a null object.") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/benchmark/KNNBenchmarkAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/benchmark/KNNBenchmarkAlgorithm.java index 611e0c41..1d20e9b2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/benchmark/KNNBenchmarkAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/benchmark/KNNBenchmarkAlgorithm.java @@ -58,6 +58,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * the original database. * * @author Erich Schubert + * @since 0.5.5 * * @param <O> Object type * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/benchmark/RangeQueryBenchmarkAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/benchmark/RangeQueryBenchmarkAlgorithm.java index 9a5532e3..98c66129 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/benchmark/RangeQueryBenchmarkAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/benchmark/RangeQueryBenchmarkAlgorithm.java @@ -89,6 +89,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * TODO: alternatively, allow using a fixed radius? * * @author Erich Schubert + * @since 0.5.5 * * @param <O> Vector type * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/benchmark/ValidateApproximativeKNNIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/benchmark/ValidateApproximativeKNNIndex.java index 64e00abd..fc1098ff 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/benchmark/ValidateApproximativeKNNIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/benchmark/ValidateApproximativeKNNIndex.java @@ -65,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * exact indexing (e.g. linear scanning). * * @author Erich Schubert + * @since 0.5.5 * * @param <O> Object type * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/AbstractClassifier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/AbstractClassifier.java index fe97c83e..c4db6887 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/AbstractClassifier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/AbstractClassifier.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * Abstract base class for algorithms. * * @author Erich Schubert + * @since 0.7.0 * * @param <O> Input type * @param <R> Result type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/Classifier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/Classifier.java index 429f016a..ebdb7fe5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/Classifier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/Classifier.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * classify a new instance of the same type. * * @author Arthur Zimek + * @since 0.7.0 * * @param <O> the type of DatabaseObjects handled by this Algorithm */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/KNNClassifier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/KNNClassifier.java index c506fa8b..84e40731 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/KNNClassifier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/KNNClassifier.java @@ -56,6 +56,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * k nearest neighbors in a database. * * @author Arthur Zimek + * @since 0.7.0 * @param <O> the type of DatabaseObjects handled by this Algorithm */ @Title("kNN-classifier") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/PriorProbabilityClassifier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/PriorProbabilityClassifier.java index 0032e8ac..df1d0f86 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/PriorProbabilityClassifier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/classification/PriorProbabilityClassifier.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * the database, without using the actual data values. * * @author Arthur Zimek + * @since 0.7.0 */ @Title("Prior Probability Classifier") @Description("Classifier to predict simply prior probabilities for all classes as defined by their relative abundance in a given database.") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/AbstractProjectedClustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/AbstractProjectedClustering.java index c63df6c3..2b17380a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/AbstractProjectedClustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/AbstractProjectedClustering.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * and {@link de.lmu.ifi.dbs.elki.algorithm.clustering.correlation.ORCLUS}. * * @author Elke Achtert + * @since 0.2 * * @param <R> the result we return * @param <V> the type of FeatureVector handled by this Algorithm diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/CanopyPreClustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/CanopyPreClustering.java index c8e17b45..49d3586f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/CanopyPreClustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/CanopyPreClustering.java @@ -61,6 +61,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/ClusteringAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/ClusteringAlgorithm.java index b0f3e2d3..a7957d1e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/ClusteringAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/ClusteringAlgorithm.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.database.Database; * database complete or is in any other sense a relaxed clustering result. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.has Clustering * @apiviz.has Model diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/ClusteringAlgorithmUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/ClusteringAlgorithmUtil.java index 8fead310..482eb40a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/ClusteringAlgorithmUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/ClusteringAlgorithmUtil.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * Utility functionality for writing clustering algorithms. * * @author Erich Schubert + * @since 0.7.0 */ public class ClusteringAlgorithmUtil { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/DBSCAN.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/DBSCAN.java index 7d802fa4..ba6cf77d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/DBSCAN.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/DBSCAN.java @@ -34,12 +34,13 @@ import de.lmu.ifi.dbs.elki.data.model.Model; import de.lmu.ifi.dbs.elki.data.type.TypeInformation; import de.lmu.ifi.dbs.elki.data.type.TypeUtil; import de.lmu.ifi.dbs.elki.database.QueryUtil; +import de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs; import de.lmu.ifi.dbs.elki.database.ids.DBIDIter; import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; import de.lmu.ifi.dbs.elki.database.ids.DBIDVar; import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDList; -import de.lmu.ifi.dbs.elki.database.ids.HashSetModifiableDBIDs; +import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDListIter; import de.lmu.ifi.dbs.elki.database.ids.ModifiableDBIDs; import de.lmu.ifi.dbs.elki.database.query.range.RangeQuery; import de.lmu.ifi.dbs.elki.database.relation.Relation; @@ -70,6 +71,8 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Arthur Zimek + * @author Erich Schubert + * @since 0.2 * @param <O> the type of Object the algorithm is applied to */ @Title("DBSCAN: Density-Based Clustering of Applications with Noise") @@ -172,9 +175,10 @@ public class DBSCAN<O> extends AbstractDistanceBasedAlgorithm<O, Clustering<Mode IndefiniteProgress clusprog = LOG.isVerbose() ? new IndefiniteProgress("Number of clusters", LOG) : null; processedIDs = DBIDUtil.newHashSet(size); + ArrayModifiableDBIDs seeds = DBIDUtil.newArray(); for(DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) { if(!processedIDs.contains(iditer)) { - expandCluster(relation, rangeQuery, iditer, objprog, clusprog); + expandCluster(relation, rangeQuery, iditer, seeds, objprog, clusprog); } if(objprog != null && clusprog != null) { objprog.setProcessed(processedIDs.size(), LOG); @@ -197,9 +201,11 @@ public class DBSCAN<O> extends AbstractDistanceBasedAlgorithm<O, Clustering<Mode * @param relation Database relation to run on * @param rangeQuery Range query to use * @param startObjectID potential seed of a new potential cluster - * @param objprog the progress object for logging the current status + * @param seeds Array to store the current seeds + * @param objprog Number of objects processed (may be {@code null}) + * @param clusprog Number of clusters found (may be {@code null}) */ - protected void expandCluster(Relation<O> relation, RangeQuery<O> rangeQuery, DBIDRef startObjectID, FiniteProgress objprog, IndefiniteProgress clusprog) { + protected void expandCluster(Relation<O> relation, RangeQuery<O> rangeQuery, DBIDRef startObjectID, ArrayModifiableDBIDs seeds, FiniteProgress objprog, IndefiniteProgress clusprog) { DoubleDBIDList neighbors = rangeQuery.getRangeForDBID(startObjectID, epsilon); ncounter += neighbors.size(); @@ -218,13 +224,13 @@ public class DBSCAN<O> extends AbstractDistanceBasedAlgorithm<O, Clustering<Mode processedIDs.add(startObjectID); // try to expand the cluster - HashSetModifiableDBIDs seeds = DBIDUtil.newHashSet(); + assert(seeds.size() == 0); + seeds.clear(); processNeighbors(neighbors.iter(), currentCluster, seeds); DBIDVar o = DBIDUtil.newVar(); while(!seeds.isEmpty()) { - seeds.pop(o); - neighbors = rangeQuery.getRangeForDBID(o, epsilon); + neighbors = rangeQuery.getRangeForDBID(seeds.pop(o), epsilon); ncounter += neighbors.size(); if(neighbors.size() >= minpts) { @@ -248,10 +254,13 @@ public class DBSCAN<O> extends AbstractDistanceBasedAlgorithm<O, Clustering<Mode * @param currentCluster Current cluster * @param seeds Seed set */ - private void processNeighbors(DBIDIter neighbor, ModifiableDBIDs currentCluster, HashSetModifiableDBIDs seeds) { + private void processNeighbors(DoubleDBIDListIter neighbor, ModifiableDBIDs currentCluster, ArrayModifiableDBIDs seeds) { + final boolean ismetric = getDistanceFunction().isMetric(); for(; neighbor.valid(); neighbor.advance()) { if(processedIDs.add(neighbor)) { - seeds.add(neighbor); + if(!ismetric || neighbor.doubleValue() > 0.) { + seeds.add(neighbor); + } } else if(!noise.remove(neighbor)) { continue; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/GriDBSCAN.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/GriDBSCAN.java new file mode 100644 index 00000000..aecb7c30 --- /dev/null +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/GriDBSCAN.java @@ -0,0 +1,913 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2016 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import java.util.Arrays; + +import de.lmu.ifi.dbs.elki.algorithm.AbstractDistanceBasedAlgorithm; +import de.lmu.ifi.dbs.elki.data.Cluster; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.NumberVector; +import de.lmu.ifi.dbs.elki.data.model.ClusterModel; +import de.lmu.ifi.dbs.elki.data.model.Model; +import de.lmu.ifi.dbs.elki.data.type.CombinedTypeInformation; +import de.lmu.ifi.dbs.elki.data.type.TypeInformation; +import de.lmu.ifi.dbs.elki.data.type.TypeUtil; +import de.lmu.ifi.dbs.elki.database.datastore.DataStoreFactory; +import de.lmu.ifi.dbs.elki.database.datastore.DataStoreUtil; +import de.lmu.ifi.dbs.elki.database.datastore.WritableDataStore; +import de.lmu.ifi.dbs.elki.database.datastore.WritableIntegerDataStore; +import de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs; +import de.lmu.ifi.dbs.elki.database.ids.DBIDIter; +import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; +import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; +import de.lmu.ifi.dbs.elki.database.ids.DBIDVar; +import de.lmu.ifi.dbs.elki.database.ids.DBIDs; +import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDList; +import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDListIter; +import de.lmu.ifi.dbs.elki.database.ids.ModifiableDBIDs; +import de.lmu.ifi.dbs.elki.database.ids.ModifiableDoubleDBIDList; +import de.lmu.ifi.dbs.elki.database.query.range.RangeQuery; +import de.lmu.ifi.dbs.elki.database.relation.ProxyView; +import de.lmu.ifi.dbs.elki.database.relation.Relation; +import de.lmu.ifi.dbs.elki.database.relation.RelationUtil; +import de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction; +import de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction; +import de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPNormDistanceFunction; +import de.lmu.ifi.dbs.elki.logging.Logging; +import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress; +import de.lmu.ifi.dbs.elki.logging.statistics.DoubleStatistic; +import de.lmu.ifi.dbs.elki.logging.statistics.LongStatistic; +import de.lmu.ifi.dbs.elki.logging.statistics.StringStatistic; +import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; +import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.CommonConstraints; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.GreaterEqualConstraint; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; +import gnu.trove.iterator.TLongObjectIterator; +import gnu.trove.map.hash.TLongObjectHashMap; + +/** + * Using Grid for Accelerating Density-Based Clustering. + * + * An accelerated DBSCAN version for numerical data and Lp-norms only, by + * partitioning the data set into overlapping grid cells. For best efficiency, + * the overlap of the grid cells must be chosen well. The authors suggest a grid + * width of 10 times epsilon. + * + * Because of partitioning the data, this version does not make use of indexes. + * + * Reference: + * <p> + * S. Mahran and K. Mahar: <br /> + * Using grid for accelerating density-based clustering.<br /> + * In 8th IEEE Int. Conf. on Computer and Information Technology, 2008. + * </p> + * + * @author Erich Schubert + * @since 0.7.1 + * + * @apiviz.composedOf Instance + * + * @param <V> the type of vector the algorithm is applied to + */ +@Reference(authors = "S. Mahran and K. Mahar", // +title = "Using grid for accelerating density-based clustering", // +booktitle = "8th IEEE Int. Conf. on Computer and Information Technology", // +url = "http://dx.doi.org/10.1109/CIT.2008.4594646") +public class GriDBSCAN<V extends NumberVector> extends AbstractDistanceBasedAlgorithm<V, Clustering<Model>> implements ClusteringAlgorithm<Clustering<Model>> { + /** + * The logger for this class. + */ + private static final Logging LOG = Logging.getLogger(GriDBSCAN.class); + + /** + * Holds the epsilon radius threshold. + */ + protected double epsilon; + + /** + * Holds the minimum cluster size. + */ + protected int minpts; + + /** + * Width of the grid cells. Must be at least 2 epsilon! + */ + protected double gridwidth; + + /** + * Constructor with parameters. + * + * @param distanceFunction Distance function + * @param epsilon Epsilon value + * @param minpts Minpts parameter + * @param gridwidth Grid width + */ + public GriDBSCAN(DistanceFunction<? super V> distanceFunction, double epsilon, int minpts, double gridwidth) { + super(distanceFunction); + this.epsilon = epsilon; + this.minpts = minpts; + this.gridwidth = gridwidth; + } + + /** + * Performs the DBSCAN algorithm on the given database. + */ + public Clustering<Model> run(Relation<V> relation) { + final DBIDs ids = relation.getDBIDs(); + + // Degenerate result: + if(ids.size() < minpts) { + Clustering<Model> result = new Clustering<>("DBSCAN Clustering", "dbscan-clustering"); + result.addToplevelCluster(new Cluster<Model>(ids, true, ClusterModel.CLUSTER)); + return result; + } + + double gridwidth = this.gridwidth; // local copy. + if(gridwidth < 2. * epsilon) { + LOG.warning("Invalid grid width (less than 2*epsilon, recommended 10*epsilon). Increasing grid width automatically."); + gridwidth = 2. * epsilon; + } + return new Instance<V>(getDistanceFunction(), epsilon, minpts, gridwidth).run(relation); + } + + /** + * Instance, for a single run. + * + * @author Erich Schubert + * + * @param <V> Vector type + */ + protected static class Instance<V extends NumberVector> { + /** + * Unprocessed IDs. + */ + protected static final int UNPROCESSED = 0; + + /** + * Noise IDs. + */ + protected static final int NOISE = 1; + + /** + * Distance function used. + */ + protected DistanceFunction<? super V> distanceFunction; + + /** + * Holds the epsilon radius threshold. + */ + protected double epsilon; + + /** + * Holds the minimum cluster size. + */ + protected int minpts; + + /** + * Width of the grid cells. Must be at least 2 epsilon! + */ + protected double gridwidth; + + /** + * Value domain. + */ + protected double[][] domain; + + /** + * Dimensionality. + */ + protected int dim; + + /** + * Grid offset. + */ + protected double[] offset; + + /** + * Number of cells per dimension. + */ + protected int[] cells; + + /** + * Data grid partitioning. + */ + TLongObjectHashMap<ModifiableDBIDs> grid; + + /** + * Core identifier objects (shared to conserve memory). + */ + private Core[] cores; + + /** + * Border identifier objects (shared to conserve memory). + */ + private Border[] borders; + + /** + * Cluster assignments. + */ + private WritableDataStore<Assignment> clusterids; + + /** + * Temporary assignments of a single run. + */ + private WritableIntegerDataStore temporary; + + /** + * Indicates that the number of grid cells has overflown. + */ + private boolean overflown; + + /** + * Constructor. + * + * @param distanceFunction Distance function + * @param epsilon Epsilon + * @param minpts MinPts + * @param gridwidth Grid width + */ + public Instance(DistanceFunction<? super V> distanceFunction, double epsilon, int minpts, double gridwidth) { + this.distanceFunction = distanceFunction; + this.epsilon = epsilon; + this.minpts = minpts; + this.gridwidth = gridwidth; + } + + /** + * Performs the DBSCAN algorithm on the given database. + * + * @param relation Relation to process + */ + public Clustering<Model> run(Relation<V> relation) { + final DBIDs ids = relation.getDBIDs(); + final int size = ids.size(); + + // Domain of the database + this.domain = RelationUtil.computeMinMax(relation); + this.dim = domain[0].length; + this.offset = new double[dim]; + this.cells = new int[dim]; + // Compute the grid start, and the number of cells in each dimension. + long numcells = computeGridBaseOffsets(); + if(numcells > size) { + LOG.warning("The generated grid has more cells than data points. This may need excessive amounts of memory."); + } + else if(numcells == 1) { + LOG.warning("All data is in a single cell. This has degenerated to a non-indexed DBSCAN!"); + } + else if(numcells <= dim * dim) { + LOG.warning("There are only " + numcells + " cells. This will likely be slower than regular DBSCAN!"); + } + + // Build the data grid. + buildGrid(relation, (int) numcells, offset); + if(grid.size() <= dim) { + LOG.warning("There are only " + grid.size() + " occupied cells. This will likely be slower than regular DBSCAN!"); + } + + // Check grid cell counts: + int mincells = checkGridCellSizes(size, numcells); + + // (Temporary) store the cluster ID assigned. + clusterids = DataStoreUtil.makeStorage(ids, DataStoreFactory.HINT_TEMP, Assignment.class); + temporary = DataStoreUtil.makeIntegerStorage(ids, DataStoreFactory.HINT_TEMP, UNPROCESSED); + final ArrayModifiableDBIDs activeSet = DBIDUtil.newArray(); + // Reserve the first two cluster ids: + int clusterid = NOISE + 1; + this.cores = new Core[2]; + this.borders = new Border[2]; + + // Reused storage for neighbors: + ModifiableDoubleDBIDList neighbors = DBIDUtil.newDistanceDBIDList(minpts << 1); + // Run DBSCAN on each cell that has enough objects. + FiniteProgress cprog = LOG.isVerbose() ? new FiniteProgress("Processing grid cells", mincells, LOG) : null; + for(TLongObjectIterator<ModifiableDBIDs> it = grid.iterator(); it.hasNext();) { + it.advance(); + ModifiableDBIDs cellids = it.value(); + if(cellids.size() < minpts) { + continue; // Too few objects. + } + temporary.clear(); // Reset to "UNPROCESSED" + ProxyView<V> rel = new ProxyView<>(cellids, relation); + RangeQuery<V> rq = rel.getRangeQuery(distanceFunction, epsilon); + FiniteProgress pprog = LOG.isVerbose() ? new FiniteProgress("Running DBSCAN", cellids.size(), LOG) : null; + for(DBIDIter id = cellids.iter(); id.valid(); id.advance()) { + // Skip already processed ids. + if(temporary.intValue(id) != UNPROCESSED) { + continue; + } + neighbors.clear(); + rq.getRangeForDBID(id, epsilon, neighbors); + if(neighbors.size() >= minpts) { + expandCluster(id, clusterid, temporary, neighbors, activeSet, rq, pprog); + ++clusterid; + } + else { + temporary.putInt(id, NOISE); + LOG.incrementProcessed(pprog); + } + } + LOG.ensureCompleted(pprog); + // Post-process DBSCAN clustering result: + updateCoreBorderObjects(clusterid); + mergeClusterInformation(cellids, temporary, clusterids); + LOG.incrementProcessed(cprog); + } + LOG.ensureCompleted(cprog); + temporary.destroy(); + + FiniteProgress pprog = LOG.isVerbose() ? new FiniteProgress("Building final result", size, LOG) : null; + ModifiableDBIDs[] clusters = new ModifiableDBIDs[clusterid]; + ModifiableDBIDs noise = DBIDUtil.newArray(); + for(DBIDIter it = ids.iter(); it.valid(); it.advance()) { + Assignment cids = clusterids.get(it); + if(cids == null) { + noise.add(it); + } + else { + if(cids instanceof MultiBorder) { + cids = ((MultiBorder) cids).getCore(); + } + else if(cids instanceof Border) { + cids = ((Border) cids).core; + } + assert (cids instanceof Core); + Core co = (Core) cids; + while(cores[co.parent].parent != co.parent) { + co = cores[co.parent = cores[co.parent].parent]; + } + ModifiableDBIDs clu = clusters[co.parent]; + if(clu == null) { + clu = clusters[co.parent] = DBIDUtil.newArray(); + } + clu.add(it); + } + LOG.incrementProcessed(pprog); + } + LOG.ensureCompleted(pprog); + clusterids.destroy(); + + Clustering<Model> result = new Clustering<>("DBSCAN Clustering", "dbscan-clustering"); + for(int i = NOISE + 1; i < clusters.length; i++) { + if(clusters[i] != null) { + result.addToplevelCluster(new Cluster<Model>(clusters[i], ClusterModel.CLUSTER)); + } + } + if(noise.size() > 0) { + result.addToplevelCluster(new Cluster<Model>(noise, true, ClusterModel.CLUSTER)); + } + return result; + } + + /** + * Update the shared arrays for core points (to conserve memory) + * + * @param clusterid Number of clusters + */ + private void updateCoreBorderObjects(int clusterid) { + int i = cores.length; + cores = Arrays.copyOf(cores, clusterid); + borders = Arrays.copyOf(borders, clusterid); + while(i < clusterid) { + cores[i] = new Core(i); + borders[i] = new Border(cores[i]); + ++i; + } + } + + /** + * Compute the grid base offset. + * + * @return Total number of grid cells + */ + private long computeGridBaseOffsets() { + StringBuffer buf = LOG.isDebuggingFinest() ? new StringBuffer() : null; + double[] min = domain[0], max = domain[1]; + long total = 1; + for(int d = 0; d < dim; d++) { + final double mi = min[d], ma = max[d], wi = ma - mi; + if(mi == Double.NEGATIVE_INFINITY || ma == Double.POSITIVE_INFINITY || mi != mi || ma != ma) { + throw new AbortException("Dimension " + d + " contains non-finite values."); + } + int c = cells[d] = Math.max(1, (int) Math.ceil(wi / gridwidth)); + offset[d] = mi - (c * gridwidth - wi) * .5; + assert (offset[d] <= mi) : "Grid inconsistent."; + assert (offset[d] + c * gridwidth >= ma) : "Grid inconsistent."; + total *= c; + if(total < 0) { + LOG.warning("Excessive amount of grid cells (long overflow)! Use larger grid cells."); + if (total < 0) { + overflown = true; + total &= 0x7FFF_FFFF_FFFF_FFFFL; + } + } + if(buf != null) { + buf.append(d).append(": min=").append(mi).append(" max=").append(ma); + double s = offset[d]; + for(int i = 0; i <= c; i++) { + buf.append(' ').append(s); + s += gridwidth; + } + buf.append('\n'); + } + } + if(buf != null) { + LOG.debugFinest(buf); + } + return total; + } + + /** + * Build the data grid. + * + * @param relation Data relation + * @param numcells Total number of cells + * @param offset Offset + */ + protected void buildGrid(Relation<V> relation, int numcells, double[] offset) { + grid = new TLongObjectHashMap<ModifiableDBIDs>(numcells >>> 2); + for(DBIDIter it = relation.iterDBIDs(); it.valid(); it.advance()) { + V obj = relation.get(it); + insertIntoGrid(it, obj, 0, 0); + } + } + + /** + * Insert a single object into the grid; potentially into multiple cells (at + * most 2^d) via recursion. + * + * @param id Object ID + * @param obj Object + * @param d Current dimension + * @param v Current cell value + */ + private void insertIntoGrid(DBIDRef id, V obj, int d, int v) { + final int cn = cells[d]; // Number of cells in this dimension + final int nd = d + 1; // Next dimension + int mi = Math.max(0, (int) Math.floor((obj.doubleValue(d) - offset[d] - epsilon) / gridwidth)); + int ma = Math.min(cn - 1, (int) Math.floor((obj.doubleValue(d) - offset[d] + epsilon) / gridwidth)); + assert (mi <= ma) : "Grid inconsistent."; + for(int i = mi; i <= ma; i++) { + int c = v * cn + i; + if(nd == cells.length) { + ModifiableDBIDs ids = grid.get(c); + if(ids == null) { + grid.put(c, ids = DBIDUtil.newArray()); + } + ids.add(id); + } + else { + insertIntoGrid(id, obj, nd, c); + } + } + } + + /** + * Perform some sanity checks on the grid cells. + * + * @param numcell Number of cells + * @param size Relation size + * @return Number of cells with minPts points + */ + protected int checkGridCellSizes(int size, long numcell) { + int tcount = 0; + int hasmin = 0; + double sqcount = 0; + for(TLongObjectIterator<ModifiableDBIDs> it = grid.iterator(); it.hasNext();) { + it.advance(); + final int s = it.value().size(); + if(s >= size >> 1) { + LOG.warning("A single cell contains half of the database (" + s// + + " objects). This will not scale very well."); + } + tcount += s; + sqcount += s * (long) s; + if(s >= minpts) { + hasmin++; + } + } + double savings = sqcount / size / size; + if(savings >= 1) { + LOG.warning("Pairwise distances within each cells are more expensive than a full DBSCAN run due to overlap!"); + } + if (overflown) { + LOG.statistics(new StringStatistic(GriDBSCAN.class.getName() + ".all-cells", "overflow")); + } else { + LOG.statistics(new LongStatistic(GriDBSCAN.class.getName() + ".all-cells", numcell)); + } + LOG.statistics(new LongStatistic(GriDBSCAN.class.getName() + ".used-cells", grid.size())); + LOG.statistics(new LongStatistic(GriDBSCAN.class.getName() + ".minpts-cells", hasmin)); + LOG.statistics(new DoubleStatistic(GriDBSCAN.class.getName() + ".redundancy", tcount / (double) size)); + LOG.statistics(new DoubleStatistic(GriDBSCAN.class.getName() + ".relative-cost", savings)); + return hasmin; + } + + /** + * Set-based expand cluster implementation. + * + * @param clusterid ID of the current cluster. + * @param clusterids Current object to cluster mapping. + * @param neighbors Neighbors acquired by initial getNeighbors call. + * @param activeSet Set to manage active candidates. + * @param rq Range query + * @param pprog Object progress + * @return cluster size + */ + protected int expandCluster(final DBIDRef seed, final int clusterid, final WritableIntegerDataStore clusterids, final ModifiableDoubleDBIDList neighbors, ArrayModifiableDBIDs activeSet, RangeQuery<V> rq, FiniteProgress pprog) { + assert (activeSet.size() == 0); + int clustersize = 1 + processCorePoint(seed, neighbors, clusterid, clusterids, activeSet); + LOG.incrementProcessed(pprog); + // run expandCluster as long as there is another seed + final DBIDVar id = DBIDUtil.newVar(); + while(!activeSet.isEmpty()) { + activeSet.pop(id); + neighbors.clear(); + // Evaluate Neighborhood predicate + rq.getRangeForDBID(id, epsilon, neighbors); + // Evaluate Core-Point predicate + if(neighbors.size() >= minpts) { + clustersize += processCorePoint(id, neighbors, clusterid, clusterids, activeSet); + } + LOG.incrementProcessed(pprog); + } + return clustersize; + } + + /** + * Process a single core point. + * + * @param seed Point to process + * @param newneighbors New neighbors + * @param clusterid Cluster to add to + * @param clusterids Cluster assignment storage. + * @param activeSet Active set of cluster seeds + * @return Number of new points added to cluster + */ + protected int processCorePoint(final DBIDRef seed, DoubleDBIDList newneighbors, final int clusterid, final WritableIntegerDataStore clusterids, ArrayModifiableDBIDs activeSet) { + clusterids.putInt(seed, clusterid); // Core point now + int clustersize = 0; + // The recursion is unrolled into iteration over the active set. + for(DoubleDBIDListIter it = newneighbors.iter(); it.valid(); it.advance()) { + final int oldassign = clusterids.intValue(it); + if(oldassign == UNPROCESSED) { + if(it.doubleValue() > 0.) { // We can skip points at distance 0. + activeSet.add(it); + } + } + else if(oldassign != NOISE) { + continue; // Member of some cluster. + } + clustersize++; + clusterids.putInt(it, -clusterid); + } + return clustersize; + } + + /** + * Merge cluster information. + * + * @param cellids IDs in current cell + * @param temporary Temporary assignments + * @param clusterids Merged cluster assignment + */ + protected void mergeClusterInformation(ModifiableDBIDs cellids, WritableIntegerDataStore temporary, WritableDataStore<Assignment> clusterids) { + FiniteProgress mprog = LOG.isVerbose() ? new FiniteProgress("Collecting result", cellids.size(), LOG) : null; + for(DBIDIter id = cellids.iter(); id.valid(); id.advance()) { + int nclus = temporary.intValue(id); + if(nclus > NOISE) { // Core point + Core core = cores[nclus]; + assert (core.parent > NOISE); + Assignment oclus = clusterids.get(id); + if(oclus == null) { // No assignment yet (= NOISE) + clusterids.put(id, core); + } + else if(oclus instanceof Core) { // Core and core - merge! + core.mergeWith((Core) oclus); + } + else if(oclus instanceof Border) { // Core and border point, merge! + core.mergeWith(((Border) oclus).core); + clusterids.put(id, core); + } + else { // Point is border for multiple clusters + assert (oclus instanceof MultiBorder); + if(LOG.isDebuggingFinest()) { + LOG.debugFinest("Multi-Merge: " + nclus + " - " + oclus + " -> " + core); + } + // Find minimum: + int m = core.parent, m2 = ((MultiBorder) oclus).getCore().parent; + m = m < m2 ? m : m2; + assert (m > NOISE); + // Execute all merges: + for(Border b : ((MultiBorder) oclus).cs) { + cores[b.core.parent].parent = m; + } + core.parent = m; + clusterids.put(id, core); + } + } + else if(nclus < 0) { // Border point + Border border = borders[-nclus]; + Assignment oclus = clusterids.get(id); + if(oclus == null) { // No assignment yet. + clusterids.put(id, border); + } + else if(oclus instanceof Core) { // Border and core point - merge + ((Core) oclus).mergeWith(border.core); + } + else if(oclus instanceof Border) { // Border and border + if(((Border) oclus).core.parent != border.core.parent) { + clusterids.put(id, new MultiBorder((Border) oclus, border)); + } + } + else { + assert (oclus instanceof MultiBorder); + clusterids.put(id, ((MultiBorder) oclus).update(border)); + } + } + else { + assert (nclus == NOISE); // Ignore noise. + } + LOG.incrementProcessed(mprog); + } + LOG.ensureCompleted(mprog); + } + } + + /** + * Point assignment. + * + * @author Erich Schubert + * + * @apiviz.exclude + */ + protected static interface Assignment { + // Empty + } + + /** + * Core point assignment. + * + * @author Erich Schubert + * + * @apiviz.exclude + */ + protected static class Core implements Assignment { + /** + * Cluster number + */ + protected int parent; + + /** + * Constructor. + * + * @param parent Cluster number + */ + protected Core(int parent) { + assert (parent > GriDBSCAN.Instance.NOISE); + this.parent = parent; + } + + /** + * Merge two cores. + * + * @param o Other core + */ + public void mergeWith(Core o) { + o.parent = this.parent = (parent < o.parent ? parent : o.parent); + } + + @Override + public String toString() { + return "Core[" + parent + "]"; + } + } + + /** + * Border point assignment. + * + * @author Erich Schubert + * + * @apiviz.exclude + */ + protected static class Border implements Assignment, Comparable<Border> { + /** + * Cluster number + */ + protected Core core; + + /** + * Constructor. + * + * @param core Cluster number + */ + protected Border(Core core) { + this.core = core; + } + + @Override + public String toString() { + return "Border[" + core.parent + "]"; + } + + @Override + public int compareTo(Border o) { + return Integer.compare(o.core.parent, this.core.parent); + } + } + + /** + * Multiple border point assignment. + * + * @author Erich Schubert + * + * @apiviz.exclude + */ + protected static class MultiBorder implements Assignment { + /** + * Cluster numbers + */ + protected Border[] cs; + + /** + * Constructor. + * + * @param i First cluster border + * @param j Second cluster border + */ + protected MultiBorder(Border i, Border j) { + assert (i.core != j.core); + this.cs = new Border[] { i, j }; + } + + /** + * Add a new border to the existing borders. + * + * @param border New border. + */ + public Assignment update(Border border) { + Arrays.sort(cs); + int j = 1; + boolean found = (cs[0].core == border.core); + for(int i = 1; i < cs.length; i++) { + if(cs[i].core != cs[i - 1].core) { + cs[j++] = cs[i]; + } + found |= (cs[i].core == border.core); + } + if(found) { + if(j == 1) { + Border r = cs[0]; + cs = null; // Prevent further use + return r; + } + if(j < cs.length) { + cs = Arrays.copyOf(cs, j); + } + return this; + } + if(j + 1 != cs.length) { + cs = Arrays.copyOf(cs, j + 1); + } + cs[j] = border; + return this; + } + + /** + * Get the core this is assigned to. + * + * @return Core + */ + public Core getCore() { + Core a = cs[0].core; + for(int i = 1; i < cs.length; i++) { + Core v = cs[i].core; + a = a.parent > v.parent ? a : v; // max, of negative values + } + assert (a.parent > GriDBSCAN.Instance.NOISE); + return a; + } + + @Override + public String toString() { + StringBuilder buf = new StringBuilder(); + buf.append("MultiBorder["); + for(Border b : cs) { + buf.append(b.core.parent).append(','); + } + buf.append(']'); + return buf.toString(); + } + } + + @Override + public TypeInformation[] getInputTypeRestriction() { + // We strictly need a vector field of fixed dimensionality! + TypeInformation type = new CombinedTypeInformation(TypeUtil.NUMBER_VECTOR_FIELD, getDistanceFunction().getInputTypeRestriction()); + return TypeUtil.array(type); + } + + @Override + protected Logging getLogger() { + return LOG; + } + + /** + * Parameterization class. + * + * @author Erich Schubert + * + * @apiviz.exclude + * + * @param <O> Vector type to use + */ + public static class Parameterizer<O extends NumberVector> extends AbstractDistanceBasedAlgorithm.Parameterizer<O> { + /** + * Parameter to control the grid width. + * + * Must be at least two times epsilon. + */ + public static final OptionID GRID_ID = new OptionID("gridbscan.gridwidth", "Width of the grid used, must be at least two times epsilon."); + + /** + * Holds the epsilon radius threshold. + */ + protected double epsilon; + + /** + * Holds the minimum cluster size. + */ + protected int minpts; + + /** + * Width of the grid cells. Must be at least 2 epsilon! + */ + protected double gridwidth; + + @Override + protected void makeOptions(Parameterization config) { + // Disabled: super.makeOptions(config); + // Because we currently only allow Lp norms: + ObjectParameter<DistanceFunction<? super O>> distanceFunctionP = makeParameterDistanceFunction(EuclideanDistanceFunction.class, LPNormDistanceFunction.class); + if(config.grab(distanceFunctionP)) { + distanceFunction = distanceFunctionP.instantiateClass(config); + } + + DoubleParameter epsilonP = new DoubleParameter(DBSCAN.Parameterizer.EPSILON_ID) // + .addConstraint(CommonConstraints.GREATER_THAN_ZERO_DOUBLE); + if(config.grab(epsilonP)) { + epsilon = epsilonP.getValue(); + } + + IntParameter minptsP = new IntParameter(DBSCAN.Parameterizer.MINPTS_ID) // + .addConstraint(CommonConstraints.GREATER_EQUAL_ONE_INT); + if(config.grab(minptsP)) { + minpts = minptsP.getValue(); + if(minpts <= 2) { + LOG.warning("DBSCAN with minPts <= 2 is equivalent to single-link clustering at a single height. Consider using larger values of minPts."); + } + } + + DoubleParameter gridP = new DoubleParameter(GRID_ID) // + .addConstraint(CommonConstraints.GREATER_THAN_ZERO_DOUBLE); + if(epsilon > 0.) { + gridP.setDefaultValue(10. * epsilon); + gridP.addConstraint(new GreaterEqualConstraint(1. * epsilon)); + } + if(config.grab(gridP)) { + gridwidth = gridP.doubleValue(); + } + } + + @Override + protected GriDBSCAN<O> makeInstance() { + return new GriDBSCAN<>(distanceFunction, epsilon, minpts, gridwidth); + } + } +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/NaiveMeanShiftClustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/NaiveMeanShiftClustering.java index 0d1e9fe2..b6b43047 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/NaiveMeanShiftClustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/NaiveMeanShiftClustering.java @@ -77,6 +77,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * </p> * * @author Erich Schubert + * @since 0.5.5 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/SNNClustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/SNNClustering.java index 2cc48637..39da3e7f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/SNNClustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/SNNClustering.java @@ -68,6 +68,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Arthur Zimek + * @since 0.2 * * @apiviz.uses SharedNearestNeighborSimilarityFunction * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/AffinityPropagationClusteringAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/AffinityPropagationClusteringAlgorithm.java index a1ef9768..0216d475 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/AffinityPropagationClusteringAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/AffinityPropagationClusteringAlgorithm.java @@ -62,6 +62,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.composedOf AffinityPropagationInitialization * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/AffinityPropagationInitialization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/AffinityPropagationInitialization.java index 5532f8c8..891b8a3e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/AffinityPropagationInitialization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/AffinityPropagationInitialization.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; * Initialization methods for affinity propagation. * * @author Erich Schubert + * @since 0.6.0 */ public interface AffinityPropagationInitialization<O> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/DistanceBasedInitializationWithMedian.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/DistanceBasedInitializationWithMedian.java index 1bdff0c3..e514df53 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/DistanceBasedInitializationWithMedian.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/DistanceBasedInitializationWithMedian.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Distance based initialization. * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/SimilarityBasedInitializationWithMedian.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/SimilarityBasedInitializationWithMedian.java index d8abe9c1..3086d4fb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/SimilarityBasedInitializationWithMedian.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/SimilarityBasedInitializationWithMedian.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Similarity based initialization. * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/AbstractBiclustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/AbstractBiclustering.java index 2a0896ea..9d1b2f91 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/AbstractBiclustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/AbstractBiclustering.java @@ -53,6 +53,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.ExceptionMessages; * of the {@link NumberVector}s. * * @author Arthur Zimek + * @since 0.2 * @param <V> a certain subtype of NumberVector - the data matrix is supposed to * consist of rows where each row relates to an object of type V and the * columns relate to the attribute values of these objects diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/ChengAndChurch.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/ChengAndChurch.java index ceb13976..cf957fc0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/ChengAndChurch.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/ChengAndChurch.java @@ -61,6 +61,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Erich Schubert + * @since 0.2 * @param <V> Vector type. */ @Reference(authors = "Y. Cheng, G. M. Church", title = "Biclustering of expression data", booktitle = "Proc. 8th International Conference on Intelligent Systems for Molecular Biology (ISMB)") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/CASH.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/CASH.java index 43c0528d..1db2d79f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/CASH.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/CASH.java @@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.algorithm.clustering.correlation; This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures - Copyright (C) 2015 + Copyright (C) 2016 Ludwig-Maximilians-Universität München Lehr- und Forschungseinheit für Datenbanksysteme ELKI Development Team @@ -95,6 +95,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Elke Achtert + * @since 0.2 * * @apiviz.has CASHInterval * @apiviz.has ParameterizationFunction @@ -109,84 +110,36 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; title = "Robust clustering in arbitraily oriented subspaces", // booktitle = "Proc. 8th SIAM Int. Conf. on Data Mining (SDM'08), Atlanta, GA, 2008", // url = "http://www.siam.org/proceedings/datamining/2008/dm08_69_AchtertBoehmDavidKroegerZimek.pdf") -public class CASH<V extends NumberVector> extends AbstractAlgorithm<Clustering<Model>>implements ClusteringAlgorithm<Clustering<Model>> { +public class CASH<V extends NumberVector> extends AbstractAlgorithm<Clustering<Model>> implements ClusteringAlgorithm<Clustering<Model>> { /** * The logger for this class. */ private static final Logging LOG = Logging.getLogger(CASH.class); /** - * Parameter to specify the threshold for minimum number of points in a - * cluster, must be an integer greater than 0. - * <p> - * Key: {@code -cash.minpts} - * </p> + * Threshold for minimum number of points in a cluster */ - public static final OptionID MINPTS_ID = new OptionID("cash.minpts", "Threshold for minimum number of points in a cluster."); + protected int minPts; /** - * Parameter to specify the maximum level for splitting the hypercube, must be - * an integer greater than 0. - * <p> - * Key: {@code -cash.maxlevel} - * </p> + * Maximum level for splitting the hypercube. */ - public static final OptionID MAXLEVEL_ID = new OptionID("cash.maxlevel", "The maximum level for splitting the hypercube."); + protected int maxLevel; /** - * Parameter to specify the minimum dimensionality of the subspaces to be - * found, must be an integer greater than 0. - * <p> - * Default value: {@code 1} - * </p> - * <p> - * Key: {@code -cash.mindim} - * </p> + * Minimum dimensionality of the subspaces to be found */ - public static final OptionID MINDIM_ID = new OptionID("cash.mindim", "The minimum dimensionality of the subspaces to be found."); + protected int minDim; /** - * Parameter to specify the maximum jitter for distance values, must be a - * double greater than 0. - * <p> - * Key: {@code -cash.jitter} - * </p> + * Maximum jitter for distance values. */ - public static final OptionID JITTER_ID = new OptionID("cash.jitter", "The maximum jitter for distance values."); + protected double jitter; /** - * Flag to indicate that an adjustment of the applied heuristic for choosing - * an interval is performed after an interval is selected. - * <p> - * Key: {@code -cash.adjust} - * </p> + * Apply adjustment heuristic for interval choosing. */ - public static final OptionID ADJUST_ID = new OptionID("cash.adjust", "Flag to indicate that an adjustment of the applied heuristic for choosing an interval " + "is performed after an interval is selected."); - - /** - * Holds the value of {@link #MINPTS_ID}. - */ - private int minPts; - - /** - * Holds the value of {@link #MAXLEVEL_ID}. - */ - private int maxLevel; - - /** - * Holds the value of {@link #MINDIM_ID}. - */ - private int minDim; - - /** - * Holds the value of {@link #JITTER_ID}. - */ - private double jitter; - - /** - * Holds the value of {@link #ADJUST_ID}. - */ - private boolean adjust; + protected boolean adjust; /** * Holds the dimensionality for noise. @@ -711,7 +664,7 @@ public class CASH<V extends NumberVector> extends AbstractAlgorithm<Clustering<M // set the parameters ListParameterization parameters = new ListParameterization(); parameters.addParameter(PCAFilteredRunner.Parameterizer.PCA_EIGENPAIR_FILTER, FirstNEigenPairFilter.class.getName()); - parameters.addParameter(FirstNEigenPairFilter.EIGENPAIR_FILTER_N, Integer.toString(dim - 1)); + parameters.addParameter(FirstNEigenPairFilter.Parameterizer.EIGENPAIR_FILTER_N, Integer.toString(dim - 1)); DependencyDerivator<DoubleVector> derivator = null; Class<DependencyDerivator<DoubleVector>> cls = ClassGenericsUtil.uglyCastIntoSubclass(DependencyDerivator.class); derivator = parameters.tryInstantiate(cls); @@ -784,7 +737,7 @@ public class CASH<V extends NumberVector> extends AbstractAlgorithm<Clustering<M ListParameterization parameters = new ListParameterization(); parameters.addParameter(PCAFilteredRunner.Parameterizer.PCA_EIGENPAIR_FILTER, FirstNEigenPairFilter.class.getName()); - parameters.addParameter(FirstNEigenPairFilter.EIGENPAIR_FILTER_N, Integer.toString(dimensionality)); + parameters.addParameter(FirstNEigenPairFilter.Parameterizer.EIGENPAIR_FILTER_N, Integer.toString(dimensionality)); DependencyDerivator<DoubleVector> derivator = null; Class<DependencyDerivator<DoubleVector>> cls = ClassGenericsUtil.uglyCastIntoSubclass(DependencyDerivator.class); derivator = parameters.tryInstantiate(cls); @@ -841,14 +794,77 @@ public class CASH<V extends NumberVector> extends AbstractAlgorithm<Clustering<M * @apiviz.exclude */ public static class Parameterizer extends AbstractParameterizer { - protected int minpts; - - protected int maxlevel; - - protected int mindim; - + /** + * Parameter to specify the threshold for minimum number of points in a + * cluster, must be an integer greater than 0. + * <p> + * Key: {@code -cash.minpts} + * </p> + */ + public static final OptionID MINPTS_ID = new OptionID("cash.minpts", "Threshold for minimum number of points in a cluster."); + + /** + * Parameter to specify the maximum level for splitting the hypercube, must + * be an integer greater than 0. + * <p> + * Key: {@code -cash.maxlevel} + * </p> + */ + public static final OptionID MAXLEVEL_ID = new OptionID("cash.maxlevel", "The maximum level for splitting the hypercube."); + + /** + * Parameter to specify the minimum dimensionality of the subspaces to be + * found, must be an integer greater than 0. + * <p> + * Default value: {@code 1} + * </p> + * <p> + * Key: {@code -cash.mindim} + * </p> + */ + public static final OptionID MINDIM_ID = new OptionID("cash.mindim", "The minimum dimensionality of the subspaces to be found."); + + /** + * Parameter to specify the maximum jitter for distance values, must be a + * double greater than 0. + * <p> + * Key: {@code -cash.jitter} + * </p> + */ + public static final OptionID JITTER_ID = new OptionID("cash.jitter", "The maximum jitter for distance values."); + + /** + * Flag to indicate that an adjustment of the applied heuristic for choosing + * an interval is performed after an interval is selected. + * <p> + * Key: {@code -cash.adjust} + * </p> + */ + public static final OptionID ADJUST_ID = new OptionID("cash.adjust", "Flag to indicate that an adjustment of the applied heuristic for choosing an interval " + "is performed after an interval is selected."); + + /** + * Threshold for minimum number of points in a cluster + */ + protected int minPts; + + /** + * Maximum level for splitting the hypercube. + */ + protected int maxLevel; + + /** + * Minimum dimensionality of the subspaces to be found + */ + protected int minDim; + + /** + * Maximum jitter for distance values. + */ protected double jitter; + /** + * Apply adjustment heuristic for interval choosing. + */ protected boolean adjust; @Override @@ -857,17 +873,17 @@ public class CASH<V extends NumberVector> extends AbstractAlgorithm<Clustering<M IntParameter minptsP = new IntParameter(MINPTS_ID); minptsP.addConstraint(CommonConstraints.GREATER_EQUAL_ONE_INT); if(config.grab(minptsP)) { - minpts = minptsP.getValue(); + minPts = minptsP.getValue(); } IntParameter maxlevelP = new IntParameter(MAXLEVEL_ID); maxlevelP.addConstraint(CommonConstraints.GREATER_EQUAL_ONE_INT); if(config.grab(maxlevelP)) { - maxlevel = maxlevelP.getValue(); + maxLevel = maxlevelP.getValue(); } IntParameter mindimP = new IntParameter(MINDIM_ID, 1); mindimP.addConstraint(CommonConstraints.GREATER_EQUAL_ONE_INT); if(config.grab(mindimP)) { - mindim = mindimP.getValue(); + minDim = mindimP.getValue(); } DoubleParameter jitterP = new DoubleParameter(JITTER_ID); jitterP.addConstraint(CommonConstraints.GREATER_THAN_ZERO_DOUBLE); @@ -882,7 +898,7 @@ public class CASH<V extends NumberVector> extends AbstractAlgorithm<Clustering<M @Override protected CASH<NumberVector> makeInstance() { - return new CASH<>(minpts, maxlevel, mindim, jitter, adjust); + return new CASH<>(minPts, maxLevel, minDim, jitter, adjust); } } } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/COPAC.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/COPAC.java index 06e64343..72de0a55 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/COPAC.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/COPAC.java @@ -67,6 +67,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Arthur Zimek + * @since 0.2 * * @apiviz.has DimensionModel * @apiviz.composedOf COPACNeighborPredicate diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/ERiC.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/ERiC.java index 8fb11eaf..f73e9e70 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/ERiC.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/ERiC.java @@ -79,6 +79,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Elke Achtert + * @since 0.2 * * @apiviz.composedOf COPAC * @apiviz.composedOf DBSCAN diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/FourC.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/FourC.java index 52d043ec..63fe9d81 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/FourC.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/FourC.java @@ -47,19 +47,20 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * 4C identifies local subgroups of data objects sharing a uniform correlation. * The algorithm is based on a combination of PCA and density-based clustering * (DBSCAN). - * + * * Reference: * <p> * C. Böhm, K. Kailing, P. Kröger, A. Zimek:<br /> * Computing Clusters of Correlation Connected Objects. <br> * In Proc. ACM SIGMOD Int. Conf. on Management of Data, Paris, France, 2004. * </p> - * + * * @author Arthur Zimek - * + * @since 0.2 + * * @apiviz.composedOf FourCNeighborPredicate * @apiviz.composedOf FourCCorePredicate - * + * * @param <V> type of NumberVector handled by this Algorithm */ @Title("4C: Computing Correlation Connected Clusters") @@ -77,7 +78,7 @@ public class FourC<V extends NumberVector> extends GeneralizedDBSCAN { /** * Constructor. - * + * * @param settings FourC settings. */ public FourC(FourC.Settings settings) { @@ -96,9 +97,9 @@ public class FourC<V extends NumberVector> extends GeneralizedDBSCAN { /** * Class wrapping the 4C parameter settings. - * + * * @author Erich Schubert - * + * * @apiviz.exclude */ public static class Settings { @@ -135,9 +136,9 @@ public class FourC<V extends NumberVector> extends GeneralizedDBSCAN { /** * Parameterization class for 4C settings. - * + * * @author Erich Schubert - * + * * @apiviz.exclude */ public static class Parameterizer extends AbstractParameterizer { @@ -178,7 +179,7 @@ public class FourC<V extends NumberVector> extends GeneralizedDBSCAN { /** * Configure the epsilon radius parameter. - * + * * @param config Parameter source */ protected void configEpsilon(Parameterization config) { @@ -191,7 +192,7 @@ public class FourC<V extends NumberVector> extends GeneralizedDBSCAN { /** * Configure the minPts aka "mu" parameter. - * + * * @param config Parameter source */ protected void configMinPts(Parameterization config) { @@ -204,18 +205,18 @@ public class FourC<V extends NumberVector> extends GeneralizedDBSCAN { /** * Configure the delta parameter. - * + * * @param config Parameter source */ protected void configDelta(Parameterization config) { // Flag for using absolute variances - Flag absoluteF = new Flag(LimitEigenPairFilter.EIGENPAIR_FILTER_ABSOLUTE); + Flag absoluteF = new Flag(LimitEigenPairFilter.Parameterizer.EIGENPAIR_FILTER_ABSOLUTE); if(config.grab(absoluteF)) { settings.absolute = absoluteF.isTrue(); } // Parameter delta - DoubleParameter deltaP = new DoubleParameter(LimitEigenPairFilter.EIGENPAIR_FILTER_DELTA) // + DoubleParameter deltaP = new DoubleParameter(LimitEigenPairFilter.Parameterizer.EIGENPAIR_FILTER_DELTA) // .addConstraint(CommonConstraints.GREATER_EQUAL_ZERO_DOUBLE); if(!settings.absolute) { deltaP.setDefaultValue(DEFAULT_DELTA); @@ -230,7 +231,7 @@ public class FourC<V extends NumberVector> extends GeneralizedDBSCAN { /** * Configure the kappa parameter. - * + * * @param config Parameter source */ protected void configKappa(Parameterization config) { @@ -244,7 +245,7 @@ public class FourC<V extends NumberVector> extends GeneralizedDBSCAN { /** * Configure the delta parameter. - * + * * @param config Parameter source */ protected void configLambda(Parameterization config) { @@ -265,9 +266,9 @@ public class FourC<V extends NumberVector> extends GeneralizedDBSCAN { /** * Parameterization class. - * + * * @author Erich Schubert - * + * * @apiviz.exclude */ public static class Parameterizer<O extends NumberVector> extends AbstractParameterizer { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/HiCO.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/HiCO.java index 0bbd012a..6a741ce1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/HiCO.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/HiCO.java @@ -74,11 +74,12 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * In: Proc. Int. Conf. on Scientific and Statistical Database Management * (SSDBM'06), Vienna, Austria, 2006. * </p> - * + * * @author Elke Achtert - * + * @since 0.3 + * * @apiviz.composedOf HiCO.Instance - * + * * @param <V> the type of NumberVector handled by the algorithm */ @Title("Mining Hierarchies of Correlation Clusters") @@ -117,7 +118,7 @@ public class HiCO<V extends NumberVector> extends GeneralizedOPTICS<V, Correlati /** * Constructor. - * + * * @param indexfactory Index factory * @param mu Mu parameter */ @@ -138,7 +139,7 @@ public class HiCO<V extends NumberVector> extends GeneralizedOPTICS<V, Correlati /** * Instance of the OPTICS algorithm. - * + * * @author Erich Schubert * * @apiviz.uses FilteredLocalPCAIndex @@ -275,7 +276,7 @@ public class HiCO<V extends NumberVector> extends GeneralizedOPTICS<V, Correlati /** * Sort new candidates by their distance, for determining the core size. - * + * * @author Erich Schubert * * @apiviz.exclude @@ -298,7 +299,7 @@ public class HiCO<V extends NumberVector> extends GeneralizedOPTICS<V, Correlati /** * Computes the correlation distance between the two subspaces defined by the * specified PCAs. - * + * * @param pca1 first PCA * @param pca2 second PCA * @param dimensionality the dimensionality of the data space @@ -370,7 +371,7 @@ public class HiCO<V extends NumberVector> extends GeneralizedOPTICS<V, Correlati * <code>v</code> at column <code>corrDim</code>. After insertion the matrix * <code>v</code> is orthonormalized and column <code>corrDim</code> of matrix * <code>e_czech</code> is set to the <code>corrDim</code>-th unit vector. - * + * * @param v the orthonormal matrix of the eigenvectors * @param e_czech the selection matrix of the strong eigenvectors * @param vector the vector to be inserted @@ -411,9 +412,9 @@ public class HiCO<V extends NumberVector> extends GeneralizedOPTICS<V, Correlati /** * Parameterization class. - * + * * @author Erich Schubert - * + * * @apiviz.exclude */ public static class Parameterizer<V extends NumberVector> extends AbstractParameterizer { @@ -421,7 +422,7 @@ public class HiCO<V extends NumberVector> extends GeneralizedOPTICS<V, Correlati * Parameter to specify the smoothing factor, must be an integer greater * than 0. The {link {@link #MU_ID}-nearest neighbor is used to compute the * correlation reachability of an object. - * + * * <p> * Key: {@code -hico.mu} * </p> @@ -515,7 +516,7 @@ public class HiCO<V extends NumberVector> extends GeneralizedOPTICS<V, Correlati ListParameterization params = new ListParameterization(); // preprocessor params.addParameter(KNNQueryFilteredPCAIndex.Factory.Parameterizer.K_ID, k); - params.addParameter(PercentageEigenPairFilter.ALPHA_ID, alpha); + params.addParameter(PercentageEigenPairFilter.Parameterizer.ALPHA_ID, alpha); ChainedParameterization chain = new ChainedParameterization(params, config); chain.errorsTo(config); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/LMCLUS.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/LMCLUS.java index 934d3fc6..0a302005 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/LMCLUS.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/LMCLUS.java @@ -79,6 +79,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * * @author Ernst Waas * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "Robert Haralick, Rave Harpaz", title = "Linear manifold clustering in high dimensional spaces by stochastic search", booktitle = "Pattern Recognition volume 40, Issue 10", url = "http://dx.doi.org/10.1016/j.patcog.2007.01.020") public class LMCLUS extends AbstractAlgorithm<Clustering<Model>> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/ORCLUS.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/ORCLUS.java index 4e5c3fbc..413675a8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/ORCLUS.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/ORCLUS.java @@ -75,6 +75,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * </p> * * @author Elke Achtert + * @since 0.2 * * @apiviz.has PCARunner * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/cash/CASHInterval.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/cash/CASHInterval.java index bf935864..42f1f474 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/cash/CASHInterval.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/cash/CASHInterval.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.logging.LoggingConfiguration; * and a set of objects ids associated with this interval. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has de.lmu.ifi.dbs.elki.algorithm.clustering.correlation.cash.CASHIntervalSplit */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/cash/CASHIntervalSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/cash/CASHIntervalSplit.java index 1edec3a9..038495f2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/cash/CASHIntervalSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/cash/CASHIntervalSplit.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.FormatUtil; * Supports the splitting of CASH intervals. * * @author Elke Achtert + * @since 0.2 */ public class CASHIntervalSplit { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/cash/ParameterizationFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/cash/ParameterizationFunction.java index 31fea80f..1b0ec58f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/cash/ParameterizationFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/cash/ParameterizationFunction.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.FormatUtil; * belonging to the normal vector n. * * @author Elke Achtert + * @since 0.2 */ public class ParameterizationFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/AbstractEMModelFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/AbstractEMModelFactory.java index 36ae7804..0b165c75 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/AbstractEMModelFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/AbstractEMModelFactory.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Abstract base class for initializing EM. * * @author Erich Schubert + * @since 0.4.0 * * @param <V> Vector type * @param <M> Model type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/DiagonalGaussianModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/DiagonalGaussianModel.java index 544362da..e31089d5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/DiagonalGaussianModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/DiagonalGaussianModel.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * Simpler model for a single Gaussian cluster, without covariances. * * @author Erich Schubert + * @since 0.7.0 */ public class DiagonalGaussianModel implements EMClusterModel<EMModel> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/DiagonalGaussianModelFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/DiagonalGaussianModelFactory.java index 3f3bf914..66fb548b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/DiagonalGaussianModelFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/DiagonalGaussianModelFactory.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * corresponds to the {@code 'VVI'} model in Mclust (R). * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has DiagonalGaussianModel * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/EM.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/EM.java index 208e8450..039c0174 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/EM.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/EM.java @@ -63,14 +63,16 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Clustering by expectation maximization (EM-Algorithm), also known as Gaussian * Mixture Modeling (GMM). * + * Reference: * <p> - * Reference: A. P. Dempster, N. M. Laird, D. B. Rubin:<br /> - * Maximum Likelihood from Incomplete Data via the EM algorithm.<br> + * A. P. Dempster, N. M. Laird, D. B. Rubin:<br /> + * Maximum Likelihood from Incomplete Data via the EM algorithm.<br /> * In Journal of the Royal Statistical Society, Series B, 39(1), 1977, pp. 1-31 * </p> * * @author Arthur Zimek * @author Erich Schubert + * @since 0.2 * * @apiviz.composedOf EMClusterModelFactory * @@ -83,7 +85,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; title = "Maximum Likelihood from Incomplete Data via the EM algorithm", // booktitle = "Journal of the Royal Statistical Society, Series B, 39(1), 1977, pp. 1-31", // url = "http://www.jstor.org/stable/2984875") -@Alias({ "de.lmu.ifi.dbs.elki.algorithm.clustering.EM", "EM" }) +@Alias("de.lmu.ifi.dbs.elki.algorithm.clustering.EM") public class EM<V extends NumberVector, M extends MeanModel> extends AbstractAlgorithm<Clustering<M>> implements ClusteringAlgorithm<Clustering<M>> { /** * The logger for this class. @@ -392,7 +394,7 @@ public class EM<V extends NumberVector, M extends MeanModel> extends AbstractAlg initializer = initialP.instantiateClass(config); } - DoubleParameter deltaP = new DoubleParameter(DELTA_ID, 1e-5)// + DoubleParameter deltaP = new DoubleParameter(DELTA_ID, 1e-7)// .addConstraint(CommonConstraints.GREATER_EQUAL_ZERO_DOUBLE); if(config.grab(deltaP)) { delta = deltaP.getValue(); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/EMClusterModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/EMClusterModel.java index aaf66839..c89d85d0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/EMClusterModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/EMClusterModel.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.data.model.MeanModel; * Models useable in EM clustering. * * @author Erich Schubert + * @since 0.3 */ public interface EMClusterModel<M extends MeanModel> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/EMClusterModelFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/EMClusterModelFactory.java index d486d5d3..a4f1e486 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/EMClusterModelFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/EMClusterModelFactory.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunctio * Factory for initializing the EM models. * * @author Erich Schubert + * @since 0.2 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/MultivariateGaussianModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/MultivariateGaussianModel.java index 4c020bc1..3b433af1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/MultivariateGaussianModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/MultivariateGaussianModel.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * Model for a single Gaussian cluster. * * @author Erich Schubert + * @since 0.7.0 */ public class MultivariateGaussianModel implements EMClusterModel<EMModel> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/MultivariateGaussianModelFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/MultivariateGaussianModelFactory.java index 8e767a0f..e47cb1ea 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/MultivariateGaussianModelFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/MultivariateGaussianModelFactory.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * {@code 'VVV'} model in Mclust (R). * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has MultivariateGaussianModel * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/SphericalGaussianModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/SphericalGaussianModel.java index 7aa5b92b..97296d45 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/SphericalGaussianModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/SphericalGaussianModel.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * Simple spherical Gaussian cluster. * * @author Erich Schubert + * @since 0.7.0 */ public class SphericalGaussianModel implements EMClusterModel<EMModel> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/SphericalGaussianModelFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/SphericalGaussianModelFactory.java index 8b2dfd57..0b32a962 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/SphericalGaussianModelFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/SphericalGaussianModelFactory.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * corresponds to the {@code 'VVI'} model in Mclust (R). * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has SphericalGaussianModel * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/AbstractRangeQueryNeighborPredicate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/AbstractRangeQueryNeighborPredicate.java index 53f70aac..aa78033d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/AbstractRangeQueryNeighborPredicate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/AbstractRangeQueryNeighborPredicate.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Abstract local model neighborhood predicate. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has Instance * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/COPACNeighborPredicate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/COPACNeighborPredicate.java index a2ec0e2e..f8aa1b97 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/COPACNeighborPredicate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/COPACNeighborPredicate.java @@ -70,6 +70,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * * @author Arthur Zimek * @author Erich Schubert + * @since 0.7.0 * * @param <V> the type of NumberVector handled by this Algorithm */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/CorePredicate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/CorePredicate.java index f87227c1..cd957770 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/CorePredicate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/CorePredicate.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * Note the Factory/Instance split of this interface. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has Instance */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/ERiCNeighborPredicate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/ERiCNeighborPredicate.java index d137ee67..cbe169ee 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/ERiCNeighborPredicate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/ERiCNeighborPredicate.java @@ -70,6 +70,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * * @author Elke Achtert * @author Erich Schubert + * @since 0.7.0 * * @param <V> the type of NumberVector handled by this Algorithm */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/EpsilonNeighborPredicate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/EpsilonNeighborPredicate.java index 8610521a..e3fdb443 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/EpsilonNeighborPredicate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/EpsilonNeighborPredicate.java @@ -59,6 +59,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has Instance * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/FourCCorePredicate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/FourCCorePredicate.java index ecd569e9..72b96fa0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/FourCCorePredicate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/FourCCorePredicate.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * </p> * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has Instance */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/FourCNeighborPredicate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/FourCNeighborPredicate.java index e9f50c41..71b4cf66 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/FourCNeighborPredicate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/FourCNeighborPredicate.java @@ -65,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * * @author Arthur Zimek * @author Erich Schubert + * @since 0.7.0 * * @param <V> the type of NumberVector handled by this Algorithm */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/GeneralizedDBSCAN.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/GeneralizedDBSCAN.java index b6b9d74f..86753fcd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/GeneralizedDBSCAN.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/GeneralizedDBSCAN.java @@ -68,6 +68,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Erich Schubert * @author Arthur Zimek + * @since 0.5.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/LSDBC.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/LSDBC.java index bd145c14..5c6ddafe 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/LSDBC.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/LSDBC.java @@ -75,6 +75,7 @@ import gnu.trove.list.array.TIntArrayList; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/MinPtsCorePredicate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/MinPtsCorePredicate.java index ff58902d..405ba28a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/MinPtsCorePredicate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/MinPtsCorePredicate.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has Instance */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/NeighborPredicate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/NeighborPredicate.java index 1e2aa716..9d760a4d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/NeighborPredicate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/NeighborPredicate.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * Note the Factory/Instance split of this interface. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has Instance */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/PreDeConCorePredicate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/PreDeConCorePredicate.java index 0ae26c40..e0cd1547 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/PreDeConCorePredicate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/PreDeConCorePredicate.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * </p> * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has Instance */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/PreDeConNeighborPredicate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/PreDeConNeighborPredicate.java index 26991ca9..9da9cc21 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/PreDeConNeighborPredicate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/PreDeConNeighborPredicate.java @@ -59,6 +59,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * * @author Peer Kröger * @author Erich Schubert + * @since 0.7.0 * * @param <V> the type of NumberVector handled by this Algorithm */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AGNES.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AGNES.java index 41de1cac..484c83b7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AGNES.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AGNES.java @@ -27,14 +27,8 @@ import de.lmu.ifi.dbs.elki.algorithm.AbstractDistanceBasedAlgorithm; import de.lmu.ifi.dbs.elki.data.type.TypeInformation; import de.lmu.ifi.dbs.elki.data.type.TypeUtil; import de.lmu.ifi.dbs.elki.database.Database; -import de.lmu.ifi.dbs.elki.database.datastore.DataStoreFactory; -import de.lmu.ifi.dbs.elki.database.datastore.DataStoreUtil; -import de.lmu.ifi.dbs.elki.database.datastore.WritableDBIDDataStore; -import de.lmu.ifi.dbs.elki.database.datastore.WritableDoubleDataStore; -import de.lmu.ifi.dbs.elki.database.datastore.WritableIntegerDataStore; import de.lmu.ifi.dbs.elki.database.ids.ArrayDBIDs; import de.lmu.ifi.dbs.elki.database.ids.DBIDArrayIter; -import de.lmu.ifi.dbs.elki.database.ids.DBIDIter; import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery; import de.lmu.ifi.dbs.elki.database.relation.Relation; @@ -57,7 +51,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * This is the naive O(n^3) algorithm. See {@link SLINK} for a much faster * algorithm (however, only for single-linkage). - * + * * This implementation uses the pointer-based representation used by SLINK, so * that the extraction algorithms we have can be used with either of them. * @@ -92,8 +86,10 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.composedOf LinkageMethod + * @apiviz.composedOf PointerHierarchyRepresentationBuilder * * @param <O> Object type */ @@ -116,7 +112,7 @@ public class AGNES<O> extends AbstractDistanceBasedAlgorithm<O, PointerHierarchy /** * Constructor. - * + * * @param distanceFunction Distance function to use * @param linkage Linkage method */ @@ -136,7 +132,7 @@ public class AGNES<O> extends AbstractDistanceBasedAlgorithm<O, PointerHierarchy /** * Run the algorithm - * + * * @param db Database * @param relation Relation * @return Clustering hierarchy @@ -162,21 +158,16 @@ public class AGNES<O> extends AbstractDistanceBasedAlgorithm<O, PointerHierarchy initializeDistanceMatrix(scratch, dq, ix, iy, square); // Initialize space for result: - WritableDBIDDataStore pi = DataStoreUtil.makeDBIDStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_STATIC); - WritableDoubleDataStore lambda = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_STATIC, Double.POSITIVE_INFINITY); - WritableIntegerDataStore csize = DataStoreUtil.makeIntegerStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, 1); - for(DBIDIter it = ids.iter(); it.valid(); it.advance()) { - pi.put(it, it); - } + PointerHierarchyRepresentationBuilder builder = new PointerHierarchyRepresentationBuilder(ids); // Repeat until everything merged into 1 cluster FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Agglomerative clustering", size - 1, LOG) : null; int wsize = size; for(int i = 1; i < size; i++) { - int x = findMerge(wsize, scratch, ix, iy, pi, lambda, csize); + int x = findMerge(wsize, scratch, ix, iy, builder); if(x == wsize - 1) { --wsize; - for(ix.seek(wsize - 1); lambda.doubleValue(ix) < Double.POSITIVE_INFINITY; ix.retract()) { + for(ix.seek(wsize - 1); builder.isLinked(ix); ix.retract()) { --wsize; } } @@ -184,12 +175,12 @@ public class AGNES<O> extends AbstractDistanceBasedAlgorithm<O, PointerHierarchy } LOG.ensureCompleted(prog); - return new PointerHierarchyRepresentationResult(ids, pi, lambda); + return builder.complete(); } /** * Compute the size of a complete x by x triangle (minus diagonal) - * + * * @param x Offset * @return Size of complete triangle */ @@ -199,7 +190,7 @@ public class AGNES<O> extends AbstractDistanceBasedAlgorithm<O, PointerHierarchy /** * Initialize a distance matrix. - * + * * @param scratch Scratch space to be used. * @param dq Distance query * @param ix Data iterator @@ -221,29 +212,27 @@ public class AGNES<O> extends AbstractDistanceBasedAlgorithm<O, PointerHierarchy /** * Perform the next merge step in AGNES. - * + * * @param size Data set size * @param scratch Scratch space. * @param ix First iterator * @param iy Second iterator - * @param pi Parent storage - * @param lambda Lambda (join distance) storage - * @param csize Cluster sizes + * @param builder Pointer representation builder * @return x, for shrinking the working set. */ - protected int findMerge(int size, double[] scratch, DBIDArrayIter ix, DBIDArrayIter iy, WritableDBIDDataStore pi, WritableDoubleDataStore lambda, WritableIntegerDataStore csize) { + protected int findMerge(int size, double[] scratch, DBIDArrayIter ix, DBIDArrayIter iy, PointerHierarchyRepresentationBuilder builder) { double mindist = Double.POSITIVE_INFINITY; int x = -1, y = -1; // Find minimum: for(int ox = 0, xbase = 0; ox < size; xbase += ox++) { // Skip if object has already joined a cluster: - if(lambda.doubleValue(ix.seek(ox)) < Double.POSITIVE_INFINITY) { + if(builder.isLinked(ix.seek(ox))) { continue; } assert(xbase == triangleSize(ox)); for(int oy = 0; oy < ox; oy++) { // Skip if object has already joined a cluster: - if(lambda.doubleValue(iy.seek(oy)) < Double.POSITIVE_INFINITY) { + if(builder.isLinked(iy.seek(oy))) { continue; } final int idx = xbase + oy; @@ -255,25 +244,23 @@ public class AGNES<O> extends AbstractDistanceBasedAlgorithm<O, PointerHierarchy } } assert(x >= 0 && y >= 0); - merge(size, scratch, ix, iy, pi, lambda, csize, mindist, x, y); + merge(size, scratch, ix, iy, builder, mindist, x, y); return x; } /** * Execute the cluster merge. - * + * * @param size Data set size * @param scratch Scratch space. * @param ix First iterator * @param iy Second iterator - * @param pi Parent storage - * @param lambda Lambda (join distance) storage - * @param csize Cluster sizes + * @param builder Hierarchy builder * @param mindist Distance that was used for merging * @param x First matrix position * @param y Second matrix position */ - protected void merge(int size, double[] scratch, DBIDArrayIter ix, DBIDArrayIter iy, WritableDBIDDataStore pi, WritableDoubleDataStore lambda, WritableIntegerDataStore csize, double mindist, int x, int y) { + protected void merge(int size, double[] scratch, DBIDArrayIter ix, DBIDArrayIter iy, PointerHierarchyRepresentationBuilder builder, double mindist, int x, int y) { // Avoid allocating memory, by reusing existing iterators: ix.seek(x); iy.seek(y); @@ -283,41 +270,39 @@ public class AGNES<O> extends AbstractDistanceBasedAlgorithm<O, PointerHierarchy // Perform merge in data structure: x -> y assert(y < x); // Since y < x, prefer keeping y, dropping x. - lambda.put(ix, mindist); - pi.put(ix, iy); + builder.add(ix, mindist, iy); // Update cluster size for y: - final int sizex = csize.intValue(ix), sizey = csize.intValue(iy); - csize.put(iy, sizex + sizey); + final int sizex = builder.getSize(ix), sizey = builder.getSize(iy); + builder.setSize(iy, sizex + sizey); // Note: this changes iy. - updateMatrix(size, scratch, iy, lambda, csize, mindist, x, y, sizex, sizey); + updateMatrix(size, scratch, iy, builder, mindist, x, y, sizex, sizey); } /** * Update the scratch distance matrix. - * + * * @param size Data set size * @param scratch Scratch matrix. * @param ij Iterator to reuse - * @param lambda Lambda (join distance) storage - * @param csize Cluster sizes + * @param builder Hierarchy builder * @param mindist Distance that was used for merging * @param x First matrix position * @param y Second matrix position * @param sizex Old size of first cluster * @param sizey Old size of second cluster */ - protected void updateMatrix(int size, double[] scratch, DBIDArrayIter ij, WritableDoubleDataStore lambda, WritableIntegerDataStore csize, double mindist, int x, int y, final int sizex, final int sizey) { + protected void updateMatrix(int size, double[] scratch, DBIDArrayIter ij, PointerHierarchyRepresentationBuilder builder, double mindist, int x, int y, final int sizex, final int sizey) { // Update distance matrix. Note: miny < minx final int xbase = triangleSize(x), ybase = triangleSize(y); // Write to (y, j), with j < y int j = 0; for(; j < y; j++) { - if(lambda.doubleValue(ij.seek(j)) < Double.POSITIVE_INFINITY) { + if(builder.isLinked(ij.seek(j))) { continue; } - final int sizej = csize.intValue(ij); + final int sizej = builder.getSize(ij); final int yb = ybase + j; scratch[yb] = linkage.combine(sizex, scratch[xbase + j], sizey, scratch[yb], sizej, mindist); } @@ -325,20 +310,20 @@ public class AGNES<O> extends AbstractDistanceBasedAlgorithm<O, PointerHierarchy // Write to (j, y), with y < j < x int jbase = triangleSize(j); for(; j < x; jbase += j++) { - if(lambda.doubleValue(ij.seek(j)) < Double.POSITIVE_INFINITY) { + if(builder.isLinked(ij.seek(j))) { continue; } - final int sizej = csize.intValue(ij); + final int sizej = builder.getSize(ij); final int jb = jbase + y; scratch[jb] = linkage.combine(sizex, scratch[xbase + j], sizey, scratch[jb], sizej, mindist); } jbase += j++; // Skip x // Write to (j, y), with y < x < j for(; j < size; jbase += j++) { - if(lambda.doubleValue(ij.seek(j)) < Double.POSITIVE_INFINITY) { + if(builder.isLinked(ij.seek(j))) { continue; } - final int sizej = csize.intValue(ij); + final int sizej = builder.getSize(ij); scratch[jbase + y] = linkage.combine(sizex, scratch[jbase + x], sizey, scratch[jbase + y], sizej, mindist); } } @@ -356,11 +341,11 @@ public class AGNES<O> extends AbstractDistanceBasedAlgorithm<O, PointerHierarchy /** * Parameterization class - * + * * @author Erich Schubert - * + * * @apiviz.exclude - * + * * @param <O> Object type */ public static class Parameterizer<O> extends AbstractDistanceBasedAlgorithm.Parameterizer<O> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AbstractHDBSCAN.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AbstractHDBSCAN.java index 8febff49..a38f629f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AbstractHDBSCAN.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AbstractHDBSCAN.java @@ -66,6 +66,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf HDBSCANAdapter * @apiviz.composedOf HeapMSTCollector @@ -107,7 +108,7 @@ public abstract class AbstractHDBSCAN<O, R extends Result> extends AbstractDista protected WritableDoubleDataStore computeCoreDists(DBIDs ids, KNNQuery<O> knnQ, int minPts) { final Logging LOG = getLogger(); final WritableDoubleDataStore coredists = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_DB); - FiniteProgress cprog = LOG.isVerbose() ? new FiniteProgress("Computing core sizes.", ids.size(), LOG) : null; + FiniteProgress cprog = LOG.isVerbose() ? new FiniteProgress("Computing core sizes", ids.size(), LOG) : null; for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) { coredists.put(iter, knnQ.getKNNForDBID(iter, minPts).getKNNDistance()); LOG.incrementProcessed(cprog); @@ -234,7 +235,7 @@ public abstract class AbstractHDBSCAN<O, R extends Result> extends AbstractDista pi.put(iter, iter); // Initialize } DBIDVar p = DBIDUtil.newVar(), q = DBIDUtil.newVar(), n = DBIDUtil.newVar(); - FiniteProgress pprog = LOG.isVerbose() ? new FiniteProgress("Converting MST to pointer representation.", heap.size(), LOG) : null; + FiniteProgress pprog = LOG.isVerbose() ? new FiniteProgress("Converting MST to pointer representation", heap.size(), LOG) : null; while(!heap.isEmpty()) { final double dist = heap.peekKey(); final long pair = heap.peekValue(); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AnderbergHierarchicalClustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AnderbergHierarchicalClustering.java index 0484b7ad..f30bd8df 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AnderbergHierarchicalClustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AnderbergHierarchicalClustering.java @@ -29,14 +29,8 @@ import de.lmu.ifi.dbs.elki.algorithm.AbstractDistanceBasedAlgorithm; import de.lmu.ifi.dbs.elki.data.type.TypeInformation; import de.lmu.ifi.dbs.elki.data.type.TypeUtil; import de.lmu.ifi.dbs.elki.database.Database; -import de.lmu.ifi.dbs.elki.database.datastore.DataStoreFactory; -import de.lmu.ifi.dbs.elki.database.datastore.DataStoreUtil; -import de.lmu.ifi.dbs.elki.database.datastore.WritableDBIDDataStore; -import de.lmu.ifi.dbs.elki.database.datastore.WritableDoubleDataStore; -import de.lmu.ifi.dbs.elki.database.datastore.WritableIntegerDataStore; import de.lmu.ifi.dbs.elki.database.ids.ArrayDBIDs; import de.lmu.ifi.dbs.elki.database.ids.DBIDArrayIter; -import de.lmu.ifi.dbs.elki.database.ids.DBIDIter; import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery; import de.lmu.ifi.dbs.elki.database.relation.Relation; @@ -52,16 +46,16 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; /** * This is a modification of the classic AGNES algorithm for hierarchical * clustering using a nearest-neighbor heuristic for acceleration. - * + * * Instead of scanning the matrix (with cost O(n^2)) to find the minimum, the * nearest neighbor of each object is remembered. On the downside, we need to * check these values at every merge, and it may now cost O(n^2) to perform a * merge, so there is no worst-case advantage to this approach. The average case * however improves from O(n^3) to O(n^2), which yields a considerable * improvement in running time. - * + * * This optimization is attributed to M. R. Anderberg. - * + * * Reference: * <p> * M. R. Anderberg<br /> @@ -71,8 +65,10 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.composedOf LinkageMethod + * @apiviz.composedOf PointerHierarchyRepresentationBuilder * * @param <O> Object type */ @@ -92,7 +88,7 @@ public class AnderbergHierarchicalClustering<O> extends AbstractDistanceBasedAlg /** * Constructor. - * + * * @param distanceFunction Distance function to use * @param linkage Linkage method */ @@ -103,7 +99,7 @@ public class AnderbergHierarchicalClustering<O> extends AbstractDistanceBasedAlg /** * Run the algorithm - * + * * @param db Database * @param relation Relation * @return Clustering hierarchy @@ -135,21 +131,16 @@ public class AnderbergHierarchicalClustering<O> extends AbstractDistanceBasedAlg initializeNNCache(scratch, bestd, besti); // Initialize space for result: - WritableDBIDDataStore pi = DataStoreUtil.makeDBIDStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_STATIC); - WritableDoubleDataStore lambda = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_STATIC, Double.POSITIVE_INFINITY); - WritableIntegerDataStore csize = DataStoreUtil.makeIntegerStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, 1); - for(DBIDIter it = ids.iter(); it.valid(); it.advance()) { - pi.put(it, it); - } + PointerHierarchyRepresentationBuilder builder = new PointerHierarchyRepresentationBuilder(ids); // Repeat until everything merged into 1 cluster FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Agglomerative clustering", size - 1, LOG) : null; int wsize = size; for(int i = 1; i < size; i++) { - int x = findMerge(wsize, scratch, ix, iy, bestd, besti, pi, lambda, csize); + int x = findMerge(wsize, scratch, ix, iy, bestd, besti, builder); if(x == wsize - 1) { --wsize; - for(ix.seek(wsize - 1); lambda.doubleValue(ix) < Double.POSITIVE_INFINITY; ix.retract()) { + for(ix.seek(wsize - 1); builder.isLinked(ix); ix.retract()) { --wsize; } } @@ -157,12 +148,12 @@ public class AnderbergHierarchicalClustering<O> extends AbstractDistanceBasedAlg } LOG.ensureCompleted(prog); - return new PointerHierarchyRepresentationResult(ids, pi, lambda); + return builder.complete(); } /** * Initialize the NN cache. - * + * * @param scratch Scatch space * @param bestd Best distance * @param besti Best index @@ -193,21 +184,19 @@ public class AnderbergHierarchicalClustering<O> extends AbstractDistanceBasedAlg /** * Perform the next merge step. - * + * * Due to the cache, this is now O(n) each time, instead of O(n*n). - * + * * @param size Data set size * @param scratch Scratch space. * @param ix First iterator * @param iy Second iterator * @param bestd Best distance * @param besti Index of best distance - * @param pi Parent storage - * @param lambda Lambda (join distance) storage - * @param csize Cluster sizes + * @param builder Hierarchy builder * @return x, for shrinking the working set. */ - protected int findMerge(int size, double[] scratch, DBIDArrayIter ix, DBIDArrayIter iy, double[] bestd, int[] besti, WritableDBIDDataStore pi, WritableDoubleDataStore lambda, WritableIntegerDataStore csize) { + protected int findMerge(int size, double[] scratch, DBIDArrayIter ix, DBIDArrayIter iy, double[] bestd, int[] besti, PointerHierarchyRepresentationBuilder builder) { double mindist = Double.POSITIVE_INFINITY; int x = -1, y = -1; // Find minimum: @@ -223,27 +212,25 @@ public class AnderbergHierarchicalClustering<O> extends AbstractDistanceBasedAlg } } assert(x >= 0 && y >= 0); - merge(size, scratch, ix, iy, bestd, besti, pi, lambda, csize, mindist, x < y ? y : x, x < y ? x : y); + merge(size, scratch, ix, iy, bestd, besti, builder, mindist, x < y ? y : x, x < y ? x : y); return x; } /** * Execute the cluster merge. - * + * * @param size Data set size * @param scratch Scratch space. * @param ix First iterator * @param iy Second iterator * @param bestd Best distance * @param besti Index of best distance - * @param pi Parent storage - * @param lambda Lambda (join distance) storage - * @param csize Cluster sizes + * @param builder Hierarchy builder * @param mindist Distance that was used for merging * @param x First matrix position * @param y Second matrix position */ - protected void merge(int size, double[] scratch, DBIDArrayIter ix, DBIDArrayIter iy, double[] bestd, int[] besti, WritableDBIDDataStore pi, WritableDoubleDataStore lambda, WritableIntegerDataStore csize, double mindist, int x, int y) { + protected void merge(int size, double[] scratch, DBIDArrayIter ix, DBIDArrayIter iy, double[] bestd, int[] besti, PointerHierarchyRepresentationBuilder builder, double mindist, int x, int y) { // Avoid allocating memory, by reusing existing iterators: ix.seek(x); iy.seek(y); @@ -253,17 +240,16 @@ public class AnderbergHierarchicalClustering<O> extends AbstractDistanceBasedAlg // Perform merge in data structure: x -> y assert(y < x); // Since y < x, prefer keeping y, dropping x. - lambda.put(ix, mindist); - pi.put(ix, iy); + builder.add(ix, mindist, iy); // Update cluster size for y: - final int sizex = csize.intValue(ix), sizey = csize.intValue(iy); - csize.put(iy, sizex + sizey); + final int sizex = builder.getSize(ix), sizey = builder.getSize(iy); + builder.setSize(iy, sizex + sizey); // Deactivate x in cache: besti[x] = -1; // Note: this changes iy. - updateMatrix(size, scratch, iy, bestd, besti, lambda, csize, mindist, x, y, sizex, sizey); + updateMatrix(size, scratch, iy, bestd, besti, builder, mindist, x, y, sizex, sizey); if(besti[y] == x) { findBest(size, scratch, bestd, besti, y); } @@ -271,31 +257,30 @@ public class AnderbergHierarchicalClustering<O> extends AbstractDistanceBasedAlg /** * Update the scratch distance matrix. - * + * * @param size Data set size * @param scratch Scratch matrix. * @param ij Iterator to reuse * @param bestd Best distance * @param besti Index of best distance - * @param lambda Lambda (join distance) storage - * @param csize Cluster sizes + * @param builder Hierarchy builder * @param mindist Distance that was used for merging * @param x First matrix position * @param y Second matrix position * @param sizex Old size of first cluster * @param sizey Old size of second cluster */ - protected void updateMatrix(int size, double[] scratch, DBIDArrayIter ij, double[] bestd, int[] besti, WritableDoubleDataStore lambda, WritableIntegerDataStore csize, double mindist, int x, int y, final int sizex, final int sizey) { + protected void updateMatrix(int size, double[] scratch, DBIDArrayIter ij, double[] bestd, int[] besti, PointerHierarchyRepresentationBuilder builder, double mindist, int x, int y, final int sizex, final int sizey) { // Update distance matrix. Note: miny < minx final int xbase = AGNES.triangleSize(x), ybase = AGNES.triangleSize(y); // Write to (y, j), with j < y int j = 0; for(; j < y; j++) { - if(lambda.doubleValue(ij.seek(j)) < Double.POSITIVE_INFINITY) { + if(builder.isLinked(ij.seek(j))) { continue; } - final int sizej = csize.intValue(ij); + final int sizej = builder.getSize(ij); final int yb = ybase + j; final double d = scratch[yb] = linkage.combine(sizex, scratch[xbase + j], sizey, scratch[yb], sizej, mindist); updateCache(size, scratch, bestd, besti, x, y, j, d); @@ -304,10 +289,10 @@ public class AnderbergHierarchicalClustering<O> extends AbstractDistanceBasedAlg // Write to (j, y), with y < j < x int jbase = AGNES.triangleSize(j); for(; j < x; jbase += j++) { - if(lambda.doubleValue(ij.seek(j)) < Double.POSITIVE_INFINITY) { + if(builder.isLinked(ij.seek(j))) { continue; } - final int sizej = csize.intValue(ij); + final int sizej = builder.getSize(ij); final int jb = jbase + y; final double d = scratch[jb] = linkage.combine(sizex, scratch[xbase + j], sizey, scratch[jb], sizej, mindist); updateCache(size, scratch, bestd, besti, x, y, j, d); @@ -315,10 +300,10 @@ public class AnderbergHierarchicalClustering<O> extends AbstractDistanceBasedAlg jbase += j++; // Skip x // Write to (j, y), with y < x < j for(; j < size; jbase += j++) { - if(lambda.doubleValue(ij.seek(j)) < Double.POSITIVE_INFINITY) { + if(builder.isLinked(ij.seek(j))) { continue; } - final int sizej = csize.intValue(ij); + final int sizej = builder.getSize(ij); final double d = scratch[jbase + y] = linkage.combine(sizex, scratch[jbase + x], sizey, scratch[jbase + y], sizej, mindist); updateCache(size, scratch, bestd, besti, x, y, j, d); } @@ -390,11 +375,11 @@ public class AnderbergHierarchicalClustering<O> extends AbstractDistanceBasedAlg /** * Parameterization class - * + * * @author Erich Schubert - * + * * @apiviz.exclude - * + * * @param <O> Object type */ public static class Parameterizer<O> extends AbstractDistanceBasedAlgorithm.Parameterizer<O> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/CLINK.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/CLINK.java index 65eba0cd..711cc5c7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/CLINK.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/CLINK.java @@ -56,6 +56,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has CompleteLinkageMethod * @@ -65,7 +66,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; title = "An Efficient Algorithm for the Complete Link Cluster Method", // booktitle = "The Computer Journal 20.4", // url = "http://dx.doi.org/10.1093/comjnl/20.4.364") -@Alias({ "CLINK", "Defays" }) +@Alias("Defays") public class CLINK<O> extends SLINK<O> { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/CentroidLinkageMethod.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/CentroidLinkageMethod.java index 9fc13e20..5d33f693 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/CentroidLinkageMethod.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/CentroidLinkageMethod.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 */ @Alias({ "centroid", "upgmc" }) @Reference(authors = "A. K. Jain and R. C. Dubes", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/CompleteLinkageMethod.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/CompleteLinkageMethod.java index 28c6841d..241137e1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/CompleteLinkageMethod.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/CompleteLinkageMethod.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Complete-linkage clustering method. * * @author Erich Schubert + * @since 0.5.0 */ @Alias({ "complete", "clink", "complete-link", "farthest-neighbor" }) public class CompleteLinkageMethod implements LinkageMethod { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/GroupAverageLinkageMethod.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/GroupAverageLinkageMethod.java index c618775e..551f84cb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/GroupAverageLinkageMethod.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/GroupAverageLinkageMethod.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.3 */ @Alias({ "upgma", "average", "average-link", "average-linkage", "UPGMA" }) @Reference(authors = "A. K. Jain and R. C. Dubes", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/HDBSCANLinearMemory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/HDBSCANLinearMemory.java index 37dfd01f..b402d65f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/HDBSCANLinearMemory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/HDBSCANLinearMemory.java @@ -74,8 +74,11 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @param <O> Object type + * + * @apiviz.has PointerDensityHierarchyRepresentationResult */ @Title("HDBSCAN: Hierarchical Density-Based Spatial Clustering of Applications with Noise") @Description("Density-Based Clustering Based on Hierarchical Density Estimates") @@ -119,7 +122,7 @@ public class HDBSCANLinearMemory<O> extends AbstractHDBSCAN<O, PointerDensityHie final int numedges = ids.size() - 1; DoubleLongHeap heap = new DoubleLongMinHeap(numedges); // 2. Build spanning tree. - FiniteProgress mprog = LOG.isVerbose() ? new FiniteProgress("Computing minimum spanning tree (n-1 edges).", numedges, LOG) : null; + FiniteProgress mprog = LOG.isVerbose() ? new FiniteProgress("Computing minimum spanning tree (n-1 edges)", numedges, LOG) : null; PrimsMinimumSpanningTree.processDense(ids,// new HDBSCANAdapter(ids, coredists, distQ), // new HeapMSTCollector(heap, mprog, LOG)); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/HierarchicalClusteringAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/HierarchicalClusteringAlgorithm.java index 0dfb31e0..80f72a69 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/HierarchicalClusteringAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/HierarchicalClusteringAlgorithm.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.database.Database; * {@link de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.extraction.ExtractFlatClusteringFromHierarchy}. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has PointerHierarchyRepresentationResult */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/LinkageMethod.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/LinkageMethod.java index ea853eec..de134e1d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/LinkageMethod.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/LinkageMethod.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.4.0 */ @Reference(authors = "G. N. Lance and W. T. Williams", // title = "A general theory of classificatory sorting strategies 1. Hierarchical systems", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/MedianLinkageMethod.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/MedianLinkageMethod.java index 6eb2e156..20f83feb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/MedianLinkageMethod.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/MedianLinkageMethod.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.3 */ @Reference(authors = "J. C. Gower", // title = "A comparison of some methods of cluster analysis", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/PointerDensityHierarchyRepresentationResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/PointerDensityHierarchyRepresentationResult.java index 581841b8..b37e82af 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/PointerDensityHierarchyRepresentationResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/PointerDensityHierarchyRepresentationResult.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * which is a density estimation. * * @author Erich Schubert + * @since 0.5.0 */ public class PointerDensityHierarchyRepresentationResult extends PointerHierarchyRepresentationResult { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/PointerHierarchyRepresentationBuilder.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/PointerHierarchyRepresentationBuilder.java new file mode 100644 index 00000000..8e15bf81 --- /dev/null +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/PointerHierarchyRepresentationBuilder.java @@ -0,0 +1,171 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical; +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import de.lmu.ifi.dbs.elki.database.datastore.DataStoreFactory; +import de.lmu.ifi.dbs.elki.database.datastore.DataStoreUtil; +import de.lmu.ifi.dbs.elki.database.datastore.WritableDBIDDataStore; +import de.lmu.ifi.dbs.elki.database.datastore.WritableDoubleDataStore; +import de.lmu.ifi.dbs.elki.database.datastore.WritableIntegerDataStore; +import de.lmu.ifi.dbs.elki.database.ids.DBIDIter; +import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; +import de.lmu.ifi.dbs.elki.database.ids.DBIDs; +import de.lmu.ifi.dbs.elki.logging.Logging; + +/** + * Class to help building a pointer hierarchy. + * + * @author Erich Schubert + * @since 0.7.1 + * + * @apiviz.has PointerHierarchyRepresentationResult + */ +public class PointerHierarchyRepresentationBuilder { + /** + * Class logger. + */ + private static final Logging LOG = Logging.getLogger(PointerHierarchyRepresentationBuilder.class); + + /** + * The DBIDs in this result. + */ + protected final DBIDs ids; + + /** + * The parent DBID relation. + */ + protected WritableDBIDDataStore parent; + + /** + * Distance to the parent object. + */ + protected WritableDoubleDataStore parentDistance; + + /** + * Last linking distance. + */ + protected double prevdist; + + /** + * Cluster size storage. May be uninitialized! + */ + protected WritableIntegerDataStore csize; + + /** + * Constructor. + * + * @param ids IDs + */ + public PointerHierarchyRepresentationBuilder(DBIDs ids) { + super(); + this.ids = ids; + this.parent = DataStoreUtil.makeDBIDStorage(ids, DataStoreFactory.HINT_DB | DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_STATIC); + this.parentDistance = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_DB | DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_STATIC, Double.POSITIVE_INFINITY); + this.prevdist = Double.NEGATIVE_INFINITY; + for(DBIDIter it = ids.iter(); it.valid(); it.advance()) { + parent.put(it, it); + } + } + + /** + * Add an element to the pointer representation. + * + * Important: If an algorithm does not produce links in an increasing fashion, + * a warning will be issued and the linking distance will be increased. + * Otherwise, the hierarchy would be misinterpreted when links are executed + * ordered by their distance. + * + * @param cur Current object + * @param distance Link distance + * @param par Parent + */ + public void add(DBIDRef cur, double distance, DBIDRef par) { + if(distance < prevdist) { + LOG.warning("Non-monotone hierarchical clustering detected. Adjusting linking distance from " + distance + " to " + prevdist); + distance = prevdist; + } + parent.putDBID(cur, par); + double olddist = parentDistance.putDouble(cur, distance); + assert (olddist == Double.POSITIVE_INFINITY) : "Object was already linked!"; + prevdist = distance; + } + + /** + * Finalize the result. + * + * @return Completed result + */ + public PointerHierarchyRepresentationResult complete() { + if(csize != null) { + csize.destroy(); + csize = null; + } + return new PointerHierarchyRepresentationResult(ids, parent, parentDistance); + } + + /** + * Get the cluster size of the current object. + * + * @param id Object id + * @return Cluster size (initially 1). + */ + public int getSize(DBIDRef id) { + if(csize == null) { + csize = DataStoreUtil.makeIntegerStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, 1); + } + return csize.intValue(id); + } + + /** + * Set the cluster size of an object. + * + * @param id Object to set + * @param size Cluster size + */ + public void setSize(DBIDRef id, int size) { + if(csize == null) { + csize = DataStoreUtil.makeIntegerStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, 1); + } + csize.putInt(id, size); + } + + /** + * Test if an object is already linked. + * + * @param id Object + * @return {@code true} if the object is already linked. + */ + public boolean isLinked(DBIDRef id) { + return parentDistance.doubleValue(id) < Double.POSITIVE_INFINITY; + } + + /** + * Get the current linking distance of an object. + * + * @param id Object + * @return Distance, or infinity + */ + public double getDistance(DBIDRef id) { + return parentDistance.doubleValue(id); + } +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/PointerHierarchyRepresentationResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/PointerHierarchyRepresentationResult.java index 2369c6e5..fbd3d6b9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/PointerHierarchyRepresentationResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/PointerHierarchyRepresentationResult.java @@ -24,8 +24,19 @@ package de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical; */ import de.lmu.ifi.dbs.elki.database.datastore.DBIDDataStore; +import de.lmu.ifi.dbs.elki.database.datastore.DataStoreFactory; +import de.lmu.ifi.dbs.elki.database.datastore.DataStoreUtil; import de.lmu.ifi.dbs.elki.database.datastore.DoubleDataStore; +import de.lmu.ifi.dbs.elki.database.datastore.IntegerDataStore; +import de.lmu.ifi.dbs.elki.database.datastore.WritableIntegerDataStore; +import de.lmu.ifi.dbs.elki.database.ids.ArrayDBIDs; +import de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs; +import de.lmu.ifi.dbs.elki.database.ids.DBIDArrayIter; +import de.lmu.ifi.dbs.elki.database.ids.DBIDIter; +import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; +import de.lmu.ifi.dbs.elki.database.ids.DBIDVar; import de.lmu.ifi.dbs.elki.database.ids.DBIDs; +import de.lmu.ifi.dbs.elki.database.ids.ModifiableDBIDs; import de.lmu.ifi.dbs.elki.result.BasicResult; /** @@ -36,7 +47,12 @@ import de.lmu.ifi.dbs.elki.result.BasicResult; * {@link de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.extraction.ExtractFlatClusteringFromHierarchy} * can be used to extract partitions from this graph. * + * This class can also compute dendrogram positions, but using a faster + * algorithm than the one proposed by Sibson 1971, using only O(n log n) time + * due to sorting, but using an additional temporary array. + * * @author Erich Schubert + * @since 0.6.0 */ public class PointerHierarchyRepresentationResult extends BasicResult { /** @@ -55,8 +71,13 @@ public class PointerHierarchyRepresentationResult extends BasicResult { DoubleDataStore parentDistance; /** + * Position storage, computed on demand. + */ + IntegerDataStore positions = null; + + /** * Constructor. - * + * * @param ids IDs processed. * @param parent Parent pointer. * @param parentDistance Distance to parent. @@ -70,7 +91,7 @@ public class PointerHierarchyRepresentationResult extends BasicResult { /** * Get the clustered DBIDs. - * + * * @return DBIDs */ public DBIDs getDBIDs() { @@ -79,7 +100,7 @@ public class PointerHierarchyRepresentationResult extends BasicResult { /** * Get the parent DBID relation. - * + * * @return Parent relation. */ public DBIDDataStore getParentStore() { @@ -88,10 +109,98 @@ public class PointerHierarchyRepresentationResult extends BasicResult { /** * Get the distance to the parent. - * + * * @return Parent distance. */ public DoubleDataStore getParentDistanceStore() { return parentDistance; } + + /** + * Get / compute the positions. + * + * @return Dendrogram positions + */ + public IntegerDataStore getPositions() { + if(positions != null) { + return positions; // Return cached. + } + ArrayDBIDs order = topologicalSort(ids, parent, parentDistance); + DBIDArrayIter it = order.iter(); + final int last = order.size() - 1; + // Subtree sizes of each element: + WritableIntegerDataStore siz = DataStoreUtil.makeIntegerStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_DB, 1); + DBIDVar v1 = DBIDUtil.newVar(); + for(it.seek(0); it.valid(); it.advance()) { + if(DBIDUtil.equal(it, parent.assignVar(it, v1))) { + continue; + } + siz.increment(v1, siz.intValue(it)); + } + // Assertion only holds for exact e.g. single linkage + //assert (siz.intValue(it.seek(last)) == ids.size()); + WritableIntegerDataStore pos = DataStoreUtil.makeIntegerStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_DB, -1); + WritableIntegerDataStore ins = DataStoreUtil.makeIntegerStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, -1); + int defins = 0; + // Place elements based on their successor + for(it.seek(last); it.valid(); it.retract()) { + int size = siz.intValue(it); + parent.assignVar(it, v1); // v1 = parent + final int ipos = ins.intValue(v1); + // Assertion only holds for exact e.g. single linkage + // assert (ipos >= 0); + if(ipos < 0 || DBIDUtil.equal(it, v1)) { + // Root: use interval [defins; defins + size] + ins.putInt(it, defins); + pos.putInt(it, defins + size - 1); + defins += size; + continue; + } + // Insertion position of parent = leftmost + pos.putInt(it, ipos + size - 1); + ins.putInt(it, ipos); + ins.increment(v1, size); + } + ins.destroy(); + return positions = pos; + } + + /** + * Perform topological sorting based on the successor order. + * + * @param oids IDs to sort + * @param parent Parent relationship. + * @param parentDistance Distance to parent. + * @return Sorted order + */ + public static ArrayDBIDs topologicalSort(DBIDs oids, DBIDDataStore parent, DoubleDataStore parentDistance) { + // We used to simply use this: + // But for e.g. Median Linkage, this would lead to problems, as links are + // not necessarily performed in ascending order anymore! + ArrayModifiableDBIDs ids = DBIDUtil.newArray(oids); + ids.sort(new DataStoreUtil.DescendingByDoubleDataStoreAndId(parentDistance)); + final int size = ids.size(); + ModifiableDBIDs seen = DBIDUtil.newHashSet(size); + ArrayModifiableDBIDs order = DBIDUtil.newArray(size); + DBIDVar v1 = DBIDUtil.newVar(), prev = DBIDUtil.newVar(); + for(DBIDIter it = ids.iter(); it.valid(); it.advance()) { + if(!seen.add(it)) { + continue; + } + order.add(it); + prev.set(it); // Copy + while(!DBIDUtil.equal(prev, parent.assignVar(prev, v1))) { + if(!seen.add(v1)) { + break; + } + order.add(v1); + prev.set(v1); // Copy + } + } + // Reverse the array: + for(int i = 0, j = size - 1; i < j; i++, j--) { + order.swap(i, j); + } + return order; + } } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/SLINK.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/SLINK.java index 71213208..f41a18bb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/SLINK.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/SLINK.java @@ -63,6 +63,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * * @author Elke Achtert * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has SingleLinkageMethod * @@ -74,7 +75,8 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; title = "SLINK: An optimally efficient algorithm for the single-link cluster method", // booktitle = "The Computer Journal 16 (1973), No. 1, p. 30-34.", // url = "http://dx.doi.org/10.1093/comjnl/16.1.30") -@Alias(value = { "de.lmu.ifi.dbs.elki.algorithm.clustering.SLINK", "clustering.SLINK", "SLINK", "single-link", "single-linkage" }) +@Alias({ "de.lmu.ifi.dbs.elki.algorithm.clustering.SLINK", "clustering.SLINK", // +"single-link", "single-linkage" }) public class SLINK<O> extends AbstractDistanceBasedAlgorithm<O, PointerHierarchyRepresentationResult>implements HierarchicalClusteringAlgorithm { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/SLINKHDBSCANLinearMemory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/SLINKHDBSCANLinearMemory.java index 8f1c6195..d89da303 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/SLINKHDBSCANLinearMemory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/SLINKHDBSCANLinearMemory.java @@ -50,22 +50,22 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; /** * Linear memory implementation of HDBSCAN clustering based on SLINK. - * + * * By not building a distance matrix, we can reduce memory usage to linear * memory only; but at the cost of roughly double the runtime (unless using * indexes) as we first need to compute all kNN distances (for core sizes), then * recompute distances when building the spanning tree. - * + * * This version uses the SLINK algorithm to directly produce the pointer * representation expected by the extraction methods. The SLINK algorithm is * closely related to Prim's minimum spanning tree, but produces the more * compact pointer representation instead of an edges list. - * + * * This implementation does <em>not</em> include the cluster extraction * discussed as Step 4. This functionality should however already be provided by * {@link de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.extraction.HDBSCANHierarchyExtraction} * . For this reason, we also do <em>not include self-edges</em>. - * + * * Reference: * <p> * R. J. G. B. Campello, D. Moulavi, and J. Sander<br /> @@ -73,8 +73,11 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * Pacific-Asia Conference on Advances in Knowledge Discovery and Data Mining, * PAKDD * </p> - * + * * @author Erich Schubert + * @since 0.6.0 + * + * @apiviz.has PointerDensityHierarchyRepresentationResult */ @Title("HDBSCAN: Hierarchical Density-Based Spatial Clustering of Applications with Noise") @Description("Density-Based Clustering Based on Hierarchical Density Estimates") @@ -90,7 +93,7 @@ public class SLINKHDBSCANLinearMemory<O> extends AbstractHDBSCAN<O, PointerDensi /** * Constructor. - * + * * @param distanceFunction Distance function * @param minPts Minimum number of points for density */ @@ -100,7 +103,7 @@ public class SLINKHDBSCANLinearMemory<O> extends AbstractHDBSCAN<O, PointerDensi /** * Run the algorithm - * + * * @param db Database * @param relation Relation * @return Clustering hierarchy @@ -143,7 +146,7 @@ public class SLINKHDBSCANLinearMemory<O> extends AbstractHDBSCAN<O, PointerDensi /** * First step: Initialize P(id) = id, L(id) = infinity. - * + * * @param id the id of the object to be inserted into the pointer * representation * @param pi Pi data store @@ -160,7 +163,7 @@ public class SLINKHDBSCANLinearMemory<O> extends AbstractHDBSCAN<O, PointerDensi /** * Second step: Determine the pairwise distances from all objects in the * pointer representation to the new object with the specified id. - * + * * @param id the id of the object to be inserted into the pointer * representation * @param processedIDs the already processed ids @@ -179,7 +182,7 @@ public class SLINKHDBSCANLinearMemory<O> extends AbstractHDBSCAN<O, PointerDensi /** * Third step: Determine the values for P and L - * + * * @param id the id of the object to be inserted into the pointer * representation * @param pi Pi data store @@ -220,7 +223,7 @@ public class SLINKHDBSCANLinearMemory<O> extends AbstractHDBSCAN<O, PointerDensi /** * Fourth step: Actualize the clusters if necessary - * + * * @param id the id of the current object * @param pi Pi data store * @param lambda Lambda data store @@ -254,11 +257,11 @@ public class SLINKHDBSCANLinearMemory<O> extends AbstractHDBSCAN<O, PointerDensi /** * Parameterization class - * + * * @author Erich Schubert - * + * * @apiviz.exclude - * + * * @param <O> Object type */ public static class Parameterizer<O> extends AbstractHDBSCAN.Parameterizer<O> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/SingleLinkageMethod.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/SingleLinkageMethod.java index f16393de..73cf4b99 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/SingleLinkageMethod.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/SingleLinkageMethod.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.3 */ @Reference(authors = "K. Florek and J. Łukaszewicz and J. Perkal and H. Steinhaus and S. Zubrzycki", // title = "Sur la liaison et la division des points d'un ensemble fini",// diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/WardLinkageMethod.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/WardLinkageMethod.java index 80194a87..ad61d6da 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/WardLinkageMethod.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/WardLinkageMethod.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "J. H. Ward Jr", // title = "Hierarchical grouping to optimize an objective function", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/WeightedAverageLinkageMethod.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/WeightedAverageLinkageMethod.java index 162d4bc9..3cb583f8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/WeightedAverageLinkageMethod.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/WeightedAverageLinkageMethod.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "A. K. Jain and R. C. Dubes", // title = "Algorithms for Clustering Data", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/extraction/ExtractFlatClusteringFromHierarchy.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/extraction/ExtractFlatClusteringFromHierarchy.java index 5f4bbd70..9d055b03 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/extraction/ExtractFlatClusteringFromHierarchy.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/extraction/ExtractFlatClusteringFromHierarchy.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; import de.lmu.ifi.dbs.elki.database.ids.ModifiableDBIDs; import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.DoubleArray; import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; @@ -69,10 +70,12 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * TODO: add an hierarchy simplification step. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses HierarchicalClusteringAlgorithm * @apiviz.uses PointerHierarchyRepresentationResult */ +@Alias("de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.ExtractFlatClusteringFromHierarchy") public class ExtractFlatClusteringFromHierarchy implements ClusteringAlgorithm<Clustering<DendrogramModel>> { /** * Class logger. @@ -182,8 +185,7 @@ public class ExtractFlatClusteringFromHierarchy implements ClusteringAlgorithm<C // Sort DBIDs by lambda. We need this for two things: // a) to determine the stop distance from "minclusters" parameter // b) to process arrows in decreasing / increasing order - ArrayModifiableDBIDs order = DBIDUtil.newArray(ids); - order.sort(new DataStoreUtil.AscendingByDoubleDataStore(lambda)); + ArrayDBIDs order = PointerHierarchyRepresentationResult.topologicalSort(ids, pi, lambda); DBIDArrayIter it = order.iter(); // Used multiple times! final int split = findSplit(order, it, lambda); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/extraction/HDBSCANHierarchyExtraction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/extraction/HDBSCANHierarchyExtraction.java index 20c5e211..80c32ae4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/extraction/HDBSCANHierarchyExtraction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/extraction/HDBSCANHierarchyExtraction.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.database.datastore.DataStoreFactory; import de.lmu.ifi.dbs.elki.database.datastore.DataStoreUtil; import de.lmu.ifi.dbs.elki.database.datastore.DoubleDataStore; import de.lmu.ifi.dbs.elki.database.datastore.WritableDataStore; +import de.lmu.ifi.dbs.elki.database.ids.ArrayDBIDs; import de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs; import de.lmu.ifi.dbs.elki.database.ids.DBIDArrayIter; import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; @@ -81,6 +82,7 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * one-element clusters to reduce garbage collection overhead. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.uses HierarchicalClusteringAlgorithm * @apiviz.uses PointerHierarchyRepresentationResult @@ -153,8 +155,7 @@ public class HDBSCANHierarchyExtraction implements ClusteringAlgorithm<Clusterin FiniteProgress progress = LOG.isVerbose() ? new FiniteProgress("Extracting clusters", ids.size(), LOG) : null; // Sort DBIDs by lambda, to process merges in increasing order. - ArrayModifiableDBIDs order = DBIDUtil.newArray(ids); - order.sort(new DataStoreUtil.AscendingByDoubleDataStore(lambda)); + ArrayDBIDs order = PointerHierarchyRepresentationResult.topologicalSort(ids, pi, lambda); WritableDataStore<TempCluster> cluster_map = DataStoreUtil.makeStorage(ids, DataStoreFactory.HINT_TEMP, TempCluster.class); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/extraction/SimplifiedHierarchyExtraction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/extraction/SimplifiedHierarchyExtraction.java index 236e7e0a..b84d1a6f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/extraction/SimplifiedHierarchyExtraction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/extraction/SimplifiedHierarchyExtraction.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.database.datastore.DataStoreFactory; import de.lmu.ifi.dbs.elki.database.datastore.DataStoreUtil; import de.lmu.ifi.dbs.elki.database.datastore.DoubleDataStore; import de.lmu.ifi.dbs.elki.database.datastore.WritableDataStore; +import de.lmu.ifi.dbs.elki.database.ids.ArrayDBIDs; import de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs; import de.lmu.ifi.dbs.elki.database.ids.DBIDArrayIter; import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; @@ -73,6 +74,7 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.uses HierarchicalClusteringAlgorithm * @apiviz.uses PointerHierarchyRepresentationResult @@ -138,8 +140,7 @@ public class SimplifiedHierarchyExtraction implements ClusteringAlgorithm<Cluste FiniteProgress progress = LOG.isVerbose() ? new FiniteProgress("Extracting clusters", ids.size(), LOG) : null; // Sort DBIDs by lambda, to process merges in increasing order. - ArrayModifiableDBIDs order = DBIDUtil.newArray(ids); - order.sort(new DataStoreUtil.AscendingByDoubleDataStore(lambda)); + ArrayDBIDs order = PointerHierarchyRepresentationResult.topologicalSort(ids, pi, lambda); WritableDataStore<TempCluster> cluster_map = DataStoreUtil.makeStorage(ids, DataStoreFactory.HINT_TEMP, TempCluster.class); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/AbstractKMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/AbstractKMeans.java index 40fb313d..5df1bee8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/AbstractKMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/AbstractKMeans.java @@ -63,6 +63,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Abstract base class for k-means implementations. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.composedOf KMeansInitialization * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/BestOfMultipleKMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/BestOfMultipleKMeans.java index 292e74db..84fb877c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/BestOfMultipleKMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/BestOfMultipleKMeans.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Stephan Baier * @author Erich Schubert + * @since 0.6.0 * * @param <V> Vector type * @param <M> Model type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/CLARA.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/CLARA.java index 4e2bf7a8..42ea12b6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/CLARA.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/CLARA.java @@ -66,6 +66,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @param <V> Vector type */ @@ -124,7 +125,7 @@ public class CLARA<V> extends KMedoidsPAM<V> { WritableIntegerDataStore bestclusters = null; Random rnd = random.getSingleThreadedRandom(); - FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Random samples.", numsamples, LOG) : null; + FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Processing random samples", numsamples, LOG) : null; for(int j = 0; j < numsamples; j++) { DBIDs rids = DBIDUtil.randomSample(ids, sampling, rnd); // Choose initial medoids diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeans.java index b242b407..697655d8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeans.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; * Some constants and options shared among kmeans family algorithms. * * @author Erich Schubert + * @since 0.2 * * @param <V> Number vector type * @param <M> Actual model type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansBatchedLloyd.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansBatchedLloyd.java index c6082176..8885fc46 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansBatchedLloyd.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansBatchedLloyd.java @@ -69,6 +69,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * blocks. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has KMeansModel * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansBisecting.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansBisecting.java index 70b6a30e..92e00e0d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansBisecting.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansBisecting.java @@ -61,6 +61,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Stephan Baier + * @since 0.6.0 * * @param <V> Vector type * @param <M> Model type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansCompare.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansCompare.java new file mode 100644 index 00000000..5632621a --- /dev/null +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansCompare.java @@ -0,0 +1,271 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.KMeansInitialization; +import de.lmu.ifi.dbs.elki.data.Cluster; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.NumberVector; +import de.lmu.ifi.dbs.elki.data.model.KMeansModel; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.database.datastore.DataStoreFactory; +import de.lmu.ifi.dbs.elki.database.datastore.DataStoreUtil; +import de.lmu.ifi.dbs.elki.database.datastore.WritableIntegerDataStore; +import de.lmu.ifi.dbs.elki.database.ids.DBIDIter; +import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; +import de.lmu.ifi.dbs.elki.database.ids.DBIDs; +import de.lmu.ifi.dbs.elki.database.ids.ModifiableDBIDs; +import de.lmu.ifi.dbs.elki.database.relation.Relation; +import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunction; +import de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SquaredEuclideanDistanceFunction; +import de.lmu.ifi.dbs.elki.logging.Logging; +import de.lmu.ifi.dbs.elki.logging.progress.IndefiniteProgress; +import de.lmu.ifi.dbs.elki.logging.statistics.DoubleStatistic; +import de.lmu.ifi.dbs.elki.logging.statistics.LongStatistic; +import de.lmu.ifi.dbs.elki.logging.statistics.StringStatistic; +import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; +import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; +import de.lmu.ifi.dbs.elki.utilities.documentation.Title; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; + +/** + * Compare-Means: Accelerated k-means by exploiting the triangle inequality and + * pairwise distances of means to prune candidate means. + * + * Reference: + * <p> + * S. J. Phillips<br /> + * Acceleration of k-means and related clustering algorithms<br /> + * Proc. 4th Int. Workshop on Algorithm Engineering and Experiments (ALENEX + * 2002) + * </p> + * + * @author Erich Schubert + * @since 0.5.0 + * + * @apiviz.has KMeansModel + * + * @param <V> vector datatype + */ +@Title("Compare-Means") +@Reference(authors = "S. J. Phillips", // +title = "Acceleration of k-means and related clustering algorithms", // +booktitle = "Proc. 4th Int. Workshop on Algorithm Engineering and Experiments (ALENEX 2002)", // +url = "http://dx.doi.org/10.1007/3-540-45643-0_13") +public class KMeansCompare<V extends NumberVector> extends AbstractKMeans<V, KMeansModel> { + /** + * The logger for this class. + */ + private static final Logging LOG = Logging.getLogger(KMeansCompare.class); + + /** + * Key for statistics logging. + */ + private static final String KEY = KMeansCompare.class.getName(); + + /** + * Constructor. + * + * @param distanceFunction distance function + * @param k k parameter + * @param maxiter Maxiter parameter + * @param initializer Initialization method + */ + public KMeansCompare(NumberVectorDistanceFunction<? super V> distanceFunction, int k, int maxiter, KMeansInitialization<? super V> initializer) { + super(distanceFunction, k, maxiter, initializer); + } + + @Override + public Clustering<KMeansModel> run(Database database, Relation<V> relation) { + if(relation.size() <= 0) { + return new Clustering<>("k-Means Clustering", "kmeans-clustering"); + } + // Choose initial means + if(LOG.isStatistics()) { + LOG.statistics(new StringStatistic(KEY + ".initialization", initializer.toString())); + } + List<Vector> means = initializer.chooseInitialMeans(database, relation, k, getDistanceFunction(), Vector.FACTORY); + // Setup cluster assignment store + List<ModifiableDBIDs> clusters = new ArrayList<>(); + for(int i = 0; i < k; i++) { + clusters.add(DBIDUtil.newHashSet((int) (relation.size() * 2. / k))); + } + WritableIntegerDataStore assignment = DataStoreUtil.makeIntegerStorage(relation.getDBIDs(), DataStoreFactory.HINT_TEMP | DataStoreFactory.HINT_HOT, -1); + double[] varsum = new double[k]; + + // Cluster distances + double[][] cdist = new double[k][k]; + + IndefiniteProgress prog = LOG.isVerbose() ? new IndefiniteProgress("K-Means iteration", LOG) : null; + DoubleStatistic varstat = LOG.isStatistics() ? new DoubleStatistic(this.getClass().getName() + ".variance-sum") : null; + LongStatistic diststat = LOG.isStatistics() ? new LongStatistic(KEY + ".distance-computations") : null; + int iteration = 0; + for(; maxiter <= 0 || iteration < maxiter; iteration++) { + LOG.incrementProcessed(prog); + recomputeSeperation(means, cdist, diststat); + boolean changed = assignToNearestCluster(relation, means, clusters, assignment, varsum, cdist, diststat); + logVarstat(varstat, varsum); + if(LOG.isStatistics()) { + LOG.statistics(diststat); + } + // Stop if no cluster assignment changed. + if(!changed) { + break; + } + // Recompute means. + means = means(clusters, means, relation); + } + LOG.setCompleted(prog); + if(LOG.isStatistics()) { + LOG.statistics(new LongStatistic(KEY + ".iterations", iteration)); + } + + // Wrap result + Clustering<KMeansModel> result = new Clustering<>("k-Means Clustering", "kmeans-clustering"); + for(int i = 0; i < clusters.size(); i++) { + DBIDs ids = clusters.get(i); + if(ids.size() == 0) { + continue; + } + KMeansModel model = new KMeansModel(means.get(i), varsum[i]); + result.addToplevelCluster(new Cluster<>(ids, model)); + } + return result; + } + + /** + * Recompute the separation of cluster means. + * + * @param means Means + * @param cdist Center-to-Center distances + * @param diststat Distance counting statistic + */ + private void recomputeSeperation(List<Vector> means, double[][] cdist, LongStatistic diststat) { + final int k = means.size(); + for(int i = 1; i < k; i++) { + Vector mi = means.get(i); + for(int j = 0; j < i; j++) { + double d = distanceFunction.distance(mi, means.get(j)); + cdist[i][j] = d; + cdist[j][i] = d; + } + } + if(diststat != null) { + diststat.increment((k * (k - 1)) >> 1); + } + } + + /** + * Reassign objects, but only if their bounds indicate it is necessary to do + * so. + * + * @param relation Data + * @param means Current means + * @param clusters Current clusters + * @param assignment Cluster assignment + * @param varsum Variance sum counter + * @param cdist Centroid distances + * @param diststat Distance statistics + * @return true when the object was reassigned + */ + private boolean assignToNearestCluster(Relation<V> relation, List<Vector> means, List<ModifiableDBIDs> clusters, WritableIntegerDataStore assignment, double[] varsum, double[][] cdist, LongStatistic diststat) { + assert (k == means.size()); + long dists = 0; + boolean changed = false; + // Reset all clusters + Arrays.fill(varsum, 0.); + for(ModifiableDBIDs cluster : clusters) { + cluster.clear(); + } + final NumberVectorDistanceFunction<?> df = getDistanceFunction(); + double mult = (df instanceof SquaredEuclideanDistanceFunction) ? 4 : 2; + for(DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) { + final int cur = assignment.intValue(iditer), ini = cur >= 0 ? cur : 0; + // Distance to current mean: + V fv = relation.get(iditer); + double mindist = df.distance(fv, means.get(ini)); + ++dists; + final double thresh = mult * mindist; + int minIndex = ini; + for(int i = 0; i < k; i++) { + if(i == ini || cdist[minIndex][i] >= thresh) { // Compare pruning + continue; + } + double dist = df.distance(fv, means.get(i)); + ++dists; + if(dist < mindist) { + minIndex = i; + mindist = dist; + } + } + varsum[minIndex] += mindist; + clusters.get(minIndex).add(iditer); + changed |= assignment.putInt(iditer, minIndex) != minIndex; + } + // Increment distance computations counter. + if(diststat != null) { + diststat.increment(dists); + } + return changed; + } + + @Override + protected Logging getLogger() { + return LOG; + } + + /** + * Parameterization class. + * + * @author Erich Schubert + * + * @apiviz.exclude + */ + public static class Parameterizer<V extends NumberVector> extends AbstractKMeans.Parameterizer<V> { + @Override + protected Logging getLogger() { + return LOG; + } + + @Override + protected void getParameterDistanceFunction(Parameterization config) { + super.getParameterDistanceFunction(config); + if(distanceFunction instanceof SquaredEuclideanDistanceFunction) { + return; // Proper choice. + } + if(distanceFunction != null && !distanceFunction.isMetric()) { + LOG.warning("Compare k-means requires a metric distance, and k-means should only be used with squared Euclidean distance!"); + } + } + + @Override + protected KMeansCompare<V> makeInstance() { + return new KMeansCompare<>(distanceFunction, k, maxiter, initializer); + } + } +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansElkan.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansElkan.java index e2dcf88c..58015327 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansElkan.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansElkan.java @@ -47,11 +47,14 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunctio import de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SquaredEuclideanDistanceFunction; import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.logging.progress.IndefiniteProgress; +import de.lmu.ifi.dbs.elki.logging.statistics.DoubleStatistic; import de.lmu.ifi.dbs.elki.logging.statistics.LongStatistic; import de.lmu.ifi.dbs.elki.logging.statistics.StringStatistic; import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; /** * Elkan's fast k-means by exploiting the triangle inequality. @@ -69,6 +72,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * </p> * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has KMeansModel * @@ -90,15 +94,22 @@ public class KMeansElkan<V extends NumberVector> extends AbstractKMeans<V, KMean private static final String KEY = KMeansElkan.class.getName(); /** + * Flag whether to compute the final variance statistic. + */ + private boolean varstat = false; + + /** * Constructor. * * @param distanceFunction distance function * @param k k parameter * @param maxiter Maxiter parameter * @param initializer Initialization method + * @param varstat Compute the variance statistic */ - public KMeansElkan(NumberVectorDistanceFunction<? super V> distanceFunction, int k, int maxiter, KMeansInitialization<? super V> initializer) { + public KMeansElkan(NumberVectorDistanceFunction<? super V> distanceFunction, int k, int maxiter, KMeansInitialization<? super V> initializer, boolean varstat) { super(distanceFunction, k, maxiter, initializer); + this.varstat = varstat; } @Override @@ -108,7 +119,7 @@ public class KMeansElkan<V extends NumberVector> extends AbstractKMeans<V, KMean } // Choose initial means if(LOG.isStatistics()) { - LOG.statistics(new StringStatistic(KEY + ".initializer", initializer.toString())); + LOG.statistics(new StringStatistic(KEY + ".initialization", initializer.toString())); } List<Vector> means = initializer.chooseInitialMeans(database, relation, k, getDistanceFunction(), Vector.FACTORY); // Setup cluster assignment store @@ -136,7 +147,7 @@ public class KMeansElkan<V extends NumberVector> extends AbstractKMeans<V, KMean double[][] cdist = new double[k][k]; IndefiniteProgress prog = LOG.isVerbose() ? new IndefiniteProgress("K-Means iteration", LOG) : null; - LongStatistic varstat = LOG.isStatistics() ? new LongStatistic(this.getClass().getName() + ".reassignments") : null; + LongStatistic rstat = LOG.isStatistics() ? new LongStatistic(this.getClass().getName() + ".reassignments") : null; int iteration = 0; for(; maxiter <= 0 || iteration < maxiter; iteration++) { LOG.incrementProcessed(prog); @@ -148,9 +159,9 @@ public class KMeansElkan<V extends NumberVector> extends AbstractKMeans<V, KMean recomputeSeperation(means, sep, cdist); // #1 changed = assignToNearestCluster(relation, means, sums, clusters, assignment, sep, cdist, upper, lower); } - if(varstat != null) { - varstat.setLong(changed); - LOG.statistics(varstat); + if(rstat != null) { + rstat.setLong(changed); + LOG.statistics(rstat); } // Stop if no cluster assignment changed. if(changed == 0) { @@ -178,6 +189,7 @@ public class KMeansElkan<V extends NumberVector> extends AbstractKMeans<V, KMean lower.destroy(); // Wrap result + double totalvariance = 0.; Clustering<KMeansModel> result = new Clustering<>("k-Means Clustering", "kmeans-clustering"); for(int i = 0; i < clusters.size(); i++) { DBIDs ids = clusters.get(i); @@ -189,9 +201,13 @@ public class KMeansElkan<V extends NumberVector> extends AbstractKMeans<V, KMean for(DBIDIter it = ids.iter(); it.valid(); it.advance()) { varsum += distanceFunction.distance(mean, relation.get(it)); } + totalvariance += varsum; KMeansModel model = new KMeansModel(mean, varsum); result.addToplevelCluster(new Cluster<>(ids, model)); } + if(LOG.isStatistics() && varstat) { + LOG.statistics(new DoubleStatistic(this.getClass().getName() + ".variance-sum", totalvariance)); + } return result; } @@ -395,6 +411,16 @@ public class KMeansElkan<V extends NumberVector> extends AbstractKMeans<V, KMean * @apiviz.exclude */ public static class Parameterizer<V extends NumberVector> extends AbstractKMeans.Parameterizer<V> { + /** + * Flag to compute the final clustering variance statistic. + */ + public static final OptionID VARSTAT_ID = new OptionID("kmeans.varstat", "Compute the final clustering variance statistic. Needs an additional full pass over the data set."); + + /** + * Compute the final variance statisic. + */ + protected boolean varstat = false; + @Override protected Logging getLogger() { return LOG; @@ -412,8 +438,17 @@ public class KMeansElkan<V extends NumberVector> extends AbstractKMeans<V, KMean } @Override + protected void makeOptions(Parameterization config) { + super.makeOptions(config); + Flag varF = new Flag(VARSTAT_ID); + if(config.grab(varF)) { + varstat = varF.isTrue(); + } + } + + @Override protected KMeansElkan<V> makeInstance() { - return new KMeansElkan<>(distanceFunction, k, maxiter, initializer); + return new KMeansElkan<>(distanceFunction, k, maxiter, initializer, varstat); } } } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansHamerly.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansHamerly.java index 1b114701..06228525 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansHamerly.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansHamerly.java @@ -46,11 +46,14 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunctio import de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SquaredEuclideanDistanceFunction; import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.logging.progress.IndefiniteProgress; +import de.lmu.ifi.dbs.elki.logging.statistics.DoubleStatistic; import de.lmu.ifi.dbs.elki.logging.statistics.LongStatistic; import de.lmu.ifi.dbs.elki.logging.statistics.StringStatistic; import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; /** * Hamerly's fast k-means by exploiting the triangle inequality. @@ -63,6 +66,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * </p> * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has KMeansModel * @@ -84,15 +88,22 @@ public class KMeansHamerly<V extends NumberVector> extends AbstractKMeans<V, KMe private static final String KEY = KMeansHamerly.class.getName(); /** + * Flag whether to compute the final variance statistic. + */ + private boolean varstat = false; + + /** * Constructor. * * @param distanceFunction distance function * @param k k parameter * @param maxiter Maxiter parameter * @param initializer Initialization method + * @param varstat Compute the variance statistic */ - public KMeansHamerly(NumberVectorDistanceFunction<? super V> distanceFunction, int k, int maxiter, KMeansInitialization<? super V> initializer) { + public KMeansHamerly(NumberVectorDistanceFunction<? super V> distanceFunction, int k, int maxiter, KMeansInitialization<? super V> initializer, boolean varstat) { super(distanceFunction, k, maxiter, initializer); + this.varstat = varstat; } @Override @@ -102,7 +113,7 @@ public class KMeansHamerly<V extends NumberVector> extends AbstractKMeans<V, KMe } // Choose initial means if(LOG.isStatistics()) { - LOG.statistics(new StringStatistic(KEY + ".initializer", initializer.toString())); + LOG.statistics(new StringStatistic(KEY + ".initialization", initializer.toString())); } List<Vector> means = initializer.chooseInitialMeans(database, relation, k, getDistanceFunction(), Vector.FACTORY); // Setup cluster assignment store @@ -124,7 +135,7 @@ public class KMeansHamerly<V extends NumberVector> extends AbstractKMeans<V, KMe double[] sep = new double[k]; IndefiniteProgress prog = LOG.isVerbose() ? new IndefiniteProgress("K-Means iteration", LOG) : null; - LongStatistic varstat = LOG.isStatistics() ? new LongStatistic(KEY + ".reassignments") : null; + LongStatistic rstat = LOG.isStatistics() ? new LongStatistic(KEY + ".reassignments") : null; int iteration = 0; for(; maxiter <= 0 || iteration < maxiter; iteration++) { LOG.incrementProcessed(prog); @@ -136,9 +147,9 @@ public class KMeansHamerly<V extends NumberVector> extends AbstractKMeans<V, KMe recomputeSeperation(means, sep); changed = assignToNearestCluster(relation, means, sums, clusters, assignment, sep, upper, lower); } - if(varstat != null) { - varstat.setLong(changed); - LOG.statistics(varstat); + if(rstat != null) { + rstat.setLong(changed); + LOG.statistics(rstat); } // Stop if no cluster assignment changed. if(changed == 0) { @@ -167,6 +178,7 @@ public class KMeansHamerly<V extends NumberVector> extends AbstractKMeans<V, KMe lower.destroy(); // Wrap result + double totalvariance = 0.; Clustering<KMeansModel> result = new Clustering<>("k-Means Clustering", "kmeans-clustering"); for(int i = 0; i < clusters.size(); i++) { DBIDs ids = clusters.get(i); @@ -178,9 +190,13 @@ public class KMeansHamerly<V extends NumberVector> extends AbstractKMeans<V, KMe for(DBIDIter it = ids.iter(); it.valid(); it.advance()) { varsum += distanceFunction.distance(mean, relation.get(it)); } + totalvariance += varsum; KMeansModel model = new KMeansModel(mean, varsum); result.addToplevelCluster(new Cluster<>(ids, model)); } + if(LOG.isStatistics() && varstat) { + LOG.statistics(new DoubleStatistic(this.getClass().getName() + ".variance-sum", totalvariance)); + } return result; } @@ -389,6 +405,16 @@ public class KMeansHamerly<V extends NumberVector> extends AbstractKMeans<V, KMe * @apiviz.exclude */ public static class Parameterizer<V extends NumberVector> extends AbstractKMeans.Parameterizer<V> { + /** + * Flag to compute the final clustering variance statistic. + */ + public static final OptionID VARSTAT_ID = new OptionID("kmeans.varstat", "Compute the final clustering variance statistic. Needs an additional full pass over the data set."); + + /** + * Compute the final variance statisic. + */ + protected boolean varstat = false; + @Override protected Logging getLogger() { return LOG; @@ -406,8 +432,17 @@ public class KMeansHamerly<V extends NumberVector> extends AbstractKMeans<V, KMe } @Override + protected void makeOptions(Parameterization config) { + super.makeOptions(config); + Flag varF = new Flag(VARSTAT_ID); + if(config.grab(varF)) { + varstat = varF.isTrue(); + } + } + + @Override protected KMeansHamerly<V> makeInstance() { - return new KMeansHamerly<>(distanceFunction, k, maxiter, initializer); + return new KMeansHamerly<>(distanceFunction, k, maxiter, initializer, varstat); } } } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansHybridLloydMacQueen.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansHybridLloydMacQueen.java index cd025b03..476f95f2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansHybridLloydMacQueen.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansHybridLloydMacQueen.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * processing and Lloyd-Style batch steps. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has KMeansModel * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansLloyd.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansLloyd.java index d8b69f54..c32f22c1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansLloyd.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansLloyd.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.logging.statistics.DoubleStatistic; import de.lmu.ifi.dbs.elki.logging.statistics.LongStatistic; import de.lmu.ifi.dbs.elki.logging.statistics.StringStatistic; import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; @@ -53,15 +54,16 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; /** * The standard k-means algorithm, using Lloyd-style bulk iterations. * + * Reference: * <p> - * Reference:<br /> - * S. Lloyd<br/> + * S. Lloyd:<br/> * Least squares quantization in PCM<br/> * IEEE Transactions on Information Theory 28 (2)<br/> * previously published as Bell Telephone Laboratories Paper * </p> * * @author Arthur Zimek + * @since 0.5.0 * * @apiviz.landmark * @apiviz.has KMeansModel @@ -74,6 +76,8 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; title = "Least squares quantization in PCM", // booktitle = "IEEE Transactions on Information Theory 28 (2): 129–137.", // url = "http://dx.doi.org/10.1109/TIT.1982.1056489") +@Alias({ "de.lmu.ifi.dbs.elki.algorithm.clustering.KMeans", // +"de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans" }) public class KMeansLloyd<V extends NumberVector> extends AbstractKMeans<V, KMeansModel> { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansMacQueen.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansMacQueen.java index 176fa311..4f22497d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansMacQueen.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansMacQueen.java @@ -58,14 +58,16 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * convergence, although MacQueen likely only meant to do a single pass over the * data. * + * Reference: * <p> - * Reference:<br /> - * J. MacQueen: Some Methods for Classification and Analysis of Multivariate - * Observations. <br /> + * J. MacQueen:<br /> + * Some Methods for Classification and Analysis of Multivariate Observations. + * <br /> * In 5th Berkeley Symp. Math. Statist. Prob., Vol. 1, 1967, pp 281-297. * </p> * * @author Erich Schubert + * @since 0.5.0 * @apiviz.has KMeansModel * * @param <V> vector type to use diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansSort.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansSort.java new file mode 100644 index 00000000..c119c4ec --- /dev/null +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansSort.java @@ -0,0 +1,284 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.KMeansInitialization; +import de.lmu.ifi.dbs.elki.data.Cluster; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.NumberVector; +import de.lmu.ifi.dbs.elki.data.model.KMeansModel; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.database.datastore.DataStoreFactory; +import de.lmu.ifi.dbs.elki.database.datastore.DataStoreUtil; +import de.lmu.ifi.dbs.elki.database.datastore.WritableIntegerDataStore; +import de.lmu.ifi.dbs.elki.database.ids.DBIDIter; +import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; +import de.lmu.ifi.dbs.elki.database.ids.DBIDs; +import de.lmu.ifi.dbs.elki.database.ids.ModifiableDBIDs; +import de.lmu.ifi.dbs.elki.database.relation.Relation; +import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunction; +import de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SquaredEuclideanDistanceFunction; +import de.lmu.ifi.dbs.elki.logging.Logging; +import de.lmu.ifi.dbs.elki.logging.progress.IndefiniteProgress; +import de.lmu.ifi.dbs.elki.logging.statistics.DoubleStatistic; +import de.lmu.ifi.dbs.elki.logging.statistics.LongStatistic; +import de.lmu.ifi.dbs.elki.logging.statistics.StringStatistic; +import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; +import de.lmu.ifi.dbs.elki.utilities.datastructures.arrays.DoubleIntegerArrayQuickSort; +import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; +import de.lmu.ifi.dbs.elki.utilities.documentation.Title; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; + +/** + * Sort-Means: Accelerated k-means by exploiting the triangle inequality and + * pairwise distances of means to prune candidate means (with sorting). + * + * Reference: + * <p> + * S. J. Phillips<br /> + * Acceleration of k-means and related clustering algorithms<br /> + * Proc. 4th Int. Workshop on Algorithm Engineering and Experiments (ALENEX + * 2002) + * </p> + * + * @author Erich Schubert + * @since 0.7.1 + * + * @apiviz.has KMeansModel + * + * @param <V> vector datatype + */ +@Title("Sort-Means") +@Reference(authors = "S. J. Phillips", // +title = "Acceleration of k-means and related clustering algorithms", // +booktitle = "Proc. 4th Int. Workshop on Algorithm Engineering and Experiments (ALENEX 2002)", // +url = "http://dx.doi.org/10.1007/3-540-45643-0_13") +public class KMeansSort<V extends NumberVector> extends AbstractKMeans<V, KMeansModel> { + /** + * The logger for this class. + */ + private static final Logging LOG = Logging.getLogger(KMeansSort.class); + + /** + * Key for statistics logging. + */ + private static final String KEY = KMeansSort.class.getName(); + + /** + * Constructor. + * + * @param distanceFunction distance function + * @param k k parameter + * @param maxiter Maxiter parameter + * @param initializer Initialization method + */ + public KMeansSort(NumberVectorDistanceFunction<? super V> distanceFunction, int k, int maxiter, KMeansInitialization<? super V> initializer) { + super(distanceFunction, k, maxiter, initializer); + } + + @Override + public Clustering<KMeansModel> run(Database database, Relation<V> relation) { + if(relation.size() <= 0) { + return new Clustering<>("k-Means Clustering", "kmeans-clustering"); + } + // Choose initial means + if(LOG.isStatistics()) { + LOG.statistics(new StringStatistic(KEY + ".initialization", initializer.toString())); + } + List<Vector> means = initializer.chooseInitialMeans(database, relation, k, getDistanceFunction(), Vector.FACTORY); + // Setup cluster assignment store + List<ModifiableDBIDs> clusters = new ArrayList<>(); + for(int i = 0; i < k; i++) { + clusters.add(DBIDUtil.newHashSet((int) (relation.size() * 2. / k))); + } + WritableIntegerDataStore assignment = DataStoreUtil.makeIntegerStorage(relation.getDBIDs(), DataStoreFactory.HINT_TEMP | DataStoreFactory.HINT_HOT, -1); + double[] varsum = new double[k]; + + // Cluster distances + double[][] cdist = new double[k][k]; + int[][] cnum = new int[k][k - 1]; + + IndefiniteProgress prog = LOG.isVerbose() ? new IndefiniteProgress("K-Means iteration", LOG) : null; + DoubleStatistic varstat = LOG.isStatistics() ? new DoubleStatistic(this.getClass().getName() + ".variance-sum") : null; + LongStatistic diststat = LOG.isStatistics() ? new LongStatistic(KEY + ".distance-computations") : null; + int iteration = 0; + for(; maxiter <= 0 || iteration < maxiter; iteration++) { + LOG.incrementProcessed(prog); + recomputeSeperation(means, cdist, cnum, diststat); + boolean changed = assignToNearestCluster(relation, means, clusters, assignment, varsum, cdist, cnum, diststat); + logVarstat(varstat, varsum); + if(LOG.isStatistics()) { + LOG.statistics(diststat); + } + // Stop if no cluster assignment changed. + if(!changed) { + break; + } + // Recompute means. + means = means(clusters, means, relation); + } + LOG.setCompleted(prog); + if(LOG.isStatistics()) { + LOG.statistics(new LongStatistic(KEY + ".iterations", iteration)); + } + + // Wrap result + Clustering<KMeansModel> result = new Clustering<>("k-Means Clustering", "kmeans-clustering"); + for(int i = 0; i < clusters.size(); i++) { + DBIDs ids = clusters.get(i); + if(ids.size() == 0) { + continue; + } + KMeansModel model = new KMeansModel(means.get(i), varsum[i]); + result.addToplevelCluster(new Cluster<>(ids, model)); + } + return result; + } + + /** + * Recompute the separation of cluster means. + * + * @param means Means + * @param cdist Center-to-Center distances + * @param cnum Center numbers + * @param diststat Distance counting statistic + */ + private void recomputeSeperation(List<Vector> means, double[][] cdist, int[][] cnum, LongStatistic diststat) { + final int k = means.size(); + for(int i = 1; i < k; i++) { + Vector mi = means.get(i); + for(int j = 0; j < i; j++) { + double d = distanceFunction.distance(mi, means.get(j)); + cdist[i][j] = d; + cdist[j][i] = d; + } + } + double[] buf = new double[k - 1]; + for(int i = 0; i < k; i++) { + System.arraycopy(cdist[i], 0, buf, 0, i); + System.arraycopy(cdist[i], i + 1, buf, i, k - i - 1); + for(int j = 0; j < buf.length; j++) { + cnum[i][j] = j < i ? j : (j + 1); + } + DoubleIntegerArrayQuickSort.sort(buf, cnum[i], k - 1); + } + if(diststat != null) { + diststat.increment((k * (k - 1)) >> 1); + } + } + + /** + * Reassign objects, but only if their bounds indicate it is necessary to do + * so. + * + * @param relation Data + * @param means Current means + * @param clusters Current clusters + * @param assignment Cluster assignment + * @param varsum Variance sum counter + * @param cdist Centroid distances + * @param cnum Centroid nearest neighbors + * @param diststat Distance statistics + * @return true when the object was reassigned + */ + private boolean assignToNearestCluster(Relation<V> relation, List<Vector> means, List<ModifiableDBIDs> clusters, WritableIntegerDataStore assignment, double[] varsum, double[][] cdist, int[][] cnum, LongStatistic diststat) { + assert (k == means.size()); + long dists = 0; + boolean changed = false; + // Reset all clusters + Arrays.fill(varsum, 0.); + for(ModifiableDBIDs cluster : clusters) { + cluster.clear(); + } + final NumberVectorDistanceFunction<?> df = getDistanceFunction(); + double mult = (df instanceof SquaredEuclideanDistanceFunction) ? 4 : 2; + for(DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) { + final int cur = assignment.intValue(iditer), ini = cur >= 0 ? cur : 0; + // Distance to current mean: + V fv = relation.get(iditer); + double mindist = df.distance(fv, means.get(ini)); + ++dists; + final double threshold = mult * mindist; + int minIndex = ini; + for(int i : cnum[ini]) { + if(cdist[minIndex][i] >= threshold) { // Sort pruning + break; // All following can only be worse. + } + double dist = df.distance(fv, means.get(i)); + ++dists; + if(dist < mindist) { + minIndex = i; + mindist = dist; + } + } + varsum[minIndex] += mindist; + clusters.get(minIndex).add(iditer); + changed |= assignment.putInt(iditer, minIndex) != minIndex; + } + // Increment distance computations counter. + if(diststat != null) { + diststat.increment(dists); + } + return changed; + } + + @Override + protected Logging getLogger() { + return LOG; + } + + /** + * Parameterization class. + * + * @author Erich Schubert + * + * @apiviz.exclude + */ + public static class Parameterizer<V extends NumberVector> extends AbstractKMeans.Parameterizer<V> { + @Override + protected Logging getLogger() { + return LOG; + } + + @Override + protected void getParameterDistanceFunction(Parameterization config) { + super.getParameterDistanceFunction(config); + if(distanceFunction instanceof SquaredEuclideanDistanceFunction) { + return; // Proper choice. + } + if(distanceFunction != null && !distanceFunction.isMetric()) { + LOG.warning("Compare k-means requires a metric distance, and k-means should only be used with squared Euclidean distance!"); + } + } + + @Override + protected KMeansSort<V> makeInstance() { + return new KMeansSort<>(distanceFunction, k, maxiter, initializer); + } + } +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMediansLloyd.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMediansLloyd.java index 6d8b5874..7e4b4524 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMediansLloyd.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMediansLloyd.java @@ -60,6 +60,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * </p> * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has MeanModel * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMedoidsEM.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMedoidsEM.java index 567d6753..cc06a4d5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMedoidsEM.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMedoidsEM.java @@ -72,6 +72,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * (this variation is likely not worth publishing on its own). * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has MedoidModel * @apiviz.composedOf KMedoidsInitialization diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMedoidsPAM.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMedoidsPAM.java index fc3bdd5f..4d45eb3d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMedoidsPAM.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMedoidsPAM.java @@ -77,6 +77,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has MedoidModel * @apiviz.composedOf KMedoidsInitialization diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/SingleAssignmentKMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/SingleAssignmentKMeans.java index 5fa88a33..b4413904 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/SingleAssignmentKMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/SingleAssignmentKMeans.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * Pseudo-k-Means variations, that assigns each object to the nearest center. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has KMeansModel * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/XMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/XMeans.java index d354327b..75a87daa 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/XMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/XMeans.java @@ -77,6 +77,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * * @author Tibor Goldschwendt * @author Erich Schubert + * @since 0.7.0 * * @param <V> Vector type * @param <M> Model type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/AbstractKMeansInitialization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/AbstractKMeansInitialization.java index 723c86cc..72f9a887 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/AbstractKMeansInitialization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/AbstractKMeansInitialization.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * Abstract base class for common k-means initializations. * * @author Erich Schubert + * @since 0.3 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestPointsInitialMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestPointsInitialMeans.java index 4fa0d004..a686f345 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestPointsInitialMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestPointsInitialMeans.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery; import de.lmu.ifi.dbs.elki.database.relation.Relation; import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunction; import de.lmu.ifi.dbs.elki.math.random.RandomFactory; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; @@ -52,9 +53,11 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; * times will be more likely to return the same local minima. * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Object type for kMedoids and kMedians */ +@Alias("de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.FarthestPointsInitialMeans") public class FarthestPointsInitialMeans<O> extends AbstractKMeansInitialization<NumberVector> implements KMedoidsInitialization<O> { /** * Discard the first vector. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestSumPointsInitialMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestSumPointsInitialMeans.java index 9cceb4f2..9f223dac 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestSumPointsInitialMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestSumPointsInitialMeans.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.math.random.RandomFactory; * times will be more likely to return the same local minima. * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Object type for kmedoids and kmedians */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FirstKInitialMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FirstKInitialMeans.java index beab423e..210994e5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FirstKInitialMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FirstKInitialMeans.java @@ -34,15 +34,18 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery; import de.lmu.ifi.dbs.elki.database.relation.Relation; import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunction; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; /** * Initialize K-means by using the first k objects as initial means. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type for KMedoids */ +@Alias("de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.FirstKInitialMeans") public class FirstKInitialMeans<O> implements KMeansInitialization<NumberVector>, KMedoidsInitialization<O> { /** * Constructor. @@ -84,4 +87,4 @@ public class FirstKInitialMeans<O> implements KMeansInitialization<NumberVector> return new FirstKInitialMeans<>(); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/KMeansInitialization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/KMeansInitialization.java index 55ffb65e..c1cd71a0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/KMeansInitialization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/KMeansInitialization.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunctio * Interface for initializing K-Means * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/KMeansPlusPlusInitialMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/KMeansPlusPlusInitialMeans.java index c1518d18..11bfef59 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/KMeansPlusPlusInitialMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/KMeansPlusPlusInitialMeans.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunction; import de.lmu.ifi.dbs.elki.logging.LoggingUtil; import de.lmu.ifi.dbs.elki.math.random.RandomFactory; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; @@ -56,6 +57,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * </p> * * @author Erich Schubert + * @since 0.5.0 * * @param <O> Vector type */ @@ -63,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; title = "k-means++: the advantages of careful seeding", // booktitle = "Proc. of the Eighteenth Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 2007", // url = "http://dx.doi.org/10.1145/1283383.1283494") +@Alias("de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansPlusPlusInitialMeans") public class KMeansPlusPlusInitialMeans<O> extends AbstractKMeansInitialization<NumberVector> implements KMedoidsInitialization<O> { /** * Constructor. @@ -232,4 +235,4 @@ public class KMeansPlusPlusInitialMeans<O> extends AbstractKMeansInitialization< return new KMeansPlusPlusInitialMeans<>(rnd); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/KMedoidsInitialization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/KMedoidsInitialization.java index 0ae3723e..2dc11c52 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/KMedoidsInitialization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/KMedoidsInitialization.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery; * this initialization will only return members of the original data set. * * @author Erich Schubert + * @since 0.5.0 * * @param <V> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/PAMInitialMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/PAMInitialMeans.java index 396d79e6..ea11330e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/PAMInitialMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/PAMInitialMeans.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.PrimitiveDistanceFunction; import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress; import de.lmu.ifi.dbs.elki.math.MathUtil; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; @@ -57,12 +58,14 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.5.0 * * @param <O> Object type for KMedoids initialization */ @Reference(title = "Clustering my means of Medoids", // authors = "Kaufman, L. and Rousseeuw, P.J.", // booktitle = "Statistical Data Analysis Based on the L_1–Norm and Related Methods") +@Alias("de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.PAMInitialMeans") public class PAMInitialMeans<O> implements KMeansInitialization<NumberVector>, KMedoidsInitialization<O> { /** * Class logger. @@ -78,6 +81,9 @@ public class PAMInitialMeans<O> implements KMeansInitialization<NumberVector>, K @Override public <T extends NumberVector, V extends NumberVector> List<V> chooseInitialMeans(Database database, Relation<T> relation, int k, NumberVectorDistanceFunction<? super T> distanceFunction, NumberVector.Factory<V> factory) { + if(relation.size() < k) { + throw new AbortException("Database has less than k objects."); + } // Ugly cast; but better than code duplication. @SuppressWarnings("unchecked") Relation<O> rel = (Relation<O>) relation; @@ -97,38 +103,33 @@ public class PAMInitialMeans<O> implements KMeansInitialization<NumberVector>, K public DBIDs chooseInitialMedoids(int k, DBIDs ids, DistanceQuery<? super O> distQ) { ArrayModifiableDBIDs medids = DBIDUtil.newArray(k); DBIDVar bestid = DBIDUtil.newVar(); - WritableDoubleDataStore mindist = null; + // We need three temporary storage arrays: + WritableDoubleDataStore mindist, bestd, tempd; + mindist = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP); + bestd = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP); + tempd = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP); // First mean is chosen by having the smallest distance sum to all others. { double best = Double.POSITIVE_INFINITY; - WritableDoubleDataStore newd = null; FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Choosing initial mean", ids.size(), LOG) : null; for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) { - if(newd == null) { - newd = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP); - } - int sum = 0; + double sum = 0, d; for(DBIDIter iter2 = ids.iter(); iter2.valid(); iter2.advance()) { - double d = distQ.distance(iter, iter2); - sum += d; - newd.putDouble(iter2, d); + sum += d = distQ.distance(iter, iter2); + tempd.putDouble(iter2, d); } if(sum < best) { best = sum; bestid.set(iter); - if(mindist != null) { - mindist.destroy(); - } - mindist = newd; - newd = null; + // Swap mindist and newd: + WritableDoubleDataStore temp = mindist; + mindist = tempd; + tempd = temp; } LOG.incrementProcessed(prog); } LOG.ensureCompleted(prog); - if(newd != null) { - newd.destroy(); - } medids.add(bestid); } assert(mindist != null); @@ -138,44 +139,40 @@ public class PAMInitialMeans<O> implements KMeansInitialization<NumberVector>, K LOG.incrementProcessed(prog); // First one was just chosen. for(int i = 1; i < k; i++) { double best = Double.POSITIVE_INFINITY; - WritableDoubleDataStore bestd = null, newd = null; + bestid.unset(); for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) { if(medids.contains(iter)) { continue; } - if(newd == null) { - newd = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP); - } - double sum = 0.; + double sum = 0., v; for(DBIDIter iter2 = ids.iter(); iter2.valid(); iter2.advance()) { - double v = MathUtil.min(distQ.distance(iter, iter2), mindist.doubleValue(iter2)); - sum += v; - newd.put(iter2, v); + sum += v = MathUtil.min(distQ.distance(iter, iter2), mindist.doubleValue(iter2)); + tempd.put(iter2, v); } if(sum < best) { best = sum; bestid.set(iter); - if(bestd != null) { - bestd.destroy(); - } - bestd = newd; - newd = null; + // Swap bestd and newd: + WritableDoubleDataStore temp = bestd; + bestd = tempd; + tempd = temp; } } - if(bestd == null) { + if(!bestid.isSet()) { throw new AbortException("No median found that improves the criterion function?!? Too many infinite distances."); } medids.add(bestid); - if(newd != null) { - newd.destroy(); - } - mindist.destroy(); - mindist = bestd; + // Swap bestd and mindist: + WritableDoubleDataStore temp = bestd; + bestd = mindist; + mindist = temp; LOG.incrementProcessed(prog); } LOG.ensureCompleted(prog); mindist.destroy(); + bestd.destroy(); + tempd.destroy(); return medids; } @@ -192,4 +189,4 @@ public class PAMInitialMeans<O> implements KMeansInitialization<NumberVector>, K return new PAMInitialMeans<>(); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/PredefinedInitialMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/PredefinedInitialMeans.java index ca8a612a..b01651b8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/PredefinedInitialMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/PredefinedInitialMeans.java @@ -38,12 +38,13 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.VectorListParameter; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleArrayListParameter; /** * Run k-means with prespecified initial means. * * @author Erich Schubert + * @since 0.7.0 */ public class PredefinedInitialMeans extends AbstractKMeansInitialization<NumberVector> { /** @@ -147,9 +148,12 @@ public class PredefinedInitialMeans extends AbstractKMeansInitialization<NumberV @Override protected void makeOptions(Parameterization config) { super.makeOptions(config); - VectorListParameter meansP = new VectorListParameter(INITIAL_MEANS); + DoubleArrayListParameter meansP = new DoubleArrayListParameter(INITIAL_MEANS); if(config.grab(meansP)) { - initialMeans = meansP.getValue(); + initialMeans = new ArrayList<>(meansP.getValue().size()); + for(double[] v : meansP.getValue()) { + initialMeans.add(new Vector(v)); + } } } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/RandomlyChosenInitialMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/RandomlyChosenInitialMeans.java index b6cfad8d..bb03b278 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/RandomlyChosenInitialMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/RandomlyChosenInitialMeans.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery; import de.lmu.ifi.dbs.elki.database.relation.Relation; import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunction; import de.lmu.ifi.dbs.elki.math.random.RandomFactory; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; /** @@ -51,12 +52,14 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * available in Biometrics). * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Vector type */ @Reference(authors = "E. W. Forgy", // title = "Cluster analysis of multivariate data: efficiency versus interpretability of classifications", // booktitle = "Biometrics 21(3)") +@Alias("de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.RandomlyChosenInitialMeans") public class RandomlyChosenInitialMeans<O> extends AbstractKMeansInitialization<NumberVector> implements KMedoidsInitialization<O> { /** * Constructor. @@ -95,4 +98,4 @@ public class RandomlyChosenInitialMeans<O> extends AbstractKMeansInitialization< return new RandomlyChosenInitialMeans<>(rnd); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/RandomlyGeneratedInitialMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/RandomlyGeneratedInitialMeans.java index bc2181e8..30d1b00f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/RandomlyGeneratedInitialMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/RandomlyGeneratedInitialMeans.java @@ -33,13 +33,16 @@ import de.lmu.ifi.dbs.elki.database.relation.RelationUtil; import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunction; import de.lmu.ifi.dbs.elki.math.MathUtil; import de.lmu.ifi.dbs.elki.math.random.RandomFactory; +import de.lmu.ifi.dbs.elki.utilities.Alias; /** * Initialize k-means by generating random vectors (within the data sets value * range). * * @author Erich Schubert + * @since 0.5.0 */ +@Alias("de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.RandomlyGeneratedInitialMeans") public class RandomlyGeneratedInitialMeans extends AbstractKMeansInitialization<NumberVector> { /** * Constructor. @@ -84,4 +87,4 @@ public class RandomlyGeneratedInitialMeans extends AbstractKMeansInitialization< return new RandomlyGeneratedInitialMeans(rnd); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/SampleKMeansInitialization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/SampleKMeansInitialization.java index ac7f7f27..f5ed00f1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/SampleKMeansInitialization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/SampleKMeansInitialization.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunctio import de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SquaredEuclideanDistanceFunction; import de.lmu.ifi.dbs.elki.logging.LoggingUtil; import de.lmu.ifi.dbs.elki.math.random.RandomFactory; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ChainedParameterization; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; @@ -53,9 +54,11 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Initialize k-means by running k-means on a sample of the data set only. * * @author Erich Schubert + * @since 0.6.0 * * @param <V> Vector type */ +@Alias("de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.SampleKMeansInitialization") public class SampleKMeansInitialization<V extends NumberVector> extends AbstractKMeansInitialization<V> { /** * Variant of kMeans to use for initialization. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/parallel/KMeansProcessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/parallel/KMeansProcessor.java index c0e34f12..f2b9db1f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/parallel/KMeansProcessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/parallel/KMeansProcessor.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.parallel.processor.Processor; * Parallel k-means implementation. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has Instance */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/parallel/ParallelLloydKMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/parallel/ParallelLloydKMeans.java index a10d45ae..e214581a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/parallel/ParallelLloydKMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/parallel/ParallelLloydKMeans.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.parallel.ParallelExecutor; * Parallel implementation of k-Means clustering. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has KMeansProcessor * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/AbstractKMeansQualityMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/AbstractKMeansQualityMeasure.java index 721b74b6..cc4c00ea 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/AbstractKMeansQualityMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/AbstractKMeansQualityMeasure.java @@ -65,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * * @author Tibor Goldschwendt * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "D. Pelleg, A. Moore", // booktitle = "X-means: Extending K-means with Efficient Estimation on the Number of Clusters", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/AkaikeInformationCriterion.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/AkaikeInformationCriterion.java index e1e72b51..aafd6173 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/AkaikeInformationCriterion.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/AkaikeInformationCriterion.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * * @author Tibor Goldschwendt * @author Erich Schubert + * @since 0.2 */ @Reference(authors = "H. Akaike", // title = "On entropy maximization principle", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/BayesianInformationCriterion.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/BayesianInformationCriterion.java index 8b21753d..22ad56d9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/BayesianInformationCriterion.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/BayesianInformationCriterion.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * * @author Tibor Goldschwendt * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "G. Schwarz", // title = "Estimating the dimension of a model", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/BayesianInformationCriterionZhao.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/BayesianInformationCriterionZhao.java index 755d7137..6a18269a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/BayesianInformationCriterionZhao.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/BayesianInformationCriterionZhao.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * * @author Tibor Goldschwendt * @author Erich Schubert + * @since 0.2 */ @Reference(authors = "Q. Zhao, M. Xu, P. Fränti", // title = "Knee Point Detection on Bayesian Information Criterion", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/KMeansQualityMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/KMeansQualityMeasure.java index bd0f12a1..100c2dfc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/KMeansQualityMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/KMeansQualityMeasure.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunctio * Important note: some measures are ascending, others are descending! * * @author Erich Schubert + * @since 0.2 * * @param <O> Input Object restriction type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/WithinClusterMeanDistanceQualityMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/WithinClusterMeanDistanceQualityMeasure.java index cd7a4d14..e7069ac0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/WithinClusterMeanDistanceQualityMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/WithinClusterMeanDistanceQualityMeasure.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunctio * The average of all average pairwise distances in a cluster. * * @author Stephan Baier + * @since 0.6.0 */ public class WithinClusterMeanDistanceQualityMeasure implements KMeansQualityMeasure<NumberVector> { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/WithinClusterVarianceQualityMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/WithinClusterVarianceQualityMeasure.java index 09017413..fbd04dbd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/WithinClusterVarianceQualityMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/WithinClusterVarianceQualityMeasure.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunctio * * @author Stephan Baier * @author Erich Schubert + * @since 0.6.0 */ public class WithinClusterVarianceQualityMeasure extends AbstractKMeansQualityMeasure<NumberVector> { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/meta/ExternalClustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/meta/ExternalClustering.java index ef8045a9..634eb057 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/meta/ExternalClustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/meta/ExternalClustering.java @@ -79,6 +79,7 @@ import gnu.trove.map.hash.TIntObjectHashMap; * considered noise clusters. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf CSVReaderFormat * @apiviz.has Clustering diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/onedimensional/KNNKernelDensityMinimaClustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/onedimensional/KNNKernelDensityMinimaClustering.java index 71167a90..4b2d5b8a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/onedimensional/KNNKernelDensityMinimaClustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/onedimensional/KNNKernelDensityMinimaClustering.java @@ -58,6 +58,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * performing kernel density estimation. * * @author Erich Schubert + * @since 0.6.0 */ public class KNNKernelDensityMinimaClustering<V extends NumberVector> extends AbstractAlgorithm<Clustering<ClusterModel>> implements ClusteringAlgorithm<Clustering<ClusterModel>> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/AbstractOPTICS.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/AbstractOPTICS.java index da4c94f1..da0a6dc3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/AbstractOPTICS.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/AbstractOPTICS.java @@ -53,6 +53,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * * @author Elke Achtert * @author Erich Schubert + * @since 0.7.0 * * @param <O> the type of DatabaseObjects handled by the algorithm */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/ClusterOrder.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/ClusterOrder.java index 93a24407..dc50b086 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/ClusterOrder.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/ClusterOrder.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.result.OrderingResult; * Class to store the result of an ordering clustering algorithm such as OPTICS. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/CorrelationClusterOrder.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/CorrelationClusterOrder.java index 6b94e358..d8bdf5a8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/CorrelationClusterOrder.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/CorrelationClusterOrder.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * * @author Elke Achtert * @author Erich Schubert + * @since 0.7.0 */ public class CorrelationClusterOrder extends ClusterOrder { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/DeLiClu.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/DeLiClu.java index e2017f85..27737f60 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/DeLiClu.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/DeLiClu.java @@ -80,6 +80,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Elke Achtert + * @since 0.7.0 * @param <NV> the type of NumberVector handled by this Algorithm */ @Title("DeliClu: Density-Based Hierarchical Clustering") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/FastOPTICS.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/FastOPTICS.java index 9ec79b29..5df5712b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/FastOPTICS.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/FastOPTICS.java @@ -73,6 +73,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * * @author Johannes Schneider * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf RandomProjectedNeighborsAndDensities */ @@ -158,7 +159,7 @@ public class FastOPTICS<V extends NumberVector> extends AbstractAlgorithm<Cluste neighs = index.getNeighs(); // get neighbors of points // compute ordering as for OPTICS - FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("OPTICS clustering.", ids.size(), LOG) : null; + FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("FastOPTICS clustering", ids.size(), LOG) : null; processed = DBIDUtil.newHashSet(ids.size()); order = new ClusterOrder(ids, "FastOPTICS Cluster Order", "fast-optics"); for(DBIDIter it = ids.iter(); it.valid(); it.advance()) { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/GeneralizedOPTICS.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/GeneralizedOPTICS.java index 771d59e8..5b47ec16 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/GeneralizedOPTICS.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/GeneralizedOPTICS.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.QuickSelect; * distances, and serves as a base for several other algorithms (HiCO, HiSC). * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf Instance * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSHeap.java index cb1265eb..a7d7b3f7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSHeap.java @@ -58,6 +58,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * * @author Elke Achtert * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf Instance * @@ -69,8 +70,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; title = "OPTICS: Ordering Points to Identify the Clustering Structure", // booktitle = "Proc. ACM SIGMOD Int. Conf. on Management of Data (SIGMOD '99)", // url = "http://dx.doi.org/10.1145/304181.304187") -@Alias({ "OPTICS", "de.lmu.ifi.dbs.elki.algorithm.clustering.OPTICS", // -"de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICS" }) +@Alias("de.lmu.ifi.dbs.elki.algorithm.clustering.OPTICS") public class OPTICSHeap<O> extends AbstractOPTICS<O> { /** * The logger for this class. @@ -213,4 +213,4 @@ public class OPTICSHeap<O> extends AbstractOPTICS<O> { return new OPTICSHeap<>(distanceFunction, epsilon, minpts); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSHeapEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSHeapEntry.java index 89e6ebb1..0b181442 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSHeapEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSHeapEntry.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; * Entry in the priority heap. * * @author Elke Achtert + * @since 0.2 * * @apiviz.exclude */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSList.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSList.java index 34d822cc..313bba79 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSList.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSList.java @@ -65,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * * @author Elke Achtert * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf OPTICSList.Instance * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSTypeAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSTypeAlgorithm.java index 695ef8fd..9b9cde62 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSTypeAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSTypeAlgorithm.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.Database; * Interface for OPTICS type algorithms, that can be analyzed by OPTICS Xi etc. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has ClusterOrder */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSXi.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSXi.java index 087876dc..7ce0bba1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSXi.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSXi.java @@ -66,12 +66,13 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; * This removes a popular type of artifacts. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf OPTICSTypeAlgorithm oneway - «runs» * @apiviz.uses ClusterOrder oneway - «reads» * @apiviz.has SteepAreaResult oneway - «produces» */ -@Alias({ "OPTICSXi", "de.lmu.ifi.dbs.elki.algorithm.clustering.OPTICSXi" }) +@Alias("de.lmu.ifi.dbs.elki.algorithm.clustering.OPTICSXi") public class OPTICSXi extends AbstractAlgorithm<Clustering<OPTICSModel>> implements ClusteringAlgorithm<Clustering<OPTICSModel>> { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/CLIQUE.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/CLIQUE.java index 86aa3b3f..c8dada62 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/CLIQUE.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/CLIQUE.java @@ -85,6 +85,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * </p> * * @author Elke Achtert + * @since 0.2 * * @apiviz.has SubspaceModel * @apiviz.has CLIQUESubspace diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DOC.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DOC.java index 896519b3..a19ea88a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DOC.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DOC.java @@ -77,6 +77,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * </p> * * @author Florian Nuecke + * @since 0.6.0 * * @apiviz.has SubspaceModel * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DiSH.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DiSH.java index 1bbd4def..7653246f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DiSH.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DiSH.java @@ -95,6 +95,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * </p> * * @author Elke Achtert + * @since 0.2 * * @apiviz.uses DiSHPreferenceVectorIndex * @apiviz.has SubspaceModel diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/HiSC.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/HiSC.java index 64bde076..088b81d9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/HiSC.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/HiSC.java @@ -69,6 +69,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * </p> * * @author Elke Achtert + * @since 0.3 * * @apiviz.uses HiSCPreferenceVectorIndex * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/P3C.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/P3C.java index 03670579..02e7792c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/P3C.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/P3C.java @@ -93,6 +93,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * * @author Florian Nuecke * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses EM * @apiviz.has SubspaceModel @@ -363,7 +364,7 @@ public class P3C<V extends NumberVector> extends AbstractAlgorithm<Clustering<Su * @return p-signatures */ private ArrayList<Signature> mergeClusterCores(final int binCount, ArrayList<Signature> signatures) { - MutableProgress mergeProgress = LOG.isVerbose() ? new MutableProgress("Merging signatures.", signatures.size(), LOG) : null; + MutableProgress mergeProgress = LOG.isVerbose() ? new MutableProgress("Merging signatures", signatures.size(), LOG) : null; // Annotate dimensions to 1-signatures for quick stopping. int[] firstdim = new int[signatures.size()]; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java index 45cc4c97..dcc84d20 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java @@ -88,6 +88,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * </p> * * @author Elke Achtert + * @since 0.2 * * @apiviz.has SubspaceModel * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PreDeCon.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PreDeCon.java index f7533443..9a98396b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PreDeCon.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PreDeCon.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Peer Kröger + * @since 0.2 * * @apiviz.has PreDeCon.Settings * @apiviz.composedOf PreDeConNeighborPredicate diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/SUBCLU.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/SUBCLU.java index b8856044..f20064be 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/SUBCLU.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/SUBCLU.java @@ -74,6 +74,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Elke Achtert + * @since 0.2 * * @apiviz.uses DBSCAN * @apiviz.uses DimensionSelectingSubspaceDistanceFunction diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/SubspaceClusteringAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/SubspaceClusteringAlgorithm.java index 453b26dc..e3f97350 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/SubspaceClusteringAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/SubspaceClusteringAlgorithm.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.data.model.SubspaceModel; * {@link SubspaceModel}, that can then be post-processed for outlier detection. * * @author Erich Schubert + * @since 0.4.0 * * @param <M> Model type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/clique/CLIQUEInterval.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/clique/CLIQUEInterval.java index 510f10a8..7305d43f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/clique/CLIQUEInterval.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/clique/CLIQUEInterval.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.FormatUtil; * Represents an interval in a certain dimension of the data space. * * @author Elke Achtert + * @since 0.2 */ public class CLIQUEInterval implements Comparable<CLIQUEInterval> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/clique/CLIQUESubspace.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/clique/CLIQUESubspace.java index cda00f8b..280702cb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/clique/CLIQUESubspace.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/clique/CLIQUESubspace.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * Represents a subspace of the original data space in the CLIQUE algorithm. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has CoverageComparator * @apiviz.composedOf CLIQUEUnit diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/clique/CLIQUEUnit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/clique/CLIQUEUnit.java index cf96670e..f7b581a7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/clique/CLIQUEUnit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/clique/CLIQUEUnit.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.database.ids.ModifiableDBIDs; * Represents a unit in the CLIQUE algorithm. * * @author Elke Achtert + * @since 0.2 * * @apiviz.composedOf CLIQUEInterval * @apiviz.composedOf ModifiableDBIDs diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByLabelClustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByLabelClustering.java index 29006f01..d2ba1b38 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByLabelClustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByLabelClustering.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.database.ids.HashSetModifiableDBIDs; import de.lmu.ifi.dbs.elki.database.ids.ModifiableDBIDs; import de.lmu.ifi.dbs.elki.database.relation.Relation; import de.lmu.ifi.dbs.elki.logging.Logging; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; @@ -65,16 +66,18 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.PatternParameter; * * If an assignment of an object to multiple clusters is desired, the labels of * the object indicating the clusters need to be separated by blanks and the - * flag {@link #MULTIPLE_ID} needs to be set. + * flag {@link Parameterizer#MULTIPLE_ID} needs to be set. * * TODO: handling of data sets with no labels? * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses de.lmu.ifi.dbs.elki.data.ClassLabel */ @Title("Clustering by label") @Description("Cluster points by a (pre-assigned!) label. For comparing results with a reference clustering.") +@Alias("de.lmu.ifi.dbs.elki.algorithm.clustering.ByLabelClustering") public class ByLabelClustering extends AbstractAlgorithm<Clustering<Model>> implements ClusteringAlgorithm<Clustering<Model>> { /** * The logger for this class. @@ -82,24 +85,12 @@ public class ByLabelClustering extends AbstractAlgorithm<Clustering<Model>> impl private static final Logging LOG = Logging.getLogger(ByLabelClustering.class); /** - * Flag to indicate that multiple cluster assignment is possible. If an - * assignment to multiple clusters is desired, the labels indicating the - * clusters need to be separated by blanks. - */ - public static final OptionID MULTIPLE_ID = new OptionID("bylabelclustering.multiple", "Flag to indicate that only subspaces with large coverage " + "(i.e. the fraction of the database that is covered by the dense units) " + "are selected, the rest will be pruned."); - - /** - * Pattern to recognize noise clusters by. - */ - public static final OptionID NOISE_ID = new OptionID("bylabelclustering.noise", "Pattern to recognize noise classes by their label."); - - /** - * Holds the value of {@link #MULTIPLE_ID}. + * Allow multiple cluster assignment. */ private boolean multiple; /** - * Holds the value of {@link #NOISE_ID}. + * Pattern to recognize noise clusters by. */ private Pattern noisepattern = null; @@ -248,8 +239,26 @@ public class ByLabelClustering extends AbstractAlgorithm<Clustering<Model>> impl * @apiviz.exclude */ public static class Parameterizer extends AbstractParameterizer { + /** + * Flag to indicate that multiple cluster assignment is possible. If an + * assignment to multiple clusters is desired, the labels indicating the + * clusters need to be separated by blanks. + */ + public static final OptionID MULTIPLE_ID = new OptionID("bylabelclustering.multiple", "Flag to indicate that only subspaces with large coverage " + "(i.e. the fraction of the database that is covered by the dense units) " + "are selected, the rest will be pruned."); + + /** + * Parameter to specify the pattern to recognize noise clusters by. + */ + public static final OptionID NOISE_ID = new OptionID("bylabelclustering.noise", "Pattern to recognize noise classes by their label."); + + /** + * Allow multiple cluster assignment. + */ protected boolean multiple; + /** + * Pattern to recognize noise clusters by. + */ protected Pattern noisepat; @Override @@ -272,4 +281,4 @@ public class ByLabelClustering extends AbstractAlgorithm<Clustering<Model>> impl return new ByLabelClustering(multiple, noisepat); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByLabelHierarchicalClustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByLabelHierarchicalClustering.java index e246c4e6..d48efe68 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByLabelHierarchicalClustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByLabelHierarchicalClustering.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.database.ids.HashSetModifiableDBIDs; import de.lmu.ifi.dbs.elki.database.ids.ModifiableDBIDs; import de.lmu.ifi.dbs.elki.database.relation.Relation; import de.lmu.ifi.dbs.elki.logging.Logging; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; @@ -64,11 +65,13 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * TODO: Noise handling (e.g. allow the user to specify a noise label pattern?) * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses de.lmu.ifi.dbs.elki.data.ClassLabel */ @Title("Hierarchical clustering by label") @Description("Cluster points by a (pre-assigned!) label. For comparing results with a reference clustering.") +@Alias("de.lmu.ifi.dbs.elki.algorithm.clustering.ByLabelHierarchicalClustering") public class ByLabelHierarchicalClustering extends AbstractAlgorithm<Clustering<Model>> implements ClusteringAlgorithm<Clustering<Model>> { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByLabelOrAllInOneClustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByLabelOrAllInOneClustering.java index 12af74ba..7de4c4f0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByLabelOrAllInOneClustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByLabelOrAllInOneClustering.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * "all-in-one" clustering. * * @author Erich Schubert + * @since 0.2 */ public class ByLabelOrAllInOneClustering extends ByLabelClustering { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByModelClustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByModelClustering.java index 9832ea4a..0583ceb5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByModelClustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/ByModelClustering.java @@ -56,6 +56,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.PatternParameter; * reference result / golden standard used by the generator). * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.uses Model */ @@ -68,12 +69,7 @@ public class ByModelClustering extends AbstractAlgorithm<Clustering<Model>> impl private static final Logging LOG = Logging.getLogger(ByModelClustering.class); /** - * Pattern to recognize noise clusters with - */ - public static final OptionID NOISE_ID = new OptionID("bymodel.noise", "Pattern to recognize noise models by their label."); - - /** - * Holds the value of {@link #NOISE_ID}. + * Pattern to recognize noise clusters with. */ private Pattern noisepattern = null; @@ -144,6 +140,14 @@ public class ByModelClustering extends AbstractAlgorithm<Clustering<Model>> impl * @apiviz.exclude */ public static class Parameterizer extends AbstractParameterizer { + /** + * Parameter to specify the pattern to recognize noise clusters with. + */ + public static final OptionID NOISE_ID = new OptionID("bymodel.noise", "Pattern to recognize noise models by their label."); + + /** + * Pattern to recognize noise clusters with + */ protected Pattern noisepat; @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/TrivialAllInOne.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/TrivialAllInOne.java index 64c103c3..188db3e9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/TrivialAllInOne.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/TrivialAllInOne.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.data.type.TypeUtil; import de.lmu.ifi.dbs.elki.database.ids.DBIDs; import de.lmu.ifi.dbs.elki.database.relation.Relation; import de.lmu.ifi.dbs.elki.logging.Logging; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; @@ -44,9 +45,11 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * Useful for evaluation and testing. * * @author Erich Schubert + * @since 0.2 */ @Title("Trivial all-in-one clustering") @Description("Returns a 'tivial' clustering which just considers all points to be one big cluster.") +@Alias("de.lmu.ifi.dbs.elki.algorithm.clustering.TrivialAllInOne") public class TrivialAllInOne extends AbstractAlgorithm<Clustering<Model>> implements ClusteringAlgorithm<Clustering<Model>> { /** * The logger for this class. @@ -77,4 +80,4 @@ public class TrivialAllInOne extends AbstractAlgorithm<Clustering<Model>> implem protected Logging getLogger() { return LOG; } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/TrivialAllNoise.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/TrivialAllNoise.java index db4cb8dd..4db4dfed 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/TrivialAllNoise.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/trivial/TrivialAllNoise.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.data.type.TypeUtil; import de.lmu.ifi.dbs.elki.database.ids.DBIDs; import de.lmu.ifi.dbs.elki.database.relation.Relation; import de.lmu.ifi.dbs.elki.logging.Logging; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; @@ -43,9 +44,11 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * Useful for evaluation and testing. * * @author Erich Schubert + * @since 0.2 */ @Title("Trivial all-noise clustering") @Description("Returns a 'trivial' clustering which just considers all points as noise points.") +@Alias("de.lmu.ifi.dbs.elki.algorithm.clustering.TrivialAllNoise") public class TrivialAllNoise extends AbstractAlgorithm<Clustering<Model>> implements ClusteringAlgorithm<Clustering<Model>> { /** * The logger for this class. @@ -76,4 +79,4 @@ public class TrivialAllNoise extends AbstractAlgorithm<Clustering<Model>> implem protected Logging getLogger() { return LOG; } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/CKMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/CKMeans.java index 14915807..3d095cbd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/CKMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/CKMeans.java @@ -57,6 +57,7 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * however, is constant. * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "S. D. Lee, B. Kao, R. Cheng", // title = "Reducing UK-means to K-means", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/CenterOfMassMetaClustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/CenterOfMassMetaClustering.java index 1187ff30..961e7fc2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/CenterOfMassMetaClustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/CenterOfMassMetaClustering.java @@ -66,6 +66,7 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @param <C> Clustering result type (inherited from inner algorithm) */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/FDBSCAN.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/FDBSCAN.java index 47f3e6bb..4c177463 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/FDBSCAN.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/FDBSCAN.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf FDBSCANNeighborPredicate */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/FDBSCANNeighborPredicate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/FDBSCANNeighborPredicate.java index a51ec92a..8fc3bd03 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/FDBSCANNeighborPredicate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/FDBSCANNeighborPredicate.java @@ -76,6 +76,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * * @author Alexander Koos * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf Instance */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/RepresentativeUncertainClustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/RepresentativeUncertainClustering.java index da377ea1..c1ee8ed8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/RepresentativeUncertainClustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/RepresentativeUncertainClustering.java @@ -104,6 +104,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.DoubleObjPair; * * @author Alexander Koos * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has RepresentativenessEvaluation */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/UKMeans.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/UKMeans.java index fc602d1f..14aee8aa 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/UKMeans.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/uncertain/UKMeans.java @@ -76,6 +76,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * </p> * * @author Klaus Arthur Schmidt + * @since 0.7.0 */ @Reference(authors = "M. Chau, R. Cheng, B. Kao, J. Ng", // title = "Uncertain data mining: An example in clustering location data", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/APRIORI.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/APRIORI.java index 64cfa509..3555e307 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/APRIORI.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/APRIORI.java @@ -23,9 +23,6 @@ package de.lmu.ifi.dbs.elki.algorithm.itemsetmining; along with this program. If not, see <http://www.gnu.org/licenses/>. */ -import gnu.trove.iterator.TLongIntIterator; -import gnu.trove.map.hash.TLongIntHashMap; - import java.util.ArrayList; import java.util.Collections; import java.util.Iterator; @@ -46,11 +43,14 @@ import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.logging.statistics.Duration; import de.lmu.ifi.dbs.elki.logging.statistics.LongStatistic; import de.lmu.ifi.dbs.elki.result.FrequentItemsetsResult; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.BitsUtil; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; +import gnu.trove.iterator.TLongIntIterator; +import gnu.trove.map.hash.TLongIntHashMap; /** * The APRIORI algorithm for Mining Association Rules. @@ -72,6 +72,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * * @author Arthur Zimek * @author Erich Schubert + * @since 0.2 * * @apiviz.has Itemset * @apiviz.uses BitVector @@ -82,6 +83,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; title = "Fast Algorithms for Mining Association Rules", // booktitle = "Proc. 20th Int. Conf. on Very Large Data Bases (VLDB '94), Santiago de Chile, Chile 1994", // url = "http://www.vldb.org/conf/1994/P487.PDF") +@Alias("de.lmu.ifi.dbs.elki.algorithm.APRIORI") public class APRIORI extends AbstractFrequentItemsetAlgorithm { /** * The logger for this class. @@ -596,4 +598,4 @@ public class APRIORI extends AbstractFrequentItemsetAlgorithm { return new APRIORI(minsupp, minlength, maxlength); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/AbstractFrequentItemsetAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/AbstractFrequentItemsetAlgorithm.java index 31947c33..4f73d247 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/AbstractFrequentItemsetAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/AbstractFrequentItemsetAlgorithm.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * Abstract base class for frequent itemset mining. * * @author Erich Schubert + * @since 0.7.0 */ public abstract class AbstractFrequentItemsetAlgorithm extends AbstractAlgorithm<FrequentItemsetsResult> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/DenseItemset.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/DenseItemset.java index d77a0915..7896bb00 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/DenseItemset.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/DenseItemset.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * APRIORI itemset. * * @author Erich Schubert + * @since 0.7.0 */ public class DenseItemset extends Itemset { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/Eclat.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/Eclat.java index 47f75c54..9e62c5ed 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/Eclat.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/Eclat.java @@ -74,6 +74,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.7.0 */ @Reference(title = "New Algorithms for Fast Discovery of Association Rules", // authors = "M.J. Zaki, S. Parthasarathy, M. Ogihara, and W. Li", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/FPGrowth.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/FPGrowth.java index 5cdde71a..a09bf551 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/FPGrowth.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/FPGrowth.java @@ -75,6 +75,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf FPTree */ @@ -194,7 +195,7 @@ public class FPGrowth extends AbstractFrequentItemsetAlgorithm { */ private int[] countItemSupport(final Relation<BitVector> relation, final int dim) { final int[] counts = new int[dim]; - FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Finding frequent 1-items.", relation.size(), LOG) : null; + FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Finding frequent 1-items", relation.size(), LOG) : null; for(DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) { SparseFeatureVector<?> bv = relation.get(iditer); // TODO: only count those which satisfy minlength? diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/Itemset.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/Itemset.java index c195a79f..7e6446e7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/Itemset.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/Itemset.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.data.type.VectorFieldTypeInformation; * APRIORI itemset. * * @author Erich Schubert + * @since 0.7.0 */ public abstract class Itemset implements Comparable<Itemset> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/OneItemset.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/OneItemset.java index 9fddd758..63ca1dde 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/OneItemset.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/OneItemset.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * APRIORI itemset. * * @author Erich Schubert + * @since 0.7.0 */ public class OneItemset extends Itemset { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/SmallDenseItemset.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/SmallDenseItemset.java index e1b8ca55..c68c65ab 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/SmallDenseItemset.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/SmallDenseItemset.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * APRIORI itemset. * * @author Erich Schubert + * @since 0.7.0 */ public class SmallDenseItemset extends Itemset { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/SparseItemset.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/SparseItemset.java index 87534439..3eada0a6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/SparseItemset.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/itemsetmining/SparseItemset.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * APRIORI itemset. * * @author Erich Schubert + * @since 0.7.0 */ public class SparseItemset extends Itemset { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/COP.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/COP.java index 7f43796b..d2ba2160 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/COP.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/COP.java @@ -83,6 +83,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Erich Schubert + * @since 0.2 * * @param <V> the type of NumberVector handled by this Algorithm */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/DWOF.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/DWOF.java index a3e9e1d2..51ca8848 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/DWOF.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/DWOF.java @@ -90,6 +90,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Omar Yousry + * @since 0.6.0 * * @param <O> the type of DatabaseObjects handled by this Algorithm */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/GaussianModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/GaussianModel.java index 25a776e0..4f6ba095 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/GaussianModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/GaussianModel.java @@ -56,6 +56,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; * <em>probability density</em> of the assumed distribution. * * @author Lisa Reichert + * @since 0.3 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/GaussianUniformMixture.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/GaussianUniformMixture.java index cb170573..190bbb55 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/GaussianUniformMixture.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/GaussianUniformMixture.java @@ -74,6 +74,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * </p> * * @author Lisa Reichert + * @since 0.3 * * @param <V> Vector Type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/OPTICSOF.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/OPTICSOF.java index 484736bb..ccde20eb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/OPTICSOF.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/OPTICSOF.java @@ -72,6 +72,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * and Data Mining (PKDD), Prague, Czech Republic * * @author Ahmed Hettab + * @since 0.3 * * @apiviz.has KNNQuery * @apiviz.has RangeQuery diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/OutlierAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/OutlierAlgorithm.java index 6d671cd0..fff0310c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/OutlierAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/OutlierAlgorithm.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; * Generic super interface for outlier detection algorithms. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/SimpleCOP.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/SimpleCOP.java index 6b8f645d..271d0467 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/SimpleCOP.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/SimpleCOP.java @@ -70,6 +70,8 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Algorithm to compute local correlation outlier probability. * * This is the simpler, original version of COP, as published in + * + * Reference: * <p> * Arthur Zimek<br /> * Correlation Clustering.<br /> @@ -78,10 +80,13 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * which has then been refined to the method published as {@link COP} * * @author Erich Schubert + * @since 0.5.5 * @param <V> the type of NumberVector handled by this Algorithm */ @Title("Simple COP: Correlation Outlier Probability") -@Reference(authors = "Arthur Zimek", title = "Correlation Clustering. PhD thesis, Chapter 18", booktitle = "") +@Reference(authors = "Arthur Zimek", // +title = "Correlation Clustering", // +booktitle = "PhD thesis, Chapter 18") public class SimpleCOP<V extends NumberVector> extends AbstractDistanceBasedAlgorithm<V, OutlierResult> implements OutlierAlgorithm { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/ABOD.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/ABOD.java index a78f76c9..946c94ad 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/ABOD.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/ABOD.java @@ -75,6 +75,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Matthias Schubert (Original Code) * @author Erich Schubert (ELKIfication) + * @since 0.2 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/FastABOD.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/FastABOD.java index 88a606d5..5ff844a5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/FastABOD.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/FastABOD.java @@ -75,6 +75,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * * @author Matthias Schubert (Original Code) * @author Erich Schubert (ELKIfication) + * @since 0.6.0 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/LBABOD.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/LBABOD.java index 945d3d46..cb0e4114 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/LBABOD.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/LBABOD.java @@ -82,6 +82,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * * @author Matthias Schubert (Original Code) * @author Erich Schubert (ELKIfication) + * @since 0.6.0 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/EMOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/EMOutlier.java index fc33d88f..62f492e3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/EMOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/EMOutlier.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.result.Result; import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; import de.lmu.ifi.dbs.elki.result.outlier.OutlierScoreMeta; import de.lmu.ifi.dbs.elki.result.outlier.ProbabilisticOutlierScore; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; import de.lmu.ifi.dbs.elki.utilities.datastructures.hierarchy.Hierarchy.Iter; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; @@ -57,6 +58,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * object is an outlier. * * @author Lisa Reichert + * @since 0.3 * * @apiviz.has EM * @@ -65,6 +67,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz // TODO: re-use an existing EM when present? @Title("EM Outlier: Outlier Detection based on the generic EM clustering") @Description("The outlier score assigned is based on the highest cluster probability obtained from EM clustering.") +@Alias("de.lmu.ifi.dbs.elki.algorithm.outlier.EMOutlier") public class EMOutlier<V extends NumberVector> extends AbstractAlgorithm<OutlierResult> implements OutlierAlgorithm { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/KMeansOutlierDetection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/KMeansOutlierDetection.java index 4db56748..b4a7b44c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/KMeansOutlierDetection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/KMeansOutlierDetection.java @@ -67,6 +67,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * publication list</a> for citation information and BibTeX templates). * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has KMeans * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/SilhouetteOutlierDetection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/SilhouetteOutlierDetection.java index 34600968..a4a3d7f1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/SilhouetteOutlierDetection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/SilhouetteOutlierDetection.java @@ -74,6 +74,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * for citation information and BibTeX templates). * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has ClusteringAlgorithm * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/AbstractDBOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/AbstractDBOutlier.java index 6a7a2922..7d7fc950 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/AbstractDBOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/AbstractDBOutlier.java @@ -53,6 +53,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * </p> * * @author Lisa Reichert + * @since 0.3 * * @param <O> the type of DatabaseObjects handled by this Algorithm */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/DBOutlierDetection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/DBOutlierDetection.java index bee17874..d9e705d8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/DBOutlierDetection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/DBOutlierDetection.java @@ -62,6 +62,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * 3.1. * * @author Lisa Reichert + * @since 0.3 * * @apiviz.has KNNQuery * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/DBOutlierScore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/DBOutlierScore.java index e1775bad..354057a4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/DBOutlierScore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/DBOutlierScore.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * </p> * * @author Lisa Reichert + * @since 0.3 * * @apiviz.has RangeQuery * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/HilOut.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/HilOut.java index c748c832..35fe19e0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/HilOut.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/HilOut.java @@ -85,6 +85,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Jonathan von Brünken * @author Erich Schubert + * @since 0.5.0 * * @apiviz.composedOf HilbertFeatures * @apiviz.uses HilFeature diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/KNNOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/KNNOutlier.java index 649ea088..41653ac3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/KNNOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/KNNOutlier.java @@ -73,6 +73,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Lisa Reichert + * @since 0.3 * * @apiviz.has KNNQuery * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/KNNWeightOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/KNNWeightOutlier.java index 3aeb6da2..5b92cef5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/KNNWeightOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/KNNWeightOutlier.java @@ -81,6 +81,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Lisa Reichert + * @since 0.3 * * @apiviz.has KNNQuery * @@ -125,7 +126,7 @@ public class KNNWeightOutlier<O> extends AbstractDistanceBasedAlgorithm<O, Outli final DistanceQuery<O> distanceQuery = database.getDistanceQuery(relation, getDistanceFunction()); KNNQuery<O> knnQuery = database.getKNNQuery(distanceQuery, k + 1); // + query point - FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Compute kNN weights.", relation.size(), LOG) : null; + FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Compute kNN weights", relation.size(), LOG) : null; DoubleMinMax minmax = new DoubleMinMax(); WritableDoubleDataStore knnw_score = DataStoreUtil.makeDoubleStorage(relation.getDBIDs(), DataStoreFactory.HINT_STATIC); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/LocalIsolationCoefficient.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/LocalIsolationCoefficient.java index 33450eb1..034f6af2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/LocalIsolationCoefficient.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/LocalIsolationCoefficient.java @@ -68,6 +68,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Erich Schubert + * @since 0.3 * * @apiviz.has KNNQuery * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/ODIN.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/ODIN.java index e249e543..534f2be1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/ODIN.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/ODIN.java @@ -65,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/ReferenceBasedOutlierDetection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/ReferenceBasedOutlierDetection.java index cf184221..304474a3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/ReferenceBasedOutlierDetection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/ReferenceBasedOutlierDetection.java @@ -81,6 +81,7 @@ import de.lmu.ifi.dbs.elki.utilities.referencepoints.ReferencePointsHeuristic; * * @author Lisa Reichert * @author Erich Schubert + * @since 0.3 * * @apiviz.composedOf ReferencePointsHeuristic */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/KNNWeightProcessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/KNNWeightProcessor.java index 60ebcd8b..3de88864 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/KNNWeightProcessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/KNNWeightProcessor.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.parallel.variables.SharedObject; * Needs the k nearest neighbors as input, for example from {@link KNNProcessor} * * @author Erich Schubert + * @since 0.7.0 */ public class KNNWeightProcessor extends AbstractDoubleProcessor { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/ParallelKNNOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/ParallelKNNOutlier.java index 3b4c17f1..96c70b60 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/ParallelKNNOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/ParallelKNNOutlier.java @@ -76,6 +76,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf KNNProcessor * @apiviz.composedOf KDistanceProcessor diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/ParallelKNNWeightOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/ParallelKNNWeightOutlier.java index 571c2038..7f86e48f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/ParallelKNNWeightOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/ParallelKNNWeightOutlier.java @@ -76,6 +76,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf KNNWeightProcessor * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/intrinsic/IDOS.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/intrinsic/IDOS.java index b462b836..442a96a1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/intrinsic/IDOS.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/intrinsic/IDOS.java @@ -70,6 +70,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p>
*
* @author Jonathan von Brünken
+ * @since 0.7.0 * @author Erich Schubert
*
* @param <O> Object type
diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/intrinsic/IntrinsicDimensionalityOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/intrinsic/IntrinsicDimensionalityOutlier.java index 1b2d25ef..04679930 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/intrinsic/IntrinsicDimensionalityOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/intrinsic/IntrinsicDimensionalityOutlier.java @@ -63,6 +63,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Please see their upcoming publications for an improved solution. * * @author Erich Schubert + * @since 0.3 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/ALOCI.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/ALOCI.java index f7edae0f..e0fefe2d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/ALOCI.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/ALOCI.java @@ -55,6 +55,7 @@ import de.lmu.ifi.dbs.elki.math.random.RandomFactory; import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; import de.lmu.ifi.dbs.elki.result.outlier.OutlierScoreMeta; import de.lmu.ifi.dbs.elki.result.outlier.QuotientOutlierScoreMeta; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; @@ -67,27 +68,31 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; /** * Fast Outlier Detection Using the "approximate Local Correlation Integral". - * + * * Outlier detection using multiple epsilon neighborhoods. - * + * * Reference: * <p> - * S. Papadimitriou, H. Kitagawa, P. B. Gibbons and C. Faloutsos:<br /> - * LOCI: Fast Outlier Detection Using the Local Correlation Integral.<br /> - * In: Proc. 19th IEEE Int. Conf. on Data Engineering (ICDE '03), Bangalore, - * India, 2003. + * S. Papadimitriou, H. Kitagawa, P. B. Gibbons and C. Faloutsos: <br /> + * LOCI: Fast Outlier Detection Using the Local Correlation Integral. <br /> + * In: Proc. 19th IEEE Int. Conf. on Data Engineering (ICDE '03) * </p> - * + * * @author Jonathan von Brünken * @author Erich Schubert - * + * @since 0.5.0 + * * @apiviz.composedOf ALOCIQuadTree - * + * * @param <O> Object type */ @Title("LOCI: Fast Outlier Detection Using the Local Correlation Integral") @Description("Algorithm to compute outliers based on the Local Correlation Integral") -@Reference(authors = "S. Papadimitriou, H. Kitagawa, P. B. Gibbons, C. Faloutsos", title = "LOCI: Fast Outlier Detection Using the Local Correlation Integral", booktitle = "Proc. 19th IEEE Int. Conf. on Data Engineering (ICDE '03), Bangalore, India, 2003", url = "http://dx.doi.org/10.1109/ICDE.2003.1260802") +@Reference(authors = "S. Papadimitriou, H. Kitagawa, P. B. Gibbons, C. Faloutsos", // +title = "LOCI: Fast Outlier Detection Using the Local Correlation Integral", // +booktitle = "Proc. 19th IEEE Int. Conf. on Data Engineering (ICDE '03)", // +url = "http://dx.doi.org/10.1109/ICDE.2003.1260802") +@Alias("de.lmu.ifi.dbs.elki.algorithm.outlier.ALOCI") public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResult> implements OutlierAlgorithm { /** * The logger for this class. @@ -121,7 +126,7 @@ public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResu /** * Constructor. - * + * * @param distanceFunction Distance function * @param nmin Minimum neighborhood size * @param alpha Alpha value @@ -246,10 +251,10 @@ public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResu /** * Method for the MDEF calculation - * + * * @param sn Sampling Neighborhood * @param cg Counting Neighborhood - * + * * @return MDEF norm */ private static double calculate_MDEF_norm(Node sn, Node cg) { @@ -294,13 +299,13 @@ public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResu /** * Simple quadtree for ALOCI. Not storing the actual objects, just the counts. - * + * * Furthermore, the quadtree can be shifted by a specified vector, wrapping * around min/max - * + * * @author Jonathan von Brünken * @author Erich Schubert - * + * * @apiviz.composedOf Node */ static class ALOCIQuadTree { @@ -326,7 +331,7 @@ public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResu /** * Constructor. - * + * * @param min Minimum coordinates * @param max Maximum coordinates * @param shift Tree shift offset @@ -364,7 +369,7 @@ public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResu /** * Bulk load the tree - * + * * @param lmin Subtree minimum (unshifted, will be modified) * @param lmax Subtree maximum (unshifted, will be modified) * @param children List of children for current parent @@ -461,7 +466,7 @@ public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResu /** * Shift and wrap a single dimension. - * + * * @param obj Object * @param dim Dimension * @param level Level (controls scaling/wraping!) @@ -476,7 +481,7 @@ public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResu /** * Find the closest node (of depth tlevel or above, if there is no node at * this depth) for the given vector. - * + * * @param vec Query vector * @param tlevel Target level * @return Node @@ -511,7 +516,7 @@ public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResu /** * Node of the ALOCI Quadtree - * + * * @author Erich Schubert */ static class Node { @@ -547,7 +552,7 @@ public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResu /** * Constructor. - * + * * @param code Node code * @param center Center vector * @param count Element count @@ -569,7 +574,7 @@ public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResu /** * Get level of node. - * + * * @return Level of node */ public int getLevel() { @@ -578,7 +583,7 @@ public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResu /** * Get count of subtree - * + * * @return subtree count */ public int getCount() { @@ -587,7 +592,7 @@ public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResu /** * Return center vector - * + * * @return center vector */ public Vector getCenter() { @@ -596,7 +601,7 @@ public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResu /** * Get sum of squares, recursively - * + * * @param levels Depth to collect * @return Sum of squares */ @@ -613,7 +618,7 @@ public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResu /** * Get cubic sum. - * + * * @param levels Level to collect * @return sum of cubes */ @@ -631,9 +636,9 @@ public class ALOCI<O extends NumberVector> extends AbstractAlgorithm<OutlierResu /** * Parameterization class. - * + * * @author Erich Schubert - * + * * @apiviz.exclude */ public static class Parameterizer<O extends NumberVector> extends AbstractParameterizer { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/COF.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/COF.java index 87019ae6..61cb915f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/COF.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/COF.java @@ -67,6 +67,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Erich Schubert + * @since 0.2 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/FlexibleLOF.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/FlexibleLOF.java index e38e8da2..eae6f530 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/FlexibleLOF.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/FlexibleLOF.java @@ -107,6 +107,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * @author Peer Kröger * @author Erich Schubert * @author Elke Achtert + * @since 0.2 * * @apiviz.has LOFResult oneway - - computes * @apiviz.has KNNQuery diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/INFLO.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/INFLO.java index 1e77cab5..375031f9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/INFLO.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/INFLO.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.math.DoubleMinMax; import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; import de.lmu.ifi.dbs.elki.result.outlier.OutlierScoreMeta; import de.lmu.ifi.dbs.elki.result.outlier.QuotientOutlierScoreMeta; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; @@ -72,6 +73,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * * @author Ahmed Hettab * @author Erich Schubert + * @since 0.3 * * @apiviz.has KNNQuery * @@ -83,6 +85,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; title = "Ranking outliers using symmetric neighborhood relationship", // booktitle = "Proc. 10th Pacific-Asia conference on Advances in Knowledge Discovery and Data Mining", // url = "http://dx.doi.org/10.1007/11731139_68") +@Alias("de.lmu.ifi.dbs.elki.algorithm.outlier.INFLO") public class INFLO<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> implements OutlierAlgorithm { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/KDEOS.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/KDEOS.java index 1583ac99..92f0d7a9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/KDEOS.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/KDEOS.java @@ -93,6 +93,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has KNNQuery * @apiviz.has KernelDensityFunction @@ -203,7 +204,7 @@ public class KDEOS<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult>im densities.put(iter, new double[knum]); } // Distribute densities: - FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Computing densities.", ids.size(), LOG) : null; + FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Computing densities", ids.size(), LOG) : null; double iminbw = (minBandwidth > 0.) ? 1. / (minBandwidth * scale) : Double.POSITIVE_INFINITY; for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) { KNNList neighbors = knnq.getKNNForDBID(iter, kmax + 1); @@ -269,7 +270,7 @@ public class KDEOS<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult>im */ protected void computeOutlierScores(KNNQuery<O> knnq, final DBIDs ids, WritableDataStore<double[]> densities, WritableDoubleDataStore kdeos, DoubleMinMax minmax) { final int knum = kmax + 1 - kmin; - FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Computing KDEOS scores.", ids.size(), LOG) : null; + FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Computing KDEOS scores", ids.size(), LOG) : null; double[][] scratch = new double[knum][kmax + 5]; MeanVariance mv = new MeanVariance(); @@ -339,32 +340,32 @@ public class KDEOS<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult>im /** * Parameter to specify the kernel density function. */ - private static final OptionID KERNEL_ID = new OptionID("kdeos.kernel", "Kernel density function to use."); + public static final OptionID KERNEL_ID = new OptionID("kdeos.kernel", "Kernel density function to use."); /** * Parameter to specify the minimum bandwidth. */ - private static final OptionID KERNEL_MIN_ID = new OptionID("kdeos.kernel.minbw", "Minimum bandwidth for kernel density estimation."); + public static final OptionID KERNEL_MIN_ID = new OptionID("kdeos.kernel.minbw", "Minimum bandwidth for kernel density estimation."); /** * Parameter to specify the kernel scaling factor. */ - private static final OptionID KERNEL_SCALE_ID = new OptionID("kdeos.kernel.scale", "Scaling factor for the kernel function."); + public static final OptionID KERNEL_SCALE_ID = new OptionID("kdeos.kernel.scale", "Scaling factor for the kernel function."); /** * Minimum value of k to analyze. */ - private static final OptionID KMIN_ID = new OptionID("kdeos.k.min", "Minimum value of k to analyze."); + public static final OptionID KMIN_ID = new OptionID("kdeos.k.min", "Minimum value of k to analyze."); /** * Maximum value of k to analyze. */ - private static final OptionID KMAX_ID = new OptionID("kdeos.k.max", "Maximum value of k to analyze."); + public static final OptionID KMAX_ID = new OptionID("kdeos.k.max", "Maximum value of k to analyze."); /** * Intrinsic dimensionality. */ - private static final OptionID IDIM_ID = new OptionID("kdeos.idim", "Intrinsic dimensionality of this data set. Use -1 for using the true data dimensionality, but values such as 0-2 often offer better performance."); + public static final OptionID IDIM_ID = new OptionID("kdeos.idim", "Intrinsic dimensionality of this data set. Use -1 for using the true data dimensionality, but values such as 0-2 often offer better performance."); /** * Kernel function to use for density estimation. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LDF.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LDF.java index 056a6ba3..c4067504 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LDF.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LDF.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.math.statistics.kernelfunctions.KernelDensityFunction import de.lmu.ifi.dbs.elki.result.outlier.BasicOutlierScoreMeta; import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; import de.lmu.ifi.dbs.elki.result.outlier.OutlierScoreMeta; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.DatabaseUtil; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; @@ -77,6 +78,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has KNNQuery * @apiviz.has KernelDensityFunction @@ -87,6 +89,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; title = "Outlier Detection with Kernel Density Functions", // booktitle = "Machine Learning and Data Mining in Pattern Recognition", // url = "http://dx.doi.org/10.1007/978-3-540-73499-4_6") +@Alias("de.lmu.ifi.dbs.elki.algorithm.outlier.LDF") public class LDF<O extends NumberVector> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> implements OutlierAlgorithm { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LDOF.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LDOF.java index b41af3bd..9dadf0e3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LDOF.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LDOF.java @@ -71,6 +71,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Arthur Zimek + * @since 0.3 * * @apiviz.has KNNQuery * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LOCI.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LOCI.java index 7b332639..f8623bcc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LOCI.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LOCI.java @@ -63,26 +63,33 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; /** * Fast Outlier Detection Using the "Local Correlation Integral". - * + * * Exact implementation only, not aLOCI. See {@link ALOCI}. - * + * * Outlier detection using multiple epsilon neighborhoods. - * + * * This implementation has O(n<sup>3</sup> log n) runtime complexity! - * - * Based on: S. Papadimitriou, H. Kitagawa, P. B. Gibbons and C. Faloutsos: - * LOCI: Fast Outlier Detection Using the Local Correlation Integral. In: Proc. - * 19th IEEE Int. Conf. on Data Engineering (ICDE '03), Bangalore, India, 2003. - * + * + * Reference: + * <p> + * S. Papadimitriou, H. Kitagawa, P. B. Gibbons and C. Faloutsos: <br /> + * LOCI: Fast Outlier Detection Using the Local Correlation Integral. <br /> + * In: Proc. 19th IEEE Int. Conf. on Data Engineering (ICDE '03) + * </p> + * * @author Erich Schubert - * + * @since 0.2 + * * @apiviz.has RangeQuery - * + * * @param <O> Object type */ @Title("LOCI: Fast Outlier Detection Using the Local Correlation Integral") @Description("Algorithm to compute outliers based on the Local Correlation Integral") -@Reference(authors = "S. Papadimitriou, H. Kitagawa, P. B. Gibbons, C. Faloutsos", title = "LOCI: Fast Outlier Detection Using the Local Correlation Integral", booktitle = "Proc. 19th IEEE Int. Conf. on Data Engineering (ICDE '03), Bangalore, India, 2003", url = "http://dx.doi.org/10.1109/ICDE.2003.1260802") +@Reference(authors = "S. Papadimitriou, H. Kitagawa, P. B. Gibbons, C. Faloutsos", // +title = "LOCI: Fast Outlier Detection Using the Local Correlation Integral", // +booktitle = "Proc. 19th IEEE Int. Conf. on Data Engineering (ICDE '03)", // +url = "http://dx.doi.org/10.1109/ICDE.2003.1260802") @Alias({ "de.lmu.ifi.dbs.elki.algorithm.outlier.LOCI" }) public class LOCI<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> implements OutlierAlgorithm { /** @@ -91,39 +98,23 @@ public class LOCI<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> im private static final Logging LOG = Logging.getLogger(LOCI.class); /** - * Parameter to specify the maximum radius of the neighborhood to be - * considered, must be suitable to the distance function specified. - */ - public static final OptionID RMAX_ID = new OptionID("loci.rmax", "The maximum radius of the neighborhood to be considered."); - - /** - * Parameter to specify the minimum neighborhood size - */ - public static final OptionID NMIN_ID = new OptionID("loci.nmin", "Minimum neighborhood size to be considered."); - - /** - * Parameter to specify the averaging neighborhood scaling. - */ - public static final OptionID ALPHA_ID = new OptionID("loci.alpha", "Scaling factor for averaging neighborhood"); - - /** - * Holds the value of {@link #RMAX_ID}. + * Maximum radius. */ private double rmax; /** - * Holds the value of {@link #NMIN_ID}. + * Minimum neighborhood size. */ - private int nmin; + private int nmin = 0; /** - * Holds the value of {@link #ALPHA_ID}. + * Scaling of averaging neighborhood. */ - private double alpha; + private double alpha = 0.5; /** * Constructor. - * + * * @param distanceFunction Distance function * @param rmax Maximum radius * @param nmin Minimum neighborhood size @@ -138,7 +129,7 @@ public class LOCI<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> im /** * Run the algorithm - * + * * @param database Database to process * @param relation Relation to process * @return Outlier result @@ -228,7 +219,7 @@ public class LOCI<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> im /** * Preprocessing step: determine the radii of interest for each point. - * + * * @param ids IDs to process * @param rangeQuery Range query * @param interestingDistances Distances of interest @@ -284,7 +275,7 @@ public class LOCI<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> im /** * Array of double-int values. - * + * * @author Erich Schubert * * @apiviz.exclude @@ -307,7 +298,7 @@ public class LOCI<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> im /** * Constructor. - * + * * @param alloc Initial allocation. */ public DoubleIntArrayList(int alloc) { @@ -318,7 +309,7 @@ public class LOCI<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> im /** * Collection size. - * + * * @return Size */ public int size() { @@ -327,7 +318,7 @@ public class LOCI<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> im /** * Get the key at the given position. - * + * * @param i Position * @return Key */ @@ -337,7 +328,7 @@ public class LOCI<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> im /** * Get the value at the given position. - * + * * @param i Position * @return Value */ @@ -347,7 +338,7 @@ public class LOCI<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> im /** * Get the value at the given position. - * + * * @param i Position * @param val New value */ @@ -357,7 +348,7 @@ public class LOCI<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> im /** * Append a key-value pair. - * + * * @param key Key to append * @param val Value to append. */ @@ -373,7 +364,7 @@ public class LOCI<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> im /** * Find the last position with a smaller or equal key. - * + * * @param search Key * @return Position */ @@ -412,18 +403,43 @@ public class LOCI<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> im /** * Parameterization class. - * + * * @author Erich Schubert - * + * * @apiviz.exclude - * + * * @param <O> Object type */ public static class Parameterizer<O> extends AbstractDistanceBasedAlgorithm.Parameterizer<O> { + /** + * Parameter to specify the maximum radius of the neighborhood to be + * considered, must be suitable to the distance function specified. + */ + public static final OptionID RMAX_ID = new OptionID("loci.rmax", "The maximum radius of the neighborhood to be considered."); + + /** + * Parameter to specify the minimum neighborhood size + */ + public static final OptionID NMIN_ID = new OptionID("loci.nmin", "Minimum neighborhood size to be considered."); + + /** + * Parameter to specify the averaging neighborhood scaling. + */ + public static final OptionID ALPHA_ID = new OptionID("loci.alpha", "Scaling factor for averaging neighborhood"); + + /** + * Maximum radius. + */ protected double rmax; + /** + * Minimum neighborhood size. + */ protected int nmin = 0; + /** + * Scaling of averaging neighborhood. + */ protected double alpha = 0.5; @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LOF.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LOF.java index 87b1be8c..52fbeafc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LOF.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LOF.java @@ -87,6 +87,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * * @author Erich Schubert * @author Elke Achtert + * @since 0.2 * * @apiviz.has KNNQuery * @@ -98,7 +99,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; title = "LOF: Identifying Density-Based Local Outliers", // booktitle = "Proc. 2nd ACM SIGMOD Int. Conf. on Management of Data (SIGMOD '00), Dallas, TX, 2000", // url = "http://dx.doi.org/10.1145/342009.335388") -@Alias({ "de.lmu.ifi.dbs.elki.algorithm.outlier.LOF", "LOF" }) +@Alias("de.lmu.ifi.dbs.elki.algorithm.outlier.LOF") public class LOF<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> implements OutlierAlgorithm { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LoOP.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LoOP.java index 48589698..16f46a33 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LoOP.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LoOP.java @@ -90,6 +90,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * </ul> * * @author Erich Schubert + * @since 0.3 * * @apiviz.has KNNQuery * @@ -101,7 +102,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; title = "LoOP: Local Outlier Probabilities", // booktitle = "Proceedings of the 18th International Conference on Information and Knowledge Management (CIKM), Hong Kong, China, 2009", // url = "http://dx.doi.org/10.1145/1645953.1646195") -@Alias({ "de.lmu.ifi.dbs.elki.algorithm.outlier.LoOP", "LoOP" }) +@Alias("de.lmu.ifi.dbs.elki.algorithm.outlier.LoOP") public class LoOP<O> extends AbstractAlgorithm<OutlierResult> implements OutlierAlgorithm { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/OnlineLOF.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/OnlineLOF.java index 715d3c0e..6a9344b3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/OnlineLOF.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/OnlineLOF.java @@ -53,6 +53,7 @@ import de.lmu.ifi.dbs.elki.logging.progress.StepProgress; import de.lmu.ifi.dbs.elki.math.DoubleMinMax; import de.lmu.ifi.dbs.elki.result.outlier.BasicOutlierScoreMeta; import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; @@ -63,10 +64,12 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * BUG: this currently does not appear to work. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has FlexibleLOF.LOFResult oneway - - updates */ // TODO: related to publication? +@Alias("de.lmu.ifi.dbs.elki.algorithm.outlier.OnlineLOF") public class OnlineLOF<O> extends FlexibleLOF<O> { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/SimpleKernelDensityLOF.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/SimpleKernelDensityLOF.java index af32988e..80c41e57 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/SimpleKernelDensityLOF.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/SimpleKernelDensityLOF.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.math.statistics.kernelfunctions.KernelDensityFunction import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; import de.lmu.ifi.dbs.elki.result.outlier.OutlierScoreMeta; import de.lmu.ifi.dbs.elki.result.outlier.QuotientOutlierScoreMeta; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.DatabaseUtil; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.CommonConstraints; @@ -66,12 +67,14 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * estimation instead of the local reachability density. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has KNNQuery * @apiviz.has KernelDensityFunction * * @param <O> the type of objects handled by this Algorithm */ +@Alias("de.lmu.ifi.dbs.elki.algorithm.outlier.SimpleKernelDensityLOF") public class SimpleKernelDensityLOF<O extends NumberVector> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> implements OutlierAlgorithm { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/SimplifiedLOF.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/SimplifiedLOF.java index 17ebdabf..5705e7aa 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/SimplifiedLOF.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/SimplifiedLOF.java @@ -68,6 +68,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has KNNQuery * @@ -77,7 +78,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; title = "Local Outlier Detection Reconsidered: a Generalized View on Locality with Applications to Spatial, Video, and Network Outlier Detection", // booktitle = "Data Mining and Knowledge Discovery, 28(1): 190–237, 2014.", // url = "http://dx.doi.org/10.1007/s10618-012-0300-z") -@Alias({ "SimplifiedLOF", "outlier.SimplifiedLOF", "de.lmu.ifi.dbs.elki.algorithm.outlier.SimplifiedLOF" }) +@Alias("de.lmu.ifi.dbs.elki.algorithm.outlier.SimpleLOF") public class SimplifiedLOF<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> implements OutlierAlgorithm { /** * The logger for this class. @@ -172,7 +173,7 @@ public class SimplifiedLOF<O> extends AbstractDistanceBasedAlgorithm<O, OutlierR * @param lofminmax Minimum and maximum scores */ private void computeSimplifiedLOFs(DBIDs ids, KNNQuery<O> knnq, WritableDoubleDataStore slrds, WritableDoubleDataStore lofs, DoubleMinMax lofminmax) { - FiniteProgress progressLOFs = LOG.isVerbose() ? new FiniteProgress("Simplified LOF scores.", ids.size(), LOG) : null; + FiniteProgress progressLOFs = LOG.isVerbose() ? new FiniteProgress("Simplified LOF scores", ids.size(), LOG) : null; for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) { final double lof; final double lrdp = slrds.doubleValue(iter); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/VarianceOfVolume.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/VarianceOfVolume.java index 3dffe213..93f62bea 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/VarianceOfVolume.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/VarianceOfVolume.java @@ -77,6 +77,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has KNNQuery * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/LOFProcessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/LOFProcessor.java index 095a1b5b..c6c7b315 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/LOFProcessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/LOFProcessor.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.parallel.variables.SharedDouble; * Processor for computing the LOF. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has Instance */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/LRDProcessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/LRDProcessor.java index e9c48cbf..c21a45af 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/LRDProcessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/LRDProcessor.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.parallel.variables.SharedDouble; * Processor for the "local reachability density" of LOF. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has Instance */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/ParallelLOF.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/ParallelLOF.java index 59b69931..04b7f1da 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/ParallelLOF.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/ParallelLOF.java @@ -71,6 +71,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has LRDProcessor * @apiviz.has LOFProcessor diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/ParallelSimplifiedLOF.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/ParallelSimplifiedLOF.java index 9be38c34..d57972e3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/ParallelSimplifiedLOF.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/ParallelSimplifiedLOF.java @@ -70,6 +70,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has SimplifiedLRDProcessor * @apiviz.has LOFProcessor diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/SimplifiedLRDProcessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/SimplifiedLRDProcessor.java index 0ee9a862..c075c674 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/SimplifiedLRDProcessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/SimplifiedLRDProcessor.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.parallel.variables.SharedDouble; * Note: we compute 1/lrd, the local reachability distance. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has Instance */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/ExternalDoubleOutlierScore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/ExternalDoubleOutlierScore.java index 2791b800..63226bc9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/ExternalDoubleOutlierScore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/ExternalDoubleOutlierScore.java @@ -73,6 +73,7 @@ import de.lmu.ifi.dbs.elki.utilities.scaling.outlier.OutlierScalingFunction; * score specified with an algorithm-specific prefix. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has ScalingFunction * @apiviz.has File diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/FeatureBagging.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/FeatureBagging.java index 6a7a41f3..1354b5c0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/FeatureBagging.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/FeatureBagging.java @@ -79,6 +79,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * * @author Erich Schubert * @author Remigius Wojdanowski + * @since 0.4.0 */ @Title("Feature Bagging for Outlier Detection") @Reference(title = "Feature Bagging for Outlier Detection", authors = "A. Lazarevic, V. Kumar", booktitle = "Proc. of the 11th ACM SIGKDD international conference on Knowledge discovery in data mining", url = "http://dx.doi.org/10.1145/1081870.1081891") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/HiCS.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/HiCS.java index 4dcf83ec..e38dd7aa 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/HiCS.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/HiCS.java @@ -94,6 +94,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * * @author Jan Brusis * @author Erich Schubert + * @since 0.5.0 * * @apiviz.composedOf GoodnessOfFitTest * @apiviz.composedOf OutlierAlgorithm diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/RescaleMetaOutlierAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/RescaleMetaOutlierAlgorithm.java index f6f3fabc..fa940477 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/RescaleMetaOutlierAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/RescaleMetaOutlierAlgorithm.java @@ -56,6 +56,7 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * Scale another outlier score using the given scaling function. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf OutlierAlgorithm */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/SimpleOutlierEnsemble.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/SimpleOutlierEnsemble.java index 591ab776..16d07d05 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/SimpleOutlierEnsemble.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/SimpleOutlierEnsemble.java @@ -64,6 +64,7 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * Simple outlier ensemble method. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.composedOf EnsembleVoting * @apiviz.uses OutlierResult oneway - - reads diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/AbstractDistanceBasedSpatialOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/AbstractDistanceBasedSpatialOutlier.java index 829c9010..3ee1d13e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/AbstractDistanceBasedSpatialOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/AbstractDistanceBasedSpatialOutlier.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Abstract base class for distance-based spatial outlier detection methods. * * @author Ahmed Hettab + * @since 0.4.0 * * @param <N> Object type for neighborhood * @param <O> Non-spatial object type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/AbstractNeighborhoodOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/AbstractNeighborhoodOutlier.java index 2be79793..0fed345b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/AbstractNeighborhoodOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/AbstractNeighborhoodOutlier.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * neighborhood. * * @author Ahmed Hettab + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuGLSBackwardSearchAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuGLSBackwardSearchAlgorithm.java index 70f0eddb..13499720 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuGLSBackwardSearchAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuGLSBackwardSearchAlgorithm.java @@ -79,6 +79,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * that make the optimization problem convex. * * @author Ahmed Hettab + * @since 0.4.0 * * @param <V> Vector type to use for distances */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMeanMultipleAttributes.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMeanMultipleAttributes.java index f0783700..2322205f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMeanMultipleAttributes.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMeanMultipleAttributes.java @@ -69,6 +69,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Ahmed Hettab + * @since 0.4.0 * * @param <N> Spatial Vector * @param <O> Attribute Vector diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMedianAlgorithm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMedianAlgorithm.java index a5cb7423..cae611b8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMedianAlgorithm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMedianAlgorithm.java @@ -65,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * Outliers. * * @author Ahmed Hettab + * @since 0.4.0 * * @param <N> Neighborhood type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMedianMultipleAttributes.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMedianMultipleAttributes.java index 1093b449..9af83939 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMedianMultipleAttributes.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMedianMultipleAttributes.java @@ -70,6 +70,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Ahmed Hettab + * @since 0.4.0 * * @param <N> Spatial Vector * @param <O> Non Spatial Vector diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMoranScatterplotOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMoranScatterplotOutlier.java index 5e8a7086..78e7fbd4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMoranScatterplotOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuMoranScatterplotOutlier.java @@ -67,6 +67,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * upper left or lower right are Spatial Outliers. * * @author Ahmed Hettab + * @since 0.4.0 * * @param <N> Neighborhood type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuRandomWalkEC.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuRandomWalkEC.java index 6892200c..793b6977 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuRandomWalkEC.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuRandomWalkEC.java @@ -75,6 +75,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Ahmed Hettab + * @since 0.4.0 * * @param <P> Spatial Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuScatterplotOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuScatterplotOutlier.java index 16cd6625..b0a31a2c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuScatterplotOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuScatterplotOutlier.java @@ -69,6 +69,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * </p> * * @author Ahmed Hettab + * @since 0.4.0 * * @param <N> Neighborhood object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuZTestOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuZTestOutlier.java index ba93c79c..13f7488d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuZTestOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/CTLuZTestOutlier.java @@ -69,6 +69,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * </p> * * @author Ahmed Hettab + * @since 0.4.0 * * @param <N> Neighborhood type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/SLOM.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/SLOM.java index c18c69e0..ff2a671d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/SLOM.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/SLOM.java @@ -62,6 +62,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * still not be too useful then), which will result in divisions by zero. * * @author Ahmed Hettab + * @since 0.4.0 * * @param <N> the type the spatial neighborhood is defined over * @param <O> the type of objects handled by the algorithm diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/SOF.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/SOF.java index 31083439..32747bf3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/SOF.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/SOF.java @@ -62,6 +62,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * A LOF variation simplified with reachDist(o,p) == dist(o,p). * * @author Ahmed Hettab + * @since 0.4.0 * * @param <N> Neighborhood object type * @param <O> Attribute object type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/TrimmedMeanApproach.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/TrimmedMeanApproach.java index 6581bb82..2e5b305b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/TrimmedMeanApproach.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/TrimmedMeanApproach.java @@ -74,6 +74,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * </p> * * @author Ahmed Hettab + * @since 0.4.0 * @param <N> Neighborhood object type */ @Title("A Trimmed Mean Approach to Finding Spatial Outliers") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/AbstractPrecomputedNeighborhood.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/AbstractPrecomputedNeighborhood.java index abf42e98..da5c3d5c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/AbstractPrecomputedNeighborhood.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/AbstractPrecomputedNeighborhood.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * Abstract base class for precomputed neighborhoods. * * @author Erich Schubert + * @since 0.4.0 */ public abstract class AbstractPrecomputedNeighborhood implements NeighborSetPredicate { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/ExtendedNeighborhood.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/ExtendedNeighborhood.java index ba37400b..8284ace8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/ExtendedNeighborhood.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/ExtendedNeighborhood.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * neighborhood. * * @author Erich Schubert + * @since 0.4.0 */ public class ExtendedNeighborhood extends AbstractPrecomputedNeighborhood { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/ExternalNeighborhood.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/ExternalNeighborhood.java index 7881633c..4d0dd24a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/ExternalNeighborhood.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/ExternalNeighborhood.java @@ -59,6 +59,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; * A precomputed neighborhood, loaded from an external file. * * @author Erich Schubert + * @since 0.4.0 */ public class ExternalNeighborhood extends AbstractPrecomputedNeighborhood { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/NeighborSetPredicate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/NeighborSetPredicate.java index d953ece1..9ae428e6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/NeighborSetPredicate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/NeighborSetPredicate.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.result.Result; * Predicate to obtain the neighbors of a reference object as set. * * @author Erich Schubert + * @since 0.4.0 */ public interface NeighborSetPredicate extends Result { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/PrecomputedKNearestNeighborNeighborhood.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/PrecomputedKNearestNeighborNeighborhood.java index 923cd39d..0a70ae85 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/PrecomputedKNearestNeighborNeighborhood.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/PrecomputedKNearestNeighborNeighborhood.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Neighborhoods based on k nearest neighbors. * * @author Ahmed Hettab + * @since 0.4.0 */ public class PrecomputedKNearestNeighborNeighborhood extends AbstractPrecomputedNeighborhood { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/weighted/LinearWeightedExtendedNeighborhood.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/weighted/LinearWeightedExtendedNeighborhood.java index b45fd3cc..54753e17 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/weighted/LinearWeightedExtendedNeighborhood.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/weighted/LinearWeightedExtendedNeighborhood.java @@ -53,6 +53,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * TODO: make actual weighting parameterizable? * * @author Erich Schubert + * @since 0.4.0 */ public class LinearWeightedExtendedNeighborhood implements WeightedNeighborSetPredicate { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/weighted/UnweightedNeighborhoodAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/weighted/UnweightedNeighborhoodAdapter.java index 5476791d..def719cf 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/weighted/UnweightedNeighborhoodAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/weighted/UnweightedNeighborhoodAdapter.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * weighted neighborhoods. * * @author Erich Schubert + * @since 0.4.0 */ public class UnweightedNeighborhoodAdapter implements WeightedNeighborSetPredicate { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/weighted/WeightedNeighborSetPredicate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/weighted/WeightedNeighborSetPredicate.java index aeb91741..3e9a301c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/weighted/WeightedNeighborSetPredicate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/spatial/neighborhood/weighted/WeightedNeighborSetPredicate.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * Neighbor predicate with weight support. * * @author Erich Schubert + * @since 0.4.0 */ public interface WeightedNeighborSetPredicate { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AbstractAggarwalYuOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AbstractAggarwalYuOutlier.java index 54fc9853..63e58864 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AbstractAggarwalYuOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AbstractAggarwalYuOutlier.java @@ -63,6 +63,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.IntIntPair; * * @author Ahmed Hettab * @author Erich Schubert + * @since 0.4.0 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AggarwalYuEvolutionary.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AggarwalYuEvolutionary.java index 829347dc..e856ce62 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AggarwalYuEvolutionary.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AggarwalYuEvolutionary.java @@ -23,8 +23,6 @@ package de.lmu.ifi.dbs.elki.algorithm.outlier.subspace; along with this program. If not, see <http://www.gnu.org/licenses/>. */ -import gnu.trove.iterator.TIntIterator; -import gnu.trove.list.array.TIntArrayList; import java.util.ArrayList; import java.util.Arrays; @@ -50,6 +48,7 @@ import de.lmu.ifi.dbs.elki.math.random.RandomFactory; import de.lmu.ifi.dbs.elki.result.outlier.InvertedOutlierScoreMeta; import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; import de.lmu.ifi.dbs.elki.result.outlier.OutlierScoreMeta; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.datastructures.heap.Heap; import de.lmu.ifi.dbs.elki.utilities.datastructures.heap.TopBoundedHeap; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; @@ -61,6 +60,8 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; +import gnu.trove.iterator.TIntIterator; +import gnu.trove.list.array.TIntArrayList; /** * Evolutionary variant (EAFOD) of the high-dimensional outlier detection @@ -75,6 +76,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * * @author Ahmed Hettab * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has EvolutionarySearch oneway - - runs * @apiviz.has Individuum oneway - - obtains @@ -85,6 +87,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; @Title("EAFOD: the evolutionary outlier detection algorithm") @Description("Outlier detection for high dimensional data") @Reference(authors = "C.C. Aggarwal, P. S. Yu", title = "Outlier detection for high dimensional data", booktitle = "Proc. ACM SIGMOD Int. Conf. on Management of Data (SIGMOD 2001), Santa Barbara, CA, 2001", url = "http://dx.doi.org/10.1145/375663.375668") +@Alias("de.lmu.ifi.dbs.elki.algorithm.outlier.AggarwalYuEvolutionary") public class AggarwalYuEvolutionary<V extends NumberVector> extends AbstractAggarwalYuOutlier<V> { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AggarwalYuNaive.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AggarwalYuNaive.java index e141ad48..3c601dda 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AggarwalYuNaive.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AggarwalYuNaive.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.math.DoubleMinMax; import de.lmu.ifi.dbs.elki.result.outlier.InvertedOutlierScoreMeta; import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; import de.lmu.ifi.dbs.elki.result.outlier.OutlierScoreMeta; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; @@ -64,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.IntIntPair; * * @author Ahmed Hettab * @author Erich Schubert + * @since 0.4.0 * * @param <V> Vector type */ @@ -71,6 +73,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.IntIntPair; @Title("BruteForce: Outlier detection for high dimensional data") @Description("Examines all possible sets of k dimensional projections") @Reference(authors = "C.C. Aggarwal, P. S. Yu", title = "Outlier detection for high dimensional data", booktitle = "Proc. ACM SIGMOD Int. Conf. on Management of Data (SIGMOD 2001), Santa Barbara, CA, 2001", url = "http://dx.doi.org/10.1145/375663.375668") +@Alias("de.lmu.ifi.dbs.elki.algorithm.outlier.AggarwalYuNaive") public class AggarwalYuNaive<V extends NumberVector> extends AbstractAggarwalYuOutlier<V> { /** * The logger for this class. @@ -188,4 +191,4 @@ public class AggarwalYuNaive<V extends NumberVector> extends AbstractAggarwalYuO return new AggarwalYuNaive<>(k, phi); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/OUTRES.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/OUTRES.java index 6f7ee1f4..66d8ef5f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/OUTRES.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/OUTRES.java @@ -83,6 +83,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * * @author Viktoria Pleintinger * @author Erich Schubert + * @since 0.5.0 * * @apiviz.composedOf KernelDensityEstimator * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/OutRankS1.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/OutRankS1.java index 54047472..4ba34c10 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/OutRankS1.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/OutRankS1.java @@ -71,6 +71,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Erich Schubert + * @since 0.5.0 */ @Title("OutRank: ranking outliers in high dimensional data") @Description("Ranking outliers in high dimensional data - score 1") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/SOD.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/SOD.java index db1a969c..8b0ac7c7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/SOD.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/SOD.java @@ -57,6 +57,7 @@ import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; import de.lmu.ifi.dbs.elki.result.outlier.OutlierScoreMeta; import de.lmu.ifi.dbs.elki.result.textwriter.TextWriteable; import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.BitsUtil; import de.lmu.ifi.dbs.elki.utilities.datastructures.heap.Heap; import de.lmu.ifi.dbs.elki.utilities.datastructures.heap.TiedTopBoundedHeap; @@ -85,6 +86,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Arthur Zimek + * @since 0.2 * * @apiviz.has SODModel oneway - - computes * @apiviz.has SharedNearestNeighborSimilarityFunction @@ -94,6 +96,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; @Title("SOD: Subspace outlier degree") @Description("Outlier Detection in Axis-Parallel Subspaces of High Dimensional Data") @Reference(authors = "H.-P. Kriegel, P. Kröger, E. Schubert, A. Zimek", title = "Outlier Detection in Axis-Parallel Subspaces of High Dimensional Data", booktitle = "Proceedings of the 13th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), Bangkok, Thailand, 2009", url = "http://dx.doi.org/10.1007/978-3-642-01307-2") +@Alias("de.lmu.ifi.dbs.elki.algorithm.outlier.SOD") public class SOD<V extends NumberVector> extends AbstractAlgorithm<OutlierResult> implements OutlierAlgorithm { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/ByLabelOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/ByLabelOutlier.java index dfd35c78..6c2fc6c2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/ByLabelOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/ByLabelOutlier.java @@ -53,6 +53,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.PatternParameter; * reference algorithm in comparisons. * * @author Erich Schubert + * @since 0.4.0 */ public class ByLabelOutlier extends AbstractAlgorithm<OutlierResult> implements OutlierAlgorithm { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialAllOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialAllOutlier.java index 5ef77e12..3a8d1528 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialAllOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialAllOutlier.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.result.outlier.ProbabilisticOutlierScore; * reference algorithm in comparisons. * * @author Erich Schubert + * @since 0.4.0 */ public class TrivialAllOutlier extends AbstractAlgorithm<OutlierResult> implements OutlierAlgorithm { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialAverageCoordinateOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialAverageCoordinateOutlier.java index 4fe722a2..06da97e3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialAverageCoordinateOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialAverageCoordinateOutlier.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.result.outlier.OutlierScoreMeta; * convert a 1d data set into a score, e.g. in geodata. * * @author Erich Schubert + * @since 0.4.0 */ public class TrivialAverageCoordinateOutlier extends AbstractAlgorithm<OutlierResult> implements OutlierAlgorithm { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialGeneratedOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialGeneratedOutlier.java index c837e246..82155c2b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialGeneratedOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialGeneratedOutlier.java @@ -64,6 +64,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * generator model information is still available. * * @author Erich Schubert + * @since 0.5.0 */ public class TrivialGeneratedOutlier extends AbstractAlgorithm<OutlierResult> implements OutlierAlgorithm { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialNoOutlier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialNoOutlier.java index e25c35f5..d5df4573 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialNoOutlier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/trivial/TrivialNoOutlier.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.result.outlier.ProbabilisticOutlierScore; * algorithm in comparisons. * * @author Erich Schubert + * @since 0.4.0 */ public class TrivialNoOutlier extends AbstractAlgorithm<OutlierResult> implements OutlierAlgorithm { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/AddSingleScale.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/AddSingleScale.java index 6f243996..9e15127e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/AddSingleScale.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/AddSingleScale.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleListParamet * FIXME: this should become part of relation metadata. * * @author Erich Schubert + * @since 0.5.0 */ @Description("Setup a scaling so that all dimensions are scaled equally in visualization.") public class AddSingleScale implements Algorithm { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/AveragePrecisionAtK.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/AveragePrecisionAtK.java index a5a9291e..8a31f956 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/AveragePrecisionAtK.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/AveragePrecisionAtK.java @@ -59,6 +59,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * at k, when ranking the objects by distance. * * @author Erich Schubert + * @since 0.5.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/DistanceQuantileSampler.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/DistanceQuantileSampler.java index 5f0ae42a..fe7b98f0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/DistanceQuantileSampler.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/DistanceQuantileSampler.java @@ -58,6 +58,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * algorithms. * * @author Erich Schubert + * @since 0.7.0 * * @param <O> Object type */ @@ -164,6 +165,8 @@ public class DistanceQuantileSampler<O> extends AbstractDistanceBasedAlgorithm<O * @author Erich Schubert * * @param <O> Object type + * + * @apiviz.exclude */ public static class Parameterizer<O> extends AbstractDistanceBasedAlgorithm.Parameterizer<O> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/DistanceStatisticsWithClasses.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/DistanceStatisticsWithClasses.java index 4cc4a35c..bb3808b8 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/DistanceStatisticsWithClasses.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/DistanceStatisticsWithClasses.java @@ -73,6 +73,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * set. * * @author Erich Schubert + * @since 0.2 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/EstimateIntrinsicDimensionality.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/EstimateIntrinsicDimensionality.java index 8bc0cfe8..f78ff82c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/EstimateIntrinsicDimensionality.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/EstimateIntrinsicDimensionality.java @@ -55,6 +55,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Note: this algorithm does not produce a result, but only logs statistics. * * @author Erich Schubert + * @since 0.7.0 * * @param <O> Data type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/EvaluateRankingQuality.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/EvaluateRankingQuality.java index 27c9d1ed..8c1ff8e3 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/EvaluateRankingQuality.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/EvaluateRankingQuality.java @@ -82,6 +82,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * TODO: Add sampling * * @author Erich Schubert + * @since 0.2 * @param <V> Vector type */ @Title("Evaluate Ranking Quality") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/EvaluateRetrievalPerformance.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/EvaluateRetrievalPerformance.java index 6ca75b0c..ec70970a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/EvaluateRetrievalPerformance.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/EvaluateRetrievalPerformance.java @@ -64,6 +64,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * distance. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has RetrievalPerformanceResult * @apiviz.composedOf KNNEvaluator diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/HopkinsStatisticClusteringTendency.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/HopkinsStatisticClusteringTendency.java index 7ce4e428..e41b77df 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/HopkinsStatisticClusteringTendency.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/HopkinsStatisticClusteringTendency.java @@ -78,6 +78,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * * @author Lisa Reichert * @author Erich Schubert + * @since 0.7.0 */ // TODO: allow using more than one k @Reference(authors = "B. Hopkins and J. G. Skellam", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/RangeQuerySelectivity.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/RangeQuerySelectivity.java index 5fb7d785..cf6294d0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/RangeQuerySelectivity.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/RangeQuerySelectivity.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * TODO: Add sampling * * @author Erich Schubert + * @since 0.7.0 * @param <V> Vector type */ public class RangeQuerySelectivity<V extends NumberVector> extends AbstractDistanceBasedAlgorithm<V, Result> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/RankingQualityHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/RankingQualityHistogram.java index bfdf190a..d009628f 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/RankingQualityHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/statistics/RankingQualityHistogram.java @@ -65,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * TODO: Add sampling * * @author Erich Schubert + * @since 0.2 * @param <O> Object type */ @Title("Ranking Quality Histogram") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/AbstractApplication.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/AbstractApplication.java index 167b2991..f0ba3652 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/AbstractApplication.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/AbstractApplication.java @@ -30,7 +30,6 @@ import java.util.Properties; import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.logging.Logging.Level; import de.lmu.ifi.dbs.elki.logging.LoggingConfiguration; -import de.lmu.ifi.dbs.elki.logging.LoggingUtil; import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; import de.lmu.ifi.dbs.elki.utilities.FormatUtil; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; @@ -41,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionUtil; import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.UnspecifiedParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.SerializedParameterization; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.TrackParameters; @@ -59,6 +59,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.StringParameter; * * @author Elke Achtert * @author Erich Schubert + * @since 0.2 * * @apiviz.uses LoggingConfiguration oneway * @apiviz.excludeSubtypes @@ -152,7 +153,7 @@ public abstract class AbstractApplication { return; } if(debugP.isDefined()) { - LoggingUtil.parseDebugParameter(debugP); + Parameterizer.parseDebugParameter(debugP); } } catch(Exception e) { @@ -375,6 +376,40 @@ public abstract class AbstractApplication { } return null; } + + /** + * Parse the option string to configure logging. + * + * @param param Parameter to process. + * + * @throws WrongParameterValueException On parsing errors + */ + public static final void parseDebugParameter(StringParameter param) throws WrongParameterValueException { + String[] opts = param.getValue().split(","); + for(String opt : opts) { + try { + String[] chunks = opt.split("="); + if(chunks.length == 1) { + try { + java.util.logging.Level level = Level.parse(chunks[0]); + LoggingConfiguration.setDefaultLevel(level); + } + catch(IllegalArgumentException e) { + LoggingConfiguration.setLevelFor(chunks[0], Level.FINEST.getName()); + } + } + else if(chunks.length == 2) { + LoggingConfiguration.setLevelFor(chunks[0], chunks[1]); + } + else { + throw new WrongParameterValueException(param, param.getValue(), "More than one '=' in debug parameter."); + } + } + catch(IllegalArgumentException e) { + throw (new WrongParameterValueException(param, param.getValue(), "Could not process value.", e)); + } + } + } @Override protected abstract AbstractApplication makeInstance(); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/ClassifierHoldoutEvaluationTask.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/ClassifierHoldoutEvaluationTask.java index c49c42c5..91570cee 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/ClassifierHoldoutEvaluationTask.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/ClassifierHoldoutEvaluationTask.java @@ -83,6 +83,7 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * TODO: add support for predefined test and training pairs! * * @author Erich Schubert + * @since 0.7.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/ConvertToBundleApplication.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/ConvertToBundleApplication.java index ad7d17dc..55057b05 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/ConvertToBundleApplication.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/ConvertToBundleApplication.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Convert an input file to the more efficient ELKI bundle format. * * @author Erich Schubert + * @since 0.5.5 */ public class ConvertToBundleApplication extends AbstractApplication { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/ELKILauncher.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/ELKILauncher.java index 6d23d902..5830a601 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/ELKILauncher.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/ELKILauncher.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.ELKIServiceRegistry; * Class to launch ELKI. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.uses AbstractApplication */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/GeneratorXMLSpec.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/GeneratorXMLSpec.java index 45e97e9f..e6a1b18a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/GeneratorXMLSpec.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/GeneratorXMLSpec.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * Generate a data set based on a specified model (using an XML specification) * * @author Erich Schubert + * @since 0.2 * * @apiviz.composedOf GeneratorXMLDatabaseConnection */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/KDDCLIApplication.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/KDDCLIApplication.java index 7138d7f4..bd5740b5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/KDDCLIApplication.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/KDDCLIApplication.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.workflow.OutputStep; * {@link de.lmu.ifi.dbs.elki.datasource.DatabaseConnection DatabaseConnection}. * * @author Arthur Zimek + * @since 0.3 * * @apiviz.composedOf KDDTask */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceInOnDiskMatrix.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceInOnDiskMatrix.java index 56b1f377..6994cac9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceInOnDiskMatrix.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceInOnDiskMatrix.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.workflow.InputStep; * Precompute an on-disk distance matrix, using double precision. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has OnDiskUpperTriangleMatrix * @apiviz.has DistanceFunction diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceKNNLists.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceKNNLists.java index dc1df9e5..d6cfc429 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceKNNLists.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceKNNLists.java @@ -56,6 +56,7 @@ import de.lmu.ifi.dbs.elki.workflow.InputStep; * Precompute the k nearest neighbors in a disk cache. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has DistanceFunction * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceRangeQueries.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceRangeQueries.java index 4ccba594..6b42b27c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceRangeQueries.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceRangeQueries.java @@ -57,6 +57,7 @@ import de.lmu.ifi.dbs.elki.workflow.InputStep; * Precompute the k nearest neighbors in a disk cache. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has DistanceFunction * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheFloatDistanceInOnDiskMatrix.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheFloatDistanceInOnDiskMatrix.java index f9d7a2c2..a12b13cb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheFloatDistanceInOnDiskMatrix.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/cache/CacheFloatDistanceInOnDiskMatrix.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.workflow.InputStep; * Precompute an on-disk distance matrix, using float precision. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has OnDiskUpperTriangleMatrix * @apiviz.has DistanceFunction diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/experiments/EvaluateIntrinsicDimensionalityEstimators.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/experiments/EvaluateIntrinsicDimensionalityEstimators.java index 27784179..3dea86bc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/experiments/EvaluateIntrinsicDimensionalityEstimators.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/experiments/EvaluateIntrinsicDimensionalityEstimators.java @@ -55,6 +55,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * estimators. * * @author Erich Schubert + * @since 0.7.0 */ public class EvaluateIntrinsicDimensionalityEstimators extends AbstractApplication { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/geo/VisualizeGeodesicDistances.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/geo/VisualizeGeodesicDistances.java index 4ecbe8c3..76776eb0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/geo/VisualizeGeodesicDistances.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/geo/VisualizeGeodesicDistances.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Niels Dörre * @author Erich Schubert + * @since 0.5.5 */ public class VisualizeGeodesicDistances extends AbstractApplication { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/ComputeKNNOutlierScores.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/ComputeKNNOutlierScores.java index 934255b4..d89d535f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/ComputeKNNOutlierScores.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/ComputeKNNOutlierScores.java @@ -105,6 +105,7 @@ import de.lmu.ifi.dbs.elki.workflow.InputStep; * </p> * * @author Erich Schubert + * @since 0.5.0 * * @param <O> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/EvaluatePrecomputedOutlierScores.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/EvaluatePrecomputedOutlierScores.java index 94abafa1..0107dc64 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/EvaluatePrecomputedOutlierScores.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/EvaluatePrecomputedOutlierScores.java @@ -77,6 +77,7 @@ import de.lmu.ifi.dbs.elki.workflow.InputStep; * * @author Erich Schubert * @author Guilherme Oliveira Campos + * @since 0.7.0 */ public class EvaluatePrecomputedOutlierScores extends AbstractApplication { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/GreedyEnsembleExperiment.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/GreedyEnsembleExperiment.java index d36da97b..6a614f99 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/GreedyEnsembleExperiment.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/greedyensemble/GreedyEnsembleExperiment.java @@ -97,6 +97,7 @@ import de.lmu.ifi.dbs.elki.workflow.InputStep; * </p> * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "E. Schubert, R. Wojdanowski, A. Zimek, H.-P. Kriegel", // title = "On Evaluation of Outlier Rankings and Outlier Scores", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/CheckELKIServices.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/CheckELKIServices.java index e18bd633..b0e17e6d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/CheckELKIServices.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/CheckELKIServices.java @@ -58,6 +58,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * implementations. * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses ELKIServiceLoader */ @@ -243,6 +244,7 @@ public class CheckELKIServices { if(parts.length > 1) { StringBuilder buf = new StringBuilder(); buf.append("Class ").append(classname); + buf.append(" in ").append(parent.getCanonicalName()); buf.append(" has the following extraneous aliases:"); for(int i = 1; i < parts.length; i++) { buf.append(' ').append(parts[i]); @@ -261,6 +263,7 @@ public class CheckELKIServices { if(buf == null) { buf = new StringBuilder(); buf.append("Class ").append(classname); + buf.append(" in ").append(parent.getCanonicalName()); buf.append(" is missing the following aliases:"); } buf.append(' ').append(a); @@ -274,6 +277,7 @@ public class CheckELKIServices { buf.append('\n'); } buf.append("Class ").append(classname); + buf.append(" in ").append(parent.getCanonicalName()); buf.append(" has the following extraneous aliases:"); for(String a : aliases) { buf.append(' ').append(a); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/CheckParameterizables.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/CheckParameterizables.java index a278f287..4c106f83 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/CheckParameterizables.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/CheckParameterizables.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * interface. * * @author Erich Schubert + * @since 0.3 * * @apiviz.landmark * @apiviz.uses AbstractParameterizer diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentParameters.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentParameters.java index eea3dad6..8325872b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentParameters.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentParameters.java @@ -57,6 +57,7 @@ import de.lmu.ifi.dbs.elki.application.AbstractApplication; import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.logging.Logging.Level; import de.lmu.ifi.dbs.elki.logging.LoggingConfiguration; +import de.lmu.ifi.dbs.elki.math.random.RandomFactory; import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; import de.lmu.ifi.dbs.elki.utilities.ELKIServiceRegistry; import de.lmu.ifi.dbs.elki.utilities.ELKIServiceScanner; @@ -70,6 +71,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.UnParameter import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ClassListParameter; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ClassParameter; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; import de.lmu.ifi.dbs.elki.utilities.xml.HTMLUtil; @@ -78,6 +80,7 @@ import de.lmu.ifi.dbs.elki.utilities.xml.HTMLUtil; * {@link Parameter}s. Used in documentation generation only. * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses Parameter */ @@ -182,7 +185,7 @@ public class DocumentParameters { throw new RuntimeException(e); } try { - PrintStream byclassstream = new PrintStream(new BufferedOutputStream(byclassfo)); + PrintStream byclassstream = new PrintStream(new BufferedOutputStream(byclassfo), false, "UTF-8"); makeByClassOverviewWiki(byclass, new WikiStream(byclassstream)); byclassstream.flush(); byclassstream.close(); @@ -245,7 +248,9 @@ public class DocumentParameters { private static void buildParameterIndex(Map<Class<?>, List<Parameter<?>>> byclass, Map<OptionID, List<Pair<Parameter<?>, Class<?>>>> byopt) { final ArrayList<TrackedParameter> options = new ArrayList<>(); ExecutorService es = Executors.newSingleThreadExecutor(); - for(final Class<?> cls : ELKIServiceRegistry.findAllImplementations(Object.class, false, true)) { + List<Class<?>> objs = ELKIServiceRegistry.findAllImplementations(Object.class, false, true); + Collections.sort(objs, new ELKIServiceScanner.ClassSorter()); + for(final Class<?> cls : objs) { // Doesn't have a proper name? if(cls.getCanonicalName() == null) { continue; @@ -720,9 +725,18 @@ public class DocumentParameters { Element maindl = htmldoc.createElement(HTMLUtil.HTML_DL_TAG); body.appendChild(maindl); - List<OptionID> opts = new ArrayList<>(byopt.keySet()); - Collections.sort(opts, new SortByOption()); + final Comparator<OptionID> osort = new SortByOption(); + final Comparator<Class<?>> csort = new ELKIServiceScanner.ClassSorter(); + Comparator<Pair<Parameter<?>, Class<?>>> psort = new Comparator<Pair<Parameter<?>, Class<?>>>() { + @Override + public int compare(Pair<Parameter<?>, Class<?>> o1, Pair<Parameter<?>, Class<?>> o2) { + int c = osort.compare(o1.first.getOptionID(), o2.first.getOptionID()); + return (c != 0) ? c : csort.compare(o1.second, o2.second); + } + }; + List<OptionID> opts = new ArrayList<>(byopt.keySet()); + Collections.sort(opts, osort); for(OptionID oid : opts) { final Parameter<?> firstopt = byopt.get(oid).get(0).getFirst(); // DT = definition term @@ -787,7 +801,9 @@ public class DocumentParameters { optdd.appendChild(p); } optdd.appendChild(classesul); - for(Pair<Parameter<?>, Class<?>> clinst : byopt.get(oid)) { + List<Pair<Parameter<?>, Class<?>>> plist = byopt.get(oid); + Collections.sort(plist, psort); + for(Pair<Parameter<?>, Class<?>> clinst : plist) { // DT definition term: option name, in TT for typewriter optics Element classli = htmldoc.createElement(HTMLUtil.HTML_LI_TAG); @@ -1020,9 +1036,11 @@ public class DocumentParameters { if(par instanceof ClassParameter<?>) { appendDefaultClassLink(htmldoc, par, p); } + else if(par instanceof RandomParameter && par.getDefaultValue() == RandomFactory.DEFAULT) { + p.appendChild(htmldoc.createTextNode("use global random seed")); + } else { - Object def = par.getDefaultValue(); - p.appendChild(htmldoc.createTextNode(def.toString())); + p.appendChild(htmldoc.createTextNode(par.getDefaultValueAsString())); } optdd.appendChild(p); } @@ -1047,9 +1065,11 @@ public class DocumentParameters { final Class<?> name = ((ClassParameter<?>) par).getDefaultValue(); out.javadocLink(name, null); } + else if(par instanceof RandomParameter && par.getDefaultValue() == RandomFactory.DEFAULT) { + out.print("use global random seed"); + } else { - Object def = par.getDefaultValue(); - out.print(def.toString()); + out.print(par.getDefaultValueAsString()); } out.println(); } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentReferences.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentReferences.java index 7d448fca..66f2bda8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentReferences.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentReferences.java @@ -60,6 +60,7 @@ import de.lmu.ifi.dbs.elki.utilities.xml.HTMLUtil; * Build a reference documentation for all available parameters. * * @author Erich Schubert + * @since 0.3 * * @apiviz.uses Reference */ @@ -105,7 +106,7 @@ public class DocumentReferences { try { File refwiki = new File(args[1]); FileOutputStream reffow = new FileOutputStream(refwiki); - PrintStream refstreamW = new PrintStream(reffow); + PrintStream refstreamW = new PrintStream(reffow, false, "UTF-8"); documentReferencesWiki(refs, refstreamW); refstreamW.flush(); refstreamW.close(); @@ -330,7 +331,28 @@ public class DocumentReferences { @Override public int compare(Pair<Reference, TreeSet<Object>> p1, Pair<Reference, TreeSet<Object>> p2) { final Object o1 = p1.second.first(), o2 = p2.second.first(); - return COMPARATOR.compare(o1, o2); + int c = COMPARATOR.compare(o1, o2); + if(c == 0) { + Reference r1 = p1.first, r2 = p2.first; + c = compareNull(r1.title(), r2.title()); + c = (c != 0) ? c : compareNull(r1.authors(), r2.authors()); + c = (c != 0) ? c : compareNull(r1.booktitle(), r2.booktitle()); + } + return c; + } + + /** + * Null-tolerant String comparison. + * + * @param s1 First string + * @param s2 Second string + * @return Order + */ + private int compareNull(String s1, String s2) { + return (s1 == s2) ? 0 // + : (s1 == null) ? -1 // + : (s2 == null) ? +1 // + : s1.compareTo(s2); } }); return refs; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/jsmap/JSONBuffer.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/jsmap/JSONBuffer.java index 740f3856..418771c2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/jsmap/JSONBuffer.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/jsmap/JSONBuffer.java @@ -29,6 +29,7 @@ import java.util.Stack; * Helper class to produce JSON output. Try hard to ensure validity of the output. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf StringBuilder * @apiviz.has JSONBuffer.JSONException diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/jsmap/JSONResultHandler.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/jsmap/JSONResultHandler.java index 316c7950..14c0b77f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/jsmap/JSONResultHandler.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/jsmap/JSONResultHandler.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * Handle results by serving them via a web server to mapping applications. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf JSONWebServer */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/jsmap/JSONWebServer.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/jsmap/JSONWebServer.java index e133e3ab..6e216e81 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/jsmap/JSONWebServer.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/jsmap/JSONWebServer.java @@ -61,6 +61,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * A simple web server to serve data base contents to a JavaScript client. * * @author Erich Schubert + * @since 0.4.0 * * TODO: use Jetty or something similar on the long run. * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/AbstractNumberVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/AbstractNumberVector.java index cffa3de9..4a228c0e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/AbstractNumberVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/AbstractNumberVector.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayLikeUtil; * AbstractNumberVector is an abstract implementation of FeatureVector. * * @author Arthur Zimek + * @since 0.2 */ public abstract class AbstractNumberVector implements NumberVector { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Bit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Bit.java index 46e85cac..13a39e37 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Bit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Bit.java @@ -29,6 +29,7 @@ import java.util.regex.Pattern; * A boolean number type. * * @author Arthur Zimek + * @since 0.2 */ public class Bit extends Number { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/BitVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/BitVector.java index 914bd5cc..ef6deeac 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/BitVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/BitVector.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Vector using a dense bit set encoding, based on {@code long[]} storage. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.composedOf Bit */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ByteVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ByteVector.java index c5e296c6..a77733b1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ByteVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ByteVector.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Vector using {@code byte[]} storage. * * @author Erich Schubert + * @since 0.2 */ public class ByteVector extends AbstractNumberVector { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ClassLabel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ClassLabel.java index 03d4743c..7bc2f257 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ClassLabel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ClassLabel.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.data.type.SimpleTypeInformation; * other classes by a classifier. * * @author Arthur Zimek + * @since 0.2 */ public abstract class ClassLabel implements Comparable<ClassLabel> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Cluster.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Cluster.java index fd2d1f68..6cd1a286 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Cluster.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Cluster.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; * @param <M> Model object type * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Clustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Clustering.java index 928ca7e3..f61bf17b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Clustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Clustering.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.hierarchy.ModifiableHierarch * or getAllClusters(). * * @author Erich Schubert + * @since 0.2 * * @apiviz.composedOf Cluster oneway - n * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/DoubleVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/DoubleVector.java index 7c8a7dbc..3824dfbb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/DoubleVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/DoubleVector.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Vector type using {@code double[]} storage for real numbers. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ExternalID.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ExternalID.java index 9b5fbd94..e8912070 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ExternalID.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ExternalID.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.data; * External ID objects. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf String */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/FeatureVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/FeatureVector.java index e3a74300..e4dc4808 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/FeatureVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/FeatureVector.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; * actually store numerical features. * * @author Erich Schubert + * @since 0.2 */ public interface FeatureVector<D> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/FloatVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/FloatVector.java index 657102c7..4cc3ca21 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/FloatVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/FloatVector.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * much memory as {@link DoubleVector}. * * @author Elke Achtert + * @since 0.2 */ public class FloatVector extends AbstractNumberVector { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/HierarchicalClassLabel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/HierarchicalClassLabel.java index 8c911a0f..79640642 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/HierarchicalClassLabel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/HierarchicalClassLabel.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.data.type.SimpleTypeInformation; * of classes. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.composedOf Comparable */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/HyperBoundingBox.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/HyperBoundingBox.java index 903249ca..33de8fd1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/HyperBoundingBox.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/HyperBoundingBox.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.FormatUtil; * HyperBoundingBox represents a hyperrectangle in the multidimensional space. * * @author Elke Achtert + * @since 0.2 */ public class HyperBoundingBox implements SpatialComparable, Externalizable { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/IntegerVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/IntegerVector.java index 5d724171..e91b0bd1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/IntegerVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/IntegerVector.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Vector type using {@code int[]} storage. * * @author Erich Schubert + * @since 0.2 */ public class IntegerVector extends AbstractNumberVector { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/LabelList.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/LabelList.java index 6b5850da..72ec61fe 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/LabelList.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/LabelList.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; * A list of string labels. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf String */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ModifiableHyperBoundingBox.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ModifiableHyperBoundingBox.java index d9a2d1c9..a117c6f4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ModifiableHyperBoundingBox.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ModifiableHyperBoundingBox.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.logging.LoggingConfiguration; * MBR class allowing modifications (as opposed to {@link HyperBoundingBox}). * * @author Marisa Thoma + * @since 0.3 */ public class ModifiableHyperBoundingBox extends HyperBoundingBox { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/NumberVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/NumberVector.java index 60a0036e..a946285b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/NumberVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/NumberVector.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * Object that is element of a real vector space of type N. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.landmark * @apiviz.has Vector diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/OneDimensionalDoubleVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/OneDimensionalDoubleVector.java index d50bcc85..5c044a0f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/OneDimensionalDoubleVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/OneDimensionalDoubleVector.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * as we want to implement the interface. * * @author Erich Schubert + * @since 0.4.0 */ public class OneDimensionalDoubleVector extends AbstractNumberVector { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ShortVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ShortVector.java index 02711118..9d275842 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ShortVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/ShortVector.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Vector type using {@code short[]} storage. * * @author Erich Schubert + * @since 0.2 */ public class ShortVector extends AbstractNumberVector { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SimpleClassLabel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SimpleClassLabel.java index 13ccc4a7..56df7df6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SimpleClassLabel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SimpleClassLabel.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; * A simple class label casting a String as it is as label. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.composedOf String */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseByteVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseByteVector.java index 53ebc1e2..dc97e6c6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseByteVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseByteVector.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * value (limited to -128..+127). * * @author Arthur Zimek + * @since 0.2 */ public class SparseByteVector extends AbstractNumberVector implements SparseNumberVector { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseDoubleVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseDoubleVector.java index 358763d7..44158a88 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseDoubleVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseDoubleVector.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * value. * * @author Arthur Zimek + * @since 0.2 */ public class SparseDoubleVector extends AbstractNumberVector implements SparseNumberVector { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseFeatureVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseFeatureVector.java index b0eee337..ba82b56f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseFeatureVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseFeatureVector.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.data; * Extended interface for sparse feature vector types. * * @author Erich Schubert + * @since 0.4.0 * */ public interface SparseFeatureVector<D> extends FeatureVector<D> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseFloatVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseFloatVector.java index 90613041..108210ce 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseFloatVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseFloatVector.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * value. * * @author Arthur Zimek + * @since 0.2 */ public class SparseFloatVector extends AbstractNumberVector implements SparseNumberVector { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseIntegerVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseIntegerVector.java index cb2ee455..aa561714 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseIntegerVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseIntegerVector.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * integer value. * * @author Arthur Zimek + * @since 0.2 */ public class SparseIntegerVector extends AbstractNumberVector implements SparseNumberVector { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseNumberVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseNumberVector.java index bbacaba0..f3252f24 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseNumberVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseNumberVector.java @@ -29,6 +29,7 @@ import gnu.trove.map.TIntDoubleMap; * Combines the SparseFeatureVector and NumberVector. * * @author Erich Schubert + * @since 0.4.0 */ public interface SparseNumberVector extends NumberVector, SparseFeatureVector<Number> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseShortVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseShortVector.java index 17624a6b..1864788e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseShortVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/SparseShortVector.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * value. * * @author Arthur Zimek + * @since 0.2 */ public class SparseShortVector extends AbstractNumberVector implements SparseNumberVector { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Subspace.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Subspace.java index 96d86a41..c18d9bb3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Subspace.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/Subspace.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * Represents a subspace of the original data space. * * @author Elke Achtert + * @since 0.2 * * @apiviz.owns de.lmu.ifi.dbs.elki.data.Subspace.DimensionComparator */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/VectorUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/VectorUtil.java index 2e42b498..5959d64c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/VectorUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/VectorUtil.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.QuickSelect; * Note: obviously, many functions are class methods or database related. * * @author Erich Schubert + * @since 0.3 * * @apiviz.uses NumberVector */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/AbstractModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/AbstractModel.java index 7d825480..db1c52c4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/AbstractModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/AbstractModel.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; * Abstract base class for Cluster Models. * * @author Erich Schubert + * @since 0.2 */ public abstract class AbstractModel implements Model { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/BiclusterModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/BiclusterModel.java index 81b3f5bf..53b49d2e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/BiclusterModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/BiclusterModel.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.data.model; * Wrapper class to provide the basic properties of a Bicluster. * * @author Arthur Zimek + * @since 0.2 */ public class BiclusterModel implements Model { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/BiclusterWithInversionsModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/BiclusterWithInversionsModel.java index bc6ae177..721b9ffe 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/BiclusterWithInversionsModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/BiclusterWithInversionsModel.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * have inverted rows. * * @author Erich Schubert + * @since 0.3 */ public class BiclusterWithInversionsModel extends BiclusterModel { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/ClusterModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/ClusterModel.java index 5081c9b5..26fb91ee 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/ClusterModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/ClusterModel.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.data.model; * static {@link #CLUSTER} object. * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CoreObjectsModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CoreObjectsModel.java index cc99f84d..7d476382 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CoreObjectsModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CoreObjectsModel.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; * DBSCAN implementation when the {@code -gdbscan.core-model} flag is set. * * @author Erich Schubert + * @since 0.3 */ public class CoreObjectsModel extends AbstractModel implements TextWriteable { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CorrelationAnalysisSolution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CorrelationAnalysisSolution.java index 7a0b4901..d2408775 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CorrelationAnalysisSolution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CorrelationAnalysisSolution.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; * dependencies. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.composedOf LinearEquationSystem * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CorrelationModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CorrelationModel.java index 9b6dfcde..1e638497 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CorrelationModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CorrelationModel.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.FormatUtil; * Cluster model using a filtered PCA result and an centroid. * * @author Erich Schubert + * @since 0.2 * * @apiviz.composedOf PCAFilteredResult * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/DendrogramModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/DendrogramModel.java index 1a339677..e129b4f3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/DendrogramModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/DendrogramModel.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; * Model for dendrograms, provides the distance to the child cluster. * * @author Elke Achtert + * @since 0.4.0 */ // TODO: comments public class DendrogramModel extends AbstractModel { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/DimensionModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/DimensionModel.java index e867fede..5b8a978f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/DimensionModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/DimensionModel.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; * Cluster model just providing a cluster dimensionality. * * @author Erich Schubert + * @since 0.2 */ public class DimensionModel extends AbstractModel implements TextWriteable { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/EMModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/EMModel.java index eabffce7..1b91e405 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/EMModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/EMModel.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; * Matrix. * * @author Erich Schubert + * @since 0.2 */ public class EMModel extends MeanModel { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/KMeansModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/KMeansModel.java index eef678cc..3bcb24c2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/KMeansModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/KMeansModel.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * produced by k-means (so the Voronoi cell visualization is sensible). * * @author Erich Schubert + * @since 0.2 */ public class KMeansModel extends MeanModel { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/LinearEquationModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/LinearEquationModel.java index 0c6f9871..afa56261 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/LinearEquationModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/LinearEquationModel.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; * Cluster model containing a linear equation system for the cluster. * * @author Erich Schubert + * @since 0.2 * * @apiviz.composedOf LinearEquationSystem */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/MeanModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/MeanModel.java index 7a5c71b9..350a8678 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/MeanModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/MeanModel.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriteable; * Cluster model that stores a mean for the cluster. * * @author Erich Schubert + * @since 0.3 */ public class MeanModel extends PrototypeModel<Vector> implements TextWriteable { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/MedoidModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/MedoidModel.java index 1654490a..add3fe2b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/MedoidModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/MedoidModel.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriteable; * Cluster model that stores a mean for the cluster. * * @author Erich Schubert + * @since 0.3 */ public class MedoidModel extends PrototypeModel<DBID> implements TextWriteable { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/Model.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/Model.java index d30eddfd..369688e1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/Model.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/Model.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.data.model; * Base interface for Model classes. * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/ModelUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/ModelUtil.java index 16b6ca27..891bc733 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/ModelUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/ModelUtil.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayLikeUtil; * Utility classes for dealing with cluster models. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.uses Model * @apiviz.uses NumberVector diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/OPTICSModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/OPTICSModel.java index 96e56f2e..02b21a30 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/OPTICSModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/OPTICSModel.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.data.model; * Model for an OPTICS cluster * * @author Erich Schubert + * @since 0.4.0 */ public class OPTICSModel extends AbstractModel { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/PrototypeModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/PrototypeModel.java index d8f836fa..8ce14e0d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/PrototypeModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/PrototypeModel.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; * Cluster model that stores a prototype for each cluster. * * @author Erich Schubert + * @since 0.3 */ public class PrototypeModel<V> extends AbstractModel implements TextWriteable { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/SubspaceModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/SubspaceModel.java index 38064c8f..bfc30205 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/SubspaceModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/SubspaceModel.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; * * @author Erich Schubert * @author Elke Achtert + * @since 0.3 * * @apiviz.composedOf Subspace */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/FeatureSelection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/FeatureSelection.java index d3c0abfe..eab1f1ea 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/FeatureSelection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/FeatureSelection.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntListParameter; * Projection class for number vectors. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.uses FeatureVector * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/LatLngToECEFProjection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/LatLngToECEFProjection.java index 3b63e257..5549dd26 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/LatLngToECEFProjection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/LatLngToECEFProjection.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * coordinates to ECEF (earth-centered earth-fixed). * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf EarthModel * @apiviz.uses NumberVector diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/LngLatToECEFProjection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/LngLatToECEFProjection.java index 56316949..22448c73 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/LngLatToECEFProjection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/LngLatToECEFProjection.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * coordinates to ECEF (earth-centered earth-fixed). * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf EarthModel * @apiviz.uses NumberVector diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/NumericalFeatureSelection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/NumericalFeatureSelection.java index caeb9de9..77cf5e47 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/NumericalFeatureSelection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/NumericalFeatureSelection.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntListParameter; * Projection class for number vectors. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.uses NumberVector * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/Projection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/Projection.java index aa057fe0..b88c4bb6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/Projection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/Projection.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.data.type.TypeInformation; * Projection interface. * * @author Erich Schubert + * @since 0.4.0 * * @param <IN> Input data type * @param <OUT> Output data type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/RandomProjection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/RandomProjection.java index 6318ce10..04fe210f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/RandomProjection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/projection/RandomProjection.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * suggested for locality sensitive hashing (LSH). * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses NumberVector * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/Polygon.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/Polygon.java index b574645c..cd58ed8d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/Polygon.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/Polygon.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.ArrayListIter; * polygons are simple. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf Vector */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/PolygonsObject.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/PolygonsObject.java index 98aae9cf..fdee5f60 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/PolygonsObject.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/PolygonsObject.java @@ -31,6 +31,7 @@ import java.util.Iterator; * Object representation consisting of (multiple) polygons. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has Polygon */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialComparable.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialComparable.java index 999c24a1..4d605472 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialComparable.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialComparable.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.data.spatial; * Defines the required methods needed for comparison of spatial objects. * * @author Elke Achtert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialSingleMaxComparator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialSingleMaxComparator.java index c773cde6..04e6d351 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialSingleMaxComparator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialSingleMaxComparator.java @@ -29,6 +29,7 @@ import java.util.Comparator; * dimension. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses SpatialComparable */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialSingleMeanComparator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialSingleMeanComparator.java index 2992d901..5b7b14ac 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialSingleMeanComparator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialSingleMeanComparator.java @@ -29,6 +29,7 @@ import java.util.Comparator; * dimension. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses SpatialComparable */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialSingleMinComparator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialSingleMinComparator.java index 2bf1f0e5..6ae90d64 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialSingleMinComparator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialSingleMinComparator.java @@ -29,6 +29,7 @@ import java.util.Comparator; * dimension. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses SpatialComparable */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialUtil.java index 59d1c282..864ef7fc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialUtil.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayAdapter; * Utility class with spatial functions. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorInterface.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorInterface.java index f7521c67..1b3175d1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorInterface.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorInterface.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.UnableToComplyException; * Interface for cluster generators * * @author Erich Schubert + * @since 0.2 */ public interface GeneratorInterface { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorInterfaceDynamic.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorInterfaceDynamic.java index 4898319a..1a9ed0f0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorInterfaceDynamic.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorInterfaceDynamic.java @@ -30,6 +30,7 @@ package de.lmu.ifi.dbs.elki.data.synthetic.bymodel; * and the generation of additional new points. * * @author Erich Schubert + * @since 0.2 */ public interface GeneratorInterfaceDynamic extends GeneratorInterface { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorMain.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorMain.java index 9db74eb7..ad5c6e67 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorMain.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorMain.java @@ -65,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.UnableToComplyException; * be as expected. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has GeneratorInterface */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorSingleCluster.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorSingleCluster.java index 850cfbcc..b4add21d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorSingleCluster.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorSingleCluster.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.UnableToComplyException; * according to the same model) * * @author Erich Schubert + * @since 0.2 * * @apiviz.composedOf Distribution * @apiviz.composedOf AffineTransformation diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorStatic.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorStatic.java index 9b25c7fb..8cf4b241 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorStatic.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/synthetic/bymodel/GeneratorStatic.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * that will return only a given set of points. * * @author Erich Schubert + * @since 0.2 */ public class GeneratorStatic implements GeneratorInterface { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/AlternativeTypeInformation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/AlternativeTypeInformation.java index 7bad02cb..14083bac 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/AlternativeTypeInformation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/AlternativeTypeInformation.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.data.type; * operator. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf TypeInformation */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/CombinedTypeInformation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/CombinedTypeInformation.java index 839b65d7..7af7532e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/CombinedTypeInformation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/CombinedTypeInformation.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.data.type; * Class that combines multiple type restrictions into one using an "and" operator. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf TypeInformation */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/FieldTypeInformation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/FieldTypeInformation.java index 00ce847b..b0375996 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/FieldTypeInformation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/FieldTypeInformation.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.data.type; * TODO: implement polygon and rectangle types! * * @author Erich Schubert + * @since 0.6.0 */ public interface FieldTypeInformation extends TypeInformation { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/MultivariateSeriesTypeInformation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/MultivariateSeriesTypeInformation.java index 72c017c5..16372da1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/MultivariateSeriesTypeInformation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/MultivariateSeriesTypeInformation.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; * Type information for multi-variate time series. * * @author Sebastian Hollizeck + * @since 0.7.0 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/NoSupportedDataTypeException.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/NoSupportedDataTypeException.java index 9ab4141e..1e899f5f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/NoSupportedDataTypeException.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/NoSupportedDataTypeException.java @@ -29,6 +29,7 @@ import java.util.Collection; * Exception thrown when no supported data type was found. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses TypeInformation oneway - - */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/SimpleTypeInformation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/SimpleTypeInformation.java index 36633198..4ff6fbae 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/SimpleTypeInformation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/SimpleTypeInformation.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; * Class wrapping a particular data type. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf ByteBufferSerializer * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/TypeInformation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/TypeInformation.java index dfbc74e4..bb1fbd08 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/TypeInformation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/TypeInformation.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.data.type; * Class wrapping a particular data type. * * @author Erich Schubert + * @since 0.4.0 */ public interface TypeInformation { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/TypeInformationSerializer.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/TypeInformationSerializer.java index 9a8d74ae..c9661419 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/TypeInformationSerializer.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/TypeInformationSerializer.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; * possible. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.composedOf SimpleTypeSerializer * @apiviz.composedOf VectorTypeSerializer diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/TypeUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/TypeUtil.java index 85c0abf7..4a6eb8d7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/TypeUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/TypeUtil.java @@ -53,6 +53,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteArrayUtil; * Utility package containing various common types. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has TypeInformation oneway - - * @apiviz.landmark diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/VectorFieldTypeInformation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/VectorFieldTypeInformation.java index e6526c61..efcb8dd7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/VectorFieldTypeInformation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/VectorFieldTypeInformation.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; * Type information to specify that a type has a fixed dimensionality. * * @author Erich Schubert + * @since 0.4.0 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/VectorTypeInformation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/VectorTypeInformation.java index c193a3fd..12276165 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/VectorTypeInformation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/type/VectorTypeInformation.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; * Construct a type information for vector spaces with fixed dimensionality. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has FeatureVector * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/AbstractUncertainObject.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/AbstractUncertainObject.java index ed5bab03..766740f9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/AbstractUncertainObject.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/AbstractUncertainObject.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.data.spatial.SpatialComparable; * * @author Alexander Koos * @author Erich Schubert + * @since 0.7.0 */ public abstract class AbstractUncertainObject implements UncertainObject { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/DiscreteUncertainObject.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/DiscreteUncertainObject.java index 5d7cfc22..c29ab470 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/DiscreteUncertainObject.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/DiscreteUncertainObject.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.data.DoubleVector; * (possibly weighted) number of samples. * * @author Erich Schubert + * @since 0.7.0 */ public interface DiscreteUncertainObject extends UncertainObject { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/SimpleGaussianContinuousUncertainObject.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/SimpleGaussianContinuousUncertainObject.java index d3958f36..bf60cd39 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/SimpleGaussianContinuousUncertainObject.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/SimpleGaussianContinuousUncertainObject.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; * TODO: currently, only a 3 sigma bounding box is supported. * * @author Erich Schubert + * @since 0.7.0 */ public class SimpleGaussianContinuousUncertainObject extends AbstractUncertainObject { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/UncertainObject.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/UncertainObject.java index ea1dfa3d..a96452b6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/UncertainObject.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/UncertainObject.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.data.spatial.SpatialComparable; * TODO: Eventually allow float precision, too. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has DoubleVector oneway - «contains/produces» */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/UniformContinuousUncertainObject.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/UniformContinuousUncertainObject.java index 7c236f70..868a745c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/UniformContinuousUncertainObject.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/UniformContinuousUncertainObject.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; * * @author Alexander Koos * @author Erich Schubert + * @since 0.7.0 */ public class UniformContinuousUncertainObject extends AbstractUncertainObject { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/UnweightedDiscreteUncertainObject.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/UnweightedDiscreteUncertainObject.java index 877361fa..6b527e4e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/UnweightedDiscreteUncertainObject.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/UnweightedDiscreteUncertainObject.java @@ -57,6 +57,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; * * @author Alexander Koos * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "N. Dalvi, C. Ré, D. Suciu", // title = "Probabilistic databases: diamonds in the dirt", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/WeightedDiscreteUncertainObject.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/WeightedDiscreteUncertainObject.java index 0b08dcbc..8657720f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/WeightedDiscreteUncertainObject.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/WeightedDiscreteUncertainObject.java @@ -73,6 +73,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; * * @author Alexander Koos * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "O. Benjelloun, A. D. Sarma, A. Halevy, J. Widom", // title = "ULDBs: Databases with uncertainty and lineage", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/AbstractDiscreteUncertainifier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/AbstractDiscreteUncertainifier.java index 4ee534cc..190ccc6a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/AbstractDiscreteUncertainifier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/AbstractDiscreteUncertainifier.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Factory class for discrete uncertain objects. * * @author Erich Schubert + * @since 0.7.0 * * @param <UO> Uncertain object type. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/SimpleGaussianUncertainifier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/SimpleGaussianUncertainifier.java index 0e7c01df..0056d687 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/SimpleGaussianUncertainifier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/SimpleGaussianUncertainifier.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; * Vector factory * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has SimpleGaussianContinuousUncertainObject */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/Uncertainifier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/Uncertainifier.java index 02a7b537..6bd584e4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/Uncertainifier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/Uncertainifier.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; * Class to derive uncertain object from exact vectors. * * @author Erich Schubert + * @since 0.7.0 * * @param <UO> Object type * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/UniformUncertainifier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/UniformUncertainifier.java index 96153685..3e141b05 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/UniformUncertainifier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/UniformUncertainifier.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; * Factory class. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has UniformContinuousUncertainObject */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/UnweightedDiscreteUncertainifier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/UnweightedDiscreteUncertainifier.java index 632c58f9..17c3d812 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/UnweightedDiscreteUncertainifier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/UnweightedDiscreteUncertainifier.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * {@link SimpleGaussianUncertainifier}). * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has UnweightedDiscreteUncertainObject */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/WeightedDiscreteUncertainifier.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/WeightedDiscreteUncertainifier.java index fb63a992..3b499de4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/WeightedDiscreteUncertainifier.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/data/uncertain/uncertainifier/WeightedDiscreteUncertainifier.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * {@link SimpleGaussianUncertainifier}). * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has WeightedDiscreteUncertainObject */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/AbstractDatabase.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/AbstractDatabase.java index 0c038369..b9424041 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/AbstractDatabase.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/AbstractDatabase.java @@ -56,6 +56,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; * <tt>-enableDebug de.lmu.ifi.dbs.elki.database=FINEST</tt> * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf DatabaseEventManager * @apiviz.has IndexFactory diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/Database.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/Database.java index d553da17..4a008919 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/Database.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/Database.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.result.HierarchicalResult; * parameters for dynamic instantiation. * * @author Elke Achtert + * @since 0.2 * * @apiviz.landmark * @apiviz.has DistanceQuery oneway - - provides diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/DatabaseEventManager.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/DatabaseEventManager.java index 3ddba18e..5251366c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/DatabaseEventManager.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/DatabaseEventManager.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.result.ResultListener; * Class to manage database events such as insertions and removals. * * @author Elke Achtert + * @since 0.4.0 * @apiviz.has ResultListener */ public class DatabaseEventManager { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/HashmapDatabase.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/HashmapDatabase.java index 90fd55ea..56ec0706 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/HashmapDatabase.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/HashmapDatabase.java @@ -60,6 +60,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Arthur Zimek * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * @apiviz.composedOf HashSetModifiableDBIDs diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ProxyDatabase.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ProxyDatabase.java index eb8dd05b..5c635f96 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ProxyDatabase.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ProxyDatabase.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * A proxy database to use e.g. for projections and partitions. * * @author Erich Schubert + * @since 0.4.0 */ public class ProxyDatabase extends AbstractDatabase { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/QueryUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/QueryUtil.java index 26262575..a3bfd071 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/QueryUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/QueryUtil.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.distance.similarityfunction.SimilarityFunction; * Static class with utilities related to querying a database. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/StaticArrayDatabase.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/StaticArrayDatabase.java index da13c5fa..cc889e6f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/StaticArrayDatabase.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/StaticArrayDatabase.java @@ -55,6 +55,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Arthur Zimek * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * @apiviz.composedOf ArrayStaticDBIDs diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/UpdatableDatabase.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/UpdatableDatabase.java index 45f7ad78..48333aab 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/UpdatableDatabase.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/UpdatableDatabase.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.UnableToComplyException; * that cannot be done in dynamic databases. * * @author Erich Schubert + * @since 0.4.0 */ public interface UpdatableDatabase extends Database { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DBIDDataStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DBIDDataStore.java index b79be1f4..8d9d08c8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DBIDDataStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DBIDDataStore.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDVar; * DBID-valued data store (avoids boxing/unboxing). * * @author Erich Schubert + * @since 0.4.0 */ public interface DBIDDataStore extends DataStore<DBID> { /** @@ -40,7 +41,7 @@ public interface DBIDDataStore extends DataStore<DBID> { */ @Override @Deprecated - public DBID get(DBIDRef id); + DBID get(DBIDRef id); /** * Retrieves an object from the storage. @@ -49,5 +50,5 @@ public interface DBIDDataStore extends DataStore<DBID> { * @param var Variable to update. * @return {@code var} */ - public DBIDVar assignVar(DBIDRef id, DBIDVar var); + DBIDVar assignVar(DBIDRef id, DBIDVar var); } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStore.java index 2c306486..e78fc591 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStore.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.result.Result; * Generic storage interface for objects indexed by {@link DBID}. * * @author Erich Schubert + * @since 0.4.0 * * @param <T> Data type */ @@ -41,5 +42,5 @@ public interface DataStore<T> extends Result { * @param id Database ID. * @return Object or {@code null} */ - public T get(DBIDRef id); + T get(DBIDRef id); }
\ No newline at end of file diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreEvent.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreEvent.java index 294a3a19..79afd440 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreEvent.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreEvent.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * {@link DataStoreListener} of the change. * * @author Erich Schubert + * @since 0.4.0 * * @see DataStore * @see DataStoreListener diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreFactory.java index 63a12693..17c3221b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreFactory.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * Use {@link #FACTORY} for a static instance. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory,interface * @apiviz.has WritableDataStore oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreIDMap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreIDMap.java index 70e0a3f6..c9501dd6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreIDMap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreIDMap.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * Interface to map DBIDs to integer record ids for use in storage. * * @author Erich Schubert + * @since 0.4.0 */ public interface DataStoreIDMap { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreListener.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreListener.java index 60a1bc16..edf37bf9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreListener.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreListener.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.database.datastore; * {@link DataStore}. * * @author Elke Achtert + * @since 0.4.0 * * @apiviz.uses DataStoreEvent oneway - - listens * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreUtil.java index 5602e0d7..7976759b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DataStoreUtil.java @@ -26,14 +26,16 @@ package de.lmu.ifi.dbs.elki.database.datastore; import java.util.Comparator; import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; +import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; import de.lmu.ifi.dbs.elki.database.ids.DBIDs; /** * Storage utility class. Mostly a shorthand for * {@link DataStoreFactory#FACTORY}. - * + * * @author Erich Schubert - * + * @since 0.4.0 + * * @apiviz.landmark * @apiviz.composedOf de.lmu.ifi.dbs.elki.database.datastore.DataStoreFactory */ @@ -41,7 +43,7 @@ public final class DataStoreUtil { /** * Make a new storage, to associate the given ids with an object of class * dataclass. - * + * * @param <T> stored data type * @param ids DBIDs to store data for * @param hints Hints for the storage manager @@ -55,7 +57,7 @@ public final class DataStoreUtil { /** * Make a new storage, to associate the given ids with an object of class * dataclass. - * + * * @param ids DBIDs to store data for * @param hints Hints for the storage manager * @return new data store @@ -67,7 +69,7 @@ public final class DataStoreUtil { /** * Make a new storage, to associate the given ids with an object of class * dataclass. - * + * * @param ids DBIDs to store data for * @param hints Hints for the storage manager * @return new data store @@ -79,7 +81,7 @@ public final class DataStoreUtil { /** * Make a new storage, to associate the given ids with an object of class * dataclass. - * + * * @param ids DBIDs to store data for * @param hints Hints for the storage manager * @param def Default value @@ -92,7 +94,7 @@ public final class DataStoreUtil { /** * Make a new storage, to associate the given ids with an object of class * dataclass. - * + * * @param ids DBIDs to store data for * @param hints Hints for the storage manager * @return new data store @@ -104,7 +106,7 @@ public final class DataStoreUtil { /** * Make a new storage, to associate the given ids with an object of class * dataclass. - * + * * @param ids DBIDs to store data for * @param hints Hints for the storage manager * @param def Default value @@ -117,7 +119,7 @@ public final class DataStoreUtil { /** * Make a new record storage, to associate the given ids with an object of * class dataclass. - * + * * @param ids DBIDs to store data for * @param hints Hints for the storage manager * @param dataclasses classes to store @@ -129,9 +131,9 @@ public final class DataStoreUtil { /** * Sort objects by a double relation - * + * * @author Erich Schubert - * + * * @apiviz.exclude */ public static class AscendingByDoubleDataStore implements Comparator<DBIDRef> { @@ -139,7 +141,7 @@ public final class DataStoreUtil { * Scores to use for sorting. */ private final DoubleDataStore scores; - + /** * Constructor. * @@ -158,9 +160,9 @@ public final class DataStoreUtil { /** * Sort objects by a double relation - * + * * @author Erich Schubert - * + * * @apiviz.exclude */ public static class DescendingByDoubleDataStore implements Comparator<DBIDRef> { @@ -168,7 +170,7 @@ public final class DataStoreUtil { * Scores to use for sorting. */ private final DoubleDataStore scores; - + /** * Constructor. * @@ -184,4 +186,64 @@ public final class DataStoreUtil { return Double.compare(scores.doubleValue(id2), scores.doubleValue(id1)); } } + + /** + * Sort objects by a double relation + * + * @author Erich Schubert + * + * @apiviz.exclude + */ + public static class AscendingByDoubleDataStoreAndId implements Comparator<DBIDRef> { + /** + * Scores to use for sorting. + */ + private final DoubleDataStore scores; + + /** + * Constructor. + * + * @param scores Scores for sorting + */ + public AscendingByDoubleDataStoreAndId(DoubleDataStore scores) { + super(); + this.scores = scores; + } + + @Override + public int compare(DBIDRef id1, DBIDRef id2) { + int c = Double.compare(scores.doubleValue(id1), scores.doubleValue(id2)); + return c != 0 ? c : DBIDUtil.compare(id1, id2); + } + } + + /** + * Sort objects by a double relation + * + * @author Erich Schubert + * + * @apiviz.exclude + */ + public static class DescendingByDoubleDataStoreAndId implements Comparator<DBIDRef> { + /** + * Scores to use for sorting. + */ + private final DoubleDataStore scores; + + /** + * Constructor. + * + * @param scores Scores for sorting + */ + public DescendingByDoubleDataStoreAndId(DoubleDataStore scores) { + super(); + this.scores = scores; + } + + @Override + public int compare(DBIDRef id1, DBIDRef id2) { + int c = Double.compare(scores.doubleValue(id2), scores.doubleValue(id1)); + return c != 0 ? c : DBIDUtil.compare(id1, id2); + } + } } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DoubleDataStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DoubleDataStore.java index 8cf6cdf1..8f52f996 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DoubleDataStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/DoubleDataStore.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * Double-valued data store (avoids boxing/unboxing). * * @author Erich Schubert + * @since 0.4.0 */ public interface DoubleDataStore extends DataStore<Double> { /** @@ -38,7 +39,7 @@ public interface DoubleDataStore extends DataStore<Double> { */ @Override @Deprecated - public Double get(DBIDRef id); + Double get(DBIDRef id); /** * Retrieves an object from the storage. @@ -46,5 +47,5 @@ public interface DoubleDataStore extends DataStore<Double> { * @param id Database ID. * @return Double value */ - public double doubleValue(DBIDRef id); + double doubleValue(DBIDRef id); }
\ No newline at end of file diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/IntegerDataStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/IntegerDataStore.java index 986f4fc8..7747bcb3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/IntegerDataStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/IntegerDataStore.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * Integer-valued data store (avoids boxing/unboxing). * * @author Erich Schubert + * @since 0.4.0 */ public interface IntegerDataStore extends DataStore<Integer> { /** @@ -38,7 +39,7 @@ public interface IntegerDataStore extends DataStore<Integer> { */ @Override @Deprecated - public Integer get(DBIDRef id); + Integer get(DBIDRef id); /** * Retrieves a value from the storage. @@ -46,5 +47,5 @@ public interface IntegerDataStore extends DataStore<Integer> { * @param id Database ID. * @return Double value */ - public int intValue(DBIDRef id); + int intValue(DBIDRef id); }
\ No newline at end of file diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/RecordStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/RecordStore.java index b98f4d13..be06aa13 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/RecordStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/RecordStore.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.database.datastore; * Represents a storage which stores multiple values per object in a record fashion. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has de.lmu.ifi.dbs.elki.database.datastore.DataStore oneway - - projectsTo */ @@ -40,5 +41,5 @@ public interface RecordStore { * @param datatype data class * @return writable storage */ - public <T> DataStore<T> getStorage(int col, Class<? super T> datatype); + <T> DataStore<T> getStorage(int col, Class<? super T> datatype); } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableDBIDDataStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableDBIDDataStore.java index 38fd8adb..df0001ec 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableDBIDDataStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableDBIDDataStore.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * Data store specialized for doubles. Avoids boxing/unboxing. * * @author Erich Schubert + * @since 0.4.0 */ public interface WritableDBIDDataStore extends DBIDDataStore, WritableDataStore<DBID> { /** @@ -39,7 +40,7 @@ public interface WritableDBIDDataStore extends DBIDDataStore, WritableDataStore< */ @Override @Deprecated - public DBID put(DBIDRef id, DBID value); + DBID put(DBIDRef id, DBID value); /** * Associates the specified value with the specified id in this storage. If @@ -49,7 +50,7 @@ public interface WritableDBIDDataStore extends DBIDDataStore, WritableDataStore< * @param id Database ID. * @param value Value to store. */ - public void putDBID(DBIDRef id, DBIDRef value); + void putDBID(DBIDRef id, DBIDRef value); /** * Associates the specified value with the specified id in this storage. If @@ -59,5 +60,5 @@ public interface WritableDBIDDataStore extends DBIDDataStore, WritableDataStore< * @param id Database ID. * @param value Value to store. */ - public void put(DBIDRef id, DBIDRef value); + void put(DBIDRef id, DBIDRef value); }
\ No newline at end of file diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableDataStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableDataStore.java index 8baf622e..33f213b8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableDataStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableDataStore.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * Writable data store. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @@ -44,13 +45,13 @@ public interface WritableDataStore<T> extends DataStore<T> { * @param value Value to store. * @return previous value */ - public T put(DBIDRef id, T value); + T put(DBIDRef id, T value); /** * Deallocate the storage, freeing the memory and notifies the registered * listeners. */ - public void destroy(); + void destroy(); /** * Delete the contents for a particular ID and notifies the registered @@ -58,5 +59,10 @@ public interface WritableDataStore<T> extends DataStore<T> { * * @param id Database ID. */ - public void delete(DBIDRef id); + void delete(DBIDRef id); + + /** + * Clear the storage (resetting it to the default value). + */ + void clear(); } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableDoubleDataStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableDoubleDataStore.java index 8a3f9e8a..ac7fa2f2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableDoubleDataStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableDoubleDataStore.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * Data store specialized for doubles. Avoids boxing/unboxing. * * @author Erich Schubert + * @since 0.4.0 */ public interface WritableDoubleDataStore extends DoubleDataStore, WritableDataStore<Double> { /** @@ -38,7 +39,7 @@ public interface WritableDoubleDataStore extends DoubleDataStore, WritableDataSt */ @Override @Deprecated - public Double put(DBIDRef id, Double value); + Double put(DBIDRef id, Double value); /** * Associates the specified value with the specified id in this storage. If @@ -49,7 +50,7 @@ public interface WritableDoubleDataStore extends DoubleDataStore, WritableDataSt * @param value Value to store. * @return previous value */ - public double putDouble(DBIDRef id, double value); + double putDouble(DBIDRef id, double value); /** * Associates the specified value with the specified id in this storage. If @@ -60,8 +61,7 @@ public interface WritableDoubleDataStore extends DoubleDataStore, WritableDataSt * @param value Value to store. * @return previous value */ - public double put(DBIDRef id, double value); - + double put(DBIDRef id, double value); /** * Increment the specified value with the specified id in this storage. @@ -69,10 +69,5 @@ public interface WritableDoubleDataStore extends DoubleDataStore, WritableDataSt * @param id Database ID. * @param value Value to add to the previous value. */ - public void increment(DBIDRef id, double value); - - /** - * Reinitialize (reset to default value). - */ - public void clear(); + void increment(DBIDRef id, double value); }
\ No newline at end of file diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableIntegerDataStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableIntegerDataStore.java index 0303f45e..09bbc77f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableIntegerDataStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableIntegerDataStore.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * Data store specialized for doubles. Avoids boxing/unboxing. * * @author Erich Schubert + * @since 0.4.0 */ public interface WritableIntegerDataStore extends IntegerDataStore, WritableDataStore<Integer> { /** @@ -38,7 +39,7 @@ public interface WritableIntegerDataStore extends IntegerDataStore, WritableData */ @Override @Deprecated - public Integer put(DBIDRef id, Integer value); + Integer put(DBIDRef id, Integer value); /** * Associates the specified value with the specified id in this storage. If @@ -49,7 +50,7 @@ public interface WritableIntegerDataStore extends IntegerDataStore, WritableData * @param value Value to store. * @return previous value */ - public int putInt(DBIDRef id, int value); + int putInt(DBIDRef id, int value); /** * Associates the specified value with the specified id in this storage. If @@ -60,7 +61,7 @@ public interface WritableIntegerDataStore extends IntegerDataStore, WritableData * @param value Value to store. * @return previous value */ - public int put(DBIDRef id, int value); + int put(DBIDRef id, int value); /** * Increment a value. @@ -68,5 +69,5 @@ public interface WritableIntegerDataStore extends IntegerDataStore, WritableData * @param id Database ID. * @param adjust Value to add to the previous value. */ - public void increment(DBIDRef id, int adjust); + void increment(DBIDRef id, int adjust); }
\ No newline at end of file diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableRecordStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableRecordStore.java index 73106b28..81148c63 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableRecordStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/WritableRecordStore.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * Represents a storage which stores multiple values per object in a record fashion. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @@ -44,7 +45,7 @@ public interface WritableRecordStore extends RecordStore { * @return writable storage */ @Override - public <T> WritableDataStore<T> getStorage(int col, Class<? super T> datatype); + <T> WritableDataStore<T> getStorage(int col, Class<? super T> datatype); /** * Remove an object from the store, all columns. @@ -52,5 +53,5 @@ public interface WritableRecordStore extends RecordStore { * @param id object ID to remove * @return success code */ - public boolean remove(DBIDRef id); + boolean remove(DBIDRef id); } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayDBIDStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayDBIDStore.java index 2c73ada4..f557f529 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayDBIDStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayDBIDStore.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDVar; * A class to answer representation queries using the stored Array. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf de.lmu.ifi.dbs.elki.database.datastore.DataStoreIDMap */ @@ -60,7 +61,7 @@ public class ArrayDBIDStore implements WritableDBIDDataStore { this.data = DBIDUtil.newArray(size); // Initialize DBIDRef inv = DBIDUtil.invalid(); - for (int i = 0; i < size; i++) { + for(int i = 0; i < size; i++) { data.add(inv); } this.idmap = idmap; @@ -106,8 +107,19 @@ public class ArrayDBIDStore implements WritableDBIDDataStore { } @Override + public void clear() { + // Re-initialize + DBIDRef inv = DBIDUtil.invalid(); + final int size = data.size(); + data.clear(); + for(int i = 0; i < size; i++) { + data.add(inv); + } + } + + @Override public void delete(DBIDRef id) { - throw new UnsupportedOperationException("Can't delete from a static array storage."); + put(id, DBIDUtil.invalid()); } @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayDoubleStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayDoubleStore.java index d1a8672e..5f6d687d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayDoubleStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayDoubleStore.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * A class to answer representation queries using the stored Array. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf de.lmu.ifi.dbs.elki.database.datastore.DataStoreIDMap */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayIntegerStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayIntegerStore.java index 6b6ac14a..b4a4d7fc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayIntegerStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayIntegerStore.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * A class to answer representation queries using the stored Array. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf de.lmu.ifi.dbs.elki.database.datastore.DataStoreIDMap */ @@ -48,6 +49,11 @@ public class ArrayIntegerStore implements WritableIntegerDataStore { private DataStoreIDMap idmap; /** + * Default value (for {@link #clear()}). + */ + private int def; + + /** * Constructor. * * @param size Size @@ -67,6 +73,7 @@ public class ArrayIntegerStore implements WritableIntegerDataStore { public ArrayIntegerStore(int size, DataStoreIDMap idmap, int def) { super(); this.data = new int[size]; + this.def = def; if(def != 0) { Arrays.fill(this.data, def); } @@ -123,7 +130,12 @@ public class ArrayIntegerStore implements WritableIntegerDataStore { @Override public void delete(DBIDRef id) { - throw new UnsupportedOperationException("Can't delete from a static array storage."); + put(id, def); + } + + @Override + public void clear() { + Arrays.fill(data, def); } @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayRecordStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayRecordStore.java index 62f07448..deb949ff 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayRecordStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayRecordStore.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * A class to answer representation queries using the stored Array. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf DataStoreIDMap * @apiviz.has ArrayRecordStore.StorageAccessor oneway - - projectsTo @@ -128,12 +129,17 @@ public class ArrayRecordStore implements WritableRecordStore { @Override public void destroy() { - throw new UnsupportedOperationException("ArrayStore record columns cannot be destroyed."); + throw new UnsupportedOperationException("ArrayStore record columns cannot (yet) be destroyed."); } @Override public void delete(DBIDRef id) { - throw new UnsupportedOperationException("ArrayStore record values cannot be deleted."); + put(id, null); + } + + @Override + public void clear() { + throw new UnsupportedOperationException("ArrayStore record columns cannot (yet) be cleared."); } @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayStore.java index 35871ed9..bbfa967f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/ArrayStore.java @@ -1,5 +1,7 @@ package de.lmu.ifi.dbs.elki.database.datastore.memory; +import java.util.Arrays; + /* This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures @@ -33,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.ObjectNotFoundException; * A class to answer representation queries using the stored Array. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf de.lmu.ifi.dbs.elki.database.datastore.DataStoreIDMap * @@ -86,7 +89,12 @@ public class ArrayStore<T> implements WritableDataStore<T> { @Override public void delete(DBIDRef id) { - throw new UnsupportedOperationException("Can't delete from a static array storage."); + put(id, null); + } + + @Override + public void clear() { + Arrays.fill(data, null); } @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDDBIDStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDDBIDStore.java index 11b3cbb2..9016e6cf 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDDBIDStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDDBIDStore.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDVar; * Writable data store for double values. * * @author Erich Schubert + * @since 0.5.0 */ public class MapIntegerDBIDDBIDStore implements WritableDBIDDataStore { /** @@ -76,17 +77,6 @@ public class MapIntegerDBIDDBIDStore implements WritableDBIDDataStore { } @Override - public void destroy() { - map.clear(); - map = null; - } - - @Override - public void delete(DBIDRef id) { - map.remove(DBIDUtil.asInteger(id)); - } - - @Override public void put(DBIDRef id, DBIDRef value) { map.put(DBIDUtil.asInteger(id), DBIDUtil.asInteger(value)); } @@ -102,4 +92,20 @@ public class MapIntegerDBIDDBIDStore implements WritableDBIDDataStore { DBIDFactory.FACTORY.assignVar(var, val); return var; } + + @Override + public void delete(DBIDRef id) { + map.remove(DBIDUtil.asInteger(id)); + } + + @Override + public void destroy() { + map.clear(); + map = null; + } + + @Override + public void clear() { + map.clear(); + } } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDDoubleStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDDoubleStore.java index 5e21f6b4..4629a942 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDDoubleStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDDoubleStore.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; * Writable data store for double values. * * @author Erich Schubert + * @since 0.5.0 */ public class MapIntegerDBIDDoubleStore implements WritableDoubleDataStore { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDIntegerStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDIntegerStore.java index 2474aa4a..37fb84c0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDIntegerStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDIntegerStore.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; * Writable data store for double values. * * @author Erich Schubert + * @since 0.5.0 */ public class MapIntegerDBIDIntegerStore implements WritableIntegerDataStore { /** @@ -112,4 +113,9 @@ public class MapIntegerDBIDIntegerStore implements WritableIntegerDataStore { public void increment(DBIDRef id, int adjust) { map.adjustOrPutValue(DBIDUtil.asInteger(id), adjust, adjust); } + + @Override + public void clear() { + map.clear(); + } } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDRecordStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDRecordStore.java index 66f885d5..6461ad97 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDRecordStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDRecordStore.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; * record. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has MapIntegerDBIDRecordStore.StorageAccessor oneway - - projectsTo */ @@ -165,7 +166,12 @@ public class MapIntegerDBIDRecordStore implements WritableRecordStore { @Override public void delete(DBIDRef id) { - throw new UnsupportedOperationException("Record storage values cannot be deleted."); + throw new UnsupportedOperationException("Record storage accessors cannot be deleted."); + } + + @Override + public void clear() { + throw new UnsupportedOperationException("Record storage accessors cannot be cleared."); } @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDStore.java index 08e31971..2d21dccb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapIntegerDBIDStore.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; * wrapper around a regular map. * * @author Erich Schubert + * @since 0.4.0 * * @param <T> Representation object type */ @@ -94,6 +95,11 @@ public class MapIntegerDBIDStore<T> implements WritableDataStore<T> { } @Override + public void clear() { + data.clear(); + } + + @Override public String getLongName() { return "raw"; } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapRecordStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapRecordStore.java index 6ed7f581..e6cf1198 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapRecordStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapRecordStore.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; * record. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has MapRecordStore.StorageAccessor oneway - - projectsTo */ @@ -90,7 +91,7 @@ public class MapRecordStore implements WritableRecordStore { @SuppressWarnings("unchecked") protected <T> T get(DBIDRef id, int index) { Object[] d = data.get(DBIDUtil.deref(id)); - if (d == null) { + if(d == null) { return null; } return (T) d[index]; @@ -108,7 +109,7 @@ public class MapRecordStore implements WritableRecordStore { @SuppressWarnings("unchecked") protected <T> T set(DBIDRef id, int index, T value) { Object[] d = data.get(DBIDUtil.deref(id)); - if (d == null) { + if(d == null) { d = new Object[rlen]; data.put(DBIDUtil.deref(id), d); } @@ -157,6 +158,11 @@ public class MapRecordStore implements WritableRecordStore { } @Override + public void clear() { + throw new UnsupportedOperationException("Record storage accessors cannot (yet) be cleared."); + } + + @Override public void delete(DBIDRef id) { throw new UnsupportedOperationException("Record storage values cannot be deleted."); } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapStore.java index 98e5fc57..758e8bec 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MapStore.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; * wrapper around a regular map. * * @author Erich Schubert + * @since 0.4.0 * * @param <T> Representation object type */ @@ -87,6 +88,11 @@ public class MapStore<T> implements WritableDataStore<T> { } @Override + public void clear() { + data.clear(); + } + + @Override public String getLongName() { return "raw"; } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MemoryDataStoreFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MemoryDataStoreFactory.java index 649de071..6e9427f5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MemoryDataStoreFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/datastore/memory/MemoryDataStoreFactory.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * in-memory. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.has ArrayStore oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ArrayDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ArrayDBIDs.java index c48e575d..8fc27ff3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ArrayDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ArrayDBIDs.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * Interface for array based DBIDs. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has DBIDArrayIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ArrayModifiableDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ArrayModifiableDBIDs.java index 498d090a..c879ae95 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ArrayModifiableDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ArrayModifiableDBIDs.java @@ -28,6 +28,7 @@ import java.util.Comparator; * Array-oriented implementation of a modifiable DBID collection. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has DBIDArrayMIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ArrayStaticDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ArrayStaticDBIDs.java index 7331edce..623b102d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ArrayStaticDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ArrayStaticDBIDs.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * Unmodifiable, indexed DBIDs. * * @author Erich Schubert + * @since 0.4.0 */ public interface ArrayStaticDBIDs extends ArrayDBIDs, StaticDBIDs { // empty. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBID.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBID.java index 3fb4cc93..66001a7a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBID.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBID.java @@ -34,6 +34,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * consistent across multiple results/databases. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDArrayIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDArrayIter.java index 9168e7c6..0f638fe0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDArrayIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDArrayIter.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.ArrayIter; * Array iterators that can also go backwards and seek. * * @author Erich Schubert + * @since 0.4.0 */ public interface DBIDArrayIter extends DBIDIter, ArrayIter { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDArrayMIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDArrayMIter.java index e4bca297..5da6b6ae 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDArrayMIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDArrayMIter.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * Modifiable array iterator. * * @author Erich Schubert + * @since 0.4.0 */ public interface DBIDArrayMIter extends DBIDArrayIter, DBIDMIter { // Nothing new, see {@link DBIDArrayIter} and {@link DBIDMIter} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDFactory.java index dc424b71..6ac06aab 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDFactory.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.FixedSizeByteBufferSerializer; * instance to use. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses DBID oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDIter.java index d2c816a2..f9e9e381 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDIter.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.Iter; * </ul> * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDMIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDMIter.java index d52e87ed..7dc3dca6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDMIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDMIter.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.MIter; * Modifiable DBID iterator. * * @author Erich Schubert + * @since 0.4.0 */ public interface DBIDMIter extends DBIDIter, MIter { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDPair.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDPair.java index 29d993ea..675f8810 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDPair.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDPair.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * using {@link de.lmu.ifi.dbs.elki.utilities.pairs.Pair} * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf de.lmu.ifi.dbs.elki.database.ids.DBID */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDRange.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDRange.java index 710ec3c6..1e515893 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDRange.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDRange.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.datastore.DataStoreIDMap; * Static DBID range. * * @author Erich Schubert + * @since 0.4.0 */ public interface DBIDRange extends ArrayStaticDBIDs, DataStoreIDMap { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDRef.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDRef.java index 80b69a1e..7f051e35 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDRef.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDRef.java @@ -31,6 +31,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * are a good example how the DBIDRef may change. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDUtil.java index ae85fa12..c9f2c1f1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDUtil.java @@ -41,11 +41,12 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; /** * DBID Utility functions. - * + * * @author Erich Schubert - * + * @since 0.4.0 + * * @apiviz.landmark - * + * * @apiviz.has DBIDs * @apiviz.has DBIDRef * @apiviz.composedOf DBIDFactory @@ -65,7 +66,7 @@ public final class DBIDUtil { /** * Get the invalid special ID. - * + * * @return invalid ID value */ public static DBIDRef invalid() { @@ -74,9 +75,9 @@ public final class DBIDUtil { /** * Import and integer as DBID. - * + * * Note: this may not be possible for some factories! - * + * * @param id Integer ID to import * @return DBID */ @@ -86,9 +87,9 @@ public final class DBIDUtil { /** * Export a DBID as int. - * + * * Note: this may not be possible for some factories! - * + * * @param id DBID to export * @return integer value */ @@ -98,7 +99,7 @@ public final class DBIDUtil { /** * Compare two DBIDs. - * + * * @param id1 First ID * @param id2 Second ID * @return Comparison result @@ -109,7 +110,7 @@ public final class DBIDUtil { /** * Test two DBIDs for equality. - * + * * @param id1 First ID * @param id2 Second ID * @return Comparison result @@ -120,7 +121,7 @@ public final class DBIDUtil { /** * Dereference a DBID reference. - * + * * @param ref DBID reference * @return DBID */ @@ -133,7 +134,7 @@ public final class DBIDUtil { /** * Format a DBID as string. - * + * * @param id DBID * @return String representation */ @@ -143,7 +144,7 @@ public final class DBIDUtil { /** * Format a DBID as string. - * + * * @param ids DBIDs * @return String representation */ @@ -163,7 +164,7 @@ public final class DBIDUtil { /** * Get a serializer for DBIDs. - * + * * @return DBID serializer */ public static ByteBufferSerializer<DBID> getDBIDSerializer() { @@ -172,7 +173,7 @@ public final class DBIDUtil { /** * Get a serializer for DBIDs with static size. - * + * * @return DBID serializer */ public static ByteBufferSerializer<DBID> getDBIDSerializerStatic() { @@ -181,7 +182,7 @@ public final class DBIDUtil { /** * Generate a single DBID. - * + * * @return A single DBID */ public static DBID generateSingleDBID() { @@ -190,7 +191,7 @@ public final class DBIDUtil { /** * Return a single DBID for reuse. - * + * * @param id DBID to deallocate */ public static void deallocateSingleDBID(DBID id) { @@ -199,7 +200,7 @@ public final class DBIDUtil { /** * Generate a static DBID range. - * + * * @param size Requested size * @return DBID range */ @@ -209,7 +210,7 @@ public final class DBIDUtil { /** * Deallocate a static DBID range. - * + * * @param range Range to deallocate */ public static void deallocateDBIDRange(DBIDRange range) { @@ -218,7 +219,7 @@ public final class DBIDUtil { /** * Make a new DBID variable. - * + * * @param val Initial value. * @return Variable */ @@ -228,7 +229,7 @@ public final class DBIDUtil { /** * Make a new DBID variable. - * + * * @return Variable */ public static DBIDVar newVar() { @@ -237,7 +238,7 @@ public final class DBIDUtil { /** * Make a new (modifiable) array of DBIDs. - * + * * @return New array */ public static ArrayModifiableDBIDs newArray() { @@ -246,7 +247,7 @@ public final class DBIDUtil { /** * Make a new (modifiable) hash set of DBIDs. - * + * * @return New hash set */ public static HashSetModifiableDBIDs newHashSet() { @@ -255,7 +256,7 @@ public final class DBIDUtil { /** * Make a new (modifiable) array of DBIDs. - * + * * @param size Size hint * @return New array */ @@ -265,7 +266,7 @@ public final class DBIDUtil { /** * Make a new (modifiable) hash set of DBIDs. - * + * * @param size Size hint * @return New hash set */ @@ -275,7 +276,7 @@ public final class DBIDUtil { /** * Make a new (modifiable) array of DBIDs. - * + * * @param existing Existing DBIDs * @return New array */ @@ -285,7 +286,7 @@ public final class DBIDUtil { /** * Make a new (modifiable) hash set of DBIDs. - * + * * @param existing Existing DBIDs * @return New hash set */ @@ -295,7 +296,7 @@ public final class DBIDUtil { /** * Compute the set intersection of two sets. - * + * * @param first First set * @param second Second set * @return result. @@ -316,7 +317,7 @@ public final class DBIDUtil { /** * Compute the set intersection size of two sets. - * + * * @param first First set * @param second Second set * @return size @@ -345,7 +346,7 @@ public final class DBIDUtil { /** * Compute the set intersection size of two sets. - * + * * @param first First set * @param second Second set * @return size @@ -362,7 +363,7 @@ public final class DBIDUtil { /** * Compute the set symmetric intersection of two sets. - * + * * @param first First set * @param second Second set * @param firstonly OUTPUT: elements only in first. MUST BE EMPTY @@ -393,7 +394,7 @@ public final class DBIDUtil { /** * Returns the union of the two specified collection of IDs. - * + * * @param ids1 the first collection * @param ids2 the second collection * @return the union of ids1 and ids2 without duplicates @@ -407,7 +408,7 @@ public final class DBIDUtil { /** * Returns the difference of the two specified collection of IDs. - * + * * @param ids1 the first collection * @param ids2 the second collection * @return the difference of ids1 minus ids2 @@ -420,7 +421,7 @@ public final class DBIDUtil { /** * Wrap an existing DBIDs collection to be unmodifiable. - * + * * @param existing Existing collection * @return Unmodifiable collection */ @@ -442,7 +443,7 @@ public final class DBIDUtil { /** * Ensure that the given DBIDs are array-indexable. - * + * * @param ids IDs * @return Array DBIDs. */ @@ -457,7 +458,7 @@ public final class DBIDUtil { /** * Ensure that the given DBIDs support fast "contains" operations. - * + * * @param ids IDs * @return Set DBIDs. */ @@ -472,7 +473,7 @@ public final class DBIDUtil { /** * Ensure modifiable. - * + * * @param ids IDs * @return Modifiable DBIDs. */ @@ -493,10 +494,10 @@ public final class DBIDUtil { /** * Make a DBID pair. - * + * * @param id1 first ID * @param id2 second ID - * + * * @return DBID pair */ public static DBIDPair newPair(DBIDRef id1, DBIDRef id2) { @@ -505,7 +506,7 @@ public final class DBIDUtil { /** * Make a DoubleDBIDPair. - * + * * @param val double value * @param id ID * @return new pair @@ -516,9 +517,9 @@ public final class DBIDUtil { /** * Create an appropriate heap for the distance type. - * + * * This will use a double heap if appropriate. - * + * * @param k K value * @return New heap of size k, appropriate for this distance type. */ @@ -528,7 +529,7 @@ public final class DBIDUtil { /** * Build a new heap from a given list. - * + * * @param exist Existing result * @return New heap */ @@ -538,7 +539,7 @@ public final class DBIDUtil { /** * Produce a random shuffling of the given DBID array. - * + * * @param ids Original DBIDs * @param rnd Random generator */ @@ -548,7 +549,7 @@ public final class DBIDUtil { /** * Produce a random shuffling of the given DBID array. - * + * * @param ids Original DBIDs * @param random Random generator */ @@ -558,22 +559,24 @@ public final class DBIDUtil { /** * Produce a random shuffling of the given DBID array. - * - * Only the first {@code limit} elements will be randomized. - * + * + * Only the first {@code limit} elements will be fully randomized, but the + * remaining objects will also be changed. + * * @param ids Original DBIDs * @param random Random generator * @param limit Shuffling limit. */ public static void randomShuffle(ArrayModifiableDBIDs ids, Random random, final int limit) { + final int end = ids.size(); for(int i = 1; i < limit; i++) { - ids.swap(i - 1, i + random.nextInt(limit - i)); + ids.swap(i - 1, i + random.nextInt(end - i)); } } /** * Produce a random sample of the given DBIDs. - * + * * @param source Original DBIDs * @param k k Parameter * @param seed Random generator seed @@ -585,7 +588,7 @@ public final class DBIDUtil { /** * Produce a random sample of the given DBIDs. - * + * * @param source Original DBIDs * @param k k Parameter * @param seed Random generator seed @@ -602,7 +605,7 @@ public final class DBIDUtil { /** * Produce a random sample of the given DBIDs. - * + * * @param source Original DBIDs * @param k k Parameter * @param rnd Random generator @@ -614,7 +617,7 @@ public final class DBIDUtil { /** * Produce a random sample of the given DBIDs. - * + * * @param source Original DBIDs * @param k k Parameter * @param random Random generator @@ -645,7 +648,7 @@ public final class DBIDUtil { ArrayModifiableDBIDs sample = DBIDUtil.newArray(source); randomShuffle(sample, random, k); // Delete trailing elements - for(int i = sample.size() - 1; i > k; i--) { + for(int i = sample.size() - 1; i >= k; i--) { sample.remove(i); } return sample; @@ -654,7 +657,7 @@ public final class DBIDUtil { /** * Produce a random sample of the given DBIDs. - * + * * @param ids Original ids * @param rate Sampling rate * @param random Random generator @@ -666,7 +669,7 @@ public final class DBIDUtil { /** * Produce a random sample of the given DBIDs. - * + * * @param ids Original ids * @param rate Sampling rate * @param random Random generator @@ -711,7 +714,7 @@ public final class DBIDUtil { /** * Randomly split IDs into {@code p} partitions of almost-equal size. - * + * * @param ids Original DBIDs * @param p Desired number of partitions. * @param rnd Random generator @@ -722,7 +725,7 @@ public final class DBIDUtil { /** * Randomly split IDs into {@code p} partitions of almost-equal size. - * + * * @param oids Original DBIDs * @param p Desired number of partitions. * @param random Random generator @@ -752,7 +755,7 @@ public final class DBIDUtil { /** * Get a subset of the KNN result. - * + * * @param list Existing list * @param k k * @return Subset @@ -769,7 +772,7 @@ public final class DBIDUtil { /** * Create a modifiable list to store distance-DBID pairs. - * + * * @param size Estimated upper list size * @return Empty list */ @@ -779,7 +782,7 @@ public final class DBIDUtil { /** * Create a modifiable list to store distance-DBID pairs. - * + * * @return Empty list */ public static ModifiableDoubleDBIDList newDistanceDBIDList() { @@ -788,7 +791,7 @@ public final class DBIDUtil { /** * Assert that the presented ids constitute a continuous {@link DBIDRange}. - * + * * @param ids ID range. * @return DBID range. * @throws AbortException diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDVar.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDVar.java index adfa9aed..80dfaf53 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDVar.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDVar.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.database.datastore.DBIDDataStore; * candidate. * * @author Erich Schubert + * @since 0.4.0 */ public interface DBIDVar extends DBIDRef, ArrayDBIDs, SetDBIDs { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDs.java index 47ab6c2b..95a07f80 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DBIDs.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * Interface for a collection of database references (IDs). * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.composedOf DBID diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDList.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDList.java index 4ac19f95..355f9c17 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDList.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDList.java @@ -50,6 +50,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * </pre> * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDListIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDListIter.java index 92fe9233..6435a048 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDListIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDListIter.java @@ -31,6 +31,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * {@link de.lmu.ifi.dbs.elki.database.ids.DBIDRef}. * * @author Erich Schubert + * @since 0.3 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDListMIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDListMIter.java index 0e371ff8..638c32ee 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDListMIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDListMIter.java @@ -26,6 +26,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * Modifiable DBIDList iterator. * * @author Erich Schubert + * @since 0.2 */ public interface DoubleDBIDListMIter extends DoubleDBIDListIter, DBIDArrayMIter { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDPair.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDPair.java index 725861d6..1a49ad56 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDPair.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/DoubleDBIDPair.java @@ -30,6 +30,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * object reference. * * @author Erich Schubert + * @since 0.2 */ public interface DoubleDBIDPair extends DBIDRef, Comparable<DoubleDBIDPair> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/EmptyDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/EmptyDBIDs.java index 5c1c3e2d..444b632c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/EmptyDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/EmptyDBIDs.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.logging.LoggingUtil; * Empty DBID collection. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf EmptyDBIDIterator */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/HashSetDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/HashSetDBIDs.java index c7deb732..e5a3c4d3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/HashSetDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/HashSetDBIDs.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * Hash-organized DBIDs * * @author Erich Schubert + * @since 0.4.0 */ public interface HashSetDBIDs extends SetDBIDs { // Empty marker interface diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/HashSetModifiableDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/HashSetModifiableDBIDs.java index e5cde131..f3a43b8b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/HashSetModifiableDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/HashSetModifiableDBIDs.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * Set-oriented implementation of a modifiable DBID collection. * * @author Erich Schubert + * @since 0.4.0 */ public interface HashSetModifiableDBIDs extends HashSetDBIDs, ModifiableDBIDs { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/KNNHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/KNNHeap.java index f2ae4c0e..73fddbb2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/KNNHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/KNNHeap.java @@ -31,6 +31,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * {@link de.lmu.ifi.dbs.elki.database.ids.DBIDUtil#newHeap}! * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/KNNList.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/KNNList.java index 94c26a5f..f23e81e2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/KNNList.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/KNNList.java @@ -51,6 +51,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * </pre> * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ModifiableDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ModifiableDBIDs.java index fa88c373..f59f1d92 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ModifiableDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ModifiableDBIDs.java @@ -25,43 +25,46 @@ package de.lmu.ifi.dbs.elki.database.ids; /** * Interface for a generic modifiable DBID collection. - * + * * Note: we had this use the Java Collections API for a long time, however this * prevented certain optimizations. So it now only mimics the Collections API * <em>deliberately</em>. - * + * * @author Erich Schubert - * + * @since 0.4.0 + * * @apiviz.has DBIDMIter */ public interface ModifiableDBIDs extends DBIDs { /** * Add DBIDs to collection. - * + * * @param ids IDs to add. - * @return {@code true} when modified + * @return {@code true} if the collection changed. */ boolean addDBIDs(DBIDs ids); /** * Remove DBIDs from collection. - * + * * @param ids IDs to remove. - * @return {@code true} when modified + * @return {@code true} if the collection changed. */ boolean removeDBIDs(DBIDs ids); /** * Add a single DBID to the collection. - * + * * @param id ID to add + * @return {@code true} if the collection changed. */ boolean add(DBIDRef id); /** * Remove a single DBID from the collection. - * + * * @param id ID to remove + * @return {@code true} if the collection changed. */ boolean remove(DBIDRef id); @@ -72,9 +75,9 @@ public interface ModifiableDBIDs extends DBIDs { /** * Get a <em>modifiable</em> DBID iterator (a more efficient API). - * + * * usage example: - * + * * <pre> * {@code * for(DBIDMIter iter = ids.iter(); iter.valid(); iter.advance()) { @@ -83,7 +86,7 @@ public interface ModifiableDBIDs extends DBIDs { * } * } * </pre> - * + * * @return modifiable iterator */ @Override @@ -93,6 +96,8 @@ public interface ModifiableDBIDs extends DBIDs { * Pop (get and remove) one DBID from the set, into a variable. * * @param outvar Output variable + * @return Always {@code outvar}, for inlining + * @throws ArrayIndexOutOfBoundsException when empty. */ - void pop(DBIDVar outvar); + DBIDVar pop(DBIDVar outvar); }
\ No newline at end of file diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ModifiableDoubleDBIDList.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ModifiableDoubleDBIDList.java index 964e18d0..8b4409ee 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ModifiableDoubleDBIDList.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/ModifiableDoubleDBIDList.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * Modifiable API for Distance-DBID results * * @author Erich Schubert + * @since 0.3 * * @apiviz.composedOf DoubleDBIDPair */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/SetDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/SetDBIDs.java index bcae4fec..cead3cb6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/SetDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/SetDBIDs.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * "contains" lookups. * * @author Erich Schubert + * @since 0.4.0 */ public interface SetDBIDs extends DBIDs { // empty marker interface diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/StaticDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/StaticDBIDs.java index f1b96812..3b4ccc16 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/StaticDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/StaticDBIDs.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.database.ids; * Unmodifiable DBIDs. * * @author Erich Schubert + * @since 0.4.0 */ public interface StaticDBIDs extends DBIDs { // Empty marker interface. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/KNNSubList.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/KNNSubList.java index 1563efd4..770c3792 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/KNNSubList.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/KNNSubList.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.database.ids.KNNList; * Sublist of an existing result to contain only the first k elements. * * @author Erich Schubert + * @since 0.5.5 */ public class KNNSubList implements KNNList { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/MaskedDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/MaskedDBIDs.java index f71498bd..b61b2a98 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/MaskedDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/MaskedDBIDs.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * View on an ArrayDBIDs masked using a BitMask for efficient mask changing. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses DBIDs */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/UnmodifiableArrayDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/UnmodifiableArrayDBIDs.java index 637ad758..698e63ab 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/UnmodifiableArrayDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/UnmodifiableArrayDBIDs.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDVar; * Unmodifiable wrapper for DBIDs. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses ArrayDBIDs * @apiviz.has UnmodifiableDBIDArrayIter diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/UnmodifiableDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/UnmodifiableDBIDs.java index 16ff1f81..7ce291e8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/UnmodifiableDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/generic/UnmodifiableDBIDs.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.database.ids.StaticDBIDs; * Unmodifiable wrapper for DBIDs. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses DBIDs * @apiviz.has UnmodifiableDBIDIter diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/AbstractIntegerDBIDFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/AbstractIntegerDBIDFactory.java index cbf29e9c..6ad8c6fe 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/AbstractIntegerDBIDFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/AbstractIntegerDBIDFactory.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.FixedSizeByteBufferSerializer; * Abstract base class for DBID factories. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses IntegerDBID oneway - - «create» * @apiviz.uses IntegerDBIDPair oneway - - «create» @@ -83,7 +84,8 @@ abstract class AbstractIntegerDBIDFactory implements DBIDFactory { @Override public String toString(DBIDRef id) { - return (id != null) ? Integer.toString(id.internalGetIndex()) : "null"; + return (id != null && id.internalGetIndex() != Integer.MIN_VALUE) // + ? Integer.toString(id.internalGetIndex()) : "null"; } @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/ArrayModifiableIntegerDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/ArrayModifiableIntegerDBIDs.java index 835bcd8d..8aa6813c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/ArrayModifiableIntegerDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/ArrayModifiableIntegerDBIDs.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * Class using a primitive int[] array as storage. * * @author Erich Schubert + * @since 0.6.0 */ class ArrayModifiableIntegerDBIDs implements ArrayModifiableDBIDs, IntegerArrayDBIDs { /** @@ -271,7 +272,7 @@ class ArrayModifiableIntegerDBIDs implements ArrayModifiableDBIDs, IntegerArrayD } @Override - public void pop(DBIDVar var) { + public DBIDVar pop(DBIDVar var) { if(size == 0) { throw new ArrayIndexOutOfBoundsException("Cannot pop() from an empty array."); } @@ -282,6 +283,7 @@ class ArrayModifiableIntegerDBIDs implements ArrayModifiableDBIDs, IntegerArrayD // less efficient, involves object creation. var.set(get(--size)); } + return var; } @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/ArrayStaticIntegerDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/ArrayStaticIntegerDBIDs.java index 210dbb15..fb171416 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/ArrayStaticIntegerDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/ArrayStaticIntegerDBIDs.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.logging.LoggingUtil; * Static (no modifications allowed) set of Database Object IDs. * * @author Erich Schubert + * @since 0.4.0 */ class ArrayStaticIntegerDBIDs implements IntegerArrayStaticDBIDs { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDKNNHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDKNNHeap.java index 7162dbc2..1fe22b71 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDKNNHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDKNNHeap.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.heap.DoubleIntegerMaxHeap; * Class to efficiently manage a kNN heap. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has DoubleIntegerDBIDKNNList * @apiviz.composedOf DoubleIntegerMaxHeap diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDKNNList.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDKNNList.java index 449497d1..e0e891e3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDKNNList.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDKNNList.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDListIter; * the results to be sorted! * * @author Erich Schubert + * @since 0.6.0 */ public class DoubleIntegerDBIDKNNList extends DoubleIntegerDBIDList implements IntegerDBIDKNNList { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDList.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDList.java index 6f551189..9c97f779 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDList.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDList.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arrays.DoubleIntegerArrayQui * Class to store double distance, integer DBID results. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses DoubleIntegerArrayQuickSort */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDListIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDListIter.java index 0cd7f33a..f944df03 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDListIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDListIter.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDListIter; * Combination interface of the DoubleDBIDListIter with IntegerDBIDIter. * * @author Erich Schubert + * @since 0.7.0 */ public interface DoubleIntegerDBIDListIter extends DoubleDBIDListIter, IntegerDBIDIter { // No additional methods. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDListKNNHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDListKNNHeap.java index 82c0f184..4ddf7ba3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDListKNNHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDListKNNHeap.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.database.ids.KNNList; * order. * * @author Erich Schubert + * @since 0.6.0 */ class DoubleIntegerDBIDListKNNHeap extends DoubleIntegerDBIDKNNList implements KNNHeap { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDListMIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDListMIter.java index 59824d85..d46b2952 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDListMIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDListMIter.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDListMIter; * Combination interface for modifiable iterators. * * @author Erich Schubert + * @since 0.4.0 */ interface DoubleIntegerDBIDListMIter extends DoubleIntegerDBIDListIter, DoubleDBIDListMIter { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDPair.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDPair.java index 7cb247ce..f18ab125 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDPair.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDPair.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDPair; * Pair containing a double value and an integer DBID. * * @author Erich Schubert + * @since 0.4.0 */ class DoubleIntegerDBIDPair implements DoubleDBIDPair, IntegerDBIDRef { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDPairKNNListHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDPairKNNListHeap.java index ee06d7fa..eb2c8267 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDPairKNNListHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDPairKNNListHeap.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.database.ids.KNNList; * Currently unused, needs benchmarking. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.composedOf DoubleIntegerDBIDPair */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDPairList.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDPairList.java index 990e572f..593ba6ed 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDPairList.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDPairList.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.database.ids.ModifiableDoubleDBIDList; * Currently unused. Needs benchmarking. * * @author Erich Schubert + * @since 0.6.0 */ class DoubleIntegerDBIDPairList implements ModifiableDoubleDBIDList, IntegerDBIDs { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerArrayDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerArrayDBIDs.java index 4afc942a..3f93a4b9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerArrayDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerArrayDBIDs.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.ArrayDBIDs; * Trivial combination interface. * * @author Erich Schubert + * @since 0.4.0 */ public interface IntegerArrayDBIDs extends IntegerDBIDs, ArrayDBIDs { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerArrayStaticDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerArrayStaticDBIDs.java index fac20bca..c3ba28da 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerArrayStaticDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerArrayStaticDBIDs.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.ArrayStaticDBIDs; * Combination of {@link ArrayStaticDBIDs} and {@link IntegerDBIDs}. * * @author Erich Schubert + * @since 0.4.0 */ interface IntegerArrayStaticDBIDs extends ArrayStaticDBIDs, IntegerArrayDBIDs { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBID.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBID.java index bdc5196b..11cc8c07 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBID.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBID.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.FixedSizeByteBufferSerializer; * consistent across multiple results/databases. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf DynamicSerializer * @apiviz.composedOf StaticSerializer @@ -100,7 +101,7 @@ final class IntegerDBID implements DBID, IntegerDBIDRef { @Override public String toString() { - return Integer.toString(id); + return (id != Integer.MIN_VALUE) ? Integer.toString(id) : "null"; } @Override @@ -111,11 +112,11 @@ final class IntegerDBID implements DBID, IntegerDBIDRef { @Override @Deprecated public boolean equals(Object obj) { - if (this == obj) { + if(this == obj) { return true; } - if (!(obj instanceof IntegerDBID)) { - if (obj instanceof DBIDRef) { + if(!(obj instanceof IntegerDBID)) { + if(obj instanceof DBIDRef) { LoggingUtil.warning("Programming error: DBID.equals(DBIDRef) is not well-defined. Use DBIDUtil.equal() instead!", new Throwable()); } return false; @@ -137,7 +138,7 @@ final class IntegerDBID implements DBID, IntegerDBIDRef { @Override public DBID get(int i) { - if (i != 0) { + if(i != 0) { throw new ArrayIndexOutOfBoundsException(); } return this; @@ -145,7 +146,7 @@ final class IntegerDBID implements DBID, IntegerDBIDRef { @Override public DBIDVar assignVar(int index, DBIDVar var) { - if (index != 0) { + if(index != 0) { throw new ArrayIndexOutOfBoundsException(); } var.set(this); @@ -165,9 +166,10 @@ final class IntegerDBID implements DBID, IntegerDBIDRef { @Override public ArrayDBIDs slice(int begin, int end) { - if (begin == 0 && end == 1) { + if(begin == 0 && end == 1) { return this; - } else { + } + else { return DBIDUtil.EMPTYDBIDS; } } @@ -232,7 +234,7 @@ final class IntegerDBID implements DBID, IntegerDBIDRef { @Override public boolean equals(Object other) { - if (other instanceof DBID) { + if(other instanceof DBID) { LoggingUtil.warning("Programming error detected: DBIDItr.equals(DBID). Use sameDBID()!", new Throwable()); } return super.equals(other); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDArrayIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDArrayIter.java index f0ac9928..4b120c8c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDArrayIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDArrayIter.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDArrayIter; * Modifiable integer array iterator. * * @author Erich Schubert + * @since 0.4.0 */ interface IntegerDBIDArrayIter extends IntegerDBIDIter, DBIDArrayIter { // Empty diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDArrayMIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDArrayMIter.java index c9234060..946484ec 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDArrayMIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDArrayMIter.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDArrayMIter; * Modifiable integer array iterator. * * @author Erich Schubert + * @since 0.4.0 */ interface IntegerDBIDArrayMIter extends IntegerDBIDArrayIter, IntegerDBIDMIter, DBIDArrayMIter { // Empty diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDArrayQuickSort.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDArrayQuickSort.java index bfbde351..7e020554 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDArrayQuickSort.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDArrayQuickSort.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.uses IntegerArrayDBIDs */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDIter.java index 687a64b2..08b7fa01 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDIter.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDIter; * Iterator for integer DBIDs. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDKNNList.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDKNNList.java index 3fb0d381..c71253de 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDKNNList.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDKNNList.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.KNNList; * Combination interface for KNNList and IntegerDBIDs. * * @author Erich Schubert + * @since 0.7.0 */ public interface IntegerDBIDKNNList extends KNNList, DoubleDBIDList, IntegerDBIDs { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDKNNSubList.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDKNNSubList.java index 4d1095e0..ac050ab9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDKNNSubList.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDKNNSubList.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDPair; * Sublist of an existing result to contain only the first k elements. * * @author Erich Schubert + * @since 0.5.5 */ public class IntegerDBIDKNNSubList implements IntegerDBIDKNNList { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDMIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDMIter.java index 6bf1cffd..bf6bfcd8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDMIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDMIter.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDMIter; * Modifiable iterator interface for integer DBIDs. * * @author Erich Schubert + * @since 0.4.0 */ interface IntegerDBIDMIter extends DBIDMIter, IntegerDBIDIter { // Empty. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDPair.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDPair.java index cd50f00e..5ed718d3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDPair.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDPair.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDVar; * DBID pair using two ints for storage. * * @author Erich Schubert + * @since 0.4.0 */ class IntegerDBIDPair implements DBIDPair, IntegerDBIDs { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDRange.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDRange.java index 2b790fb5..b7a21419 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDRange.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDRange.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.database.ids.SetDBIDs; * Representing a DBID range allocation. * * @author Erich Schubert + * @since 0.4.0 */ final class IntegerDBIDRange implements IntegerDBIDs, DBIDRange, SetDBIDs { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDRef.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDRef.java index da21b007..e2cb0b2e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDRef.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDRef.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * DBID reference that references an integer value. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDVar.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDVar.java index 12e320e9..b2721a20 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDVar.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDVar.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.logging.LoggingUtil; * should come for free! * * @author Erich Schubert + * @since 0.4.0 */ class IntegerDBIDVar implements DBIDVar, IntegerDBIDs { /** @@ -165,7 +166,7 @@ class IntegerDBIDVar implements DBIDVar, IntegerDBIDs { @Override public String toString() { - return Integer.toString(id); + return (id != Integer.MIN_VALUE) ? Integer.toString(id) : "null"; } @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDs.java index 3146f829..50c2b950 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/IntegerDBIDs.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * Integer DBID collection. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has IntegerDBIDIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/ReusingDBIDFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/ReusingDBIDFactory.java index 02819f0f..ac4715a8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/ReusingDBIDFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/ReusingDBIDFactory.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * TODO: manage fragmentation of ranges? * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/SimpleDBIDFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/SimpleDBIDFactory.java index b49ab39a..99b96b03 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/SimpleDBIDFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/SimpleDBIDFactory.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * negative values. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.stereotype factory diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/TrivialDBIDFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/TrivialDBIDFactory.java index c3e77e99..e9c3b30c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/TrivialDBIDFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/TrivialDBIDFactory.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * sequence. All IDs will be positive. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.stereotype factory diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/TroveHashSetModifiableDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/TroveHashSetModifiableDBIDs.java index 2fc54afd..912a501b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/TroveHashSetModifiableDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/TroveHashSetModifiableDBIDs.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.Iter; * Implementation using GNU Trove Int Hash Sets. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has Itr */ @@ -158,7 +159,7 @@ class TroveHashSetModifiableDBIDs implements HashSetModifiableDBIDs, IntegerDBID } @Override - public void pop(DBIDVar outvar) { + public DBIDVar pop(DBIDVar outvar) { if(store.size() == 0) { throw new ArrayIndexOutOfBoundsException("Cannot pop() from an empty array."); } @@ -167,9 +168,8 @@ class TroveHashSetModifiableDBIDs implements HashSetModifiableDBIDs, IntegerDBID while(i-- > 0 && (states[i] != TPrimitiveHash.FULL)) { ; // Not occupied. Continue } - if(i < 0) { - outvar.unset(); - return; + if(i < 0) { // Should never happen because size > 0 + throw new ArrayIndexOutOfBoundsException("Cannot pop() from an empty array."); } final int val = store._set[i]; if(outvar instanceof IntegerDBIDVar) { @@ -180,6 +180,7 @@ class TroveHashSetModifiableDBIDs implements HashSetModifiableDBIDs, IntegerDBID } // Unfortunately, not visible: store.removeAt(i); store.remove(val); + return outvar; } /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/UnmodifiableIntegerArrayDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/UnmodifiableIntegerArrayDBIDs.java index b7c1fb87..402b780e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/UnmodifiableIntegerArrayDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/UnmodifiableIntegerArrayDBIDs.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDVar; * Unmodifiable wrapper for DBIDs. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses IntegerArrayDBIDs * @apiviz.has UnmodifiableDBIDIter diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/UnmodifiableIntegerDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/UnmodifiableIntegerDBIDs.java index 2c4ad2f6..cd48f2b3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/UnmodifiableIntegerDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/ids/integer/UnmodifiableIntegerDBIDs.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.database.ids.StaticDBIDs; * Unmodifiable wrapper for DBIDs. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses IntegerDBIDs * @apiviz.has UnmodifiableDBIDIter diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/DatabaseQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/DatabaseQuery.java index 703f0abd..f37694fe 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/DatabaseQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/DatabaseQuery.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.database.query; * Will only contain elemental stuff such as some hints. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/DistanceSimilarityQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/DistanceSimilarityQuery.java index 5f0ea430..aae16b79 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/DistanceSimilarityQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/DistanceSimilarityQuery.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.database.query.similarity.SimilarityQuery; * combined implementations of both. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/LinearScanQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/LinearScanQuery.java index ad580c97..fa4b43b7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/LinearScanQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/LinearScanQuery.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.database.query; * Marker interface for linear scan (slow, non-accelerated) queries. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses de.lmu.ifi.dbs.elki.database.Database */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/AbstractDatabaseDistanceQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/AbstractDatabaseDistanceQuery.java index f37c7cc7..a52da9af 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/AbstractDatabaseDistanceQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/AbstractDatabaseDistanceQuery.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * Run a database query in a database context. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Database object type. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/AbstractDistanceQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/AbstractDistanceQuery.java index b6ea580a..77aeccb4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/AbstractDistanceQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/AbstractDistanceQuery.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * distances. * * @author Erich Schubert + * @since 0.4.0 * * @param O Input object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/DBIDDistanceQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/DBIDDistanceQuery.java index 2cb55529..3185376b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/DBIDDistanceQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/DBIDDistanceQuery.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.DBIDDistanceFunction; * Run a distance query based on DBIDs * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.uses DBIDDistanceFunction diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/DBIDRangeDistanceQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/DBIDRangeDistanceQuery.java index 5976d247..70c17202 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/DBIDRangeDistanceQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/DBIDRangeDistanceQuery.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.DBIDRangeDistanceFunction; * Run a distance query based on DBIDRanges * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.uses DBIDRangeDistanceFunction @@ -59,6 +60,7 @@ public class DBIDRangeDistanceQuery extends DBIDDistanceQuery { public DBIDRangeDistanceQuery(Relation<DBID> relation, DBIDRangeDistanceFunction distanceFunction) { super(relation, distanceFunction); this.range = DBIDUtil.assertRange(relation.getDBIDs()); + distanceFunction.checkRange(this.range); this.distanceFunction = distanceFunction; } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/DistanceQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/DistanceQuery.java index c1ce98a1..6eac7fa8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/DistanceQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/DistanceQuery.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction; * distances. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/PrimitiveDistanceQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/PrimitiveDistanceQuery.java index 1dbd0dff..a91c7e43 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/PrimitiveDistanceQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/PrimitiveDistanceQuery.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.PrimitiveDistanceFunction; * Run a database query in a database context. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.uses PrimitiveDistanceFunction diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/PrimitiveDistanceSimilarityQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/PrimitiveDistanceSimilarityQuery.java index ccea951b..bb2c7d8c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/PrimitiveDistanceSimilarityQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/PrimitiveDistanceSimilarityQuery.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.distance.similarityfunction.PrimitiveSimilarityFuncti * Combination query class, for convenience. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses PrimitiveSimilarityFunction * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/SpatialDistanceQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/SpatialDistanceQuery.java index 21e0deda..9ddc5bdb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/SpatialDistanceQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/SpatialDistanceQuery.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.SpatialPrimitiveDistanceFun * Query interface for spatial distance queries. * * @author Erich Schubert + * @since 0.4.0 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/SpatialPrimitiveDistanceQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/SpatialPrimitiveDistanceQuery.java index f7272014..50ff7992 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/SpatialPrimitiveDistanceQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/distance/SpatialPrimitiveDistanceQuery.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.SpatialPrimitiveDistanceFun /** * Distance query for spatial distance functions * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses SpatialPrimitiveDistanceFunction * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/AbstractDistanceKNNQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/AbstractDistanceKNNQuery.java index 883e4e74..69856801 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/AbstractDistanceKNNQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/AbstractDistanceKNNQuery.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * Instance for the query on a particular database. * * @author Erich Schubert + * @since 0.4.0 */ public abstract class AbstractDistanceKNNQuery<O> implements KNNQuery<O> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/KNNQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/KNNQuery.java index 67010016..cf214a4e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/KNNQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/KNNQuery.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.database.query.DatabaseQuery; * The interface of an actual instance. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.has KNNList oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/LinearScanDistanceKNNQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/LinearScanDistanceKNNQuery.java index 31e27242..8e362b56 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/LinearScanDistanceKNNQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/LinearScanDistanceKNNQuery.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery; * Instance of this query for a particular database. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.has DistanceQuery diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/LinearScanEuclideanDistanceKNNQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/LinearScanEuclideanDistanceKNNQuery.java index e4ca590d..807b194f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/LinearScanEuclideanDistanceKNNQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/LinearScanEuclideanDistanceKNNQuery.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SquaredEuclideanD * retrieve the query object from the relation only once! * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses PrimitiveDistanceQuery * @apiviz.uses EuclideanDistanceFunction diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/LinearScanPrimitiveDistanceKNNQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/LinearScanPrimitiveDistanceKNNQuery.java index ccb52533..a1234a43 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/LinearScanPrimitiveDistanceKNNQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/LinearScanPrimitiveDistanceKNNQuery.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.PrimitiveDistanceFunction; * retrieve the query object from the relation only once! * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses PrimitiveDistanceQuery * @apiviz.uses PrimitiveDistanceFunction diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/PreprocessorKNNQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/PreprocessorKNNQuery.java index 6a851b80..10957258 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/PreprocessorKNNQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/knn/PreprocessorKNNQuery.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * Instance for a particular database, invoking the preprocessor. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Data object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/AbstractDistanceRangeQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/AbstractDistanceRangeQuery.java index af121f59..809ccf25 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/AbstractDistanceRangeQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/AbstractDistanceRangeQuery.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * instance * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Database object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/LinearScanDistanceRangeQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/LinearScanDistanceRangeQuery.java index 809d563b..bab6521c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/LinearScanDistanceRangeQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/LinearScanDistanceRangeQuery.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery; * Default linear scan range query class. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.has DistanceQuery diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/LinearScanEuclideanDistanceRangeQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/LinearScanEuclideanDistanceRangeQuery.java index d89b3b60..74e0bc6b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/LinearScanEuclideanDistanceRangeQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/LinearScanEuclideanDistanceRangeQuery.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SquaredEuclideanD * Optimized linear scan for Euclidean distance range queries. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses SquaredEuclideanDistanceFunction * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/LinearScanPrimitiveDistanceRangeQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/LinearScanPrimitiveDistanceRangeQuery.java index 80828bd8..aff636fa 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/LinearScanPrimitiveDistanceRangeQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/LinearScanPrimitiveDistanceRangeQuery.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.PrimitiveDistanceFunction; * once from the relation. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses PrimitiveDistanceQuery * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/RangeQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/RangeQuery.java index 3dfe9c5e..f5cf8525 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/RangeQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/range/RangeQuery.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.database.query.DatabaseQuery; * called "range queries". * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.uses DoubleDBIDList oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/AbstractRKNNQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/AbstractRKNNQuery.java index 32d19c76..36550fe4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/AbstractRKNNQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/AbstractRKNNQuery.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * Instance for the query on a particular database. * * @author Erich Schubert + * @since 0.4.0 */ public abstract class AbstractRKNNQuery<O> implements RKNNQuery<O> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/LinearScanRKNNQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/LinearScanRKNNQuery.java index 60a64552..bd16a8a1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/LinearScanRKNNQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/LinearScanRKNNQuery.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.database.query.knn.KNNQuery; * Default linear scan RKNN query class. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.has KNNQuery diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/PreprocessorRKNNQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/PreprocessorRKNNQuery.java index 2f971854..4be95a39 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/PreprocessorRKNNQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/PreprocessorRKNNQuery.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * Instance for a particular database, invoking the preprocessor. * * @author Elke Achtert + * @since 0.4.0 */ public class PreprocessorRKNNQuery<O> implements RKNNQuery<O> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/RKNNQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/RKNNQuery.java index a0822585..c45aa782 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/RKNNQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/rknn/RKNNQuery.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.database.query.DatabaseQuery; * Abstract reverse kNN Query interface. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses DoubleDBIDList oneway - - «create» * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/AbstractDBIDSimilarityQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/AbstractDBIDSimilarityQuery.java index 142d0577..f30c4cdb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/AbstractDBIDSimilarityQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/AbstractDBIDSimilarityQuery.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * Run a database query in a database context. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Database object type. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/AbstractSimilarityQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/AbstractSimilarityQuery.java index 44e10020..08b51dcc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/AbstractSimilarityQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/AbstractSimilarityQuery.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * similarity functions. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Input object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/PrimitiveSimilarityQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/PrimitiveSimilarityQuery.java index b961222c..450f674e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/PrimitiveSimilarityQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/PrimitiveSimilarityQuery.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.distance.similarityfunction.PrimitiveSimilarityFuncti * Run a database query in a database context. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has PrimitiveSimilarityFunction * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/SimilarityQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/SimilarityQuery.java index 9f9e2531..7dbf7403 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/SimilarityQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/query/similarity/SimilarityQuery.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.distance.similarityfunction.SimilarityFunction; * similarity functions. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/AbstractRelation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/AbstractRelation.java index 9022c2d0..21694a4c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/AbstractRelation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/AbstractRelation.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * Abstract base class for relations. * * @author Erich Schubert + * @since 0.7.0 * * @param <O> Data type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ConvertToStringView.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ConvertToStringView.java index df4da4ef..6ab6753c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ConvertToStringView.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ConvertToStringView.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * representation. * * @author Erich Schubert + * @since 0.4.0 */ public class ConvertToStringView extends AbstractRelation<String> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/DBIDView.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/DBIDView.java index f2a3b741..612b0755 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/DBIDView.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/DBIDView.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * Pseudo-representation that is the object ID itself. * * @author Erich Schubert + * @since 0.4.0 */ public class DBIDView extends AbstractRelation<DBID> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/DoubleRelation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/DoubleRelation.java index 73641b9c..35ce7bc4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/DoubleRelation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/DoubleRelation.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * Interface for double-valued relations. * * @author Erich Schubert + * @since 0.7.0 */ public interface DoubleRelation extends ModifiableRelation<Double> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/MaterializedDoubleRelation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/MaterializedDoubleRelation.java index 0d9c2a21..2b2d6ef7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/MaterializedDoubleRelation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/MaterializedDoubleRelation.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * set(), remove the DBID, then delete(). * * @author Erich Schubert + * @since 0.4.0 */ public class MaterializedDoubleRelation extends AbstractRelation<Double>implements DoubleRelation { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/MaterializedRelation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/MaterializedRelation.java index a7aa2995..463c5c26 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/MaterializedRelation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/MaterializedRelation.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * TODO: is this semantic sane? * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Data type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ModifiableRelation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ModifiableRelation.java index 0127fa66..98cd93a5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ModifiableRelation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ModifiableRelation.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * creation (i.e. notifying them of inserts and deletions). * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Data type. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ProjectedView.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ProjectedView.java index 513dab9d..170d5ad2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ProjectedView.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ProjectedView.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * Projected relation view (non-materialized) * * @author Erich Schubert + * @since 0.4.0 * * @param <IN> Vector type * @param <OUT> Vector type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ProxyView.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ProxyView.java index 51306d52..03221e94 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ProxyView.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/ProxyView.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * passed on to the wrapped representation. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/Relation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/Relation.java index 88b4b18d..9bc9eff2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/Relation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/Relation.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.result.HierarchicalResult; * An object representation from a database. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses DBIDRef * @apiviz.exclude TooltipStringVisualization diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/RelationUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/RelationUtil.java index ac9fed6d..2dd8c62e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/RelationUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/database/relation/RelationUtil.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * Utility functions for handling database relation. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.uses Relation oneway * @apiviz.has CollectionFromRelation diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/AbstractDatabaseConnection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/AbstractDatabaseConnection.java index e75187d4..72c1ff98 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/AbstractDatabaseConnection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/AbstractDatabaseConnection.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * already provides the setting of the database according to parameters. * * @author Elke Achtert + * @since 0.2 * * @apiviz.uses ObjectFilter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/ArrayAdapterDatabaseConnection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/ArrayAdapterDatabaseConnection.java index 316ead88..a9cb0cd1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/ArrayAdapterDatabaseConnection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/ArrayAdapterDatabaseConnection.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * Note: this class is not parameterizable, but can only be used from Java. * * @author Erich Schubert + * @since 0.5.0 */ public class ArrayAdapterDatabaseConnection implements DatabaseConnection { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/BundleDatabaseConnection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/BundleDatabaseConnection.java index 58d2bbf7..2abd6f83 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/BundleDatabaseConnection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/BundleDatabaseConnection.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; * indexes. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.composedOf BundleReader */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/ConcatenateFilesDatabaseConnection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/ConcatenateFilesDatabaseConnection.java index ce639606..c5f98815 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/ConcatenateFilesDatabaseConnection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/ConcatenateFilesDatabaseConnection.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileListParameter * Database that will loading multiple files, concatenating the results. * * @author Erich Schubert + * @since 0.5.0 */ public class ConcatenateFilesDatabaseConnection extends AbstractDatabaseConnection { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/DBIDRangeDatabaseConnection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/DBIDRangeDatabaseConnection.java index 117a9eaa..2a50859e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/DBIDRangeDatabaseConnection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/DBIDRangeDatabaseConnection.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * This is useful when using e.g. a distance matrix to access external data. * * @author Erich Schubert + * @since 0.5.0 */ @Description("This class generates a sequence of DBIDs to 'load' into a database. This is useful when using an external data matrix, and not requiring access to the actual vectors.") public class DBIDRangeDatabaseConnection implements DatabaseConnection { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/DatabaseConnection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/DatabaseConnection.java index 77adf35b..42b62315 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/DatabaseConnection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/DatabaseConnection.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.datasource.bundle.MultipleObjectsBundle; * an intermediate connection to a database system. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.landmark * @apiviz.has MultipleObjectsBundle diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/EmptyDatabaseConnection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/EmptyDatabaseConnection.java index 4fb02813..f1198774 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/EmptyDatabaseConnection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/EmptyDatabaseConnection.java @@ -25,6 +25,7 @@ package de.lmu.ifi.dbs.elki.datasource; import de.lmu.ifi.dbs.elki.datasource.bundle.MultipleObjectsBundle; import de.lmu.ifi.dbs.elki.logging.Logging; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; @@ -32,9 +33,11 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * Pseudo database that is empty. * * @author Erich Schubert + * @since 0.3 */ @Title("Empty Database") @Description("Dummy data source that does not provide any objects.") +@Alias("de.lmu.ifi.dbs.elki.database.connection.EmptyDatabaseConnection") public class EmptyDatabaseConnection extends AbstractDatabaseConnection { /** * Static logger @@ -59,4 +62,4 @@ public class EmptyDatabaseConnection extends AbstractDatabaseConnection { protected Logging getLogger() { return LOG; } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/ExternalIDJoinDatabaseConnection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/ExternalIDJoinDatabaseConnection.java index 771f6c80..a04fb46d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/ExternalIDJoinDatabaseConnection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/ExternalIDJoinDatabaseConnection.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectListParamet * Joins multiple data sources by their label * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses ExternalID */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/FileBasedDatabaseConnection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/FileBasedDatabaseConnection.java index 3fffb19d..a96b5f16 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/FileBasedDatabaseConnection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/FileBasedDatabaseConnection.java @@ -31,7 +31,10 @@ import java.io.InputStream; import java.util.List; import de.lmu.ifi.dbs.elki.datasource.filter.ObjectFilter; +import de.lmu.ifi.dbs.elki.datasource.parser.ArffParser; +import de.lmu.ifi.dbs.elki.datasource.parser.NumberVectorLabelParser; import de.lmu.ifi.dbs.elki.datasource.parser.Parser; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.FileUtil; import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; @@ -42,9 +45,11 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; * File based database connection based on the parser to be set. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.landmark */ +@Alias("de.lmu.ifi.dbs.elki.database.connection.FileBasedDatabaseConnection") public class FileBasedDatabaseConnection extends InputStreamDatabaseConnection { /** * Constructor. @@ -115,12 +120,18 @@ public class FileBasedDatabaseConnection extends InputStreamDatabaseConnection { @Override protected void makeOptions(Parameterization config) { + Class<? extends Parser> defaultParser = NumberVectorLabelParser.class; // Add the input file first, for usability reasons. final FileParameter inputParam = new FileParameter(INPUT_ID, FileParameter.FileType.INPUT_FILE); if(config.grab(inputParam)) { infile = inputParam.getValue(); + String nam = infile.getName(); + if(nam != null && (nam.endsWith(".arff") || nam.endsWith(".arff.gz"))) { + defaultParser = ArffParser.class; + } } - super.makeOptions(config); + configParser(config, Parser.class, defaultParser); + configFilters(config); } @Override @@ -128,4 +139,4 @@ public class FileBasedDatabaseConnection extends InputStreamDatabaseConnection { return new FileBasedDatabaseConnection(filters, parser, infile); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/GeneratorXMLDatabaseConnection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/GeneratorXMLDatabaseConnection.java index 8d3df23b..201122ce 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/GeneratorXMLDatabaseConnection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/GeneratorXMLDatabaseConnection.java @@ -75,6 +75,7 @@ import de.lmu.ifi.dbs.elki.utilities.xml.XMLNodeIterator; * supported) data sets that satisfy a given specification file. * * @author Erich Schubert + * @since 0.2 * * @apiviz.composedOf GeneratorMain */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/InputStreamDatabaseConnection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/InputStreamDatabaseConnection.java index 444e15af..e82a2354 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/InputStreamDatabaseConnection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/InputStreamDatabaseConnection.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * Database connection expecting input from an input stream such as stdin. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.uses Parser oneway - - runs */ @@ -132,7 +133,6 @@ public class InputStreamDatabaseConnection extends AbstractDatabaseConnection { public static class Parameterizer extends AbstractDatabaseConnection.Parameterizer { @Override protected void makeOptions(Parameterization config) { - super.makeOptions(config); configParser(config, Parser.class, NumberVectorLabelParser.class); configFilters(config); } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/LabelJoinDatabaseConnection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/LabelJoinDatabaseConnection.java index 2e9e5fc9..28f010e3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/LabelJoinDatabaseConnection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/LabelJoinDatabaseConnection.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectListParamet * Joins multiple data sources by their label * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses LabelList */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/MultipleObjectsBundleDatabaseConnection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/MultipleObjectsBundleDatabaseConnection.java index 249135c8..94b9aaa0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/MultipleObjectsBundleDatabaseConnection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/MultipleObjectsBundleDatabaseConnection.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.datasource.bundle.MultipleObjectsBundle; * database. * * @author Erich Schubert + * @since 0.4.0 */ public class MultipleObjectsBundleDatabaseConnection implements DatabaseConnection { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/PresortedBlindJoinDatabaseConnection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/PresortedBlindJoinDatabaseConnection.java index 1f36c0bf..2c7a0dc9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/PresortedBlindJoinDatabaseConnection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/PresortedBlindJoinDatabaseConnection.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectListParamet * sources are ordered appropriately! * * @author Erich Schubert + * @since 0.5.0 */ @Description("Blindly joins multiple data sources, assuming they are ordered the same way.") public class PresortedBlindJoinDatabaseConnection extends AbstractDatabaseConnection { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/RandomDoubleVectorDatabaseConnection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/RandomDoubleVectorDatabaseConnection.java index 701f51c5..a34f8fe4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/RandomDoubleVectorDatabaseConnection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/RandomDoubleVectorDatabaseConnection.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * Produce a database of random double vectors with each dimension in [0:1]. * * @author Erich Schubert + * @since 0.4.0 */ public class RandomDoubleVectorDatabaseConnection extends AbstractDatabaseConnection { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleMeta.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleMeta.java index 041961ae..2be09983 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleMeta.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleMeta.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.data.type.SimpleTypeInformation; * it improves code readability and type safety. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf SimpleTypeInformation */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleReader.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleReader.java index e0534408..a9ee6dce 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleReader.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleReader.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; * TODO: resize buffer when necessary? * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.uses MappedByteBuffer - - «reads» * @apiviz.uses FileChannel - - «reads» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleStreamSource.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleStreamSource.java index 7e98c135..9254e9da 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleStreamSource.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleStreamSource.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDVar; * Soruce for a bundle stream * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf BundleMeta * @apiviz.has BundleStreamSource.Event diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleWriter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleWriter.java index f4c2ece3..f5e3af9d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleWriter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/BundleWriter.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; * Bundle streams that add new columns are not supported. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.uses BundleStreamSource - - «reads» * @apiviz.uses WritableByteChannel - - «writes» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/MultipleObjectsBundle.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/MultipleObjectsBundle.java index a910fb56..507ef6a6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/MultipleObjectsBundle.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/MultipleObjectsBundle.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * with multiple representations outside of any index structure. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/ObjectBundle.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/ObjectBundle.java index 46ab032e..3af418c4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/ObjectBundle.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/ObjectBundle.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDVar; * Shared API for both single-object and multi-object packages. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf BundleMeta */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/SingleObjectBundle.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/SingleObjectBundle.java index 0f93bcd1..0eacf962 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/SingleObjectBundle.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/SingleObjectBundle.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDVar; * representations outside of any index structure. * * @author Erich Schubert + * @since 0.4.0 */ public class SingleObjectBundle implements ObjectBundle { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/StreamFromBundle.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/StreamFromBundle.java index 10762d4b..085aacdf 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/StreamFromBundle.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/StreamFromBundle.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDVar; * To use this, invoke {@link MultipleObjectsBundle#asStream()}. * * @author Erich Schubert + * @since 0.4.0 */ public class StreamFromBundle implements BundleStreamSource { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractConversionFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractConversionFilter.java index 57eb6501..dbb492d5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractConversionFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractConversionFilter.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * Abstract base class for simple conversion filters such as normalizations and projections. * * @author Erich Schubert + * @since 0.4.0 * * @param <I> Input object type * @param <O> Input object type @@ -74,7 +75,7 @@ public abstract class AbstractConversionFilter<I, O> implements ObjectFilter { // When necessary, perform an initialization scan if(prepareStart(castType)) { - FiniteProgress pprog = logger.isVerbose() ? new FiniteProgress("Preparing normalization.", objects.dataLength(), logger) : null; + FiniteProgress pprog = logger.isVerbose() ? new FiniteProgress("Preparing normalization", objects.dataLength(), logger) : null; for(Object o : column) { @SuppressWarnings("unchecked") final I obj = (I) o; @@ -90,7 +91,7 @@ public abstract class AbstractConversionFilter<I, O> implements ObjectFilter { bundle.appendColumn(convertedType(castType), castColumn); // Normalization scan - FiniteProgress nprog = logger.isVerbose() ? new FiniteProgress("Data normalization.", objects.dataLength(), logger) : null; + FiniteProgress nprog = logger.isVerbose() ? new FiniteProgress("Data normalization", objects.dataLength(), logger) : null; for(int i = 0; i < objects.dataLength(); i++) { @SuppressWarnings("unchecked") final I obj = (I) column.get(i); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractStreamConversionFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractStreamConversionFilter.java index 19aa0d53..57b8474a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractStreamConversionFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractStreamConversionFilter.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.datasource.bundle.BundleMeta; * projections. * * @author Erich Schubert + * @since 0.5.0 * * @param <I> Input object type * @param <O> Input object type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractStreamFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractStreamFilter.java index f2cf7e62..19d8ce05 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractStreamFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractStreamFilter.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.datasource.bundle.MultipleObjectsBundle; * Abstract base class for streaming filters. * * @author Erich Schubert + * @since 0.4.0 */ public abstract class AbstractStreamFilter implements StreamFilter { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractVectorConversionFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractVectorConversionFilter.java index 4c4e92bd..4da87ed1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractVectorConversionFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractVectorConversionFilter.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.data.type.SimpleTypeInformation; * Abstract class for filters that produce number vectors. * * @author Erich Schubert + * @since 0.4.0 * * @param <I> Input vector type * @param <O> Output vector type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractVectorStreamConversionFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractVectorStreamConversionFilter.java index b5111a22..80edde67 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractVectorStreamConversionFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/AbstractVectorStreamConversionFilter.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.data.type.SimpleTypeInformation; * Abstract base class for streaming filters that produce vectors. * * @author Erich Schubert + * @since 0.4.0 * * @param <I> Input type * @param <O> Output vector type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/FilterUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/FilterUtil.java index d8da0f62..2dc97ef0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/FilterUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/FilterUtil.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.logging.LoggingUtil; * Utilities for implementing filters. * * @author Erich Schubert + * @since 0.4.0 */ public final class FilterUtil { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/FixedDBIDsFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/FixedDBIDsFilter.java index f6ae4a41..0177acb4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/FixedDBIDsFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/FixedDBIDsFilter.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * the bundle by adding a column of DBID type to the bundle. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has DBIDRange oneway - - «produces» */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/NoOpFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/NoOpFilter.java index 872daf19..c8c77e0e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/NoOpFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/NoOpFilter.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.datasource.bundle.MultipleObjectsBundle; * just use this dummy filter as first parameter. * * @author Erich Schubert + * @since 0.4.0 */ public class NoOpFilter extends AbstractStreamFilter { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/ObjectFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/ObjectFilter.java index cbf5fa85..ed541778 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/ObjectFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/ObjectFilter.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.datasource.bundle.MultipleObjectsBundle; * Object filters as part of the input step. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/StreamFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/StreamFilter.java index 2e07c52c..9157967e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/StreamFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/StreamFilter.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.datasource.bundle.BundleStreamSource; * keep a reference to earlier data. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/DropNaNFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/DropNaNFilter.java index 8eb54ab4..21300cea 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/DropNaNFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/DropNaNFilter.java @@ -44,8 +44,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * TODO: add support for sparse vectors. * * @author Erich Schubert + * @since 0.4.0 */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.DropNaNFilter" }) +@Alias("de.lmu.ifi.dbs.elki.datasource.filter.DropNaNFilter") public class DropNaNFilter extends AbstractStreamFilter { /** * Class logger diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/NoMissingValuesFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/NoMissingValuesFilter.java index 32b92a8a..a7c425e4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/NoMissingValuesFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/NoMissingValuesFilter.java @@ -36,8 +36,10 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * A filter to remove entries that have missing values. * * @author Erich Schubert + * @since 0.4.0 */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.NoMissingValuesFilter" }) +@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.FilterNoMissingValuesFilter", // +"de.lmu.ifi.dbs.elki.datasource.filter.NoMissingValuesFilter" }) public class NoMissingValuesFilter extends AbstractStreamFilter { /** * Class logger @@ -130,4 +132,4 @@ public class NoMissingValuesFilter extends AbstractStreamFilter { return new NoMissingValuesFilter(); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/ReplaceNaNWithRandomFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/ReplaceNaNWithRandomFilter.java index 6ee9e220..a5222d8f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/ReplaceNaNWithRandomFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/ReplaceNaNWithRandomFilter.java @@ -48,8 +48,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * TODO: add support for sparse vectors. * * @author Erich Schubert + * @since 0.4.0 */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.ReplaceNaNWithRandomFilter" }) +@Alias("de.lmu.ifi.dbs.elki.datasource.filter.ReplaceNaNWithRandomFilter") public class ReplaceNaNWithRandomFilter extends AbstractStreamFilter { /** * Class logger diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/VectorDimensionalityFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/VectorDimensionalityFilter.java index d0bafa31..33a9c13f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/VectorDimensionalityFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/cleaning/VectorDimensionalityFilter.java @@ -44,10 +44,10 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * Filter to remove all vectors that do not have the desired dimensionality. * * @author Erich Schubert + * @since 0.7.0 * * @param <V> Vector type */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.VectorDimensionalityFilter" }) public class VectorDimensionalityFilter<V extends NumberVector> extends AbstractStreamFilter { /** * Class logger. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/AbstractNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/AbstractNormalization.java index e0cd3f09..0e6f783b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/AbstractNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/AbstractNormalization.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.LinearEquationSystem; * Abstract super class for all normalizations. * * @author Elke Achtert + * @since 0.4.0 * * @param <V> Object type processed */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/AbstractStreamNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/AbstractStreamNormalization.java index 1e61a206..e8b099ce 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/AbstractStreamNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/AbstractStreamNormalization.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.LinearEquationSystem; * Abstract super class for all normalizations. * * @author Erich Schubert + * @since 0.4.0 * * @param <V> Object type processed */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/NonNumericFeaturesException.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/NonNumericFeaturesException.java index 16175bc8..4f8cfb56 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/NonNumericFeaturesException.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/NonNumericFeaturesException.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.datasource.filter.normalization; * features have been expected. * * @author Arthur Zimek + * @since 0.4.0 */ public class NonNumericFeaturesException extends Exception { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/Normalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/Normalization.java index 26393bd9..ea08a93e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/Normalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/Normalization.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.LinearEquationSystem; * dependencies quantitatively adapted to the original space. * * @author Arthur Zimek + * @since 0.4.0 * * @apiviz.landmark * @apiviz.has NonNumericFeaturesException diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseBetaNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseBetaNormalization.java index 2500a370..1b9b9d6d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseBetaNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseBetaNormalization.java @@ -59,13 +59,13 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectListParamet * this. * * @author Erich Schubert + * @since 0.6.0 * * @param <V> vector type * * @apiviz.uses NumberVector * @apiviz.uses DistributionEstimator */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseBetaNormalization"}) public class AttributeWiseBetaNormalization<V extends NumberVector> implements Normalization<V> { /** * Class logger. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseCDFNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseCDFNormalization.java index d4028f1e..6d2f77e8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseCDFNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseCDFNormalization.java @@ -64,6 +64,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectListParamet * but they do not detail how to obtain an appropriate function `F`. * * @author Erich Schubert + * @since 0.6.0 * @param <V> vector type * * @apiviz.uses NumberVector diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseErfNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseErfNormalization.java index 83d24244..a099e533 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseErfNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseErfNormalization.java @@ -36,12 +36,14 @@ import de.lmu.ifi.dbs.elki.utilities.Alias; * sense when you have data that has been mean-variance normalized before. * * @author Erich Schubert + * @since 0.4.0 * * @param <V> Object type * * @apiviz.uses NumberVector */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseErfNormalization"}) +@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseErfNormalization", // +"de.lmu.ifi.dbs.elki.datasource.filter.AttributeWiseErfNormalization" }) public class AttributeWiseErfNormalization<V extends NumberVector> extends AbstractNormalization<V> { /** * Class logger. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseMADNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseMADNormalization.java index cdb60a4d..165aa4a1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseMADNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseMADNormalization.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.ExceptionMessages; * robust towards outliers, and only slightly more expensive to compute. * * @author Erich Schubert + * @since 0.6.0 * @param <V> vector type * * @apiviz.uses NumberVector @@ -111,7 +112,7 @@ public class AttributeWiseMADNormalization<V extends NumberVector> implements No // Scratch space for testing: double[] test = new double[castColumn.size()]; - FiniteProgress dprog = LOG.isVerbose() ? new FiniteProgress("Analyzing data.", dim, LOG) : null; + FiniteProgress dprog = LOG.isVerbose() ? new FiniteProgress("Analyzing data", dim, LOG) : null; // We iterate over dimensions, this kind of filter needs fast random // access. for(int d = 0; d < dim; d++) { @@ -147,7 +148,7 @@ public class AttributeWiseMADNormalization<V extends NumberVector> implements No } LOG.ensureCompleted(dprog); - FiniteProgress nprog = LOG.isVerbose() ? new FiniteProgress("Data normalization.", objects.dataLength(), LOG) : null; + FiniteProgress nprog = LOG.isVerbose() ? new FiniteProgress("Data normalization", objects.dataLength(), LOG) : null; // Normalization scan double[] buf = new double[dim]; for(int i = 0; i < objects.dataLength(); i++) { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseMeanNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseMeanNormalization.java index 350f6188..4aedfe3d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseMeanNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseMeanNormalization.java @@ -38,11 +38,11 @@ import de.lmu.ifi.dbs.elki.utilities.FormatUtil; * attribute is scaled to have the same mean (but 0 is not changed). * * @author Erich Schubert + * @since 0.7.0 * @param <V> vector type * * @apiviz.uses NumberVector */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseMeanNormalization"}) public class AttributeWiseMeanNormalization<V extends NumberVector> extends AbstractNormalization<V> { /** * Class logger. @@ -204,4 +204,4 @@ public class AttributeWiseMeanNormalization<V extends NumberVector> extends Abst protected SimpleTypeInformation<? super V> getInputTypeRestriction() { return TypeUtil.NUMBER_VECTOR_FIELD; } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseMinMaxNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseMinMaxNormalization.java index 7981d4f5..8fbff47e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseMinMaxNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseMinMaxNormalization.java @@ -44,11 +44,13 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleListParamet * given minimum and maximum in each dimension. * * @author Elke Achtert + * @since 0.4.0 * @param <V> vector type * * @apiviz.uses NumberVector */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseMinMaxNormalization" }) +@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseMinMaxNormalization", // +"de.lmu.ifi.dbs.elki.datasource.filter.AttributeWiseMinMaxNormalization" }) public class AttributeWiseMinMaxNormalization<V extends NumberVector> extends AbstractNormalization<V> { /** * Class logger. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseVarianceNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseVarianceNormalization.java index e997b907..d53f7ffd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseVarianceNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/AttributeWiseVarianceNormalization.java @@ -46,11 +46,13 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleListParamet * given mean and standard deviation in each dimension. * * @author Erich Schubert + * @since 0.4.0 * @param <V> vector type * * @apiviz.uses NumberVector */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseVarianceNormalization", "z" }) +@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseVarianceNormalization", // +"z", "de.lmu.ifi.dbs.elki.datasource.filter.AttributeWiseVarianceNormalization" }) public class AttributeWiseVarianceNormalization<V extends NumberVector> extends AbstractNormalization<V> { /** * Class logger. @@ -277,4 +279,4 @@ public class AttributeWiseVarianceNormalization<V extends NumberVector> extends return new AttributeWiseVarianceNormalization<>(mean, stddev); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/IntegerRankTieNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/IntegerRankTieNormalization.java index 03c98023..d9733b78 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/IntegerRankTieNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/IntegerRankTieNormalization.java @@ -45,8 +45,9 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arrays.IntegerComparator; * then, followed by the next on "4") * * @author Erich Schubert + * @since 0.5.0 */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.IntegerRankTieNormalization"}) +@Alias("de.lmu.ifi.dbs.elki.datasource.filter.normalization.RankTieNormalization") public class IntegerRankTieNormalization implements ObjectFilter { /** * Constructor. @@ -147,4 +148,4 @@ public class IntegerRankTieNormalization implements ObjectFilter { return (vx < vy) ? -1 : (vx == vy) ? 0 : +1; } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/InverseDocumentFrequencyNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/InverseDocumentFrequencyNormalization.java index 3ebce57d..6b730fc1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/InverseDocumentFrequencyNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/columnwise/InverseDocumentFrequencyNormalization.java @@ -38,12 +38,14 @@ import de.lmu.ifi.dbs.elki.utilities.Alias; * frequency (IDF). See also: TF-IDF for text analysis. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses SparseNumberVector * * @param <V> Vector type */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.InverseDocumentFrequencyNormalization" }) +@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.InverseDocumentFrequencyNormalization", // +"de.lmu.ifi.dbs.elki.datasource.filter.InverseDocumentFrequencyNormalization" }) public class InverseDocumentFrequencyNormalization<V extends SparseNumberVector> extends AbstractNormalization<V> { /** * Class logger. @@ -127,4 +129,4 @@ public class InverseDocumentFrequencyNormalization<V extends SparseNumberVector> protected Logging getLogger() { return LOG; } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/HellingerHistogramNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/HellingerHistogramNormalization.java index a79a3047..352e96dd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/HellingerHistogramNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/HellingerHistogramNormalization.java @@ -39,10 +39,10 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * {@link de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic.HellingerDistanceFunction} * * @author Erich Schubert + * @since 0.7.0 * * @param <V> vector type */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.HellingerHistogramNormalization" }) public class HellingerHistogramNormalization<V extends NumberVector> extends AbstractStreamNormalization<V> { /** * Static instance. @@ -94,4 +94,4 @@ public class HellingerHistogramNormalization<V extends NumberVector> extends Abs return STATIC; } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceLogRankNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceLogRankNormalization.java index 8f46b156..d8d0ff95 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceLogRankNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceLogRankNormalization.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * largest is 1, but using log_2(1+x). * * @author Erich Schubert + * @since 0.7.0 * * @param <V> vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceMeanVarianceNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceMeanVarianceNormalization.java index a546ccd8..fa1eb6d1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceMeanVarianceNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceMeanVarianceNormalization.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Normalize vectors such that they have zero mean and unit variance. * * @author Erich Schubert + * @since 0.7.0 * * @param <V> vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceMinMaxNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceMinMaxNormalization.java index f0b1ceea..fbbd4d46 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceMinMaxNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceMinMaxNormalization.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Normalize vectors such that the smallest attribute is 0, the largest is 1. * * @author Erich Schubert + * @since 0.7.0 * * @param <V> vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceRankNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceRankNormalization.java index f6058ecb..bd85d912 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceRankNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/InstanceRankNormalization.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * largest is 1. * * @author Erich Schubert + * @since 0.7.0 * * @param <V> vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/LengthNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/LengthNormalization.java index df00683e..b82d1eba 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/LengthNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/LengthNormalization.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Heidi Kolb * @author Erich Schubert + * @since 0.5.0 * * @param <V> vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/Log1PlusNormalization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/Log1PlusNormalization.java index 04e27e73..737869ae 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/Log1PlusNormalization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/normalization/instancewise/Log1PlusNormalization.java @@ -41,10 +41,10 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * By default b=1, and thus the transformation is log2(1+|x|). * * @author Erich Schubert + * @since 0.5.0 * * @param <V> vector type */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.Log1PlusNormalization" }) public class Log1PlusNormalization<V extends NumberVector> extends AbstractStreamNormalization<V> { /** * Static instance. @@ -116,4 +116,4 @@ public class Log1PlusNormalization<V extends NumberVector> extends AbstractStrea return new Log1PlusNormalization<>(boost); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/ByLabelFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/ByLabelFilter.java index 381001c0..962e3a7a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/ByLabelFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/ByLabelFilter.java @@ -42,10 +42,12 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.PatternParameter; * A filter to select data set by their label. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses LabelList oneway - - «reads» */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.ByLabelFilter" }) +@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.ByLabelFilter", // +"de.lmu.ifi.dbs.elki.datasource.filter.FilterByLabelFilter" }) public class ByLabelFilter extends AbstractStreamFilter { /** * Class logger @@ -195,4 +197,4 @@ public class ByLabelFilter extends AbstractStreamFilter { return new ByLabelFilter(pattern, inverted); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/RandomSamplingStreamFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/RandomSamplingStreamFilter.java index faf6276f..9418a6c1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/RandomSamplingStreamFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/RandomSamplingStreamFilter.java @@ -40,8 +40,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * Subsampling stream filter. * * @author Erich Schubert + * @since 0.5.0 */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.RandomSamplingStreamFilter" }) +@Alias("de.lmu.ifi.dbs.elki.datasource.filter.RandomSamplingStreamFilter") public class RandomSamplingStreamFilter extends AbstractStreamFilter { /** * Probability diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/ShuffleObjectsFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/ShuffleObjectsFilter.java index 1d86a59d..16afb512 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/ShuffleObjectsFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/ShuffleObjectsFilter.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * A filter to shuffle the dataset. * * @author Erich Schubert + * @since 0.4.0 */ @Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.ShuffleObjectsFilter" }) public class ShuffleObjectsFilter implements ObjectFilter { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/SortByLabelFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/SortByLabelFilter.java index d1a7beb8..5b833c07 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/SortByLabelFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/selection/SortByLabelFilter.java @@ -39,10 +39,11 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * A filter to sort the data set by some label. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses de.lmu.ifi.dbs.elki.data.LabelList oneway - - «reads» */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.SortByLabelFilter" }) +@Alias("de.lmu.ifi.dbs.elki.datasource.filter.SortByLabelFilter") public class SortByLabelFilter implements ObjectFilter { /** * Class logger diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/AbstractSupervisedProjectionVectorFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/AbstractSupervisedProjectionVectorFilter.java index bd89e7f1..3854ee7d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/AbstractSupervisedProjectionVectorFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/AbstractSupervisedProjectionVectorFilter.java @@ -23,9 +23,6 @@ package de.lmu.ifi.dbs.elki.datasource.filter.transform; along with this program. If not, see <http://www.gnu.org/licenses/>. */ -import gnu.trove.list.TIntList; -import gnu.trove.list.array.TIntArrayList; - import java.util.HashMap; import java.util.Iterator; import java.util.List; @@ -42,12 +39,13 @@ import de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.ClassLabelFilter; import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.math.linearalgebra.Matrix; import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; -import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayLikeUtil; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.CommonConstraints; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; +import gnu.trove.list.TIntList; +import gnu.trove.list.array.TIntArrayList; /** * Base class for supervised projection methods. @@ -56,6 +54,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * * @author Angela Peng * @author Erich Schubert + * @since 0.6.0 * * @param <V> Vector type */ @@ -113,7 +112,7 @@ public abstract class AbstractSupervisedProjectionVectorFilter<V extends NumberV List<V> vectorcolumn = (List<V>) column; final VectorFieldTypeInformation<?> vtype = (VectorFieldTypeInformation<?>) type; @SuppressWarnings("unchecked") - NumberVector.Factory<V> factory = (NumberVector.Factory<V> ) vtype.getFactory(); + NumberVector.Factory<V> factory = (NumberVector.Factory<V>) vtype.getFactory(); int dim = vtype.getDimensionality(); if(tdim > dim) { @@ -127,7 +126,7 @@ public abstract class AbstractSupervisedProjectionVectorFilter<V extends NumberV Matrix proj = computeProjectionMatrix(vectorcolumn, classcolumn, dim); for(int i = 0; i < dataLength; i++) { final Vector pv = proj.times(vectorcolumn.get(i).getColumnVector()); - V filteredObj = factory.newNumberVector(pv, ArrayLikeUtil.VECTORADAPTER); + V filteredObj = factory.newNumberVector(pv); vectorcolumn.set(i, filteredObj); } bundle.appendColumn(convertedType(type, factory), column); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/ClassicMultidimensionalScalingTransform.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/ClassicMultidimensionalScalingTransform.java index af1aa3af..8c1d161c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/ClassicMultidimensionalScalingTransform.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/ClassicMultidimensionalScalingTransform.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * instead. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.composedOf SingularValueDecomposition * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/FastMultidimensionalScalingTransform.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/FastMultidimensionalScalingTransform.java index 121e500b..7270b3ac 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/FastMultidimensionalScalingTransform.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/FastMultidimensionalScalingTransform.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * This implementation is O(n^2), and uses O(n^2) memory. * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Data type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/GlobalPrincipalComponentAnalysisTransform.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/GlobalPrincipalComponentAnalysisTransform.java index 86b30c0c..20b64eb0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/GlobalPrincipalComponentAnalysisTransform.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/GlobalPrincipalComponentAnalysisTransform.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * {@link Parameterizer#FILTER_ID} parameter! * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.composedOf PCARunner * @apiviz.composedOf CovarianceMatrix diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/HistogramJitterFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/HistogramJitterFilter.java index 609ee0c9..a88ec88d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/HistogramJitterFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/HistogramJitterFilter.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.data.type.TypeUtil; import de.lmu.ifi.dbs.elki.datasource.filter.AbstractVectorStreamConversionFilter; import de.lmu.ifi.dbs.elki.math.random.RandomFactory; import de.lmu.ifi.dbs.elki.math.statistics.distribution.ExponentialDistribution; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; @@ -52,10 +53,12 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * to control the degradation amount. * * @author Erich Schubert + * @since 0.5.5 * * @param <V> Vector type */ @Description("Add uniform Jitter to a dataset, while preserving the total vector sum.") +@Alias("de.lmu.ifi.dbs.elki.datasource.filter.HistogramJitterFilter") public class HistogramJitterFilter<V extends NumberVector> extends AbstractVectorStreamConversionFilter<V, V> { /** * Jitter amount. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/LatLngToECEFFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/LatLngToECEFFilter.java index e82f07d1..9284f4ab 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/LatLngToECEFFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/LatLngToECEFFilter.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Z), such that Euclidean distance is line-of-sight. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses NumberVector * @apiviz.composedOf EarthModel diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/LinearDiscriminantAnalysisFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/LinearDiscriminantAnalysisFilter.java index 58e29021..08ebcc8b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/LinearDiscriminantAnalysisFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/LinearDiscriminantAnalysisFilter.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * * @author Angela Peng * @author Erich Schubert + * @since 0.6.0 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/LngLatToECEFFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/LngLatToECEFFilter.java index fae5ee9f..7fcabaaf 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/LngLatToECEFFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/LngLatToECEFFilter.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Z), such that Euclidean distance is line-of-sight. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses NumberVector * @apiviz.composedOf EarthModel diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/NumberVectorFeatureSelectionFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/NumberVectorFeatureSelectionFilter.java index e2a03544..2716b830 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/NumberVectorFeatureSelectionFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/NumberVectorFeatureSelectionFilter.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntListParameter; * </p> * * @author Arthur Zimek + * @since 0.4.0 * * @apiviz.uses NumberVector * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/NumberVectorRandomFeatureSelectionFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/NumberVectorRandomFeatureSelectionFilter.java index fff1f44a..fca5aa73 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/NumberVectorRandomFeatureSelectionFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/NumberVectorRandomFeatureSelectionFilter.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * randomly selected subset of attributes. * * @author Arthur Zimek + * @since 0.4.0 * * @apiviz.uses NumberVector * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/PerturbationFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/PerturbationFilter.java index 680cd023..afae04a2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/PerturbationFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/PerturbationFilter.java @@ -67,6 +67,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.LongParameter; * </p> * * @author Arthur Zimek + * @since 0.7.0 */ @Title("Data Perturbation for Outlier Detection Ensembles") @Description("A filter to perturb a datasset on read by an additive noise component, implemented for use in an outlier ensemble (this reference).") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/ProjectionFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/ProjectionFilter.java index ed87b8db..2074929e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/ProjectionFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/ProjectionFilter.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Apply a projection to the data. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.composedOf Projection * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/ClassLabelFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/ClassLabelFilter.java index 4e48adbc..33b715dc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/ClassLabelFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/ClassLabelFilter.java @@ -44,11 +44,12 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Class that turns a label column into a class label column. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses LabelList oneway - - «reads» * @apiviz.has ClassLabel */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.ClassLabelFilter" }) +@Alias("de.lmu.ifi.dbs.elki.datasource.filter.ClassLabelFilter") public class ClassLabelFilter implements ObjectFilter { /** * The index of the label to be used as class label, null if no class label is diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/ClassLabelFromPatternFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/ClassLabelFromPatternFilter.java index 0d3279ce..1eab3804 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/ClassLabelFromPatternFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/ClassLabelFromPatternFilter.java @@ -44,8 +44,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.StringParameter; * Streaming filter to derive an outlier class label. * * @author Erich Schubert + * @since 0.6.0 */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.ClassLabelFromPatternFilter" }) +@Alias("de.lmu.ifi.dbs.elki.datasource.filter.ClassLabelFromPatternFilter") public class ClassLabelFromPatternFilter extends AbstractStreamFilter { /** * Current meta data diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/ExternalIDFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/ExternalIDFilter.java index 72ac5578..b6baaebf 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/ExternalIDFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/ExternalIDFilter.java @@ -42,11 +42,12 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * Class that turns a label column into an external ID column. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses LabelList oneway - - «reads» * @apiviz.has ExternalID oneway - - «produces» */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.ExternalIDFilter" }) +@Alias("de.lmu.ifi.dbs.elki.datasource.filter.ExternalIDFilter") public class ExternalIDFilter implements ObjectFilter { /** * The index of the label to be used as external Id. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/MultivariateTimeSeriesFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/MultivariateTimeSeriesFilter.java index 4ee50783..5d4e253b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/MultivariateTimeSeriesFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/MultivariateTimeSeriesFilter.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * Class to "fold" a flat number vector into a multivariate time series. * * @author Erich Schubert + * @since 0.7.0 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/SparseVectorFieldFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/SparseVectorFieldFilter.java index 86092f7c..f174eb70 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/SparseVectorFieldFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/SparseVectorFieldFilter.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.Alias; * the maximum dimensionality for each vector. * * @author Erich Schubert + * @since 0.5.0 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/SplitNumberVectorFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/SplitNumberVectorFilter.java index bf1e415f..95e3fd6a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/SplitNumberVectorFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/SplitNumberVectorFilter.java @@ -45,12 +45,13 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntListParameter; * Split an existing column into two types. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses NumberVector * * @param <V> Vector type */ -@Alias({ "de.lmu.ifi.dbs.elki.datasource.filter.normalization.SplitNumberVectorFilter" }) +@Alias("de.lmu.ifi.dbs.elki.datasource.filter.SplitNumberVectorFilter") public class SplitNumberVectorFilter<V extends NumberVector> implements ObjectFilter { /** * Selected dimensions. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/UncertainSplitFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/UncertainSplitFilter.java index 0ae85cd2..68dcf218 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/UncertainSplitFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/UncertainSplitFilter.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * uncertain observation. * * @author Erich Schubert + * @since 0.7.0 */ public class UncertainSplitFilter extends AbstractConversionFilter<NumberVector, UnweightedDiscreteUncertainObject> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/UncertainifyFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/UncertainifyFilter.java index e45b964c..ccd8e72f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/UncertainifyFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/UncertainifyFilter.java @@ -57,6 +57,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * * @author Alexander Koos * @author Erich Schubert + * @since 0.7.0 * * @param <UO> Uncertain object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/WeightedUncertainSplitFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/WeightedUncertainSplitFilter.java index 48df989b..0a10b036 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/WeightedUncertainSplitFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/typeconversions/WeightedUncertainSplitFilter.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * interpret as uncertain observation. * * @author Erich Schubert + * @since 0.7.0 */ public class WeightedUncertainSplitFilter extends AbstractConversionFilter<NumberVector, WeightedDiscreteUncertainObject> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/AbstractStreamingParser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/AbstractStreamingParser.java index 642a7cf1..3671a447 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/AbstractStreamingParser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/AbstractStreamingParser.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * Base class for streaming parsers. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses CSVReaderFormat * @apiviz.composedOf TokenizedReader diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/ArffParser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/ArffParser.java index 515c68c4..9a2cf786 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/ArffParser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/ArffParser.java @@ -68,6 +68,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.PatternParameter; * TODO: allow optional class labels. * * @author Erich Schubert + * @since 0.4.0 */ public class ArffParser implements Parser { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/BitVectorLabelParser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/BitVectorLabelParser.java index e6060bb4..ddef1548 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/BitVectorLabelParser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/BitVectorLabelParser.java @@ -23,12 +23,14 @@ package de.lmu.ifi.dbs.elki.datasource.parser; along with this program. If not, see <http://www.gnu.org/licenses/>. */ -import gnu.trove.list.array.TLongArrayList; + import de.lmu.ifi.dbs.elki.data.BitVector; import de.lmu.ifi.dbs.elki.data.LabelList; import de.lmu.ifi.dbs.elki.logging.Logging; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; +import gnu.trove.list.array.TLongArrayList; /** * Parser for parsing one BitVector per line, bits separated by whitespace. @@ -37,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * Bit. Lines starting with "#" will be ignored. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.has BitVector */ @@ -47,6 +50,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; "If this fails, it will be appended to a label. " + // "(Thus, any label must not be parseable as Bit.) " + // "Empty lines and lines beginning with \"#\" will be ignored.") +@Alias("de.lmu.ifi.dbs.elki.parser.BitVectorLabelParser") public class BitVectorLabelParser extends NumberVectorLabelParser<BitVector> implements Parser { /** * Class logger diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/CSVReaderFormat.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/CSVReaderFormat.java index c0adbabd..5104f83d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/CSVReaderFormat.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/CSVReaderFormat.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.StringParameter; * * @author Arthur Zimek * @author Erich Schubert + * @since 0.2 * * @apiviz.has TokenizedReader */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/CategorialDataAsNumberVectorParser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/CategorialDataAsNumberVectorParser.java index 86054b86..9f6f9c42 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/CategorialDataAsNumberVectorParser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/CategorialDataAsNumberVectorParser.java @@ -40,6 +40,7 @@ import gnu.trove.map.hash.TObjectIntHashMap; * TODO: specify handling for numerical values. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.landmark * @apiviz.has NumberVector diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/ClusteringVectorParser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/ClusteringVectorParser.java index e6b8d82b..26dd9acc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/ClusteringVectorParser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/ClusteringVectorParser.java @@ -73,6 +73,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * TODO: support noise, via negative cluster numbers? * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has Clustering */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/LibSVMFormatParser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/LibSVMFormatParser.java index fab7bc60..8e5dae65 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/LibSVMFormatParser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/LibSVMFormatParser.java @@ -53,6 +53,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * <tt>#</tt>. * * @author Erich Schubert + * @since 0.7.0 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/NumberVectorLabelParser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/NumberVectorLabelParser.java index aaca0190..f3584932 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/NumberVectorLabelParser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/NumberVectorLabelParser.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.data.type.VectorFieldTypeInformation; import de.lmu.ifi.dbs.elki.data.type.VectorTypeInformation; import de.lmu.ifi.dbs.elki.datasource.bundle.BundleMeta; import de.lmu.ifi.dbs.elki.logging.Logging; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.BitsUtil; import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.DoubleArray; import de.lmu.ifi.dbs.elki.utilities.datastructures.hash.Unique; @@ -59,12 +60,15 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Arthur Zimek * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * @apiviz.has NumberVector * * @param <V> the type of NumberVector used */ +@Alias({ "de.lmu.ifi.dbs.elki.parser.NumberVectorLabelParser", // +"de.lmu.ifi.dbs.elki.parser.RealVectorLabelParser" }) public class NumberVectorLabelParser<V extends NumberVector> extends AbstractStreamingParser { /** * Logging class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/Parser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/Parser.java index c9ba4d1a..649fb1fe 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/Parser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/Parser.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.datasource.bundle.MultipleObjectsBundle; * A Parser shall provide a ParsingResult by parsing an InputStream. * * @author Arthur Zimek + * @since 0.4.0 * * @apiviz.landmark * @apiviz.uses InputStream diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/SimplePolygonParser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/SimplePolygonParser.java index 4abd76c6..e291214c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/SimplePolygonParser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/SimplePolygonParser.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.FormatUtil; * Unparseable parts will be treated as labels. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has PolygonsObject */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/SimpleTransactionParser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/SimpleTransactionParser.java index 6fb96359..5fbf8af7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/SimpleTransactionParser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/SimpleTransactionParser.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * of tokens. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has BitVector */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/SparseNumberVectorLabelParser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/SparseNumberVectorLabelParser.java index 478a9686..f6061fa6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/SparseNumberVectorLabelParser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/SparseNumberVectorLabelParser.java @@ -70,6 +70,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Arthur Zimek + * @since 0.2 * * @apiviz.has SparseNumberVector * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/StreamingParser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/StreamingParser.java index a189cd86..a3cb7a99 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/StreamingParser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/StreamingParser.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.datasource.bundle.BundleStreamSource; * combination with filters. * * @author Erich Schubert + * @since 0.4.0 */ public interface StreamingParser extends Parser, BundleStreamSource { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/StringParser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/StringParser.java index 0110ea9a..8750df85 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/StringParser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/StringParser.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.PatternParameter; * * @author Felix Stahlberg * @author Erich Schubert + * @since 0.6.0 */ @Title("String Parser") @Description("Parses new line separated strings") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/TermFrequencyParser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/TermFrequencyParser.java index da0aca26..ccaac348 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/TermFrequencyParser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/datasource/parser/TermFrequencyParser.java @@ -53,6 +53,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * {@link SimpleTransactionParser} instead. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has SparseNumberVector */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractDBIDRangeDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractDBIDRangeDistanceFunction.java index b858f6dd..330f1f6a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractDBIDRangeDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractDBIDRangeDistanceFunction.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * within a consecutive range. This is beneficial for external distances. * * @author Erich Schubert + * @since 0.7.0 */ public abstract class AbstractDBIDRangeDistanceFunction extends AbstractDatabaseDistanceFunction<DBID> implements DBIDRangeDistanceFunction { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractDatabaseDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractDatabaseDistanceFunction.java index 3bd107ca..851e7dc6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractDatabaseDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractDatabaseDistanceFunction.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * Abstract super class for distance functions needing a database context. * * @author Elke Achtert + * @since 0.4.0 * * @apiviz.has AbstractDatabaseDistanceFunction.Instance * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractIndexBasedDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractIndexBasedDistanceFunction.java index 73eed528..1676364e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractIndexBasedDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractIndexBasedDistanceFunction.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Abstract super class for distance functions needing a database index. * * @author Elke Achtert + * @since 0.4.0 * * @apiviz.has AbstractIndexBasedDistanceFunction.Instance * @apiviz.composedOf IndexFactory diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractNumberVectorDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractNumberVectorDistanceFunction.java index b4de6fbf..56dd19ea 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractNumberVectorDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractNumberVectorDistanceFunction.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.data.type.TypeUtil; * on number vectors and returning double values. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractNumberVectorNorm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractNumberVectorNorm.java index 59273fc5..7af85c0e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractNumberVectorNorm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractNumberVectorNorm.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.data.NumberVector; * norms. * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractPrimitiveDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractPrimitiveDistanceFunction.java index a19199b9..e06e2c5b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractPrimitiveDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractPrimitiveDistanceFunction.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * AbstractDistanceFunction provides some methods valid for any extending class. * * @author Arthur Zimek + * @since 0.4.0 * * @apiviz.excludeSubtypes * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractSpatialDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractSpatialDistanceFunction.java index a36faa3f..e73cb7bc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractSpatialDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractSpatialDistanceFunction.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * distance functions easier. * * @author Erich Schubert + * @since 0.4.0 */ public abstract class AbstractSpatialDistanceFunction extends AbstractNumberVectorDistanceFunction implements SpatialPrimitiveDistanceFunction<NumberVector> { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractSpatialNorm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractSpatialNorm.java index b8915ef1..bc3fc200 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractSpatialNorm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/AbstractSpatialNorm.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * distance functions easier. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/ArcCosineDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/ArcCosineDistanceFunction.java index b8227739..a51544e7 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/ArcCosineDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/ArcCosineDistanceFunction.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * value, i.e., <code>arccos(<v1,v2>)</code>. * * @author Arthur Zimek + * @since 0.2 */ @Alias({ "arccos" }) public class ArcCosineDistanceFunction extends AbstractSpatialDistanceFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/BrayCurtisDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/BrayCurtisDistanceFunction.java index 46770514..dafe9c65 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/BrayCurtisDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/BrayCurtisDistanceFunction.java @@ -67,6 +67,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * TODO: add a version optimized for sparse vectors / binary data. * * @author Erich Schubert + * @since 0.4.0 */ @Alias({ "bray-curtis", "braycurtis", "sorensen", "dice", "sorensen-dice" }) @Reference(authors = "J. R. Bray and J. T. Curtis", title = "An ordination of the upland forest communities of southern Wisconsin", booktitle = "Ecological monographs 27.4", url = "http://dx.doi.org/10.2307/1942268") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/CanberraDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/CanberraDistanceFunction.java index 530ee70d..f373e2e1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/CanberraDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/CanberraDistanceFunction.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.4.0 */ @Reference(authors = "G. N. Lance, W. T. Williams", // title = "Computer programs for hierarchical polythetic classification (similarity analyses)", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/ClarkDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/ClarkDistanceFunction.java index 128d7e80..56f7de86 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/ClarkDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/ClarkDistanceFunction.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.4.0 */ @Reference(authors = "M.-M. Deza and E. Deza", title = "Dictionary of distances", booktitle = "Dictionary of distances") public class ClarkDistanceFunction extends AbstractSpatialDistanceFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/CosineDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/CosineDistanceFunction.java index b0f55abd..ec9a9bf6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/CosineDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/CosineDistanceFunction.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * <code>1-(cosine similarity)</code>. * * @author Arthur Zimek + * @since 0.2 */ @Alias({ "cosine" }) public class CosineDistanceFunction extends AbstractSpatialDistanceFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/DBIDDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/DBIDDistanceFunction.java index 4a1803da..8f3ee417 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/DBIDDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/DBIDDistanceFunction.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * Example: external precomputed distances * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.uses DBID oneway - - defined on diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/DBIDRangeDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/DBIDRangeDistanceFunction.java index 23284d1a..6c121ce5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/DBIDRangeDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/DBIDRangeDistanceFunction.java @@ -1,5 +1,7 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction; +import de.lmu.ifi.dbs.elki.database.ids.DBIDRange; + /* This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures @@ -34,6 +36,7 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction; * Example: external precomputed distances * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.uses de.lmu.ifi.dbs.elki.database.ids.DBIDRange oneway - - defined on @@ -47,4 +50,12 @@ public interface DBIDRangeDistanceFunction extends DBIDDistanceFunction { * @return Distance */ double distance(int i1, int i2); + + /** + * Validate the range of DBIDs to use. This will log a warning if an obvious + * mismatch was found. + * + * @param range DBID range + */ + void checkRange(DBIDRange range); }
\ No newline at end of file diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/DistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/DistanceFunction.java index d53c9e26..375083d1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/DistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/DistanceFunction.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * Base interface for any kind of distances. * * @author Erich Schubert + * @since 0.2 * * @param <O> Object type * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/IndexBasedDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/IndexBasedDistanceFunction.java index 8b41f956..9e24c934 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/IndexBasedDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/IndexBasedDistanceFunction.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; * Distance function relying on an index (such as preprocessed neighborhoods). * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.stereotype factory diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/Kulczynski1DistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/Kulczynski1DistanceFunction.java index 2baa2466..da8ea270 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/Kulczynski1DistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/Kulczynski1DistanceFunction.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.4.0 */ @Reference(authors = "M.-M. Deza and E. Deza", title = "Dictionary of distances", booktitle = "Dictionary of distances") public class Kulczynski1DistanceFunction extends AbstractSpatialDistanceFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/LorentzianDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/LorentzianDistanceFunction.java index cbb193ac..fdf6de66 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/LorentzianDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/LorentzianDistanceFunction.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.4.0 */ @Reference(authors = "M.-M. Deza and E. Deza", title = "Dictionary of distances", booktitle = "Dictionary of distances") public class LorentzianDistanceFunction extends AbstractSpatialNorm { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/MatrixWeightedDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/MatrixWeightedDistanceFunction.java index 40b8b900..006e2bd0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/MatrixWeightedDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/MatrixWeightedDistanceFunction.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * Weighted distance for feature vectors. * * @author Elke Achtert + * @since 0.2 */ // TODO: Factory with parameterizable weight matrix? public class MatrixWeightedDistanceFunction extends AbstractNumberVectorDistanceFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/Norm.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/Norm.java index f25c91be..ba7724a6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/Norm.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/Norm.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction; * Abstract interface for a mathematical norm. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/NumberVectorDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/NumberVectorDistanceFunction.java index 3b6021e0..7840d0b8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/NumberVectorDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/NumberVectorDistanceFunction.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.data.NumberVector; * vectors. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/PrimitiveDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/PrimitiveDistanceFunction.java index 2a3ae0c1..0995e7b9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/PrimitiveDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/PrimitiveDistanceFunction.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.data.type.SimpleTypeInformation; * Primitive distance function that is defined on some kind of object. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/RandomStableDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/RandomStableDistanceFunction.java index e1eafbad..d6ced169 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/RandomStableDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/RandomStableDistanceFunction.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * metrical. * * @author Erich Schubert + * @since 0.4.0 */ public class RandomStableDistanceFunction extends AbstractDatabaseDistanceFunction<DBID> implements DBIDDistanceFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/SharedNearestNeighborJaccardDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/SharedNearestNeighborJaccardDistanceFunction.java index c11a3448..691a7373 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/SharedNearestNeighborJaccardDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/SharedNearestNeighborJaccardDistanceFunction.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * coefficient, which is a proper distance metric. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses * de.lmu.ifi.dbs.elki.index.preprocessed.snn.SharedNearestNeighborIndex diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/SpatialPrimitiveDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/SpatialPrimitiveDistanceFunction.java index 2611c36f..d8d246e1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/SpatialPrimitiveDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/SpatialPrimitiveDistanceFunction.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * API for a spatial primitive distance function. * * @author Erich Schubert + * @since 0.4.0 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/WeightedCanberraDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/WeightedCanberraDistanceFunction.java index bd4fb5db..8c2b382e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/WeightedCanberraDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/WeightedCanberraDistanceFunction.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleListParamet * Weighted Canberra distance function, a variation of Manhattan distance. * * @author Erich Schubert + * @since 0.4.0 */ public class WeightedCanberraDistanceFunction extends AbstractSpatialDistanceFunction implements WeightedNumberVectorDistanceFunction<NumberVector> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/WeightedNumberVectorDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/WeightedNumberVectorDistanceFunction.java index 682b394a..2890292b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/WeightedNumberVectorDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/WeightedNumberVectorDistanceFunction.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; * Distance functions where each dimension is assigned a weight. * * @author Erich Schubert + * @since 0.4.0 * * @param <V> Vector type, usually NumberVector or above. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/AbstractSimilarityAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/AbstractSimilarityAdapter.java index f77c4927..31138c4d 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/AbstractSimilarityAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/AbstractSimilarityAdapter.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * equation. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has Instance * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/ArccosSimilarityAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/ArccosSimilarityAdapter.java index 4931c4e8..87cadf1a 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/ArccosSimilarityAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/ArccosSimilarityAdapter.java @@ -28,17 +28,20 @@ import de.lmu.ifi.dbs.elki.database.query.similarity.SimilarityQuery; import de.lmu.ifi.dbs.elki.database.relation.Relation; import de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction; import de.lmu.ifi.dbs.elki.distance.similarityfunction.NormalizedSimilarityFunction; +import de.lmu.ifi.dbs.elki.utilities.Alias; /** * Adapter from a normalized similarity function to a distance function using * <code>arccos(sim)</code>. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has Instance * * @param <O> Object class to process. */ +@Alias("de.lmu.ifi.dbs.elki.distance.distancefunction.adapter.SimilarityAdapterArccos") public class ArccosSimilarityAdapter<O> extends AbstractSimilarityAdapter<O> { /** * Constructor. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/LinearAdapterLinear.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/LinearAdapterLinear.java index 63b681e9..4d1f76c4 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/LinearAdapterLinear.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/LinearAdapterLinear.java @@ -28,17 +28,20 @@ import de.lmu.ifi.dbs.elki.database.query.similarity.SimilarityQuery; import de.lmu.ifi.dbs.elki.database.relation.Relation; import de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction; import de.lmu.ifi.dbs.elki.distance.similarityfunction.NormalizedSimilarityFunction; +import de.lmu.ifi.dbs.elki.utilities.Alias; /** * Adapter from a normalized similarity function to a distance function using * <code>1 - sim</code>. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has Instance * * @param <O> Object class to process. */ +@Alias("de.lmu.ifi.dbs.elki.distance.distancefunction.adapter.SimilarityAdapterLinear") public class LinearAdapterLinear<O> extends AbstractSimilarityAdapter<O> { /** * Constructor. @@ -98,4 +101,4 @@ public class LinearAdapterLinear<O> extends AbstractSimilarityAdapter<O> { return NORMALIZED_SIMILARITY; } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/LnSimilarityAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/LnSimilarityAdapter.java index f3002e1a..1ccc3749 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/LnSimilarityAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/adapter/LnSimilarityAdapter.java @@ -28,17 +28,20 @@ import de.lmu.ifi.dbs.elki.database.query.similarity.SimilarityQuery; import de.lmu.ifi.dbs.elki.database.relation.Relation; import de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction; import de.lmu.ifi.dbs.elki.distance.similarityfunction.NormalizedSimilarityFunction; +import de.lmu.ifi.dbs.elki.utilities.Alias; /** * Adapter from a normalized similarity function to a distance function using * <code>-log(sim)</code>. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has Instance * * @param <O> object class to process. */ +@Alias("de.lmu.ifi.dbs.elki.distance.distancefunction.adapter.SimilarityAdapterLn") public class LnSimilarityAdapter<O> extends AbstractSimilarityAdapter<O> { /** * Constructor. @@ -98,4 +101,4 @@ public class LnSimilarityAdapter<O> extends AbstractSimilarityAdapter<O> { return NORMALIZED_SIMILARITY; } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/colorhistogram/HSBHistogramQuadraticDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/colorhistogram/HSBHistogramQuadraticDistanceFunction.java index ec5e4a90..48383915 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/colorhistogram/HSBHistogramQuadraticDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/colorhistogram/HSBHistogramQuadraticDistanceFunction.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntListParameter; * </p> * * @author Erich Schubert + * @since 0.3 */ @Reference(authors = "J. R. Smith, S. F. Chang", title = "VisualSEEk: a fully automated content-based image query system", booktitle = "Proceedings of the fourth ACM international conference on Multimedia 1997", url = "http://dx.doi.org/10.1145/244130.244151") public class HSBHistogramQuadraticDistanceFunction extends MatrixWeightedDistanceFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/colorhistogram/HistogramIntersectionDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/colorhistogram/HistogramIntersectionDistanceFunction.java index e4141684..ba5e129b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/colorhistogram/HistogramIntersectionDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/colorhistogram/HistogramIntersectionDistanceFunction.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * International Journal of Computer Vision, 7(1), 32, 1991 * * @author Erich Schubert + * @since 0.3 */ @Title("Color histogram intersection distance") @Description("Distance function for color histograms that emphasizes 'strong' bins.") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/colorhistogram/RGBHistogramQuadraticDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/colorhistogram/RGBHistogramQuadraticDistanceFunction.java index 70935d28..01540f98 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/colorhistogram/RGBHistogramQuadraticDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/colorhistogram/RGBHistogramQuadraticDistanceFunction.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Erich Schubert + * @since 0.3 */ @Reference(authors = "J. Hafner, H. S.Sawhney, W. Equits, M. Flickner, W. Niblack", title = "Efficient Color Histogram Indexing for Quadratic Form Distance Functions", booktitle = "IEEE Trans. on Pattern Analysis and Machine Intelligence, Vol. 17, No. 7, July 1995", url = "http://dx.doi.org/10.1109/34.391417") public class RGBHistogramQuadraticDistanceFunction extends MatrixWeightedDistanceFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/AbsolutePearsonCorrelationDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/AbsolutePearsonCorrelationDistanceFunction.java index c0033742..df2c3018 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/AbsolutePearsonCorrelationDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/AbsolutePearsonCorrelationDistanceFunction.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * uncorrelated. * * @author Erich Schubert + * @since 0.3 */ public class AbsolutePearsonCorrelationDistanceFunction extends AbstractNumberVectorDistanceFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/AbsoluteUncenteredCorrelationDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/AbsoluteUncenteredCorrelationDistanceFunction.java index 50321129..b37719db 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/AbsoluteUncenteredCorrelationDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/AbsoluteUncenteredCorrelationDistanceFunction.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * but uses a fixed mean of 0 instead of the sample mean. * * @author Erich Schubert + * @since 0.4.0 */ public class AbsoluteUncenteredCorrelationDistanceFunction extends AbstractNumberVectorDistanceFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/PearsonCorrelationDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/PearsonCorrelationDistanceFunction.java index 0a0c6dc9..0bcafa43 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/PearsonCorrelationDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/PearsonCorrelationDistanceFunction.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * will be intermediate (around 1). * * @author Arthur Zimek + * @since 0.3 */ public class PearsonCorrelationDistanceFunction extends AbstractNumberVectorDistanceFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/SquaredPearsonCorrelationDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/SquaredPearsonCorrelationDistanceFunction.java index ea1cede4..f98235d4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/SquaredPearsonCorrelationDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/SquaredPearsonCorrelationDistanceFunction.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * 1). * * @author Arthur Zimek + * @since 0.3 */ public class SquaredPearsonCorrelationDistanceFunction extends AbstractNumberVectorDistanceFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/SquaredUncenteredCorrelationDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/SquaredUncenteredCorrelationDistanceFunction.java index 5f39b0ad..0828c82a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/SquaredUncenteredCorrelationDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/SquaredUncenteredCorrelationDistanceFunction.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * but uses a fixed mean of 0 instead of the sample mean. * * @author Erich Schubert + * @since 0.4.0 */ public class SquaredUncenteredCorrelationDistanceFunction extends AbstractNumberVectorDistanceFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/UncenteredCorrelationDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/UncenteredCorrelationDistanceFunction.java index 83bb7e7d..e5f6dd18 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/UncenteredCorrelationDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/UncenteredCorrelationDistanceFunction.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * uses a fixed mean of 0 instead of the sample mean. * * @author Erich Schubert + * @since 0.3 */ public class UncenteredCorrelationDistanceFunction extends AbstractNumberVectorDistanceFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/WeightedPearsonCorrelationDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/WeightedPearsonCorrelationDistanceFunction.java index 60ed0638..70c8f34e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/WeightedPearsonCorrelationDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/WeightedPearsonCorrelationDistanceFunction.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleListParamet * * @author Arthur Zimek * @author Erich Schubert + * @since 0.3 */ public class WeightedPearsonCorrelationDistanceFunction extends AbstractNumberVectorDistanceFunction implements WeightedNumberVectorDistanceFunction<NumberVector> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/WeightedSquaredPearsonCorrelationDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/WeightedSquaredPearsonCorrelationDistanceFunction.java index 4ec94227..108f8f97 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/WeightedSquaredPearsonCorrelationDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/WeightedSquaredPearsonCorrelationDistanceFunction.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleListParamet * * @author Arthur Zimek * @author Erich Schubert + * @since 0.3 */ public class WeightedSquaredPearsonCorrelationDistanceFunction extends AbstractNumberVectorDistanceFunction implements WeightedNumberVectorDistanceFunction<NumberVector> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/AsciiDistanceParser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/AsciiDistanceParser.java index 2122f43b..61552730 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/AsciiDistanceParser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/AsciiDistanceParser.java @@ -29,6 +29,7 @@ import java.io.InputStream; import de.lmu.ifi.dbs.elki.datasource.parser.CSVReaderFormat; import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.logging.progress.IndefiniteProgress; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; @@ -41,11 +42,12 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * Parser for parsing one distance value per line. * * A line must have the following format: {@code id1 id2 distanceValue}, where - * id1 and id2 are integers representing the two ids belonging to the distance - * value. Lines starting with "#" will be ignored. + * id1 and id2 are integers starting at 0 representing the two ids belonging to + * the distance value. Lines starting with "#" will be ignored. * * @author Elke Achtert * @author Erich Schubert + * @since 0.2 * * @apiviz.uses CSVReaderFormat * @apiviz.composedOf TokenizedReader @@ -54,8 +56,11 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz */ @Title("Number Distance Parser") @Description("Parser for the following line format:\n" // - + "id1 id2 distanceValue, where id1 and is2 are integers representing the two ids belonging to the distance value.\n" // - + "The ids and the distance value are separated by whitespace. Empty lines and lines beginning with \"#\" will be ignored.") ++ "id1 id2 distanceValue, where id1 and is2 are integers starting at 0 representing the two ids belonging to the distance value.\n" // ++ "The ids and the distance value are separated by whitespace. Empty lines and lines beginning with \"#\" will be ignored.") +@Alias({ "de.lmu.ifi.dbs.elki.datasource.parser.NumberDistanceParser", // +"de.lmu.ifi.dbs.elki.distance.distancefunction.external.NumberDistanceParser", // +"de.lmu.ifi.dbs.elki.parser.NumberDistanceParser" }) public class AsciiDistanceParser implements DistanceParser { /** * The logger for this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DiskCacheBasedDoubleDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DiskCacheBasedDoubleDistanceFunction.java index 6bfd6df0..5ad01b72 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DiskCacheBasedDoubleDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DiskCacheBasedDoubleDistanceFunction.java @@ -26,7 +26,9 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction.external; import java.io.File; import java.io.IOException; +import de.lmu.ifi.dbs.elki.database.ids.DBIDRange; import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractDBIDRangeDistanceFunction; +import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.persistent.OnDiskUpperTriangleMatrix; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; @@ -42,11 +44,15 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; * matrix of an external binary matrix file. * * @author Erich Schubert + * @since 0.2 */ @Title("File based double distance for database objects.") @Description("Loads double distance values from an external matrix.") public class DiskCacheBasedDoubleDistanceFunction extends AbstractDBIDRangeDistanceFunction { - // TODO: constructor with file. + /** + * Class logger. + */ + private static final Logging LOG = Logging.getLogger(DiskCacheBasedDoubleDistanceFunction.class); /** * Magic to identify double cache matrices @@ -68,6 +74,17 @@ public class DiskCacheBasedDoubleDistanceFunction extends AbstractDBIDRangeDista this.cache = cache; } + /** + * Constructor. + * + * @param matrixfile File name + * @throws IOException + */ + public DiskCacheBasedDoubleDistanceFunction(File matrixfile) throws IOException { + super(); + this.cache = new OnDiskUpperTriangleMatrix(matrixfile, DOUBLE_CACHE_MAGIC, 0, ByteArrayUtil.SIZE_DOUBLE, false); + } + @Override public double distance(int i1, int i2) { // the smaller id is the first key @@ -84,6 +101,13 @@ public class DiskCacheBasedDoubleDistanceFunction extends AbstractDBIDRangeDista } @Override + public void checkRange(DBIDRange range) { + if(cache.getMatrixSize() < range.size()) { + LOG.warning("Distance matrix has size " + cache.getMatrixSize() + " but range has size: " + range.size()); + } + } + + @Override public boolean equals(Object obj) { if(obj == null) { return false; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DiskCacheBasedFloatDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DiskCacheBasedFloatDistanceFunction.java index de8d96b4..b6731a30 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DiskCacheBasedFloatDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DiskCacheBasedFloatDistanceFunction.java @@ -26,7 +26,9 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction.external; import java.io.File; import java.io.IOException; +import de.lmu.ifi.dbs.elki.database.ids.DBIDRange; import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractDBIDRangeDistanceFunction; +import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.persistent.OnDiskUpperTriangleMatrix; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; @@ -41,11 +43,15 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; * of an external binary matrix file. * * @author Erich Schubert + * @since 0.2 */ @Title("File based float distance for database objects.") @Description("Loads float distance values from an external matrix.") public class DiskCacheBasedFloatDistanceFunction extends AbstractDBIDRangeDistanceFunction { - // TODO: constructor with file. + /** + * Class logger. + */ + private static final Logging LOG = Logging.getLogger(DiskCacheBasedFloatDistanceFunction.class); /** * Magic to identify double cache matrices @@ -67,6 +73,17 @@ public class DiskCacheBasedFloatDistanceFunction extends AbstractDBIDRangeDistan this.cache = cache; } + /** + * Constructor. + * + * @param matrixfile File name + * @throws IOException + */ + public DiskCacheBasedFloatDistanceFunction(File matrixfile) throws IOException { + super(); + this.cache = new OnDiskUpperTriangleMatrix(matrixfile, FLOAT_CACHE_MAGIC, 0, ByteArrayUtil.SIZE_FLOAT, false); + } + @Override public double distance(int i1, int i2) { // the smaller id is the first key @@ -94,6 +111,13 @@ public class DiskCacheBasedFloatDistanceFunction extends AbstractDBIDRangeDistan return this.cache.equals(other.cache); } + @Override + public void checkRange(DBIDRange range) { + if(cache.getMatrixSize() < range.size()) { + LOG.warning("Distance matrix has size " + cache.getMatrixSize() + " but range has size: " + range.size()); + } + } + /** * Parameterization class. * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DistanceCacheWriter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DistanceCacheWriter.java index cd73b73e..3d83db66 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DistanceCacheWriter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DistanceCacheWriter.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction.external; * Interface to plug in the cache storage into the parser. * * @author Erich Schubert + * @since 0.4.0 */ public interface DistanceCacheWriter { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DistanceParser.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DistanceParser.java index 28234d75..d495427b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DistanceParser.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/DistanceParser.java @@ -30,6 +30,7 @@ import java.io.InputStream; * InputStream. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.uses DistanceCacheWriter oneway - - «create» */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedDoubleDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedDoubleDistanceFunction.java index 4f872766..cbbf7fa2 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedDoubleDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedDoubleDistanceFunction.java @@ -1,5 +1,28 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction.external; +import java.io.BufferedInputStream; +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.io.InputStream; + +import de.lmu.ifi.dbs.elki.database.ids.DBID; +import de.lmu.ifi.dbs.elki.database.ids.DBIDRange; +import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery; +import de.lmu.ifi.dbs.elki.database.relation.Relation; +import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractDBIDRangeDistanceFunction; +import de.lmu.ifi.dbs.elki.logging.Logging; +import de.lmu.ifi.dbs.elki.utilities.FileUtil; +import de.lmu.ifi.dbs.elki.utilities.documentation.Description; +import de.lmu.ifi.dbs.elki.utilities.documentation.Title; +import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; +import gnu.trove.impl.Constants; + /* This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures @@ -26,26 +49,6 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction.external; import gnu.trove.map.TLongDoubleMap; import gnu.trove.map.hash.TLongDoubleHashMap; -import java.io.BufferedInputStream; -import java.io.File; -import java.io.FileInputStream; -import java.io.IOException; -import java.io.InputStream; - -import de.lmu.ifi.dbs.elki.database.ids.DBID; -import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery; -import de.lmu.ifi.dbs.elki.database.relation.Relation; -import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractDBIDRangeDistanceFunction; -import de.lmu.ifi.dbs.elki.utilities.FileUtil; -import de.lmu.ifi.dbs.elki.utilities.documentation.Description; -import de.lmu.ifi.dbs.elki.utilities.documentation.Title; -import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; - /** * Distance function that is based on double distances given by a distance * matrix of an external ASCII file. @@ -58,6 +61,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Elke Achtert * @author Erich Schubert + * @since 0.2 * * @apiviz.composedOf DistanceCacheWriter */ @@ -65,6 +69,11 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; @Description("Loads double distance values from an external text file.") public class FileBasedDoubleDistanceFunction extends AbstractDBIDRangeDistanceFunction { /** + * Class logger. + */ + private static final Logging LOG = Logging.getLogger(FileBasedDoubleDistanceFunction.class); + + /** * The distance cache */ private TLongDoubleMap cache; @@ -80,6 +89,11 @@ public class FileBasedDoubleDistanceFunction extends AbstractDBIDRangeDistanceFu private File matrixfile; /** + * Minimum and maximum IDs seen. + */ + private int min, max; + + /** * Constructor. * * @param parser Parser @@ -106,18 +120,25 @@ public class FileBasedDoubleDistanceFunction extends AbstractDBIDRangeDistanceFu @Override public double distance(int i1, int i2) { - if(i1 == i2) { - return 0.; - } - return cache.get(makeKey(i1, i2)); + return (i1 == i2) ? 0. : cache.get(makeKey(i1 + min, i2 + min)); } private void loadCache(DistanceParser parser, File matrixfile) throws IOException { InputStream in = new BufferedInputStream(FileUtil.tryGzipInput(new FileInputStream(matrixfile))); - cache = new TLongDoubleHashMap(); + cache = new TLongDoubleHashMap(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1L, Double.POSITIVE_INFINITY); + min = Integer.MAX_VALUE; + max = Integer.MIN_VALUE; parser.parse(in, new DistanceCacheWriter() { @Override public void put(int id1, int id2, double distance) { + if(id1 < id2) { + min = id1 < min ? id1 : min; + max = id2 > max ? id2 : max; + } + else { + min = id2 < min ? id2 : min; + max = id1 > max ? id1 : max; + } cache.put(makeKey(id1, id2), distance); } @@ -126,6 +147,9 @@ public class FileBasedDoubleDistanceFunction extends AbstractDBIDRangeDistanceFu return cache.containsKey(makeKey(id1, id2)); } }); + if(min != 0) { + LOG.verbose("Distance matrix is supposed to be 0-indexed. Choosing offset " + min + " to compensate."); + } } /** @@ -142,6 +166,14 @@ public class FileBasedDoubleDistanceFunction extends AbstractDBIDRangeDistanceFu } @Override + public void checkRange(DBIDRange range) { + final int size = max + 1 - min; + if(size < range.size()) { + LOG.warning("Distance matrix has size " + size + " but range has size: " + range.size()); + } + } + + @Override public boolean equals(Object obj) { if(obj == null) { return false; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedFloatDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedFloatDistanceFunction.java index d14afb5d..51ae874e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedFloatDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedFloatDistanceFunction.java @@ -1,5 +1,27 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction.external; +import java.io.BufferedInputStream; +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.io.InputStream; + +import de.lmu.ifi.dbs.elki.database.ids.DBID; +import de.lmu.ifi.dbs.elki.database.ids.DBIDRange; +import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery; +import de.lmu.ifi.dbs.elki.database.relation.Relation; +import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractDBIDRangeDistanceFunction; +import de.lmu.ifi.dbs.elki.logging.Logging; +import de.lmu.ifi.dbs.elki.utilities.FileUtil; +import de.lmu.ifi.dbs.elki.utilities.documentation.Description; +import de.lmu.ifi.dbs.elki.utilities.documentation.Title; +import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; +import gnu.trove.impl.Constants; + /* This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures @@ -26,25 +48,6 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction.external; import gnu.trove.map.TLongFloatMap; import gnu.trove.map.hash.TLongFloatHashMap; -import java.io.BufferedInputStream; -import java.io.File; -import java.io.FileInputStream; -import java.io.IOException; -import java.io.InputStream; - -import de.lmu.ifi.dbs.elki.database.ids.DBID; -import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery; -import de.lmu.ifi.dbs.elki.database.relation.Relation; -import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractDBIDRangeDistanceFunction; -import de.lmu.ifi.dbs.elki.utilities.FileUtil; -import de.lmu.ifi.dbs.elki.utilities.documentation.Description; -import de.lmu.ifi.dbs.elki.utilities.documentation.Title; -import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; - /** * Distance function that is based on float distances given by a distance matrix * of an external ASCII file. @@ -57,6 +60,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Elke Achtert * @author Erich Schubert + * @since 0.2 * * @apiviz.composedOf DistanceCacheWriter */ @@ -64,6 +68,11 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; @Description("Loads float distance values from an external text file.") public class FileBasedFloatDistanceFunction extends AbstractDBIDRangeDistanceFunction { /** + * Class logger. + */ + private static final Logging LOG = Logging.getLogger(FileBasedFloatDistanceFunction.class); + + /** * The distance cache */ private TLongFloatMap cache; @@ -79,6 +88,11 @@ public class FileBasedFloatDistanceFunction extends AbstractDBIDRangeDistanceFun private File matrixfile; /** + * Minimum and maximum IDs seen. + */ + private int min, max; + + /** * Constructor. * * @param parser Parser @@ -105,15 +119,25 @@ public class FileBasedFloatDistanceFunction extends AbstractDBIDRangeDistanceFun @Override public double distance(int i1, int i2) { - return (i1 == i2) ? 0. : cache.get(makeKey(i1, i2)); + return (i1 == i2) ? 0. : cache.get(makeKey(i1 + min, i2 + min)); } private void loadCache(DistanceParser parser, File matrixfile) throws IOException { InputStream in = new BufferedInputStream(FileUtil.tryGzipInput(new FileInputStream(matrixfile))); - cache = new TLongFloatHashMap(); + cache = new TLongFloatHashMap(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1L, Float.POSITIVE_INFINITY); + min = Integer.MAX_VALUE; + max = Integer.MIN_VALUE; parser.parse(in, new DistanceCacheWriter() { @Override public void put(int id1, int id2, double distance) { + if(id1 < id2) { + min = id1 < min ? id1 : min; + max = id2 > max ? id2 : max; + } + else { + min = id2 < min ? id2 : min; + max = id1 > max ? id1 : max; + } cache.put(makeKey(id1, id2), (float) distance); } @@ -122,6 +146,9 @@ public class FileBasedFloatDistanceFunction extends AbstractDBIDRangeDistanceFun return cache.containsKey(makeKey(id1, id2)); } }); + if(min != 0) { + LOG.verbose("Distance matrix is supposed to be 0-indexed. Choosing offset " + min + " to compensate."); + } } /** @@ -138,6 +165,14 @@ public class FileBasedFloatDistanceFunction extends AbstractDBIDRangeDistanceFun } @Override + public void checkRange(DBIDRange range) { + final int size = max + 1 - min; + if(size < range.size()) { + LOG.warning("Distance matrix has size " + size + " but range has size: " + range.size()); + } + } + + @Override public boolean equals(Object obj) { if(obj == null) { return false; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/geo/DimensionSelectingLatLngDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/geo/DimensionSelectingLatLngDistanceFunction.java index 203e9e1c..8e8f9310 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/geo/DimensionSelectingLatLngDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/geo/DimensionSelectingLatLngDistanceFunction.java @@ -56,6 +56,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf EarthModel */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/geo/LatLngDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/geo/LatLngDistanceFunction.java index 2ccb13ec..b7528a41 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/geo/LatLngDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/geo/LatLngDistanceFunction.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf EarthModel */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/geo/LngLatDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/geo/LngLatDistanceFunction.java index 2e1f0c13..faf541a1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/geo/LngLatDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/geo/LngLatDistanceFunction.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf EarthModel */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/histogram/HistogramMatchDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/histogram/HistogramMatchDistanceFunction.java index 089460f3..cd1d0be5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/histogram/HistogramMatchDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/histogram/HistogramMatchDistanceFunction.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.4.0 */ @Reference(authors = "L.N. Vaserstein", // title = "Markov processes over denumerable products of spaces describing large systems of automata", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/histogram/KolmogorovSmirnovDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/histogram/KolmogorovSmirnovDistanceFunction.java index a078eae3..7645e5fd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/histogram/KolmogorovSmirnovDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/histogram/KolmogorovSmirnovDistanceFunction.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * i.e. they should be some 1-dimensional histogram. * * @author Erich Schubert + * @since 0.4.0 */ public class KolmogorovSmirnovDistanceFunction extends AbstractNumberVectorDistanceFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/EuclideanDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/EuclideanDistanceFunction.java index 422ea5d0..d17756f9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/EuclideanDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/EuclideanDistanceFunction.java @@ -32,8 +32,10 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Euclidean distance for {@link NumberVector}s. * * @author Arthur Zimek + * @since 0.2 */ -@Alias({ "euclidean", "euclid", "l2", "EuclideanDistanceFunction", "de.lmu.ifi.dbs.elki.distance.distancefunction.EuclideanDistanceFunction" }) +@Alias({ "euclidean", "euclid", "l2", // +"de.lmu.ifi.dbs.elki.distance.distancefunction.EuclideanDistanceFunction" }) public class EuclideanDistanceFunction extends LPIntegerNormDistanceFunction { /** * Static instance. Use this! diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/LPIntegerNormDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/LPIntegerNormDistanceFunction.java index 055e96cf..56d03b41 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/LPIntegerNormDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/LPIntegerNormDistanceFunction.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * machine version. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/LPNormDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/LPNormDistanceFunction.java index 88b5edc5..aa8b9e80 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/LPNormDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/LPNormDistanceFunction.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * LP-Norm for {@link NumberVector}s. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/ManhattanDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/ManhattanDistanceFunction.java index f0562aa0..f82514ac 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/ManhattanDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/ManhattanDistanceFunction.java @@ -32,8 +32,10 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Manhattan distance for {@link NumberVector}s. * * @author Arthur Zimek + * @since 0.2 */ -@Alias({ "taxicab", "cityblock", "l1", "ManhattanDistanceFunction", "de.lmu.ifi.dbs.elki.distance.distancefunction.ManhattanDistanceFunction" }) +@Alias({ "taxicab", "cityblock", "l1", // +"de.lmu.ifi.dbs.elki.distance.distancefunction.ManhattanDistanceFunction" }) public class ManhattanDistanceFunction extends LPIntegerNormDistanceFunction { /** * The static instance to use. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/MaximumDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/MaximumDistanceFunction.java index 84c1e7a2..dce6a67e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/MaximumDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/MaximumDistanceFunction.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Maximum distance for {@link NumberVector}s. * * @author Erich Schubert + * @since 0.3 */ @Alias({ "maximum", "max", "chebyshev", "de.lmu.ifi.dbs.elki.distance.distancefunction.MaximumDistanceFunction" }) public class MaximumDistanceFunction extends LPNormDistanceFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/MinimumDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/MinimumDistanceFunction.java index 1d218718..3ce7da42 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/MinimumDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/MinimumDistanceFunction.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Maximum distance for {@link NumberVector}s. * * @author Erich Schubert + * @since 0.3 */ @Alias({ "minimum", "min", "de.lmu.ifi.dbs.elki.distance.distancefunction.MinimumDistanceFunction" }) public class MinimumDistanceFunction extends AbstractSpatialNorm { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseEuclideanDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseEuclideanDistanceFunction.java index b6085f9a..91960751 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseEuclideanDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseEuclideanDistanceFunction.java @@ -24,13 +24,16 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski; */ import de.lmu.ifi.dbs.elki.data.SparseNumberVector; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; /** * Euclidean distance function, optimized for {@link SparseNumberVector}s. * * @author Erich Schubert + * @since 0.5.0 */ +@Alias("de.lmu.ifi.dbs.elki.distance.distancefunction.SparseEuclideanDistanceFunction") public class SparseEuclideanDistanceFunction extends SparseLPNormDistanceFunction { /** * Static instance diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseLPNormDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseLPNormDistanceFunction.java index 28e3e33e..97ffe515 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseLPNormDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseLPNormDistanceFunction.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.data.type.SimpleTypeInformation; import de.lmu.ifi.dbs.elki.data.type.TypeUtil; import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractPrimitiveDistanceFunction; import de.lmu.ifi.dbs.elki.distance.distancefunction.Norm; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.CommonConstraints; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; @@ -37,8 +38,10 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * LP-Norm, optimized for {@link SparseNumberVector}s. * * @author Erich Schubert + * @since 0.5.0 */ // TODO: implement SpatialDistanceFunction +@Alias("de.lmu.ifi.dbs.elki.distance.distancefunction.SparseLPNormDistanceFunction") public class SparseLPNormDistanceFunction extends AbstractPrimitiveDistanceFunction<SparseNumberVector> implements Norm<SparseNumberVector> { /** * P parameter and its inverse. @@ -153,4 +156,4 @@ public class SparseLPNormDistanceFunction extends AbstractPrimitiveDistanceFunct return new SparseLPNormDistanceFunction(p); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseManhattanDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseManhattanDistanceFunction.java index ffb6bdfc..a83a0ac4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseManhattanDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseManhattanDistanceFunction.java @@ -24,13 +24,16 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski; */ import de.lmu.ifi.dbs.elki.data.SparseNumberVector; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; /** * Manhattan distance, optimized for {@link SparseNumberVector}s. * * @author Erich Schubert + * @since 0.5.0 */ +@Alias("de.lmu.ifi.dbs.elki.distance.distancefunction.SparseManhattanDistanceFunction") public class SparseManhattanDistanceFunction extends SparseLPNormDistanceFunction { /** * Static instance @@ -112,4 +115,4 @@ public class SparseManhattanDistanceFunction extends SparseLPNormDistanceFunctio return SparseManhattanDistanceFunction.STATIC; } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseMaximumDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseMaximumDistanceFunction.java index 237453c8..5a33c6aa 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseMaximumDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SparseMaximumDistanceFunction.java @@ -23,13 +23,16 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski; along with this program. If not, see <http://www.gnu.org/licenses/>. */ import de.lmu.ifi.dbs.elki.data.SparseNumberVector; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; /** * Maximum distance, optimized for {@link SparseNumberVector}s. * * @author Erich Schubert + * @since 0.5.0 */ +@Alias("de.lmu.ifi.dbs.elki.distance.distancefunction.SparseMaximumDistanceFunction") public class SparseMaximumDistanceFunction extends SparseLPNormDistanceFunction { /** * Static instance @@ -123,4 +126,4 @@ public class SparseMaximumDistanceFunction extends SparseLPNormDistanceFunction return SparseMaximumDistanceFunction.STATIC; } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SquaredEuclideanDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SquaredEuclideanDistanceFunction.java index 387dfa86..7714282c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SquaredEuclideanDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SquaredEuclideanDistanceFunction.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * computing the square root. * * @author Arthur Zimek + * @since 0.2 */ @Alias({ "squaredeuclidean", "de.lmu.ifi.dbs.elki.distance.distancefunction.SquaredEuclideanDistanceFunction" }) public class SquaredEuclideanDistanceFunction extends AbstractSpatialNorm { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedEuclideanDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedEuclideanDistanceFunction.java index 3fbfc28e..fe163c43 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedEuclideanDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedEuclideanDistanceFunction.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleListParamet * Weighted Euclidean distance for {@link NumberVector}s. * * @author Erich Schubert + * @since 0.4.0 */ public class WeightedEuclideanDistanceFunction extends WeightedLPNormDistanceFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedLPNormDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedLPNormDistanceFunction.java index 6f9a99c2..dc75a0bd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedLPNormDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedLPNormDistanceFunction.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.data.spatial.SpatialComparable; import de.lmu.ifi.dbs.elki.data.type.SimpleTypeInformation; import de.lmu.ifi.dbs.elki.data.type.VectorFieldTypeInformation; import de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedNumberVectorDistanceFunction; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleListParameter; @@ -37,7 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleListParamet * Weighted version of the Minkowski L_p norm distance for {@link NumberVector}. * * @author Erich Schubert + * @since 0.4.0 */ +@Alias("de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedLPNormDistanceFunction") public class WeightedLPNormDistanceFunction extends LPNormDistanceFunction implements WeightedNumberVectorDistanceFunction<NumberVector> { /** * Weight array diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedManhattanDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedManhattanDistanceFunction.java index 473c24fb..2d2483a6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedManhattanDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedManhattanDistanceFunction.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleListParamet * {@link NumberVector}s. * * @author Erich Schubert + * @since 0.4.0 */ public class WeightedManhattanDistanceFunction extends WeightedLPNormDistanceFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedMaximumDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedMaximumDistanceFunction.java index 14f1d899..71a4bf7e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedMaximumDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedMaximumDistanceFunction.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleListParamet * {@link NumberVector}s. * * @author Erich Schubert + * @since 0.4.0 */ public class WeightedMaximumDistanceFunction extends WeightedLPNormDistanceFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedSquaredEuclideanDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedSquaredEuclideanDistanceFunction.java index b57e0317..9e6a5868 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedSquaredEuclideanDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/WeightedSquaredEuclideanDistanceFunction.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.data.NumberVector; import de.lmu.ifi.dbs.elki.data.spatial.SpatialComparable; import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractSpatialNorm; import de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedNumberVectorDistanceFunction; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleListParameter; @@ -38,7 +39,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleListParamet * same rankings as Euclidean distance, but saves computing the square root. * * @author Arthur Zimek + * @since 0.4.0 */ +@Alias("de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedSquaredEuclideanDistanceFunction") public class WeightedSquaredEuclideanDistanceFunction extends AbstractSpatialNorm implements WeightedNumberVectorDistanceFunction<NumberVector> { /** * Weight array diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/ChiSquaredDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/ChiSquaredDistanceFunction.java index 06b7bf79..5eb40eea 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/ChiSquaredDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/ChiSquaredDistanceFunction.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.4.0 */ @Alias("chisq") @Reference(authors = "J. Puzicha, J.M. Buhmann, Y. Rubner, C. Tomasi", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/HellingerDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/HellingerDistanceFunction.java index f955520a..ba191a46 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/HellingerDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/HellingerDistanceFunction.java @@ -55,6 +55,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * TODO: support acceleration for sparse vectors * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "E. Hellinger", // title = "Neue Begründung der Theorie quadratischer Formen von unendlichvielen Veränderlichen", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/JeffreyDivergenceDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/JeffreyDivergenceDistanceFunction.java index 55f9a476..16814c4c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/JeffreyDivergenceDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/JeffreyDivergenceDistanceFunction.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.4.0 */ @Reference(authors = "J. Puzicha, J.M. Buhmann, Y. Rubner, C. Tomasi", // title = "Empirical evaluation of dissimilarity measures for color and texture", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/JensenShannonDivergenceDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/JensenShannonDivergenceDistanceFunction.java index 18eb33bf..6b20a3f7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/JensenShannonDivergenceDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/JensenShannonDivergenceDistanceFunction.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * scaled by half. * * @author Erich Schubert + * @since 0.6.0 */ public class JensenShannonDivergenceDistanceFunction extends JeffreyDivergenceDistanceFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/KullbackLeiblerDivergenceAsymmetricDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/KullbackLeiblerDivergenceAsymmetricDistanceFunction.java index 48cd39e4..064fc6df 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/KullbackLeiblerDivergenceAsymmetricDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/KullbackLeiblerDivergenceAsymmetricDistanceFunction.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.4.0 */ @Reference(authors = "S. Kullback", title = "Information theory and statistics", booktitle = "Information theory and statistics, Courier Dover Publications, 1997.") @Alias("kl") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/KullbackLeiblerDivergenceReverseAsymmetricDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/KullbackLeiblerDivergenceReverseAsymmetricDistanceFunction.java index 1e96ee0e..4bfe9521 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/KullbackLeiblerDivergenceReverseAsymmetricDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/KullbackLeiblerDivergenceReverseAsymmetricDistanceFunction.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.4.0 */ @Reference(authors = "S. Kullback", title = "Information theory and statistics", booktitle = "Information theory and statistics, Courier Dover Publications, 1997.") @Alias("kli") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/SqrtJensenShannonDivergenceDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/SqrtJensenShannonDivergenceDistanceFunction.java index ca99a4c8..b792f97c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/SqrtJensenShannonDivergenceDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/SqrtJensenShannonDivergenceDistanceFunction.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.4.0 */ @Reference(authors = "D. M. Endres, J. E. Schindelin", title = "A new metric for probability distributions", booktitle = "IEEE Transactions on Information Theory, 49(7)", url = "http://dx.doi.org/10.1109/TIT.2003.813506") public class SqrtJensenShannonDivergenceDistanceFunction extends AbstractNumberVectorDistanceFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/set/AbstractSetDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/set/AbstractSetDistanceFunction.java index 814d144e..bce8437c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/set/AbstractSetDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/set/AbstractSetDistanceFunction.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractPrimitiveDistanceFu * Abstract base class for set distance functions. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/set/HammingDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/set/HammingDistanceFunction.java index 4d467db9..a04c5d37 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/set/HammingDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/set/HammingDistanceFunction.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * TODO: add a sparse (but not binary) optimized version? * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "R. W. Hamming", // title = "Error detecting and error correcting codes", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/set/JaccardSimilarityDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/set/JaccardSimilarityDistanceFunction.java index 954339ec..c13b4af0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/set/JaccardSimilarityDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/set/JaccardSimilarityDistanceFunction.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunction; import de.lmu.ifi.dbs.elki.distance.distancefunction.PrimitiveDistanceFunction; import de.lmu.ifi.dbs.elki.distance.similarityfunction.NormalizedPrimitiveSimilarityFunction; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; /** @@ -56,12 +57,14 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Vector type */ @Reference(authors = "P. Jaccard", // title = "Distribution de la florine alpine dans la Bassin de Dranses et dans quelques regiones voisines", // booktitle = "Bulletin del la Société Vaudoise des Sciences Naturelles") +@Alias("de.lmu.ifi.dbs.elki.distance.similarityfunction.JaccardPrimitiveSimilarityFunction") public class JaccardSimilarityDistanceFunction<O extends FeatureVector<?>> extends AbstractSetDistanceFunction<O> implements NormalizedPrimitiveSimilarityFunction<O>, NumberVectorDistanceFunction<O>, PrimitiveDistanceFunction<O> { /** * Constructor. No parameters. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/LevenshteinDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/LevenshteinDistanceFunction.java index 5a6aa5f6..a2b098e5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/LevenshteinDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/LevenshteinDistanceFunction.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Felix Stahlberg * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses String */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/NormalizedLevenshteinDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/NormalizedLevenshteinDistanceFunction.java index 8a48038d..f2b3d7db 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/NormalizedLevenshteinDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/NormalizedLevenshteinDistanceFunction.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Felix Stahlberg * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses String */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/AbstractDimensionsSelectingDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/AbstractDimensionsSelectingDistanceFunction.java index 98d753ff..17f493cd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/AbstractDimensionsSelectingDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/AbstractDimensionsSelectingDistanceFunction.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntListParameter; * Selected dimensions are encuded as bits in a {@code long[]}. * * @author Elke Achtert + * @since 0.2 * @param <V> the type of FeatureVector to compute the distances in between */ public abstract class AbstractDimensionsSelectingDistanceFunction<V extends FeatureVector<?>> extends AbstractPrimitiveDistanceFunction<V> implements PrimitiveDistanceFunction<V>, DimensionSelectingSubspaceDistanceFunction<V> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/DimensionSelectingSubspaceDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/DimensionSelectingSubspaceDistanceFunction.java index e96dfd33..0e46d953 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/DimensionSelectingSubspaceDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/DimensionSelectingSubspaceDistanceFunction.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction; * Interface for dimension selecting subspace distance functions. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/OnedimensionalDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/OnedimensionalDistanceFunction.java index 58b16354..e37287e3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/OnedimensionalDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/OnedimensionalDistanceFunction.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.data.spatial.SpatialComparable; import de.lmu.ifi.dbs.elki.data.type.VectorFieldTypeInformation; import de.lmu.ifi.dbs.elki.data.type.VectorTypeInformation; import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractSpatialNorm; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.BitsUtil; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; @@ -40,7 +41,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * absolute difference of their values in a specified dimension only. * * @author Elke Achtert + * @since 0.2 */ +@Alias("de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionSelectingDistanceFunction") public class OnedimensionalDistanceFunction extends AbstractSpatialNorm implements DimensionSelectingSubspaceDistanceFunction<NumberVector> { /** * The dimension to be considered for distance computation. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceEuclideanDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceEuclideanDistanceFunction.java index baa67c60..57895724 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceEuclideanDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceEuclideanDistanceFunction.java @@ -25,6 +25,7 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction.subspace; import de.lmu.ifi.dbs.elki.data.NumberVector; import de.lmu.ifi.dbs.elki.data.spatial.SpatialComparable; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.BitsUtil; /** @@ -32,7 +33,9 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * dimensions. * * @author Elke Achtert + * @since 0.2 */ +@Alias("de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionsSelectingEuclideanDistanceFunction") public class SubspaceEuclideanDistanceFunction extends SubspaceLPNormDistanceFunction { /** * Constructor. @@ -144,4 +147,4 @@ public class SubspaceEuclideanDistanceFunction extends SubspaceLPNormDistanceFun return new SubspaceEuclideanDistanceFunction(dimensions); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceLPNormDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceLPNormDistanceFunction.java index 69ca26a2..f3102c76 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceLPNormDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceLPNormDistanceFunction.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * dimensions. * * @author Elke Achtert + * @since 0.2 */ public class SubspaceLPNormDistanceFunction extends AbstractDimensionsSelectingDistanceFunction<NumberVector> implements SpatialPrimitiveDistanceFunction<NumberVector>, Norm<NumberVector>, NumberVectorDistanceFunction<NumberVector> { /** @@ -198,4 +199,4 @@ public class SubspaceLPNormDistanceFunction extends AbstractDimensionsSelectingD return new SubspaceLPNormDistanceFunction(p, dimensions); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceManhattanDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceManhattanDistanceFunction.java index 4e2e1ed5..87168695 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceManhattanDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceManhattanDistanceFunction.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * dimensions. * * @author Elke Achtert + * @since 0.5.0 */ public class SubspaceManhattanDistanceFunction extends SubspaceLPNormDistanceFunction { /** @@ -130,4 +131,4 @@ public class SubspaceManhattanDistanceFunction extends SubspaceLPNormDistanceFun return new SubspaceManhattanDistanceFunction(dimensions); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceMaximumDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceMaximumDistanceFunction.java index edf88ef6..e24ff4cc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceMaximumDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/subspace/SubspaceMaximumDistanceFunction.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * dimensions. * * @author Elke Achtert + * @since 0.5.0 */ public class SubspaceMaximumDistanceFunction extends SubspaceLPNormDistanceFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/AbstractEditDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/AbstractEditDistanceFunction.java index 6eb4a0cf..37d611a4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/AbstractEditDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/AbstractEditDistanceFunction.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Edit Distance for FeatureVectors. * * @author Thomas Bernecker + * @since 0.2 */ public abstract class AbstractEditDistanceFunction extends AbstractNumberVectorDistanceFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DTWDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DTWDistanceFunction.java index b3a1e19f..deddb490 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DTWDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DTWDistanceFunction.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * * @author Thomas Bernecker * @author Erich Schubert + * @since 0.2 */ @Title("Dynamic Time Warping Distance Function") @Reference(authors = "Berndt, D. and Clifford, J.", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DerivativeDTWDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DerivativeDTWDistanceFunction.java index c21997cb..4116fb94 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DerivativeDTWDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DerivativeDTWDistanceFunction.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * </p> * * @author Lara Hirschbeck, Daniel Kolb + * @since 0.2 */ @Title("Derivative dynamic time warping") @Reference(authors = "E. J. Keogh and M. J. Pazzani", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/EDRDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/EDRDistanceFunction.java index c6d01419..afc7b8de 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/EDRDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/EDRDistanceFunction.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * </p> * * @author Thomas Bernecker + * @since 0.2 */ @Title("Edit Distance on Real Sequence") @Reference(authors = "L. Chen and M. T. Özsu and V. Oria", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/ERPDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/ERPDistanceFunction.java index 39341d1e..93fd98bd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/ERPDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/ERPDistanceFunction.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * </p> * * @author Thomas Bernecker + * @since 0.2 */ @Title("Edit Distance with Real Penalty") @Reference(authors = "L. Chen and R. Ng", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/LCSSDistanceFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/LCSSDistanceFunction.java index 2d71ba1c..12e2752d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/LCSSDistanceFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/LCSSDistanceFunction.java @@ -68,6 +68,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * * * @author Thomas Bernecker + * @since 0.2 */ @Title("Longest Common Subsequence distance function") @Reference(authors = "M. Vlachos, M. Hadjieleftheriou, D. Gunopulos, E. Keogh", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractDBIDSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractDBIDSimilarityFunction.java index 9a4f2f58..9c440aee 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractDBIDSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractDBIDSimilarityFunction.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * Abstract super class for distance functions needing a preprocessor. * * @author Elke Achtert + * @since 0.4.0 */ public abstract class AbstractDBIDSimilarityFunction extends AbstractPrimitiveSimilarityFunction<DBID> implements DBIDSimilarityFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractIndexBasedSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractIndexBasedSimilarityFunction.java index 014ed7c9..16ba4e7f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractIndexBasedSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractIndexBasedSimilarityFunction.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Abstract super class for distance functions needing a preprocessor. * * @author Elke Achtert + * @since 0.4.0 * * @apiviz.uses IndexFactory * @apiviz.has Instance oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractPrimitiveSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractPrimitiveSimilarityFunction.java index 0cfb7c2a..7f1775ed 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractPrimitiveSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractPrimitiveSimilarityFunction.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * Base implementation of a similarity function. * * @author Arthur Zimek + * @since 0.4.0 * * @apiviz.excludeSubtypes * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractVectorSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractVectorSimilarityFunction.java index 1550c6c3..a09aff09 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractVectorSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/AbstractVectorSimilarityFunction.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.data.type.TypeUtil; * Abstract base class for double-valued primitive similarity functions. * * @author Erich Schubert + * @since 0.4.0 */ public abstract class AbstractVectorSimilarityFunction extends AbstractPrimitiveSimilarityFunction<NumberVector> implements PrimitiveSimilarityFunction<NumberVector> { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/DBIDSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/DBIDSimilarityFunction.java index cd8c8a0e..3db8b672 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/DBIDSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/DBIDSimilarityFunction.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBID; * function defined over object IDs. * * @author Elke Achtert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.uses DBID oneway - - defined on diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/FractionalSharedNearestNeighborSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/FractionalSharedNearestNeighborSimilarityFunction.java index 046d3725..36195869 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/FractionalSharedNearestNeighborSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/FractionalSharedNearestNeighborSimilarityFunction.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * Strings that define a non-negative Integer. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.has * de.lmu.ifi.dbs.elki.index.preprocessed.snn.SharedNearestNeighborIndex diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/IndexBasedSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/IndexBasedSimilarityFunction.java index 989178b5..1b79330d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/IndexBasedSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/IndexBasedSimilarityFunction.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.index.Index; * Interface for preprocessor/index based similarity functions. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has Instance oneway - - «create» * @apiviz.landmark diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/InvertedDistanceSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/InvertedDistanceSimilarityFunction.java index 3238b263..2e921066 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/InvertedDistanceSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/InvertedDistanceSimilarityFunction.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; * 1/distance. * * @author Erich Schubert + * @since 0.5.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/Kulczynski1SimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/Kulczynski1SimilarityFunction.java index a4f43310..1f84efcb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/Kulczynski1SimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/Kulczynski1SimilarityFunction.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "M.-M. Deza and E. Deza", title = "Dictionary of distances", booktitle = "Dictionary of distances") public class Kulczynski1SimilarityFunction extends AbstractVectorSimilarityFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/Kulczynski2SimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/Kulczynski2SimilarityFunction.java index 29fedb2e..15ab839f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/Kulczynski2SimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/Kulczynski2SimilarityFunction.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * TODO: add an optimized version for binary data. * * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "M.-M. Deza and E. Deza", title = "Dictionary of distances", booktitle = "Dictionary of distances") public class Kulczynski2SimilarityFunction extends AbstractVectorSimilarityFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/NormalizedPrimitiveSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/NormalizedPrimitiveSimilarityFunction.java index 9f7fd624..d43d095e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/NormalizedPrimitiveSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/NormalizedPrimitiveSimilarityFunction.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.distance.similarityfunction; * limited to the 0-1 value range. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/NormalizedSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/NormalizedSimilarityFunction.java index 0194b614..28dc1722 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/NormalizedSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/NormalizedSimilarityFunction.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.distance.similarityfunction; * produce values in the range of [0:1]. * * @author Erich Schubert + * @since 0.2 * @param <O> object type */ public interface NormalizedSimilarityFunction<O> extends SimilarityFunction<O> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/PrimitiveSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/PrimitiveSimilarityFunction.java index 308711f0..085e245a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/PrimitiveSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/PrimitiveSimilarityFunction.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.data.type.SimpleTypeInformation; * function. * * @author Elke Achtert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/SharedNearestNeighborSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/SharedNearestNeighborSimilarityFunction.java index c48b1dd3..6bb6f37b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/SharedNearestNeighborSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/SharedNearestNeighborSimilarityFunction.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * Strings that define a non-negative Integer. * * @author Arthur Zimek + * @since 0.2 * * @apiviz.has * de.lmu.ifi.dbs.elki.index.preprocessed.snn.SharedNearestNeighborIndex diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/SimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/SimilarityFunction.java index 95a8d59d..2315ec85 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/SimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/SimilarityFunction.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * function. * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusterIntersectionSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusterIntersectionSimilarityFunction.java index e7758720..dd5d0dcd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusterIntersectionSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusterIntersectionSimilarityFunction.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Measure the similarity of clusters via the intersection size. * * @author Erich Schubert + * @since 0.7.0 */ public class ClusterIntersectionSimilarityFunction extends AbstractPrimitiveSimilarityFunction<Cluster<?>> implements PrimitiveDistanceFunction<Cluster<?>> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusterJaccardSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusterJaccardSimilarityFunction.java index f67e4bc3..79993a5a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusterJaccardSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusterJaccardSimilarityFunction.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "P. Jaccard", // title = "Distribution de la florine alpine dans la Bassin de Dranses et dans quelques regiones voisines", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringAdjustedRandIndexSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringAdjustedRandIndexSimilarityFunction.java index 5d742ad1..255168fb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringAdjustedRandIndexSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringAdjustedRandIndexSimilarityFunction.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "Rand, W. M.", // title = "Objective Criteria for the Evaluation of Clustering Methods", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringBCubedF1SimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringBCubedF1SimilarityFunction.java index d4806cc4..58f7c3d9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringBCubedF1SimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringBCubedF1SimilarityFunction.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "Bagga, A. and Baldwin, B.", // title = "Entity-based cross-document coreferencing using the Vector Space Model", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringDistanceSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringDistanceSimilarityFunction.java index cc207a26..890c24db 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringDistanceSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringDistanceSimilarityFunction.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.distance.similarityfunction.PrimitiveSimilarityFuncti * Distance and similarity measure for clusterings. * * @author Erich Schubert + * @since 0.6.0 */ public interface ClusteringDistanceSimilarityFunction extends PrimitiveSimilarityFunction<Clustering<?>>, PrimitiveDistanceFunction<Clustering<?>> { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringFowlkesMallowsSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringFowlkesMallowsSimilarityFunction.java index e23fd289..0b9e99a7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringFowlkesMallowsSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringFowlkesMallowsSimilarityFunction.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "Fowlkes, E.B. and Mallows, C.L.", // title = "A method for comparing two hierarchical clusterings", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringRandIndexSimilarityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringRandIndexSimilarityFunction.java index 4719d1f6..13572924 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringRandIndexSimilarityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/cluster/ClusteringRandIndexSimilarityFunction.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "Rand, W. M.", // title = "Objective Criteria for the Evaluation of Clustering Methods", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/KernelMatrix.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/KernelMatrix.java index d747bc01..24195f7a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/KernelMatrix.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/KernelMatrix.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Matrix; * Kernel matrix representation. * * @author Simon Paradies + * @since 0.2 * * @apiviz.uses PrimitiveSimilarityFunction */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/LaplaceKernelFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/LaplaceKernelFunction.java index 1e0f3515..3a26e43a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/LaplaceKernelFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/LaplaceKernelFunction.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Laplace / exponential radial basis function kernel. * * @author Erich Schubert + * @since 0.2 */ public class LaplaceKernelFunction extends AbstractVectorSimilarityFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/LinearKernelFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/LinearKernelFunction.java index ca0d62fd..39380c11 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/LinearKernelFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/LinearKernelFunction.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * {@link de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction} * * @author Simon Paradies + * @since 0.2 */ public class LinearKernelFunction extends PolynomialKernelFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/PolynomialKernelFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/PolynomialKernelFunction.java index 9fe6b943..16249ec8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/PolynomialKernelFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/PolynomialKernelFunction.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * vectors V1 and V2 defined by (V1^T*V2)^degree. * * @author Simon Paradies + * @since 0.2 */ public class PolynomialKernelFunction extends AbstractVectorSimilarityFunction implements PrimitiveDistanceFunction<NumberVector> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/RadialBasisFunctionKernelFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/RadialBasisFunctionKernelFunction.java index c786f77d..b8bfa7e4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/RadialBasisFunctionKernelFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/RadialBasisFunctionKernelFunction.java @@ -37,8 +37,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Gaussian radial basis function kernel (RBF Kernel). * * @author Erich Schubert + * @since 0.2 */ -@Alias({ "rbf" }) +@Alias("rbf") public class RadialBasisFunctionKernelFunction extends AbstractVectorSimilarityFunction { /** * Scaling factor gamma. (= - 1/(2sigma^2)) diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/RationalQuadraticKernelFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/RationalQuadraticKernelFunction.java index 91264881..ea8c746e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/RationalQuadraticKernelFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/RationalQuadraticKernelFunction.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * RBF kernel ({@link RadialBasisFunctionKernelFunction}). * * @author Erich Schubert + * @since 0.2 */ public class RationalQuadraticKernelFunction extends AbstractVectorSimilarityFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/SigmoidKernelFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/SigmoidKernelFunction.java index 82eb5ea6..7a752a3a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/SigmoidKernelFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/SigmoidKernelFunction.java @@ -26,6 +26,7 @@ package de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel; import de.lmu.ifi.dbs.elki.data.NumberVector; import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractNumberVectorDistanceFunction; import de.lmu.ifi.dbs.elki.distance.similarityfunction.AbstractVectorSimilarityFunction; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; @@ -36,7 +37,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * perceptron MLP kernel). * * @author Erich Schubert + * @since 0.2 */ +@Alias("sigmoid") public class SigmoidKernelFunction extends AbstractVectorSimilarityFunction { /** * Scaling factor c, bias theta @@ -59,7 +62,7 @@ public class SigmoidKernelFunction extends AbstractVectorSimilarityFunction { public double similarity(NumberVector o1, NumberVector o2) { final int dim = AbstractNumberVectorDistanceFunction.dimensionality(o1, o2); double sim = 0.; - for (int i = 0; i < dim; i++) { + for(int i = 0; i < dim; i++) { final double v = o1.doubleValue(i) * o2.doubleValue(i); sim += v; } @@ -93,11 +96,11 @@ public class SigmoidKernelFunction extends AbstractVectorSimilarityFunction { protected void makeOptions(Parameterization config) { super.makeOptions(config); final DoubleParameter cP = new DoubleParameter(C_ID, 1.); - if (config.grab(cP)) { + if(config.grab(cP)) { c = cP.doubleValue(); } final DoubleParameter thetaP = new DoubleParameter(THETA_ID, 0.); - if (config.grab(thetaP)) { + if(config.grab(thetaP)) { theta = thetaP.doubleValue(); } } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/AutomaticEvaluation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/AutomaticEvaluation.java index 484b55c5..0763f69e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/AutomaticEvaluation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/AutomaticEvaluation.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.utilities.scaling.LinearScaling; * Evaluator that tries to auto-run a number of evaluation methods. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/Evaluator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/Evaluator.java index ad8d06db..636b4c8a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/Evaluator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/Evaluator.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.result.ResultProcessor; * evaluations, ... * * @author Erich Schubert + * @since 0.2 * * @apiviz.excludeSubtypes */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/NoAutomaticEvaluation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/NoAutomaticEvaluation.java index c2fd7811..e6cd96a2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/NoAutomaticEvaluation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/NoAutomaticEvaluation.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * evaluation to run. * * @author Erich Schubert + * @since 0.2 */ public class NoAutomaticEvaluation implements Evaluator { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/ConfusionMatrix.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/ConfusionMatrix.java index 78be5b52..73098bc5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/ConfusionMatrix.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/ConfusionMatrix.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.data.ClassLabel; * can be derived from a confusion matrix. * * @author Arthur Zimek + * @since 0.7.0 */ public class ConfusionMatrix { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/ConfusionMatrixEvaluationResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/ConfusionMatrixEvaluationResult.java index 87ad6df3..02d35025 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/ConfusionMatrixEvaluationResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/ConfusionMatrixEvaluationResult.java @@ -30,10 +30,13 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; /** * Provides the prediction performance measures for a classifier based on the * confusion matrix. - * + * * Note: this API is non-final, and will be refactored soon. * * @author Arthur Zimek + * @since 0.7.0 + * + * @apiviz.composedOf ConfusionMatrix */ public class ConfusionMatrixEvaluationResult implements Result, TextWriteable { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/AbstractHoldout.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/AbstractHoldout.java index cbe90475..bff2fa7f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/AbstractHoldout.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/AbstractHoldout.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * Split a data set for holdout evaluation. * * @author Erich Schubert + * @since 0.7.0 */ public abstract class AbstractHoldout implements Holdout { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/DisjointCrossValidation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/DisjointCrossValidation.java index c3c1df82..ecb872ac 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/DisjointCrossValidation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/DisjointCrossValidation.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * perform cross-validation. The test sets are guaranteed to be disjoint. * * @author Arthur Zimek + * @since 0.7.0 */ public class DisjointCrossValidation extends RandomizedHoldout { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/Holdout.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/Holdout.java index 69de2f9e..c2656147 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/Holdout.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/Holdout.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.datasource.bundle.MultipleObjectsBundle; * pairs of training and test data sets. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses MultipleObjectsBundle * @apiviz.has TrainingAndTestSet diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/LeaveOneOut.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/LeaveOneOut.java index ae638a39..e67d4a14 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/LeaveOneOut.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/LeaveOneOut.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.datasource.bundle.MultipleObjectsBundle; * remaining instances are training instances. * * @author Arthur Zimek + * @since 0.7.0 */ public class LeaveOneOut extends AbstractHoldout { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/RandomizedCrossValidation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/RandomizedCrossValidation.java index 868462d9..2921fc22 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/RandomizedCrossValidation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/RandomizedCrossValidation.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * to perform cross-validation. The test sets are not guaranteed to be disjoint. * * @author Arthur Zimek + * @since 0.7.0 */ public class RandomizedCrossValidation extends RandomizedHoldout { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/RandomizedHoldout.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/RandomizedHoldout.java index dd390421..aca68ed6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/RandomizedHoldout.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/RandomizedHoldout.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * A holdout providing a seed for randomized operations. * * @author Arthur Zimek + * @since 0.3 */ public abstract class RandomizedHoldout extends AbstractHoldout { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/StratifiedCrossValidation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/StratifiedCrossValidation.java index 3e0c4b2b..60af8179 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/StratifiedCrossValidation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/StratifiedCrossValidation.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * deterministic. * * @author Arthur Zimek + * @since 0.7.0 */ public class StratifiedCrossValidation extends AbstractHoldout { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/TrainingAndTestSet.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/TrainingAndTestSet.java index 7ee58663..3c1af309 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/TrainingAndTestSet.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/classification/holdout/TrainingAndTestSet.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.datasource.bundle.MultipleObjectsBundle; * training and test set are provided in labels. * * @author Arthur Zimek + * @since 0.7.0 */ public class TrainingAndTestSet { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/BCubed.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/BCubed.java index e4958527..4cf9ec0e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/BCubed.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/BCubed.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Sascha Goldhofer + * @since 0.5.0 */ @Reference(authors = "A. Bagga and B. Baldwin", // title = "Entity-based cross-document coreferencing using the Vector Space Model", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/ClusterContingencyTable.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/ClusterContingencyTable.java index e063b967..b269d2f9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/ClusterContingencyTable.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/ClusterContingencyTable.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * Class storing the contingency table and related data on two clusterings. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/EditDistance.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/EditDistance.java index 85764e2e..e07c84eb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/EditDistance.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/EditDistance.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Sascha Goldhofer + * @since 0.5.0 */ @Reference(authors = "Pantel, P. and Lin, D.", title = "Document clustering with committees", booktitle = "Proc. 25th ACM SIGIR conference on Research and development in information retrieval", url = "http://dx.doi.org/10.1145/564376.564412") public class EditDistance { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/Entropy.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/Entropy.java index b7770f71..17e3abca 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/Entropy.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/Entropy.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Sascha Goldhofer + * @since 0.5.0 */ @Reference(authors = "Meilă, M.", // title = "Comparing clusterings by the variation of information", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/EvaluateClustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/EvaluateClustering.java index a4c46191..473e713c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/EvaluateClustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/EvaluateClustering.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.result.EvaluationResult; import de.lmu.ifi.dbs.elki.result.Result; import de.lmu.ifi.dbs.elki.result.ResultHierarchy; import de.lmu.ifi.dbs.elki.result.ResultUtil; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.FormatUtil; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; @@ -48,11 +49,13 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Evaluate a clustering result by comparing it to an existing cluster label. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.uses ClusterContingencyTable * @apiviz.has EvaluateClustering.ScoreResult oneway - - «create» */ +@Alias("de.lmu.ifi.dbs.elki.evaluation.paircounting.EvaluatePairCountingFMeasure") public class EvaluateClustering implements Evaluator { /** * Logger for debug output. @@ -313,4 +316,4 @@ public class EvaluateClustering implements Evaluator { return new EvaluateClustering(referencealg, noiseSpecialHandling, !selfPairing); } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/LogClusterSizes.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/LogClusterSizes.java index 9b4c2512..2b801cfb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/LogClusterSizes.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/LogClusterSizes.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.hierarchy.Hierarchy.Iter; * cluster sizes and the number of clusters. * * @author Erich Schubert + * @since 0.7.0 */ public class LogClusterSizes implements Evaluator { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/PairCounting.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/PairCounting.java index 3025f367..26f2d5db 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/PairCounting.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/PairCounting.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * Pair-counting measures. * * @author Erich Schubert + * @since 0.5.0 */ public class PairCounting { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/SetMatchingPurity.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/SetMatchingPurity.java index bbef4b5f..46bddd77 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/SetMatchingPurity.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/SetMatchingPurity.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Sascha Goldhofer + * @since 0.5.0 */ @Reference(authors = "Meilă, M", // title = "Comparing clusterings", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/extractor/ExtractFlatClusteringFromHierarchyEvaluator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/extractor/ExtractFlatClusteringFromHierarchyEvaluator.java index 258b983d..60f22623 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/extractor/ExtractFlatClusteringFromHierarchyEvaluator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/extractor/ExtractFlatClusteringFromHierarchyEvaluator.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * from the same clustering, this can be useful. * * @author Erich Schubert + * @since 0.7.0 */ public class ExtractFlatClusteringFromHierarchyEvaluator implements Evaluator { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/extractor/HDBSCANHierarchyExtractionEvaluator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/extractor/HDBSCANHierarchyExtractionEvaluator.java index 4fa9f44f..456d1fc6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/extractor/HDBSCANHierarchyExtractionEvaluator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/extractor/HDBSCANHierarchyExtractionEvaluator.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * from the same clustering, this can be useful. * * @author Erich Schubert + * @since 0.7.0 */ public class HDBSCANHierarchyExtractionEvaluator implements Evaluator { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/extractor/SimplifiedHierarchyExtractionEvaluator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/extractor/SimplifiedHierarchyExtractionEvaluator.java index 871ab121..0644a16c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/extractor/SimplifiedHierarchyExtractionEvaluator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/extractor/SimplifiedHierarchyExtractionEvaluator.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * from the same clustering, this can be useful. * * @author Erich Schubert + * @since 0.7.0 */ public class SimplifiedHierarchyExtractionEvaluator implements Evaluator { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateCIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateCIndex.java index e43d9cc5..a96dfc91 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateCIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateCIndex.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction; import de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction; import de.lmu.ifi.dbs.elki.evaluation.Evaluator; import de.lmu.ifi.dbs.elki.logging.Logging; +import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress; import de.lmu.ifi.dbs.elki.logging.statistics.DoubleStatistic; import de.lmu.ifi.dbs.elki.logging.statistics.LongStatistic; import de.lmu.ifi.dbs.elki.logging.statistics.StringStatistic; @@ -43,7 +44,9 @@ import de.lmu.ifi.dbs.elki.result.EvaluationResult.MeasurementGroup; import de.lmu.ifi.dbs.elki.result.Result; import de.lmu.ifi.dbs.elki.result.ResultHierarchy; import de.lmu.ifi.dbs.elki.result.ResultUtil; -import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.DoubleArray; +import de.lmu.ifi.dbs.elki.utilities.datastructures.heap.DoubleHeap; +import de.lmu.ifi.dbs.elki.utilities.datastructures.heap.DoubleMaxHeap; +import de.lmu.ifi.dbs.elki.utilities.datastructures.heap.DoubleMinHeap; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; @@ -53,10 +56,13 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; /** * Compute the C-index of a data set. + * + * Note: This requires pairwise distance computations, so it is not recommended + * to use this on larger data sets. * * Reference: * <p> - * L. J. Hubert and J.R. Levin <br /> + * L. J. Hubert and J. R. Levin <br /> * A general statistical framework for assessing categorical clustering in free * recall<br /> * Psychological Bulletin, Vol. 83(6) @@ -64,6 +70,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Stephan Baier * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf NoiseHandling */ @@ -115,15 +122,9 @@ public class EvaluateCIndex<O> implements Evaluator { public double evaluateClustering(Database db, Relation<? extends O> rel, DistanceQuery<O> dq, Clustering<?> c) { List<? extends Cluster<?>> clusters = c.getAllClusters(); - // theta is the sum, w the number of within group distances - double theta = 0; - int w = 0; - int ignorednoise = 0; - int isize = clusters.size() <= 1 ? rel.size() : rel.size() / (clusters.size() - 1); - DoubleArray pairDists = new DoubleArray(isize); - - for(int i = 0; i < clusters.size(); i++) { - Cluster<?> cluster = clusters.get(i); + // Count ignored noise, and within-cluster distances + int ignorednoise = 0, w = 0; + for(Cluster<?> cluster : clusters) { if(cluster.size() <= 1 || cluster.isNoise()) { switch(noiseOption){ case IGNORE_NOISE: @@ -135,41 +136,51 @@ public class EvaluateCIndex<O> implements Evaluator { break; // Treat like a cluster } } - for(DBIDIter it1 = cluster.getIDs().iter(); it1.valid(); it1.advance()) { - O obj = rel.get(it1); - // Compare object to every cluster, but only once - for(int j = i; j < clusters.size(); j++) { - Cluster<?> ocluster = clusters.get(j); - if(ocluster.size() <= 1 || ocluster.isNoise()) { - switch(noiseOption){ - case IGNORE_NOISE: - continue; // Ignore this cluster. - case TREAT_NOISE_AS_SINGLETONS: - case MERGE_NOISE: - break; // Treat like a cluster - } - } - for(DBIDIter it2 = ocluster.getIDs().iter(); it2.valid(); it2.advance()) { - if(DBIDUtil.compare(it1, it2) <= 0) { // Only once. - continue; - } - double dist = dq.distance(obj, rel.get(it2)); - pairDists.add(dist); - if(ocluster == cluster) { // Within-cluster distances. - theta += dist; - w++; - } + w += (cluster.size() * (cluster.size() - 1)) >>> 1; + } + + double theta = 0.; // Sum of within-cluster distances + double min = 0, max = 0; // Sum of larges and smallest + if(w <= (rel.size() * (rel.size() - 1L)) >>> 2) { + DoubleHeap maxDists = new DoubleMinHeap(w); // Careful: REALLY minHeap! + DoubleHeap minDists = new DoubleMaxHeap(w); // Careful: REALLY maxHeap! + + FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Processing clusters for C-Index", clusters.size(), LOG) : null; + for(int i = 0; i < clusters.size(); i++) { + Cluster<?> cluster = clusters.get(i); + if(cluster.size() <= 1 || cluster.isNoise()) { + switch(noiseOption){ + case IGNORE_NOISE: + LOG.incrementProcessed(prog); + continue; // Ignore + case TREAT_NOISE_AS_SINGLETONS: + processSingleton(cluster, rel, dq, maxDists, minDists, w); + LOG.incrementProcessed(prog); + continue; + case MERGE_NOISE: + break; // Treat like a cluster, below } } + theta += processCluster(cluster, clusters, i, dq, maxDists, minDists, w); + LOG.incrementProcessed(prog); } - } + LOG.ensureCompleted(prog); - // Simulate best and worst cases: - pairDists.sort(); - double min = 0, max = 0; - for(int i = 0, j = pairDists.size() - 1; i < w; i++, j--) { - min += pairDists.get(i); - max += pairDists.get(j); + // Simulate best and worst cases: + assert (minDists.size() == w); + assert (maxDists.size() == w); + for(DoubleHeap.UnsortedIter it = minDists.unsortedIter(); it.valid(); it.advance()) { + min += it.get(); + } + for(DoubleHeap.UnsortedIter it = maxDists.unsortedIter(); it.valid(); it.advance()) { + max += it.get(); + } + assert (max >= min); + } + else { + // Since we have fewer cross-cluster distances than within-cluster + // distances, min=max and cIndex = 0. + theta = min = max = 0; } double cIndex = (max > min) ? (theta - min) / (max - min) : 0.; @@ -189,6 +200,52 @@ public class EvaluateCIndex<O> implements Evaluator { return cIndex; } + protected double processCluster(Cluster<?> cluster, List<? extends Cluster<?>> clusters, int i, DistanceQuery<O> dq, DoubleHeap maxDists, DoubleHeap minDists, int w) { + double theta = 0.; + for(DBIDIter it1 = cluster.getIDs().iter(); it1.valid(); it1.advance()) { + // Compare object to every cluster, but only once + for(int j = i; j < clusters.size(); j++) { + Cluster<?> ocluster = clusters.get(j); + if(ocluster.size() <= 1 || ocluster.isNoise()) { + switch(noiseOption){ + case IGNORE_NOISE: + continue; // Ignore this cluster. + case TREAT_NOISE_AS_SINGLETONS: + break; // Treat like a cluster + case MERGE_NOISE: + break; // Treat like a cluster + } + } + for(DBIDIter it2 = ocluster.getIDs().iter(); it2.valid(); it2.advance()) { + if(DBIDUtil.compare(it1, it2) <= 0) { // Only once. + continue; + } + double dist = dq.distance(it1, it2); + minDists.add(dist, w); + maxDists.add(dist, w); + if(ocluster == cluster) { // Within-cluster distances. + theta += dist; + } + } + } + } + return theta; + } + + protected void processSingleton(Cluster<?> cluster, Relation<? extends O> rel, DistanceQuery<O> dq, DoubleHeap maxDists, DoubleHeap minDists, int w) { + // All other objects are in other clusters! + for(DBIDIter it1 = cluster.getIDs().iter(); it1.valid(); it1.advance()) { + for(DBIDIter it2 = rel.iterDBIDs(); it2.valid(); it2.advance()) { + if(DBIDUtil.compare(it1, it2) <= 0) { // Only once. + continue; + } + double dist = dq.distance(it1, it2); + minDists.add(dist, w); + maxDists.add(dist, w); + } + } + } + @Override public void processNewResult(ResultHierarchy hier, Result result) { List<Clustering<?>> crs = ResultUtil.getClusteringResults(result); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateConcordantPairs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateConcordantPairs.java index c5d2c199..119e9006 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateConcordantPairs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateConcordantPairs.java @@ -73,6 +73,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Stephan Baier * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf NoiseHandling */ @@ -312,7 +313,7 @@ public class EvaluateConcordantPairs<O> implements Evaluator { /** * Parameter for the option, how noise should be treated. */ - public static final OptionID NOISE_ID = new OptionID("davies-bouldin.noisehandling", "option, how noise should be treated."); + public static final OptionID NOISE_ID = new OptionID("concordant-pairs.noisehandling", "Control how noise should be treated."); /** * Distance function to use. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateDaviesBouldin.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateDaviesBouldin.java index ddeef150..d652a13a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateDaviesBouldin.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateDaviesBouldin.java @@ -63,6 +63,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Stephan Baier + * @since 0.7.0 * * @apiviz.composedOf NoiseHandling */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluatePBMIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluatePBMIndex.java index 2c3a20e0..5a893887 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluatePBMIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluatePBMIndex.java @@ -67,6 +67,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Stephan Baier * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf NoiseHandling */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateSilhouette.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateSilhouette.java index b40e6086..257ff1ea 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateSilhouette.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateSilhouette.java @@ -92,6 +92,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * TODO: keep all silhouette values, and allow visualization! * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf NoiseHandling * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateSimplifiedSilhouette.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateSimplifiedSilhouette.java index a3f7e889..7ae8193c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateSimplifiedSilhouette.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateSimplifiedSilhouette.java @@ -60,6 +60,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Stephan Baier * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf NoiseHandling */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateSquaredErrors.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateSquaredErrors.java index eec64fc4..0ea8cbf8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateSquaredErrors.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateSquaredErrors.java @@ -87,6 +87,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * by k-means. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf NoiseHandling */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateVarianceRatioCriteria.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateVarianceRatioCriteria.java index a48a410c..e8935593 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateVarianceRatioCriteria.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateVarianceRatioCriteria.java @@ -65,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; * * @author Stephan Baier * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf NoiseHandling */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/NoiseHandling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/NoiseHandling.java index 7145ed94..759636d8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/NoiseHandling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/NoiseHandling.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.evaluation.clustering.internal; * * @author Stephan Baier * @author Erich Schubert + * @since 0.7.0 */ public enum NoiseHandling { /** Merge all noise into a cluster */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/pairsegments/ClusterPairSegmentAnalysis.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/pairsegments/ClusterPairSegmentAnalysis.java index 08d92c28..50deb3ce 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/pairsegments/ClusterPairSegmentAnalysis.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/pairsegments/ClusterPairSegmentAnalysis.java @@ -29,17 +29,31 @@ import de.lmu.ifi.dbs.elki.evaluation.Evaluator; import de.lmu.ifi.dbs.elki.result.Result; import de.lmu.ifi.dbs.elki.result.ResultHierarchy; import de.lmu.ifi.dbs.elki.result.ResultUtil; +import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; /** * Evaluate clustering results by building segments for their pairs: shared * pairs and differences. * + * Reference: + * <p> + * Evaluation of Clusterings – Metrics and Visual Support<br /> + * Elke Achtert, Sascha Goldhofer, Hans-Peter Kriegel, Erich Schubert, Arthur + * Zimek<br /> + * In: Proc. 28th International Conference on Data Engineering (ICDE) 2012 + * </p> + * * @author Sascha Goldhofer * @author Erich Schubert + * @since 0.5.0 * * @apiviz.uses Clustering * @apiviz.uses Segments */ +@Reference(title = "Evaluation of Clusterings – Metrics and Visual Support", // +authors = "Elke Achtert, Sascha Goldhofer, Hans-Peter Kriegel, Erich Schubert, Arthur Zimek", // +booktitle = "Proc. 28th International Conference on Data Engineering (ICDE) 2012", // +url = "http://dx.doi.org/10.1109/ICDE.2012.128") public class ClusterPairSegmentAnalysis implements Evaluator { /** * Constructor. @@ -55,7 +69,7 @@ public class ClusterPairSegmentAnalysis implements Evaluator { public void processNewResult(ResultHierarchy hier, Result result) { // Get all new clusterings // TODO: handle clusterings added later, too. Can we update the result? - + List<Clustering<?>> clusterings = ResultUtil.getClusteringResults(result); // Abort if not enough clusterings to compare if(clusterings.size() < 2) { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/pairsegments/Segment.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/pairsegments/Segment.java index 1ed31b03..4df28760 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/pairsegments/Segment.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/pairsegments/Segment.java @@ -33,6 +33,10 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * * As such, for each ring (= clustering), a cluster number (or the constant * {@link #UNCLUSTERED}) is stored. + * + * @author Sascha Goldhofer + * @author Erich Schubert + * @since 0.5.0 */ public class Segment implements Comparable<Segment> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/pairsegments/Segments.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/pairsegments/Segments.java index 8b91d5f6..5b59b17f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/pairsegments/Segments.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/pairsegments/Segments.java @@ -59,8 +59,8 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * a corresponding object Segment. * </p> * + * Reference: * <p> - * Reference:<br /> * Evaluation of Clusterings – Metrics and Visual Support<br /> * Elke Achtert, Sascha Goldhofer, Hans-Peter Kriegel, Erich Schubert, Arthur * Zimek<br /> @@ -68,17 +68,21 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * <p> - * Details on the experimental setup can be found at: <a - * href="http://elki.dbs.ifi.lmu.de/wiki/Examples/ClusterEvaluation" - * >wiki/Examples/ClusterEvaluation</a> + * Details on the experimental setup can be found at: + * <a href="http://elki.dbs.ifi.lmu.de/wiki/Examples/ClusterEvaluation" >wiki/ + * Examples/ClusterEvaluation</a> * </p> * * @author Sascha Goldhofer * @author Erich Schubert + * @since 0.5.0 * * @apiviz.composedOf Segment */ -@Reference(title = "Evaluation of Clusterings – Metrics and Visual Support", authors = "Elke Achtert, Sascha Goldhofer, Hans-Peter Kriegel, Erich Schubert, Arthur Zimek", booktitle = "Proc. 28th International Conference on Data Engineering (ICDE) 2012", url = "http://dx.doi.org/10.1109/ICDE.2012.128") +@Reference(title = "Evaluation of Clusterings – Metrics and Visual Support", // +authors = "Elke Achtert, Sascha Goldhofer, Hans-Peter Kriegel, Erich Schubert, Arthur Zimek", // +booktitle = "Proc. 28th International Conference on Data Engineering (ICDE) 2012", // +url = "http://dx.doi.org/10.1109/ICDE.2012.128") public class Segments extends BasicResult implements Iterable<Segment> { /** * Class logger diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/histogram/ComputeOutlierHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/histogram/ComputeOutlierHistogram.java index 8a6bd542..64a1ce3c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/histogram/ComputeOutlierHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/histogram/ComputeOutlierHistogram.java @@ -66,6 +66,7 @@ import de.lmu.ifi.dbs.elki.utilities.scaling.outlier.OutlierScalingFunction; * * @author Lisa Reichert * @author Erich Schubert + * @since 0.3 * * @apiviz.landmark * @apiviz.uses OutlierResult diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/index/IndexPurity.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/index/IndexPurity.java index bde4eaa3..30d3590d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/index/IndexPurity.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/index/IndexPurity.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.utilities.DatabaseUtil; * capabilities using the Gini index. * * @author Erich Schubert + * @since 0.5.0 */ public class IndexPurity implements Evaluator { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/index/IndexStatistics.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/index/IndexStatistics.java index a137b455..5e01462f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/index/IndexStatistics.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/index/IndexStatistics.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * information. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.has IndexMetaResult oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/JudgeOutlierScores.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/JudgeOutlierScores.java index 6674293d..6c84be65 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/JudgeOutlierScores.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/JudgeOutlierScores.java @@ -60,6 +60,7 @@ import de.lmu.ifi.dbs.elki.utilities.scaling.outlier.OutlierScalingFunction; * hits. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.has ScoreResult oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierPrecisionAtKCurve.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierPrecisionAtKCurve.java index 3ce0e782..a52b829a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierPrecisionAtKCurve.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierPrecisionAtKCurve.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.PatternParameter; * method. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has PrecisionAtKCurve */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierPrecisionRecallCurve.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierPrecisionRecallCurve.java index 3b1d7375..576a0c9b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierPrecisionRecallCurve.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierPrecisionRecallCurve.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.PatternParameter; * method. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has PRCurve */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierROCCurve.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierROCCurve.java index f0ebcd88..540cba6d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierROCCurve.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierROCCurve.java @@ -62,13 +62,15 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.PatternParameter; * clustering obtained via the given class label. * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * * @apiviz.uses OutlierResult * @apiviz.has ROCResult oneway - - «create» */ -@Alias({ "ComputeROCCurve", "de.lmu.ifi.dbs.elki.evaluation.roc.ComputeROCCurve" }) +@Alias({ "de.lmu.ifi.dbs.elki.evaluation.roc.ComputeROCCurve", // +"de.lmu.ifi.dbs.elki.evaluation.ComputeROCCurve" }) public class OutlierROCCurve implements Evaluator { /** * The label we use for marking ROCAUC values. @@ -142,7 +144,8 @@ public class OutlierROCCurve implements Evaluator { if(nonefound) { return; - // logger.warning("No results found to process with ROC curve analyzer. Got "+iterables.size()+" iterables, "+orderings.size()+" orderings."); + // logger.warning("No results found to process with ROC curve analyzer. + // Got "+iterables.size()+" iterables, "+orderings.size()+" orderings."); } } @@ -209,6 +212,7 @@ public class OutlierROCCurve implements Evaluator { * </p> */ public static final OptionID POSITIVE_CLASS_NAME_ID = new OptionID("rocauc.positive", "Class label for the 'positive' class."); + /** * Pattern for positive class. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierRankingEvaluation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierRankingEvaluation.java index 43612178..407b4ec9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierRankingEvaluation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierRankingEvaluation.java @@ -57,6 +57,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.PatternParameter; * Evaluate outlier scores by their ranking * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierSmROCCurve.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierSmROCCurve.java index b39211df..49ff1a42 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierSmROCCurve.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierSmROCCurve.java @@ -67,6 +67,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.PatternParameter; * </p> * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.uses OutlierResult * @apiviz.has SmROCResult oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierThresholdClustering.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierThresholdClustering.java index 9220d06e..9993e457 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierThresholdClustering.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/OutlierThresholdClustering.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.utilities.scaling.outlier.OutlierScalingFunction; * dataset. * * @author Erich Schubert + * @since 0.5.0 */ public class OutlierThresholdClustering implements Evaluator { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/AbstractScoreEvaluation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/AbstractScoreEvaluation.java index 9f8e66df..bebb3e71 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/AbstractScoreEvaluation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/AbstractScoreEvaluation.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; * Abstract base class for evaluating a scoring result. * * @author Erich Schubert + * @since 0.7.0 */ public abstract class AbstractScoreEvaluation implements ScoreEvaluation { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/AveragePrecisionEvaluation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/AveragePrecisionEvaluation.java index fadcb3cf..51fe6c59 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/AveragePrecisionEvaluation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/AveragePrecisionEvaluation.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Evaluate using average precision. * * @author Erich Schubert + * @since 0.7.0 */ public class AveragePrecisionEvaluation extends AbstractScoreEvaluation { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/MaximumF1Evaluation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/MaximumF1Evaluation.java index dce8a84b..4d96eaaa 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/MaximumF1Evaluation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/MaximumF1Evaluation.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Evaluate using the maximum F1 score. * * @author Erich Schubert + * @since 0.7.0 */ public class MaximumF1Evaluation extends AbstractScoreEvaluation { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/PrecisionAtKEvaluation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/PrecisionAtKEvaluation.java index 3850dd3a..ba6786b9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/PrecisionAtKEvaluation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/PrecisionAtKEvaluation.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * (BEP). * * @author Erich Schubert + * @since 0.7.0 */ public class PrecisionAtKEvaluation extends AbstractScoreEvaluation { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/ROCEvaluation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/ROCEvaluation.java index 32551238..416ecda1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/ROCEvaluation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/ROCEvaluation.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * has been used the wrong way, and should be used backwards. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has XYCurve */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/ScoreEvaluation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/ScoreEvaluation.java index 2f989609..053033e9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/ScoreEvaluation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/ScoreEvaluation.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.Iter; * Compute ranking/scoring based evaluation measures. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has ScoreIter * @apiviz.uses Predicate diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/AbstractVectorIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/AbstractVectorIter.java index f75844a0..70e6618c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/AbstractVectorIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/AbstractVectorIter.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.ArrayIter; * Class to iterate over a number vector in decreasing order. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf NumberVector */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DBIDRefIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DBIDRefIter.java index 3b246327..918a235c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DBIDRefIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DBIDRefIter.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; * A score iterator wrapping a DBIDRef object. * * @author Erich Schubert + * @since 0.4.0 */ public interface DBIDRefIter { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DBIDsTest.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DBIDsTest.java index 9e1b29e9..d1c65fbe 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DBIDsTest.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DBIDsTest.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.evaluation.scores.ScoreEvaluation.Predicate; * @apiviz.composedOf DBIDs * * @author Erich Schubert + * @since 0.7.0 */ public class DBIDsTest implements Predicate<DBIDRefIter> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DecreasingVectorIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DecreasingVectorIter.java index 953f656c..9da00a3e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DecreasingVectorIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DecreasingVectorIter.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arrays.IntegerComparator; * Class to iterate over a number vector in decreasing order. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf NumberVector */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DistanceResultAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DistanceResultAdapter.java index cd1a5142..53a165ba 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DistanceResultAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/DistanceResultAdapter.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.evaluation.scores.ScoreEvaluation.ScoreIter; * ties. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf DoubleDBIDListIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/FilteredDistanceResultAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/FilteredDistanceResultAdapter.java index 28c23251..4309e138 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/FilteredDistanceResultAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/FilteredDistanceResultAdapter.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDListIter; * appropriately, the score is only used to detect ties. * * @author Erich Schubert + * @since 0.7.0 */ public class FilteredDistanceResultAdapter extends DistanceResultAdapter { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/IncreasingVectorIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/IncreasingVectorIter.java index 091a6fa1..d94c2990 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/IncreasingVectorIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/IncreasingVectorIter.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arrays.IntegerComparator; * Class to iterate over a number vector in decreasing order. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf NumberVector */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/OutlierScoreAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/OutlierScoreAdapter.java index 6dcf516a..3ff35876 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/OutlierScoreAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/OutlierScoreAdapter.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; * The ROC values would be incorrect then anyway! * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf OutlierResult */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/SimpleAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/SimpleAdapter.java index e91f0f6d..681cdcdd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/SimpleAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/SimpleAdapter.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.evaluation.scores.ScoreEvaluation.ScoreIter; * The ROC values would be incorrect then anyway! * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf DBIDIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/VectorNonZero.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/VectorNonZero.java index 343fa662..52753243 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/VectorNonZero.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/VectorNonZero.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.data.NumberVector; * @apiviz.composedOf NumberVector * * @author Erich Schubert + * @since 0.7.0 */ public class VectorNonZero extends VectorOverThreshold { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/VectorOverThreshold.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/VectorOverThreshold.java index e35db2ee..b77df57b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/VectorOverThreshold.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/VectorOverThreshold.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.evaluation.scores.ScoreEvaluation.Predicate; * @apiviz.composedOf NumberVector * * @author Erich Schubert + * @since 0.7.0 */ public class VectorOverThreshold implements Predicate<AbstractVectorIter> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/VectorZero.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/VectorZero.java index 08e694f9..aeead25b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/VectorZero.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/scores/adapter/VectorZero.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.evaluation.scores.ScoreEvaluation.Predicate; * @apiviz.composedOf NumberVector * * @author Erich Schubert + * @since 0.7.0 */ public class VectorZero implements Predicate<IncreasingVectorIter> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/similaritymatrix/ComputeSimilarityMatrixImage.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/similaritymatrix/ComputeSimilarityMatrixImage.java index d7883620..a5cf462c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/similaritymatrix/ComputeSimilarityMatrixImage.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/evaluation/similaritymatrix/ComputeSimilarityMatrixImage.java @@ -65,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.scaling.ScalingFunction; * Compute a similarity matrix for a distance function. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has SimilarityMatrix oneway - - «create» * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/GUIUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/GUIUtil.java index b7d4ee18..210f4e2e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/GUIUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/GUIUtil.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * GUI utilities. * * @author Erich Schubert + * @since 0.5.5 */ public final class GUIUtil { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/AbstractParameterConfigurator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/AbstractParameterConfigurator.java index d1d89d69..9905ad59 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/AbstractParameterConfigurator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/AbstractParameterConfigurator.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * Abstract class to produce a configurator for a particular parameter. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has StockIcon * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/AbstractSingleParameterConfigurator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/AbstractSingleParameterConfigurator.java index de040cc7..bb298994 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/AbstractSingleParameterConfigurator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/AbstractSingleParameterConfigurator.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * Base class for MiniGUI input helpers * * @author Erich Schubert + * @since 0.4.0 * * @param <T> Parameter type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ClassListParameterConfigurator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ClassListParameterConfigurator.java index ddc25f2e..0d76aa95 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ClassListParameterConfigurator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ClassListParameterConfigurator.java @@ -56,6 +56,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * Additionally, the classes can in turn have additional parameters. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses ClassListParameter * @apiviz.uses ClassTree diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ClassParameterConfigurator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ClassParameterConfigurator.java index 7bc81fed..07f1e14f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ClassParameterConfigurator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ClassParameterConfigurator.java @@ -59,6 +59,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * Additionally, the classes can in turn have additional parameters. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses ClassParameter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ConfiguratorPanel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ConfiguratorPanel.java index 873417a0..b07aed06 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ConfiguratorPanel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ConfiguratorPanel.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * A panel that contains configurators for parameters. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.has de.lmu.ifi.dbs.elki.gui.configurator.ParameterConfigurator diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/EnumParameterConfigurator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/EnumParameterConfigurator.java index 416b47bb..95ae3a04 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/EnumParameterConfigurator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/EnumParameterConfigurator.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.EnumParameter; * TODO: offer radio buttons when just a few choices are available? * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses EnumParameter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/FileParameterConfigurator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/FileParameterConfigurator.java index f7218f35..9d3d53e5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/FileParameterConfigurator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/FileParameterConfigurator.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; * Provide a configuration panel to choose a file with a file selector button. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses FileParameter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/FlagParameterConfigurator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/FlagParameterConfigurator.java index 052c6ac6..5b3d42c7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/FlagParameterConfigurator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/FlagParameterConfigurator.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; * Provide a configuration panel to modify a boolean via a checkbox. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses Flag */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ParameterConfigurator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ParameterConfigurator.java index 217f3632..88b93d25 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ParameterConfigurator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/ParameterConfigurator.java @@ -29,12 +29,40 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.TrackParameters; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; +/** + * Interface for different configuration assistants for the multistep GUI. + * + * @author Erich Schubert + * @since 0.4.0 + */ public interface ParameterConfigurator { + /** + * Add a parameter to the panel. + * + * @param owner Owning ("parent") object + * @param param Parameter + * @param track Parameter tracker + */ public void addParameter(Object owner, Parameter<?> param, TrackParameters track); + /** + * Add a change listener + * + * @param listener Change listener + */ public void addChangeListener(ChangeListener listener); + /** + * Remove a change listener + * + * @param listener Change listener + */ public void removeChangeListener(ChangeListener listener); + /** + * Append the parameters to a list. + * + * @param params Parameter list (output) + */ public void appendParameters(ListParameterization params); }
\ No newline at end of file diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/TextParameterConfigurator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/TextParameterConfigurator.java index 27c9d531..6c86f18a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/TextParameterConfigurator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/configurator/TextParameterConfigurator.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * Provide a configuration panel to input an arbitrary text parameter. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses Parameter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/icons/StockIcon.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/icons/StockIcon.java index c0c7b91c..de450f4a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/icons/StockIcon.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/icons/StockIcon.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.logging.LoggingUtil; * Stock icon library for use in the GUI. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/minigui/MiniGUI.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/minigui/MiniGUI.java index 6edaa95d..7cba1e97 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/minigui/MiniGUI.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/minigui/MiniGUI.java @@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.gui.minigui; This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures - Copyright (C) 2015 + Copyright (C) 2016 Ludwig-Maximilians-Universität München Lehr- und Forschungseinheit für Datenbanksysteme ELKI Development Team @@ -36,7 +36,6 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.List; -import java.util.logging.Level; import javax.swing.AbstractAction; import javax.swing.AbstractListModel; @@ -46,8 +45,10 @@ import javax.swing.ImageIcon; import javax.swing.JButton; import javax.swing.JComboBox; import javax.swing.JFrame; +import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JScrollPane; +import javax.swing.JTextField; import javax.swing.KeyStroke; import javax.swing.SwingWorker; import javax.swing.event.TableModelEvent; @@ -81,6 +82,7 @@ import de.lmu.ifi.dbs.elki.workflow.OutputStep; * Minimal GUI built around a table-based parameter editor. * * @author Erich Schubert + * @since 0.3 * * @apiviz.composedOf SettingsComboboxModel * @apiviz.composedOf LoggingStep @@ -140,6 +142,11 @@ public class MiniGUI extends AbstractApplication { protected SavedSettingsFile store = new SavedSettingsFile(SAVED_SETTINGS_FILENAME); /** + * Combo box for choosing the application to run. + */ + protected JComboBox<String> appCombo; + + /** * Combo box for saved settings. */ protected JComboBox<String> savedCombo; @@ -160,12 +167,22 @@ public class MiniGUI extends AbstractApplication { private Class<? extends AbstractApplication> maincls = KDDCLIApplication.class; /** + * Command line output field. + */ + private JTextField commandLine; + + /** + * Prefix for application package. + */ + private String APP_PREFIX = AbstractApplication.class.getPackage().getName() + "."; + + /** * Constructor. */ public MiniGUI() { super(); // Create and set up the window. - frame = new JFrame("ELKI MiniGUI"); + frame = new JFrame("ELKI MiniGUI Command Line Builder"); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); try { frame.setIconImage(new ImageIcon(KDDTask.class.getResource("elki-icon.png")).getImage()); @@ -178,138 +195,11 @@ public class MiniGUI extends AbstractApplication { panel.setOpaque(true); // content panes must be opaque panel.setLayout(new GridBagLayout()); - { - // Button panel - JPanel buttonPanel = new JPanel(); - buttonPanel.setLayout(new BoxLayout(buttonPanel, BoxLayout.X_AXIS)); - - // Combo box for saved settings - savedSettingsModel = new SettingsComboboxModel(store); - savedCombo = new JComboBox<>(savedSettingsModel); - savedCombo.setEditable(true); - savedCombo.setSelectedItem("[Saved Settings]"); - buttonPanel.add(savedCombo); - - // button to load settings - JButton loadButton = new JButton("Load"); - loadButton.setMnemonic(KeyEvent.VK_L); - loadButton.addActionListener(new ActionListener() { - @Override - public void actionPerformed(ActionEvent e) { - String key = savedSettingsModel.getSelectedItem(); - ArrayList<String> settings = store.get(key); - if(settings != null) { - outputArea.clear(); - outputArea.publish("Parameters: " + FormatUtil.format(settings, " ") + NEWLINE, Level.INFO); - doSetParameters(settings); - } - } - }); - buttonPanel.add(loadButton); - // button to save settings - JButton saveButton = new JButton("Save"); - saveButton.setMnemonic(KeyEvent.VK_S); - saveButton.addActionListener(new ActionListener() { - @Override - public void actionPerformed(ActionEvent e) { - String key = savedSettingsModel.getSelectedItem(); - // Stop editing the table. - parameterTable.editCellAt(-1, -1); - store.put(key, parameters.serializeParameters()); - try { - store.save(); - } - catch(IOException e1) { - LOG.exception(e1); - } - savedSettingsModel.update(); - } - }); - buttonPanel.add(saveButton); - // button to remove saved settings - JButton removeButton = new JButton("Remove"); - removeButton.setMnemonic(KeyEvent.VK_E); - removeButton.addActionListener(new ActionListener() { - @Override - public void actionPerformed(ActionEvent e) { - String key = savedSettingsModel.getSelectedItem(); - store.remove(key); - try { - store.save(); - } - catch(IOException e1) { - LOG.exception(e1); - } - savedCombo.setSelectedItem("[Saved Settings]"); - savedSettingsModel.update(); - } - }); - buttonPanel.add(removeButton); - - // button to launch the task - runButton = new JButton("Run Task"); - runButton.setMnemonic(KeyEvent.VK_R); - runButton.addActionListener(new ActionListener() { - @Override - public void actionPerformed(ActionEvent e) { - startTask(); - } - }); - buttonPanel.add(runButton); - - GridBagConstraints constraints = new GridBagConstraints(); - constraints.fill = GridBagConstraints.HORIZONTAL; - constraints.gridx = 0; - constraints.gridy = 1; - constraints.weightx = 1.0; - constraints.weighty = 0.01; - panel.add(buttonPanel, constraints); - } - - { - // Setup parameter storage and table model - this.parameters = new DynamicParameters(); - ParametersModel parameterModel = new ParametersModel(parameters); - parameterModel.addTableModelListener(new TableModelListener() { - @Override - public void tableChanged(TableModelEvent e) { - // logger.debug("Change event."); - updateParameterTable(); - } - }); - - // Create parameter table - parameterTable = new ParameterTable(frame, parameterModel, parameters); - // Create the scroll pane and add the table to it. - JScrollPane scrollPane = new JScrollPane(parameterTable); - - // Add the scroll pane to this panel. - GridBagConstraints constraints = new GridBagConstraints(); - constraints.fill = GridBagConstraints.BOTH; - constraints.gridx = 0; - constraints.gridy = 0; - constraints.weightx = 1; - constraints.weighty = 1; - panel.add(scrollPane, constraints); - } - - { - // setup text output area - outputArea = new LogPanel(); - - // Create the scroll pane and add the table to it. - JScrollPane outputPane = new JScrollPane(outputArea); - outputPane.setPreferredSize(new Dimension(800, 400)); - - // Add the output pane to the bottom - GridBagConstraints constraints = new GridBagConstraints(); - constraints.fill = GridBagConstraints.BOTH; - constraints.gridx = 0; - constraints.gridy = 2; - constraints.weightx = 1; - constraints.weighty = 1; - panel.add(outputPane, constraints); - } + setupAppChooser(); + setupParameterTable(); + setupLoadSaveButtons(); + setupCommandLine(); + setupLoggingArea(); // load saved settings (we wanted to have the logger first!) try { @@ -349,14 +239,222 @@ public class MiniGUI extends AbstractApplication { } /** + * Setup the application chooser. + */ + private void setupAppChooser() { + // Configurator to choose the main application + appCombo = new JComboBox<>(); + for(Class<?> clz : ELKIServiceRegistry.findAllImplementations(AbstractApplication.class)) { + String nam = clz.getCanonicalName(); + if(nam == null || clz.getCanonicalName().contains("GUI")) { + continue; + } + if(nam.startsWith(APP_PREFIX)) { + nam = nam.substring(APP_PREFIX.length()); + } + appCombo.addItem(nam); + } + appCombo.setEditable(true); + String sel = maincls.getCanonicalName(); + if(sel.startsWith(APP_PREFIX)) { + sel = sel.substring(APP_PREFIX.length()); + } + appCombo.setSelectedItem(sel); + appCombo.addActionListener(new ActionListener() { + @Override + public void actionPerformed(ActionEvent e) { + if("comboBoxChanged".equals(e.getActionCommand())) { + Class<? extends AbstractApplication> clz = ELKIServiceRegistry.findImplementation(AbstractApplication.class, (String) appCombo.getSelectedItem()); + if(clz != null) { + maincls = clz; + updateParameterTable(); + } + else { + LOG.warning("Main class name not found."); + } + } + } + }); + + GridBagConstraints constraints = new GridBagConstraints(); + constraints.fill = GridBagConstraints.BOTH; + constraints.gridx = 0; + constraints.gridy = 0; + constraints.weightx = 1; + constraints.weighty = .01; + panel.add(appCombo, constraints); + } + + /** + * Setup the parameter table + */ + private void setupParameterTable() { + // Setup parameter storage and table model + this.parameters = new DynamicParameters(); + ParametersModel parameterModel = new ParametersModel(parameters); + parameterModel.addTableModelListener(new TableModelListener() { + @Override + public void tableChanged(TableModelEvent e) { + // logger.debug("Change event."); + updateParameterTable(); + } + }); + + // Create parameter table + parameterTable = new ParameterTable(frame, parameterModel, parameters); + // Create the scroll pane and add the table to it. + JScrollPane scrollPane = new JScrollPane(parameterTable); + + // Add the scroll pane to this panel. + GridBagConstraints constraints = new GridBagConstraints(); + constraints.fill = GridBagConstraints.BOTH; + constraints.gridx = 0; + constraints.gridy = 1; + constraints.weightx = 1; + constraints.weighty = 1; + panel.add(scrollPane, constraints); + } + + /** + * Create the load and save buttons. + */ + private void setupLoadSaveButtons() { + // Button panel + JPanel buttonPanel = new JPanel(); + buttonPanel.setLayout(new BoxLayout(buttonPanel, BoxLayout.X_AXIS)); + + // Combo box for saved settings + savedSettingsModel = new SettingsComboboxModel(store); + savedCombo = new JComboBox<>(savedSettingsModel); + savedCombo.setEditable(true); + savedCombo.setSelectedItem("[Saved Settings]"); + buttonPanel.add(savedCombo); + + // button to load settings + JButton loadButton = new JButton("Load"); + loadButton.setMnemonic(KeyEvent.VK_L); + loadButton.addActionListener(new ActionListener() { + @Override + public void actionPerformed(ActionEvent e) { + String key = savedSettingsModel.getSelectedItem(); + ArrayList<String> settings = store.get(key); + if(settings != null) { + doSetParameters(settings); + } + } + }); + buttonPanel.add(loadButton); + // button to save settings + JButton saveButton = new JButton("Save"); + saveButton.setMnemonic(KeyEvent.VK_S); + saveButton.addActionListener(new ActionListener() { + @Override + public void actionPerformed(ActionEvent e) { + String key = savedSettingsModel.getSelectedItem(); + // Stop editing the table. + parameterTable.editCellAt(-1, -1); + ArrayList<String> list = new ArrayList<>(parameters.size() * 2 + 1); + list.add(maincls.getCanonicalName()); + parameters.serializeParameters(list); + store.put(key, list); + try { + store.save(); + } + catch(IOException e1) { + LOG.exception(e1); + } + savedSettingsModel.update(); + } + }); + buttonPanel.add(saveButton); + // button to remove saved settings + JButton removeButton = new JButton("Remove"); + removeButton.setMnemonic(KeyEvent.VK_E); + removeButton.addActionListener(new ActionListener() { + @Override + public void actionPerformed(ActionEvent e) { + String key = savedSettingsModel.getSelectedItem(); + store.remove(key); + try { + store.save(); + } + catch(IOException e1) { + LOG.exception(e1); + } + savedCombo.setSelectedItem("[Saved Settings]"); + savedSettingsModel.update(); + } + }); + buttonPanel.add(removeButton); + + // button to launch the task + runButton = new JButton("Run Task"); + runButton.setMnemonic(KeyEvent.VK_R); + runButton.addActionListener(new ActionListener() { + @Override + public void actionPerformed(ActionEvent e) { + startTask(); + } + }); + buttonPanel.add(runButton); + + GridBagConstraints constraints = new GridBagConstraints(); + constraints.fill = GridBagConstraints.HORIZONTAL; + constraints.gridx = 0; + constraints.gridy = 2; + constraints.weightx = 1.0; + constraints.weighty = 0.01; + panel.add(buttonPanel, constraints); + } + + /** + * Setup command line field + */ + private void setupCommandLine() { + // setup text output area + commandLine = new JTextField(); + commandLine.setEditable(false); // FIXME: Make editable! + + // Add the output pane to the bottom + GridBagConstraints constraints = new GridBagConstraints(); + constraints.fill = GridBagConstraints.BOTH; + constraints.gridx = 0; + constraints.gridy = 3; + constraints.weightx = 1; + constraints.weighty = .01; + panel.add(commandLine, constraints); + } + + /** + * Setup logging area + */ + private void setupLoggingArea() { + // setup text output area + outputArea = new LogPanel(); + + // Create the scroll pane and add the table to it. + JScrollPane outputPane = new JScrollPane(outputArea); + outputPane.setPreferredSize(new Dimension(800, 400)); + + // Add the output pane to the bottom + GridBagConstraints constraints = new GridBagConstraints(); + constraints.fill = GridBagConstraints.BOTH; + constraints.gridx = 0; + constraints.gridy = 4; + constraints.weightx = 1; + constraints.weighty = 1; + panel.add(outputPane, constraints); + } + + /** * Serialize the parameter table and run setParameters(). */ protected void updateParameterTable() { parameterTable.setEnabled(false); - ArrayList<String> params = parameters.serializeParameters(); - outputArea.clear(); - outputArea.publish("Parameters: " + FormatUtil.format(params, " ") + NEWLINE, Level.INFO); - doSetParameters(params); + ArrayList<String> list = new ArrayList<String>(parameters.size() * 2 + 1); + list.add(maincls.getCanonicalName()); + parameters.serializeParameters(list); + doSetParameters(list); parameterTable.setEnabled(true); } @@ -366,6 +464,16 @@ public class MiniGUI extends AbstractApplication { * @param params Parameters */ protected void doSetParameters(List<String> params) { + if(params.size() > 0) { + String first = params.get(0); + if(!first.startsWith("-")) { + Class<? extends AbstractApplication> c = ELKIServiceRegistry.findImplementation(AbstractApplication.class, first); + if(c != null) { + maincls = c; + params.remove(0); + } + } + } SerializedParameterization config = new SerializedParameterization(params); TrackParameters track = new TrackParameters(config); track.tryInstantiate(LoggingStep.class); @@ -380,6 +488,13 @@ public class MiniGUI extends AbstractApplication { List<String> remainingParameters = config.getRemainingParameters(); + outputArea.clear(); + String mainnam = maincls.getCanonicalName(); + if(mainnam.startsWith(APP_PREFIX)) { + mainnam = mainnam.substring(APP_PREFIX.length()); + } + commandLine.setText(format(mainnam, params)); + // update table: parameterTable.removeEditor(); parameterTable.setEnabled(false); @@ -403,6 +518,97 @@ public class MiniGUI extends AbstractApplication { } /** + * Format objects to a command line. + * + * @param params Parameters to format (Strings, or list of strings) + * @return Formatted string + */ + private String format(Object... params) { + StringBuilder buf = new StringBuilder(); + for(Object p : params) { + if(p instanceof String) { + formatTo(buf, (String) p); + } + else if(p instanceof List) { + formatTo(buf, (List<?>) p); + } + else { + LOG.warning("Incorrect object type: " + p.getClass()); + } + } + return buf.toString(); + } + + /** + * Format a list of strings to a buffer. + * + * @param buf Output buffer + * @param params List of strings + */ + private void formatTo(StringBuilder buf, List<?> params) { + for(Object p : params) { + if(p instanceof String) { + formatTo(buf, (String) p); + } + else { + LOG.warning("Incorrect object type: " + p.getClass()); + } + } + } + + /** + * Format a single string for the command line. + * + * @param buf Output buffer + * @param s String + */ + private void formatTo(StringBuilder buf, String s) { + if(s == null || s.length() == 0) { + return; + } + if(buf.length() > 0) { + buf.append(' '); + } + // Test for escaping necessary + int escape = 0; + for(int i = 0, l = s.length(); i < l; i++) { + char c = s.charAt(i); + if(c == '\\') { + escape |= 8; + } + else if(c <= ' ' || c >= 128 || c == '<' || c == '>' || c == '|' || c == '$') { + escape |= 1; + } + else if(c == '"') { + escape |= 2; + } + else if(c == '\'') { + escape |= 4; + } + } + if(escape == 0) { + buf.append(s); // No escaping. + } + else if((escape & 10) == 0) { + buf.append('"').append(s).append('"'); + } + else if((escape & 12) == 0) { + buf.append('\'').append(s).append('\''); + } + else { // Full escaping. + buf.append('"'); + for(int i = 0, l = s.length(); i < l; i++) { + char c = s.charAt(i); + if(c == '"' || c == '\\' || c == '$') { + buf.append('\\'); + } + buf.append(c); + } + buf.append('"'); + } + } + + /** * Auto-load the last task from the history file. */ protected void loadLatest() { @@ -420,14 +626,13 @@ public class MiniGUI extends AbstractApplication { protected void startTask() { parameterTable.editCellAt(-1, -1); parameterTable.setEnabled(false); - final ArrayList<String> params = parameters.serializeParameters(); + final ArrayList<String> params = new ArrayList<>(parameters.size() * 2); + parameters.serializeParameters(params); parameterTable.setEnabled(true); runButton.setEnabled(false); outputArea.clear(); - outputArea.publish("Running: " + FormatUtil.format(params, " ") + NEWLINE, Level.INFO); - SwingWorker<Void, Void> r = new SwingWorker<Void, Void>() { @Override public Void doInBackground() { @@ -493,6 +698,34 @@ public class MiniGUI extends AbstractApplication { * @param args command line parameters */ public static void main(final String[] args) { + // Detect the common problem of an incomplete class path: + try { + Class<?> clz = ClassLoader.getSystemClassLoader().loadClass("de.lmu.ifi.dbs.elki.database.ids.DBIDUtil"); + clz.getMethod("newHashSet").invoke(null); + } + catch(ReflectiveOperationException e) { + StringBuilder msg = new StringBuilder(); + msg.append("Your Java class path is incomplete.\n"); + if(e.getCause() != null) { + msg.append(e.getCause().toString()).append("\n"); + } + else { + msg.append(e.toString()).append("\n"); + } + msg.append("Make sure you have all the required jars on the classpath.\n"); + msg.append("On the home page, you can find a 'elki-bundle' which should include everything."); + JOptionPane.showMessageDialog(null, msg, "ClassPath incomplete", JOptionPane.ERROR_MESSAGE); + return; + } + // Detect the broken Ubuntu jAyatana hack; + String toolopt = System.getenv("JAVA_TOOL_OPTION"); + if(toolopt != null && toolopt.indexOf("jayatana") >= 0) { + StringBuilder msg = new StringBuilder(); + msg.append("The Ubuntu JAyatana 'global menu support' hack is known to cause problems with many Java applications.\n"); + msg.append("Please unset JAVA_TOOL_OPTION."); + JOptionPane.showMessageDialog(null, msg, "Incompatible with JAyatana", JOptionPane.ERROR_MESSAGE); + return; + } GUIUtil.logUncaughtExceptions(LOG); GUIUtil.setLookAndFeel(); OutputStep.setDefaultHandlerVisualizer(); @@ -549,7 +782,7 @@ public class MiniGUI extends AbstractApplication { * * @apiviz.composedOf de.lmu.ifi.dbs.elki.gui.util.SavedSettingsFile */ - class SettingsComboboxModel extends AbstractListModel<String>implements ComboBoxModel<String> { + class SettingsComboboxModel extends AbstractListModel<String> implements ComboBoxModel<String> { /** * Serial version. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/MultiStepGUI.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/MultiStepGUI.java index dacbe361..36aa79fe 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/MultiStepGUI.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/MultiStepGUI.java @@ -61,6 +61,7 @@ import de.lmu.ifi.dbs.elki.workflow.OutputStep; * Experimenter-style multi step GUI. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.composedOf AlgorithmTabPanel diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/AlgorithmTabPanel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/AlgorithmTabPanel.java index c0dda863..fb9bd116 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/AlgorithmTabPanel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/AlgorithmTabPanel.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * Panel to handle data processing * * @author Erich Schubert + * @since 0.4.0 */ public class AlgorithmTabPanel extends ParameterTabPanel { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/EvaluationTabPanel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/EvaluationTabPanel.java index 65d53d20..8a8d10b5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/EvaluationTabPanel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/EvaluationTabPanel.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.workflow.EvaluationStep; * Panel to handle result evaluation * * @author Erich Schubert + * @since 0.4.0 */ public class EvaluationTabPanel extends ParameterTabPanel { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/InputTabPanel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/InputTabPanel.java index 7a3ea1f5..cd83a860 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/InputTabPanel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/InputTabPanel.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.workflow.InputStep; * Panel to handle data input. * * @author Erich Schubert + * @since 0.4.0 */ public class InputTabPanel extends ParameterTabPanel { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/LoggingTabPanel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/LoggingTabPanel.java index 2dcc38d4..902995ce 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/LoggingTabPanel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/LoggingTabPanel.java @@ -24,9 +24,8 @@ package de.lmu.ifi.dbs.elki.gui.multistep.panels; */ import de.lmu.ifi.dbs.elki.application.AbstractApplication; -import de.lmu.ifi.dbs.elki.logging.LoggingConfiguration; -import de.lmu.ifi.dbs.elki.logging.LoggingUtil; import de.lmu.ifi.dbs.elki.logging.Logging.Level; +import de.lmu.ifi.dbs.elki.logging.LoggingConfiguration; import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; @@ -36,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.StringParameter; * Panel to handle logging * * @author Erich Schubert + * @since 0.4.0 */ public class LoggingTabPanel extends ParameterTabPanel { /** @@ -62,7 +62,7 @@ public class LoggingTabPanel extends ParameterTabPanel { // FIXME: add second level of verbosity! if (config.grab(debugParam)) { try { - LoggingUtil.parseDebugParameter(debugParam); + AbstractApplication.Parameterizer.parseDebugParameter(debugParam); } catch (WrongParameterValueException e) { de.lmu.ifi.dbs.elki.logging.LoggingUtil.exception(e); } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/OutputTabPanel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/OutputTabPanel.java index cedc5765..29fdf7ff 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/OutputTabPanel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/OutputTabPanel.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.workflow.OutputStep; * Panel to handle result output / visualization * * @author Erich Schubert + * @since 0.4.0 */ public class OutputTabPanel extends ParameterTabPanel { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/ParameterTabPanel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/ParameterTabPanel.java index caf9c066..f6985f4f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/ParameterTabPanel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/ParameterTabPanel.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.TrackParame * Abstract panel, showing particular options. * * @author Erich Schubert + * @since 0.4.0 */ public abstract class ParameterTabPanel extends JPanel implements ChangeListener { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/SavedSettingsTabPanel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/SavedSettingsTabPanel.java index 0ea2a34f..ec7b66e6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/SavedSettingsTabPanel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/multistep/panels/SavedSettingsTabPanel.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.SerializedP * Tab panel to manage saved settings. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf SavedSettingsTabPanel.SettingsComboboxModel */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/ClassTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/ClassTree.java index 8c524cdd..3c2a6373 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/ClassTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/ClassTree.java @@ -31,15 +31,16 @@ import javax.swing.tree.TreeNode; /** * Build a tree of available classes for use in Swing UIs. - * + * * @author Erich Schubert - * + * @since 0.7.0 + * * @apiviz.has TreeNode */ public class ClassTree { /** * Build the class tree for a given set of choices. - * + * * @param choices Class choices * @param rootpkg Root package name (to strip / hide) * @return Root node. @@ -59,7 +60,8 @@ public class ClassTree { for(Class<?> impl : choices) { String name = impl.getName(); name = (prefix != null && name.startsWith(prefix)) ? name.substring(prefix.length()) : name; - MutableTreeNode c = new ClassNode(impl.getName().substring(impl.getPackage().getName().length() + 1), name); + int plen = (impl.getPackage() != null) ? impl.getPackage().getName().length() + 1 : 0; + MutableTreeNode c = new ClassNode(impl.getName().substring(plen), name); MutableTreeNode p = null; int l = name.lastIndexOf('.'); @@ -96,7 +98,7 @@ public class ClassTree { /** * Simplify the tree. - * + * * @param cur Current node * @param prefix Prefix to add * @return Replacement node @@ -133,9 +135,9 @@ public class ClassTree { /** * Tree node representing a single class. - * + * * @author Erich Schubert - * + * * @apiviz.exclude */ public static class PackageNode extends DefaultMutableTreeNode { @@ -151,7 +153,7 @@ public class ClassTree { /** * Current class name. - * + * * @param display Displayed name * @param pkgname Actual class name */ @@ -162,7 +164,7 @@ public class ClassTree { /** * Return the package name. - * + * * @return Package name */ public String getPackageName() { @@ -172,9 +174,9 @@ public class ClassTree { /** * Tree node representing a single class. - * + * * @author Erich Schubert - * + * * @apiviz.exclude */ public static class ClassNode extends DefaultMutableTreeNode { @@ -190,7 +192,7 @@ public class ClassTree { /** * Current class name. - * + * * @param display Displayed name * @param clsname Actual class name */ @@ -201,7 +203,7 @@ public class ClassTree { /** * Return the class name. - * + * * @return Class name */ public String getClassName() { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/DynamicParameters.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/DynamicParameters.java index 2aae45d4..10cc79a3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/DynamicParameters.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/DynamicParameters.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.StringParameter; * correct. * * @author Erich Schubert + * @since 0.3 * * @apiviz.owns de.lmu.ifi.dbs.elki.gui.util.DynamicParameters.RemainingOptions */ @@ -206,10 +207,9 @@ public class DynamicParameters { /** * Serialize parameters into an array list to pass to setParameters() * - * @return Array list of String parameters. + * @param p Output list (will not be emptied) */ - public synchronized ArrayList<String> serializeParameters() { - ArrayList<String> p = new ArrayList<>(2 * parameters.size()); + public synchronized void serializeParameters(ArrayList<String> p) { for(Node t : parameters) { if(t.param != null) { if(t.param instanceof RemainingOptions) { @@ -232,7 +232,6 @@ public class DynamicParameters { } } } - return p; } /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/LogPane.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/LogPane.java index 17c52cea..c42a2ed7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/LogPane.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/LogPane.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.logging.progress.ProgressLogRecord; * {@link #becomeDefaultLogger()} to register as default logger in ELKI. * * @author Erich Schubert + * @since 0.3 * * @apiviz.uses LoggingConfiguration * @apiviz.uses de.lmu.ifi.dbs.elki.logging.ELKILogRecord diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/LogPanel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/LogPanel.java index dbe87b58..9507c8eb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/LogPanel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/LogPanel.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.logging.progress.StepProgress; * Panel that contains a text logging pane ({@link LogPane}) and progress bars. * * @author Erich Schubert + * @since 0.3 * * @apiviz.owns LogPane * @apiviz.uses LoggingConfiguration diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/ParameterTable.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/ParameterTable.java index a08341db..a5782ca9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/ParameterTable.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/ParameterTable.java @@ -73,6 +73,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * Class showing a table of ELKI parameters. * * @author Erich Schubert + * @since 0.3 * * @apiviz.composedOf ParametersModel * @apiviz.owns de.lmu.ifi.dbs.elki.gui.util.ParameterTable.ColorfulRenderer diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/ParametersModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/ParametersModel.java index d864cc9b..66593c20 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/ParametersModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/ParametersModel.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * A Swing TableModel that uses a {@link DynamicParameters} object as storage. * * @author Erich Schubert + * @since 0.3 */ public class ParametersModel extends AbstractTableModel { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/SavedSettingsFile.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/SavedSettingsFile.java index f8f4c990..6f31a2c6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/SavedSettingsFile.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/SavedSettingsFile.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * Class to manage saved settings in a text file. * * @author Erich Schubert + * @since 0.3 */ public class SavedSettingsFile implements Iterable<Pair<String, ArrayList<String>>> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/TreePopup.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/TreePopup.java index 19413c53..6bfb6a2a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/TreePopup.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/gui/util/TreePopup.java @@ -62,6 +62,7 @@ import javax.swing.tree.TreeModel; * Popup menu that contains a JTree. * * @author Erich Schubert + * @since 0.7.0 */ public class TreePopup extends JPopupMenu { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/AbstractIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/AbstractIndex.java index 63be2b06..8db3abe9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/AbstractIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/AbstractIndex.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * Abstract base class for indexes with some implementation defaults. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.excludeSubtypes * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/AbstractRefiningIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/AbstractRefiningIndex.java index c5a032c3..e0264cf7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/AbstractRefiningIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/AbstractRefiningIndex.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.logging.statistics.Counter; * The number of refinements will be counted as individual page accesses. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.excludeSubtypes * @apiviz.has AbstractRangeQuery diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/DistanceIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/DistanceIndex.java index f6fc929f..2fa6feff 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/DistanceIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/DistanceIndex.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction; * caches) * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/DynamicIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/DynamicIndex.java index 8179b5df..306b0a1f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/DynamicIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/DynamicIndex.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * Index that supports dynamic insertions and removals. * * @author Erich Schubert + * @since 0.2 * * @apiviz.excludeSubtypes */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/Index.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/Index.java index b312eb37..d6f9ee16 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/Index.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/Index.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.result.Result; * See also: {@link IndexFactory}, {@link DynamicIndex} * * @author Elke Achtert + * @since 0.2 * * @apiviz.excludeSubtypes */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/IndexFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/IndexFactory.java index 154974f9..1a1d3fb2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/IndexFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/IndexFactory.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * Factory interface for indexes. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory,interface * @apiviz.has Index oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/KNNIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/KNNIndex.java index aa99e8e4..e3a29bf5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/KNNIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/KNNIndex.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.query.knn.KNNQuery; * Index with support for kNN queries. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/PagedIndexFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/PagedIndexFactory.java index 75c11499..e421e252 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/PagedIndexFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/PagedIndexFactory.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Abstract base class for tree-based indexes. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory,interface * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/RKNNIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/RKNNIndex.java index 71909004..770d1170 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/RKNNIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/RKNNIndex.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.query.rknn.RKNNQuery; * Index with support for kNN queries. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/RangeIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/RangeIndex.java index 464c3589..56845f37 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/RangeIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/RangeIndex.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.query.range.RangeQuery; * Index with support for kNN queries. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/distancematrix/PrecomputedDistanceMatrix.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/distancematrix/PrecomputedDistanceMatrix.java index 44ed6c84..4dbb79ea 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/distancematrix/PrecomputedDistanceMatrix.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/distancematrix/PrecomputedDistanceMatrix.java @@ -23,17 +23,31 @@ package de.lmu.ifi.dbs.elki.index.distancematrix; along with this program. If not, see <http://www.gnu.org/licenses/>. */ +import java.util.ArrayList; +import java.util.List; + import de.lmu.ifi.dbs.elki.data.type.TypeInformation; +import de.lmu.ifi.dbs.elki.database.ids.ArrayDBIDs; import de.lmu.ifi.dbs.elki.database.ids.DBIDArrayIter; +import de.lmu.ifi.dbs.elki.database.ids.DBIDIter; import de.lmu.ifi.dbs.elki.database.ids.DBIDRange; import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; +import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; import de.lmu.ifi.dbs.elki.database.ids.DBIDs; +import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDList; +import de.lmu.ifi.dbs.elki.database.ids.KNNHeap; +import de.lmu.ifi.dbs.elki.database.ids.KNNList; +import de.lmu.ifi.dbs.elki.database.ids.ModifiableDoubleDBIDList; import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery; +import de.lmu.ifi.dbs.elki.database.query.knn.KNNQuery; +import de.lmu.ifi.dbs.elki.database.query.range.RangeQuery; import de.lmu.ifi.dbs.elki.database.relation.Relation; import de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction; import de.lmu.ifi.dbs.elki.index.AbstractIndex; import de.lmu.ifi.dbs.elki.index.DistanceIndex; import de.lmu.ifi.dbs.elki.index.IndexFactory; +import de.lmu.ifi.dbs.elki.index.KNNIndex; +import de.lmu.ifi.dbs.elki.index.RangeIndex; import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress; import de.lmu.ifi.dbs.elki.logging.statistics.LongStatistic; @@ -45,21 +59,24 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; /** * Distance matrix, for precomputing similarity for a small data set. - * + * * This class uses a linear memory layout (not a ragged array), and assumes * symmetry as well as strictness. This way, it only stores the upper triangle * matrix with double precision. It has to store (n-1) * (n-2) distance values * in memory, requiring 8 * (n-1) * (n-2) bytes. Since Java has a size limit of * arrays of 31 bits (signed integer), we can store at most 2^16 objects * (precisely, 65536 objects) in a single array, which needs about 16 GB of RAM. - * + * * @author Erich Schubert - * + * @since 0.7.0 + * * @apiviz.has PrecomputedDistanceQuery - * + * @apiviz.has PrecomputedKNNQuery + * @apiviz.has PrecomputedRangeQuery + * * @param <O> Object type */ -public class PrecomputedDistanceMatrix<O> extends AbstractIndex<O>implements DistanceIndex<O> { +public class PrecomputedDistanceMatrix<O> extends AbstractIndex<O> implements DistanceIndex<O>, RangeIndex<O>, KNNIndex<O> { /** * Class logger. */ @@ -92,7 +109,7 @@ public class PrecomputedDistanceMatrix<O> extends AbstractIndex<O>implements Dis /** * Constructor. - * + * * @param relation Data relation * @param distanceFunction Distance function */ @@ -119,7 +136,7 @@ public class PrecomputedDistanceMatrix<O> extends AbstractIndex<O>implements Dis distanceQuery = distanceFunction.instantiate(relation); - int msize = triangleSize(size); + final int msize = triangleSize(size); matrix = new double[msize]; DBIDArrayIter ix = ids.iter(), iy = ids.iter(); @@ -140,7 +157,7 @@ public class PrecomputedDistanceMatrix<O> extends AbstractIndex<O>implements Dis /** * Compute the size of a complete x by x triangle (minus diagonal) - * + * * @param x Offset * @return Size of complete triangle */ @@ -150,7 +167,7 @@ public class PrecomputedDistanceMatrix<O> extends AbstractIndex<O>implements Dis /** * Array offset computation. - * + * * @param x X parameter * @param y Y parameter * @return Array offset @@ -184,9 +201,25 @@ public class PrecomputedDistanceMatrix<O> extends AbstractIndex<O>implements Dis return null; } + @Override + public KNNQuery<O> getKNNQuery(DistanceQuery<O> distanceQuery, Object... hints) { + if(this.distanceQuery.getDistanceFunction().equals(distanceQuery.getDistanceFunction())) { + return new PrecomputedKNNQuery(); + } + return null; + } + + @Override + public RangeQuery<O> getRangeQuery(DistanceQuery<O> distanceQuery, Object... hints) { + if(this.distanceQuery.getDistanceFunction().equals(distanceQuery.getDistanceFunction())) { + return new PrecomputedRangeQuery(); + } + return null; + } + /** * Distance query using the precomputed matrix. - * + * * @author Erich Schubert */ private class PrecomputedDistanceQuery implements DistanceQuery<O> { @@ -223,12 +256,115 @@ public class PrecomputedDistanceMatrix<O> extends AbstractIndex<O>implements Dis } /** + * Range query using the distance matrix. + * + * @author Erich Schubert + */ + private class PrecomputedRangeQuery implements RangeQuery<O> { + @Override + public DoubleDBIDList getRangeForDBID(DBIDRef id, double range) { + ModifiableDoubleDBIDList ret = DBIDUtil.newDistanceDBIDList(); + getRangeForDBID(id, range, ret); + ret.sort(); + return ret; + } + + @Override + public void getRangeForDBID(DBIDRef id, double range, ModifiableDoubleDBIDList result) { + result.add(0., id); + DBIDArrayIter it = ids.iter(); + + final int x = ids.getOffset(id); + // Case y < x: triangleSize(x) + y + int pos = triangleSize(x); + for(int y = 0; y < x; y++) { + final double dist = matrix[pos]; + if(dist <= range) { + result.add(dist, it.seek(y)); + } + pos++; + } + assert (pos == triangleSize(x + 1)); + // Case y > x: triangleSize(y) + x + pos = triangleSize(x + 1) + x; + for(int y = x + 1; y < size; y++) { + final double dist = matrix[pos]; + if(dist <= range) { + result.add(dist, it.seek(y)); + } + pos += y; + } + } + + @Override + public DoubleDBIDList getRangeForObject(O obj, double range) { + throw new AbortException("Preprocessor KNN query only supports ID queries."); + } + + @Override + public void getRangeForObject(O obj, double range, ModifiableDoubleDBIDList result) { + throw new AbortException("Preprocessor KNN query only supports ID queries."); + } + } + + /** + * kNN query using the distance matrix. + * + * @author Erich Schubert + */ + private class PrecomputedKNNQuery implements KNNQuery<O> { + @Override + public KNNList getKNNForDBID(DBIDRef id, int k) { + KNNHeap heap = DBIDUtil.newHeap(k); + heap.insert(0., id); + DBIDArrayIter it = ids.iter(); + double max = Double.POSITIVE_INFINITY; + final int x = ids.getOffset(id); + // Case y < x: triangleSize(x) + y + int pos = triangleSize(x); + for(int y = 0; y < x; y++) { + final double dist = matrix[pos]; + if(dist <= max) { + max = heap.insert(dist, it.seek(y)); + } + pos++; + } + assert (pos == triangleSize(x + 1)); + // Case y > x: triangleSize(y) + x + pos = triangleSize(x + 1) + x; + for(int y = x + 1; y < size; y++) { + final double dist = matrix[pos]; + if(dist <= max) { + max = heap.insert(dist, it.seek(y)); + } + pos += y; + } + return heap.toKNNList(); + } + + @Override + public List<? extends KNNList> getKNNForBulkDBIDs(ArrayDBIDs ids, int k) { + // TODO: optimize + List<KNNList> ret = new ArrayList<>(ids.size()); + for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) { + ret.add(getKNNForDBID(iter, k)); + } + return ret; + } + + @Override + public KNNList getKNNForObject(O obj, int k) { + throw new AbortException("Preprocessor KNN query only supports ID queries."); + } + } + + /** * Factory for the index. - * + * * @author Erich Schubert - * + * * @apiviz.has PrecomputedDistanceMatrix - * + * * @param <O> Object type */ public static class Factory<O> implements IndexFactory<O, PrecomputedDistanceMatrix<O>> { @@ -239,7 +375,7 @@ public class PrecomputedDistanceMatrix<O> extends AbstractIndex<O>implements Dis /** * Constructor. - * + * * @param distanceFunction Distance function */ public Factory(DistanceFunction<? super O> distanceFunction) { @@ -259,11 +395,11 @@ public class PrecomputedDistanceMatrix<O> extends AbstractIndex<O>implements Dis /** * Parameterizer. - * + * * @author Erich Schubert - * + * * @apiviz.exclude - * + * * @param <O> Object type */ public static class Parameterizer<O> extends AbstractParameterizer { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/idistance/InMemoryIDistanceIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/idistance/InMemoryIDistanceIndex.java index 2fca801c..6ced1fbd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/idistance/InMemoryIDistanceIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/idistance/InMemoryIDistanceIndex.java @@ -87,6 +87,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.DoubleIntPair; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/invertedlist/InMemoryInvertedIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/invertedlist/InMemoryInvertedIndex.java index 7a3087ba..101b7ed1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/invertedlist/InMemoryInvertedIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/invertedlist/InMemoryInvertedIndex.java @@ -60,6 +60,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Simple index using inverted lists. * * @author Erich Schubert + * @since 0.7.0 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/InMemoryLSHIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/InMemoryLSHIndex.java index b55799af..a1940da7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/InMemoryLSHIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/InMemoryLSHIndex.java @@ -63,6 +63,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Locality Sensitive Hashing. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LocalitySensitiveHashFunctionFamily * @apiviz.has Instance @@ -169,7 +170,7 @@ public class InMemoryLSHIndex<V> implements IndexFactory<V, InMemoryLSHIndex<V>. // TODO: We assume all hash functions have the same dimensionality. double[] buf = new double[hashfunctions.get(0).getNumberOfProjections()]; - FiniteProgress progress = LOG.isVerbose() ? new FiniteProgress("Building LSH index.", relation.size(), LOG) : null; + FiniteProgress progress = LOG.isVerbose() ? new FiniteProgress("Building LSH index", relation.size(), LOG) : null; int expect = Math.max(2, (int) Math.ceil(relation.size() / (double) numberOfBuckets)); for(DBIDIter iter = relation.getDBIDs().iter(); iter.valid(); iter.advance()) { V obj = relation.get(iter); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/AbstractProjectedHashFunctionFamily.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/AbstractProjectedHashFunctionFamily.java index 7d9b09e6..521b16c4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/AbstractProjectedHashFunctionFamily.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/AbstractProjectedHashFunctionFamily.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * Abstract base class for projection based hash functions. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses RandomProjectionFamily * @apiviz.has MultipleProjectionsLocalitySensitiveHashFunction diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/CosineHashFunctionFamily.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/CosineHashFunctionFamily.java index b46e30ae..78cf7eb4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/CosineHashFunctionFamily.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/CosineHashFunctionFamily.java @@ -65,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * </p> * * @author Evgeniy Faerman + * @since 0.6.0 */ @Reference(authors = "M.S. Charikar", // title = "Similarity estimation techniques from rounding algorithms", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/EuclideanHashFunctionFamily.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/EuclideanHashFunctionFamily.java index e50766b0..620d2ef1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/EuclideanHashFunctionFamily.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/EuclideanHashFunctionFamily.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses GaussianRandomProjectionFamily */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/LocalitySensitiveHashFunctionFamily.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/LocalitySensitiveHashFunctionFamily.java index 4c232df4..94a9e181 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/LocalitySensitiveHashFunctionFamily.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/LocalitySensitiveHashFunctionFamily.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.index.lsh.hashfunctions.LocalitySensitiveHashFunction * LSH family of hash functions. * * @author Erich Schubert + * @since 0.6.0 * * @param <V> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/ManhattanHashFunctionFamily.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/ManhattanHashFunctionFamily.java index fbc122af..95577790 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/ManhattanHashFunctionFamily.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/ManhattanHashFunctionFamily.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses CauchyRandomProjectionFamily */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfunctions/CosineLocalitySensitiveHashFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfunctions/CosineLocalitySensitiveHashFunction.java index ae0af49e..9a68c7d6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfunctions/CosineLocalitySensitiveHashFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfunctions/CosineLocalitySensitiveHashFunction.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Evgeniy Faerman + * @since 0.3 */ @Reference(authors = "M.S. Charikar", // title = "Similarity estimation techniques from rounding algorithms", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfunctions/LocalitySensitiveHashFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfunctions/LocalitySensitiveHashFunction.java index 51dcd216..cb1c1584 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfunctions/LocalitySensitiveHashFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfunctions/LocalitySensitiveHashFunction.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.index.lsh.hashfunctions; * Hash functions as used by locality sensitive hashing. * * @author Erich Schubert + * @since 0.6.0 * * @param <V> Data type to hash. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfunctions/MultipleProjectionsLocalitySensitiveHashFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfunctions/MultipleProjectionsLocalitySensitiveHashFunction.java index a4976e59..ad266f19 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfunctions/MultipleProjectionsLocalitySensitiveHashFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/lsh/hashfunctions/MultipleProjectionsLocalitySensitiveHashFunction.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "M. Datar and N. Immorlica and P. Indyk and V. S. Mirrokni", // title = "Locality-sensitive hashing scheme based on p-stable distributions", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/AbstractPreprocessorIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/AbstractPreprocessorIndex.java index 7377955b..3892c896 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/AbstractPreprocessorIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/AbstractPreprocessorIndex.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * object storage for preprocessing results. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf WritableDataStore * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/LocalProjectionIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/LocalProjectionIndex.java index af5fbcc9..66b30c9d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/LocalProjectionIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/LocalProjectionIndex.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.ProjectionResult; * Abstract index interface for local projections * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has ProjectionResult * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/fastoptics/RandomProjectedNeighborsAndDensities.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/fastoptics/RandomProjectedNeighborsAndDensities.java index e24852a9..f5615331 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/fastoptics/RandomProjectedNeighborsAndDensities.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/fastoptics/RandomProjectedNeighborsAndDensities.java @@ -85,6 +85,7 @@ import gnu.trove.list.array.TIntArrayList; * * @author Johannes Schneider * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "J. Schneider and M. Vlachos", // title = "Fast parameterless density-based clustering via random projections", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/AbstractMaterializeKNNPreprocessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/AbstractMaterializeKNNPreprocessor.java index 343f17b7..6d156c63 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/AbstractMaterializeKNNPreprocessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/AbstractMaterializeKNNPreprocessor.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Abstract base class for KNN Preprocessors. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/CachedDoubleDistanceKNNPreprocessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/CachedDoubleDistanceKNNPreprocessor.java index ae7ce384..7d9f6b19 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/CachedDoubleDistanceKNNPreprocessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/CachedDoubleDistanceKNNPreprocessor.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; * Preprocessor that loads an existing cached kNN result. * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/KNNChangeEvent.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/KNNChangeEvent.java index 953a3baa..0963229a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/KNNChangeEvent.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/KNNChangeEvent.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * subscribed {@link KNNListener} of the change. * * @author Elke Achtert + * @since 0.4.0 * * @apiviz.has DBIDs * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/KNNJoinMaterializeKNNPreprocessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/KNNJoinMaterializeKNNPreprocessor.java index 8a6af2fd..895d80c8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/KNNJoinMaterializeKNNPreprocessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/KNNJoinMaterializeKNNPreprocessor.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * Class to materialize the kNN using a spatial join on an R-tree. * * @author Erich Schubert + * @since 0.5.0 * * @param <V> vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/KNNListener.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/KNNListener.java index 40e772b1..166c4286 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/KNNListener.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/KNNListener.java @@ -30,6 +30,7 @@ import java.util.EventListener; * objects have been changed due to insertion or removals of objects. * * @author Elke Achtert + * @since 0.4.0 * * @apiviz.uses KNNChangeEvent oneway - - */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/MaterializeKNNAndRKNNPreprocessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/MaterializeKNNAndRKNNPreprocessor.java index c2577bf8..71098362 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/MaterializeKNNAndRKNNPreprocessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/MaterializeKNNAndRKNNPreprocessor.java @@ -67,6 +67,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * of the nearest neighbors! * * @author Elke Achtert + * @since 0.4.0 * * @param <O> the type of database objects the preprocessor can be applied to * @param the type of distance the used distance function will return diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/MaterializeKNNPreprocessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/MaterializeKNNPreprocessor.java index 5f21a165..24d4e677 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/MaterializeKNNPreprocessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/MaterializeKNNPreprocessor.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDIter; import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; import de.lmu.ifi.dbs.elki.database.ids.DBIDs; +import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDListIter; import de.lmu.ifi.dbs.elki.database.ids.KNNHeap; import de.lmu.ifi.dbs.elki.database.ids.KNNList; import de.lmu.ifi.dbs.elki.database.ids.SetDBIDs; @@ -46,6 +47,7 @@ import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress; import de.lmu.ifi.dbs.elki.logging.progress.StepProgress; import de.lmu.ifi.dbs.elki.logging.statistics.Duration; import de.lmu.ifi.dbs.elki.logging.statistics.LongStatistic; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; @@ -56,6 +58,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * Used for example by {@link de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LOF}. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has DistanceFunction * @apiviz.has KNNQuery @@ -65,6 +68,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; */ @Title("Materialize kNN Neighborhood preprocessor") @Description("Materializes the k nearest neighbors of objects of a database.") +@Alias("de.lmu.ifi.dbs.elki.preprocessing.MaterializeKNNPreprocessor") public class MaterializeKNNPreprocessor<O> extends AbstractMaterializeKNNPreprocessor<O> implements DynamicIndex { /** * Logger to use. @@ -105,14 +109,15 @@ public class MaterializeKNNPreprocessor<O> extends AbstractMaterializeKNNPreproc */ @Override protected void preprocess() { + final Logging log = getLogger(); // Could be subclass createStorage(); ArrayDBIDs ids = DBIDUtil.ensureArray(relation.getDBIDs()); - if(LOG.isStatistics()) { - LOG.statistics(new LongStatistic(this.getClass().getName() + ".k", k)); + if(log.isStatistics()) { + log.statistics(new LongStatistic(this.getClass().getName() + ".k", k)); } - Duration duration = LOG.isStatistics() ? LOG.newDuration(this.getClass().getName() + ".precomputation-time").begin() : null; + Duration duration = log.isStatistics() ? log.newDuration(this.getClass().getName() + ".precomputation-time").begin() : null; FiniteProgress progress = getLogger().isVerbose() ? new FiniteProgress("Materializing k nearest neighbors (k=" + k + ")", ids.size(), getLogger()) : null; // Try bulk List<? extends KNNList> kNNList = null; @@ -122,20 +127,30 @@ public class MaterializeKNNPreprocessor<O> extends AbstractMaterializeKNNPreproc int i = 0; for(DBIDIter id = ids.iter(); id.valid(); id.advance(), i++) { storage.put(id, kNNList.get(i)); - getLogger().incrementProcessed(progress); + log.incrementProcessed(progress); } } } else { + final boolean ismetric = getDistanceQuery().getDistanceFunction().isMetric(); for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) { + if(ismetric && storage.get(iter) != null) { + log.incrementProcessed(progress); + continue; // Previously computed (duplicate point?) + } KNNList knn = knnQuery.getKNNForDBID(iter, k); storage.put(iter, knn); - getLogger().incrementProcessed(progress); + if(ismetric) { + for(DoubleDBIDListIter it = knn.iter(); it.valid() && it.doubleValue() == 0.; it.advance()) { + storage.put(it, knn); // Reuse + } + } + log.incrementProcessed(progress); } } - getLogger().ensureCompleted(progress); + log.ensureCompleted(progress); if(duration != null) { - LOG.statistics(duration.end()); + log.statistics(duration.end()); } } @@ -172,11 +187,12 @@ public class MaterializeKNNPreprocessor<O> extends AbstractMaterializeKNNPreproc * @param ids the ids of the newly inserted objects */ protected void objectsInserted(DBIDs ids) { - StepProgress stepprog = getLogger().isVerbose() ? new StepProgress(3) : null; + final Logging log = getLogger(); // Could be subclass + StepProgress stepprog = log.isVerbose() ? new StepProgress(3) : null; ArrayDBIDs aids = DBIDUtil.ensureArray(ids); // materialize the new kNNs - getLogger().beginStep(stepprog, 1, "New insertions ocurred, materialize their new kNNs."); + log.beginStep(stepprog, 1, "New insertions ocurred, materialize their new kNNs."); // Bulk-query kNNs List<? extends KNNList> kNNList = knnQuery.getKNNForBulkDBIDs(aids, k); // Store in storage @@ -186,14 +202,14 @@ public class MaterializeKNNPreprocessor<O> extends AbstractMaterializeKNNPreproc } // update the affected kNNs - getLogger().beginStep(stepprog, 2, "New insertions ocurred, update the affected kNNs."); + log.beginStep(stepprog, 2, "New insertions ocurred, update the affected kNNs."); ArrayDBIDs rkNN_ids = updateKNNsAfterInsertion(ids); // inform listener - getLogger().beginStep(stepprog, 3, "New insertions ocurred, inform listeners."); + log.beginStep(stepprog, 3, "New insertions ocurred, inform listeners."); fireKNNsInserted(ids, rkNN_ids); - getLogger().setCompleted(stepprog); + log.setCompleted(stepprog); } /** @@ -267,23 +283,24 @@ public class MaterializeKNNPreprocessor<O> extends AbstractMaterializeKNNPreproc * @param ids the ids of the removed objects */ protected void objectsRemoved(DBIDs ids) { - StepProgress stepprog = getLogger().isVerbose() ? new StepProgress(3) : null; + final Logging log = getLogger(); + StepProgress stepprog = log.isVerbose() ? new StepProgress(3) : null; // delete the materialized (old) kNNs - getLogger().beginStep(stepprog, 1, "New deletions ocurred, remove their materialized kNNs."); + log.beginStep(stepprog, 1, "New deletions ocurred, remove their materialized kNNs."); for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) { storage.delete(iter); } // update the affected kNNs - getLogger().beginStep(stepprog, 2, "New deletions ocurred, update the affected kNNs."); + log.beginStep(stepprog, 2, "New deletions ocurred, update the affected kNNs."); ArrayDBIDs rkNN_ids = updateKNNsAfterDeletion(ids); // inform listener - getLogger().beginStep(stepprog, 3, "New deletions ocurred, inform listeners."); + log.beginStep(stepprog, 3, "New deletions ocurred, inform listeners."); fireKNNsRemoved(ids, rkNN_ids); - getLogger().ensureCompleted(stepprog); + log.ensureCompleted(stepprog); } /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/MetricalIndexApproximationMaterializeKNNPreprocessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/MetricalIndexApproximationMaterializeKNNPreprocessor.java index a78b06e0..7823d872 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/MetricalIndexApproximationMaterializeKNNPreprocessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/MetricalIndexApproximationMaterializeKNNPreprocessor.java @@ -59,6 +59,7 @@ import gnu.trove.map.hash.TObjectDoubleHashMap; * TODO correct handling of datastore events * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses MetricalIndexTree * @@ -99,7 +100,7 @@ public class MetricalIndexApproximationMaterializeKNNPreprocessor<O extends Numb } List<E> leaves = index.getLeaves(); - FiniteProgress progress = getLogger().isVerbose() ? new FiniteProgress("Processing leaf nodes.", leaves.size(), getLogger()) : null; + FiniteProgress progress = getLogger().isVerbose() ? new FiniteProgress("Processing leaf nodes", leaves.size(), getLogger()) : null; for(E leaf : leaves) { N node = index.getNode(leaf); int size = node.getNumEntries(); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/NaiveProjectedKNNPreprocessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/NaiveProjectedKNNPreprocessor.java index 6b946474..f4911aef 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/NaiveProjectedKNNPreprocessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/NaiveProjectedKNNPreprocessor.java @@ -79,6 +79,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * </p> * * @author Erich Schubert + * @since 0.7.0 * @apiviz.has NaiveProjectedKNNQuery */ @Reference(authors = "E. Schubert, A. Zimek, H.-P. Kriegel", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/PartitionApproximationMaterializeKNNPreprocessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/PartitionApproximationMaterializeKNNPreprocessor.java index cdb314dc..b8a9f6fe 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/PartitionApproximationMaterializeKNNPreprocessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/PartitionApproximationMaterializeKNNPreprocessor.java @@ -55,6 +55,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * Used for example by {@link de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LOF}. * * @author Erich Schubert + * @since 0.2 * * @param <O> the type of database objects the preprocessor can be applied to */ @@ -103,7 +104,7 @@ public class PartitionApproximationMaterializeKNNPreprocessor<O> extends Abstrac // Produce a random shuffling of the IDs: ArrayDBIDs[] parts = DBIDUtil.randomSplit(relation.getDBIDs(), partitions, rnd); - FiniteProgress progress = LOG.isVerbose() ? new FiniteProgress("Processing partitions.", partitions, LOG) : null; + FiniteProgress progress = LOG.isVerbose() ? new FiniteProgress("Processing partitions", partitions, LOG) : null; for(int part = 0; part < partitions; part++) { final ArrayDBIDs ids = parts[part]; final int size = ids.size(); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/RandomSampleKNNPreprocessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/RandomSampleKNNPreprocessor.java index 39eb23f3..33a0c070 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/RandomSampleKNNPreprocessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/RandomSampleKNNPreprocessor.java @@ -59,6 +59,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * </p> * * @author Erich Schubert + * @since 0.5.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/SpacefillingKNNPreprocessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/SpacefillingKNNPreprocessor.java index 8aa1368c..22b378ae 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/SpacefillingKNNPreprocessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/SpacefillingKNNPreprocessor.java @@ -88,6 +88,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has SpaceFillingKNNQuery */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/SpacefillingMaterializeKNNPreprocessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/SpacefillingMaterializeKNNPreprocessor.java index 4b3864eb..257bda32 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/SpacefillingMaterializeKNNPreprocessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/SpacefillingMaterializeKNNPreprocessor.java @@ -77,6 +77,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * </p> * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "E. Schubert, A. Zimek, H.-P. Kriegel", // title = "Fast and Scalable Outlier Detection with Approximate Nearest Neighbor Ensembles", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/SpatialApproximationMaterializeKNNPreprocessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/SpatialApproximationMaterializeKNNPreprocessor.java index 3706035c..49cdf239 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/SpatialApproximationMaterializeKNNPreprocessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/knn/SpatialApproximationMaterializeKNNPreprocessor.java @@ -23,8 +23,6 @@ package de.lmu.ifi.dbs.elki.index.preprocessed.knn; along with this program. If not, see <http://www.gnu.org/licenses/>. */ -import gnu.trove.impl.Constants; -import gnu.trove.map.hash.TObjectDoubleHashMap; import java.util.Collection; import java.util.List; @@ -49,9 +47,12 @@ import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress; import de.lmu.ifi.dbs.elki.math.MeanVariance; import de.lmu.ifi.dbs.elki.result.ResultUtil; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; +import gnu.trove.impl.Constants; +import gnu.trove.map.hash.TObjectDoubleHashMap; /** * A preprocessor for annotation of the k nearest neighbors (and their @@ -62,6 +63,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * TODO correct handling of datastore events * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses SpatialIndexTree * @@ -70,6 +72,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; */ @Title("Spatial Approximation Materialize kNN Preprocessor") @Description("Caterializes the (approximate) k nearest neighbors of objects of a database using a spatial approximation.") +@Alias("de.lmu.ifi.dbs.elki.preprocessing.SpatialApproximationMaterializeKNNPreprocessor") public class SpatialApproximationMaterializeKNNPreprocessor<O extends NumberVector, N extends SpatialNode<N, E>, E extends SpatialEntry> extends AbstractMaterializeKNNPreprocessor<O> { /** * Logger to use @@ -105,7 +108,7 @@ public class SpatialApproximationMaterializeKNNPreprocessor<O extends NumberVect } List<E> leaves = index.getLeaves(); - FiniteProgress progress = getLogger().isVerbose() ? new FiniteProgress("Processing leaf nodes.", leaves.size(), getLogger()) : null; + FiniteProgress progress = getLogger().isVerbose() ? new FiniteProgress("Processing leaf nodes", leaves.size(), getLogger()) : null; for(E leaf : leaves) { N node = index.getNode(leaf); int size = node.getNumEntries(); @@ -217,4 +220,4 @@ public class SpatialApproximationMaterializeKNNPreprocessor<O extends NumberVect } } } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/localpca/AbstractFilteredPCAIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/localpca/AbstractFilteredPCAIndex.java index f1da979e..3f7f6d93 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/localpca/AbstractFilteredPCAIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/localpca/AbstractFilteredPCAIndex.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Elke Achtert * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has PCAFilteredRunner * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/localpca/FilteredLocalPCAIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/localpca/FilteredLocalPCAIndex.java index c6504f54..9adef2e8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/localpca/FilteredLocalPCAIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/localpca/FilteredLocalPCAIndex.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.pca.PCAFilteredResult; * Interface for an index providing local PCA results. * * @author Erich Schubert + * @since 0.4.0 * * @param <NV> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/localpca/KNNQueryFilteredPCAIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/localpca/KNNQueryFilteredPCAIndex.java index 8e81d368..8dc06940 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/localpca/KNNQueryFilteredPCAIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/localpca/KNNQueryFilteredPCAIndex.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * * @author Elke Achtert * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * @apiviz.uses KNNQuery diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/AbstractPreferenceVectorIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/AbstractPreferenceVectorIndex.java index af1359d5..401a872f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/AbstractPreferenceVectorIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/AbstractPreferenceVectorIndex.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.index.preprocessed.AbstractPreprocessorIndex; * Abstract base class for preference vector based algorithms. * * @author Erich Schubert + * @since 0.4.0 * * @param <NV> Number vector */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/DiSHPreferenceVectorIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/DiSHPreferenceVectorIndex.java index 0653e1bb..5e0a954e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/DiSHPreferenceVectorIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/DiSHPreferenceVectorIndex.java @@ -70,6 +70,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * database. * * @author Elke Achtert + * @since 0.4.0 * * @param <V> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/HiSCPreferenceVectorIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/HiSCPreferenceVectorIndex.java index a196e5d4..54b01a0b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/HiSCPreferenceVectorIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/HiSCPreferenceVectorIndex.java @@ -56,6 +56,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * database. * * @author Elke Achtert + * @since 0.4.0 * * @see HiSC * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/PreferenceVectorIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/PreferenceVectorIndex.java index 3a4ed850..896783c3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/PreferenceVectorIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/PreferenceVectorIndex.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.index.IndexFactory; * Interface for an index providing preference vectors. * * @author Erich Schubert + * @since 0.4.0 * * @param <NV> Vector type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/snn/SharedNearestNeighborIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/snn/SharedNearestNeighborIndex.java index 2b689d8d..22ebacc1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/snn/SharedNearestNeighborIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/snn/SharedNearestNeighborIndex.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.index.IndexFactory; * Interface for an index providing nearest neighbor sets. * * @author Erich Schubert + * @since 0.4.0 */ public interface SharedNearestNeighborIndex<O> extends Index { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/snn/SharedNearestNeighborPreprocessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/snn/SharedNearestNeighborPreprocessor.java index 81ce777d..7e65ff80 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/snn/SharedNearestNeighborPreprocessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/snn/SharedNearestNeighborPreprocessor.java @@ -63,6 +63,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * * @author Arthur Zimek * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has DistanceFunction * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/LatLngAsECEFIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/LatLngAsECEFIndex.java index e3bf3d88..3c38ea2d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/LatLngAsECEFIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/LatLngAsECEFIndex.java @@ -74,6 +74,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * {@link DatabaseQuery#HINT_EXACT} is set, it will not be used. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.composedOf LatLngToECEFProjection * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/LngLatAsECEFIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/LngLatAsECEFIndex.java index 794ecdd6..d247b4bf 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/LngLatAsECEFIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/LngLatAsECEFIndex.java @@ -74,6 +74,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * {@link DatabaseQuery#HINT_EXACT} is set, it will not be used. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.composedOf LngLatToECEFProjection * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/PINN.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/PINN.java index 61ab9e56..7c3dbb28 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/PINN.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/PINN.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.composedOf AchlioptasRandomProjectionFamily * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/ProjectedIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/ProjectedIndex.java index 090d00ac..daab827d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/ProjectedIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/projected/ProjectedIndex.java @@ -79,6 +79,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * FIXME: add refinement to bulk queries! * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.composedOf Projection * @apiviz.has ProjectedKNNQuery diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/AbstractDirectoryEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/AbstractDirectoryEntry.java index 7918ed7d..9732469a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/AbstractDirectoryEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/AbstractDirectoryEntry.java @@ -31,6 +31,7 @@ import java.io.ObjectOutput; * Abstract superclass for entries in an tree based index structure. * * @author Elke Achtert + * @since 0.2 */ public abstract class AbstractDirectoryEntry implements DirectoryEntry { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/AbstractLeafEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/AbstractLeafEntry.java index 0ef87f34..b99adc16 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/AbstractLeafEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/AbstractLeafEntry.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; * Abstract superclass for entries in an tree based index structure. * * @author Elke Achtert + * @since 0.2 */ public abstract class AbstractLeafEntry implements LeafEntry { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/AbstractNode.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/AbstractNode.java index e1bbdb29..b2922e55 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/AbstractNode.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/AbstractNode.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * Abstract superclass for nodes in an tree based index structure. * * @author Elke Achtert + * @since 0.2 * @param <E> the type of Entry used in the index */ public abstract class AbstractNode<E extends Entry> extends AbstractExternalizablePage implements Node<E> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/BreadthFirstEnumeration.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/BreadthFirstEnumeration.java index ee86c3fa..14c3e434 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/BreadthFirstEnumeration.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/BreadthFirstEnumeration.java @@ -32,6 +32,7 @@ import java.util.Queue; * Breadth first enumeration over the nodes of an index structure. * * @author Elke Achtert + * @since 0.2 * * @apiviz.uses IndexTree * @apiviz.has IndexTreePath diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/DirectoryEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/DirectoryEntry.java index cc335e90..2edf3fa5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/DirectoryEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/DirectoryEntry.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.index.tree; * Directory Entry * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.excludeSubtypes */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/Entry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/Entry.java index 47369bac..8558842e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/Entry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/Entry.java @@ -30,6 +30,7 @@ import java.io.Externalizable; * represent a node or a data object. * * @author Elke Achtert + * @since 0.2 * @apiviz.excludeSubtypes */ public interface Entry extends Externalizable { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/IndexTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/IndexTree.java index dd38bb6f..2024fa4c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/IndexTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/IndexTree.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * Abstract super class for all tree based index classes. * * @author Elke Achtert + * @since 0.2 * * @apiviz.composedOf PageFile * @apiviz.has Node oneway - - contains diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/IndexTreePath.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/IndexTreePath.java index 02aa2c68..91737ac8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/IndexTreePath.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/IndexTreePath.java @@ -29,6 +29,7 @@ import java.util.ArrayList; * Represents a path to a node in an index structure. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has Entry oneway - - «contains» * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/LeafEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/LeafEntry.java index 8be982bd..b8e10035 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/LeafEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/LeafEntry.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBID; * Leaf entry * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.excludeSubtypes */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/Node.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/Node.java index 34ddfbeb..aaacfc2a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/Node.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/Node.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.persistent.Page; * has to provide an enumeration over its children. * * @author Elke Achtert + * @since 0.2 * * @apiviz.composedOf Entry * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/TreeIndexHeader.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/TreeIndexHeader.java index 0e40d2c1..44c520ea 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/TreeIndexHeader.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/TreeIndexHeader.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.persistent.DefaultPageHeader; * information is needed for persistent storage. * * @author Elke Achtert + * @since 0.2 */ public class TreeIndexHeader extends DefaultPageHeader { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/MetricalIndexTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/MetricalIndexTree.java index cd0be5e0..fffd7020 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/MetricalIndexTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/MetricalIndexTree.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.persistent.PageFile; * Abstract super class for all metrical index classes. * * @author Elke Achtert + * @since 0.2 * * @param <O> the type of objects stored in the index * @param <N> the type of nodes used in the metrical index diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/AbstractCoverTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/AbstractCoverTree.java index 84878486..891b353d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/AbstractCoverTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/AbstractCoverTree.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Abstract base class for cover tree variants. * * @author Erich Schubert + * @since 0.7.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/CoverTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/CoverTree.java index ca20af1e..ca07889b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/CoverTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/CoverTree.java @@ -70,6 +70,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * TODO: allow insertions and removals, as in the original publication. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has CoverTreeRangeQuery * @apiviz.has CoverTreeKNNQuery diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/SimplifiedCoverTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/SimplifiedCoverTree.java index a3daba34..2b85283f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/SimplifiedCoverTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/SimplifiedCoverTree.java @@ -71,6 +71,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.heap.DoubleObjectMinHeap; * TODO: allow insertions and removals, as in the original publication. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has CoverTreeRangeQuery * @apiviz.has CoverTreeKNNQuery diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/AbstractMTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/AbstractMTree.java index 7282a39a..073596ad 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/AbstractMTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/AbstractMTree.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.DoubleIntPair; * Abstract super class for all M-Tree variants. * * @author Elke Achtert + * @since 0.2 * * @apiviz.composedOf MTreeSettings * @apiviz.composedOf Statistics diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/AbstractMTreeFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/AbstractMTreeFactory.java index 0a7eb7cf..b3207656 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/AbstractMTreeFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/AbstractMTreeFactory.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Abstract factory for various MTrees * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses AbstractMTree oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/AbstractMTreeNode.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/AbstractMTreeNode.java index d065891b..32ee5980 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/AbstractMTreeNode.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/AbstractMTreeNode.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.logging.LoggingConfiguration; * Abstract super class for nodes in M-Tree variants. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has MTreeEntry oneway - - contains * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeDirectoryEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeDirectoryEntry.java index 46b556e5..604c9356 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeDirectoryEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeDirectoryEntry.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.index.tree.AbstractDirectoryEntry; * the routing object of the entry to its parent's routing object in the M-Tree. * * @author Elke Achtert + * @since 0.2 */ public class MTreeDirectoryEntry extends AbstractDirectoryEntry implements MTreeEntry { private static final long serialVersionUID = 2; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeEntry.java index 8578ad54..d53dcf28 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeEntry.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.index.tree.Entry; * Defines the requirements for an entry in an M-Tree node. * * @author Elke Achtert + * @since 0.2 */ public interface MTreeEntry extends Entry { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeLeafEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeLeafEntry.java index c52216be..dfa43a13 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeLeafEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeLeafEntry.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.index.tree.AbstractLeafEntry; * M-Tree. * * @author Elke Achtert + * @since 0.2 */ public class MTreeLeafEntry extends AbstractLeafEntry implements MTreeEntry { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeSettings.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeSettings.java index e139ad43..8f66f079 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeSettings.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeSettings.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.strategies.split.MT * Class to store the MTree settings. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type * @param <N> Node type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTree.java index dd55b525..0646ba3b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTree.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.persistent.PageFile; * k is less than or equal to the given parameter. * * @author Elke Achtert + * @since 0.2 * @param <O> the type of DatabaseObject to be stored in the metrical index * @param <N> the type of MetricalNode used in the metrical index * @param <E> the type of MetricalEntry used in the metrical index diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTreeUnified.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTreeUnified.java index b3fc0f5f..462a4ed1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTreeUnified.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTreeUnified.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.persistent.PageFile; * k is less than or equal to the given parameter. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has MkTreeHeader oneway * @apiviz.composedOf MkTreeSettings diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTreeUnifiedFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTreeUnifiedFactory.java index 577ca31f..5e98fc10 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTreeUnifiedFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTreeUnifiedFactory.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * Abstract factory for various Mk-Trees * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses AbstractMkTreeUnified oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/MkTreeHeader.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/MkTreeHeader.java index 74b34471..f7a08db2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/MkTreeHeader.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/MkTreeHeader.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.index.tree.TreeIndexHeader; * This information is needed for persistent storage. * * @author Elke Achtert + * @since 0.2 */ public class MkTreeHeader extends TreeIndexHeader { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/MkTreeSettings.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/MkTreeSettings.java index a3410291..1f94da0a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/MkTreeSettings.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/MkTreeSettings.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeSettings; * Class with settings for MkTrees. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type * @param <N> Node type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppDirectoryEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppDirectoryEntry.java index a8cf62e0..3dc8786e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppDirectoryEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppDirectoryEntry.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeDirectoryEntry * of its knn-distances. * * @author Elke Achtert + * @since 0.2 */ class MkAppDirectoryEntry extends MTreeDirectoryEntry implements MkAppEntry { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppEntry.java index 53f769e1..88a4bc07 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppEntry.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeEntry; * provided. * * @author Elke Achtert + * @since 0.2 * * @apiviz.composedOf PolynomialApproximation */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppLeafEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppLeafEntry.java index 098e82ac..e5d92d00 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppLeafEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppLeafEntry.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeLeafEntry; * knn-distances. * * @author Elke Achtert + * @since 0.2 */ class MkAppLeafEntry extends MTreeLeafEntry implements MkAppEntry { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTree.java index ac9a00bb..14755f4b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTree.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteArrayUtil; * parameter k < kmax. * * @author Elke Achtert + * @since 0.2 * * @apiviz.composedOf MkAppTreeSettings * @apiviz.has MkAppTreeNode oneway - - contains diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeFactory.java index b6a5792d..0c960da8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeFactory.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * Factory for a MkApp-Tree * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses MkAppTreeIndex oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeIndex.java index 7e9f2332..0ecf04e4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeIndex.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.persistent.PageFile; * MkAppTree used as database index. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeNode.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeNode.java index cb798e46..4d37e326 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeNode.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeNode.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.FormatUtil; * Represents a node in an MkApp-Tree. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has MkAppEntry oneway - - contains * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeSettings.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeSettings.java index 993b198f..a373d472 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeSettings.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeSettings.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.mktrees.MkTreeSetti * Settings class for the MkApp Tree. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/PolynomialApproximation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/PolynomialApproximation.java index fa795da7..b89e643d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/PolynomialApproximation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/PolynomialApproximation.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.FormatUtil; * for knn-distances consisting of parameters b0, ..., bp. * * @author Elke Achtert + * @since 0.2 */ public class PolynomialApproximation implements Externalizable { private static final long serialVersionUID = 1; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/ApproximationLine.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/ApproximationLine.java index d11415d2..f4567186 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/ApproximationLine.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/ApproximationLine.java @@ -33,6 +33,7 @@ import java.io.ObjectOutput; * axes intercept t and a start value for k. * * @author Elke Achtert + * @since 0.2 */ public class ApproximationLine implements Externalizable { private static final long serialVersionUID = 1; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/ConvexHull.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/ConvexHull.java index f0e202e1..36490bc0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/ConvexHull.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/ConvexHull.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.mktrees.mkcop; * Holds the lower and upper hull for some values. * * @author Elke Achtert + * @since 0.2 */ public class ConvexHull { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPDirectoryEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPDirectoryEntry.java index 012728a3..92f514bc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPDirectoryEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPDirectoryEntry.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeDirectoryEntry * its knn-distances. * * @author Elke Achtert + * @since 0.2 */ class MkCoPDirectoryEntry extends MTreeDirectoryEntry implements MkCoPEntry { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPEntry.java index 05f93438..0a112325 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPEntry.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeEntry; * provided. * * @author Elke Achtert + * @since 0.2 * * @apiviz.composedOf ApproximationLine */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPLeafEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPLeafEntry.java index dbb463c8..fc7a10b5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPLeafEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPLeafEntry.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeLeafEntry; * approximation of its knn-distances. * * @author Elke Achtert + * @since 0.2 */ class MkCoPLeafEntry extends MTreeLeafEntry implements MkCoPEntry { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPTree.java index 322b832e..1165b9d5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPTree.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteArrayUtil; * parameter k < kmax. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has MkCoPTreeNode oneway - - contains * @apiviz.has ConvexHull diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPTreeIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPTreeIndex.java index c0de7232..b17490a1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPTreeIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPTreeIndex.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.persistent.PageFile; * MkCoPTree used as database index. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPTreeNode.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPTreeNode.java index 890887b7..0a23e15b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPTreeNode.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPTreeNode.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.AbstractMTreeNode; * Represents a node in an MkCop-Tree. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has MkCoPEntry oneway - - contains * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCopTreeFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCopTreeFactory.java index d16dfa50..e8ac44f6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCopTreeFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCopTreeFactory.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * Factory for a MkCoPTree-Tree * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses MkCoPTreeIndex oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxDirectoryEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxDirectoryEntry.java index 0fb9e0c6..c1aaa975 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxDirectoryEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxDirectoryEntry.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeDirectoryEntry * the underlying MkMax-Tree node. * * @author Elke Achtert + * @since 0.2 */ class MkMaxDirectoryEntry extends MTreeDirectoryEntry implements MkMaxEntry { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxEntry.java index 867343f4..b5dc4232 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxEntry.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeEntry; * neighbor distance of the underlying data object or MkMax-Tree node. * * @author Elke Achtert + * @since 0.2 */ interface MkMaxEntry extends MTreeEntry { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxLeafEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxLeafEntry.java index 699a6a2a..e5883f0c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxLeafEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxLeafEntry.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeLeafEntry; * the underlying data object. * * @author Elke Achtert + * @since 0.2 */ class MkMaxLeafEntry extends MTreeLeafEntry implements MkMaxEntry { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTree.java index 3f2c807e..d2c64e43 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTree.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.DoubleIntPair; * in each entry of a node. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has MkMaxTreeNode oneway - - contains * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTreeFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTreeFactory.java index c8d0dc72..ee15dff6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTreeFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTreeFactory.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; * Factory for MkMaxTrees * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses MkMaxTreeIndex oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTreeIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTreeIndex.java index 21e2d9df..6182ae26 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTreeIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTreeIndex.java @@ -53,6 +53,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.NotImplementedException; * MkMax tree * * @author Elke Achtert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTreeNode.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTreeNode.java index 1e044098..3781bbd4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTreeNode.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTreeNode.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.AbstractMTreeNode; * Represents a node in an {@link MkMaxTree}. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has MkMaxEntry oneway - - contains * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabDirectoryEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabDirectoryEntry.java index 54345ca6..c16095e9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabDirectoryEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabDirectoryEntry.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeDirectoryEntry * parameters k <= k_max. * * @author Elke Achtert + * @since 0.2 */ class MkTabDirectoryEntry extends MTreeDirectoryEntry implements MkTabEntry { private static final long serialVersionUID = 2; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabEntry.java index 09dbb94c..2b2a247d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabEntry.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeEntry; * parameters k <= k_max of the underlying data object or MkTab-Tree node. * * @author Elke Achtert + * @since 0.2 */ interface MkTabEntry extends MTreeEntry { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabLeafEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabLeafEntry.java index 39627445..e3881745 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabLeafEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabLeafEntry.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeLeafEntry; * parameters k <= k_max. * * @author Elke Achtert + * @since 0.2 */ class MkTabLeafEntry extends MTreeLeafEntry implements MkTabEntry { private static final long serialVersionUID = 2; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTree.java index 5f99fc95..e45fea67 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTree.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteArrayUtil; * of a node. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has MkTabTreeNode oneway - - contains * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTreeFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTreeFactory.java index ce4a1513..ad182b78 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTreeFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTreeFactory.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; * Factory for MkTabTrees * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses MkTabTreeIndex oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTreeIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTreeIndex.java index 7fcc05fc..bef30432 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTreeIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTreeIndex.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.persistent.PageFile; * MkTabTree used as database index. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTreeNode.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTreeNode.java index be7f0790..9c62f487 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTreeNode.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTreeNode.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.AbstractMTreeNode; * Represents a node in a MkMax-Tree. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has MkTabEntry oneway - - contains * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTree.java index e7a1bdfa..631388b0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTree.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * </p> * * @author Elke Achtert + * @since 0.2 * * @apiviz.has MTreeNode oneway - - contains * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTreeFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTreeFactory.java index a65d96c7..faa1cd95 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTreeFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTreeFactory.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; * Factory for a M-Tree * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses MTreeIndex oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTreeIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTreeIndex.java index 8d73bd58..d8b2bddd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTreeIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTreeIndex.java @@ -55,6 +55,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteArrayUtil; * Class for using an m-tree as database index. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTreeNode.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTreeNode.java index db8f4a19..b8dd882d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTreeNode.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTreeNode.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeEntry; * Represents a node in an M-Tree. * * @author Elke Achtert + * @since 0.2 * @param <O> Object type */ public class MTreeNode<O> extends AbstractMTreeNode<O, MTreeNode<O>, MTreeEntry> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MTreeQueryUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MTreeQueryUtil.java index 44446fe3..35f2b40a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MTreeQueryUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MTreeQueryUtil.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.AbstractMTree; * Query utility classes for MTrees. * * @author Erich Schubert + * @since 0.5.5 */ public final class MTreeQueryUtil { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MetricalIndexKNNQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MetricalIndexKNNQuery.java index cd574b0e..73a21b69 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MetricalIndexKNNQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MetricalIndexKNNQuery.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.heap.ComparableMinHeap; * Instance of a KNN query for a particular spatial index. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses AbstractMTree * @apiviz.uses DoubleMTreeDistanceSearchCandidate diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MetricalIndexRangeQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MetricalIndexRangeQuery.java index 392b3e38..5b57ea4b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MetricalIndexRangeQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MetricalIndexRangeQuery.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeEntry; * Instance of a range query for a particular spatial index. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses AbstractMTree * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MkTreeRKNNQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MkTreeRKNNQuery.java index 9a2527f7..b69e4701 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MkTreeRKNNQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/query/MkTreeRKNNQuery.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.NotImplementedException; * Instance of a rKNN query for a particular spatial index. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses AbstractMkTree */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/insert/MTreeInsert.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/insert/MTreeInsert.java index cf460fd8..c51979e1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/insert/MTreeInsert.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/insert/MTreeInsert.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeEntry; * FIXME: move this to the actual insert. * * @author Erich Schubert + * @since 0.2 */ public interface MTreeInsert<O, N extends AbstractMTreeNode<O, N, E>, E extends MTreeEntry> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/insert/MinimumEnlargementInsert.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/insert/MinimumEnlargementInsert.java index 22bd611f..58ab4f4f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/insert/MinimumEnlargementInsert.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/insert/MinimumEnlargementInsert.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "P. Ciaccia, M. Patella, P. Zezula", // title = "M-tree: An Efficient Access Method for Similarity Search in Metric Spaces", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/Assignments.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/Assignments.java index 7095bd0a..d2fd6570 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/Assignments.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/Assignments.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeEntry; * Encapsulates the attributes of an assignment during a split. * * @author Elke Achtert + * @since 0.2 * * @apiviz.composedOf DistanceEntry * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/DistanceEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/DistanceEntry.java index 79d4668a..ac55a1d3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/DistanceEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/DistanceEntry.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.index.tree.Entry; * belonging to this entry. * * @author Elke Achtert + * @since 0.2 * * @apiviz.uses Entry * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MLBDistSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MLBDistSplit.java index f07ed672..648c97ee 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MLBDistSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MLBDistSplit.java @@ -26,6 +26,7 @@ package de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.strategies.split; import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.AbstractMTree; import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.AbstractMTreeNode; import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeEntry; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; /** @@ -41,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Elke Achtert + * @since 0.2 * * @param <O> the type of DatabaseObject to be stored in the M-Tree * @param <N> the type of AbstractMTreeNode used in the M-Tree @@ -50,6 +52,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; title = "M-tree: An Efficient Access Method for Similarity Search in Metric Spaces", // booktitle = "VLDB'97, Proceedings of 23rd International Conference on Very Large Data Bases, August 25-29, 1997, Athens, Greece", // url = "http://www.vldb.org/conf/1997/P426.PDF") +@Alias("de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.split.MLBDistSplit") public class MLBDistSplit<O, N extends AbstractMTreeNode<O, N, E>, E extends MTreeEntry> extends MTreeSplit<O, N, E> { /** * Creates a new split object. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MMRadSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MMRadSplit.java index 16687a20..6ef4e97a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MMRadSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MMRadSplit.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Elke Achtert + * @since 0.2 * * @param <O> the type of objects to be stored in the M-Tree * @param <N> the type of AbstractMTreeNode used in the M-Tree diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MRadSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MRadSplit.java index e364c61f..a53e02de 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MRadSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MRadSplit.java @@ -26,6 +26,7 @@ package de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.strategies.split; import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.AbstractMTree; import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.AbstractMTreeNode; import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeEntry; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; /** @@ -41,12 +42,14 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Elke Achtert + * @since 0.2 * * @param <O> the type of DatabaseObject to be stored in the M-Tree * @param <N> the type of AbstractMTreeNode used in the M-Tree * @param <E> the type of MetricalEntry used in the M-Tree */ @Reference(authors = "P. Ciaccia, M. Patella, P. Zezula", title = "M-tree: An Efficient Access Method for Similarity Search in Metric Spaces", booktitle = "VLDB'97, Proceedings of 23rd International Conference on Very Large Data Bases, August 25-29, 1997, Athens, Greece", url = "http://www.vldb.org/conf/1997/P426.PDF") +@Alias("de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.split.MRadSplit") public class MRadSplit<O, N extends AbstractMTreeNode<O, N, E>, E extends MTreeEntry> extends MTreeSplit<O, N, E> { /** * Creates a new split object. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MTreeSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MTreeSplit.java index 01c612c0..30487846 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MTreeSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/MTreeSplit.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arrays.DoubleIntegerArrayQui * Abstract super class for splitting a node in an M-Tree. * * @author Elke Achtert + * @since 0.2 * * @apiviz.composedOf Assignments * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/RandomSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/RandomSplit.java index e7c6dbca..27970b25 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/RandomSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/strategies/split/RandomSplit.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * </p> * * @author Elke Achtert + * @since 0.2 * * @param <O> the type of DatabaseObject to be stored in the M-Tree * @param <N> the type of AbstractMTreeNode used in the M-Tree diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/query/DoubleDistanceSearchCandidate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/query/DoubleDistanceSearchCandidate.java index 46dbe003..a5d422f7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/query/DoubleDistanceSearchCandidate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/query/DoubleDistanceSearchCandidate.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.index.tree.query; * implementation). * * @author Erich Schubert + * @since 0.4.0 */ public class DoubleDistanceSearchCandidate implements Comparable<DoubleDistanceSearchCandidate> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/query/DoubleMTreeDistanceSearchCandidate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/query/DoubleMTreeDistanceSearchCandidate.java index bdd1e0f5..08562d4d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/query/DoubleMTreeDistanceSearchCandidate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/query/DoubleMTreeDistanceSearchCandidate.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBID; * covering radius. * * @author Elke Achtert + * @since 0.4.0 */ public class DoubleMTreeDistanceSearchCandidate extends DoubleDistanceSearchCandidate { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/query/GenericMTreeDistanceSearchCandidate.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/query/GenericMTreeDistanceSearchCandidate.java index 575436db..2cdad822 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/query/GenericMTreeDistanceSearchCandidate.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/query/GenericMTreeDistanceSearchCandidate.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBID; * FIXME: Class naming in this package is inconsistent. * * @author Elke Achtert + * @since 0.4.0 */ public class GenericMTreeDistanceSearchCandidate implements Comparable<GenericMTreeDistanceSearchCandidate> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialDirectoryEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialDirectoryEntry.java index 56fd0e0c..71bfef66 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialDirectoryEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialDirectoryEntry.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.index.tree.AbstractDirectoryEntry; * spatial node. * * @author Elke Achtert + * @since 0.2 */ public class SpatialDirectoryEntry extends AbstractDirectoryEntry implements SpatialEntry { private static final long serialVersionUID = 1; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialEntry.java index 4122b90c..07d6bc17 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialEntry.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.index.tree.Entry; * Defines the requirements for an entry in a node of a Spatial Index. * * @author Elke Achtert + * @since 0.2 */ public interface SpatialEntry extends Entry, SpatialComparable { // Emtpy - just combining the two interfaces above. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialIndexTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialIndexTree.java index 52a92916..13acb8e4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialIndexTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialIndexTree.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.persistent.PageFile; * Abstract super class for all spatial index tree classes. * * @author Elke Achtert + * @since 0.2 * * @apiviz.landmark * @apiviz.has SpatialNode oneway - - contains diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialNode.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialNode.java index af88b35f..f2a584d1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialNode.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialNode.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.index.tree.Node; * leaf node. * * @author Elke Achtert + * @since 0.2 * * @apiviz.composedOf SpatialEntry * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialPair.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialPair.java index 0d4884ad..4f008337 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialPair.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialPair.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * which are spatial nodes or data objects. * * @author Elke Achtert + * @since 0.4.0 */ public class SpatialPair<K, V extends SpatialComparable> extends Pair<K, V> implements SpatialComparable { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialPointLeafEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialPointLeafEntry.java index 705c54d6..bc25c0cd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialPointLeafEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/SpatialPointLeafEntry.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * and the values of the underlying data object. * * @author Elke Achtert + * @since 0.2 */ public class SpatialPointLeafEntry extends AbstractLeafEntry implements SpatialEntry, NumberVector { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/MinimalisticMemoryKDTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/MinimalisticMemoryKDTree.java index 11bcb17a..90b07c9e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/MinimalisticMemoryKDTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/MinimalisticMemoryKDTree.java @@ -83,6 +83,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * TODO: add support for weighted Minkowski distances. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has KDTreeKNNQuery * @apiviz.has KDTreeRangeQuery diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/SmallMemoryKDTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/SmallMemoryKDTree.java index d44731f0..ca7c5821 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/SmallMemoryKDTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/SmallMemoryKDTree.java @@ -79,6 +79,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * TODO: add support for weighted Minkowski distances. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has KDTreeKNNQuery * @apiviz.has KDTreeRangeQuery diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRStarTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRStarTree.java index 5c3530ec..fd7fd8b5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRStarTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRStarTree.java @@ -59,6 +59,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * FeatureVector) is intentional, because we have spatial requirements. * * @author Elke Achtert + * @since 0.2 * * @apiviz.landmark * @apiviz.has AbstractRStarTreeNode oneway - - contains diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRStarTreeFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRStarTreeFactory.java index ae0e3389..44175e99 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRStarTreeFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRStarTreeFactory.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Abstract factory for R*-Tree based trees. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses AbstractRStarTree oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRStarTreeNode.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRStarTreeNode.java index 77de9df4..56f85ae3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRStarTreeNode.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRStarTreeNode.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.logging.LoggingConfiguration; * Abstract superclass for nodes in a R*-Tree. * * @author Elke Achtert + * @since 0.2 * @param <N> Node type * @param <E> Entry type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRTreeSettings.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRTreeSettings.java index f8c6e732..87bad4ac 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRTreeSettings.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/AbstractRTreeSettings.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.split.Top * Class to wrap common Rtree settings. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.composedOf BulkSplit * @apiviz.composedOf SplitStrategy diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/NonFlatRStarTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/NonFlatRStarTree.java index 5d65d605..bdb68439 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/NonFlatRStarTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/NonFlatRStarTree.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.persistent.PageFile; * Abstract superclass for all non-flat R*-Tree variants. * * @author Elke Achtert + * @since 0.2 * * @param <N> Node type * @param <E> Entry type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluDirectoryEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluDirectoryEntry.java index b8792abd..c4e941bf 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluDirectoryEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluDirectoryEntry.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.index.tree.spatial.SpatialDirectoryEntry; * objects. * * @author Elke Achtert + * @since 0.2 */ public class DeLiCluDirectoryEntry extends SpatialDirectoryEntry implements DeLiCluEntry { private static final long serialVersionUID = 1; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluEntry.java index f6fc3fb6..feb4501d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluEntry.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.index.tree.spatial.SpatialEntry; * contains handled or unhandled data objects. * * @author Elke Achtert + * @since 0.2 */ public interface DeLiCluEntry extends SpatialEntry { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluLeafEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluLeafEntry.java index 4a02c4fd..d973a226 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluLeafEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluLeafEntry.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.index.tree.spatial.SpatialPointLeafEntry; * whether this entry's node contains handled or unhandled data objects. * * @author Elke Achtert + * @since 0.2 */ public class DeLiCluLeafEntry extends SpatialPointLeafEntry implements DeLiCluEntry { private static final long serialVersionUID = 1; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluNode.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluNode.java index 72fdd154..994b5777 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluNode.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluNode.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.AbstractRStarTreeNod * Represents a node in a DeLiClu-Tree. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has DeLiCluEntry oneway - - contains */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluTree.java index dafa4992..a977be40 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluTree.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.persistent.PageFile; * algorithm. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has DeLiCluNode oneway - - contains */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluTreeFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluTreeFactory.java index 66a59352..3e706658 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluTreeFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluTreeFactory.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.persistent.PageFileFactory; * Factory for DeLiClu R*-Trees. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses DeLiCluTreeIndex oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluTreeIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluTreeIndex.java index 436e38fd..7f078906 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluTreeIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluTreeIndex.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * The common use of the DeLiClu tree: indexing number vectors. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTree.java index 7f0e77ab..01b4a594 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTree.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.persistent.PageFile; * to search for certain object in the structure and ensures persistence. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has FlatRStarTreeNode oneway - - contains */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTreeFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTreeFactory.java index 88505f0c..ad4406ad 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTreeFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTreeFactory.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.persistent.PageFileFactory; * Factory for flat R*-Trees. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses FlatRStarTreeIndex oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTreeIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTreeIndex.java index 21f4baea..7bfa77f4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTreeIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTreeIndex.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.persistent.PageFile; * The common use of the flat rstar tree: indexing number vectors. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTreeNode.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTreeNode.java index 0ad3af21..2ae002d8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTreeNode.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/flat/FlatRStarTreeNode.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; * Represents a node in a flat R*-Tree. * * @author Elke Achtert + * @since 0.2 */ public class FlatRStarTreeNode extends AbstractRStarTreeNode<FlatRStarTreeNode, SpatialEntry> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/EuclideanRStarTreeKNNQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/EuclideanRStarTreeKNNQuery.java index 25884cdf..30e41ff3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/EuclideanRStarTreeKNNQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/EuclideanRStarTreeKNNQuery.java @@ -58,6 +58,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.uses EuclideanDistanceFunction * @apiviz.uses SquaredEuclideanDistanceFunction diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/EuclideanRStarTreeRangeQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/EuclideanRStarTreeRangeQuery.java index 70112d7e..9c04d2a5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/EuclideanRStarTreeRangeQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/EuclideanRStarTreeRangeQuery.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses EuclideanDistanceFunction * @apiviz.uses SquaredEuclideanDistanceFunction diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/RStarTreeKNNQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/RStarTreeKNNQuery.java index bb1a57a4..763841ef 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/RStarTreeKNNQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/RStarTreeKNNQuery.java @@ -65,6 +65,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses AbstractRStarTree * @apiviz.uses SpatialPrimitiveDistanceFunction diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/RStarTreeRangeQuery.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/RStarTreeRangeQuery.java index b8929011..0319e809 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/RStarTreeRangeQuery.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/RStarTreeRangeQuery.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses AbstractRStarTree * @apiviz.uses SpatialPrimitiveDistanceFunction diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/RStarTreeUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/RStarTreeUtil.java index ee8cd6f0..9808bf30 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/RStarTreeUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/RStarTreeUtil.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.AbstractRStarTree; * Utility class for RStar trees * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNDirectoryEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNDirectoryEntry.java index 9b422334..93b32af8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNDirectoryEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNDirectoryEntry.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.index.tree.spatial.SpatialDirectoryEntry; * underlying RdKNN-Tree node. * * @author Elke Achtert + * @since 0.2 * @param Distance type */ public class RdKNNDirectoryEntry extends SpatialDirectoryEntry implements RdKNNEntry { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNEntry.java index 9d98dcd0..b85a1c92 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNEntry.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.index.tree.spatial.SpatialEntry; * data object or RdKNN-Tree node. * * @author Elke Achtert + * @since 0.2 */ interface RdKNNEntry extends SpatialEntry { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNLeafEntry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNLeafEntry.java index 44c65c5f..491d6cfe 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNLeafEntry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNLeafEntry.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.index.tree.spatial.SpatialPointLeafEntry; * data object. * * @author Elke Achtert + * @since 0.2 */ public class RdKNNLeafEntry extends SpatialPointLeafEntry implements RdKNNEntry { private static final long serialVersionUID = 2; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNNode.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNNode.java index ce4ac0dd..6a887047 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNNode.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNNode.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.AbstractRStarTreeNod * Represents a node in a RDkNN-Tree. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has RdKNNEntry oneway - - contains */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNTree.java index b9485503..04e45424 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNTree.java @@ -74,6 +74,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.DoubleObjPair; * TODO: noch nicht fertig!!! * * @author Elke Achtert + * @since 0.2 * * @apiviz.has RdKNNNode * @apiviz.has RdKNNTreeHeader diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNTreeFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNTreeFactory.java index fbe03399..9ccdea59 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNTreeFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNTreeFactory.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Factory for RdKNN R*-Trees. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.stereotype factory * @apiviz.uses RdKNNTree oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNTreeHeader.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNTreeHeader.java index 4b2b8c5f..94af7721 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNTreeHeader.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdKNNTreeHeader.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.index.tree.TreeIndexHeader; * needed for persistent storage. * * @author Elke Achtert + * @since 0.2 */ class RdKNNTreeHeader extends TreeIndexHeader { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdkNNSettings.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdkNNSettings.java index 0cee0c4a..931428b7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdkNNSettings.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rdknn/RdkNNSettings.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.AbstractRTreeSetting * Settings for the RdKNN Tree. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTree.java index b4e19638..986ade9d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTree.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * for certain object in the structure and ensures persistence. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has RStarTreeNode oneway - - contains */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTreeFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTreeFactory.java index aacb94c5..efdbdcc9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTreeFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTreeFactory.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.Alias; * Factory for regular R*-Trees. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark factory * @apiviz.uses RStarTreeIndex oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTreeIndex.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTreeIndex.java index 17c7b942..dfa39915 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTreeIndex.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTreeIndex.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.persistent.PageFile; * The common use of the rstar tree: indexing number vectors. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTreeNode.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTreeNode.java index d5d01542..14361c87 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTreeNode.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTreeNode.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.AbstractRStarTreeNod * Represents a node in an R*-Tree. * * @author Elke Achtert + * @since 0.2 */ public class RStarTreeNode extends AbstractRStarTreeNode<RStarTreeNode, SpatialEntry> { private static final long serialVersionUID = 1; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/AbstractBulkSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/AbstractBulkSplit.java index 0c218c7e..75b55eba 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/AbstractBulkSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/AbstractBulkSplit.java @@ -30,6 +30,7 @@ import java.util.List; * Encapsulates the required parameters for a bulk split of a spatial index. * * @author Elke Achtert + * @since 0.4.0 */ public abstract class AbstractBulkSplit implements BulkSplit { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/AdaptiveSortTileRecursiveBulkSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/AdaptiveSortTileRecursiveBulkSplit.java index 55b8d5ec..0eda00fd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/AdaptiveSortTileRecursiveBulkSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/AdaptiveSortTileRecursiveBulkSplit.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * See {@link SortTileRecursiveBulkSplit} for the original STR bulk load. * * @author Erich Schubert + * @since 0.5.0 */ public class AdaptiveSortTileRecursiveBulkSplit extends AbstractBulkSplit { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/BulkSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/BulkSplit.java index 84432746..0688fb1c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/BulkSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/BulkSplit.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.data.spatial.SpatialComparable; * Interface for a bulk split strategy. * * @author Erich Schubert + * @since 0.4.0 */ public interface BulkSplit { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/FileOrderBulkSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/FileOrderBulkSplit.java index ad77ceab..0c937b06 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/FileOrderBulkSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/FileOrderBulkSplit.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * before. * * @author Erich Schubert + * @since 0.5.0 */ public class FileOrderBulkSplit extends AbstractBulkSplit { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/MaxExtensionBulkSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/MaxExtensionBulkSplit.java index 3ad7a333..2bd67601 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/MaxExtensionBulkSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/MaxExtensionBulkSplit.java @@ -31,6 +31,7 @@ import java.util.List; import de.lmu.ifi.dbs.elki.data.spatial.SpatialComparable; import de.lmu.ifi.dbs.elki.data.spatial.SpatialSingleMinComparator; import de.lmu.ifi.dbs.elki.logging.Logging; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; /** @@ -38,9 +39,11 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * dimensions with maximum extension. * * @author Elke Achtert + * @since 0.4.0 * * @apiviz.composedOf SpatialSingleMinComparator */ +@Alias("de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.bulk.MaxExtensionBulkSplit") public class MaxExtensionBulkSplit extends AbstractBulkSplit { /** * Logger. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/MaxExtensionSortTileRecursiveBulkSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/MaxExtensionSortTileRecursiveBulkSplit.java index eeb3c050..e98ff4c2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/MaxExtensionSortTileRecursiveBulkSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/MaxExtensionSortTileRecursiveBulkSplit.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * further, by also varying the fan-out degree. * * @author Erich Schubert + * @since 0.5.0 */ public class MaxExtensionSortTileRecursiveBulkSplit extends AbstractBulkSplit { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/OneDimSortBulkSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/OneDimSortBulkSplit.java index 439bd9c7..111cb71c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/OneDimSortBulkSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/OneDimSortBulkSplit.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "Roussopoulos, N. and Leifker, D.", title = "Direct spatial search on pictorial databases using packed R-trees", booktitle = "ACM SIGMOD Record 14-4", url = "http://dx.doi.org/10.1145/971699.318900") public class OneDimSortBulkSplit extends AbstractBulkSplit { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/SortTileRecursiveBulkSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/SortTileRecursiveBulkSplit.java index ed9e919e..7f074023 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/SortTileRecursiveBulkSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/SortTileRecursiveBulkSplit.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "Leutenegger, S.T. and Lopez, M.A. and Edgington, J.", title = "STR: A simple and efficient algorithm for R-tree packing", booktitle = "Proc. 13th International Conference on Data Engineering, 1997", url = "http://dx.doi.org/10.1109/ICDE.1997.582015") @Alias({"str", "STR"}) diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/SpatialSortBulkSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/SpatialSortBulkSplit.java index f2b39179..f0a85de7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/SpatialSortBulkSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/SpatialSortBulkSplit.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * @apiviz.composedOf SpatialSorter * * @author Erich Schubert + * @since 0.5.0 */ @Reference(title = "On packing R-trees", authors = "Kamel, I. and Faloutsos, C.", booktitle = "Proc. of the second international conference on Information and knowledge management", url = "http://dx.doi.org/10.1145/170088.170403") public class SpatialSortBulkSplit extends AbstractBulkSplit { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/ApproximativeLeastOverlapInsertionStrategy.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/ApproximativeLeastOverlapInsertionStrategy.java index 2897c5a4..9eab98d4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/ApproximativeLeastOverlapInsertionStrategy.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/ApproximativeLeastOverlapInsertionStrategy.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.DoubleIntPair; * @author Erich Schubert * @author Franz Graf * @author Marisa Thoma + * @since 0.5.0 */ @Reference(authors = "N. Beckmann, H.-P. Kriegel, R. Schneider, B. Seeger", title = "The R*-tree: an efficient and robust access method for points and rectangles", booktitle = "Proceedings of the 1990 ACM SIGMOD International Conference on Management of Data, Atlantic City, NJ, May 23-25, 1990", url = "http://dx.doi.org/10.1145/93597.98741") public class ApproximativeLeastOverlapInsertionStrategy extends LeastOverlapInsertionStrategy { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/CombinedInsertionStrategy.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/CombinedInsertionStrategy.java index 04221d8b..f53092b8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/CombinedInsertionStrategy.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/CombinedInsertionStrategy.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ClassParameter; * </p> * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "N. Beckmann, H.-P. Kriegel, R. Schneider, B. Seeger", title = "The R*-tree: an efficient and robust access method for points and rectangles", booktitle = "Proceedings of the 1990 ACM SIGMOD International Conference on Management of Data, Atlantic City, NJ, May 23-25, 1990", url = "http://dx.doi.org/10.1145/93597.98741") public class CombinedInsertionStrategy implements InsertionStrategy { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/InsertionStrategy.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/InsertionStrategy.java index 552206bf..b564ad1d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/InsertionStrategy.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/InsertionStrategy.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayAdapter; * RTree insertion strategy interface. * * @author Erich Schubert + * @since 0.5.0 */ public interface InsertionStrategy { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/LeastEnlargementInsertionStrategy.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/LeastEnlargementInsertionStrategy.java index ef17e816..fdad1bda 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/LeastEnlargementInsertionStrategy.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/LeastEnlargementInsertionStrategy.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "Antonin Guttman", title = "R-Trees: A Dynamic Index Structure For Spatial Searching", booktitle = "Proceedings of the 1984 ACM SIGMOD international conference on Management of data", url = "http://dx.doi.org/10.1145/971697.602266") public class LeastEnlargementInsertionStrategy implements InsertionStrategy { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/LeastEnlargementWithAreaInsertionStrategy.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/LeastEnlargementWithAreaInsertionStrategy.java index 9c90169d..70543731 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/LeastEnlargementWithAreaInsertionStrategy.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/LeastEnlargementWithAreaInsertionStrategy.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "N. Beckmann, H.-P. Kriegel, R. Schneider, B. Seeger", title = "The R*-tree: an efficient and robust access method for points and rectangles", booktitle = "Proceedings of the 1990 ACM SIGMOD International Conference on Management of Data, Atlantic City, NJ, May 23-25, 1990", url = "http://dx.doi.org/10.1145/93597.98741") public class LeastEnlargementWithAreaInsertionStrategy implements InsertionStrategy { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/LeastOverlapInsertionStrategy.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/LeastOverlapInsertionStrategy.java index 794f32a1..69e68446 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/LeastOverlapInsertionStrategy.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/insert/LeastOverlapInsertionStrategy.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "N. Beckmann, H.-P. Kriegel, R. Schneider, B. Seeger", title = "The R*-tree: an efficient and robust access method for points and rectangles", booktitle = "Proceedings of the 1990 ACM SIGMOD International Conference on Management of Data, Atlantic City, NJ, May 23-25, 1990", url = "http://dx.doi.org/10.1145/93597.98741") public class LeastOverlapInsertionStrategy implements InsertionStrategy { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/overflow/LimitedReinsertOverflowTreatment.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/overflow/LimitedReinsertOverflowTreatment.java index 23db999c..2023fb44 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/overflow/LimitedReinsertOverflowTreatment.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/overflow/LimitedReinsertOverflowTreatment.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * reinsertions to happen only once per level. * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "N. Beckmann, H.-P. Kriegel, R. Schneider, B. Seeger", title = "The R*-tree: an efficient and robust access method for points and rectangles", booktitle = "Proceedings of the 1990 ACM SIGMOD International Conference on Management of Data, Atlantic City, NJ, May 23-25, 1990", url = "http://dx.doi.org/10.1145/93597.98741") public class LimitedReinsertOverflowTreatment implements OverflowTreatment { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/overflow/OverflowTreatment.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/overflow/OverflowTreatment.java index 8c9fc962..4c275503 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/overflow/OverflowTreatment.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/overflow/OverflowTreatment.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.AbstractRStarTreeNod * Reinsertion strategy to resolve overflows in the RStarTree. * * @author Erich Schubert + * @since 0.5.0 */ public interface OverflowTreatment { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/overflow/SplitOnlyOverflowTreatment.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/overflow/SplitOnlyOverflowTreatment.java index 9670daa1..d6470884 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/overflow/SplitOnlyOverflowTreatment.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/overflow/SplitOnlyOverflowTreatment.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Always split, as in the original R-Tree * * @author Erich Schubert + * @since 0.5.0 */ public class SplitOnlyOverflowTreatment implements OverflowTreatment { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/AbstractPartialReinsert.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/AbstractPartialReinsert.java index 9f65bdd8..13cf20e4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/AbstractPartialReinsert.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/AbstractPartialReinsert.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * parameter to partially reinsert entries. * * @author Erich Schubert + * @since 0.5.0 */ public abstract class AbstractPartialReinsert implements ReinsertStrategy { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/CloseReinsert.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/CloseReinsert.java index 2021b117..ae043992 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/CloseReinsert.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/CloseReinsert.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.DoubleIntPair; * The strategy preferred by the R*-Tree * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "N. Beckmann, H.-P. Kriegel, R. Schneider, B. Seeger", // title = "The R*-tree: an efficient and robust access method for points and rectangles", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/FarReinsert.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/FarReinsert.java index 52241deb..40b7b894 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/FarReinsert.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/FarReinsert.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.DoubleIntPair; * Alternative strategy mentioned in the R*-tree * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "N. Beckmann, H.-P. Kriegel, R. Schneider, B. Seeger", // title = "The R*-tree: an efficient and robust access method for points and rectangles", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/ReinsertStrategy.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/ReinsertStrategy.java index c4650b89..cb63a3d9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/ReinsertStrategy.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/reinsert/ReinsertStrategy.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayAdapter; * Reinsertion strategy to resolve overflows in the RStarTree. * * @author Erich Schubert + * @since 0.5.0 */ public interface ReinsertStrategy { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/AngTanLinearSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/AngTanLinearSplit.java index 73e3a8e5..08b40acc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/AngTanLinearSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/AngTanLinearSplit.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "C. H. Ang and T. C. Tan", title = "New linear node splitting algorithm for R-trees", booktitle = "Proceedings of the 5th International Symposium on Advances in Spatial Databases", url = "http://dx.doi.org/10.1007/3-540-63238-7_38") public class AngTanLinearSplit implements SplitStrategy { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/GreeneSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/GreeneSplit.java index f6d15f18..e415bb35 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/GreeneSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/GreeneSplit.java @@ -50,6 +50,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.DoubleIntPair; * </p> * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "Diane Greene", title = "An implementation and performance analysis of spatial data access methods", booktitle = "Proceedings of the Fifth International Conference on Data Engineering", url = "http://dx.doi.org/10.1109/ICDE.1989.47268") public class GreeneSplit implements SplitStrategy { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/RTreeLinearSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/RTreeLinearSplit.java index c7ec5412..6849207f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/RTreeLinearSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/RTreeLinearSplit.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "Antonin Guttman", title = "R-Trees: A Dynamic Index Structure For Spatial Searching", booktitle = "Proceedings of the 1984 ACM SIGMOD international conference on Management of data", url = "http://dx.doi.org/10.1145/971697.602266") public class RTreeLinearSplit implements SplitStrategy { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/RTreeQuadraticSplit.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/RTreeQuadraticSplit.java index 351c97f5..16037a4a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/RTreeQuadraticSplit.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/RTreeQuadraticSplit.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "Antonin Guttman", title = "R-Trees: A Dynamic Index Structure For Spatial Searching", booktitle = "Proceedings of the 1984 ACM SIGMOD international conference on Management of data", url = "http://dx.doi.org/10.1145/971697.602266") public class RTreeQuadraticSplit implements SplitStrategy { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/SplitStrategy.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/SplitStrategy.java index 080da97a..f63f89dd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/SplitStrategy.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/SplitStrategy.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayAdapter; * Generic interface for split strategies. * * @author Erich Schubert + * @since 0.4.0 */ public interface SplitStrategy { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/TopologicalSplitter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/TopologicalSplitter.java index d1808962..5ab9b73b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/TopologicalSplitter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/split/TopologicalSplitter.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.data.HyperBoundingBox; import de.lmu.ifi.dbs.elki.data.ModifiableHyperBoundingBox; import de.lmu.ifi.dbs.elki.data.spatial.SpatialComparable; import de.lmu.ifi.dbs.elki.data.spatial.SpatialUtil; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.BitsUtil; import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayAdapter; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; @@ -39,10 +40,12 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.DoubleIntPair; * Encapsulates the required parameters for a topological split of a R*-Tree. * * @author Elke Achtert + * @since 0.4.0 * * @apiviz.has Split */ @Reference(authors = "N. Beckmann, H.-P. Kriegel, R. Schneider, B. Seeger", title = "The R*-tree: an efficient and robust access method for points and rectangles", booktitle = "Proceedings of the 1990 ACM SIGMOD International Conference on Management of Data, Atlantic City, NJ, May 23-25, 1990", url = "http://dx.doi.org/10.1145/93597.98741") +@Alias("de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.util.TopologicalSplitter") public class TopologicalSplitter implements SplitStrategy { /** * Static instance. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/util/NodeArrayAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/util/NodeArrayAdapter.java index f0f887a4..973edf86 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/util/NodeArrayAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/util/NodeArrayAdapter.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayAdapter; * Access the entries of a node as array-like. * * @author Erich Schubert + * @since 0.4.0 */ public class NodeArrayAdapter implements ArrayAdapter<SpatialEntry, AbstractNode<? extends SpatialEntry>> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/DAFile.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/DAFile.java index 17101dec..9c3e4b1b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/DAFile.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/DAFile.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteArrayUtil; * * @author Thomas Bernecker * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "Hans-Peter Kriegel, Peer Kröger, Matthias Schubert, Ziyue Zhu", title = "Efficient Query Processing in Arbitrary Subspaces Using Vector Approximations", booktitle = "Proc. 18th Int. Conf. on Scientific and Statistical Database Management (SSDBM 06), Wien, Austria, 2006", url = "http://dx.doi.org/10.1109/SSDBM.2006.23") public class DAFile { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/PartialVAFile.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/PartialVAFile.java index fdc262d0..c0d1945d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/PartialVAFile.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/PartialVAFile.java @@ -82,6 +82,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.DoubleObjPair; * * @author Thomas Bernecker * @author Erich Schubert + * @since 0.5.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VAFile.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VAFile.java index 91516e97..2933a077 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VAFile.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VAFile.java @@ -71,6 +71,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * * @author Thomas Bernecker * @author Erich Schubert + * @since 0.5.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VALPNormDistance.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VALPNormDistance.java index ae341e4b..76f2448c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VALPNormDistance.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VALPNormDistance.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.data.NumberVector; * Lp-Norm distance function for partially computed objects. * * @author Erich Schubert + * @since 0.5.0 */ public class VALPNormDistance { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VectorApproximation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VectorApproximation.java index 9913cade..5025d415 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VectorApproximation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VectorApproximation.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteArrayUtil; * * @author Thomas Bernecker * @author Erich Schubert + * @since 0.5.0 */ public class VectorApproximation { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/CLISmartHandler.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/CLISmartHandler.java index f434cee4..de496674 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/CLISmartHandler.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/CLISmartHandler.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.logging.progress.ProgressTracker; * Handler that handles output to the console with clever formatting. * * @author Erich Schubert + * @since 0.2 * * @apiviz.composedOf ProgressTracker * @apiviz.uses LogRecord oneway - - processes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/ELKILogRecord.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/ELKILogRecord.java index c181e449..87de3faa 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/ELKILogRecord.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/ELKILogRecord.java @@ -27,9 +27,6 @@ import java.util.logging.Level; import java.util.logging.LogRecord; import java.util.logging.Logger; -import de.lmu.ifi.dbs.elki.application.AbstractApplication; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.AbstractParameterization; - /** * Base {@link LogRecord} class used in ELKI. * @@ -37,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.AbstractPar * additional classes when determining the 'origin' of a log message. * * @author Erich Schubert + * @since 0.2 */ public class ELKILogRecord extends LogRecord { /** @@ -52,7 +50,15 @@ public class ELKILogRecord extends LogRecord { /** * Classes to ignore when finding the relevant caller. */ - public static final String[] IGNORE_CLASSES = { Logger.class.getCanonicalName(), Logging.class.getCanonicalName(), LoggingUtil.class.getCanonicalName(), ELKILogRecord.class.getCanonicalName(), AbstractParameterization.class.getCanonicalName(), AbstractApplication.class.getCanonicalName() }; + public static final String[] IGNORE_CLASSES = { // + Logger.class.getCanonicalName(), // + Logging.class.getCanonicalName(), // + LoggingUtil.class.getCanonicalName(), // + ELKILogRecord.class.getCanonicalName(), // + // Avoid dependencies on these packages: + "de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.AbstractParameterization", // + "de.lmu.ifi.dbs.elki.application.AbstractApplication", // + }; /** * Name of this class. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/ErrorFormatter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/ErrorFormatter.java index 2344669e..376b3b95 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/ErrorFormatter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/ErrorFormatter.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.logging.progress.ProgressLogRecord; * Format a log record for error output, including a stack trace if available. * * @author Erich Schubert + * @since 0.5.0 */ // TODO: make more configurable and handle suppressed exceptions public class ErrorFormatter extends Formatter { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/Logging.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/Logging.java index ca59ad18..a57dd4cc 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/Logging.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/Logging.java @@ -53,6 +53,7 @@ import de.lmu.ifi.dbs.elki.logging.statistics.UnsynchronizedLongCounter; * {@link ELKILogRecord}! * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses LoggingConfiguration * @apiviz.uses ELKILogRecord oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/LoggingConfiguration.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/LoggingConfiguration.java index 86f7c528..c2d200ea 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/LoggingConfiguration.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/LoggingConfiguration.java @@ -24,6 +24,7 @@ package de.lmu.ifi.dbs.elki.logging; */ import java.io.File; +import java.io.FileInputStream; import java.io.FileNotFoundException; import java.io.InputStream; import java.util.Properties; @@ -32,12 +33,12 @@ import java.util.logging.LogManager; import java.util.logging.Logger; import de.lmu.ifi.dbs.elki.logging.Logging.Level; -import de.lmu.ifi.dbs.elki.utilities.FileUtil; /** * Facility for configuration of logging. * * @author Erich Schubert + * @since 0.2 */ public final class LoggingConfiguration { /** @@ -107,36 +108,62 @@ public final class LoggingConfiguration { LogManager logManager = LogManager.getLogManager(); Logger logger = Logger.getLogger(LoggingConfiguration.class.getName()); // allow null as package name. - if (pkg == null) { + if(pkg == null) { pkg = ""; } // Load logging configuration from current directory String cfgfile = name; - if (new File(name).exists()) { + if(new File(name).exists()) { cfgfile = name; - } else { + } + else { // Fall back to full path / resources. cfgfile = pkg.replace('.', File.separatorChar) + File.separatorChar + name; } try { - InputStream cfgdata = FileUtil.openSystemFile(cfgfile); + InputStream cfgdata = openSystemFile(cfgfile); logManager.readConfiguration(cfgdata); // also load as properties for us, to get debug flag. - InputStream cfgdata2 = FileUtil.openSystemFile(cfgfile); + InputStream cfgdata2 = openSystemFile(cfgfile); Properties cfgprop = new Properties(); cfgprop.load(cfgdata2); DEBUG = Boolean.parseBoolean(cfgprop.getProperty("debug")); logger.info("Logging configuration read."); - } catch (FileNotFoundException e) { + } + catch(FileNotFoundException e) { logger.log(Level.SEVERE, "Could not find logging configuration file: " + cfgfile, e); - } catch (Exception e) { + } + catch(Exception e) { logger.log(Level.SEVERE, "Failed to configure logging from file: " + cfgfile, e); } } /** + * Private copy from FileUtil, to avoid cross-dependencies. Try to open a + * file, first trying the file system, then falling back to the classpath. + * + * @param filename File name in system notation + * @return Input stream + * @throws FileNotFoundException When no file was found. + */ + private static InputStream openSystemFile(String filename) throws FileNotFoundException { + try { + return new FileInputStream(filename); + } + catch(FileNotFoundException e) { + // try with classloader + String resname = filename.replace(File.separatorChar, '/'); + InputStream result = ClassLoader.getSystemResourceAsStream(resname); + if(result == null) { + throw e; + } + return result; + } + } + + /** * Assert that logging was configured. */ public static void assertConfigured() { @@ -149,23 +176,24 @@ public final class LoggingConfiguration { * @param verbose verbosity level. */ public static void setVerbose(java.util.logging.Level verbose) { - if (verbose.intValue() <= Level.VERBOSE.intValue()) { + if(verbose.intValue() <= Level.VERBOSE.intValue()) { // decrease to VERBOSE if it was higher, otherwise further to VERYVERBOSE - if (LOGGER_GLOBAL_TOP.getLevel() == null || LOGGER_GLOBAL_TOP.getLevel().intValue() > verbose.intValue()) { + if(LOGGER_GLOBAL_TOP.getLevel() == null || LOGGER_GLOBAL_TOP.getLevel().intValue() > verbose.intValue()) { LOGGER_GLOBAL_TOP.setLevel(verbose); } - if (LOGGER_ELKI_TOP.getLevel() == null || LOGGER_ELKI_TOP.getLevel().intValue() > verbose.intValue()) { + if(LOGGER_ELKI_TOP.getLevel() == null || LOGGER_ELKI_TOP.getLevel().intValue() > verbose.intValue()) { LOGGER_ELKI_TOP.setLevel(verbose); } - } else { + } + else { // re-increase to given level if it was verbose or "very verbose". - if (LOGGER_GLOBAL_TOP.getLevel() != null && (// + if(LOGGER_GLOBAL_TOP.getLevel() != null && (// Level.VERBOSE.equals(LOGGER_GLOBAL_TOP.getLevel()) || // Level.VERYVERBOSE.equals(LOGGER_GLOBAL_TOP.getLevel()) // )) { LOGGER_GLOBAL_TOP.setLevel(verbose); } - if (LOGGER_ELKI_TOP.getLevel() != null && (// + if(LOGGER_ELKI_TOP.getLevel() != null && (// Level.VERBOSE.equals(LOGGER_ELKI_TOP.getLevel()) || // Level.VERYVERBOSE.equals(LOGGER_ELKI_TOP.getLevel()) // )) { @@ -179,13 +207,13 @@ public final class LoggingConfiguration { */ public static void setStatistics() { // decrease to INFO if it was higher - if (LOGGER_GLOBAL_TOP.getLevel() == null || LOGGER_GLOBAL_TOP.getLevel().intValue() > Level.STATISTICS.intValue()) { + if(LOGGER_GLOBAL_TOP.getLevel() == null || LOGGER_GLOBAL_TOP.getLevel().intValue() > Level.STATISTICS.intValue()) { LOGGER_GLOBAL_TOP.setLevel(Level.STATISTICS); } - if (LOGGER_ELKI_TOP.getLevel() == null || LOGGER_ELKI_TOP.getLevel().intValue() > Level.STATISTICS.intValue()) { + if(LOGGER_ELKI_TOP.getLevel() == null || LOGGER_ELKI_TOP.getLevel().intValue() > Level.STATISTICS.intValue()) { LOGGER_ELKI_TOP.setLevel(Level.STATISTICS); } - if (LOGGER_TIME_TOP.getLevel() == null || LOGGER_TIME_TOP.getLevel().intValue() > Level.STATISTICS.intValue()) { + if(LOGGER_TIME_TOP.getLevel() == null || LOGGER_TIME_TOP.getLevel().intValue() > Level.STATISTICS.intValue()) { LOGGER_TIME_TOP.setLevel(Level.STATISTICS); } } @@ -209,8 +237,8 @@ public final class LoggingConfiguration { */ public static void replaceDefaultHandler(Handler handler) { Logger rootlogger = LogManager.getLogManager().getLogger(""); - for (Handler h : rootlogger.getHandlers()) { - if (h instanceof CLISmartHandler) { + for(Handler h : rootlogger.getHandlers()) { + if(h instanceof CLISmartHandler) { rootlogger.removeHandler(h); } } @@ -226,7 +254,7 @@ public final class LoggingConfiguration { */ public static void setLevelFor(String pkg, String level) throws IllegalArgumentException { Logger logr = Logger.getLogger(pkg); - if (logr == null) { + if(logr == null) { throw new IllegalArgumentException("Logger not found."); } // Can also throw an IllegalArgumentException diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/LoggingUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/LoggingUtil.java index 5f9cb39b..576fa817 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/LoggingUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/LoggingUtil.java @@ -27,9 +27,6 @@ import java.util.logging.Level; import java.util.logging.LogRecord; import java.util.logging.Logger; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.StringParameter; - /** * This final class contains some static convenience methods for logging. * @@ -38,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.StringParameter; * loop constructs. * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses ELKILogRecord oneway - - «create» */ @@ -177,38 +175,4 @@ public final class LoggingUtil { return null; } - - /** - * Parse the option string to configure logging. - * - * @param param Parameter to process. - * - * @throws WrongParameterValueException On parsing errors - */ - public static final void parseDebugParameter(StringParameter param) throws WrongParameterValueException { - String[] opts = param.getValue().split(","); - for(String opt : opts) { - try { - String[] chunks = opt.split("="); - if(chunks.length == 1) { - try { - Level level = Level.parse(chunks[0]); - LoggingConfiguration.setDefaultLevel(level); - } - catch(IllegalArgumentException e) { - LoggingConfiguration.setLevelFor(chunks[0], Level.FINEST.getName()); - } - } - else if(chunks.length == 2) { - LoggingConfiguration.setLevelFor(chunks[0], chunks[1]); - } - else { - throw new WrongParameterValueException(param, param.getValue(), "More than one '=' in debug parameter."); - } - } - catch(IllegalArgumentException e) { - throw (new WrongParameterValueException(param, param.getValue(), "Could not process value.", e)); - } - } - } }
\ No newline at end of file diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/MessageFormatter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/MessageFormatter.java index e0074f4f..5dc87173 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/MessageFormatter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/MessageFormatter.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.logging.progress.ProgressLogRecord; * origin information. Usually, the formatter will try to ensure a newline at the end. * * @author Arthur Zimek + * @since 0.2 */ public class MessageFormatter extends Formatter { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/OutputStreamLogger.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/OutputStreamLogger.java index adee9b1e..0b48093c 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/OutputStreamLogger.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/OutputStreamLogger.java @@ -37,6 +37,7 @@ import java.nio.charset.CharsetEncoder; * This is meant to wrap logging output to the console. * * @author Erich Schubert + * @since 0.2 */ public class OutputStreamLogger extends OutputStreamWriter { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/AbstractProgress.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/AbstractProgress.java index 526dac3f..7171c668 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/AbstractProgress.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/AbstractProgress.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * Abstract base class for FiniteProgress objects. * * @author Erich Schubert + * @since 0.2 */ public abstract class AbstractProgress implements Progress { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/FiniteProgress.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/FiniteProgress.java index 2b1f1018..014535ee 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/FiniteProgress.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/FiniteProgress.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * progress suitable as a message for printing to the command line interface. * * @author Arthur Zimek + * @since 0.2 */ public class FiniteProgress extends AbstractProgress { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/IndefiniteProgress.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/IndefiniteProgress.java index eeebf4bb..34969e31 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/IndefiniteProgress.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/IndefiniteProgress.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * Progress class without a fixed destination value. * * @author Erich Schubert + * @since 0.2 */ public class IndefiniteProgress extends AbstractProgress { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/MutableProgress.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/MutableProgress.java index 74f5d4f0..47c426f7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/MutableProgress.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/MutableProgress.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * Progress class with a moving target. * * @author Erich Schubert + * @since 0.2 */ public class MutableProgress extends AbstractProgress { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/Progress.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/Progress.java index 25e5129a..8d41a59d 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/Progress.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/Progress.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.logging.progress; * Generic Progress logging interface. * * @author Erich Schubert + * @since 0.2 */ public interface Progress { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/ProgressLogRecord.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/ProgressLogRecord.java index cea0ecf1..773b4175 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/ProgressLogRecord.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/ProgressLogRecord.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.logging.ELKILogRecord; * Log record for progress messages. * * @author Erich Schubert + * @since 0.3 * * @apiviz.has Progress */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/ProgressTracker.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/ProgressTracker.java index 04f0c430..64e47019 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/ProgressTracker.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/ProgressTracker.java @@ -33,6 +33,7 @@ import java.util.List; * Class to keep track of "alive" progresses. * * @author Erich Schubert + * @since 0.3 * * @apiviz.uses Progress oneway - - tracks */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/StepProgress.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/StepProgress.java index ff01d027..1532bba6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/StepProgress.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/StepProgress.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * This progress class is used for multi-step processing. * * @author Erich Schubert + * @since 0.4.0 */ public class StepProgress extends FiniteProgress { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/AbstractStatistic.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/AbstractStatistic.java index 72b477ed..bcd7d101 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/AbstractStatistic.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/AbstractStatistic.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.logging.statistics; * Abstract base class for statistics tracking. * * @author Erich Schubert + * @since 0.3 */ public abstract class AbstractStatistic implements Statistic { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/AtomicLongCounter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/AtomicLongCounter.java index dfdc9e7f..3e9e88da 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/AtomicLongCounter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/AtomicLongCounter.java @@ -29,6 +29,7 @@ import java.util.concurrent.atomic.AtomicLong; * Class to count events in a thread-safe counter. * * @author Erich Schubert + * @since 0.5.0 */ public class AtomicLongCounter extends AbstractStatistic implements Counter { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/Counter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/Counter.java index 21692d54..91b4fc1d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/Counter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/Counter.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.logging.statistics; * Simple statistic by counting. For example: invocations of a method. * * @author Erich Schubert + * @since 0.2 */ public interface Counter extends Statistic { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/DoubleStatistic.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/DoubleStatistic.java index d3257edd..89b8229e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/DoubleStatistic.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/DoubleStatistic.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.logging.statistics; * Trivial double-valued statistic. * * @author Erich Schubert + * @since 0.5.0 */ public class DoubleStatistic extends AbstractStatistic { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/Duration.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/Duration.java index 1b8769e6..30162d70 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/Duration.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/Duration.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.logging.statistics; * TODO: add support for different time units? * * @author Erich Schubert + * @since 0.2 */ public interface Duration extends Statistic { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/LongStatistic.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/LongStatistic.java index 409b17f6..ffb70f3c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/LongStatistic.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/LongStatistic.java @@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.logging.statistics; This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures - Copyright (C) 2015 + Copyright (C) 2016 Ludwig-Maximilians-Universität München Lehr- und Forschungseinheit für Datenbanksysteme ELKI Development Team @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.logging.statistics; * Trivial long-valued statistic. * * @author Erich Schubert + * @since 0.5.0 */ public class LongStatistic extends AbstractStatistic { /** @@ -63,6 +64,15 @@ public class LongStatistic extends AbstractStatistic { this.value = value; } + /** + * Increment counter. + * + * @param inc Increment + */ + public void increment(long inc) { + this.value += inc; + } + @Override public String formatValue() { return Long.toString(value); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/MillisTimeDuration.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/MillisTimeDuration.java index d6637d52..2a268fd8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/MillisTimeDuration.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/MillisTimeDuration.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.logging.statistics; * Class that tracks the runtime of a task with {@code System.nanoTime()} * * @author Erich Schubert + * @since 0.5.0 */ public class MillisTimeDuration extends AbstractStatistic implements Duration { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/NanoDuration.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/NanoDuration.java index ca09324b..03a9f9eb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/NanoDuration.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/NanoDuration.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.logging.statistics; * Class that tracks the runtime of a task with {@code System.nanoTime()} * * @author Erich Schubert + * @since 0.5.0 */ public class NanoDuration extends AbstractStatistic implements Duration { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/Statistic.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/Statistic.java index 3a826ccf..5a256e24 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/Statistic.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/Statistic.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.logging.statistics; * Abstract base interface for statistics tracking. * * @author Erich Schubert + * @since 0.4.0 */ public interface Statistic { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/StringStatistic.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/StringStatistic.java index af7b12d8..81ec6ff1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/StringStatistic.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/StringStatistic.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.logging.statistics; * Trivial string based statistic. * * @author Erich Schubert + * @since 0.4.0 */ public class StringStatistic extends AbstractStatistic { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/UnsynchronizedLongCounter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/UnsynchronizedLongCounter.java index 69164053..3cd7ee54 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/UnsynchronizedLongCounter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/logging/statistics/UnsynchronizedLongCounter.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.logging.statistics; * Class to count events in a thread-safe counter. * * @author Erich Schubert + * @since 0.5.0 */ public class UnsynchronizedLongCounter extends AbstractStatistic implements Counter { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/DoubleMinMax.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/DoubleMinMax.java index 7fc67833..e65957d8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/DoubleMinMax.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/DoubleMinMax.java @@ -29,6 +29,7 @@ import java.util.Collection; * Class to find the minimum and maximum double values in data. * * @author Erich Schubert + * @since 0.2 */ public class DoubleMinMax { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/IntegerMinMax.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/IntegerMinMax.java index c80b0516..12b83945 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/IntegerMinMax.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/IntegerMinMax.java @@ -30,6 +30,7 @@ import java.util.Collection; * * @author Erich Schubert * @author Arthur Zimek + * @since 0.2 */ public class IntegerMinMax { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/MathUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/MathUtil.java index deb3ed2c..2c9f0301 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/MathUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/MathUtil.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * * @author Arthur Zimek * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark */ @@ -1046,16 +1047,15 @@ public final class MathUtil { return Math.pow(x, p); } double tmp = x, ret = (p & 1) == 1 ? x : 1.; - p >>= 1; while(true) { + tmp *= tmp; + p >>= 1; if(p == 1) { return ret * tmp; } if((p & 1) != 0) { ret *= tmp; } - tmp *= tmp; - p >>= 1; } } @@ -1072,16 +1072,15 @@ public final class MathUtil { return (int) Math.pow(x, p); } int tmp = x, ret = (p & 1) == 1 ? x : 1; - p >>= 1; while(true) { + tmp *= tmp; + p >>= 1; if(p == 1) { return ret * tmp; } if((p & 1) != 0) { ret *= tmp; } - tmp *= tmp; - p >>= 1; } } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/Mean.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/Mean.java index da8bde38..0eb7f3f0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/Mean.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/Mean.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.4.0 */ @Reference(authors = "B. P. Welford", // title = "Note on a method for calculating corrected sums of squares and products", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/MeanVariance.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/MeanVariance.java index 5a1cd7e6..6b5f893d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/MeanVariance.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/MeanVariance.java @@ -56,6 +56,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * </p> * * @author Erich Schubert + * @since 0.2 */ @Reference(authors = "B. P. Welford", // title = "Note on a method for calculating corrected sums of squares and products", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/MeanVarianceMinMax.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/MeanVarianceMinMax.java index fcd96f02..46ad82e0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/MeanVarianceMinMax.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/MeanVarianceMinMax.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * Class collecting mean, variance, minimum and maximum statistics. * * @author Erich Schubert + * @since 0.5.0 */ public class MeanVarianceMinMax extends MeanVariance { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/PearsonCorrelation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/PearsonCorrelation.java index b2821bdd..9bfe38ae 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/PearsonCorrelation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/PearsonCorrelation.java @@ -31,6 +31,7 @@ package de.lmu.ifi.dbs.elki.math; * slightly more memory (by using arrays) but essentially does the same. * * @author Erich Schubert + * @since 0.5.0 */ public class PearsonCorrelation { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/Primes.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/Primes.java index 2a717634..adebf820 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/Primes.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/Primes.java @@ -31,6 +31,7 @@ package de.lmu.ifi.dbs.elki.math; * classes. * * @author Erich Schubert + * @since 0.5.5 */ public final class Primes { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/SinCosTable.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/SinCosTable.java index 842f7152..f224a8b3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/SinCosTable.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/SinCosTable.java @@ -33,6 +33,7 @@ package de.lmu.ifi.dbs.elki.math; * TODO: add caching * * @author Erich Schubert + * @since 0.5.5 */ public abstract class SinCosTable { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/StatisticalMoments.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/StatisticalMoments.java index df188a7f..f9146314 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/StatisticalMoments.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/StatisticalMoments.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * </p> * * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "T. B. Terriberry", title = "Computing Higher-Order Moments Online", booktitle = "Online - Technical Note", url = "http://people.xiph.org/~tterribe/notes/homs.html") public class StatisticalMoments extends MeanVarianceMinMax { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/CovarianceDimensionSimilarity.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/CovarianceDimensionSimilarity.java index 08f4ad86..10c0713e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/CovarianceDimensionSimilarity.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/CovarianceDimensionSimilarity.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Class to compute the dimension similarity based on covariances. * * @author Erich Schubert + * @since 0.5.5 */ public class CovarianceDimensionSimilarity implements DimensionSimilarity<NumberVector> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/DimensionSimilarity.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/DimensionSimilarity.java index 7e772838..1bc08dbe 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/DimensionSimilarity.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/DimensionSimilarity.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * dimensions in parallel coordinate plots. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.uses DimensionSimilarityMatrix - - «writes» * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/DimensionSimilarityMatrix.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/DimensionSimilarityMatrix.java index 89d0d4eb..6e57ad00 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/DimensionSimilarityMatrix.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/DimensionSimilarityMatrix.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Matrix; * Class representing a similarity matrix between dimensions. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.uses PrimsMinimumSpanningTree */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/HSMDimensionSimilarity.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/HSMDimensionSimilarity.java index 4627c785..e4e55b9b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/HSMDimensionSimilarity.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/HSMDimensionSimilarity.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Erich Schubert * @author Robert Rödler + * @since 0.5.5 */ @Reference(authors = "A. Tatu, G. Albuquerque, M. Eisemann, P. Bak, H. Theisel, M. A. Magnor, and D. A. Keim", // title = "Automated Analytical Methods to Support Visual Exploration of High-Dimensional Data", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/HiCSDimensionSimilarity.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/HiCSDimensionSimilarity.java index 1c024fc8..0e0ddcaa 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/HiCSDimensionSimilarity.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/HiCSDimensionSimilarity.java @@ -70,6 +70,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * * @author Erich Schubert * @author Robert Rödler + * @since 0.5.5 */ @Reference(authors = "Elke Achtert, Hans-Peter Kriegel, Erich Schubert, Arthur Zimek", // title = "Interactive Data Mining with 3D-Parallel-Coordinate-Trees", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/MCEDimensionSimilarity.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/MCEDimensionSimilarity.java index 048f960d..88adbf9d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/MCEDimensionSimilarity.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/MCEDimensionSimilarity.java @@ -52,6 +52,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.5.5 */ @Reference(authors = "D. Guo", // title = "Coordinating computational and visual approaches for interactive feature selection and multivariate clustering", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/SURFINGDimensionSimilarity.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/SURFINGDimensionSimilarity.java index d7aa8ca6..4474239c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/SURFINGDimensionSimilarity.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/SURFINGDimensionSimilarity.java @@ -62,6 +62,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Robert Rödler * @author Erich Schubert + * @since 0.5.5 * * @apiviz.uses SubspaceEuclideanDistanceFunction */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/SlopeDimensionSimilarity.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/SlopeDimensionSimilarity.java index eeb7906d..55205fcc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/SlopeDimensionSimilarity.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/SlopeDimensionSimilarity.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Erich Schubert * @author Robert Rödler + * @since 0.5.5 */ @Reference(authors = "Elke Achtert, Hans-Peter Kriegel, Erich Schubert, Arthur Zimek", // title = "Interactive Data Mining with 3D-Parallel-Coordinate-Trees", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/SlopeInversionDimensionSimilarity.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/SlopeInversionDimensionSimilarity.java index 52b73350..aee0a9db 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/SlopeInversionDimensionSimilarity.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/dimensionsimilarity/SlopeInversionDimensionSimilarity.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Erich Schubert * @author Robert Rödler + * @since 0.5.5 */ @Reference(authors = "Elke Achtert, Hans-Peter Kriegel, Erich Schubert, Arthur Zimek", // title = "Interactive Data Mining with 3D-Parallel-Coordinate-Trees", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/AbstractEarthModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/AbstractEarthModel.java index 34652bd4..9122755b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/AbstractEarthModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/AbstractEarthModel.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Abstract base class for earth models with shared glue code. * * @author Erich Schubert + * @since 0.6.0 */ public abstract class AbstractEarthModel implements EarthModel { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/Clarke1858SpheroidEarthModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/Clarke1858SpheroidEarthModel.java index 4bc5560e..186c3c3a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/Clarke1858SpheroidEarthModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/Clarke1858SpheroidEarthModel.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Flattening: 1 / 294.26068 * * @author Erich Schubert + * @since 0.3 */ @Alias({ "Clarke1858" }) public class Clarke1858SpheroidEarthModel extends AbstractEarthModel { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/Clarke1880SpheroidEarthModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/Clarke1880SpheroidEarthModel.java index b204c8c4..ef1a0d2d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/Clarke1880SpheroidEarthModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/Clarke1880SpheroidEarthModel.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Flattening: 1 / 293.465 * * @author Erich Schubert + * @since 0.3 */ @Alias({ "Clarke1880" }) public class Clarke1880SpheroidEarthModel extends AbstractEarthModel { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/EarthModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/EarthModel.java index 332ddf64..8eb697b0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/EarthModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/EarthModel.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; * API for handling different earth models. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses SphereUtil */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/GRS67SpheroidEarthModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/GRS67SpheroidEarthModel.java index d8468a6b..7770933f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/GRS67SpheroidEarthModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/GRS67SpheroidEarthModel.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Flattening: 1 / 298.25 * * @author Erich Schubert + * @since 0.3 */ @Alias({ "GRS67", "GRS-67" }) public class GRS67SpheroidEarthModel extends AbstractEarthModel { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/GRS80SpheroidEarthModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/GRS80SpheroidEarthModel.java index 591dd923..8d9b59a5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/GRS80SpheroidEarthModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/GRS80SpheroidEarthModel.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Flattening: 1 / 298.257222101 * * @author Erich Schubert + * @since 0.3 */ @Alias({ "GRS-80", "GRS80" }) public class GRS80SpheroidEarthModel extends AbstractEarthModel { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphereUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphereUtil.java index 8fcd4d97..98a674f0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphereUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphereUtil.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * * @author Erich Schubert * @author Niels Dörre + * @since 0.5.5 */ @Reference(authors = "Ed Williams", title = "Aviation Formulary", booktitle = "", url = "http://williams.best.vwh.net/avform.htm") public final class SphereUtil { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphericalCosineEarthModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphericalCosineEarthModel.java index c8cc694a..f4b51dca 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphericalCosineEarthModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphericalCosineEarthModel.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * faster but less accurate than the Haversince or Vincenty's formula. * * @author Erich Schubert + * @since 0.6.0 */ public class SphericalCosineEarthModel extends AbstractEarthModel { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphericalHaversineEarthModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphericalHaversineEarthModel.java index db0c39c9..56e581a9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphericalHaversineEarthModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphericalHaversineEarthModel.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * faster but less accurate than Vincenty's formula. * * @author Erich Schubert + * @since 0.6.0 */ public class SphericalHaversineEarthModel extends AbstractEarthModel { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphericalVincentyEarthModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphericalVincentyEarthModel.java index 7f627425..439b8e77 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphericalVincentyEarthModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/SphericalVincentyEarthModel.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * A simple spherical earth model using radius 6371009 m. * * @author Erich Schubert + * @since 0.6.0 */ public class SphericalVincentyEarthModel extends AbstractEarthModel { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/WGS72SpheroidEarthModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/WGS72SpheroidEarthModel.java index 43763328..3a23cf47 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/WGS72SpheroidEarthModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/WGS72SpheroidEarthModel.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Flattening: 1 / 298.26 * * @author Erich Schubert + * @since 0.3 */ @Alias({ "WGS72", "WGS-72" }) public class WGS72SpheroidEarthModel extends AbstractEarthModel { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/WGS84SpheroidEarthModel.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/WGS84SpheroidEarthModel.java index 522e769a..2265353a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/WGS84SpheroidEarthModel.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geodesy/WGS84SpheroidEarthModel.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Flattening: 1 / 298.257223563 * * @author Erich Schubert + * @since 0.3 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/AlphaShape.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/AlphaShape.java index aefb9149..c02efca1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/AlphaShape.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/AlphaShape.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * Compute the alpha-Shape of a point set, using Delaunay triangulation. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.uses SweepHullDelaunay2D * @apiviz.has Polygon diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/GrahamScanConvexHull2D.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/GrahamScanConvexHull2D.java index c3f69807..529ae2fe 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/GrahamScanConvexHull2D.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/GrahamScanConvexHull2D.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * classic Grahams scan. Also computes a bounding box. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has Polygon */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/PrimsMinimumSpanningTree.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/PrimsMinimumSpanningTree.java index 578f7d12..06596cde 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/PrimsMinimumSpanningTree.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/PrimsMinimumSpanningTree.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.composedOf Adapter * @apiviz.composedOf Collector diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/SweepHullDelaunay2D.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/SweepHullDelaunay2D.java index b404ebfb..cb2d498a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/SweepHullDelaunay2D.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/SweepHullDelaunay2D.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.IntIntPair; * Note: This implementation does not check or handle duplicate points! * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.has Polygon */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/XYCurve.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/XYCurve.java index f3af2c8e..8c05e62e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/XYCurve.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/XYCurve.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.DoubleArray; * the curve while adding points. * * @author Erich Schubert + * @since 0.5.0 */ public class XYCurve implements Result, TextWriteable { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/XYPlot.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/XYPlot.java index 412f19ee..76c367ff 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/XYPlot.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/geometry/XYPlot.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.result.Result; * generation. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf Curve */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/AffineTransformation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/AffineTransformation.java index 74b19d2c..e00e3802 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/AffineTransformation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/AffineTransformation.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * transformation. * * @author Erich Schubert + * @since 0.2 * * @apiviz.composedOf Matrix * @apiviz.uses Matrix diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/Centroid.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/Centroid.java index 2e7ba977..dfc0f2a2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/Centroid.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/Centroid.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.database.relation.RelationUtil; * easier to use APIs. * * @author Erich Schubert + * @since 0.4.0 */ public class Centroid extends Vector { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/CholeskyDecomposition.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/CholeskyDecomposition.java index ef0d5ef7..ce0f8ab0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/CholeskyDecomposition.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/CholeskyDecomposition.java @@ -23,7 +23,6 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra; along with this program. If not, see <http://www.gnu.org/licenses/>. */ - /** * Cholesky Decomposition. * <P> @@ -34,6 +33,9 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra; * a partial decomposition and sets an internal flag that may be queried by the * isSPD() method. * + * @author Arthur Zimek + * @since 0.2 + * * @apiviz.uses Matrix - - transforms */ @SuppressWarnings("serial") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/CovarianceMatrix.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/CovarianceMatrix.java index 1e40430f..566e0e11 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/CovarianceMatrix.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/CovarianceMatrix.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.database.relation.RelationUtil; * stabilized covariance matrix builder! * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses Vector oneway * @apiviz.uses NumberVector oneway diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/EigenPair.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/EigenPair.java index f2d6cec3..df4da275 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/EigenPair.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/EigenPair.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.FormatUtil; * eigenvalue. This class is used to sort eigenpairs. * * @author Elke Achtert + * @since 0.2 * * @apiviz.composedOf Matrix */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/EigenvalueDecomposition.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/EigenvalueDecomposition.java index fde453c6..88ab0688 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/EigenvalueDecomposition.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/EigenvalueDecomposition.java @@ -39,7 +39,10 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * the eigenvectors in the sense that A*V = V*D, i.e. A.times(V) equals * V.times(D). The matrix V may be badly conditioned, or even singular, so the * validity of the equation A = V*D*inverse(V) depends upon V.cond(). - * + * + * @author Arthur Zimek + * @since 0.2 + * * @apiviz.uses Matrix - - transforms */ public class EigenvalueDecomposition implements java.io.Serializable { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/LUDecomposition.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/LUDecomposition.java index be33769e..361e315e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/LUDecomposition.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/LUDecomposition.java @@ -36,6 +36,9 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra; * decomposition is in the solution of square systems of simultaneous linear * equations. This will fail if isNonsingular() returns false. * + * @author Arthur Zimek + * @since 0.2 + * * @apiviz.uses Matrix - - transforms */ public class LUDecomposition implements java.io.Serializable { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/LinearEquationSystem.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/LinearEquationSystem.java index da723177..3d273520 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/LinearEquationSystem.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/LinearEquationSystem.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.IntIntPair; * Class for systems of linear equations. * * @author Elke Achtert + * @since 0.2 */ public class LinearEquationSystem { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/Matrix.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/Matrix.java index cb828e50..9f6ecde9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/Matrix.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/Matrix.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.DoubleArray; * * @author Elke Achtert * @author Erich Schubert + * @since 0.2 * * @apiviz.uses Vector * @apiviz.landmark diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/ProjectedCentroid.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/ProjectedCentroid.java index cc850ce4..b519ca9e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/ProjectedCentroid.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/ProjectedCentroid.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * easier to use APIs. * * @author Erich Schubert + * @since 0.4.0 */ public class ProjectedCentroid extends Centroid { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/ProjectionResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/ProjectionResult.java index ca1c05c2..67958078 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/ProjectionResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/ProjectionResult.java @@ -30,6 +30,7 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra; * This can either come from a full PCA, or just from an axis-parallel subspace selection * * @author Erich Schubert + * @since 0.4.0 */ // TODO: cleanup public interface ProjectionResult { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/QRDecomposition.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/QRDecomposition.java index 541987e7..be07df37 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/QRDecomposition.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/QRDecomposition.java @@ -36,6 +36,9 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * decomposition is in the least squares solution of nonsquare systems of * simultaneous linear equations. This will fail if isFullRank() returns false. * + * @author Arthur Zimek + * @since 0.2 + * * @apiviz.uses Matrix - - transforms */ public class QRDecomposition implements java.io.Serializable { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/SingularValueDecomposition.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/SingularValueDecomposition.java index 6b311ed1..2514acc6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/SingularValueDecomposition.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/SingularValueDecomposition.java @@ -39,6 +39,9 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * fail. The matrix condition number and the effective numerical rank can be * computed from this decomposition. * + * @author Arthur Zimek + * @since 0.2 + * * @apiviz.uses Matrix - - transforms */ public class SingularValueDecomposition { @@ -326,7 +329,7 @@ public class SingularValueDecomposition { // Perform the task indicated by kase. switch(kase){ - + // Deflate negligible s(p). case 1: { double f = e[p - 2]; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/SortedEigenPairs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/SortedEigenPairs.java index a4cca9de..e028793c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/SortedEigenPairs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/SortedEigenPairs.java @@ -33,6 +33,7 @@ import java.util.List; * eigenvectors (and -values). * * @author Elke Achtert + * @since 0.2 * * @apiviz.composedOf de.lmu.ifi.dbs.elki.math.linearalgebra.EigenPair */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/VMath.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/VMath.java index a6d4ea77..31456eff 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/VMath.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/VMath.java @@ -31,6 +31,7 @@ import java.util.Arrays; * usage and VM overhead. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/Vector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/Vector.java index 06198e4a..80e7e219 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/Vector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/Vector.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferSerializer; * A mathematical vector object, along with mathematical operations. * * @author Elke Achtert + * @since 0.2 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/FittingFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/FittingFunction.java index a0da0c7b..13aa185a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/FittingFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/FittingFunction.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra.fitting; * Interface for a function used in Levenberg-Marquard-Fitting * * @author Erich Schubert + * @since 0.2 */ public interface FittingFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/FittingFunctionResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/FittingFunctionResult.java index bf17e4c3..52f340a8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/FittingFunctionResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/FittingFunctionResult.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra.fitting; * Result returned by a fitting function. * * @author Erich Schubert + * @since 0.2 */ public class FittingFunctionResult { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/GaussianFittingFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/GaussianFittingFunction.java index 6cdcff18..7d12cdff 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/GaussianFittingFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/GaussianFittingFunction.java @@ -58,6 +58,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * number of parameters (which obviously needs to be a multiple of 3) * * @author Erich Schubert + * @since 0.2 */ public class GaussianFittingFunction implements FittingFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/LevenbergMarquardtMethod.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/LevenbergMarquardtMethod.java index b77f3b79..0ca9a643 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/LevenbergMarquardtMethod.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/fitting/LevenbergMarquardtMethod.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.LinearEquationSystem; * Which supposedly offers increased robustness. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has FittingFunction * @apiviz.uses FittingFunctionResult oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/AbstractCovarianceMatrixBuilder.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/AbstractCovarianceMatrixBuilder.java index 8190eea5..3874b91b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/AbstractCovarianceMatrixBuilder.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/AbstractCovarianceMatrixBuilder.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Matrix; * Mostly the specification of an interface. * * @author Erich Schubert + * @since 0.2 */ public abstract class AbstractCovarianceMatrixBuilder implements CovarianceMatrixBuilder { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/CompositeEigenPairFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/CompositeEigenPairFilter.java index c56217f8..bd88dcb8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/CompositeEigenPairFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/CompositeEigenPairFilter.java @@ -36,15 +36,11 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectListParamet * eigenpair filters. * * @author Elke Achtert + * @since 0.2 */ // todo parameter comments public class CompositeEigenPairFilter implements EigenPairFilter { /** - * The list of filters to use. - */ - public static final OptionID EIGENPAIR_FILTER_COMPOSITE_LIST = new OptionID("pca.filter.composite.list", "A comma separated list of the class names of the filters to be used. " + "The specified filters will be applied sequentially in the given order."); - - /** * The filters to be applied. */ private List<EigenPairFilter> filters; @@ -86,6 +82,10 @@ public class CompositeEigenPairFilter implements EigenPairFilter { */ public static class Parameterizer extends AbstractParameterizer { /** + * The list of filters to use. + */ + public static final OptionID EIGENPAIR_FILTER_COMPOSITE_LIST = new OptionID("pca.filter.composite.list", "A comma separated list of the class names of the filters to be used. " + "The specified filters will be applied sequentially in the given order."); + /** * The filters to be applied. */ private List<EigenPairFilter> filters = null; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/CovarianceMatrixBuilder.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/CovarianceMatrixBuilder.java index e3d10297..c2b40a85 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/CovarianceMatrixBuilder.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/CovarianceMatrixBuilder.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Matrix; * Interface for computing covariance matrixes on a data set. * * @author Erich Schubert + * @since 0.2 */ public interface CovarianceMatrixBuilder { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/DropEigenPairFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/DropEigenPairFilter.java index 7d642b86..40a171df 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/DropEigenPairFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/DropEigenPairFilter.java @@ -37,16 +37,17 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; /** * The "drop" filter looks for the largest drop in normalized relative * eigenvalues. - * + * * Let s_1 .. s_n be the eigenvalues. - * + * * Let a_k := 1/(n-k) sum_{i=k..n} s_i - * + * * Then r_k := s_k / a_k is the relative eigenvalue. - * + * * The drop filter searches for argmax_k r_k / r_{k+1} - * + * * @author Erich Schubert + * @since 0.2 */ @Title("Drop EigenPair Filter") public class DropEigenPairFilter implements EigenPairFilter { @@ -63,7 +64,7 @@ public class DropEigenPairFilter implements EigenPairFilter { /** * Constructor. - * + * * @param walpha */ public DropEigenPairFilter(double walpha) { @@ -121,9 +122,9 @@ public class DropEigenPairFilter implements EigenPairFilter { /** * Parameterization class. - * + * * @author Erich Schubert - * + * * @apiviz.exclude */ public static class Parameterizer extends AbstractParameterizer { @@ -132,7 +133,7 @@ public class DropEigenPairFilter implements EigenPairFilter { @Override protected void makeOptions(Parameterization config) { super.makeOptions(config); - DoubleParameter walphaP = new DoubleParameter(WeakEigenPairFilter.EIGENPAIR_FILTER_WALPHA, DEFAULT_WALPHA); + DoubleParameter walphaP = new DoubleParameter(WeakEigenPairFilter.Parameterizer.EIGENPAIR_FILTER_WALPHA, DEFAULT_WALPHA); walphaP.addConstraint(CommonConstraints.GREATER_EQUAL_ZERO_DOUBLE); if (config.grab(walphaP)) { walpha = walphaP.getValue(); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/EigenPairFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/EigenPairFilter.java index b0a244f6..7b3886e5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/EigenPairFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/EigenPairFilter.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.SortedEigenPairs; * and weak eigenpairs having small variances. * * @author Elke Achtert + * @since 0.2 * * @apiviz.uses SortedEigenPairs oneway - - reads * @apiviz.uses FilteredEigenPairs oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/FilteredEigenPairs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/FilteredEigenPairs.java index b8343a24..fcc09c7c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/FilteredEigenPairs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/FilteredEigenPairs.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.EigenPair; * by an eigenpair filter. * * @author Elke Achtert + * @since 0.2 * * @apiviz.has EigenPair */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/FirstNEigenPairFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/FirstNEigenPairFilter.java index d2251f28..ca7d288e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/FirstNEigenPairFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/FirstNEigenPairFilter.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * eigenpairs, where n is a user specified number. * * @author Elke Achtert + * @since 0.2 */ // todo parameter comments @Title("First n Eigenpair filter") @@ -53,11 +54,6 @@ public class FirstNEigenPairFilter implements EigenPairFilter { private static final Logging LOG = Logging.getLogger(FirstNEigenPairFilter.class); /** - * Paremeter n - */ - public static final OptionID EIGENPAIR_FILTER_N = new OptionID("pca.filter.n", "The number of strong eigenvectors: n eigenvectors with the n highest" + "eigenvalues are marked as strong eigenvectors."); - - /** * The threshold for strong eigenvectors: n eigenvectors with the n highest * eigenvalues are marked as strong eigenvectors. */ @@ -114,6 +110,10 @@ public class FirstNEigenPairFilter implements EigenPairFilter { */ public static class Parameterizer extends AbstractParameterizer { /** + * Paremeter n + */ + public static final OptionID EIGENPAIR_FILTER_N = new OptionID("pca.filter.n", "The number of strong eigenvectors: n eigenvectors with the n highest" + "eigenvalues are marked as strong eigenvectors."); + /** * The number of eigenpairs to keep. */ protected int n = 0; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/LimitEigenPairFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/LimitEigenPairFilter.java index 779ceb2e..a4047473 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/LimitEigenPairFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/LimitEigenPairFilter.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; * others are marked as strong eigenpairs. * * @author Elke Achtert + * @since 0.2 */ @Title("Limit-based Eigenpair Filter") @Description("Filters all eigenpairs, which are lower than a given value.") @@ -58,16 +59,6 @@ public class LimitEigenPairFilter implements EigenPairFilter { private static final Logging LOG = Logging.getLogger(LimitEigenPairFilter.class); /** - * "absolute" Flag - */ - public static final OptionID EIGENPAIR_FILTER_ABSOLUTE = new OptionID("pca.filter.absolute", "Flag to mark delta as an absolute value."); - - /** - * Parameter delta - */ - public static final OptionID EIGENPAIR_FILTER_DELTA = new OptionID("pca.filter.delta", "The threshold for strong Eigenvalues. If not otherwise specified, delta " + "is a relative value w.r.t. the (absolute) highest Eigenvalues and has to be " + "a double between 0 and 1. To mark delta as an absolute value, use " + "the option -" + EIGENPAIR_FILTER_ABSOLUTE.getName() + "."); - - /** * The default value for delta. */ public static final double DEFAULT_DELTA = 0.01; @@ -154,6 +145,16 @@ public class LimitEigenPairFilter implements EigenPairFilter { */ public static class Parameterizer extends AbstractParameterizer { /** + * "absolute" Flag + */ + public static final OptionID EIGENPAIR_FILTER_ABSOLUTE = new OptionID("pca.filter.absolute", "Flag to mark delta as an absolute value."); + + /** + * Parameter delta + */ + public static final OptionID EIGENPAIR_FILTER_DELTA = new OptionID("pca.filter.delta", "The threshold for strong Eigenvalues. If not otherwise specified, delta " + "is a relative value w.r.t. the (absolute) highest Eigenvalues and has to be " + "a double between 0 and 1. To mark delta as an absolute value, use " + "the option -" + EIGENPAIR_FILTER_ABSOLUTE.getName() + "."); + + /** * Threshold for strong eigenpairs, can be absolute or relative. */ private double delta; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/NormalizingEigenPairFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/NormalizingEigenPairFilter.java index fb95a68c..9f77f747 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/NormalizingEigenPairFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/NormalizingEigenPairFilter.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Title; * eigenvector> * eigenvalue = 1, where <,> is the standard dot product * * @author Simon Paradies + * @since 0.2 */ @Title("Perecentage based Eigenpair filter") @Description("Normalizes all eigenpairs, consisting of eigenvalue e and eigenvector v such that <v,v> * e = 1, where <,> is the standard dot product.") diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAFilteredAutotuningRunner.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAFilteredAutotuningRunner.java index 600fcf95..4abd1c6d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAFilteredAutotuningRunner.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAFilteredAutotuningRunner.java @@ -55,6 +55,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * exhibit the clearest correlation. * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "Hans-Peter Kriegel, Peer Kröger, Erich Schubert, Arthur Zimek", // title = "A General Framework for Increasing the Robustness of PCA-based Correlation Clustering Algorithms",// diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAFilteredResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAFilteredResult.java index f7ec9e79..1b7d6910 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAFilteredResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAFilteredResult.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.SortedEigenPairs; * subspace and an "error" subspace. * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAFilteredRunner.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAFilteredRunner.java index e7c31cf6..d61c7830 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAFilteredRunner.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAFilteredRunner.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * regular runner, but afterwards, an {@link EigenPairFilter} is applied. * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * @apiviz.has PCAFilteredResult oneway - - «create» diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAResult.java index 4c0de355..72268972 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCAResult.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.SortedEigenPairs; * Result class for Principal Component Analysis with some convenience methods * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * @apiviz.has SortedEigenPairs diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCARunner.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCARunner.java index bdd4f32f..c4195506 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCARunner.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PCARunner.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * to a weighted covariance matrix builder) * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * @apiviz.uses PCAResult oneway - - «create» @@ -53,18 +54,6 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; */ public class PCARunner { /** - * Parameter to specify the class to compute the covariance matrix, must be a - * subclass of {@link CovarianceMatrixBuilder}. - * <p> - * Default value: {@link CovarianceMatrixBuilder} - * </p> - * <p> - * Key: {@code -pca.covariance} - * </p> - */ - public static final OptionID PCA_COVARIANCE_MATRIX = new OptionID("pca.covariance", "Class used to compute the covariance matrix."); - - /** * The covariance computation class. */ protected CovarianceMatrixBuilder covarianceMatrixBuilder; @@ -161,6 +150,17 @@ public class PCARunner { */ public static class Parameterizer extends AbstractParameterizer { /** + * Parameter to specify the class to compute the covariance matrix, must be a + * subclass of {@link CovarianceMatrixBuilder}. + * <p> + * Default value: {@link CovarianceMatrixBuilder} + * </p> + * <p> + * Key: {@code -pca.covariance} + * </p> + */ + public static final OptionID PCA_COVARIANCE_MATRIX = new OptionID("pca.covariance", "Class used to compute the covariance matrix."); + /** * The covariance computation class. */ protected CovarianceMatrixBuilder covarianceMatrixBuilder; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PercentageEigenPairFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PercentageEigenPairFilter.java index c32ad6fc..8b445b97 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PercentageEigenPairFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/PercentageEigenPairFilter.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * eigenpairs. * * @author Elke Achtert + * @since 0.2 */ @Title("Percentage based Eigenpair filter") @Description("Sorts the eigenpairs in decending order of their eigenvalues and returns the first eigenpairs, whose sum of eigenvalues is higher than the given percentage of the sum of all eigenvalues.") @@ -54,18 +55,6 @@ public class PercentageEigenPairFilter implements EigenPairFilter { private static final Logging LOG = Logging.getLogger(PercentageEigenPairFilter.class); /** - * The threshold for 'strong' eigenvectors: the 'strong' eigenvectors explain - * a portion of at least alpha of the total variance. - * <p> - * Default value: {@link #DEFAULT_ALPHA} - * </p> - * <p> - * Key: {@code -pca.filter.alpha} - * </p> - */ - public static final OptionID ALPHA_ID = new OptionID("pca.filter.alpha", "The share (0.0 to 1.0) of variance that needs to be explained by the 'strong' eigenvectors." + "The filter class will choose the number of strong eigenvectors by this share."); - - /** * The default value for alpha. */ public static final double DEFAULT_ALPHA = 0.85; @@ -145,6 +134,17 @@ public class PercentageEigenPairFilter implements EigenPairFilter { */ public static class Parameterizer extends AbstractParameterizer { /** + * The threshold for 'strong' eigenvectors: the 'strong' eigenvectors explain + * a portion of at least alpha of the total variance. + * <p> + * Default value: {@link #DEFAULT_ALPHA} + * </p> + * <p> + * Key: {@code -pca.filter.alpha} + * </p> + */ + public static final OptionID ALPHA_ID = new OptionID("pca.filter.alpha", "The share (0.0 to 1.0) of variance that needs to be explained by the 'strong' eigenvectors." + "The filter class will choose the number of strong eigenvectors by this share."); + /** * The threshold for strong eigenvectors: the strong eigenvectors explain a * portion of at least alpha of the total variance. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/ProgressiveEigenPairFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/ProgressiveEigenPairFilter.java index 16b6d72e..242c00f4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/ProgressiveEigenPairFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/ProgressiveEigenPairFilter.java @@ -46,48 +46,44 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * gives better results when clusters of different dimensionality exist, since * different percentage alpha levels might be appropriate for different * dimensionalities. - * + * * Example calculations of alpha levels: - * + * * In a 3D space, a progressive alpha value of 0.5 equals: - * + * * - 1D subspace: 50 % + 1/3 of remainder = 0.667 - * + * * - 2D subspace: 50 % + 2/3 of remainder = 0.833 - * + * * In a 4D space, a progressive alpha value of 0.5 equals: - * + * * - 1D subspace: 50% + 1/4 of remainder = 0.625 - * + * * - 2D subspace: 50% + 2/4 of remainder = 0.750 - * + * * - 3D subspace: 50% + 3/4 of remainder = 0.875 - * + * * Reasoning why this improves over PercentageEigenPairFilter: - * + * * In a 100 dimensional space, a single Eigenvector representing over 85% of the * total variance is highly significant, whereas the strongest 85 Eigenvectors * together will by definition always represent at least 85% of the variance. * PercentageEigenPairFilter can thus not be used with these parameters and * detect both dimensionalities correctly. - * + * * The second parameter introduced here, walpha, serves a different function: It * prevents the eigenpair filter to use a statistically weak Eigenvalue just to * reach the intended level, e.g. 84% + 1% >= 85% when 1% is statistically very * weak. - * + * * @author Erich Schubert - * + * @since 0.2 + * */ @Title("Progressive Eigenpair Filter") @Description("Sorts the eigenpairs in decending order of their eigenvalues and returns the first eigenpairs, whose sum of eigenvalues explains more than the a certain percentage of the unexpected variance, where the percentage increases with subspace dimensionality.") public class ProgressiveEigenPairFilter implements EigenPairFilter { /** - * Parameter progressive alpha. - */ - public static final OptionID EIGENPAIR_FILTER_PALPHA = new OptionID("pca.filter.progressivealpha", "The share (0.0 to 1.0) of variance that needs to be explained by the 'strong' eigenvectors." + "The filter class will choose the number of strong eigenvectors by this share."); - - /** * The default value for alpha. */ public static final double DEFAULT_PALPHA = 0.5; @@ -110,7 +106,7 @@ public class ProgressiveEigenPairFilter implements EigenPairFilter { /** * Constructor. - * + * * @param palpha palpha * @param walpha walpha */ @@ -177,13 +173,18 @@ public class ProgressiveEigenPairFilter implements EigenPairFilter { /** * Parameterization class. - * + * * @author Erich Schubert - * + * * @apiviz.exclude */ public static class Parameterizer extends AbstractParameterizer { /** + * Parameter progressive alpha. + */ + public static final OptionID EIGENPAIR_FILTER_PALPHA = new OptionID("pca.filter.progressivealpha", "The share (0.0 to 1.0) of variance that needs to be explained by the 'strong' eigenvectors." + "The filter class will choose the number of strong eigenvectors by this share."); + + /** * The threshold for strong eigenvectors: the strong eigenvectors explain a * portion of at least alpha of the total variance. */ @@ -204,7 +205,7 @@ public class ProgressiveEigenPairFilter implements EigenPairFilter { palpha = palphaP.getValue(); } - DoubleParameter walphaP = new DoubleParameter(WeakEigenPairFilter.EIGENPAIR_FILTER_WALPHA, DEFAULT_WALPHA); + DoubleParameter walphaP = new DoubleParameter(WeakEigenPairFilter.Parameterizer.EIGENPAIR_FILTER_WALPHA, DEFAULT_WALPHA); walphaP.addConstraint(CommonConstraints.GREATER_EQUAL_ZERO_DOUBLE); if(config.grab(walphaP)) { walpha = walphaP.getValue(); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/RANSACCovarianceMatrixBuilder.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/RANSACCovarianceMatrixBuilder.java index 291f91b6..5553936b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/RANSACCovarianceMatrixBuilder.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/RANSACCovarianceMatrixBuilder.java @@ -74,6 +74,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * </p> * * @author Erich Schubert + * @since 0.5.5 */ @Reference(authors = "Hans-Peter Kriegel, Peer Kröger, Erich Schubert, Arthur Zimek", // title = "Outlier Detection in Arbitrarily Oriented Subspaces", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/RelativeEigenPairFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/RelativeEigenPairFilter.java index 54361c4f..3011a7d8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/RelativeEigenPairFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/RelativeEigenPairFilter.java @@ -50,16 +50,12 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * dimensionalities. * * @author Erich Schubert + * @since 0.2 */ @Title("Relative EigenPair Filter") @Description("Sorts the eigenpairs in decending order of their eigenvalues and returns those eigenpairs, whose eigenvalue is " + "above the average ('expected') eigenvalue of the remaining eigenvectors.") public class RelativeEigenPairFilter implements EigenPairFilter { /** - * Parameter relative alpha. - */ - public static final OptionID EIGENPAIR_FILTER_RALPHA = new OptionID("pca.filter.relativealpha", "The sensitivity niveau for weak eigenvectors: An eigenvector which is at less than " + "the given share of the statistical average variance is considered weak."); - - /** * The default value for ralpha. */ public static final double DEFAULT_RALPHA = 1.1; @@ -123,6 +119,10 @@ public class RelativeEigenPairFilter implements EigenPairFilter { * @apiviz.exclude */ public static class Parameterizer extends AbstractParameterizer { + /** + * Parameter relative alpha. + */ + public static final OptionID EIGENPAIR_FILTER_RALPHA = new OptionID("pca.filter.relativealpha", "The sensitivity niveau for weak eigenvectors: An eigenvector which is at less than " + "the given share of the statistical average variance is considered weak."); protected double ralpha; @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/SignificantEigenPairFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/SignificantEigenPairFilter.java index dfc5347d..64dac360 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/SignificantEigenPairFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/SignificantEigenPairFilter.java @@ -39,18 +39,19 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * The SignificantEigenPairFilter sorts the eigenpairs in descending order of * their eigenvalues and chooses the contrast of an Eigenvalue to the remaining * Eigenvalues is maximal. - * + * * It is closely related to the WeakEigenPairFilter and RelativeEigenPairFilter. * But while the RelativeEigenPairFilter chooses the highest dimensionality that * satisfies the relative alpha levels, the SignificantEigenPairFilter will * chose the local dimensionality such that the 'contrast' is maximal. - * + * * There are some situations where one or the other is superior, especially when * it comes to handling nested clusters and strong global correlations that are * not too interesting. These benefits usually only make a difference at higher * dimensionalities. - * + * * @author Erich Schubert + * @since 0.2 */ @Title("Significant EigenPair Filter") @Description("Sorts the eigenpairs in decending order of their eigenvalues and looks for the maxmimum contrast of current Eigenvalue / average of remaining Eigenvalues.") @@ -68,7 +69,7 @@ public class SignificantEigenPairFilter implements EigenPairFilter { /** * Constructor. - * + * * @param walpha */ public SignificantEigenPairFilter(double walpha) { @@ -122,9 +123,9 @@ public class SignificantEigenPairFilter implements EigenPairFilter { /** * Parameterization class. - * + * * @author Erich Schubert - * + * * @apiviz.exclude */ public static class Parameterizer extends AbstractParameterizer { @@ -133,7 +134,7 @@ public class SignificantEigenPairFilter implements EigenPairFilter { @Override protected void makeOptions(Parameterization config) { super.makeOptions(config); - DoubleParameter walphaP = new DoubleParameter(WeakEigenPairFilter.EIGENPAIR_FILTER_WALPHA, DEFAULT_WALPHA); + DoubleParameter walphaP = new DoubleParameter(WeakEigenPairFilter.Parameterizer.EIGENPAIR_FILTER_WALPHA, DEFAULT_WALPHA); walphaP.addConstraint(CommonConstraints.GREATER_EQUAL_ZERO_DOUBLE); if(config.grab(walphaP)) { walpha = walphaP.getValue(); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/StandardCovarianceMatrixBuilder.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/StandardCovarianceMatrixBuilder.java index 677a88eb..ea1a6787 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/StandardCovarianceMatrixBuilder.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/StandardCovarianceMatrixBuilder.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Matrix; * Reasonable default choice for a {@link CovarianceMatrixBuilder} * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses CovarianceMatrix */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/WeakEigenPairFilter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/WeakEigenPairFilter.java index 51d89450..8f76531e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/WeakEigenPairFilter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/WeakEigenPairFilter.java @@ -42,19 +42,12 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * as "strong", the others as "weak". * * @author Erich Schubert + * @since 0.2 */ @Title("Weak Eigenpair Filter") @Description("Sorts the eigenpairs in decending order of their eigenvalues and returns those eigenpairs, whose eigenvalue is above the average ('expected') eigenvalue.") public class WeakEigenPairFilter implements EigenPairFilter { /** - * OptionID for the weak alpha value of {@link WeakEigenPairFilter}, - * {@link de.lmu.ifi.dbs.elki.math.linearalgebra.pca.ProgressiveEigenPairFilter} - * and - * {@link de.lmu.ifi.dbs.elki.math.linearalgebra.pca.SignificantEigenPairFilter} - */ - public static final OptionID EIGENPAIR_FILTER_WALPHA = new OptionID("pca.filter.weakalpha", "The minimum strength of the statistically expected variance (1/n) share an eigenvector " + "needs to have to be considered 'strong'."); - - /** * The default value for walpha. */ public static final double DEFAULT_WALPHA = 0.95; @@ -119,6 +112,13 @@ public class WeakEigenPairFilter implements EigenPairFilter { */ public static class Parameterizer extends AbstractParameterizer { /** + * OptionID for the weak alpha value of {@link WeakEigenPairFilter}, + * {@link de.lmu.ifi.dbs.elki.math.linearalgebra.pca.ProgressiveEigenPairFilter} + * and + * {@link de.lmu.ifi.dbs.elki.math.linearalgebra.pca.SignificantEigenPairFilter} + */ + public static final OptionID EIGENPAIR_FILTER_WALPHA = new OptionID("pca.filter.weakalpha", "The minimum strength of the statistically expected variance (1/n) share an eigenvector " + "needs to have to be considered 'strong'."); + /** * The threshold for strong eigenvectors: the strong eigenvectors explain a * portion of at least alpha of the total variance. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/WeightedCovarianceMatrixBuilder.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/WeightedCovarianceMatrixBuilder.java index a5b7d545..eba61671 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/WeightedCovarianceMatrixBuilder.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/WeightedCovarianceMatrixBuilder.java @@ -60,6 +60,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Computer Science 5069, Springer * * @author Erich Schubert + * @since 0.2 * * @apiviz.has WeightFunction * @apiviz.has PrimitiveDistanceFunction @@ -73,17 +74,6 @@ booktitle = "Proceedings of the 20th International Conference on Scientific and url = "http://dx.doi.org/10.1007/978-3-540-69497-7_27") public class WeightedCovarianceMatrixBuilder extends AbstractCovarianceMatrixBuilder { /** - * Parameter to specify the weight function to use in weighted PCA, must - * implement - * {@link de.lmu.ifi.dbs.elki.math.linearalgebra.pca.weightfunctions.WeightFunction} - * . - * <p> - * Key: {@code -pca.weight} - * </p> - */ - public static final OptionID WEIGHT_ID = new OptionID("pca.weight", "Weight function to use in weighted PCA."); - - /** * Holds the weight function. */ protected WeightFunction weightfunction; @@ -205,6 +195,16 @@ public class WeightedCovarianceMatrixBuilder extends AbstractCovarianceMatrixBui */ public static class Parameterizer extends AbstractParameterizer { /** + * Parameter to specify the weight function to use in weighted PCA, must + * implement + * {@link de.lmu.ifi.dbs.elki.math.linearalgebra.pca.weightfunctions.WeightFunction} + * . + * <p> + * Key: {@code -pca.weight} + * </p> + */ + public static final OptionID WEIGHT_ID = new OptionID("pca.weight", "Weight function to use in weighted PCA."); + /** * Weight function. */ protected WeightFunction weightfunction = null; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ConstantWeight.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ConstantWeight.java index 693cdb2e..71ae52ed 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ConstantWeight.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ConstantWeight.java @@ -30,6 +30,7 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra.pca.weightfunctions; * The result is always 1.0 * * @author Erich Schubert + * @since 0.2 */ public final class ConstantWeight implements WeightFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ErfcStddevWeight.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ErfcStddevWeight.java index 03423603..76e24d18 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ErfcStddevWeight.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ErfcStddevWeight.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.math.statistics.distribution.NormalDistribution; * erfc(1 / sqrt(2) * distance / stddev) * * @author Erich Schubert + * @since 0.2 */ public final class ErfcStddevWeight implements WeightFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ErfcWeight.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ErfcWeight.java index b7bc1c67..11acb0af 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ErfcWeight.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ErfcWeight.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.math.statistics.distribution.NormalDistribution; * scaling. * * @author Erich Schubert + * @since 0.2 */ public final class ErfcWeight implements WeightFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ExponentialStddevWeight.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ExponentialStddevWeight.java index 3b265d47..fce17896 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ExponentialStddevWeight.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ExponentialStddevWeight.java @@ -34,6 +34,7 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra.pca.weightfunctions; * not squared. * * @author Erich Schubert + * @since 0.2 */ public final class ExponentialStddevWeight implements WeightFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ExponentialWeight.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ExponentialWeight.java index c67e35d7..c45d5cac 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ExponentialWeight.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/ExponentialWeight.java @@ -36,6 +36,7 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra.pca.weightfunctions; * -2.3025850929940455 is log(-.1) to achieve the intended range of 1.0 - 0.1 * * @author Erich Schubert + * @since 0.2 */ public final class ExponentialWeight implements WeightFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/GaussStddevWeight.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/GaussStddevWeight.java index bf78b576..d8f67639 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/GaussStddevWeight.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/GaussStddevWeight.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * with factor being 1 / sqrt(2 * PI) * * @author Erich Schubert + * @since 0.2 */ public final class GaussStddevWeight implements WeightFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/GaussWeight.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/GaussWeight.java index fcad89a3..70826d0e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/GaussWeight.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/GaussWeight.java @@ -31,6 +31,7 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra.pca.weightfunctions; * exp(-2.3025850929940455 * (distance/max)^2) * * @author Erich Schubert + * @since 0.2 */ public final class GaussWeight implements WeightFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/InverseLinearWeight.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/InverseLinearWeight.java index 3fb8e9e0..f2c27d5a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/InverseLinearWeight.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/InverseLinearWeight.java @@ -33,6 +33,7 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra.pca.weightfunctions; * This function has increasing weight, from 0.1 to 1.0 at distance == max. * * @author Erich Schubert + * @since 0.2 */ public final class InverseLinearWeight implements WeightFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/InverseProportionalStddevWeight.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/InverseProportionalStddevWeight.java index a4d4a28e..952e7a56 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/InverseProportionalStddevWeight.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/InverseProportionalStddevWeight.java @@ -30,6 +30,7 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra.pca.weightfunctions; * 1 / (1 + distance/stddev) * * @author Erich Schubert + * @since 0.2 */ public final class InverseProportionalStddevWeight implements WeightFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/InverseProportionalWeight.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/InverseProportionalWeight.java index fb1d71ba..810d17a9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/InverseProportionalWeight.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/InverseProportionalWeight.java @@ -30,6 +30,7 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra.pca.weightfunctions; * 1 / (1 + distance/max) * * @author Erich Schubert + * @since 0.2 */ public final class InverseProportionalWeight implements WeightFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/LinearWeight.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/LinearWeight.java index a37617b5..bc92660e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/LinearWeight.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/LinearWeight.java @@ -31,6 +31,7 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra.pca.weightfunctions; * 1 - 0.9 * (distance/max) * * @author Erich Schubert + * @since 0.2 */ public final class LinearWeight implements WeightFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/QuadraticStddevWeight.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/QuadraticStddevWeight.java index e35e9a67..c02d78f1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/QuadraticStddevWeight.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/QuadraticStddevWeight.java @@ -33,6 +33,7 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra.pca.weightfunctions; * max(0.0, 1.0 - (distance/(3*stddev))^2 * * @author Erich Schubert + * @since 0.2 */ public final class QuadraticStddevWeight implements WeightFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/QuadraticWeight.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/QuadraticWeight.java index 87bd552b..d764ef08 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/QuadraticWeight.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/QuadraticWeight.java @@ -31,6 +31,7 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra.pca.weightfunctions; * 1.0 - 0.9 * (distance/max)^2 * * @author Erich Schubert + * @since 0.2 */ public final class QuadraticWeight implements WeightFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/WeightFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/WeightFunction.java index 49bced02..afc04fb9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/WeightFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/WeightFunction.java @@ -30,6 +30,7 @@ package de.lmu.ifi.dbs.elki.math.linearalgebra.pca.weightfunctions; * normalized according to the maximum or standard deviation. * * @author Erich Schubert + * @since 0.2 */ public interface WeightFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/AbstractRandomProjectionFamily.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/AbstractRandomProjectionFamily.java index 00597ac2..7ce235de 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/AbstractRandomProjectionFamily.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/AbstractRandomProjectionFamily.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * Abstract base class for random projection families. * * @author Erich Schubert + * @since 0.3 */ public abstract class AbstractRandomProjectionFamily implements RandomProjectionFamily { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/AchlioptasRandomProjectionFamily.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/AchlioptasRandomProjectionFamily.java index e3504419..4c74bbfb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/AchlioptasRandomProjectionFamily.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/AchlioptasRandomProjectionFamily.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * TODO: faster implementation exploiting sparsity. * * @author Erich Schubert + * @since 0.6.0 */ @Reference(title = "Database-friendly random projections: Johnson-Lindenstrauss with binary coins", // authors = "D. Achlioptas", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/CauchyRandomProjectionFamily.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/CauchyRandomProjectionFamily.java index 699478ac..47fddeab 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/CauchyRandomProjectionFamily.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/CauchyRandomProjectionFamily.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "M. Datar and N. Immorlica and P. Indyk and V. S. Mirrokni", // title = "Locality-sensitive hashing scheme based on p-stable distributions", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/GaussianRandomProjectionFamily.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/GaussianRandomProjectionFamily.java index facfe427..e5277d5e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/GaussianRandomProjectionFamily.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/GaussianRandomProjectionFamily.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "M. Datar and N. Immorlica and P. Indyk and V. S. Mirrokni", // title = "Locality-sensitive hashing scheme based on p-stable distributions", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/RandomProjectionFamily.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/RandomProjectionFamily.java index 95a59276..e97e32f6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/RandomProjectionFamily.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/RandomProjectionFamily.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.data.NumberVector; * Interface for random projection families. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has Projection */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/RandomSubsetProjectionFamily.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/RandomSubsetProjectionFamily.java index dae7e0cb..15ecfec4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/RandomSubsetProjectionFamily.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/RandomSubsetProjectionFamily.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "L. Breiman", // title = "Bagging predictors", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/SimplifiedRandomHyperplaneProjectionFamily.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/SimplifiedRandomHyperplaneProjectionFamily.java index 5a505f66..3916659a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/SimplifiedRandomHyperplaneProjectionFamily.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/randomprojections/SimplifiedRandomHyperplaneProjectionFamily.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * * @author Evgeniy Faerman * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "M. Henzinger", // title = "Finding near-duplicate web pages: a large-scale evaluation of algorithms", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/FastNonThreadsafeRandom.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/FastNonThreadsafeRandom.java index 72f6be0b..a3632102 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/FastNonThreadsafeRandom.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/FastNonThreadsafeRandom.java @@ -29,6 +29,7 @@ import java.util.Random; * seeds. This implementation is <em>no longer thread-safe</em> (but faster)! * * @author Erich Schubert + * @since 0.6.0 */ public class FastNonThreadsafeRandom extends Random { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/RandomFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/RandomFactory.java index ca8f5a36..c75ac19b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/RandomFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/RandomFactory.java @@ -36,6 +36,7 @@ import java.util.Random; * scientific experiments are not likely to be adversarial. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has Random * @apiviz.has FastNonThreadsafeRandom @@ -44,7 +45,12 @@ public class RandomFactory { /** * Global default factory */ - public static RandomFactory DEFAULT = new RandomFactory(getGlobalSeed()); + public static RandomFactory DEFAULT = new RandomFactory(getGlobalSeed()) { + @Override + public String toString() { + return "GlobalRandom[" + Long.toString(this.seed) + "]"; + } + }; /** * Initialize the default random. @@ -59,7 +65,7 @@ public class RandomFactory { /** * Seed. */ - private long seed; + protected long seed; /** * Factory method: Get a random factory for the given seed. @@ -101,4 +107,9 @@ public class RandomFactory { public Random getSingleThreadedRandom() { return new FastNonThreadsafeRandom(seed++); } + + @Override + public String toString() { + return "Random[" + Long.toString(seed) + "]"; + } }
\ No newline at end of file diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/XorShift1024NonThreadsafeRandom.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/XorShift1024NonThreadsafeRandom.java index 4cafbfba..e6d28167 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/XorShift1024NonThreadsafeRandom.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/XorShift1024NonThreadsafeRandom.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "S. Vigna", // title = "An experimental exploration of Marsaglia's xorshift generators, scrambled", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/XorShift64NonThreadsafeRandom.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/XorShift64NonThreadsafeRandom.java index 4063fe03..7716d178 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/XorShift64NonThreadsafeRandom.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/random/XorShift64NonThreadsafeRandom.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "S. Vigna", // title = "An experimental exploration of Marsaglia's xorshift generators, scrambled", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/scales/LinearScale.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/scales/LinearScale.java index 94aead3b..629ac96a 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/scales/LinearScale.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/scales/LinearScale.java @@ -35,6 +35,7 @@ import java.util.Locale; * values. * * @author Erich Schubert + * @since 0.2 * */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/scales/Scales.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/scales/Scales.java index deb2a85c..7ed49882 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/scales/Scales.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/scales/Scales.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * able to automatically choose log scales when appropriate. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has LinearScale oneway - - computes */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/AbstractSpatialSorter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/AbstractSpatialSorter.java index 8c5a580f..7a9e4d31 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/AbstractSpatialSorter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/AbstractSpatialSorter.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.data.spatial.SpatialComparable; * Abstract base class for spatial sorters, offering shared functionality. * * @author Erich Schubert + * @since 0.5.0 */ public abstract class AbstractSpatialSorter implements SpatialSorter { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/BinarySplitSpatialSorter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/BinarySplitSpatialSorter.java index a1b8ea9b..e549c072 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/BinarySplitSpatialSorter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/BinarySplitSpatialSorter.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.5.0 */ @Reference(authors = "J. L. Bentley", title = "Multidimensional binary search trees used for associative searching", booktitle = "Communications of the ACM, Vol. 18 Issue 9, Sept. 1975", url = "http://dx.doi.org/10.1145/361002.361007") public class BinarySplitSpatialSorter extends AbstractSpatialSorter { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/HilbertSpatialSorter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/HilbertSpatialSorter.java index f3207233..b8eebf17 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/HilbertSpatialSorter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/HilbertSpatialSorter.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.composedOf HilbertRef */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/PeanoSpatialSorter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/PeanoSpatialSorter.java index 490c9470..2b9f6982 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/PeanoSpatialSorter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/PeanoSpatialSorter.java @@ -31,9 +31,9 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; /** * Bulk-load an R-tree index by presorting the objects with their position on * the Peano curve. - * + * * The basic shape of this space-filling curve looks like this: - * + * * <pre> * 3---4 9 * | | | @@ -41,14 +41,14 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * | | | * 1 6---7 * </pre> - * + * * Which then expands to the next level as: - * + * * <pre> * +-+ +-+ +-+ +-+ E * | | | | | | | | | * | +-+ +-+ | | +-+ - * | | | + * | | | * | +-+ +-+ | | +-+ * | | | | | | | | | * +-+ | | +-+ +-+ | @@ -57,19 +57,22 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * | | | | | | | | | * S +-+ +-+ +-+ +-+ * </pre> - * + * * and so on. - * + * * Reference: * <p> * G. Peano<br /> * Sur une courbe, qui remplit toute une aire plane<br /> * Mathematische Annalen, 36(1) * </p> - * + * * @author Erich Schubert + * @since 0.5.0 */ -@Reference(authors = "G. Peano", title = "Sur une courbe, qui remplit toute une aire plane", booktitle = "Mathematische Annalen, 36(1)") +@Reference(authors = "G. Peano", // +title = "Sur une courbe, qui remplit toute une aire plane", // +booktitle = "Mathematische Annalen, 36(1)") public class PeanoSpatialSorter extends AbstractSpatialSorter { /** * Constructor. @@ -80,12 +83,12 @@ public class PeanoSpatialSorter extends AbstractSpatialSorter { @Override public <T extends SpatialComparable> void sort(List<T> objs, int start, int end, double[] minmax, int[] dims) { - peanoSort(objs, start, end, minmax, dims, 0, BitsUtil.zero(dims.length), false); + peanoSort(objs, start, end, minmax, dims, 0, BitsUtil.zero(minmax.length >> 1), false); } /** * Sort by Peano curve. - * + * * @param objs Objects * @param start Start index * @param end End diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/SpatialSorter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/SpatialSorter.java index 0745729c..14139f97 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/SpatialSorter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/SpatialSorter.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.data.spatial.SpatialComparable; * Interface for spatial sorting - ZCurves, Peano curves, Hilbert curves, ... * * @author Erich Schubert + * @since 0.5.0 */ public interface SpatialSorter { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/ZCurveSpatialSorter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/ZCurveSpatialSorter.java index d5fd10cf..08b68c5f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/ZCurveSpatialSorter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/ZCurveSpatialSorter.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.data.spatial.SpatialComparable; * materialization of the Z indexes. * * @author Erich Schubert + * @since 0.5.0 */ public class ZCurveSpatialSorter extends AbstractSpatialSorter { private static final double STOPVAL = 1E-10; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/ZCurveTransformer.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/ZCurveTransformer.java index 29c8ae72..94a6b12c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/ZCurveTransformer.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/ZCurveTransformer.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.database.relation.RelationUtil; * Class to transform a relation to its Z coordinates. * * @author Erich Schubert + * @since 0.5.0 */ public class ZCurveTransformer { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/KernelDensityEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/KernelDensityEstimator.java index 52087f8e..20f3bee0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/KernelDensityEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/KernelDensityEstimator.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.math.statistics.kernelfunctions.KernelDensityFunction * Estimates a density using a variable width kernel density estimation. * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses KernelDensityFunction */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/LinearRegression.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/LinearRegression.java index d6818129..faee3050 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/LinearRegression.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/LinearRegression.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.DoubleDoublePair; /** * * @author Arthur Zimek + * @since 0.2 */ // TODO: arthur comment // TODO: use covariance matrix, add incremental API? diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/MultipleLinearRegression.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/MultipleLinearRegression.java index 45aad7a2..42bbc712 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/MultipleLinearRegression.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/MultipleLinearRegression.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.FormatUtil; * is defined to be y = b0 + b1*x1 + b2*x2 + ... + bp*xp + e. * * @author Elke Achtert + * @since 0.2 */ public class MultipleLinearRegression { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/PolynomialRegression.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/PolynomialRegression.java index 53f02d19..3ccc5453 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/PolynomialRegression.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/PolynomialRegression.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * + b1*x1 + b2*x2 + ... + bp*xp + e * * @author Elke Achtert + * @since 0.2 */ public class PolynomialRegression extends MultipleLinearRegression { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/ProbabilityWeightedMoments.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/ProbabilityWeightedMoments.java index 30357c9c..382600d7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/ProbabilityWeightedMoments.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/ProbabilityWeightedMoments.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "J.R.M. Hosking, J. R. Wallis, and E. F. Wood", title = "Estimation of the generalized extreme-value distribution by the method of probability-weighted moments.", booktitle = "Technometrics 27.3", url = "http://dx.doi.org/10.1080/00401706.1985.10488049") public class ProbabilityWeightedMoments { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/AbstractDependenceMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/AbstractDependenceMeasure.java index 2b76b7fe..2c177328 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/AbstractDependenceMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/AbstractDependenceMeasure.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * Abstract base class for dependence measures. * * @author Erich Schubert + * @since 0.7.0 */ public abstract class AbstractDependenceMeasure implements DependenceMeasure { // In your subclass, you will need to implement at least this method: diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/CorrelationDependenceMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/CorrelationDependenceMeasure.java index e2d434b5..b67757ee 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/CorrelationDependenceMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/CorrelationDependenceMeasure.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Pearson product-moment correlation coefficient. * * @author Erich Schubert + * @since 0.7.0 */ public class CorrelationDependenceMeasure extends AbstractDependenceMeasure { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/DependenceMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/DependenceMeasure.java index 10bd7565..be2741fe 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/DependenceMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/DependenceMeasure.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * Measure the dependence of two variables. * * @author Erich Schubert + * @since 0.5.0 */ public interface DependenceMeasure { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/DistanceCorrelationDependenceMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/DistanceCorrelationDependenceMeasure.java index 289c0045..c1fdac6a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/DistanceCorrelationDependenceMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/DistanceCorrelationDependenceMeasure.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Marie Kiermeier * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "Székely, G. J., Rizzo, M. L., & Bakirov, N. K.", // title = "Measuring and testing dependence by correlation of distances", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/HSMDependenceMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/HSMDependenceMeasure.java index b90dbc22..6adf498c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/HSMDependenceMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/HSMDependenceMeasure.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Erich Schubert * @author Robert Rödler + * @since 0.5.5 */ @Reference(authors = "A. Tatu, G. Albuquerque, M. Eisemann, P. Bak, H. Theisel, M. A. Magnor, and D. A. Keim", // title = "Automated Analytical Methods to Support Visual Exploration of High-Dimensional Data", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/HiCSDependenceMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/HiCSDependenceMeasure.java index ea06698f..335c0182 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/HiCSDependenceMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/HiCSDependenceMeasure.java @@ -63,6 +63,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * * @author Erich Schubert * @author Robert Rödler + * @since 0.7.0 */ @Reference(authors = "Elke Achtert, Hans-Peter Kriegel, Erich Schubert, Arthur Zimek", // title = "Interactive Data Mining with 3D-Parallel-Coordinate-Trees", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/HoeffdingsDDependenceMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/HoeffdingsDDependenceMeasure.java index 63f618cc..6fc96223 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/HoeffdingsDDependenceMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/HoeffdingsDDependenceMeasure.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Yinchong Yang * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "W. Hoeffding", // title = "A non-parametric test of independence", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/JensenShannonEquiwidthDependenceMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/JensenShannonEquiwidthDependenceMeasure.java index e988100d..3d0d779a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/JensenShannonEquiwidthDependenceMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/JensenShannonEquiwidthDependenceMeasure.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * TODO: Offer normalized and non-normalized variants? * * @author Erich Schubert + * @since 0.7.0 */ public class JensenShannonEquiwidthDependenceMeasure extends AbstractDependenceMeasure { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/MCEDependenceMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/MCEDependenceMeasure.java index 471c1135..6058adec 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/MCEDependenceMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/MCEDependenceMeasure.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "D. Guo", // title = "Coordinating computational and visual approaches for interactive feature selection and multivariate clustering", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/MutualInformationEquiwidthDependenceMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/MutualInformationEquiwidthDependenceMeasure.java index c1aa786d..e4145704 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/MutualInformationEquiwidthDependenceMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/MutualInformationEquiwidthDependenceMeasure.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * For a median-based discretization, see {@link MCEDependenceMeasure}. * * @author Erich Schubert + * @since 0.7.0 */ public class MutualInformationEquiwidthDependenceMeasure extends AbstractDependenceMeasure { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SURFINGDependenceMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SURFINGDependenceMeasure.java index c37ad125..9019e087 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SURFINGDependenceMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SURFINGDependenceMeasure.java @@ -59,6 +59,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Robert Rödler * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "Elke Achtert, Hans-Peter Kriegel, Erich Schubert, Arthur Zimek", // title = "Interactive Data Mining with 3D-Parallel-Coordinate-Trees", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SlopeDependenceMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SlopeDependenceMeasure.java index a5f7e60e..b3cc9e39 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SlopeDependenceMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SlopeDependenceMeasure.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Erich Schubert * @author Robert Rödler + * @since 0.7.0 */ @Reference(authors = "Elke Achtert, Hans-Peter Kriegel, Erich Schubert, Arthur Zimek", // title = "Interactive Data Mining with 3D-Parallel-Coordinate-Trees", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SlopeInversionDependenceMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SlopeInversionDependenceMeasure.java index f99984c8..0aa62ad7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SlopeInversionDependenceMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SlopeInversionDependenceMeasure.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Erich Schubert * @author Robert Rödler + * @since 0.7.0 */ @Reference(authors = "Elke Achtert, Hans-Peter Kriegel, Erich Schubert, Arthur Zimek", // title = "Interactive Data Mining with 3D-Parallel-Coordinate-Trees", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SpearmanCorrelationDependenceMeasure.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SpearmanCorrelationDependenceMeasure.java index 3a6a162f..3942e7e1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SpearmanCorrelationDependenceMeasure.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SpearmanCorrelationDependenceMeasure.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Spearman rank-correlation coefficient, also known as Spearmans Rho. * * @author Erich Schubert + * @since 0.7.0 */ public class SpearmanCorrelationDependenceMeasure extends AbstractDependenceMeasure { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/AbstractDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/AbstractDistribution.java index ef3e1dff..e7ed8a6f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/AbstractDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/AbstractDistribution.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * Abstract base class for distributions. * * @author Erich Schubert + * @since 0.6.0 */ public abstract class AbstractDistribution implements Distribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/BetaDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/BetaDistribution.java index 374ca717..d8242c0d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/BetaDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/BetaDistribution.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * * @author Jan Brusis * @author Erich Schubert + * @since 0.5.0 */ public class BetaDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/CauchyDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/CauchyDistribution.java index 808c3b00..c5edbfb6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/CauchyDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/CauchyDistribution.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Cauchy distribution. * * @author Erich Schubert + * @since 0.6.0 */ public class CauchyDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ChiDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ChiDistribution.java index 5bbcbe2b..2cc397bf 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ChiDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ChiDistribution.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Chi distribution. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.composedOf ChiSquaredDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ChiSquaredDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ChiSquaredDistribution.java index 28ccdc4b..ae6ad53b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ChiSquaredDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ChiSquaredDistribution.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Chi-Squared distribution (a specialization of the Gamma distribution). * * @author Erich Schubert + * @since 0.2 */ public class ChiSquaredDistribution extends GammaDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ConstantDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ConstantDistribution.java index c0bb98e8..10f5f377 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ConstantDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ConstantDistribution.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Pseudo distribution, that has a unique constant value. * * @author Erich Schubert + * @since 0.5.0 */ public class ConstantDistribution implements Distribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/Distribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/Distribution.java index 9edf4b68..84cd64e8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/Distribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/Distribution.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.math.statistics.distribution; * Statistical distributions, with their common functions. * * @author Erich Schubert + * @since 0.2 */ public interface Distribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ExponentialDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ExponentialDistribution.java index 828416d7..055d4e1f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ExponentialDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ExponentialDistribution.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Exponential distribution. * * @author Erich Schubert + * @since 0.5.5 */ public class ExponentialDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ExponentiallyModifiedGaussianDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ExponentiallyModifiedGaussianDistribution.java index a764e304..f373d219 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ExponentiallyModifiedGaussianDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ExponentiallyModifiedGaussianDistribution.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * is a combination of a normal distribution and an exponential distribution. * * @author Erich Schubert + * @since 0.6.0 */ @Alias({ "exgaussian" }) public class ExponentiallyModifiedGaussianDistribution extends AbstractDistribution { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GammaDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GammaDistribution.java index 92af5a88..c6573016 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GammaDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GammaDistribution.java @@ -28,6 +28,7 @@ import java.util.Random; import de.lmu.ifi.dbs.elki.logging.LoggingUtil; import de.lmu.ifi.dbs.elki.math.MathUtil; import de.lmu.ifi.dbs.elki.math.random.RandomFactory; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; @@ -37,7 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Gamma Distribution, with random generation and density functions. * * @author Erich Schubert + * @since 0.4.0 */ +@Alias("de.lmu.ifi.dbs.elki.data.synthetic.bymodel.distribution.GammaDistribution") public class GammaDistribution extends AbstractDistribution { /** * Euler–Mascheroni constant diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedExtremeValueDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedExtremeValueDistribution.java index dea33d54..ff2d8b2d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedExtremeValueDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedExtremeValueDistribution.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * from the scipy definition by having the negative shape. * * @author Erich Schubert + * @since 0.6.0 */ public class GeneralizedExtremeValueDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedLogisticAlternateDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedLogisticAlternateDistribution.java index 3c4eb761..6000a1b2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedLogisticAlternateDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedLogisticAlternateDistribution.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Where {@code shape=0} yields the regular logistic distribution. * * @author Erich Schubert + * @since 0.6.0 */ public class GeneralizedLogisticAlternateDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedLogisticDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedLogisticDistribution.java index 6cb53dc9..162b47ea 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedLogisticDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedLogisticDistribution.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Where {@code shape=1} yields the regular logistic distribution. * * @author Erich Schubert + * @since 0.6.0 */ public class GeneralizedLogisticDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedParetoDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedParetoDistribution.java index 1765ffb3..2e4a7505 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedParetoDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedParetoDistribution.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * distributions. * * @author Erich Schubert + * @since 0.6.0 */ public class GeneralizedParetoDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GumbelDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GumbelDistribution.java index d5712582..81c0f45f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GumbelDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GumbelDistribution.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Gumbel distribution, also known as Log-Weibull distribution. * * @author Erich Schubert + * @since 0.6.0 */ public class GumbelDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/HaltonUniformDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/HaltonUniformDistribution.java index 242815b0..e021a6f1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/HaltonUniformDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/HaltonUniformDistribution.java @@ -64,6 +64,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * for example by adding scrambling. * * @author Erich Schubert + * @since 0.5.5 */ @Reference(title = "Randomized halton sequences", authors = "Wang, X. and Hickernell, F.J.", booktitle = "Mathematical and Computer Modelling Vol. 32 (7)", url = "http://dx.doi.org/10.1016/S0895-7177(00)00178-3") public class HaltonUniformDistribution implements Distribution { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/KappaDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/KappaDistribution.java index f9d723d8..81cc8191 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/KappaDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/KappaDistribution.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * TODO: add references. * * @author Erich Schubert + * @since 0.6.0 */ public class KappaDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LaplaceDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LaplaceDistribution.java index c3826cb3..92db5dd7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LaplaceDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LaplaceDistribution.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Laplace distribution also known as double exponential distribution * * @author Erich Schubert + * @since 0.5.5 */ @Alias("DoubleExponentialDistribution") public class LaplaceDistribution extends AbstractDistribution { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogGammaAlternateDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogGammaAlternateDistribution.java index b7c38566..63f67adc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogGammaAlternateDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogGammaAlternateDistribution.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Note: this matches the loggamma of SciPy. * * @author Erich Schubert + * @since 0.6.0 */ public class LogGammaAlternateDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogGammaDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogGammaDistribution.java index 60fa5292..f8796fe2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogGammaDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogGammaDistribution.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Note: this is a different loggamma than scipy uses. * * @author Erich Schubert + * @since 0.6.0 */ public class LogGammaDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogLogisticDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogLogisticDistribution.java index c2dfcc64..c7cba5ac 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogLogisticDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogLogisticDistribution.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Log-Logistic distribution also known as Fisk distribution. * * @author Erich Schubert + * @since 0.6.0 */ @Alias({ "fisk", "loglog" }) public class LogLogisticDistribution extends AbstractDistribution { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogNormalDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogNormalDistribution.java index 86f2ea43..d5a2d099 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogNormalDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogNormalDistribution.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * <tt>scipy.stats.lognorm(logstddev, shift, math.exp(logmean))</tt> * * @author Erich Schubert + * @since 0.6.0 */ @Alias({ "lognormal" }) public class LogNormalDistribution extends AbstractDistribution { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogisticDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogisticDistribution.java index 6dcafddb..b8e4f5bc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogisticDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogisticDistribution.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Logistic distribution. * * @author Erich Schubert + * @since 0.6.0 */ @Alias({ "log" }) public class LogisticDistribution extends AbstractDistribution { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/NormalDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/NormalDistribution.java index 56c14eca..126db305 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/NormalDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/NormalDistribution.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Gaussian distribution aka normal distribution * * @author Erich Schubert + * @since 0.5.0 */ @Alias({ "GaussianDistribution", "normal", "gauss" }) public class NormalDistribution extends AbstractDistribution { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/PoissonDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/PoissonDistribution.java index 59bb5ba7..a67fdde1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/PoissonDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/PoissonDistribution.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * </p> * * @author Erich Schubert + * @since 0.5.0 */ public class PoissonDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/RayleighDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/RayleighDistribution.java index 0ef431e0..832952e7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/RayleighDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/RayleighDistribution.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Rayleigh distribution. * * @author Erich Schubert + * @since 0.6.0 */ public class RayleighDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/SkewGeneralizedNormalDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/SkewGeneralizedNormalDistribution.java index 8cfb3e38..0cb5bcd8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/SkewGeneralizedNormalDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/SkewGeneralizedNormalDistribution.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * multiple that go by the name of a "Generalized Normal Distribution". * * @author Erich Schubert + * @since 0.6.0 */ public class SkewGeneralizedNormalDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/StudentsTDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/StudentsTDistribution.java index ced66f37..0bde3300 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/StudentsTDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/StudentsTDistribution.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * FIXME: add quantile and random function! * * @author Jan Brusis + * @since 0.5.0 */ public class StudentsTDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/UniformDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/UniformDistribution.java index 875ee737..301dc8dd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/UniformDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/UniformDistribution.java @@ -26,6 +26,7 @@ package de.lmu.ifi.dbs.elki.math.statistics.distribution; import java.util.Random; import de.lmu.ifi.dbs.elki.math.random.RandomFactory; +import de.lmu.ifi.dbs.elki.utilities.Alias; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; @@ -34,7 +35,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Uniform distribution. * * @author Erich Schubert + * @since 0.2 */ +@Alias("de.lmu.ifi.dbs.elki.data.synthetic.bymodel.distribution.UniformDistribution") public class UniformDistribution extends AbstractDistribution { /** * Minimum diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/WaldDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/WaldDistribution.java index b96f133e..11135fed 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/WaldDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/WaldDistribution.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Inverse Gaussian distribution aka Wald distribution * * @author Erich Schubert + * @since 0.6.0 */ @Alias({ "InverseGaussianDistribution", "invgauss" }) public class WaldDistribution extends AbstractDistribution { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/WeibullDistribution.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/WeibullDistribution.java index 86ac24d9..34791481 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/WeibullDistribution.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/WeibullDistribution.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Weibull distribution. * * @author Erich Schubert + * @since 0.6.0 */ public class WeibullDistribution extends AbstractDistribution { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractExpMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractExpMADEstimator.java index 5ec6aaf3..6c08abd8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractExpMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractExpMADEstimator.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * Abstract base class for estimators based on the median and MAD. * * @author Erich Schubert + * @since 0.6.0 * * @param <D> Distribution to generate. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLMMEstimator.java index 03e21b13..86455d52 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLMMEstimator.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * Abstract base class for L-Moments based estimators (LMM). * * @author Erich Schubert + * @since 0.5.0 * * @param <D> Distribution class. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLogMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLogMADEstimator.java index 8e6ca26d..170b4fab 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLogMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLogMADEstimator.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * Abstract base class for estimators based on the median and MAD. * * @author Erich Schubert + * @since 0.6.0 * * @param <D> Distribution to generate. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLogMOMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLogMOMEstimator.java index ad260a6f..9d6e5983 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLogMOMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLogMOMEstimator.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * Abstract base class for estimators based on the statistical moments. * * @author Erich Schubert + * @since 0.5.0 * * @param <D> Distribution to generate. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLogMeanVarianceEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLogMeanVarianceEstimator.java index b76176e4..464d7072 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLogMeanVarianceEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractLogMeanVarianceEstimator.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * only). * * @author Erich Schubert + * @since 0.5.0 * * @param <D> Distribution to estimate. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractMADEstimator.java index 9c630990..746408bb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractMADEstimator.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * Abstract base class for estimators based on the median and MAD. * * @author Erich Schubert + * @since 0.6.0 * * @param <D> Distribution to generate. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractMOMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractMOMEstimator.java index 8caf4cda..d9ca2dff 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractMOMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractMOMEstimator.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * Abstract base class for estimators based on the statistical moments. * * @author Erich Schubert + * @since 0.5.0 * * @param <D> Distribution to generate. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractMeanVarianceEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractMeanVarianceEstimator.java index e9058df4..20abf67d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractMeanVarianceEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/AbstractMeanVarianceEstimator.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * only). * * @author Erich Schubert + * @since 0.5.0 * * @param <D> Distribution to estimate. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/CauchyMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/CauchyMADEstimator.java index 9ced6b54..f4db08ff 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/CauchyMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/CauchyMADEstimator.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has CauchyDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/DistributionEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/DistributionEstimator.java index b31acf66..91d29c0e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/DistributionEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/DistributionEstimator.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * Estimate distribution parameters from a sample. * * @author Erich Schubert + * @since 0.5.0 * * @param <D> Distribution type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/EMGOlivierNorbergEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/EMGOlivierNorbergEstimator.java index 38aa5380..f1fa5d95 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/EMGOlivierNorbergEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/EMGOlivierNorbergEstimator.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Naive distribution estimation using mean and sample variance. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has ExponentiallyModifiedGaussianDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExpMADDistributionEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExpMADDistributionEstimator.java index b2a935c2..51f5e46c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExpMADDistributionEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExpMADDistributionEstimator.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.math.statistics.distribution.Distribution; * exponentiated data. * * @author Erich Schubert + * @since 0.5.0 * * @param <D> Distribution estimated. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialLMMEstimator.java index c33bbdfd..88ba769a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialLMMEstimator.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has ExponentialDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialMADEstimator.java index e639dd63..6c2d21e0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialMADEstimator.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has ExponentialDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialMOMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialMOMEstimator.java index cce8c503..726c85b8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialMOMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialMOMEstimator.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * maximum-likelihood estimate (MLE), but not very robust. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has ExponentialDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialMedianEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialMedianEstimator.java index 0bda6711..17db5724 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialMedianEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/ExponentialMedianEstimator.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has ExponentialDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaChoiWetteEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaChoiWetteEstimator.java index 3714b89c..cc746ece 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaChoiWetteEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaChoiWetteEstimator.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has GammaDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaLMMEstimator.java index 8024a326..29f2af63 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaLMMEstimator.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has GammaDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaMADEstimator.java index 7032ede8..90076359 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaMADEstimator.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has GammaDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaMOMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaMOMEstimator.java index 11aeb527..346a0fd4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaMOMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GammaMOMEstimator.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has GammaDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GeneralizedExtremeValueLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GeneralizedExtremeValueLMMEstimator.java index 1e60f8be..79020a59 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GeneralizedExtremeValueLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GeneralizedExtremeValueLMMEstimator.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has GeneralizedExtremeValueDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GeneralizedLogisticAlternateLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GeneralizedLogisticAlternateLMMEstimator.java index 1b9c3879..276f538a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GeneralizedLogisticAlternateLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GeneralizedLogisticAlternateLMMEstimator.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has GeneralizedLogisticAlternateDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GeneralizedParetoLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GeneralizedParetoLMMEstimator.java index c32f1de0..aa999b1f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GeneralizedParetoLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GeneralizedParetoLMMEstimator.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has GeneralizedParetoDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GumbelLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GumbelLMMEstimator.java index d721d083..2b29b079 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GumbelLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GumbelLMMEstimator.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has GumbelDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GumbelMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GumbelMADEstimator.java index 2e1b4f99..7e7cd8a9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GumbelMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/GumbelMADEstimator.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has GumbelDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LMMDistributionEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LMMDistributionEstimator.java index 1480d96f..0118b403 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LMMDistributionEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LMMDistributionEstimator.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.math.statistics.distribution.Distribution; * (LMM). * * @author Erich Schubert + * @since 0.5.0 * * @param <D> Distribution class. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LaplaceLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LaplaceLMMEstimator.java index c9c6d0bb..dc63ed27 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LaplaceLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LaplaceLMMEstimator.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Estimate Laplace distribution parameters using the method of L-Moments (LMM). * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LaplaceDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LaplaceMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LaplaceMADEstimator.java index 63355fb5..c09ad3ca 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LaplaceMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LaplaceMADEstimator.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LaplaceDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LaplaceMLEEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LaplaceMLEEstimator.java index 42316b32..42f27d83 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LaplaceMLEEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LaplaceMLEEstimator.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LaplaceDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaAlternateExpMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaAlternateExpMADEstimator.java index 2b742ed2..43a2b83e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaAlternateExpMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaAlternateExpMADEstimator.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * A modified algorithm for LogGamma distributions. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LogGammaAlternateDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaChoiWetteEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaChoiWetteEstimator.java index 80d02555..2f1577df 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaChoiWetteEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaChoiWetteEstimator.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LogGammaDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaLogMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaLogMADEstimator.java index db228b37..7458b485 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaLogMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaLogMADEstimator.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * A modified algorithm for LogGamma distributions. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LogGammaDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaLogMOMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaLogMOMEstimator.java index 193cc5ab..1e8c3b87 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaLogMOMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogGammaLogMOMEstimator.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * transformed values. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LogGammaDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogLogisticMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogLogisticMADEstimator.java index 942cb6af..a10ad4e4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogLogisticMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogLogisticMADEstimator.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LogLogisticDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogMADDistributionEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogMADDistributionEstimator.java index 596315b3..d66d02a5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogMADDistributionEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogMADDistributionEstimator.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.math.statistics.distribution.Distribution; * Distribuition estimators that use the method of moments (MOM) in logspace. * * @author Erich Schubert + * @since 0.5.0 * * @param <D> Distribution estimated. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogMOMDistributionEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogMOMDistributionEstimator.java index bd9ec4b2..3e6d9896 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogMOMDistributionEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogMOMDistributionEstimator.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.statistics.distribution.Distribution; * i.e. that only need the statistical moments of a data set after logarithms. * * @author Erich Schubert + * @since 0.5.0 * * @param <D> Distribution estimated. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalBilkovaLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalBilkovaLMMEstimator.java index 4b6d62d5..658655dc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalBilkovaLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalBilkovaLMMEstimator.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * generalized normal distribution, as used by Hosking. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LogNormalDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLMMEstimator.java index 57c5c745..854053c0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLMMEstimator.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LogNormalDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLevenbergMarquardtKDEEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLevenbergMarquardtKDEEstimator.java index a8b84c1a..2c571e39 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLevenbergMarquardtKDEEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLevenbergMarquardtKDEEstimator.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * observed. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LogNormalDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLogMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLogMADEstimator.java index 11c3c7ed..2f7e3850 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLogMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLogMADEstimator.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LogNormalDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLogMOMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLogMOMEstimator.java index 6888e4ad..93ebdca3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLogMOMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogNormalLogMOMEstimator.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * This is a maximum-likelihood-estimator (MLE). * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LogNormalDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogisticLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogisticLMMEstimator.java index 7c4f20be..30c85bb4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogisticLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogisticLMMEstimator.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LogisticDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogisticMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogisticMADEstimator.java index 1524e698..7d56fc5d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogisticMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/LogisticMADEstimator.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LogisticDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/MADDistributionEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/MADDistributionEstimator.java index 80112d22..9ffb26fc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/MADDistributionEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/MADDistributionEstimator.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.math.statistics.distribution.Distribution; * need the statistical moments of a data set. * * @author Erich Schubert + * @since 0.5.0 * * @param <D> Distribution estimated. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/MOMDistributionEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/MOMDistributionEstimator.java index a85dfbd2..1968ee63 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/MOMDistributionEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/MOMDistributionEstimator.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.statistics.distribution.Distribution; * need the statistical moments of a data set. * * @author Erich Schubert + * @since 0.5.0 * * @param <D> Distribution estimated. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/MeanVarianceDistributionEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/MeanVarianceDistributionEstimator.java index 128f2ece..10c638d7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/MeanVarianceDistributionEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/MeanVarianceDistributionEstimator.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MeanVariance; * These can implicitely (obviously) also handle full statistical moments. * * @author Erich Schubert + * @since 0.5.0 * * @param <D> Distribution type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalLMMEstimator.java index 0a569de5..96dcf336 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalLMMEstimator.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has NormalDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalLevenbergMarquardtKDEEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalLevenbergMarquardtKDEEstimator.java index 5f6e5672..54a83355 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalLevenbergMarquardtKDEEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalLevenbergMarquardtKDEEstimator.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * observed. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has NormalDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalMADEstimator.java index 6bb5a9ea..cdbebc5b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalMADEstimator.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has NormalDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalMOMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalMOMEstimator.java index 7f5f179b..12aeaecf 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalMOMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/NormalMOMEstimator.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * extreme values. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has NormalDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/RayleighLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/RayleighLMMEstimator.java index a7afad4c..cd96506f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/RayleighLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/RayleighLMMEstimator.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * the method of L-Moments (LMM). * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has RayleighDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/RayleighMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/RayleighMADEstimator.java index 39babfe4..bcd67e0d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/RayleighMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/RayleighMADEstimator.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has RayleighDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/RayleighMLEEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/RayleighMLEEstimator.java index 4891f9bd..c0f54916 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/RayleighMLEEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/RayleighMLEEstimator.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * maximum likelihood estimate. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has RayleighDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/SkewGNormalLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/SkewGNormalLMMEstimator.java index 15e51d40..2000e841 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/SkewGNormalLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/SkewGNormalLMMEstimator.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has SkewGeneralizedNormalDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformEnhancedMinMaxEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformEnhancedMinMaxEstimator.java index 8b12ace1..b33b70da 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformEnhancedMinMaxEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformEnhancedMinMaxEstimator.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * enhances the interval appropriately. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has UniformDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformLMMEstimator.java index 5008eb85..c7134ee1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformLMMEstimator.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * L-Moments (LMM). * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has UniformDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformMADEstimator.java index 781f72ec..29004489 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformMADEstimator.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has UniformDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformMinMaxEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformMinMaxEstimator.java index a40c4686..e140ec2c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformMinMaxEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/UniformMinMaxEstimator.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Estimate the uniform distribution by computing min and max. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has UniformDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WaldMLEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WaldMLEstimator.java index d8147006..1088dd37 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WaldMLEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WaldMLEstimator.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Estimate parameter of the Wald distribution. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has WaldDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WaldMOMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WaldMOMEstimator.java index 1ccfdf08..da56827f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WaldMOMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WaldMOMEstimator.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Estimate parameter of the Wald distribution. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has WaldDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WeibullLMMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WeibullLMMEstimator.java index 4ea8faa7..0756c113 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WeibullLMMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WeibullLMMEstimator.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * (LMM). * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has WeibullDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WeibullLogMADEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WeibullLogMADEstimator.java index 8dd068e0..22f6effc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WeibullLogMADEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WeibullLogMADEstimator.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has WeibullDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WeibullLogMOMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WeibullLogMOMEstimator.java index dd02dea4..3a96dcfd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WeibullLogMOMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/WeibullLogMOMEstimator.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * doesn't use "the" statistical moments. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has WeibullDistribution - - estimates */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/meta/BestFitEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/meta/BestFitEstimator.java index 81e2abfd..c3409d9b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/meta/BestFitEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/meta/BestFitEstimator.java @@ -87,6 +87,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * choose whichever works best. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses MOMDistributionEstimator * @apiviz.uses MADDistributionEstimator diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/meta/TrimmedEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/meta/TrimmedEstimator.java index ed1ffab8..54fda81c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/meta/TrimmedEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/meta/TrimmedEstimator.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * analyzes it using another estimator. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses DistributionEstimator * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/meta/WinsorisingEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/meta/WinsorisingEstimator.java index ad8e532d..56a7ee94 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/meta/WinsorisingEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/estimator/meta/WinsorisingEstimator.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * </p> * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.uses DistributionEstimator * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/AbstractIntrinsicDimensionalityEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/AbstractIntrinsicDimensionalityEstimator.java index 4bea246b..c3dde05f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/AbstractIntrinsicDimensionalityEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/AbstractIntrinsicDimensionalityEstimator.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * Abstract base class for ID estimators. * * @author Erich Schubert + * @since 0.7.0 */ public abstract class AbstractIntrinsicDimensionalityEstimator implements IntrinsicDimensionalityEstimator { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/AggregatedHillEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/AggregatedHillEstimator.java index 732d74ab..2cd35e60 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/AggregatedHillEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/AggregatedHillEstimator.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Jonathan von Brünken * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "R. Huisman and K. G. Koedijk and C. J. M. Kool and F. Palm", // title = "Tail-Index Estimates in Small Samples", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/EnsembleEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/EnsembleEstimator.java index 019580fa..83dbb8bc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/EnsembleEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/EnsembleEstimator.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * This is an experimental estimator. Please cite ELKI when using. * * @author Erich Schubert + * @since 0.7.0 */ public class EnsembleEstimator extends AbstractIntrinsicDimensionalityEstimator { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/GEDEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/GEDEstimator.java index 2514006c..82e5486b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/GEDEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/GEDEstimator.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Jonathan von Brünken * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "M. E. Houle, H. Kashima, M. Nett", // title = "Generalized expansion dimension", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/HillEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/HillEstimator.java index 228aa5c0..0d761b8e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/HillEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/HillEstimator.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Jonathan von Brünken * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "B. M. Hill", // title = "A simple general approach to inference about the tail of a distribution", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/IntrinsicDimensionalityEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/IntrinsicDimensionalityEstimator.java index 978869b0..159b5c98 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/IntrinsicDimensionalityEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/IntrinsicDimensionalityEstimator.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.NumberArrayAdapter * Estimate the intrinsic dimensionality from a distance list. * * @author Erich Schubert + * @since 0.7.0 */ public interface IntrinsicDimensionalityEstimator { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/LMomentsEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/LMomentsEstimator.java index 671b3e36..1435945d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/LMomentsEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/LMomentsEstimator.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Jonathan von Brünken * @author Erich Schubert + * @since 0.7.0 */ public class LMomentsEstimator extends AbstractIntrinsicDimensionalityEstimator { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/MOMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/MOMEstimator.java index 174d4bf7..8379f56b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/MOMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/MOMEstimator.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "L. Amsaleg and O. Chelly and T. Furon and S. Girard and M. E. Houle and K. Kawarabayashi and M. Nett", // title = "Estimating Local Intrinsic Dimensionality", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/PWM2Estimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/PWM2Estimator.java index 5d16fa48..f8176ec8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/PWM2Estimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/PWM2Estimator.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * this. This hack causes this estimator to have a bias to underestimate the ID. * * @author Erich Schubert + * @since 0.7.0 */ public class PWM2Estimator extends AbstractIntrinsicDimensionalityEstimator { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/PWMEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/PWMEstimator.java index 9c9db16b..bcc6a21e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/PWMEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/PWMEstimator.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Jonathan von Brünken * @author Erich Schubert + * @since 0.7.0 */ public class PWMEstimator extends AbstractIntrinsicDimensionalityEstimator { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/RVEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/RVEstimator.java index 52976bf4..dcff6031 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/RVEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/RVEstimator.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Oussama Chelly + * @since 0.7.0 */ @Reference(authors = "L. Amsaleg and O. Chelly and T. Furon and S. Girard and M. E. Houle and K. Kawarabayashi and M. Nett", // title = "Estimating Local Intrinsic Dimensionality", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/ZipfEstimator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/ZipfEstimator.java index c5bd60a2..21cdb93f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/ZipfEstimator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/intrinsicdimensionality/ZipfEstimator.java @@ -55,6 +55,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * TODO: possible to improve numerical precision via log1p? * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "M. Kratz and S. I. Resnick", // title = "On Least Squares Estimates of an Exponential Tail Coefficient", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/BiweightKernelDensityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/BiweightKernelDensityFunction.java index d9252e86..7dd76cc0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/BiweightKernelDensityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/BiweightKernelDensityFunction.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Biweight (Quartic) kernel density estimator. * * @author Erich Schubert + * @since 0.6.0 */ @Alias({ "biweight", "quartic" }) public final class BiweightKernelDensityFunction implements KernelDensityFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/CosineKernelDensityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/CosineKernelDensityFunction.java index b51b308e..eaabde55 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/CosineKernelDensityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/CosineKernelDensityFunction.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Cosine kernel density estimator. * * @author Erich Schubert + * @since 0.6.0 */ public final class CosineKernelDensityFunction implements KernelDensityFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/EpanechnikovKernelDensityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/EpanechnikovKernelDensityFunction.java index b83ce76c..cde35380 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/EpanechnikovKernelDensityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/EpanechnikovKernelDensityFunction.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Epanechnikov kernel density estimator. * * @author Erich Schubert + * @since 0.6.0 */ @Alias({ "epanechnikov" }) public final class EpanechnikovKernelDensityFunction implements KernelDensityFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/GaussianKernelDensityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/GaussianKernelDensityFunction.java index adf9189e..5ec0fe94 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/GaussianKernelDensityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/GaussianKernelDensityFunction.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Gaussian kernel density estimator. * * @author Erich Schubert + * @since 0.6.0 */ public final class GaussianKernelDensityFunction implements KernelDensityFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/KernelDensityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/KernelDensityFunction.java index c53d5da1..ecc8567d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/KernelDensityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/KernelDensityFunction.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * Note: as of now, this API does not support asymmetric kernels. * * @author Erich Schubert + * @since 0.6.0 */ public interface KernelDensityFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/TriangularKernelDensityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/TriangularKernelDensityFunction.java index 0175f163..923f45e1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/TriangularKernelDensityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/TriangularKernelDensityFunction.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Triangular kernel density estimator. * * @author Erich Schubert + * @since 0.6.0 */ public final class TriangularKernelDensityFunction implements KernelDensityFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/TricubeKernelDensityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/TricubeKernelDensityFunction.java index c2cf5152..472646a0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/TricubeKernelDensityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/TricubeKernelDensityFunction.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Tricube kernel density estimator. * * @author Erich Schubert + * @since 0.6.0 */ public final class TricubeKernelDensityFunction implements KernelDensityFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/TriweightKernelDensityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/TriweightKernelDensityFunction.java index fd3b38e3..2573723f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/TriweightKernelDensityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/TriweightKernelDensityFunction.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Triweight kernel density estimator. * * @author Erich Schubert + * @since 0.6.0 */ @Alias({ "triweight" }) public final class TriweightKernelDensityFunction implements KernelDensityFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/UniformKernelDensityFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/UniformKernelDensityFunction.java index a27d0ba4..bf07911d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/UniformKernelDensityFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/kernelfunctions/UniformKernelDensityFunction.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * Uniform / Rectangular kernel density estimator. * * @author Erich Schubert + * @since 0.6.0 */ public final class UniformKernelDensityFunction implements KernelDensityFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/AndersonDarlingTest.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/AndersonDarlingTest.java index de418391..174563b7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/AndersonDarlingTest.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/AndersonDarlingTest.java @@ -62,6 +62,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "T. W. Anderson, and D. A. Darling", // title = "Asymptotic theory of certain 'goodness of fit' criteria based on stochastic processes", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/GoodnessOfFitTest.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/GoodnessOfFitTest.java index 2882390a..a1c9aa7a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/GoodnessOfFitTest.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/GoodnessOfFitTest.java @@ -33,6 +33,7 @@ package de.lmu.ifi.dbs.elki.math.statistics.tests; * * @author Jan Brusis * @author Erich Schubert + * @since 0.5.0 */ public interface GoodnessOfFitTest { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/KolmogorovSmirnovTest.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/KolmogorovSmirnovTest.java index 3e2d98e4..f0b2ea95 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/KolmogorovSmirnovTest.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/KolmogorovSmirnovTest.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * difference of the empirical CDFs. * * @author Erich Schubert + * @since 0.5.0 */ public class KolmogorovSmirnovTest implements GoodnessOfFitTest { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/StandardizedTwoSampleAndersonDarlingTest.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/StandardizedTwoSampleAndersonDarlingTest.java index d2f9777c..a2b83496 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/StandardizedTwoSampleAndersonDarlingTest.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/StandardizedTwoSampleAndersonDarlingTest.java @@ -57,6 +57,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "F. W. Scholz, and M. A. Stephens", // title = "K-sample Anderson–Darling tests", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/WelchTTest.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/WelchTTest.java index 91049bad..50e55f58 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/WelchTTest.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/math/statistics/tests/WelchTTest.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * * @author Jan Brusis * @author Erich Schubert + * @since 0.5.0 * * @apiviz.uses StudentsTDistribution */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/Executor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/Executor.java index c6659aad..93461872 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/Executor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/Executor.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.parallel.variables.SharedVariable; * Processor executor. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.uses de.lmu.ifi.dbs.elki.parallel.processor.Processor * @apiviz.uses SharedVariable diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/ParallelCore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/ParallelCore.java index 074a3562..9e84da8a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/ParallelCore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/ParallelCore.java @@ -36,6 +36,7 @@ import java.util.concurrent.atomic.AtomicInteger; * TODO: make configurable how many threads are used. * * @author Erich Schubert + * @since 0.7.0 */ public class ParallelCore { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/ParallelExecutor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/ParallelExecutor.java index f3da8bc0..dc7c8b1c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/ParallelExecutor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/ParallelExecutor.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.parallel.variables.SharedVariable.Instance; * TODO: add progress * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has BlockArrayRunner * @apiviz.uses ParallelCore diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/SingleThreadedExecutor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/SingleThreadedExecutor.java index 21c695f1..82acc4e7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/SingleThreadedExecutor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/SingleThreadedExecutor.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.parallel.variables.SharedVariable.Instance; * Currently not used. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has SingleThreadedRunner */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/AbstractDoubleProcessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/AbstractDoubleProcessor.java index 8d640af2..c7d56f65 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/AbstractDoubleProcessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/AbstractDoubleProcessor.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.parallel.variables.SharedDouble; * Abstract base class for processors that output double values. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has Instance * @apiviz.uses SharedDouble diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/DoubleMinMaxProcessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/DoubleMinMaxProcessor.java index b751b9e3..35fb6517 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/DoubleMinMaxProcessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/DoubleMinMaxProcessor.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.parallel.variables.SharedDouble; * Sink collecting minimum and maximum values. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has Instance * @apiviz.uses SharedDouble diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/KDistanceProcessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/KDistanceProcessor.java index 0b68a88a..4166a225 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/KDistanceProcessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/KDistanceProcessor.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.parallel.variables.SharedObject; * Needs the k nearest neighbors as input, for example from {@link KNNProcessor}. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has Instance * @apiviz.uses KNNList diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/KNNProcessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/KNNProcessor.java index d8d25bdc..86ab87e8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/KNNProcessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/KNNProcessor.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.parallel.variables.SharedObject; * Processor to compute the kNN of each object. * * @author Erich Schubert + * @since 0.7.0 * * @param <O> Object type * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/Processor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/Processor.java index a2bd7c3e..024bab94 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/Processor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/Processor.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.parallel.Executor; * Class to represent a processor factory. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has Instance */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/WriteDataStoreProcessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/WriteDataStoreProcessor.java index 06bac212..710b83a5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/WriteDataStoreProcessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/WriteDataStoreProcessor.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.parallel.variables.SharedObject; * Output channel to store data in a {@link WritableDataStore}. * * @author Erich Schubert + * @since 0.7.0 * * @param <T> data type * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/WriteDoubleDataStoreProcessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/WriteDoubleDataStoreProcessor.java index ff9f25c9..2967de33 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/WriteDoubleDataStoreProcessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/WriteDoubleDataStoreProcessor.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.parallel.variables.SharedDouble; * Write double values into a {@link WritableDoubleDataStore}. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has Instance * @apiviz.uses SharedDouble diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/WriteIntegerDataStoreProcessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/WriteIntegerDataStoreProcessor.java index e71d6736..b6403ba7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/WriteIntegerDataStoreProcessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/processor/WriteIntegerDataStoreProcessor.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.parallel.variables.SharedInteger; * Write int values into a {@link WritableIntegerDataStore}. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has Instance * @apiviz.uses SharedInteger diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedDouble.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedDouble.java index ea76297a..b0f75c66 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedDouble.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedDouble.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.parallel.variables; * Direct channel connecting two processors. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has SharedDouble.Instance */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedInteger.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedInteger.java index 43471144..bb10e600 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedInteger.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedInteger.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.parallel.variables; * Direct channel connecting two processors. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has SharedInteger.Instance */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedObject.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedObject.java index 83404cce..dd047f95 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedObject.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedObject.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.parallel.variables; * Variable to share between different processors (within one thread only!) * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has SharedObject.Instance * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedVariable.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedVariable.java index fd5808fb..6499c82b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedVariable.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/parallel/variables/SharedVariable.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.parallel.variables; * Shared variables storing a particular type. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.has SharedVariable.Instance * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractExternalizablePage.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractExternalizablePage.java index ee4b5972..c7be2809 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractExternalizablePage.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractExternalizablePage.java @@ -31,6 +31,7 @@ import java.io.ObjectOutput; * Abstract superclass for pages. * * @author Elke Achtert + * @since 0.2 */ // todo elke revise comments public abstract class AbstractExternalizablePage implements ExternalizablePage { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractPageFile.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractPageFile.java index 6a47ac38..78978763 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractPageFile.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractPageFile.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.logging.statistics.Counter; * (in-memory and on-disk). * * @author Erich Schubert + * @since 0.4.0 * * @param <P> page type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractPageFileFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractPageFileFactory.java index a52b21bc..26bb95d2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractPageFileFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractPageFileFactory.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * Abstract page file factory. * * @author Erich Schubert + * @since 0.6.0 * * @param <P> Page type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractStoringPageFile.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractStoringPageFile.java index a26d9a4f..3b0b4f8f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractStoringPageFile.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractStoringPageFile.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.logging.statistics.LongStatistic; * objects that implement the <code>Page</code> interface. * * @author Elke Achtert + * @since 0.4.0 * * @param <P> Page type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/DefaultPageHeader.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/DefaultPageHeader.java index 0d6b8950..5e056f05 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/DefaultPageHeader.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/DefaultPageHeader.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteArrayUtil; * Default implementation of a page header. * * @author Elke Achtert + * @since 0.2 */ public class DefaultPageHeader implements PageHeader { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/ExternalizablePage.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/ExternalizablePage.java index 8c9c124d..3ffc4a35 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/ExternalizablePage.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/ExternalizablePage.java @@ -29,6 +29,7 @@ import java.io.Externalizable; * Base interface for externalizable pages. * * @author Erich Schubert + * @since 0.4.0 */ // TODO: replace with the newer ByteSerializers public interface ExternalizablePage extends Page, Externalizable { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/LRUCache.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/LRUCache.java index e9fd7db4..5c78e3ae 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/LRUCache.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/LRUCache.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * object is dropped. * * @author Elke Achtert + * @since 0.2 * * @apiviz.uses PageFile * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/LRUCachePageFileFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/LRUCachePageFileFactory.java index fa248a52..396166c8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/LRUCachePageFileFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/LRUCachePageFileFactory.java @@ -1,12 +1,5 @@ package de.lmu.ifi.dbs.elki.persistent; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.CommonConstraints; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; - /* This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures @@ -30,10 +23,18 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; along with this program. If not, see <http://www.gnu.org/licenses/>. */ +import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.CommonConstraints; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; + /** * Page file factory for memory page files. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has LRUCache * @apiviz.composedOf PageFileFactory diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/MemoryPageFile.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/MemoryPageFile.java index f0b37914..e6ed70c5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/MemoryPageFile.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/MemoryPageFile.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * Implemented as a Map with keys representing the ids of the saved pages. * * @author Elke Achtert + * @since 0.2 * * @param <P> Page type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/MemoryPageFileFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/MemoryPageFileFactory.java index 3323fd38..1f55cfab 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/MemoryPageFileFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/MemoryPageFileFactory.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.persistent; * Page file factory for memory page files. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has MemoryPageFile * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskArray.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskArray.java index d379dc9a..448561d1 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskArray.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskArray.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteArrayUtil; * by the actual data. * * @author Erich Schubert + * @since 0.2 * * @apiviz.composedOf RandomAccessFile */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskArrayPageFile.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskArrayPageFile.java index 5c2a56c2..111b6490 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskArrayPageFile.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskArrayPageFile.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteBufferInputStream; * single file. All pages are stored in a specified directory. * * @author Elke Achtert + * @since 0.2 * * @apiviz.composedOf OnDiskArray * @apiviz.composedOf PageHeader diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskArrayPageFileFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskArrayPageFileFactory.java index d5351d3e..3b60c51d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskArrayPageFileFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskArrayPageFileFactory.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; * Page file factory for disk-based page files. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has OnDiskArrayPageFile * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskUpperTriangleMatrix.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskUpperTriangleMatrix.java index 4faa1e67..9cd7acdf 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskUpperTriangleMatrix.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/OnDiskUpperTriangleMatrix.java @@ -34,6 +34,7 @@ import java.nio.ByteBuffer; * @apiviz.composedOf OnDiskArray * * @author Erich Schubert + * @since 0.2 */ public class OnDiskUpperTriangleMatrix { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/Page.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/Page.java index 042fa893..a0c7e596 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/Page.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/Page.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.persistent; * persistently saved. * * @author Elke Achtert + * @since 0.2 * * @apiviz.excludeSubtypes */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PageFile.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PageFile.java index af791951..366ac6c4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PageFile.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PageFile.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.persistent; * Page file interface. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has Page * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PageFileFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PageFileFactory.java index df84defc..49400571 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PageFileFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PageFileFactory.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.persistent; * Factory interface for generating page files. * * @author Erich Schubert + * @since 0.4.0 * * @param <P> Page type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PageHeader.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PageHeader.java index 582ccfc6..1171b41e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PageHeader.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PageHeader.java @@ -31,6 +31,7 @@ import java.io.RandomAccessFile; * must at least store the size of a page in Bytes. * * @author Elke Achtert + * @since 0.2 */ public interface PageHeader { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PersistentPageFile.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PersistentPageFile.java index c6068edc..3103693f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PersistentPageFile.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PersistentPageFile.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * single file. All pages are stored in a specified directory. * * @author Elke Achtert + * @since 0.2 * * @apiviz.composedOf PageHeader * @apiviz.composedOf RandomAccessFile diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PersistentPageFileFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PersistentPageFileFactory.java index 4d44381a..405db531 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PersistentPageFileFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/persistent/PersistentPageFileFactory.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter; * Page file factory for disk-based page files. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has PersistentPageFile * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/AbstractHierarchicalResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/AbstractHierarchicalResult.java index e45c8106..80fee1a5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/AbstractHierarchicalResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/AbstractHierarchicalResult.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.result; * Abstract class for a result object with hierarchy * * @author Erich Schubert + * @since 0.4.0 */ public abstract class AbstractHierarchicalResult implements HierarchicalResult { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/BasicResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/BasicResult.java index 527b086c..c0db5ae2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/BasicResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/BasicResult.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.result; * stores the required short and long result names. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ClusteringVectorDumper.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ClusteringVectorDumper.java index b2f27abb..f4988e72 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ClusteringVectorDumper.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ClusteringVectorDumper.java @@ -62,6 +62,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.StringParameter; * {@link de.lmu.ifi.dbs.elki.algorithm.clustering.meta.ExternalClustering}. * * @author Erich Schubert + * @since 0.7.0 */ public class ClusteringVectorDumper implements ResultHandler { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/CollectionResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/CollectionResult.java index 0128e533..d1a86481 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/CollectionResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/CollectionResult.java @@ -32,6 +32,7 @@ import java.util.Iterator; * For example, a list of NumberVectors. * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/DBIDSelection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/DBIDSelection.java index c2cb809a..47bb25eb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/DBIDSelection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/DBIDSelection.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * * @author Heidi Kolb * @author Erich Schubert + * @since 0.4.0 */ public class DBIDSelection { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/DiscardResultHandler.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/DiscardResultHandler.java index 5b395de8..2fdbb009 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/DiscardResultHandler.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/DiscardResultHandler.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.result; * benchmarks. * * @author Erich Schubert + * @since 0.2 */ public class DiscardResultHandler implements ResultHandler { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/EvaluationResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/EvaluationResult.java index 8790a3f5..7cf49e1b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/EvaluationResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/EvaluationResult.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; * Abstract evaluation result. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf EvaluationResult.MeasurementGroup */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/FrequentItemsetsResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/FrequentItemsetsResult.java index ae34e4c6..e0f8a314 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/FrequentItemsetsResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/FrequentItemsetsResult.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; * Result class for Apriori Algorithm. * * @author Erich Schubert + * @since 0.2 */ public class FrequentItemsetsResult extends BasicResult implements TextWriteable { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/HierarchicalResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/HierarchicalResult.java index 383c3ad1..b7611d94 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/HierarchicalResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/HierarchicalResult.java @@ -31,6 +31,7 @@ package de.lmu.ifi.dbs.elki.result; * delegate is to keep the APIs simpler, and thus make ELKI development easier. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf ResultHierarchy */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/HistogramResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/HistogramResult.java index fde386e5..5065e2e0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/HistogramResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/HistogramResult.java @@ -29,6 +29,7 @@ import java.util.Collection; * Histogram result. * * @author Erich Schubert + * @since 0.3 * * @param <O> Object class (e.g. {@link de.lmu.ifi.dbs.elki.data.DoubleVector}) */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/IterableResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/IterableResult.java index 8d5d6c61..3126569e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/IterableResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/IterableResult.java @@ -30,6 +30,7 @@ import java.util.Iterator; * (At least when the class O is TextWriteable) * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/KMLOutputHandler.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/KMLOutputHandler.java index de5fc586..121cff56 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/KMLOutputHandler.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/KMLOutputHandler.java @@ -96,6 +96,7 @@ import de.lmu.ifi.dbs.elki.workflow.OutputStep; * different result types. * * @author Erich Schubert + * @since 0.4.0 */ // TODO: make configurable color scheme @Reference(authors = "E. Achtert, A. Hettab, H.-P. Kriegel, E. Schubert, A. Zimek", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/LogResultStructureResultHandler.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/LogResultStructureResultHandler.java index 0660672b..d10fa0f1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/LogResultStructureResultHandler.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/LogResultStructureResultHandler.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Description; * TODO: transform this into an evaluator, then visualize, too? * * @author Erich Schubert + * @since 0.5.5 */ @Description("Development result handler that merely logs the structure of the result tree.") public class LogResultStructureResultHandler implements ResultHandler { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/OrderingFromDataStore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/OrderingFromDataStore.java index 004b2e8f..000956ba 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/OrderingFromDataStore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/OrderingFromDataStore.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * Result class providing an ordering backed by a hashmap. * * @author Erich Schubert + * @since 0.2 * * @param <T> Data type in hash map */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/OrderingResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/OrderingResult.java index ae5a84b9..cb153b7d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/OrderingResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/OrderingResult.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * Interface for a result providing an object ordering. * * @author Erich Schubert + * @since 0.2 */ public interface OrderingResult extends Result { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/PixmapResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/PixmapResult.java index ce9800dc..04a100e7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/PixmapResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/PixmapResult.java @@ -30,6 +30,7 @@ import java.io.File; * Result encapsulating a single image. * * @author Erich Schubert + * @since 0.4.0 */ public interface PixmapResult extends Result { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/RangeSelection.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/RangeSelection.java index 301df6c1..164317d7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/RangeSelection.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/RangeSelection.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDs; * * @author Heidi Kolb * @author Erich Schubert + * @since 0.4.0 */ public class RangeSelection extends DBIDSelection { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ReferencePointsResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ReferencePointsResult.java index 082456cf..c6d7a7d3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ReferencePointsResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ReferencePointsResult.java @@ -29,6 +29,7 @@ import java.util.Collection; * Result used in passing the reference points to the visualizers. * * @author Erich Schubert + * @since 0.3 * * @param <O> data type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/Result.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/Result.java index 6a1bd402..ab6a9c82 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/Result.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/Result.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.result; * Interface for arbitrary result objects. * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultHandler.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultHandler.java index 3455056f..f228bd74 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultHandler.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultHandler.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.result; * Interface for any class that can handle results * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * @apiviz.uses Result oneway - - processes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultHierarchy.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultHierarchy.java index 5c8b1ab4..97108674 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultHierarchy.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultHierarchy.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.hierarchy.ModifiableHierarch * Class to store a hierarchy of result objects. * * @author Erich Schubert + * @since 0.4.0 */ // TODO: add listener merging! public class ResultHierarchy extends HashMapHierarchy<Result> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultListener.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultListener.java index 8dc3d637..2bdaf23b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultListener.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultListener.java @@ -29,6 +29,7 @@ import java.util.EventListener; * Listener interface invoked when new results are added to the result tree. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has Result */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultProcessor.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultProcessor.java index 9e7b255a..7ffd520a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultProcessor.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultProcessor.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.result; * Interface for any class that can handle results * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses Result oneway - - processes */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultUtil.java index f59e9977..3a394d86 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultUtil.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.hierarchy.Hierarchy; * Utilities for handling result objects * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses Result oneway - - filters */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultWriter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultWriter.java index bbbec518..39b081c4 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultWriter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ResultWriter.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.workflow.OutputStep; * Note: these classes need to be rewritten. Contributions welcome! * * @author Erich Schubert + * @since 0.2 */ public class ResultWriter implements ResultHandler { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/SamplingResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/SamplingResult.java index 973714fe..10ecaf5c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/SamplingResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/SamplingResult.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * Wrapper for storing the current database sample. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf DBIDs */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ScalesResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ScalesResult.java index 3617eb9d..b89a3dc1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ScalesResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/ScalesResult.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.math.scales.Scales; * Class to keep shared scales across visualizers. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf LinearScale */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/SelectionResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/SelectionResult.java index 783cd41d..43bbe201 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/SelectionResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/SelectionResult.java @@ -30,6 +30,7 @@ package de.lmu.ifi.dbs.elki.result; * DBIDSelection object should be seen as static contents of this result. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf DBIDSelection */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/SettingsResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/SettingsResult.java index 6a1f5f91..3b6bb147 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/SettingsResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/SettingsResult.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.TrackedPara * particular result. * * @author Erich Schubert + * @since 0.3 */ public class SettingsResult extends BasicResult { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/BasicOutlierScoreMeta.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/BasicOutlierScoreMeta.java index bb44a657..a150b462 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/BasicOutlierScoreMeta.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/BasicOutlierScoreMeta.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * {@link OutlierScoreMeta} interface. * * @author Erich Schubert + * @since 0.3 */ public class BasicOutlierScoreMeta implements OutlierScoreMeta { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/InvertedOutlierScoreMeta.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/InvertedOutlierScoreMeta.java index 0a55e07d..d8d7f2a3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/InvertedOutlierScoreMeta.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/InvertedOutlierScoreMeta.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.result.outlier; * Class to signal a value-inverted outlier score, i.e. low values are outliers. * * @author Erich Schubert + * @since 0.3 */ public class InvertedOutlierScoreMeta extends BasicOutlierScoreMeta { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/OrderingFromRelation.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/OrderingFromRelation.java index 99c0a48e..86911e6b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/OrderingFromRelation.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/OrderingFromRelation.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.result.OrderingResult; * Ordering obtained from an outlier score. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses DoubleRelation */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/OutlierResult.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/OutlierResult.java index 3aa2337d..daa62fe3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/OutlierResult.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/OutlierResult.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.result.OrderingResult; * parts. * * @author Erich Schubert + * @since 0.3 * * @apiviz.landmark * @apiviz.composedOf OutlierScoreMeta diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/OutlierScoreMeta.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/OutlierScoreMeta.java index 4ce606bf..8f7a0e5c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/OutlierScoreMeta.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/OutlierScoreMeta.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.result.Result; * return {@link Double#NEGATIVE_INFINITY} or {@link Double#POSITIVE_INFINITY}. * * @author Erich Schubert + * @since 0.3 */ public interface OutlierScoreMeta extends Result { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/ProbabilisticOutlierScore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/ProbabilisticOutlierScore.java index bc71379f..2d15dee4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/ProbabilisticOutlierScore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/ProbabilisticOutlierScore.java @@ -30,6 +30,7 @@ package de.lmu.ifi.dbs.elki.result.outlier; * But the baseline may be different from 0.0! * * @author Erich Schubert + * @since 0.3 */ public class ProbabilisticOutlierScore implements OutlierScoreMeta { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/QuotientOutlierScoreMeta.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/QuotientOutlierScoreMeta.java index 7a5ba0ff..53e9c98f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/QuotientOutlierScoreMeta.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/QuotientOutlierScoreMeta.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.result.outlier; * Score for outlier values generated by a quotient. * * @author Erich Schubert + * @since 0.3 * */ public class QuotientOutlierScoreMeta extends BasicOutlierScoreMeta { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/MultipleFilesOutput.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/MultipleFilesOutput.java index 833e95a2..57bb3454 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/MultipleFilesOutput.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/MultipleFilesOutput.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * Manage output to multiple files. * * @author Erich Schubert + * @since 0.2 */ public class MultipleFilesOutput implements StreamFactory { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/SingleStreamOutput.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/SingleStreamOutput.java index 299a665d..764d0e04 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/SingleStreamOutput.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/SingleStreamOutput.java @@ -35,6 +35,7 @@ import java.util.zip.GZIPOutputStream; * Class to output all result data to a single stream (e.g. Stdout, single file) * * @author Erich Schubert + * @since 0.2 */ public class SingleStreamOutput implements StreamFactory { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/StreamFactory.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/StreamFactory.java index 2f0b51a4..91800a93 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/StreamFactory.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/StreamFactory.java @@ -32,6 +32,7 @@ import java.io.PrintStream; * Note: these classes need to be rewritten. Contributions welcome! * * @author Erich Schubert + * @since 0.2 */ public interface StreamFactory { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriteable.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriteable.java index 90e54841..1559971a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriteable.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriteable.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter; * human reading and storage in CSV files. * * @author Erich Schubert + * @since 0.2 */ //TODO: split TextWriteable interface into data writing and metadata writing? public interface TextWriteable { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriter.java index cca91f75..49aeb2fa 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriter.java @@ -59,8 +59,10 @@ import de.lmu.ifi.dbs.elki.result.ResultUtil; import de.lmu.ifi.dbs.elki.result.SettingsResult; import de.lmu.ifi.dbs.elki.result.textwriter.naming.NamingScheme; import de.lmu.ifi.dbs.elki.result.textwriter.naming.SimpleEnumeratingScheme; +import de.lmu.ifi.dbs.elki.result.textwriter.writers.TextWriterDoubleArray; import de.lmu.ifi.dbs.elki.result.textwriter.writers.TextWriterDoubleDoublePair; import de.lmu.ifi.dbs.elki.result.textwriter.writers.TextWriterIgnore; +import de.lmu.ifi.dbs.elki.result.textwriter.writers.TextWriterIntArray; import de.lmu.ifi.dbs.elki.result.textwriter.writers.TextWriterObjectArray; import de.lmu.ifi.dbs.elki.result.textwriter.writers.TextWriterObjectInline; import de.lmu.ifi.dbs.elki.result.textwriter.writers.TextWriterPair; @@ -69,8 +71,8 @@ import de.lmu.ifi.dbs.elki.result.textwriter.writers.TextWriterVector; import de.lmu.ifi.dbs.elki.utilities.HandlerList; import de.lmu.ifi.dbs.elki.utilities.datastructures.hierarchy.Hierarchy; import de.lmu.ifi.dbs.elki.utilities.exceptions.UnableToComplyException; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.TrackedParameter; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.SerializedParameterization; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.TrackedParameter; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ClassParameter; import de.lmu.ifi.dbs.elki.utilities.pairs.DoubleDoublePair; import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; @@ -81,6 +83,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * Note: these classes need to be rewritten. Contributions welcome! * * @author Erich Schubert + * @since 0.2 * * @apiviz.landmark * @apiviz.uses TextWriterStream oneway - - writesTo @@ -107,6 +110,8 @@ public class TextWriter { writers.insertHandler(Pair.class, new TextWriterPair()); writers.insertHandler(DoubleDoublePair.class, new TextWriterDoubleDoublePair()); writers.insertHandler(FeatureVector.class, trivialwriter); + writers.insertHandler(double[].class, new TextWriterDoubleArray()); + writers.insertHandler(int[].class, new TextWriterIntArray()); // these object can be serialized inline with toString() writers.insertHandler(String.class, trivialwriter); writers.insertHandler(Double.class, trivialwriter); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterStream.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterStream.java index f6476e52..98237e3e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterStream.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterStream.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.HandlerList; * Representation of an output stream to a text file. * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses de.lmu.ifi.dbs.elki.result.textwriter.StreamFactory oneway - - * wraps diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterWriterInterface.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterWriterInterface.java index 4d9109eb..ffb36758 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterWriterInterface.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterWriterInterface.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.UnableToComplyException; * Base class for object writers. * * @author Erich Schubert + * @since 0.2 * * @param <O> Object type (usually the class itself) */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/naming/NamingScheme.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/naming/NamingScheme.java index 1524d32a..e8c6285c 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/naming/NamingScheme.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/naming/NamingScheme.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.data.Cluster; * Naming scheme implementation for clusterings. * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses Cluster */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/naming/SimpleEnumeratingScheme.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/naming/SimpleEnumeratingScheme.java index 7aa62404..794c40a2 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/naming/SimpleEnumeratingScheme.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/naming/SimpleEnumeratingScheme.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.data.Clustering; * as name, and add an enumeration postfix * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses Clustering */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterDoubleArray.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterDoubleArray.java new file mode 100644 index 00000000..cfadd3ef --- /dev/null +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterDoubleArray.java @@ -0,0 +1,51 @@ +package de.lmu.ifi.dbs.elki.result.textwriter.writers; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; +import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterWriterInterface; +import de.lmu.ifi.dbs.elki.utilities.FormatUtil; + +/** + * Write a double array. + * + * @author Erich Schubert + * @since 0.2 + */ +public class TextWriterDoubleArray extends TextWriterWriterInterface<double[]> { + /** + * Serialize an object into the inline section. + */ + @Override + public void write(TextWriterStream out, String label, double[] v) { + StringBuilder buf = new StringBuilder(); + if(label != null) { + buf.append(label).append('='); + } + if(v != null) { + FormatUtil.formatTo(buf, v, " "); + } + out.inlinePrintNoQuotes(buf.toString()); + } +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterDoubleDoublePair.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterDoubleDoublePair.java index c827cf7e..75f9394f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterDoubleDoublePair.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterDoubleDoublePair.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.DoubleDoublePair; * Write a pair * * @author Erich Schubert + * @since 0.2 * */ public class TextWriterDoubleDoublePair extends TextWriterWriterInterface<DoubleDoublePair> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterIgnore.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterIgnore.java index 6f3a67ce..a632d43a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterIgnore.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterIgnore.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterWriterInterface; * Ignore the given object when serializing to text. * * @author Erich Schubert + * @since 0.2 */ public class TextWriterIgnore extends TextWriterWriterInterface<Object> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterIntArray.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterIntArray.java new file mode 100644 index 00000000..2e275f46 --- /dev/null +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterIntArray.java @@ -0,0 +1,51 @@ +package de.lmu.ifi.dbs.elki.result.textwriter.writers; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterStream; +import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterWriterInterface; +import de.lmu.ifi.dbs.elki.utilities.FormatUtil; + +/** + * Write a double array. + * + * @author Erich Schubert + * @since 0.2 + */ +public class TextWriterIntArray extends TextWriterWriterInterface<int[]> { + /** + * Serialize an object into the inline section. + */ + @Override + public void write(TextWriterStream out, String label, int[] v) { + StringBuilder buf = new StringBuilder(); + if(label != null) { + buf.append(label).append('='); + } + if(v != null) { + FormatUtil.formatTo(buf, v, " "); + } + out.inlinePrintNoQuotes(buf.toString()); + } +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectArray.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectArray.java index bfac06c3..67a4635f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectArray.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectArray.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterWriterInterface; * Write an object into the inline section, using the objects toString method. * * @author Erich Schubert + * @since 0.2 * */ public class TextWriterObjectArray<T> extends TextWriterWriterInterface<T[]> { @@ -40,7 +41,7 @@ public class TextWriterObjectArray<T> extends TextWriterWriterInterface<T[]> { public void write(TextWriterStream out, String label, T[] v) { StringBuilder buf = new StringBuilder(); if(label != null) { - buf.append(label).append("="); + buf.append(label).append('='); } if(v != null) { for (T o : v) { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectComment.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectComment.java index 519fd41d..338dfd98 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectComment.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectComment.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterWriterInterface; * method. * * @author Erich Schubert + * @since 0.2 * */ public class TextWriterObjectComment extends TextWriterWriterInterface<Object> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectInline.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectInline.java index 8782e49f..1e5f5268 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectInline.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectInline.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterWriterInterface; * Write an object into the inline section, using the objects toString method. * * @author Erich Schubert + * @since 0.2 * */ public class TextWriterObjectInline extends TextWriterWriterInterface<Object> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterPair.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterPair.java index 3870dcf6..ff428381 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterPair.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterPair.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * Write a pair * * @author Erich Schubert + * @since 0.2 * */ public class TextWriterPair extends TextWriterWriterInterface<Pair<?,?>> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterTextWriteable.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterTextWriteable.java index fe99f668..29c653df 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterTextWriteable.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterTextWriteable.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterWriterInterface; * Write an object, using the objects own {@link TextWriteable} interface. * * @author Erich Schubert + * @since 0.2 * * @apiviz.uses TextWriteable */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterVector.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterVector.java index 568f4e30..a4b2d0ef 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterVector.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterVector.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.result.textwriter.TextWriterWriterInterface; * Write an object into the inline section, using the objects toString method. * * @author Erich Schubert + * @since 0.2 */ public class TextWriterVector extends TextWriterWriterInterface<Vector> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/Alias.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/Alias.java index ea5d864d..ba4e385a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/Alias.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/Alias.java @@ -33,6 +33,7 @@ import java.lang.annotation.Target; * This interface defines alias names for classes. * * @author Erich Schubert + * @since 0.3 */ @Documented @Retention(RetentionPolicy.RUNTIME) diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/BitsUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/BitsUtil.java index 205336df..5869ab4c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/BitsUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/BitsUtil.java @@ -37,6 +37,7 @@ import java.util.Arrays; * <code>I</code> modify in-place. * * @author Erich Schubert + * @since 0.5.0 */ public final class BitsUtil { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ClassGenericsUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ClassGenericsUtil.java index 8c938e02..e746114d 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ClassGenericsUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ClassGenericsUtil.java @@ -61,6 +61,8 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * developer should use {@link #instantiate} instead. * </p> * + * @author Erich Schubert + * @since 0.2 */ public final class ClassGenericsUtil { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/DatabaseUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/DatabaseUtil.java index a4976b5d..e4f708d9 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/DatabaseUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/DatabaseUtil.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.index.preprocessed.knn.MaterializeKNNPreprocessor; * covariances etc. * * @author Erich Schubert + * @since 0.2 */ public final class DatabaseUtil { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ELKIServiceLoader.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ELKIServiceLoader.java index dd3a9ba6..bdddac1d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ELKIServiceLoader.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ELKIServiceLoader.java @@ -29,7 +29,6 @@ import java.net.URL; import java.util.Enumeration; import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; -import de.lmu.ifi.dbs.elki.utilities.io.BufferedLineReader; /** * Class that emulates the behavior of an java ServiceLoader, except that the @@ -37,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.io.BufferedLineReader; * also we need to do the instantiations our way with the parameterizable API. * * @author Erich Schubert + * @since 0.5.0 */ public class ELKIServiceLoader { /** @@ -79,11 +79,35 @@ public class ELKIServiceLoader { Enumeration<URL> configfiles = cl.getResources(fullName); while(configfiles.hasMoreElements()) { URL nextElement = configfiles.nextElement(); + char[] buf = new char[0x4000]; try ( - InputStreamReader is = new InputStreamReader(nextElement.openStream(), "utf-8"); - BufferedLineReader r = new BufferedLineReader(is)) { - while(r.nextLine()) { - parseLine(parent, r.getBuffer(), nextElement); + InputStreamReader is = new InputStreamReader(nextElement.openStream(), "UTF-8");) { + int start = 0, cur = 0, valid = is.read(buf, 0, buf.length); + char c; + while(cur < valid) { + // Find newline or end + while(cur < valid && (c = buf[cur]) != '\n' && c != '\r') { + cur++; + } + if(cur == valid && is.ready()) { + // Move consumed buffer contents: + if(start > 0) { + System.arraycopy(buf, start, buf, 0, valid - start); + valid -= start; + cur -= start; + start = 0; + } + else if(valid == buf.length) { + throw new IOException("Buffer size exceeded. Maximum line length in service files is: " + buf.length + " in file: " + fullName); + } + valid = is.read(buf, valid, buf.length - valid); + continue; + } + parseLine(parent, buf, start, cur, nextElement); + while(cur < valid && ((c = buf[cur]) == '\n' || c == '\r')) { + cur++; + } + start = cur; } } catch(IOException x) { @@ -103,38 +127,33 @@ public class ELKIServiceLoader { * @param line Line to read * @param nam File name for error reporting */ - private static void parseLine(Class<?> parent, CharSequence line, URL nam) { - if(line == null) { - return; - } - int begin = 0, end = line.length(); - while(begin < end && line.charAt(begin) == ' ') { + private static void parseLine(Class<?> parent, char[] line, int begin, int end, URL nam) { + while(begin < end && line[begin] == ' ') { begin++; } - if(begin >= end || line.charAt(begin) == '#') { + if(begin >= end || line[begin] == '#') { return; // Empty/comment lines are okay, continue } - assert(begin == 0 || line.charAt(begin - 1) == ' '); // Find end of class name: int cend = begin + 1; - while(cend < end && line.charAt(cend) != ' ') { + while(cend < end && line[cend] != ' ') { cend++; } // Class name: - String cname = line.subSequence(begin, cend).toString(); + String cname = new String(line, begin, cend - begin); ELKIServiceRegistry.register(parent, cname); for(int abegin = cend + 1, aend = -1; abegin < end; abegin = aend + 1) { // Skip whitespace: - while(abegin < end && line.charAt(abegin) == ' ') { + while(abegin < end && line[abegin] == ' ') { abegin++; } // Find next whitespace: aend = abegin + 1; - while(aend < end && line.charAt(aend) != ' ') { + while(aend < end && line[aend] != ' ') { aend++; } if(abegin < aend) { - ELKIServiceRegistry.registerAlias(parent, line.subSequence(abegin, aend).toString(), cname); + ELKIServiceRegistry.registerAlias(parent, new String(line, abegin, aend - abegin), cname); } } return; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ELKIServiceRegistry.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ELKIServiceRegistry.java index 512de9d1..841dd41a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ELKIServiceRegistry.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ELKIServiceRegistry.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * Registry of available implementations in ELKI. * * @author Erich Schubert + * @since 0.7.0 */ public class ELKIServiceRegistry { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ELKIServiceScanner.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ELKIServiceScanner.java index 1bd139c4..05083a60 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ELKIServiceScanner.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ELKIServiceScanner.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.logging.Logging; * A collection of inspection-related utility functions. * * @author Erich Schubert + * @since 0.7.0 */ public class ELKIServiceScanner { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/FileUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/FileUtil.java index 5ad6d392..17a0e2c2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/FileUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/FileUtil.java @@ -35,6 +35,7 @@ import java.util.zip.GZIPInputStream; * Various static helper methods to deal with files and file names. * * @author Erich Schubert + * @since 0.2 */ public final class FileUtil { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/FormatUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/FormatUtil.java index ad385bcb..dc634eb2 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/FormatUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/FormatUtil.java @@ -38,6 +38,10 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; /** * Utility methods for output formatting of various number objects + * + * @author Arthur Zimek + * @author Erich Schubert + * @since 0.2 */ public final class FormatUtil { /** @@ -321,22 +325,33 @@ public final class FormatUtil { /** * Formats the int array a for printing purposes. * + * @param buf The buffer to serialize to * @param a the int array to be formatted - * @param sep the separator between the single values of the float array, e.g. - * ',' - * @return a String representing the int array a + * @param sep the separator between the single values of the array, e.g. ',' + * @return The output buffer {@code buf} */ - public static String format(int[] a, String sep) { + public static StringBuilder formatTo(StringBuilder buf, int[] a, String sep) { if(a.length == 0) { - return ""; + return buf; } - StringBuilder buffer = new StringBuilder(); - buffer.append(a[0]); + buf.append(a[0]); for(int i = 1; i < a.length; i++) { - buffer.append(sep); - buffer.append(a[i]); + buf.append(sep); + buf.append(a[i]); } - return buffer.toString(); + return buf; + } + + /** + * Formats the int array a for printing purposes. + * + * @param a the int array to be formatted + * @param sep the separator between the single values of the array, e.g. ',' + * @return a String representing the int array a + */ + public static String format(int[] a, String sep) { + return (a == null) ? "null" : (a.length == 0) ? "" : // + formatTo(new StringBuilder(), a, sep).toString(); } /** @@ -1302,8 +1317,8 @@ public final class FormatUtil { * Infinity pattern, with any capitalization */ private static final char[] INFINITY_PATTERN = { // - 'I', 'n', 'f', 'i', 'n', 'i', 't', 'y', // - 'i', 'N', 'F', 'I', 'N', 'I', 'T', 'Y' }; + 'I', 'n', 'f', 'i', 'n', 'i', 't', 'y', // + 'i', 'N', 'F', 'I', 'N', 'I', 'T', 'Y' }; /** Length of pattern */ private static final int INFINITY_LENGTH = INFINITY_PATTERN.length >> 1; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/HandlerList.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/HandlerList.java index e85d9bbd..f82ba9f3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/HandlerList.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/HandlerList.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * query object can be cast to the handlers restriction class. * * @author Erich Schubert + * @since 0.2 * * @param <H> Parent class/interface for all handlers */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/Util.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/Util.java index 5ed07ec3..24a94ec3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/Util.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/Util.java @@ -33,6 +33,10 @@ import java.util.Random; * classes. * * @see de.lmu.ifi.dbs.elki.utilities + * + * @author Arthur Zimek + * @author Erich Schubert + * @since 0.2 */ public final class Util { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/QuickSelect.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/QuickSelect.java index 070876ca..1d852688 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/QuickSelect.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/QuickSelect.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.database.ids.ModifiableDoubleDBIDList; * Charles Antony Richard Hoare * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.uses ArrayModifiableDBIDs * @apiviz.uses List diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ArrayAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ArrayAdapter.java index 5a2a1056..fd8624de 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ArrayAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ArrayAdapter.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike; * Adapter for array-like things. For example, arrays and lists. * * @author Erich Schubert + * @since 0.4.0 * * @param <T> Item type * @param <A> Array object type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ArrayDBIDsAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ArrayDBIDsAdapter.java index a6881e43..640d5c70 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ArrayDBIDsAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ArrayDBIDsAdapter.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBID; * Use a DBID array in a generic array-like context. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses ArrayDBIDs */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ArrayLikeUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ArrayLikeUtil.java index dc4f3b1c..386243f6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ArrayLikeUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ArrayLikeUtil.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * reorganizing the objects into a real array. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.landmark * @apiviz.composedOf ArrayAdapter diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/DoubleArray.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/DoubleArray.java index 2f827bb3..ca225b41 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/DoubleArray.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/DoubleArray.java @@ -27,12 +27,28 @@ import java.util.Arrays; /** * Array of double values. * - * TODO: add remove, sort etc. - * * @author Erich Schubert + * @since 0.7.0 */ public class DoubleArray implements NumberArrayAdapter<Double, DoubleArray> { /** + * Maximum array size permitted by Java. + * + * This is JVM dependent, but 2^31 - 5 is the usual OpenJDK8 value. + */ + private static final int MAX_ARRAY_SIZE = Integer.MAX_VALUE - 5; + + /** + * Last value where we can grow by 50%. + */ + private static final int LAST_GROW_SIZE = 0x5555_5551; + + // Assert that these values match. + static { + assert (LAST_GROW_SIZE + (LAST_GROW_SIZE >>> 1) + 1 <= MAX_ARRAY_SIZE); + } + + /** * (Reused) store for numerical attributes. */ public double[] data; @@ -55,6 +71,12 @@ public class DoubleArray implements NumberArrayAdapter<Double, DoubleArray> { * @param initialsize Initial size. */ public DoubleArray(int initialsize) { + if(initialsize < 0) { + initialsize = 11; + } + else if(initialsize > MAX_ARRAY_SIZE) { + initialsize = MAX_ARRAY_SIZE; + } this.data = new double[initialsize]; this.size = 0; } @@ -80,18 +102,31 @@ public class DoubleArray implements NumberArrayAdapter<Double, DoubleArray> { } /** - * Add a numeric attribute value. + * Append a value. * * @param attribute Attribute value. */ public void add(double attribute) { if(data.length == size) { - data = Arrays.copyOf(data, size << 1); + grow(); } data[size++] = attribute; } /** + * Grow the current array. + * + * @throws OutOfMemoryError + */ + private void grow() throws OutOfMemoryError { + if(data.length == MAX_ARRAY_SIZE) { + throw new OutOfMemoryError("Array size has reached the Java maximum."); + } + final int newsize = (size >= LAST_GROW_SIZE) ? MAX_ARRAY_SIZE : (size + (size >> 1) + 1); + data = Arrays.copyOf(data, newsize); + } + + /** * Get the value at this position. * * @param pos Position @@ -144,8 +179,12 @@ public class DoubleArray implements NumberArrayAdapter<Double, DoubleArray> { */ public void insert(int pos, double val) { if(size == data.length) { - double[] oldd = data; - data = new double[size << 1]; + if(data.length == MAX_ARRAY_SIZE) { + throw new OutOfMemoryError("Array size has reached the Java maximum."); + } + final int newsize = (size >= LAST_GROW_SIZE) ? MAX_ARRAY_SIZE : (size + (size >> 1) + 1); + final double[] oldd = data; + data = new double[newsize]; System.arraycopy(oldd, 0, data, 0, pos); System.arraycopy(oldd, pos, data, pos + 1, size - pos); } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/DoubleArrayAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/DoubleArrayAdapter.java index 719aea8a..221335e9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/DoubleArrayAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/DoubleArrayAdapter.java @@ -26,6 +26,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike; * Use a double array as, well, double array in the ArrayAdapter API. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.exclude */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ExtendedArray.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ExtendedArray.java index 4dfd1ecb..047e5f06 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ExtendedArray.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ExtendedArray.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike; * Class to extend an array with a single element virtually. * * @author Erich Schubert + * @since 0.5.0 * * @param <T> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/FeatureVectorAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/FeatureVectorAdapter.java index 59df30ad..338358f1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/FeatureVectorAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/FeatureVectorAdapter.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.data.FeatureVector; * Use the static instance from {@link ArrayLikeUtil}! * * @author Erich Schubert + * @since 0.4.0 * * @param <F> Feature type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/FlatMatrixAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/FlatMatrixAdapter.java index 487f2d84..1c33872d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/FlatMatrixAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/FlatMatrixAdapter.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Matrix; * Use a matrix as array, by flattening it into a sequence. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.exclude */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/FloatArrayAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/FloatArrayAdapter.java index fd82178a..6f4bfa78 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/FloatArrayAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/FloatArrayAdapter.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike; * Use a double array as, well, double array in the ArrayAdapter API. * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.exclude */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/IdentityArrayAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/IdentityArrayAdapter.java index 3766492d..d81d68f3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/IdentityArrayAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/IdentityArrayAdapter.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike; * Use the static instance from {@link ArrayLikeUtil}! * * @author Erich Schubert + * @since 0.4.0 * * @param <T> Item type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/IntegerArray.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/IntegerArray.java new file mode 100644 index 00000000..15393114 --- /dev/null +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/IntegerArray.java @@ -0,0 +1,264 @@ +package de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike; +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import java.util.Arrays; + +/** + * Array of int values. + * + * @author Erich Schubert + * @since 0.7.0 + */ +public class IntegerArray implements NumberArrayAdapter<Integer, IntegerArray> { + /** + * Maximum array size permitted by Java. + * + * This is JVM dependent, but 2^31 - 5 is the usual OpenJDK8 value. + */ + private static final int MAX_ARRAY_SIZE = Integer.MAX_VALUE - 5; + + /** + * Last value where we can grow by 50%. + */ + private static final int LAST_GROW_SIZE = 0x5555_5551; + + // Assert that these values match. + static { + assert (LAST_GROW_SIZE + (LAST_GROW_SIZE >>> 1) + 1 <= MAX_ARRAY_SIZE); + } + + /** + * (Reused) store for numerical attributes. + */ + public int[] data; + + /** + * Number of numerical attributes. + */ + public int size; + + /** + * Constructor. + */ + public IntegerArray() { + this(11); + } + + /** + * Constructor. + * + * @param initialsize Initial size. + */ + public IntegerArray(int initialsize) { + if(initialsize < 0) { + initialsize = 11; + } + else if(initialsize > MAX_ARRAY_SIZE) { + initialsize = MAX_ARRAY_SIZE; + } + this.data = new int[initialsize]; + this.size = 0; + } + + /** + * Constructor from an existing array. + * + * The new array will be allocated as small as possible, so modifications will + * cause a resize! + * + * @param existing Existing array + */ + public IntegerArray(IntegerArray existing) { + this.data = Arrays.copyOf(existing.data, existing.size); + this.size = existing.size; + } + + /** + * Reset the numeric attribute counter. + */ + public void clear() { + size = 0; + } + + /** + * Append a value. + * + * @param attribute Attribute value. + */ + public void add(int attribute) { + if(data.length == size) { + grow(); + } + data[size++] = attribute; + } + + /** + * Grow the current array. + * + * @throws OutOfMemoryError + */ + private void grow() throws OutOfMemoryError { + if(data.length == MAX_ARRAY_SIZE) { + throw new OutOfMemoryError("Array size has reached the Java maximum."); + } + final int newsize = (size >= LAST_GROW_SIZE) ? MAX_ARRAY_SIZE : (size + (size >> 1) + 1); + data = Arrays.copyOf(data, newsize); + } + + /** + * Get the value at this position. + * + * @param pos Position + * @return Value + */ + public int get(int pos) { + if(pos < 0 || pos >= size) { + throw new ArrayIndexOutOfBoundsException(pos); + } + return data[pos]; + } + + /** + * Set the value at this position. + * + * @param pos Position + * @param value Value + */ + public void set(int pos, int value) { + if(pos < 0 || pos > size) { + throw new ArrayIndexOutOfBoundsException(pos); + } + if(pos == size) { + add(value); + return; + } + data[pos] = value; + } + + /** + * Remove a range from the array. + * + * @param start Start + * @param len Length + */ + public void remove(int start, int len) { + final int end = start + len; + if(end > size) { + throw new ArrayIndexOutOfBoundsException(size); + } + System.arraycopy(data, end, data, start, size - end); + size -= len; + } + + /** + * Insert a value at the given position. + * + * @param pos Insert position + * @param val Value to insert + */ + public void insert(int pos, int val) { + if(size == data.length) { + if(data.length == MAX_ARRAY_SIZE) { + throw new OutOfMemoryError("Array size has reached the Java maximum."); + } + final int newsize = (size >= LAST_GROW_SIZE) ? MAX_ARRAY_SIZE : (size + (size >> 1) + 1); + final int[] oldd = data; + data = new int[newsize]; + System.arraycopy(oldd, 0, data, 0, pos); + System.arraycopy(oldd, pos, data, pos + 1, size - pos); + } + else { + System.arraycopy(data, pos, data, pos + 1, size - pos); + } + data[pos] = val; + size++; + } + + /** + * Get the size of the array. + * + * @return Size + */ + public int size() { + return size; + } + + /** + * Sort the contents. + */ + public void sort() { + Arrays.sort(data, 0, size); + } + + // NumberArrayAdapter: + + @Override + public int size(IntegerArray array) { + return array.size; + } + + @Override + public Integer get(IntegerArray array, int off) throws IndexOutOfBoundsException { + return array.data[off]; + } + + @Override + public double getDouble(IntegerArray array, int off) throws IndexOutOfBoundsException { + return (double) array.data[off]; + } + + @Override + public float getFloat(IntegerArray array, int off) throws IndexOutOfBoundsException { + return (float) array.data[off]; + } + + @Override + public int getInteger(IntegerArray array, int off) throws IndexOutOfBoundsException { + return array.data[off]; + } + + @Override + public short getShort(IntegerArray array, int off) throws IndexOutOfBoundsException { + return (short) array.data[off]; + } + + @Override + public long getLong(IntegerArray array, int off) throws IndexOutOfBoundsException { + return (long) array.data[off]; + } + + @Override + public byte getByte(IntegerArray array, int off) throws IndexOutOfBoundsException { + return (byte) array.data[off]; + } + + /** + * Return a copy of the contents as array. + * + * @return Copy of the contents. + */ + public int[] toArray() { + return Arrays.copyOf(data, size); + } +}
\ No newline at end of file diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ListArrayAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ListArrayAdapter.java index 242caa48..7e92978a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ListArrayAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/ListArrayAdapter.java @@ -30,6 +30,7 @@ import java.util.List; * Use the static instance from {@link ArrayLikeUtil}! * * @author Erich Schubert + * @since 0.4.0 * * @param <T> Data object type. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/NumberArrayAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/NumberArrayAdapter.java index 532862cc..c0777fbd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/NumberArrayAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/NumberArrayAdapter.java @@ -26,6 +26,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike; * Adapter for arrays of numbers, to avoid boxing. * * @author Erich Schubert + * @since 0.5.0 * * @param <N> Number type * @param <A> Array type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/NumberListArrayAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/NumberListArrayAdapter.java index e712ac9a..4c0fec71 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/NumberListArrayAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/NumberListArrayAdapter.java @@ -32,6 +32,7 @@ import java.util.List; * Use the static instance from {@link ArrayLikeUtil}! * * @author Erich Schubert + * @since 0.5.0 * * @param <T> Data object type. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/NumberVectorAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/NumberVectorAdapter.java index 8192f3b8..bb66c33e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/NumberVectorAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/NumberVectorAdapter.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.data.NumberVector; * Use the static instance from {@link ArrayLikeUtil}! * * @author Erich Schubert + * @since 0.5.0 */ public class NumberVectorAdapter implements NumberArrayAdapter<Number, NumberVector> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/SingleSubsetArrayAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/SingleSubsetArrayAdapter.java index 3d8e8c3e..cd905948 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/SingleSubsetArrayAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/SingleSubsetArrayAdapter.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike; * Single-item subset adapter * * @author Erich Schubert + * @since 0.4.0 * * @param <T> Entry type * @param <A> Array type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/SubsetArrayAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/SubsetArrayAdapter.java index 077a0e8d..1299d178 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/SubsetArrayAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/SubsetArrayAdapter.java @@ -26,6 +26,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike; * Subset array adapter (allows reordering and projection). * * @author Erich Schubert + * @since 0.4.0 * * @param <T> Entry type * @param <A> Array type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/SubsetNumberArrayAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/SubsetNumberArrayAdapter.java index 8a1a064b..7d1d1890 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/SubsetNumberArrayAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/SubsetNumberArrayAdapter.java @@ -26,6 +26,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike; * Subset array adapter (allows reordering and projection) * * @author Erich Schubert + * @since 0.4.0 * * @param <T> Entry type * @param <A> Array type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/VectorAdapter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/VectorAdapter.java index 26da061a..48705ece 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/VectorAdapter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/VectorAdapter.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * Use the static instance from {@link ArrayLikeUtil}! * * @author Erich Schubert + * @since 0.5.0 */ public class VectorAdapter implements NumberArrayAdapter<Double, Vector> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/DoubleIntegerArrayQuickSort.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/DoubleIntegerArrayQuickSort.java index a48a175b..47bc1281 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/DoubleIntegerArrayQuickSort.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/DoubleIntegerArrayQuickSort.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.arrays; * best of 5 heuristic. * * @author Erich Schubert + * @since 0.5.5 */ public class DoubleIntegerArrayQuickSort { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/IntegerArrayQuickSort.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/IntegerArrayQuickSort.java index ece63ea6..c1b64097 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/IntegerArrayQuickSort.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/IntegerArrayQuickSort.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * objects. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.uses IntegerComparator */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/IntegerComparator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/IntegerComparator.java index 11f79e45..2cb8e755 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/IntegerComparator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/IntegerComparator.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.arrays; * Interface for comparing two Integer. * * @author Erich Schubert + * @since 0.4.0 */ public interface IntegerComparator { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hash/Unique.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hash/Unique.java index 5e991156..294d7220 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hash/Unique.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hash/Unique.java @@ -33,6 +33,7 @@ import java.util.Arrays; * allows retrieving existing values. * * @author Erich Schubert + * @since 0.7.0 * * @param <E> */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparableMaxHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparableMaxHeap.java index 968251d6..54f6821b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparableMaxHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparableMaxHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has UnsortedIter * @param <K> Key type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparableMinHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparableMinHeap.java index 8cd4ef0a..4a1cc8a9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparableMinHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparableMinHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has UnsortedIter * @param <K> Key type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparatorMaxHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparatorMaxHeap.java index f3cc6d56..78c00bc5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparatorMaxHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparatorMaxHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has UnsortedIter * @param <K> Key type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparatorMinHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparatorMinHeap.java index 12a15d46..466c3e7b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparatorMinHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ComparatorMinHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has UnsortedIter * @param <K> Key type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleHeap.java index ba853032..76927fc3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleHeap.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.Iter; * Basic in-memory heap for double values. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has UnsortedIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleIntegerHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleIntegerHeap.java index 2adc17fd..96ca70c2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleIntegerHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleIntegerHeap.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.Iter; * Basic in-memory heap interface, for double keys and int values. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has UnsortedIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleIntegerMaxHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleIntegerMaxHeap.java index b0e62c30..ae40da63 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleIntegerMaxHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleIntegerMaxHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has UnsortedIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleIntegerMinHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleIntegerMinHeap.java index d94b63c1..bfc21240 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleIntegerMinHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleIntegerMinHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has UnsortedIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleLongHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleLongHeap.java index 551c4131..f4011bcd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleLongHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleLongHeap.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.Iter; * Basic in-memory heap interface, for double keys and long values. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has UnsortedIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleLongMaxHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleLongMaxHeap.java index b0f0af50..88a7ee7c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleLongMaxHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleLongMaxHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has UnsortedIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleLongMinHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleLongMinHeap.java index fcc3526d..7fc2a5dd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleLongMinHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleLongMinHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has UnsortedIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleMaxHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleMaxHeap.java index d1a6ed0f..92a1ba9c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleMaxHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleMaxHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has UnsortedIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleMinHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleMinHeap.java index f4c53260..3c8eda0b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleMinHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleMinHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has UnsortedIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleObjectHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleObjectHeap.java index 77a380bf..a822cb64 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleObjectHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleObjectHeap.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.Iter; * Basic in-memory heap interface, for double keys and V values. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has UnsortedIter * @param <V> Value type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleObjectMaxHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleObjectMaxHeap.java index 96b03a67..6e8e5c02 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleObjectMaxHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleObjectMaxHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has UnsortedIter * @param <V> Value type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleObjectMinHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleObjectMinHeap.java index c04fb7cb..b87e6281 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleObjectMinHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleObjectMinHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has UnsortedIter * @param <V> Value type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoublePriorityObject.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoublePriorityObject.java index 342c064d..cd8ef1cb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoublePriorityObject.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoublePriorityObject.java @@ -31,6 +31,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.heap; * the priority. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Stored object type. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/Heap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/Heap.java index 5f6b27c2..fe8aaa53 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/Heap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/Heap.java @@ -36,6 +36,7 @@ import java.util.Comparator; * O(n log n). This is implemented via a simple validTo counter. * * @author Erich Schubert + * @since 0.4.0 * * @param <E> Element type. Should be {@link java.lang.Comparable} or a * {@link java.util.Comparator} needs to be given. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerHeap.java index c7e897d8..4a1a7ca7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerHeap.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.Iter; * Basic in-memory heap for int values. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has UnsortedIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerMaxHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerMaxHeap.java index a4e54147..54af796b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerMaxHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerMaxHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has UnsortedIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerMinHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerMinHeap.java index 0e56e2e1..17ece116 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerMinHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerMinHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has UnsortedIter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerObjectHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerObjectHeap.java index defacf83..08eecf02 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerObjectHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerObjectHeap.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.Iter; * Basic in-memory heap interface, for int keys and V values. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has UnsortedIter * @param <V> Value type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerObjectMaxHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerObjectMaxHeap.java index ce3d7809..7f62c277 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerObjectMaxHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerObjectMaxHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has UnsortedIter * @param <V> Value type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerObjectMinHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerObjectMinHeap.java index c087d7d2..b46dadaa 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerObjectMinHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerObjectMinHeap.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.math.MathUtil; * Binary heap for primitive types. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.has UnsortedIter * @param <V> Value type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerPriorityObject.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerPriorityObject.java index c809e113..4e7c21c2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerPriorityObject.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerPriorityObject.java @@ -31,6 +31,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.heap; * the priority. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Stored object type. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ObjectHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ObjectHeap.java index 8b00dbbe..20ee0547 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ObjectHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/ObjectHeap.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.Iter; * Basic in-memory heap for K values. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has UnsortedIter * @param <K> Key type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TiedTopBoundedHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TiedTopBoundedHeap.java index f9628f1a..ea1a356a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TiedTopBoundedHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TiedTopBoundedHeap.java @@ -33,6 +33,7 @@ import java.util.List; * elements. * * @author Erich Schubert + * @since 0.4.0 * * @param <E> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TiedTopBoundedUpdatableHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TiedTopBoundedUpdatableHeap.java index 88036e00..83261ef5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TiedTopBoundedUpdatableHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TiedTopBoundedUpdatableHeap.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * elements. * * @author Erich Schubert + * @since 0.4.0 * * @param <E> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TopBoundedHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TopBoundedHeap.java index 9fd95a1b..b884c58a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TopBoundedHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TopBoundedHeap.java @@ -30,6 +30,7 @@ import java.util.Comparator; * {@code k} Elements only. * * @author Erich Schubert + * @since 0.4.0 * * @param <E> Element type. Should be {@link Comparable} or a {@link Comparator} * needs to be given. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TopBoundedUpdatableHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TopBoundedUpdatableHeap.java index 80b5768a..ff0dd369 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TopBoundedUpdatableHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TopBoundedUpdatableHeap.java @@ -30,6 +30,7 @@ import java.util.Comparator; * {@code k} Elements only. * * @author Erich Schubert + * @since 0.4.0 * * @param <E> Element type. Should be {@link Comparable} or a {@link Comparator} * needs to be given. diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/UpdatableHeap.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/UpdatableHeap.java index be089725..4af70021 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/UpdatableHeap.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/UpdatableHeap.java @@ -32,6 +32,7 @@ import java.util.Comparator; * A heap as used in OPTICS that allows updating entries. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/FilteredIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/FilteredIter.java index 67876387..aac710e8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/FilteredIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/FilteredIter.java @@ -26,6 +26,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.hierarchy; * Filtered iterator. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf Hierarchy.Iter * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/HashMapHierarchy.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/HashMapHierarchy.java index 59ec00f0..2f478866 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/HashMapHierarchy.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/HashMapHierarchy.java @@ -29,6 +29,7 @@ import java.util.HashMap; * Centralized hierarchy implementation, using a HashMap of Lists. * * @author Erich Schubert + * @since 0.6.0 * * @param <O> Object type (arbitrary!) */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/Hierarchy.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/Hierarchy.java index 6c932451..04d1cd5b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/Hierarchy.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/Hierarchy.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.hierarchy; * object, i.e. {@code hierarchy.iterChildren(object);}. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has Iter * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/ModifiableHierarchy.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/ModifiableHierarchy.java index 3496e41c..4b3af7c2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/ModifiableHierarchy.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/ModifiableHierarchy.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.hierarchy; * Modifiable Hierarchy. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/StackedIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/StackedIter.java index 52ecc0e3..93aa71b7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/StackedIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/StackedIter.java @@ -26,6 +26,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.hierarchy; * Filtered iterator. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf Hierarchy * @apiviz.composedOf Hierarchy.Iter diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/AbstractObjDynamicHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/AbstractObjDynamicHistogram.java index 9c2f3a60..d07e078b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/AbstractObjDynamicHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/AbstractObjDynamicHistogram.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * into the histogram. * * @author Erich Schubert + * @since 0.5.5 * * @param <T> Data type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/AbstractObjStaticHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/AbstractObjStaticHistogram.java index 709f7ceb..743bb179 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/AbstractObjStaticHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/AbstractObjStaticHistogram.java @@ -30,6 +30,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.histogram; * left and right. * * @author Erich Schubert + * @since 0.5.5 * * @param <T> Data type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/AbstractStaticHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/AbstractStaticHistogram.java index b0728ddb..a1a81174 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/AbstractStaticHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/AbstractStaticHistogram.java @@ -31,6 +31,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.histogram; * adapted for multiple use cases. * * @author Erich Schubert + * @since 0.5.5 */ public abstract class AbstractStaticHistogram implements Histogram { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleArrayStaticHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleArrayStaticHistogram.java index 7ea5b623..4e0081d5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleArrayStaticHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleArrayStaticHistogram.java @@ -29,6 +29,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>. * primitive in Java. * * @author Erich Schubert + * @since 0.5.5 */ public final class DoubleArrayStaticHistogram extends AbstractObjStaticHistogram<double[]> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleDynamicHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleDynamicHistogram.java index 2f2e6a02..88a70ad9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleDynamicHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleDynamicHistogram.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * bins to the data fed into the histogram. * * @author Erich Schubert + * @since 0.5.5 */ public class DoubleDynamicHistogram extends DoubleStaticHistogram { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleHistogram.java index 9a26c264..84f06713 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleHistogram.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.histogram; * Histogram storing double values. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has Iter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleStaticHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleStaticHistogram.java index 63ba3e21..6d4dc22b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleStaticHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleStaticHistogram.java @@ -32,6 +32,7 @@ import java.util.Arrays; * left and right. * * @author Erich Schubert + * @since 0.5.5 */ public class DoubleStaticHistogram extends AbstractStaticHistogram implements DoubleHistogram { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/FloatDynamicHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/FloatDynamicHistogram.java index 261c7a7f..007ef6e6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/FloatDynamicHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/FloatDynamicHistogram.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * bins to the data fed into the histogram. * * @author Erich Schubert + * @since 0.5.5 */ public class FloatDynamicHistogram extends FloatStaticHistogram { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/FloatHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/FloatHistogram.java index 81edb88c..18e992b8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/FloatHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/FloatHistogram.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.histogram; * Histogram storing float values. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has Iter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/FloatStaticHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/FloatStaticHistogram.java index 6e4d78f5..079e8e0e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/FloatStaticHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/FloatStaticHistogram.java @@ -32,6 +32,7 @@ import java.util.Arrays; * left and right. * * @author Erich Schubert + * @since 0.5.5 */ public class FloatStaticHistogram extends AbstractStaticHistogram implements FloatHistogram { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/Histogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/Histogram.java index a8fd60c0..1632fc45 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/Histogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/Histogram.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.ArrayIter; * to be shared for primitive types, too! * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has Iter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntArrayStaticHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntArrayStaticHistogram.java index d3d278ee..8e838b4e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntArrayStaticHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntArrayStaticHistogram.java @@ -29,6 +29,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>. * primitive in Java. * * @author Erich Schubert + * @since 0.5.5 */ public final class IntArrayStaticHistogram extends AbstractObjStaticHistogram<int[]> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntDynamicHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntDynamicHistogram.java index 4d3a5045..13ab7b35 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntDynamicHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntDynamicHistogram.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * bins to the data fed into the histogram. * * @author Erich Schubert + * @since 0.5.5 */ public class IntDynamicHistogram extends IntStaticHistogram { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntHistogram.java index d448c852..ce2b39aa 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntHistogram.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.histogram; * Histogram storing int values. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has Iter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntStaticHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntStaticHistogram.java index bd367837..3cbe83bc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntStaticHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/IntStaticHistogram.java @@ -32,6 +32,7 @@ import java.util.Arrays; * left and right. * * @author Erich Schubert + * @since 0.5.5 */ public class IntStaticHistogram extends AbstractStaticHistogram implements IntHistogram { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongArrayStaticHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongArrayStaticHistogram.java index 907fa7ca..a922935a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongArrayStaticHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongArrayStaticHistogram.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.histogram; * primitive in Java. * * @author Erich Schubert + * @since 0.5.5 */ public final class LongArrayStaticHistogram extends AbstractObjStaticHistogram<long[]> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongDynamicHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongDynamicHistogram.java index 78385a30..cc5b5dc6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongDynamicHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongDynamicHistogram.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * bins to the data fed into the histogram. * * @author Erich Schubert + * @since 0.5.5 */ public class LongDynamicHistogram extends LongStaticHistogram { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongHistogram.java index ec1ba994..893e0f47 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongHistogram.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.histogram; * Histogram storing long values. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has Iter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongStaticHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongStaticHistogram.java index ae37dbcc..9cc201ae 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongStaticHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/LongStaticHistogram.java @@ -32,6 +32,7 @@ import java.util.Arrays; * left and right. * * @author Erich Schubert + * @since 0.5.5 */ public class LongStaticHistogram extends AbstractStaticHistogram implements LongHistogram { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/MeanVarianceStaticHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/MeanVarianceStaticHistogram.java index f3d054cd..5adcc9bd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/MeanVarianceStaticHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/MeanVarianceStaticHistogram.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.math.MeanVariance; * left and right. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.composedOf MeanVariance */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ObjHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ObjHistogram.java index e1d75b76..2ce2926f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ObjHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ObjHistogram.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.histogram; * Basic interface for object based histograms (static and flexible). * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has Iter * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ShortDynamicHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ShortDynamicHistogram.java index 8fd1ffbd..d0a932a1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ShortDynamicHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ShortDynamicHistogram.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.BitsUtil; * bins to the data fed into the histogram. * * @author Erich Schubert + * @since 0.5.5 */ public class ShortDynamicHistogram extends ShortStaticHistogram { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ShortHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ShortHistogram.java index 706d43e8..14e1ec55 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ShortHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ShortHistogram.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.histogram; * Histogram storing short values. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.has Iter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ShortStaticHistogram.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ShortStaticHistogram.java index 4c49f595..ebfc6365 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ShortStaticHistogram.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ShortStaticHistogram.java @@ -32,6 +32,7 @@ import java.util.Arrays; * left and right. * * @author Erich Schubert + * @since 0.5.5 */ public class ShortStaticHistogram extends AbstractStaticHistogram implements ShortHistogram { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/ArrayIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/ArrayIter.java index d3deb054..3f26f417 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/ArrayIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/ArrayIter.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.iterator; * Array iterators can also go backwards and seek. * * @author Erich Schubert + * @since 0.2 * * @apiviz.excludeSubtypes */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/ArrayListIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/ArrayListIter.java index 175ccfb2..441eaee4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/ArrayListIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/ArrayListIter.java @@ -32,6 +32,7 @@ import java.util.List; * access and seeking (i.e. ArrayLists, but not Linked Lists!) * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.excludeSubtypes * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/Iter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/Iter.java index d362ff37..23cf34fe 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/Iter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/Iter.java @@ -52,6 +52,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.iterator; * </pre> * * @author Erich Schubert + * @since 0.5.0 * * @apiviz.landmark * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/MIter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/MIter.java index b7b69cc7..557870de 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/MIter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/iterator/MIter.java @@ -40,6 +40,7 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures.iterator; * </pre> * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.excludeSubtypes */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/UnionFind.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/UnionFind.java index bbba1c8e..55b0b561 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/UnionFind.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/UnionFind.java @@ -27,9 +27,10 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDRef; import de.lmu.ifi.dbs.elki.database.ids.DBIDs; /** - * Union-find implementations in ELKI + * Union-find implementations in ELKI, for DBID objects. * * @author Erich Schubert + * @since 0.7.0 */ public interface UnionFind { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/UnionFindUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/UnionFindUtil.java index ee403a66..38ec2559 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/UnionFindUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/UnionFindUtil.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.StaticDBIDs; * Union-find algorithm factory, to choose the best implementation. * * @author Erich Schubert + * @since 0.7.0 */ public class UnionFindUtil { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionInteger.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionInteger.java new file mode 100644 index 00000000..b7fc8478 --- /dev/null +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionInteger.java @@ -0,0 +1,174 @@ +package de.lmu.ifi.dbs.elki.utilities.datastructures.unionfind; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2016 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import java.util.Arrays; + +import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; +import gnu.trove.list.TIntList; +import gnu.trove.list.array.TIntArrayList; + +/** + * Union-find algorithm for primitive integers, with optimizations. + * + * This is the weighted quick union approach, weighted by count and using + * path-halving for optimization. + * + * Reference: + * <p> + * R. Sedgewick<br /> + * 1.3 Union-Find Algorithms<br /> + * Algorithms in C, Parts 1-4 + * </p> + * + * @author Erich Schubert + * @since 0.7.0 + */ +@Reference(authors = "R. Sedgewick", // +title = "1.3 Union-Find Algorithms", // +booktitle = "Algorithms in C, Parts 1-4") +public class WeightedQuickUnionInteger { + /** + * Number of used indexes. + */ + private int used; + + /** + * Parent element + */ + private int[] parent; + + /** + * Weight, for optimization. + */ + private int[] weight; + + /** + * Initial size. + */ + private static final int INITIAL_SIZE = 51; + + /** + * Constructor. + */ + public WeightedQuickUnionInteger() { + weight = new int[INITIAL_SIZE]; + parent = new int[INITIAL_SIZE]; + } + + /** + * Occupy the next unused index. + * + * @param weight Initial weight. + * @return Next unused index. + */ + public int nextIndex(int weight) { + if(used == parent.length) { + int nsize = used + (used >> 1); + this.weight = Arrays.copyOf(this.weight, nsize); + this.parent = Arrays.copyOf(this.parent, nsize); + } + this.weight[used] = weight; + this.parent[used] = used; + return used++; + } + + /** + * Find the parent of an object. + * + * @param cur Current entry + * @return Parent entry + */ + public int find(int cur) { + assert (cur >= 0 && cur < parent.length); + int p = parent[cur], tmp; + while(cur != p) { + tmp = p; + p = parent[cur] = parent[p]; // Perform simple path compression. + cur = tmp; + } + return cur; + } + + /** + * Join the components of elements p and q. + * + * @param first First element + * @param second Second element + * @return Component id. + */ + public int union(int first, int second) { + int firstComponent = find(first), secondComponent = find(second); + if(firstComponent == secondComponent) { + return firstComponent; + } + final int w1 = weight[firstComponent], w2 = weight[secondComponent]; + if(w1 > w2) { + parent[secondComponent] = firstComponent; + weight[firstComponent] += w2; + return firstComponent; + } + else { + parent[firstComponent] = secondComponent; + weight[secondComponent] += w1; + return secondComponent; + } + } + + /** + * Test if two components are connected. + * + * @param first First element + * @param second Second element + * @return {@code true} if they are in the same component. + */ + public boolean isConnected(int first, int second) { + return find(first) == find(second); + } + + /** + * Collect all component root elements. + * + * @return Root elements + */ + public TIntList getRoots() { + TIntList roots = new TIntArrayList(); + for(int i = 0; i < used; i++) { + // roots or one element in component + if(parent[i] == i) { + roots.add(i); + } + } + return roots; + } + + /** + * Number of allocated indexes. + * + * @return Index number. + */ + public int size() { + return used; + } +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionRangeDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionRangeDBIDs.java index 60c719e2..5440e2b5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionRangeDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionRangeDBIDs.java @@ -51,6 +51,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * * @author Evgeniy Faerman * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "R. Sedgewick", // title = "1.3 Union-Find Algorithms", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionStaticDBIDs.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionStaticDBIDs.java index 0e4dd24b..9ed8d618 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionStaticDBIDs.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionStaticDBIDs.java @@ -60,6 +60,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * * @author Evgeniy Faerman * @author Erich Schubert + * @since 0.7.0 */ @Reference(authors = "R. Sedgewick", // title = "1.3 Union-Find Algorithms", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Description.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Description.java index 163af834..1b4963bd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Description.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Description.java @@ -33,6 +33,7 @@ import java.lang.annotation.Target; * Class/algorithm description * * @author Erich Schubert + * @since 0.3 */ @Documented @Retention(RetentionPolicy.RUNTIME) diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/DocumentationUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/DocumentationUtil.java index 0fbc3b96..6caa488b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/DocumentationUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/DocumentationUtil.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.utilities.documentation; * Utilities for extracting documentation from class annotations. * * @author Erich Schubert + * @since 0.3 * * @apiviz.uses de.lmu.ifi.dbs.elki.utilities.documentation.Title * @apiviz.uses de.lmu.ifi.dbs.elki.utilities.documentation.Description diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Reference.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Reference.java index 9c84661e..9e8a37ff 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Reference.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Reference.java @@ -33,6 +33,7 @@ import java.lang.annotation.Target; * Annotation to specify a reference. * * @author Erich Schubert + * @since 0.3 */ @Documented @Retention(RetentionPolicy.RUNTIME) diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Restricted.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Restricted.java index 29955acf..a1725b64 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Restricted.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Restricted.java @@ -34,6 +34,7 @@ import java.lang.annotation.Target; * associated patents, and therefore must not be included in the release. * * @author Erich Schubert + * @since 0.3 */ @Documented @Retention(RetentionPolicy.RUNTIME) diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Title.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Title.java index 77889f03..5e7af068 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Title.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/documentation/Title.java @@ -33,6 +33,7 @@ import java.lang.annotation.Target; * Simple interface to provide a nicer title for the class. * * @author Erich Schubert + * @since 0.3 */ @Documented @Retention(RetentionPolicy.RUNTIME) diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVoting.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVoting.java index 994b8a1b..12e15692 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVoting.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVoting.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.ensemble; * Interface for ensemble voting rules * * @author Erich Schubert + * @since 0.4.0 */ public interface EnsembleVoting { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingInverseMultiplicative.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingInverseMultiplicative.java index 0b4c245f..f0238cc1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingInverseMultiplicative.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingInverseMultiplicative.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * {@code 1-product(1-s_i)} * * @author Erich Schubert + * @since 0.5.0 */ public class EnsembleVotingInverseMultiplicative implements EnsembleVoting { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMax.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMax.java index 67e86277..ba59c1c1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMax.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMax.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.ensemble; * Simple combination rule, by taking the maximum. * * @author Erich Schubert + * @since 0.2 */ public class EnsembleVotingMax implements EnsembleVoting { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMean.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMean.java index 8eec61e4..bf26f9ed 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMean.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMean.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.ensemble; * Simple combination rule, by taking the mean * * @author Erich Schubert + * @since 0.2 */ public class EnsembleVotingMean implements EnsembleVoting { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMedian.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMedian.java index ddd81d40..d48bd474 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMedian.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMedian.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * Note: median is very similar to a <em>majority voting</em>! * * @author Erich Schubert + * @since 0.4.0 */ public class EnsembleVotingMedian implements EnsembleVoting { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMin.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMin.java index 99f193c1..2916be9b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMin.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMin.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.utilities.ensemble; * Simple combination rule, by taking the minimum. * * @author Erich Schubert + * @since 0.5.0 */ public class EnsembleVotingMin implements EnsembleVoting { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMultiplicative.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMultiplicative.java index 5e4f34cd..adfa5b71 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMultiplicative.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/ensemble/EnsembleVotingMultiplicative.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * {@code product(s_i)} * * @author Erich Schubert + * @since 0.5.0 */ public class EnsembleVotingMultiplicative implements EnsembleVoting { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/APIViolationException.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/APIViolationException.java index b6a56a48..82632083 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/APIViolationException.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/APIViolationException.java @@ -36,6 +36,7 @@ package de.lmu.ifi.dbs.elki.utilities.exceptions; * the Java compiler). * * @author Erich Schubert + * @since 0.4.0 */ public class APIViolationException extends AbortException { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/AbortException.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/AbortException.java index 678abdd9..764c68e8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/AbortException.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/AbortException.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.utilities.exceptions; * Exception for aborting some process and transporting a message. * * @author Arthur Zimek + * @since 0.2 */ public class AbortException extends RuntimeException { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/ExceptionMessages.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/ExceptionMessages.java index 68560813..c0302f97 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/ExceptionMessages.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/ExceptionMessages.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.exceptions; * Interface to collect exception messages that are used in several cases. * * @author Arthur Zimek + * @since 0.2 */ public interface ExceptionMessages { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/NotImplementedException.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/NotImplementedException.java index 89f33361..ac116a38 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/NotImplementedException.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/NotImplementedException.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.utilities.exceptions; * See {@link ExceptionMessages} for common explanations. * * @author Erich Schubert + * @since 0.4.0 */ public class NotImplementedException extends AbortException { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/ObjectNotFoundException.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/ObjectNotFoundException.java index f44c11b9..1275c6ae 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/ObjectNotFoundException.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/ObjectNotFoundException.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBID; * Exception thrown when the requested object was not found in the database. * * @author Erich Schubert + * @since 0.4.0 */ public class ObjectNotFoundException extends RuntimeException { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/UnableToComplyException.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/UnableToComplyException.java index ee00ff06..c004e401 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/UnableToComplyException.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/exceptions/UnableToComplyException.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.utilities.exceptions; * General Exception to state inability to execute an operation. * * @author Arthur Zimek + * @since 0.2 */ @SuppressWarnings("serial") public class UnableToComplyException extends Exception { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/BufferedLineReader.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/BufferedLineReader.java index b93c28bf..d387093e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/BufferedLineReader.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/BufferedLineReader.java @@ -28,12 +28,13 @@ import java.io.InputStreamReader; /** * Class for buffered IO, avoiding some of the overheads of the Java API. - * + * * The main difference to the standard Java API is that this implementation will * reuse the buffer. <b>After a call to {@code nextLine()}, the buffer will be * overwitten!</b> - * + * * @author Erich Schubert + * @since 0.7.0 */ public class BufferedLineReader implements AutoCloseable { /** @@ -44,7 +45,7 @@ public class BufferedLineReader implements AutoCloseable { /** * The buffer we read the data into. */ - protected StringBuilder buf = new StringBuilder(); + protected StringBuilder buf = new StringBuilder(1024); /** * Current line number. @@ -98,9 +99,9 @@ public class BufferedLineReader implements AutoCloseable { /** * Reset to a new line reader. - * + * * <b>A previous reader will not be closed automatically!</b> - * + * * @param r New reader */ public void reset(LineReader r) { @@ -110,9 +111,9 @@ public class BufferedLineReader implements AutoCloseable { /** * Reset to a new line reader. - * + * * <b>A previous stream will not be closed automatically!</b> - * + * * @param in New input stream reader */ public void reset(InputStream in) { @@ -122,9 +123,9 @@ public class BufferedLineReader implements AutoCloseable { /** * Reset to a new line reader. - * + * * <b>A previous stream will not be closed automatically!</b> - * + * * @param in New input stream reader */ public void reset(InputStreamReader in) { @@ -134,9 +135,9 @@ public class BufferedLineReader implements AutoCloseable { /** * Get the reader buffer. - * + * * <b>After a call to {@code nextLine()}, the buffer will be overwitten!</b> - * + * * @return Buffer. */ public CharSequence getBuffer() { @@ -145,7 +146,7 @@ public class BufferedLineReader implements AutoCloseable { /** * Get the current line number. - * + * * @return Current line number */ public int getLineNumber() { @@ -154,7 +155,7 @@ public class BufferedLineReader implements AutoCloseable { /** * Read the next line. - * + * * @return {@code true} if another line was read successfully. * @throws IOException on IO errors. */ @@ -179,7 +180,7 @@ public class BufferedLineReader implements AutoCloseable { /** * Get the length of the string, not taking trailing linefeeds into account. - * + * * @param line Input line * @return Length */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteArrayUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteArrayUtil.java index 49493e33..8cb7570a 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteArrayUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteArrayUtil.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * {@link java.io.ByteArrayOutputStream} * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.landmark * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteBufferInputStream.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteBufferInputStream.java index 138957bd..1fcb1f3c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteBufferInputStream.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteBufferInputStream.java @@ -30,6 +30,7 @@ import java.nio.ByteBuffer; * Wrap an existing ByteBuffer as InputStream. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has ByteBuffer */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteBufferOutputStream.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteBufferOutputStream.java index 3e2b397c..8e07f075 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteBufferOutputStream.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteBufferOutputStream.java @@ -30,6 +30,7 @@ import java.nio.ByteBuffer; * Wrap an existing ByteBuffer as OutputStream. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has ByteBuffer */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteBufferSerializer.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteBufferSerializer.java index 94f882ab..c58d6063 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteBufferSerializer.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/ByteBufferSerializer.java @@ -30,6 +30,7 @@ import java.nio.ByteBuffer; * Class to convert from and to byte arrays (in index structures). * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has ByteBuffer - - oneway «serializes to/from» * @apiviz.excludeSubtypes diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FixedSizeByteBufferSerializer.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FixedSizeByteBufferSerializer.java index ac966c7e..e360fc43 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FixedSizeByteBufferSerializer.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FixedSizeByteBufferSerializer.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.io; * Serializers with a fixed length serialization. * * @author Erich Schubert + * @since 0.4.0 * @apiviz.excludeSubtypes * * @param <T> Type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/LineReader.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/LineReader.java index 3bec4ad4..01b1336d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/LineReader.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/LineReader.java @@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.utilities.io; This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures - Copyright (C) 2015 + Copyright (C) 2016 Ludwig-Maximilians-Universität München Lehr- und Forschungseinheit für Datenbanksysteme ELKI Development Team @@ -30,43 +30,52 @@ import java.io.Reader; /** * Fast class to read a file, line per line. - * + * * Lines must be split using Unix newlines <code>\n</code>, linefeeds * <code>\r</code> are ignored. - * + * * This is a rather minimal implementation, which supposedly pays off in * performance. In particular, this class allows recycling the buffer, which * will yield less object allocations and thus less garbage collection. - * + * * Usage example: - * + * * <pre> * StringBuilder buf = new StringBuilder(); * LineReader reader = new LineReader(inputStream); * // Clear buffer, and append next line. - * while(reader.readLine(buf.delete(0, buf.length()))) { + * while(reader.readLine(buf.setLength(0))) { * // process string in buffer. * } * </pre> - * + * * @author Erich Schubert + * @since 0.7.0 */ public class LineReader implements AutoCloseable { - /** Buffer size to use */ + /** + * Default buffer size to use + */ final static int BUFFER_SIZE = 4096; - /** Input stream to read from */ + /** + * Input stream to read from + */ Reader in; - /** Character buffer */ - char[] buffer = new char[BUFFER_SIZE]; + /** + * Character buffer + */ + char[] buffer; - /** Current position, and length of buffer */ + /** + * Current position, and length of buffer + */ int pos = 0, end = 0; /** * Constructor - * + * * @param in Stream */ public LineReader(InputStream in) { @@ -75,16 +84,37 @@ public class LineReader implements AutoCloseable { /** * Constructor - * + * * @param in Reader */ public LineReader(Reader in) { + this(in, BUFFER_SIZE); + } + + /** + * Constructor + * + * @param in Reader + * @param buffersize Buffer size + */ + public LineReader(InputStream in, int buffersize) { + this(new InputStreamReader(in), buffersize); + } + + /** + * Constructor + * + * @param in Reader + * @param buffersize Buffer size + */ + public LineReader(Reader in, int buffersize) { this.in = in; + this.buffer = new char[buffersize]; } /** * Read a line into the given buffer. - * + * * @param buf Buffer. * @return {@code true} if some characters have been read. */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/TokenizedReader.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/TokenizedReader.java index f9363d57..0afcb9ab 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/TokenizedReader.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/TokenizedReader.java @@ -31,6 +31,7 @@ import java.util.regex.Pattern; * Reader that will tokenize the input data as desired. * * @author Erich Schubert + * @since 0.7.0 * * @apiviz.composedOf Tokenizer */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/Tokenizer.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/Tokenizer.java index 67339cd2..b86923d7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/Tokenizer.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/Tokenizer.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.iterator.Iter; * String tokenizer. * * @author Erich Schubert + * @since 0.6.0 */ public class Tokenizer implements Iter { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/AbstractParameterizer.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/AbstractParameterizer.java index f8a7b390..a3559e86 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/AbstractParameterizer.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/AbstractParameterizer.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * Abstract base class that handles the parameterization of a class. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses Parameterization * @apiviz.has de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/InternalParameterizationErrors.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/InternalParameterizationErrors.java index 3301c31c..9173cc24 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/InternalParameterizationErrors.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/InternalParameterizationErrors.java @@ -32,6 +32,7 @@ import java.util.Collection; * This is meant for reporting re-parameterization errors. * * @author Erich Schubert + * @since 0.3 */ public class InternalParameterizationErrors extends ParameterException { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/NoParameterValueException.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/NoParameterValueException.java index 50ad6215..36c23718 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/NoParameterValueException.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/NoParameterValueException.java @@ -25,6 +25,9 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling; /** * Thrown by OptionHandler in case of incorrect parameter-array. + * + * @author Arthur Zimek + * @since 0.2 */ public class NoParameterValueException extends ParameterException { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/OptionID.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/OptionID.java index 20cdc6c7..67c6326e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/OptionID.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/OptionID.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling; * within this class. * * @author Elke Achtert + * @since 0.2 */ public final class OptionID { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/OptionUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/OptionUtil.java index a72035f9..2f0def2b 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/OptionUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/OptionUtil.java @@ -39,6 +39,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; /** * Utility functions related to Option handling. * + * @author Erich Schubert + * @since 0.2 + * * @apiviz.uses Parameter */ public final class OptionUtil { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/ParameterException.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/ParameterException.java index 2a456fed..9527b946 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/ParameterException.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/ParameterException.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling; * Abstract super class for all exceptions thrown during parameterization. * * @author Elke Achtert + * @since 0.2 */ @SuppressWarnings("serial") public abstract class ParameterException extends Exception { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/Parameterizer.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/Parameterizer.java index 2931309f..c0134b40 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/Parameterizer.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/Parameterizer.java @@ -31,6 +31,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * To instantiate a class, use {@link Parameterization#tryInstantiate(Class)}! * * @author Erich Schubert + * @since 0.4.0 */ public interface Parameterizer { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/UnspecifiedParameterException.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/UnspecifiedParameterException.java index c7a9909c..5569a648 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/UnspecifiedParameterException.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/UnspecifiedParameterException.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * Exception when a required parameter was not given. * * @author Erich Schubert + * @since 0.2 */ public class UnspecifiedParameterException extends WrongParameterValueException { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/UnusedParameterException.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/UnusedParameterException.java index 016cdf76..7cd86f8c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/UnusedParameterException.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/UnusedParameterException.java @@ -23,9 +23,11 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling; along with this program. If not, see <http://www.gnu.org/licenses/>. */ - /** * Thrown by OptionHandler in case of request of an unused parameter. + * + * @author Arthur Zimek + * @since 0.2 */ @SuppressWarnings("serial") public class UnusedParameterException extends ParameterException { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/WrongParameterValueException.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/WrongParameterValueException.java index c0bd4b40..cd24cf66 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/WrongParameterValueException.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/WrongParameterValueException.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * Thrown by a Parameterizable object in case of wrong parameter format. * * @author Steffi Wanka + * @since 0.2 */ public class WrongParameterValueException extends ParameterException { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/AbstractNumberConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/AbstractNumberConstraint.java index b08da639..815ccdef 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/AbstractNumberConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/AbstractNumberConstraint.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints; * Abstract super class for constraints dealing with a certain number value. * * @author Elke Achtert + * @since 0.2 * * @apiviz.uses * de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.NumberParameter diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/AllOrNoneMustBeSetGlobalConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/AllOrNoneMustBeSetGlobalConstraint.java index f468af92..3430fd81 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/AllOrNoneMustBeSetGlobalConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/AllOrNoneMustBeSetGlobalConstraint.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * parameters ({@link Parameter}) must be set, or none of them. * * @author Steffi Wanka + * @since 0.2 */ public class AllOrNoneMustBeSetGlobalConstraint implements GlobalParameterConstraint { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/CommonConstraints.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/CommonConstraints.java index 3507e946..09df14df 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/CommonConstraints.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/CommonConstraints.java @@ -27,6 +27,7 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints; * Class storing a number of very common constraints. * * @author Erich Schubert + * @since 0.6.0 * * @apiviz.landmark * @apiviz.composedOf ParameterConstraint diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/EqualSizeGlobalConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/EqualSizeGlobalConstraint.java index ae817a7a..e6257e47 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/EqualSizeGlobalConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/EqualSizeGlobalConstraint.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ListParameter; * ) must have equal list sizes. * * @author Steffi Wanka + * @since 0.2 */ public class EqualSizeGlobalConstraint implements GlobalParameterConstraint { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/EqualStringConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/EqualStringConstraint.java index 52ac3ff6..e7379b6a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/EqualStringConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/EqualStringConstraint.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException * ) to be tested is equal to the specified constraint-strings. * * @author Steffi Wanka + * @since 0.2 * * @apiviz.uses de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.StringParameter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GlobalListSizeConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GlobalListSizeConstraint.java index 05d391b3..21669a38 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GlobalListSizeConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GlobalListSizeConstraint.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ListParameter; * specified by the integer parameter ({@link IntParameter}) given. * * @author Steffi Wanka + * @since 0.2 */ public class GlobalListSizeConstraint implements GlobalParameterConstraint { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GlobalParameterConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GlobalParameterConstraint.java index c01802bc..ae1ea824 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GlobalParameterConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GlobalParameterConstraint.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; * The proper constraint test should be implemented in the method {@link #test()}. * </p> * @author Steffi Wanka + * @since 0.2 * */ public interface GlobalParameterConstraint { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GlobalVectorListElementSizeConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GlobalVectorListElementSizeConstraint.java index 79d67a2c..b162fc4a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GlobalVectorListElementSizeConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GlobalVectorListElementSizeConstraint.java @@ -23,24 +23,24 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints; along with this program. If not, see <http://www.gnu.org/licenses/>. */ -import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.VectorListParameter; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleArrayListParameter; /** * Global parameter constraint for testing if the dimensions of each vector - * specified by a given vector list parameter ({@link VectorListParameter}) + * specified by a given vector list parameter ({@link DoubleArrayListParameter}) * correspond to the value of a integer parameter ({@link IntParameter}) given. * * @author Steffi Wanka + * @since 0.2 */ public class GlobalVectorListElementSizeConstraint implements GlobalParameterConstraint { /** * Vector list parameter. */ - private VectorListParameter vector; + private DoubleArrayListParameter vector; /** * Integer parameter providing the size constraint. @@ -56,7 +56,7 @@ public class GlobalVectorListElementSizeConstraint implements GlobalParameterCon * @param vector the vector list parameter * @param sizeConstraint the integer parameter providing the size constraint */ - public GlobalVectorListElementSizeConstraint(VectorListParameter vector, IntParameter sizeConstraint) { + public GlobalVectorListElementSizeConstraint(DoubleArrayListParameter vector, IntParameter sizeConstraint) { this.vector = vector; this.size = sizeConstraint; } @@ -73,9 +73,12 @@ public class GlobalVectorListElementSizeConstraint implements GlobalParameterCon return; } - for(Vector vec : vector.getValue()) { - if(vec.getDimensionality() != size.intValue()) { - throw new WrongParameterValueException("Global Parameter Constraint Error.\n" + "The vectors of vector list parameter " + vector.getName() + " have not the required dimension of " + size.getValue() + " given by integer parameter " + size.getName() + "."); + for(double[] vec : vector.getValue()) { + if(vec.length != size.intValue()) { + throw new WrongParameterValueException("Global Parameter Constraint Error.\n" // + + "The vectors of vector list parameter " + vector.getName() // + + " have not the required dimension of " + size.getValue() // + + " given by integer parameter " + size.getName() + "."); } } } @@ -84,4 +87,4 @@ public class GlobalVectorListElementSizeConstraint implements GlobalParameterCon public String getDescription() { return "The dimensionality of the vectors of vector list parameter " + vector.getName() + " must have the value of integer parameter " + size.getName(); } -}
\ No newline at end of file +} diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GreaterConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GreaterConstraint.java index 002ff4f3..b9e445d1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GreaterConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GreaterConstraint.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.NumberParameter; * constraint value. * * @author Steffi Wanka + * @since 0.2 */ public class GreaterConstraint extends AbstractNumberConstraint<Number> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GreaterEqualConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GreaterEqualConstraint.java index fab416d4..a8791f97 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GreaterEqualConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/GreaterEqualConstraint.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.NumberParameter; * than the specified constraint value. * * @author Steffi Wanka + * @since 0.2 */ public class GreaterEqualConstraint extends AbstractNumberConstraint<Number> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessConstraint.java index c63fa1ea..c2b73d1d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessConstraint.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.NumberParameter; * constraint value. * * @author Steffi Wanka + * @since 0.2 */ public class LessConstraint extends AbstractNumberConstraint<Number> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessEqualConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessEqualConstraint.java index 8aef29b4..a8c210d4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessEqualConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessEqualConstraint.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.NumberParameter; * the specified constraint value. * * @author Steffi Wanka + * @since 0.2 */ public class LessEqualConstraint extends AbstractNumberConstraint<Number> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessEqualGlobalConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessEqualGlobalConstraint.java index c3f4ef09..10f12988 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessEqualGlobalConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessEqualGlobalConstraint.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.NumberParameter; * the value of the second number parameter ({@link NumberParameter}). * * @author Steffi Wanka + * @since 0.2 * @param <T> Number type */ public class LessEqualGlobalConstraint<T extends Number> implements GlobalParameterConstraint { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessGlobalConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessGlobalConstraint.java index 0ab9fbae..57b9d473 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessGlobalConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/LessGlobalConstraint.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.NumberParameter; * value of the second number parameter ({@link NumberParameter}) given. * * @author Steffi Wanka + * @since 0.2 * @param <T> Number type */ public class LessGlobalConstraint<T extends Number> implements GlobalParameterConstraint { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ListEachConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ListEachConstraint.java index 764b1773..ff1aba69 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ListEachConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ListEachConstraint.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; * Applies constraints to all elements of a list. * * @author Erich Schubert + * @since 0.5.5 * * @apiviz.composedOf ParameterConstraint oneway 1 n */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ListParameterNoDuplicateValueConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ListParameterNoDuplicateValueConstraint.java index e0dfe3e1..f5c052b6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ListParameterNoDuplicateValueConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ListParameterNoDuplicateValueConstraint.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException * is not allowed to have duplicate values. * * @author Arthur Zimek + * @since 0.5.5 */ public class ListParameterNoDuplicateValueConstraint<T extends Object> implements ParameterConstraint<List<T>> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ListSizeConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ListSizeConstraint.java index 0969ac06..c9f273de 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ListSizeConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ListSizeConstraint.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ListParameter; * FIXME: Unfortunately, we cannot have good type safety anymore right now. * * @author Steffi Wanka + * @since 0.2 * * @apiviz.uses * de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ListParameter diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/NoDuplicateValueGlobalConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/NoDuplicateValueGlobalConstraint.java index 4efd6118..55ea5363 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/NoDuplicateValueGlobalConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/NoDuplicateValueGlobalConstraint.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * parameters ({@link NumberParameter}) are not allowed to have the same value. * * @author Steffi Wanka + * @since 0.2 */ public class NoDuplicateValueGlobalConstraint implements GlobalParameterConstraint { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/OneMustBeSetGlobalConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/OneMustBeSetGlobalConstraint.java index af35e3e9..9ed325f4 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/OneMustBeSetGlobalConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/OneMustBeSetGlobalConstraint.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * set. * * @author Steffi Wanka + * @since 0.2 */ public class OneMustBeSetGlobalConstraint implements GlobalParameterConstraint { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/OnlyOneIsAllowedToBeSetGlobalConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/OnlyOneIsAllowedToBeSetGlobalConstraint.java index c37a05f2..58c69dd9 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/OnlyOneIsAllowedToBeSetGlobalConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/OnlyOneIsAllowedToBeSetGlobalConstraint.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * parameters ({@link Parameter}) is allowed to be set. * * @author Steffi Wanka + * @since 0.2 */ public class OnlyOneIsAllowedToBeSetGlobalConstraint implements GlobalParameterConstraint { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ParameterConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ParameterConstraint.java index 99009941..9061533b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ParameterConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ParameterConstraint.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; * </p> * * @author Steffi Wanka + * @since 0.2 * @param <T> the type of the parameter the constraint applies to */ public interface ParameterConstraint<T> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ParameterFlagGlobalConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ParameterFlagGlobalConstraint.java index 03e4b9e1..3de8ecb2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ParameterFlagGlobalConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/ParameterFlagGlobalConstraint.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * not. * * @author Steffi Wanka + * @since 0.2 * * @apiviz.uses de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag * @apiviz.uses diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/StringLengthConstraint.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/StringLengthConstraint.java index 50417b21..7a6acd32 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/StringLengthConstraint.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/constraints/StringLengthConstraint.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException * . * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.StringParameter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/AbstractParameterization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/AbstractParameterization.java index 4980af5f..67180790 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/AbstractParameterization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/AbstractParameterization.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * Abstract class with shared code for parameterization handling. * * @author Erich Schubert + * @since 0.3 */ public abstract class AbstractParameterization implements Parameterization { // TODO: refactor "tryInstantiate" even in a higher class? diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ChainedParameterization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ChainedParameterization.java index 98cfa5a9..f4f8ca3c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ChainedParameterization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ChainedParameterization.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * for examples. * * @author Erich Schubert + * @since 0.3 */ public class ChainedParameterization extends AbstractParameterization { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/EmptyParameterization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/EmptyParameterization.java index fe1de0be..c89a1420 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/EmptyParameterization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/EmptyParameterization.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * Parameterization handler that only allows the use of default values. * * @author Erich Schubert + * @since 0.3 */ public class EmptyParameterization extends AbstractParameterization { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ListParameterization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ListParameterization.java index c67533a6..542c98ef 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ListParameterization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ListParameterization.java @@ -33,24 +33,25 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; -import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; /** * Parameterization handler using a List and OptionIDs, for programmatic use. * * @author Erich Schubert + * @since 0.3 */ public class ListParameterization extends AbstractParameterization { /** * The actual parameters, for storage */ - LinkedList<Pair<OptionID, Object>> parameters = new LinkedList<>(); + List<ParameterPair> parameters; /** * Default constructor. */ public ListParameterization() { super(); + this.parameters = new LinkedList<>(); } /** @@ -58,10 +59,11 @@ public class ListParameterization extends AbstractParameterization { * * @param dbParameters existing parameter collection */ - public ListParameterization(Collection<Pair<OptionID, Object>> dbParameters) { + public ListParameterization(Collection<ParameterPair> dbParameters) { this(); - for (Pair<OptionID, Object> pair : dbParameters) { - addParameter(pair.first, pair.second); + this.parameters = new LinkedList<>(); + for(ParameterPair pair : dbParameters) { + addParameter(pair.option, pair.value); } } @@ -71,7 +73,7 @@ public class ListParameterization extends AbstractParameterization { * @param optionid Option ID */ public void addFlag(OptionID optionid) { - parameters.add(new Pair<OptionID, Object>(optionid, Flag.SET)); + parameters.add(new ParameterPair(optionid, Flag.SET)); } /** @@ -81,7 +83,7 @@ public class ListParameterization extends AbstractParameterization { * @param value Value */ public void addParameter(OptionID optionid, Object value) { - parameters.add(new Pair<>(optionid, value)); + parameters.add(new ParameterPair(optionid, value)); } /** @@ -90,7 +92,7 @@ public class ListParameterization extends AbstractParameterization { * @param flag Flag to add, if set */ public void forwardOption(Flag flag) { - if (flag.isDefined() && flag.getValue().booleanValue()) { + if(flag.isDefined() && flag.getValue().booleanValue()) { addFlag(flag.getOptionID()); } } @@ -101,19 +103,19 @@ public class ListParameterization extends AbstractParameterization { * @param param Parameter to add */ public void forwardOption(Parameter<?> param) { - if (param.isDefined()) { + if(param.isDefined()) { addParameter(param.getOptionID(), param.getValue()); } } @Override public boolean setValueForOption(Parameter<?> opt) throws ParameterException { - Iterator<Pair<OptionID, Object>> iter = parameters.iterator(); - while (iter.hasNext()) { - Pair<OptionID, Object> pair = iter.next(); - if (pair.first == opt.getOptionID()) { + Iterator<ParameterPair> iter = parameters.iterator(); + while(iter.hasNext()) { + ParameterPair pair = iter.next(); + if(pair.option == opt.getOptionID()) { iter.remove(); - opt.setValue(pair.second); + opt.setValue(pair.value); return true; } } @@ -125,7 +127,7 @@ public class ListParameterization extends AbstractParameterization { * * @return Unused parameters. */ - public List<Pair<OptionID, Object>> getRemainingParameters() { + public List<ParameterPair> getRemainingParameters() { return parameters; } @@ -145,9 +147,9 @@ public class ListParameterization extends AbstractParameterization { @Override public String toString() { StringBuilder buf = new StringBuilder(); - for (Pair<OptionID, Object> pair : parameters) { - buf.append('-').append(pair.getFirst().toString()).append(' '); - buf.append(pair.getSecond().toString()).append(' '); + for(ParameterPair pair : parameters) { + buf.append('-').append(pair.option.toString()).append(' '); + buf.append(pair.value.toString()).append(' '); } return buf.toString(); } @@ -159,16 +161,53 @@ public class ListParameterization extends AbstractParameterization { */ public ArrayList<String> serialize() { ArrayList<String> params = new ArrayList<>(); - for (Pair<OptionID, Object> pair : parameters) { - params.add("-" + pair.getFirst().toString()); - if (pair.getSecond() instanceof String) { - params.add((String) pair.getSecond()); - } else if (pair.getSecond() instanceof Class) { - params.add(((Class<?>) pair.getSecond()).getCanonicalName()); - } else { // Fallback: - params.add(pair.getSecond().toString()); + for(ParameterPair pair : parameters) { + params.add("-" + pair.option.toString()); + if(pair.value instanceof String) { + params.add((String) pair.value); + } + else if(pair.value instanceof Class) { + params.add(((Class<?>) pair.value).getCanonicalName()); + } + else { // Fallback: + params.add(pair.value.toString()); } } return params; } + + /** + * Parameter pair, package-private. + * + * @author Erich Schubert + * + * @apiviz.exclude + */ + static final class ParameterPair { + /** + * Option key. + */ + public OptionID option; + + /** + * Option value. + */ + public Object value; + + /** + * Constructor. + * + * @param key Option key + * @param value Option value + */ + public ParameterPair(OptionID key, Object value) { + this.option = key; + this.value = value; + } + + @Override + public String toString() { + return "-" + option.getName() + " " + value; + } + } } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/MergedParameterization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/MergedParameterization.java index 4faa3c60..926e660f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/MergedParameterization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/MergedParameterization.java @@ -23,17 +23,16 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization; along with this program. If not, see <http://www.gnu.org/licenses/>. */ -import java.util.Collection; import java.util.ArrayList; +import java.util.Collection; import java.util.List; import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; import de.lmu.ifi.dbs.elki.utilities.optionhandling.InternalParameterizationErrors; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.GlobalParameterConstraint; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization.ParameterPair; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; -import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; /** * This configuration can be "rewound" to allow the same values to be consumed @@ -42,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair; * e.g. in visualization classes. * * @author Erich Schubert + * @since 0.3 */ // TODO: Can we merge MergedParameterization and TrackParameters into one? public class MergedParameterization implements Parameterization { @@ -58,7 +58,7 @@ public class MergedParameterization implements Parameterization { /** * Parameters to rewind. */ - final private List<Pair<OptionID, Object>> used; + final private List<ParameterPair> used; /** * Constructor. @@ -79,7 +79,7 @@ public class MergedParameterization implements Parameterization { * @param current Current parameterization to re-used * @param used Used parameters list. */ - private MergedParameterization(Parameterization inner, ListParameterization current, List<Pair<OptionID, Object>> used) { + private MergedParameterization(Parameterization inner, ListParameterization current, List<ParameterPair> used) { super(); this.inner = inner; this.current = current; @@ -91,8 +91,8 @@ public class MergedParameterization implements Parameterization { */ public void rewind() { synchronized(used) { - for(Pair<OptionID, Object> pair : used) { - current.addParameter(pair.first, pair.second); + for(ParameterPair pair : used) { + current.addParameter(pair.option, pair.value); } used.clear(); } @@ -102,7 +102,7 @@ public class MergedParameterization implements Parameterization { public boolean setValueForOption(Parameter<?> opt) throws ParameterException { try { if(current.setValueForOption(opt)) { - used.add(new Pair<OptionID, Object>(opt.getOptionID(), opt.getValue())); + used.add(new ParameterPair(opt.getOptionID(), opt.getValue())); return true; } } @@ -110,10 +110,10 @@ public class MergedParameterization implements Parameterization { current.reportError(e); } if(inner.setValueForOption(opt)) { - used.add(new Pair<OptionID, Object>(opt.getOptionID(), opt.getValue())); + used.add(new ParameterPair(opt.getOptionID(), opt.getValue())); return true; } - used.add(new Pair<OptionID, Object>(opt.getOptionID(), opt.getDefaultValue())); + used.add(new ParameterPair(opt.getOptionID(), opt.getDefaultValue())); return false; } @@ -128,7 +128,7 @@ public class MergedParameterization implements Parameterization { public Collection<ParameterException> getErrors() { return current.getErrors(); } - + @Override public boolean hasErrors() { return current.hasErrors(); @@ -142,11 +142,11 @@ public class MergedParameterization implements Parameterization { @Override public boolean grab(Parameter<?> opt) { try { - if (setValueForOption(opt)) { + if(setValueForOption(opt)) { return true; } // Try default value instead. - if (opt.tryDefaultValue()) { + if(opt.tryDefaultValue()) { return true; } // No value available. @@ -175,7 +175,7 @@ public class MergedParameterization implements Parameterization { return ClassGenericsUtil.tryInstantiate(r, c, this); } catch(Exception e) { - reportError(new InternalParameterizationErrors("Error instantiating internal class: "+c.getName(), e)); + reportError(new InternalParameterizationErrors("Error instantiating internal class: " + c.getName(), e)); return null; } } @@ -186,7 +186,7 @@ public class MergedParameterization implements Parameterization { return ClassGenericsUtil.tryInstantiate(c, c, this); } catch(Exception e) { - reportError(new InternalParameterizationErrors("Error instantiating internal class: "+c.getName(), e)); + reportError(new InternalParameterizationErrors("Error instantiating internal class: " + c.getName(), e)); return null; } } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/Parameterization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/Parameterization.java index f165942e..29c22e27 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/Parameterization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/Parameterization.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * @apiviz.uses ParameterException * * @author Erich Schubert + * @since 0.3 */ public interface Parameterization { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/SerializedParameterization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/SerializedParameterization.java index b5ba3e58..2837983d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/SerializedParameterization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/SerializedParameterization.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * When building parameter lists, use {@link ListParameterization} where possible. * * @author Erich Schubert + * @since 0.3 */ public class SerializedParameterization extends AbstractParameterization { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/TrackParameters.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/TrackParameters.java index 5429ea8b..4b8ea073 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/TrackParameters.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/TrackParameters.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * All actual Parameterization operations are forwarded to the inner class. * * @author Erich Schubert + * @since 0.3 * * @apiviz.composedOf TrackedParameter */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/TrackedParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/TrackedParameter.java index caa87440..e039f492 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/TrackedParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/TrackedParameter.java @@ -28,6 +28,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * Class containing an object, and the associated value. * * @author Erich Schubert + * @since 0.3 */ public class TrackedParameter { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/UnParameterization.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/UnParameterization.java index a1d58676..ea48655c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/UnParameterization.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/UnParameterization.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * in a non-recursive way. * * @author Erich Schubert + * @since 0.3 */ public class UnParameterization implements Parameterization { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/AbstractParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/AbstractParameter.java index d78d0dcc..17d17c6d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/AbstractParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/AbstractParameter.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.ParameterConstra * * @author Steffi Wanka * @author Erich Schubert + * @since 0.3 * * @apiviz.composedOf OptionID * @apiviz.uses ParameterConstraint diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ClassListParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ClassListParameter.java index d9d1a3a2..b0ce1bc7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ClassListParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ClassListParameter.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * * @author Steffi Wanka * @author Erich Schubert + * @since 0.3 * * @apiviz.uses ELKIServiceRegistry * @@ -96,6 +97,23 @@ public class ClassListParameter<C> extends ListParameter<ClassListParameter<C>, return buf.toString(); } + @Override + public String getDefaultValueAsString() { + StringBuilder buf = new StringBuilder(); + final String defPackage = restrictionClass.getPackage().getName() + "."; + for(Class<? extends C> c : getDefaultValue()) { + if(buf.length() > 0) { + buf.append(LIST_SEP); + } + String name = c.getName(); + if(name.startsWith(defPackage)) { + name = name.substring(defPackage.length()); + } + buf.append(name); + } + return buf.toString(); + } + @SuppressWarnings("unchecked") @Override protected List<Class<? extends C>> parseValue(Object obj) throws ParameterException { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ClassParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ClassParameter.java index 6f562838..39e0daae 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ClassParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ClassParameter.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * * @author Steffi Wanka * @author Erich Schubert + * @since 0.2 * * @apiviz.uses ELKIServiceRegistry * diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/VectorListParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/DoubleArrayListParameter.java index b6d999fb..696adbff 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/VectorListParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/DoubleArrayListParameter.java @@ -3,7 +3,7 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters; This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures - Copyright (C) 2015 + Copyright (C) 2016 Ludwig-Maximilians-Universität München Lehr- und Forschungseinheit für Datenbanksysteme ELKI Development Team @@ -23,12 +23,11 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters; */ import java.util.ArrayList; +import java.util.Arrays; import java.util.Iterator; import java.util.List; -import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; import de.lmu.ifi.dbs.elki.utilities.FormatUtil; -import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.DoubleArray; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException; @@ -39,8 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.ParameterConstra * * @author Steffi Wanka * @author Erich Schubert + * @since 0.3 */ -public class VectorListParameter extends ListParameter<VectorListParameter, List<Vector>> { +public class DoubleArrayListParameter extends ListParameter<DoubleArrayListParameter, List<double[]>> { /** * Constructs a vector list parameter with the given name and description. * @@ -48,7 +48,7 @@ public class VectorListParameter extends ListParameter<VectorListParameter, List * @param constraint Constraint * @param defaultValue Default value */ - public VectorListParameter(OptionID optionID, ParameterConstraint<List<Vector>> constraint, List<Vector> defaultValue) { + public DoubleArrayListParameter(OptionID optionID, ParameterConstraint<List<double[]>> constraint, List<double[]> defaultValue) { super(optionID, defaultValue); addConstraint(constraint); } @@ -60,7 +60,7 @@ public class VectorListParameter extends ListParameter<VectorListParameter, List * @param constraint Constraint * @param optional Optional flag */ - public VectorListParameter(OptionID optionID, ParameterConstraint<List<Vector>> constraint, boolean optional) { + public DoubleArrayListParameter(OptionID optionID, ParameterConstraint<List<double[]>> constraint, boolean optional) { super(optionID, optional); addConstraint(constraint); } @@ -71,7 +71,7 @@ public class VectorListParameter extends ListParameter<VectorListParameter, List * @param optionID Option ID * @param constraint Constraint */ - public VectorListParameter(OptionID optionID, ParameterConstraint<List<Vector>> constraint) { + public DoubleArrayListParameter(OptionID optionID, ParameterConstraint<List<double[]>> constraint) { super(optionID); addConstraint(constraint); } @@ -82,11 +82,9 @@ public class VectorListParameter extends ListParameter<VectorListParameter, List * @param optionID Option ID * @param defaultValue Default value */ - // Indiscernible from optionID, constraints - /* - * public VectorListParameter(OptionID optionID, List<Vector> defaultValue) { - * super(optionID, defaultValue); } - */ + public DoubleArrayListParameter(OptionID optionID, List<double[]> defaultValue) { + super(optionID, defaultValue); + } /** * Constructs a vector list parameter with the given name and description. @@ -94,7 +92,7 @@ public class VectorListParameter extends ListParameter<VectorListParameter, List * @param optionID Option ID * @param optional Optional flag */ - public VectorListParameter(OptionID optionID, boolean optional) { + public DoubleArrayListParameter(OptionID optionID, boolean optional) { super(optionID, optional); } @@ -103,17 +101,17 @@ public class VectorListParameter extends ListParameter<VectorListParameter, List * * @param optionID Option ID */ - public VectorListParameter(OptionID optionID) { + public DoubleArrayListParameter(OptionID optionID) { super(optionID); } @Override public String getValueAsString() { StringBuilder buf = new StringBuilder(); - List<Vector> val = getValue(); - Iterator<Vector> valiter = val.iterator(); + List<double[]> val = getValue(); + Iterator<double[]> valiter = val.iterator(); while(valiter.hasNext()) { - buf.append(FormatUtil.format(valiter.next().getArrayRef(), LIST_SEP)); + buf.append(FormatUtil.format(valiter.next(), LIST_SEP)); // Append separation character if(valiter.hasNext()) { buf.append(VECTOR_SEP); @@ -122,47 +120,47 @@ public class VectorListParameter extends ListParameter<VectorListParameter, List return buf.toString(); } - @SuppressWarnings("unchecked") @Override - protected List<Vector> parseValue(Object obj) throws ParameterException { - try { - List<?> l = List.class.cast(obj); - // do extra validation: - for(Object o : l) { - List<?> v = List.class.cast(o); - for(Object c : v) { - if(!(c instanceof Double)) { - throw new WrongParameterValueException("Wrong parameter format for parameter \"" + getName() + "\". Given list contains objects of different type!"); - } - } + public String getDefaultValueAsString() { + StringBuilder buf = new StringBuilder(); + List<double[]> val = getDefaultValue(); + Iterator<double[]> valiter = val.iterator(); + while(valiter.hasNext()) { + buf.append(FormatUtil.format(valiter.next(), LIST_SEP)); + // Append separation character + if(valiter.hasNext()) { + buf.append(VECTOR_SEP); } - // TODO: can we use reflection to get extra checks? - // TODO: Should we copy the list and vectors? - return (List<Vector>) l; - } - catch(ClassCastException e) { - // continue with other attempts. } + return buf.toString(); + } + + @Override + protected List<double[]> parseValue(Object obj) throws ParameterException { if(obj instanceof String) { String[] vectors = VECTOR_SPLIT.split((String) obj); if(vectors.length == 0) { throw new WrongParameterValueException("Wrong parameter format! Given list of vectors for parameter \"" + getName() + "\" is empty!"); } - ArrayList<Vector> vecs = new ArrayList<>(); + ArrayList<double[]> vecs = new ArrayList<>(); - DoubleArray vectorCoord = new DoubleArray(); + double[] buf = new double[11]; + int used = 0; for(String vector : vectors) { - vectorCoord.clear(); + used = 0; String[] coordinates = SPLIT.split(vector); for(String coordinate : coordinates) { try { - vectorCoord.add(FormatUtil.parseDouble(coordinate)); + if(used == buf.length) { + buf = Arrays.copyOf(buf, buf.length << 1); + } + buf[used++] = FormatUtil.parseDouble(coordinate); } catch(NumberFormatException e) { throw new WrongParameterValueException("Wrong parameter format! Coordinates of vector \"" + vector + "\" are not valid!"); } } - vecs.add(new Vector(vectorCoord.toArray())); + vecs.add(Arrays.copyOf(buf, used)); } return vecs; } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/DoubleListParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/DoubleListParameter.java index 074bb0ed..a9fe5471 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/DoubleListParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/DoubleListParameter.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException * * @author Steffi Wanka * @author Erich Schubert + * @since 0.3 */ public class DoubleListParameter extends ListParameter<DoubleListParameter, double[]> { /** @@ -60,6 +61,11 @@ public class DoubleListParameter extends ListParameter<DoubleListParameter, doub } @Override + public String getDefaultValueAsString() { + return FormatUtil.format(getDefaultValue(), LIST_SEP); + } + + @Override protected double[] parseValue(Object obj) throws ParameterException { if(obj instanceof double[]) { return double[].class.cast(obj); diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/DoubleParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/DoubleParameter.java index a28f8d38..ef7d4a88 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/DoubleParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/DoubleParameter.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException * * @author Steffi Wanka * @author Erich Schubert + * @since 0.2 */ public class DoubleParameter extends NumberParameter<DoubleParameter, Double> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/EnumParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/EnumParameter.java index 0cad6e11..d1fafa79 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/EnumParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/EnumParameter.java @@ -60,6 +60,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException * </p> * * @author Florian Nuecke + * @since 0.4.0 * * @param <E> Enum type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/FileListParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/FileListParameter.java index e5f1b021..cc6d885f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/FileListParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/FileListParameter.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException * * @author Steffi Wanka * @author Erich Schubert + * @since 0.3 */ public class FileListParameter extends ListParameter<FileListParameter, List<File>> { /** @@ -89,6 +90,20 @@ public class FileListParameter extends ListParameter<FileListParameter, List<Fil return buf.toString(); } + @Override + public String getDefaultValueAsString() { + StringBuilder buf = new StringBuilder(); + List<File> val = getDefaultValue(); + Iterator<File> veciter = val.iterator(); + while(veciter.hasNext()) { + buf.append(veciter.next()); + if (veciter.hasNext()) { + buf.append(LIST_SEP); + } + } + return buf.toString(); + } + @SuppressWarnings("unchecked") @Override protected List<File> parseValue(Object obj) throws ParameterException { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/FileParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/FileParameter.java index 0e865f2d..9571a018 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/FileParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/FileParameter.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException * * @author Steffi Wanka * @author Erich Schubert + * @since 0.3 */ // TODO: turn FileType into a Constraint? public class FileParameter extends AbstractParameter<FileParameter, File> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/Flag.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/Flag.java index 8d83ed2c..d1e29eb7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/Flag.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/Flag.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException * * @author Steffi Wanka * @author Erich Schubert + * @since 0.3 */ public class Flag extends AbstractParameter<Flag, Boolean> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/IntListParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/IntListParameter.java index 756dbb90..59bfb3a5 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/IntListParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/IntListParameter.java @@ -23,7 +23,6 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters; along with this program. If not, see <http://www.gnu.org/licenses/>. */ -import de.lmu.ifi.dbs.elki.utilities.BitsUtil; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException; @@ -33,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException * * @author Elke Achtert * @author Erich Schubert + * @since 0.2 */ public class IntListParameter extends ListParameter<IntListParameter, int[]> { /** @@ -70,6 +70,21 @@ public class IntListParameter extends ListParameter<IntListParameter, int[]> { } @Override + public String getDefaultValueAsString() { + int[] val = getDefaultValue(); + if(val.length == 0) { + return ""; + } + StringBuilder buf = new StringBuilder(); + buf.append(val[0]); + for(int i = 1; i < val.length; i++) { + buf.append(LIST_SEP); + buf.append(val[i]); + } + return buf.toString(); + } + + @Override protected int[] parseValue(Object obj) throws ParameterException { if(obj instanceof int[]) { return (int[]) obj; @@ -95,7 +110,7 @@ public class IntListParameter extends ListParameter<IntListParameter, int[]> { /** * Returns a string representation of the parameter's type. - * + * * @return "<int_1,...,int_n>" */ @Override @@ -105,7 +120,9 @@ public class IntListParameter extends ListParameter<IntListParameter, int[]> { /** * Get the values as a bitmask. - * + * + * See also: {@link de.lmu.ifi.dbs.elki.utilities.BitsUtil} + * * @return Bitmask */ public long[] getValueAsBitSet() { @@ -114,9 +131,9 @@ public class IntListParameter extends ListParameter<IntListParameter, int[]> { for(int d : value) { maxd = (d > maxd) ? d : maxd; } - long[] dimensions = BitsUtil.zero(maxd); + long[] dimensions = new long[(maxd >>> 6) + 1]; for(int d : value) { - BitsUtil.setI(dimensions, d); + dimensions[d >>> 6] |= 1L << (d & 0x3F); } return dimensions; } diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/IntParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/IntParameter.java index d6adf273..9ed15e95 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/IntParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/IntParameter.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException * * @author Steffi Wanka * @author Erich Schubert + * @since 0.3 */ public class IntParameter extends NumberParameter<IntParameter, Integer> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ListParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ListParameter.java index 097475fb..82c4a46d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ListParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ListParameter.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; * * @author Steffi Wanka * @author Erich Schubert + * @since 0.2 * * @param <THIS> Type self-reference * @param <T> List type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/LongParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/LongParameter.java index 11aff3cb..f44f759d 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/LongParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/LongParameter.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException * * @author Steffi Wanka * @author Erich Schubert + * @since 0.2 */ public class LongParameter extends NumberParameter<LongParameter, Long> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/NumberParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/NumberParameter.java index c71db779..bb5c6864 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/NumberParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/NumberParameter.java @@ -30,6 +30,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; * * @author Steffi Wanka * @author Erich Schubert + * @since 0.2 * * @param <THIS> type self-reference * @param <T> the type of a possible value (i.e., the type of the option) diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ObjectListParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ObjectListParameter.java index baaa2765..d31c4117 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ObjectListParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ObjectListParameter.java @@ -37,6 +37,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * Parameter that represents a list of objects (in contrast to a class list parameter, they will be instanced at most once.) * * @author Erich Schubert + * @since 0.3 * * @param <C> Class type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ObjectParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ObjectParameter.java index 40d5b49a..aa0e4a17 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ObjectParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ObjectParameter.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz * * @author Steffi Wanka * @author Erich Schubert + * @since 0.3 * @param <C> Class type */ public class ObjectParameter<C> extends ClassParameter<C> { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/Parameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/Parameter.java index 9c2d7ea8..99751076 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/Parameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/Parameter.java @@ -1,10 +1,5 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.UnspecifiedParameterException; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.ParameterConstraint; - /* This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures @@ -28,6 +23,11 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.ParameterConstra along with this program. If not, see <http://www.gnu.org/licenses/>. */ +import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.UnspecifiedParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.ParameterConstraint; + /** * Interface for the parameter of a class. * @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.ParameterConstra * * @author Steffi Wanka * @author Erich Schubert + * @since 0.3 * * @apiviz.composedOf OptionID * @apiviz.uses ParameterConstraint diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/PatternParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/PatternParameter.java index 3c010db6..f2160d53 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/PatternParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/PatternParameter.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException * * @author Steffi Wanka * @author Erich Schubert + * @since 0.3 */ public class PatternParameter extends AbstractParameter<PatternParameter, Pattern> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/RandomParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/RandomParameter.java index 0d5f3741..5e7d6c66 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/RandomParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/RandomParameter.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException * Parameter for random generators and/or random seeds. * * @author Erich Schubert + * @since 0.5.5 */ public class RandomParameter extends AbstractParameter<RandomParameter, RandomFactory> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/StringParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/StringParameter.java index 0f06beef..7882c9ee 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/StringParameter.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/StringParameter.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException * * @author Steffi Wanka * @author Erich Schubert + * @since 0.3 */ public class StringParameter extends AbstractParameter<StringParameter, String> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/DoubleDoublePair.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/DoubleDoublePair.java index af10137b..bdfd2b1c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/DoubleDoublePair.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/DoubleDoublePair.java @@ -29,6 +29,7 @@ import java.util.Comparator; * Pair storing two doubles. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has Comparator */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/DoubleIntPair.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/DoubleIntPair.java index 08d0fadd..8f8481b0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/DoubleIntPair.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/DoubleIntPair.java @@ -29,6 +29,7 @@ import java.util.Comparator; * Pair storing an integer and a double. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has Comparator */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/DoubleObjPair.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/DoubleObjPair.java index 5fdd005e..ccbc38d0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/DoubleObjPair.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/DoubleObjPair.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.utilities.pairs; * Pair storing a native double value and an arbitrary object. * * @author Erich Schubert + * @since 0.4.0 * * @param <O> Object type */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/IntDoublePair.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/IntDoublePair.java index 2b8fd6cf..61993a15 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/IntDoublePair.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/IntDoublePair.java @@ -29,6 +29,7 @@ import java.util.Comparator; * Pair storing an integer and a double. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has Comparator */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/IntIntPair.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/IntIntPair.java index e7fd6db8..10a458d0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/IntIntPair.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/IntIntPair.java @@ -29,6 +29,7 @@ import java.util.Comparator; * Pair storing two integers. * * @author Erich Schubert + * @since 0.2 * * @apiviz.has Comparator */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/Pair.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/Pair.java index 28f7fdaa..40b049f2 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/Pair.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/pairs/Pair.java @@ -36,6 +36,7 @@ import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; * meaningful field names and comparators. * * @author Erich Schubert + * @since 0.2 * * @param <FIRST> first type * @param <SECOND> second type diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/AxisBasedReferencePoints.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/AxisBasedReferencePoints.java index 026cf048..337197a3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/AxisBasedReferencePoints.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/AxisBasedReferencePoints.java @@ -43,6 +43,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * surrounding cube. * * @author Erich Schubert + * @since 0.3 */ public class AxisBasedReferencePoints implements ReferencePointsHeuristic { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/FullDatabaseReferencePoints.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/FullDatabaseReferencePoints.java index aed7845f..9e4b9c8f 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/FullDatabaseReferencePoints.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/FullDatabaseReferencePoints.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.database.relation.RelationUtil; * Strategy to use the complete database as reference points. * * @author Erich Schubert + * @since 0.3 */ public class FullDatabaseReferencePoints implements ReferencePointsHeuristic { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/GridBasedReferencePoints.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/GridBasedReferencePoints.java index 1d614bff..45e3c66b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/GridBasedReferencePoints.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/GridBasedReferencePoints.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * Grid-based strategy to pick reference points. * * @author Erich Schubert + * @since 0.3 */ public class GridBasedReferencePoints implements ReferencePointsHeuristic { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/RandomGeneratedReferencePoints.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/RandomGeneratedReferencePoints.java index 9de4e5e8..9b287443 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/RandomGeneratedReferencePoints.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/RandomGeneratedReferencePoints.java @@ -25,6 +25,7 @@ package de.lmu.ifi.dbs.elki.utilities.referencepoints; import java.util.ArrayList; import java.util.Collection; +import java.util.Random; import de.lmu.ifi.dbs.elki.data.NumberVector; import de.lmu.ifi.dbs.elki.database.relation.Relation; @@ -41,8 +42,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; /** * Reference points generated randomly within the used data space. - * + * * @author Erich Schubert + * @since 0.3 */ public class RandomGeneratedReferencePoints implements ReferencePointsHeuristic { /** @@ -62,7 +64,7 @@ public class RandomGeneratedReferencePoints implements ReferencePointsHeuristic /** * Constructor. - * + * * @param samplesize Size of desired sample set * @param scale Scaling factor * @param rnd Random generator @@ -86,14 +88,14 @@ public class RandomGeneratedReferencePoints implements ReferencePointsHeuristic mean[d] -= delta[d] * .5; } + Random rand = rnd.getSingleThreadedRandom(); ArrayList<Vector> result = new ArrayList<>(samplesize); double[] vec = new double[dim]; for(int i = 0; i < samplesize; i++) { for(int d = 0; d < dim; d++) { - vec[d] = mean[d] + (Math.random() - 0.5) * scale * delta[d]; + vec[d] = mean[d] + (rand.nextDouble() - 0.5) * scale * delta[d]; } Vector newp = new Vector(vec); - // logger.debug("New reference point: " + FormatUtil.format(vec)); result.add(newp); } @@ -102,9 +104,9 @@ public class RandomGeneratedReferencePoints implements ReferencePointsHeuristic /** * Parameterization class. - * + * * @author Erich Schubert - * + * * @apiviz.exclude */ public static class Parameterizer extends AbstractParameterizer { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/RandomSampleReferencePoints.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/RandomSampleReferencePoints.java index a8b17234..14d91a55 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/RandomSampleReferencePoints.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/RandomSampleReferencePoints.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.RandomParameter; * Random-Sampling strategy for picking reference points. * * @author Erich Schubert + * @since 0.3 */ public class RandomSampleReferencePoints implements ReferencePointsHeuristic { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/ReferencePointsHeuristic.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/ReferencePointsHeuristic.java index 2b417d84..00cef7dc 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/ReferencePointsHeuristic.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/ReferencePointsHeuristic.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.database.relation.Relation; * Simple Interface for an heuristic to pick reference points. * * @author Erich Schubert + * @since 0.3 */ public interface ReferencePointsHeuristic { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/StarBasedReferencePoints.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/StarBasedReferencePoints.java index f1e1c1fb..2b35108b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/StarBasedReferencePoints.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/referencepoints/StarBasedReferencePoints.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; * Star-based strategy to pick reference points. * * @author Erich Schubert + * @since 0.3 */ public class StarBasedReferencePoints implements ReferencePointsHeuristic { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/ClipScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/ClipScaling.java index 3917c550..74558293 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/ClipScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/ClipScaling.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * maximum. * * @author Erich Schubert + * @since 0.3 */ public class ClipScaling implements StaticScalingFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/GammaScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/GammaScaling.java index 36fc8eed..7efc5318 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/GammaScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/GammaScaling.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * * @author Erich Schubert * @author Remigius Wojdanowski + * @since 0.3 */ public class GammaScaling implements StaticScalingFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/IdentityScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/IdentityScaling.java index c66a2c7d..46832321 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/IdentityScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/IdentityScaling.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.utilities.scaling; * The trivial "identity" scaling function. * * @author Erich Schubert + * @since 0.3 */ public class IdentityScaling implements StaticScalingFunction { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/LinearScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/LinearScaling.java index de0b5c02..4a65a49a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/LinearScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/LinearScaling.java @@ -29,6 +29,7 @@ import de.lmu.ifi.dbs.elki.math.DoubleMinMax; * Simple linear scaling function. * * @author Erich Schubert + * @since 0.3 */ public class LinearScaling implements StaticScalingFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/MinusLogScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/MinusLogScaling.java index 2c79d8bf..0c8262b0 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/MinusLogScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/MinusLogScaling.java @@ -28,6 +28,7 @@ package de.lmu.ifi.dbs.elki.utilities.scaling; * Scaling function to invert values by computing -1 * Math.log(x) * * @author Erich Schubert + * @since 0.3 */ public class MinusLogScaling implements StaticScalingFunction { @Override diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/ScalingFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/ScalingFunction.java index fce71ffc..9928dcc1 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/ScalingFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/ScalingFunction.java @@ -36,6 +36,7 @@ package de.lmu.ifi.dbs.elki.utilities.scaling; * {@code prepare} statement. * * @author Erich Schubert + * @since 0.3 */ public interface ScalingFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/StaticScalingFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/StaticScalingFunction.java index 72f8c6a7..34c44b88 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/StaticScalingFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/StaticScalingFunction.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.utilities.scaling; * But will always map x to the same f(x) (given the same parameters). * * @author Erich Schubert + * @since 0.3 * */ public interface StaticScalingFunction extends ScalingFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/COPOutlierScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/COPOutlierScaling.java index 122e93b2..ea4dc752 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/COPOutlierScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/COPOutlierScaling.java @@ -58,6 +58,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * </p> * * @author Erich Schubert + * @since 0.6.0 */ @Reference(authors = "H.-P. Kriegel, P. Kröger, E. Schubert, A. Zimek", title = "Interpreting and Unifying Outlier Scores", booktitle = "Proc. 11th SIAM International Conference on Data Mining (SDM), Mesa, AZ, 2011", url = "http://siam.omnibooksonline.com/2011datamining/data/papers/018.pdf") public class COPOutlierScaling implements OutlierScalingFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/HeDESNormalizationOutlierScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/HeDESNormalizationOutlierScaling.java index 2e778500..be9012a8 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/HeDESNormalizationOutlierScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/HeDESNormalizationOutlierScaling.java @@ -35,6 +35,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * Normalization used by HeDES * * @author Erich Schubert + * @since 0.4.0 */ @Reference(authors = "H. V. Nguyen, H. H. Ang, V. Gopalkrishnan", title = "Mining Outliers with Ensemble of Heterogeneous Detectors on Random Subspaces", booktitle = "Proc. 15th International Conference on Database Systems for Advanced Applications (DASFAA 2010)", url = "http://dx.doi.org/10.1007/978-3-642-12026-8_29") public class HeDESNormalizationOutlierScaling implements OutlierScalingFunction { diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/LogRankingPseudoOutlierScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/LogRankingPseudoOutlierScaling.java index a2533119..ab63eabd 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/LogRankingPseudoOutlierScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/LogRankingPseudoOutlierScaling.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * a normal distribution. * * @author Erich Schubert + * @since 0.4.0 */ public class LogRankingPseudoOutlierScaling implements OutlierScalingFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MinusLogGammaScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MinusLogGammaScaling.java index 00c2a9f0..002ff917 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MinusLogGammaScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MinusLogGammaScaling.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer; * </p> * * @author Erich Schubert + * @since 0.3 */ @Reference(authors = "H.-P. Kriegel, P. Kröger, E. Schubert, A. Zimek", // title = "Interpreting and Unifying Outlier Scores", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MinusLogStandardDeviationScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MinusLogStandardDeviationScaling.java index 2c01b2a1..b6645231 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MinusLogStandardDeviationScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MinusLogStandardDeviationScaling.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.3 */ @Reference(authors = "H.-P. Kriegel, P. Kröger, E. Schubert, A. Zimek", // title = "Interpreting and Unifying Outlier Scores", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MixtureModelOutlierScalingFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MixtureModelOutlierScalingFunction.java index 0271f3f3..dd915b7a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MixtureModelOutlierScalingFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MixtureModelOutlierScalingFunction.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.4.0 */ @Reference(authors = "J. Gao, P.-N. Tan", // title = "Converting Output Scores from Outlier Detection Algorithms into Probability Estimates", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MultiplicativeInverseScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MultiplicativeInverseScaling.java index adaf0659..c566d373 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MultiplicativeInverseScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/MultiplicativeInverseScaling.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.3 */ @Reference(authors = "H.-P. Kriegel, P. Kröger, E. Schubert, A. Zimek", // title = "Interpreting and Unifying Outlier Scores", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierGammaScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierGammaScaling.java index 0ac8f6fe..732a54f3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierGammaScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierGammaScaling.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag; * </p> * * @author Erich Schubert + * @since 0.3 */ @Reference(authors = "H.-P. Kriegel, P. Kröger, E. Schubert, A. Zimek", // title = "Interpreting and Unifying Outlier Scores", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierLinearScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierLinearScaling.java index d7feb2b4..34480521 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierLinearScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierLinearScaling.java @@ -47,6 +47,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter; * maximum values. * * @author Erich Schubert + * @since 0.3 */ public class OutlierLinearScaling implements OutlierScalingFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierMinusLogScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierMinusLogScaling.java index 4ccbe77d..c3f7697e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierMinusLogScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierMinusLogScaling.java @@ -46,6 +46,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.3 */ @Reference(authors = "H.-P. Kriegel, P. Kröger, E. Schubert, A. Zimek", // title = "Interpreting and Unifying Outlier Scores", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierScalingFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierScalingFunction.java index 6e05d7c6..e6ae2491 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierScalingFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierScalingFunction.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.scaling.ScalingFunction; * scaling function. * * @author Erich Schubert + * @since 0.3 */ public interface OutlierScalingFunction extends ScalingFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierSqrtScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierSqrtScaling.java index 8da3bd35..4339e2aa 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierSqrtScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/OutlierSqrtScaling.java @@ -41,6 +41,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * mapping onto 0:1 using the minimum values seen. * * @author Erich Schubert + * @since 0.3 */ public class OutlierSqrtScaling implements OutlierScalingFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/RankingPseudoOutlierScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/RankingPseudoOutlierScaling.java index 75a532f7..0b12b0c7 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/RankingPseudoOutlierScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/RankingPseudoOutlierScaling.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException; * a normal distribution. * * @author Erich Schubert + * @since 0.4.0 */ public class RankingPseudoOutlierScaling implements OutlierScalingFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/SigmoidOutlierScalingFunction.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/SigmoidOutlierScalingFunction.java index 748fddd4..6855d879 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/SigmoidOutlierScalingFunction.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/SigmoidOutlierScalingFunction.java @@ -48,6 +48,7 @@ import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; * </p> * * @author Erich Schubert + * @since 0.4.0 */ @Reference(authors = "J. Gao, P.-N. Tan", // title = "Converting Output Scores from Outlier Detection Algorithms into Probability Estimates", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/SqrtStandardDeviationScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/SqrtStandardDeviationScaling.java index 1387d69f..0fe9e86a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/SqrtStandardDeviationScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/SqrtStandardDeviationScaling.java @@ -57,6 +57,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * </p> * * @author Erich Schubert + * @since 0.3 */ @Reference(authors = "H.-P. Kriegel, P. Kröger, E. Schubert, A. Zimek", // title = "Interpreting and Unifying Outlier Scores", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/StandardDeviationScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/StandardDeviationScaling.java index b6ef5e3a..524c93f6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/StandardDeviationScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/StandardDeviationScaling.java @@ -54,6 +54,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter; * </p> * * @author Erich Schubert + * @since 0.3 */ @Reference(authors = "H.-P. Kriegel, P. Kröger, E. Schubert, A. Zimek", // title = "Interpreting and Unifying Outlier Scores", // diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/TopKOutlierScaling.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/TopKOutlierScaling.java index 7ac19a1b..1f867e4a 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/TopKOutlierScaling.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/outlier/TopKOutlierScaling.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; * Outlier scaling function that only keeps the top k outliers. * * @author Erich Schubert + * @since 0.3 */ public class TopKOutlierScaling implements OutlierScalingFunction { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/DOMCloner.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/DOMCloner.java index 85f81561..6fecd67c 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/DOMCloner.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/DOMCloner.java @@ -33,6 +33,7 @@ import org.w3c.dom.Node; * Class for cloning XML document, with filter capabilites * * @author Erich Schubert + * @since 0.5.0 */ public class DOMCloner { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/HTMLUtil.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/HTMLUtil.java index 4522df6f..376f00cb 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/HTMLUtil.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/HTMLUtil.java @@ -40,6 +40,7 @@ import org.w3c.dom.Element; * Class with HTML related utility functions, in particular HTML generation. * * @author Erich Schubert + * @since 0.2 */ public final class HTMLUtil { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/XMLNodeIterator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/XMLNodeIterator.java index 10b14c8b..af272678 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/XMLNodeIterator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/XMLNodeIterator.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.ExceptionMessages; * Simple adapter class to iterate over a DOM tree nodes children. * * @author Erich Schubert + * @since 0.2 */ public final class XMLNodeIterator implements Iterator<Node> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/XMLNodeListIterator.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/XMLNodeListIterator.java index 7566ccb4..f1ada456 100755 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/XMLNodeListIterator.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/XMLNodeListIterator.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.ExceptionMessages; * Simple adapter class to iterate over a DOM tree nodes children. * * @author Erich Schubert + * @since 0.2 */ public final class XMLNodeListIterator implements Iterator<Node> { /** diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/AlgorithmStep.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/AlgorithmStep.java index d3b8cc48..223ee5b3 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/AlgorithmStep.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/AlgorithmStep.java @@ -45,6 +45,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectListParamet * The "algorithms" step, where data is analyzed. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has Algorithm * @apiviz.has Result diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/EvaluationStep.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/EvaluationStep.java index 99f57fd1..fab93f05 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/EvaluationStep.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/EvaluationStep.java @@ -42,6 +42,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectListParamet * The "evaluation" step, where data is analyzed. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has Evaluator * @apiviz.uses Result diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/InputStep.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/InputStep.java index b7de345b..6680e2a6 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/InputStep.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/InputStep.java @@ -34,6 +34,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * Data input step of the workflow. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.has Database */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/LoggingStep.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/LoggingStep.java index 167f8c8b..8641b69b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/LoggingStep.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/LoggingStep.java @@ -38,6 +38,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.StringParameter; * Pseudo-step to configure logging / verbose mode. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses LoggingConfiguration */ diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/OutputStep.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/OutputStep.java index 9d58129a..3448bf1b 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/OutputStep.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/OutputStep.java @@ -39,6 +39,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectListParamet * The "output" step, where data is analyzed. * * @author Erich Schubert + * @since 0.4.0 * * @apiviz.uses ResultHierarchy * @apiviz.has ResultHandler @@ -90,7 +91,7 @@ public class OutputStep implements WorkflowStep { Class<? extends ResultHandler> clz; try { clz = (Class<? extends ResultHandler>) ClassLoader.getSystemClassLoader().loadClass(// - "de.lmu.ifi.dbs.elki.visualization.gui.ResultVisualizer"); + "de.lmu.ifi.dbs.elki.result.AutomaticVisualization"); } catch(ClassNotFoundException e) { clz = ResultWriter.class; diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/WorkflowStep.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/WorkflowStep.java index b001d8e3..9e305c4e 100644 --- a/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/WorkflowStep.java +++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/workflow/WorkflowStep.java @@ -29,6 +29,7 @@ package de.lmu.ifi.dbs.elki.workflow; * A logical grouping of classes with no real functionality. * * @author Erich Schubert + * @since 0.4.0 */ public interface WorkflowStep { // Empty diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.AbstractNumberVectorDistanceBasedAlgorithm b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.AbstractNumberVectorDistanceBasedAlgorithm index e2fc2d93..ea8a208f 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.AbstractNumberVectorDistanceBasedAlgorithm +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.AbstractNumberVectorDistanceBasedAlgorithm @@ -1,7 +1,9 @@ de.lmu.ifi.dbs.elki.algorithm.DependencyDerivator +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansSort +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansCompare de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansHamerly de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansElkan -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansLloyd +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansLloyd de.lmu.ifi.dbs.elki.algorithm.clustering.KMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.parallel.ParallelLloydKMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansMacQueen de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMediansLloyd diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.AbstractPrimitiveDistanceBasedAlgorithm b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.AbstractPrimitiveDistanceBasedAlgorithm deleted file mode 100644 index e69de29b..00000000 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.AbstractPrimitiveDistanceBasedAlgorithm +++ /dev/null diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.Algorithm b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.Algorithm index 252a7a42..55895bea 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.Algorithm +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.Algorithm @@ -2,21 +2,24 @@ de.lmu.ifi.dbs.elki.algorithm.NullAlgorithm de.lmu.ifi.dbs.elki.algorithm.clustering.CanopyPreClustering de.lmu.ifi.dbs.elki.algorithm.clustering.DBSCAN de.lmu.ifi.dbs.elki.algorithm.clustering.affinitypropagation.AffinityPropagationClusteringAlgorithm -de.lmu.ifi.dbs.elki.algorithm.clustering.em.EM de.lmu.ifi.dbs.elki.algorithm.clustering.EM EM +de.lmu.ifi.dbs.elki.algorithm.clustering.em.EM de.lmu.ifi.dbs.elki.algorithm.clustering.EM de.lmu.ifi.dbs.elki.algorithm.clustering.gdbscan.GeneralizedDBSCAN de.lmu.ifi.dbs.elki.algorithm.clustering.gdbscan.LSDBC +de.lmu.ifi.dbs.elki.algorithm.clustering.GriDBSCAN de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.extraction.HDBSCANHierarchyExtraction de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.extraction.SimplifiedHierarchyExtraction -de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.extraction.ExtractFlatClusteringFromHierarchy -de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.SLINK de.lmu.ifi.dbs.elki.algorithm.clustering.SLINK clustering.SLINK SLINK single-link single-linkage +de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.extraction.ExtractFlatClusteringFromHierarchy de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.ExtractFlatClusteringFromHierarchy +de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.SLINK de.lmu.ifi.dbs.elki.algorithm.clustering.SLINK clustering.SLINK single-link single-linkage de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.AnderbergHierarchicalClustering de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.AGNES HAC NaiveAgglomerativeHierarchicalClustering de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.NaiveAgglomerativeHierarchicalClustering -de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.CLINK CLINK Defays +de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.CLINK Defays de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.SLINKHDBSCANLinearMemory de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.HDBSCANLinearMemory +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansSort +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansCompare de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansHamerly de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansElkan -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansLloyd +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansLloyd de.lmu.ifi.dbs.elki.algorithm.clustering.KMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.parallel.ParallelLloydKMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansMacQueen de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMediansLloyd @@ -31,8 +34,8 @@ de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.SingleAssignmentKMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.XMeans de.lmu.ifi.dbs.elki.algorithm.clustering.NaiveMeanShiftClustering de.lmu.ifi.dbs.elki.algorithm.clustering.optics.DeLiClu de.lmu.ifi.dbs.elki.algorithm.clustering.DeLiClu -de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSXi OPTICSXi de.lmu.ifi.dbs.elki.algorithm.clustering.OPTICSXi -de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSHeap OPTICS de.lmu.ifi.dbs.elki.algorithm.clustering.OPTICS de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICS +de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSXi de.lmu.ifi.dbs.elki.algorithm.clustering.OPTICSXi +de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSHeap de.lmu.ifi.dbs.elki.algorithm.clustering.OPTICS de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSList de.lmu.ifi.dbs.elki.algorithm.clustering.optics.FastOPTICS de.lmu.ifi.dbs.elki.algorithm.clustering.SNNClustering @@ -54,24 +57,24 @@ de.lmu.ifi.dbs.elki.algorithm.clustering.subspace.PreDeCon de.lmu.ifi.dbs.elki.algorithm.clustering.subspace.PROCLUS de.lmu.ifi.dbs.elki.algorithm.clustering.subspace.SUBCLU de.lmu.ifi.dbs.elki.algorithm.clustering.meta.ExternalClustering -de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.ByLabelClustering -de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.ByLabelHierarchicalClustering +de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.ByLabelClustering de.lmu.ifi.dbs.elki.algorithm.clustering.ByLabelClustering +de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.ByLabelHierarchicalClustering de.lmu.ifi.dbs.elki.algorithm.clustering.ByLabelHierarchicalClustering de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.ByModelClustering -de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.TrivialAllInOne -de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.TrivialAllNoise +de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.TrivialAllInOne de.lmu.ifi.dbs.elki.algorithm.clustering.TrivialAllInOne +de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.TrivialAllNoise de.lmu.ifi.dbs.elki.algorithm.clustering.TrivialAllNoise de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.ByLabelOrAllInOneClustering de.lmu.ifi.dbs.elki.algorithm.clustering.uncertain.FDBSCAN de.lmu.ifi.dbs.elki.algorithm.clustering.uncertain.CKMeans de.lmu.ifi.dbs.elki.algorithm.clustering.uncertain.UKMeans de.lmu.ifi.dbs.elki.algorithm.clustering.uncertain.RepresentativeUncertainClustering de.lmu.ifi.dbs.elki.algorithm.clustering.uncertain.CenterOfMassMetaClustering -de.lmu.ifi.dbs.elki.algorithm.itemsetmining.APRIORI +de.lmu.ifi.dbs.elki.algorithm.itemsetmining.APRIORI de.lmu.ifi.dbs.elki.algorithm.APRIORI de.lmu.ifi.dbs.elki.algorithm.itemsetmining.Eclat de.lmu.ifi.dbs.elki.algorithm.itemsetmining.FPGrowth de.lmu.ifi.dbs.elki.algorithm.outlier.anglebased.ABOD de.lmu.ifi.dbs.elki.algorithm.outlier.ABOD abod de.lmu.ifi.dbs.elki.algorithm.outlier.anglebased.FastABOD de.lmu.ifi.dbs.elki.algorithm.outlier.FastABOD fastabod de.lmu.ifi.dbs.elki.algorithm.outlier.anglebased.LBABOD de.lmu.ifi.dbs.elki.algorithm.outlier.LBABOD lb-abod -de.lmu.ifi.dbs.elki.algorithm.outlier.clustering.EMOutlier +de.lmu.ifi.dbs.elki.algorithm.outlier.clustering.EMOutlier de.lmu.ifi.dbs.elki.algorithm.outlier.EMOutlier de.lmu.ifi.dbs.elki.algorithm.outlier.clustering.KMeansOutlierDetection de.lmu.ifi.dbs.elki.algorithm.outlier.clustering.SilhouetteOutlierDetection de.lmu.ifi.dbs.elki.algorithm.outlier.COP @@ -90,27 +93,27 @@ de.lmu.ifi.dbs.elki.algorithm.outlier.GaussianModel de.lmu.ifi.dbs.elki.algorithm.outlier.GaussianUniformMixture de.lmu.ifi.dbs.elki.algorithm.outlier.OPTICSOF de.lmu.ifi.dbs.elki.algorithm.outlier.SimpleCOP -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LOF de.lmu.ifi.dbs.elki.algorithm.outlier.LOF LOF +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LOF de.lmu.ifi.dbs.elki.algorithm.outlier.LOF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.parallel.ParallelLOF -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.ALOCI +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.ALOCI de.lmu.ifi.dbs.elki.algorithm.outlier.ALOCI de.lmu.ifi.dbs.elki.algorithm.outlier.lof.COF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.FlexibleLOF -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.INFLO +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.INFLO de.lmu.ifi.dbs.elki.algorithm.outlier.INFLO de.lmu.ifi.dbs.elki.algorithm.outlier.lof.KDEOS -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LDF +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LDF de.lmu.ifi.dbs.elki.algorithm.outlier.LDF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LDOF de.lmu.ifi.dbs.elki.algorithm.outlier.LDOF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LOCI de.lmu.ifi.dbs.elki.algorithm.outlier.LOCI -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LoOP de.lmu.ifi.dbs.elki.algorithm.outlier.LoOP LoOP -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.OnlineLOF -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.SimplifiedLOF SimplifiedLOF outlier.SimplifiedLOF de.lmu.ifi.dbs.elki.algorithm.outlier.SimplifiedLOF +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LoOP de.lmu.ifi.dbs.elki.algorithm.outlier.LoOP +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.OnlineLOF de.lmu.ifi.dbs.elki.algorithm.outlier.OnlineLOF +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.SimplifiedLOF de.lmu.ifi.dbs.elki.algorithm.outlier.SimpleLOF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.parallel.ParallelSimplifiedLOF -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.SimpleKernelDensityLOF +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.SimpleKernelDensityLOF de.lmu.ifi.dbs.elki.algorithm.outlier.SimpleKernelDensityLOF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.VarianceOfVolume -de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.AggarwalYuEvolutionary -de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.AggarwalYuNaive +de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.AggarwalYuEvolutionary de.lmu.ifi.dbs.elki.algorithm.outlier.AggarwalYuEvolutionary +de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.AggarwalYuNaive de.lmu.ifi.dbs.elki.algorithm.outlier.AggarwalYuNaive de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.OUTRES de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.OutRankS1 -de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.SOD +de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.SOD de.lmu.ifi.dbs.elki.algorithm.outlier.SOD de.lmu.ifi.dbs.elki.algorithm.outlier.spatial.CTLuGLSBackwardSearchAlgorithm de.lmu.ifi.dbs.elki.algorithm.outlier.spatial.CTLuMeanMultipleAttributes de.lmu.ifi.dbs.elki.algorithm.outlier.spatial.CTLuMedianAlgorithm @@ -146,7 +149,7 @@ de.lmu.ifi.dbs.elki.algorithm.statistics.RangeQuerySelectivity de.lmu.ifi.dbs.elki.algorithm.statistics.RankingQualityHistogram # de.lmu.ifi.dbs.elki.algorithm.DummyAlgorithm de.lmu.ifi.dbs.elki.algorithm.DependencyDerivator -de.lmu.ifi.dbs.elki.algorithm.KNNDistancesSampler +de.lmu.ifi.dbs.elki.algorithm.KNNDistancesSampler de.lmu.ifi.dbs.elki.algorithm.KNNDistanceOrder de.lmu.ifi.dbs.elki.algorithm.KNNJoin de.lmu.ifi.dbs.elki.algorithm.MaterializeDistances de.lmu.ifi.dbs.elki.algorithm.benchmark.KNNBenchmarkAlgorithm diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.DistanceBasedAlgorithm b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.DistanceBasedAlgorithm index 4c14d6a2..4243bfca 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.DistanceBasedAlgorithm +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.DistanceBasedAlgorithm @@ -2,15 +2,18 @@ de.lmu.ifi.dbs.elki.algorithm.clustering.CanopyPreClustering de.lmu.ifi.dbs.elki.algorithm.clustering.DBSCAN de.lmu.ifi.dbs.elki.algorithm.clustering.NaiveMeanShiftClustering de.lmu.ifi.dbs.elki.algorithm.clustering.gdbscan.LSDBC -de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.SLINK de.lmu.ifi.dbs.elki.algorithm.clustering.SLINK clustering.SLINK SLINK single-link single-linkage +de.lmu.ifi.dbs.elki.algorithm.clustering.GriDBSCAN +de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.SLINK de.lmu.ifi.dbs.elki.algorithm.clustering.SLINK clustering.SLINK single-link single-linkage de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.AnderbergHierarchicalClustering de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.AGNES HAC NaiveAgglomerativeHierarchicalClustering de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.NaiveAgglomerativeHierarchicalClustering -de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.CLINK CLINK Defays +de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.CLINK Defays de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.HDBSCANLinearMemory de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.SLINKHDBSCANLinearMemory +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansSort +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansCompare de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansHamerly de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansElkan -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansLloyd +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansLloyd de.lmu.ifi.dbs.elki.algorithm.clustering.KMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.parallel.ParallelLloydKMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansMacQueen de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMediansLloyd @@ -23,7 +26,7 @@ de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansBatchedLloyd de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansHybridLloydMacQueen de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.SingleAssignmentKMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.XMeans -de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSHeap OPTICS de.lmu.ifi.dbs.elki.algorithm.clustering.OPTICS de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICS +de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSHeap de.lmu.ifi.dbs.elki.algorithm.clustering.OPTICS de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSList de.lmu.ifi.dbs.elki.algorithm.clustering.optics.DeLiClu de.lmu.ifi.dbs.elki.algorithm.clustering.DeLiClu de.lmu.ifi.dbs.elki.algorithm.outlier.clustering.SilhouetteOutlierDetection @@ -41,17 +44,17 @@ de.lmu.ifi.dbs.elki.algorithm.outlier.distance.parallel.ParallelKNNWeightOutlier de.lmu.ifi.dbs.elki.algorithm.outlier.DWOF de.lmu.ifi.dbs.elki.algorithm.outlier.OPTICSOF de.lmu.ifi.dbs.elki.algorithm.outlier.SimpleCOP -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LOF de.lmu.ifi.dbs.elki.algorithm.outlier.LOF LOF +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LOF de.lmu.ifi.dbs.elki.algorithm.outlier.LOF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.parallel.ParallelLOF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.COF -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.INFLO +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.INFLO de.lmu.ifi.dbs.elki.algorithm.outlier.INFLO de.lmu.ifi.dbs.elki.algorithm.outlier.lof.KDEOS -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LDF +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LDF de.lmu.ifi.dbs.elki.algorithm.outlier.LDF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LDOF de.lmu.ifi.dbs.elki.algorithm.outlier.LDOF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LOCI de.lmu.ifi.dbs.elki.algorithm.outlier.LOCI -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.SimplifiedLOF SimplifiedLOF outlier.SimplifiedLOF de.lmu.ifi.dbs.elki.algorithm.outlier.SimplifiedLOF +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.SimplifiedLOF de.lmu.ifi.dbs.elki.algorithm.outlier.SimpleLOF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.parallel.ParallelSimplifiedLOF -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.SimpleKernelDensityLOF +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.SimpleKernelDensityLOF de.lmu.ifi.dbs.elki.algorithm.outlier.SimpleKernelDensityLOF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.VarianceOfVolume de.lmu.ifi.dbs.elki.algorithm.outlier.spatial.CTLuGLSBackwardSearchAlgorithm de.lmu.ifi.dbs.elki.algorithm.outlier.spatial.CTLuRandomWalkEC @@ -71,6 +74,6 @@ de.lmu.ifi.dbs.elki.algorithm.benchmark.RangeQueryBenchmarkAlgorithm de.lmu.ifi.dbs.elki.algorithm.benchmark.ValidateApproximativeKNNIndex de.lmu.ifi.dbs.elki.algorithm.classification.KNNClassifier de.lmu.ifi.dbs.elki.algorithm.DependencyDerivator -de.lmu.ifi.dbs.elki.algorithm.KNNDistancesSampler +de.lmu.ifi.dbs.elki.algorithm.KNNDistancesSampler de.lmu.ifi.dbs.elki.algorithm.KNNDistanceOrder de.lmu.ifi.dbs.elki.algorithm.KNNJoin de.lmu.ifi.dbs.elki.algorithm.MaterializeDistances diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.ClusteringAlgorithm b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.ClusteringAlgorithm index e35a6a81..de499672 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.ClusteringAlgorithm +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.ClusteringAlgorithm @@ -2,14 +2,17 @@ de.lmu.ifi.dbs.elki.algorithm.clustering.CanopyPreClustering de.lmu.ifi.dbs.elki.algorithm.clustering.DBSCAN de.lmu.ifi.dbs.elki.algorithm.clustering.gdbscan.GeneralizedDBSCAN de.lmu.ifi.dbs.elki.algorithm.clustering.gdbscan.LSDBC +de.lmu.ifi.dbs.elki.algorithm.clustering.GriDBSCAN de.lmu.ifi.dbs.elki.algorithm.clustering.affinitypropagation.AffinityPropagationClusteringAlgorithm -de.lmu.ifi.dbs.elki.algorithm.clustering.em.EM de.lmu.ifi.dbs.elki.algorithm.clustering.EM EM +de.lmu.ifi.dbs.elki.algorithm.clustering.em.EM de.lmu.ifi.dbs.elki.algorithm.clustering.EM de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.extraction.HDBSCANHierarchyExtraction de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.extraction.SimplifiedHierarchyExtraction -de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.extraction.ExtractFlatClusteringFromHierarchy +de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.extraction.ExtractFlatClusteringFromHierarchy de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.ExtractFlatClusteringFromHierarchy +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansSort +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansCompare de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansHamerly de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansElkan -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansLloyd +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansLloyd de.lmu.ifi.dbs.elki.algorithm.clustering.KMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.parallel.ParallelLloydKMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansMacQueen de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMediansLloyd @@ -23,7 +26,7 @@ de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansHybridLloydMacQueen de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.SingleAssignmentKMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.XMeans de.lmu.ifi.dbs.elki.algorithm.clustering.NaiveMeanShiftClustering -de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSXi OPTICSXi de.lmu.ifi.dbs.elki.algorithm.clustering.OPTICSXi +de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSXi de.lmu.ifi.dbs.elki.algorithm.clustering.OPTICSXi de.lmu.ifi.dbs.elki.algorithm.clustering.SNNClustering de.lmu.ifi.dbs.elki.algorithm.clustering.biclustering.ChengAndChurch de.lmu.ifi.dbs.elki.algorithm.clustering.correlation.CASH @@ -40,11 +43,11 @@ de.lmu.ifi.dbs.elki.algorithm.clustering.subspace.PreDeCon de.lmu.ifi.dbs.elki.algorithm.clustering.subspace.PROCLUS de.lmu.ifi.dbs.elki.algorithm.clustering.subspace.SUBCLU de.lmu.ifi.dbs.elki.algorithm.clustering.meta.ExternalClustering -de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.ByLabelClustering -de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.ByLabelHierarchicalClustering +de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.ByLabelClustering de.lmu.ifi.dbs.elki.algorithm.clustering.ByLabelClustering +de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.ByLabelHierarchicalClustering de.lmu.ifi.dbs.elki.algorithm.clustering.ByLabelHierarchicalClustering de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.ByModelClustering -de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.TrivialAllInOne -de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.TrivialAllNoise +de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.TrivialAllInOne de.lmu.ifi.dbs.elki.algorithm.clustering.TrivialAllInOne +de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.TrivialAllNoise de.lmu.ifi.dbs.elki.algorithm.clustering.TrivialAllNoise de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.ByLabelOrAllInOneClustering de.lmu.ifi.dbs.elki.algorithm.clustering.uncertain.FDBSCAN de.lmu.ifi.dbs.elki.algorithm.clustering.uncertain.CKMeans diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.HierarchicalClusteringAlgorithm b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.HierarchicalClusteringAlgorithm index c4585e42..9f436243 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.HierarchicalClusteringAlgorithm +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.HierarchicalClusteringAlgorithm @@ -1,6 +1,6 @@ -de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.SLINK de.lmu.ifi.dbs.elki.algorithm.clustering.SLINK clustering.SLINK SLINK single-link single-linkage +de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.SLINK de.lmu.ifi.dbs.elki.algorithm.clustering.SLINK clustering.SLINK single-link single-linkage de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.AnderbergHierarchicalClustering de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.AGNES HAC NaiveAgglomerativeHierarchicalClustering de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.NaiveAgglomerativeHierarchicalClustering -de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.CLINK CLINK Defays +de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.CLINK Defays de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.HDBSCANLinearMemory de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.SLINKHDBSCANLinearMemory diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans index 7e811cfd..8f0d1004 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans @@ -1,6 +1,8 @@ +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansSort +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansCompare de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansHamerly de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansElkan -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansLloyd +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansLloyd de.lmu.ifi.dbs.elki.algorithm.clustering.KMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.parallel.ParallelLloydKMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansMacQueen de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMediansLloyd diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.KMeansInitialization b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.KMeansInitialization index 6a5305b4..adb9a44d 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.KMeansInitialization +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.KMeansInitialization @@ -1,9 +1,9 @@ -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.RandomlyChosenInitialMeans -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.FirstKInitialMeans -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.KMeansPlusPlusInitialMeans -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.SampleKMeansInitialization -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.FarthestPointsInitialMeans +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.RandomlyChosenInitialMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.RandomlyChosenInitialMeans +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.FirstKInitialMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.FirstKInitialMeans +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.KMeansPlusPlusInitialMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansPlusPlusInitialMeans +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.SampleKMeansInitialization de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.SampleKMeansInitialization +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.FarthestPointsInitialMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.FarthestPointsInitialMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.FarthestSumPointsInitialMeans -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.RandomlyGeneratedInitialMeans +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.RandomlyGeneratedInitialMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.RandomlyGeneratedInitialMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.PredefinedInitialMeans -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.PAMInitialMeans +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.PAMInitialMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.PAMInitialMeans diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.KMedoidsInitialization b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.KMedoidsInitialization index 29d84566..a142b64d 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.KMedoidsInitialization +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.KMedoidsInitialization @@ -1,6 +1,6 @@ -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.PAMInitialMeans -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.RandomlyChosenInitialMeans -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.FirstKInitialMeans -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.KMeansPlusPlusInitialMeans -de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.FarthestPointsInitialMeans +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.PAMInitialMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.PAMInitialMeans +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.RandomlyChosenInitialMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.RandomlyChosenInitialMeans +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.FirstKInitialMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.FirstKInitialMeans +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.KMeansPlusPlusInitialMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansPlusPlusInitialMeans +de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.FarthestPointsInitialMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.FarthestPointsInitialMeans de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.FarthestSumPointsInitialMeans
\ No newline at end of file diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSTypeAlgorithm b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSTypeAlgorithm index dcd0c73a..04ab94f6 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSTypeAlgorithm +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSTypeAlgorithm @@ -1,4 +1,4 @@ -de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSHeap OPTICS de.lmu.ifi.dbs.elki.algorithm.clustering.OPTICS de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICS +de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSHeap de.lmu.ifi.dbs.elki.algorithm.clustering.OPTICS de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICSList de.lmu.ifi.dbs.elki.algorithm.clustering.optics.DeLiClu de.lmu.ifi.dbs.elki.algorithm.clustering.DeLiClu de.lmu.ifi.dbs.elki.algorithm.clustering.optics.FastOPTICS diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.outlier.OutlierAlgorithm b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.outlier.OutlierAlgorithm index 7b806549..a7a48700 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.outlier.OutlierAlgorithm +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.algorithm.outlier.OutlierAlgorithm @@ -1,7 +1,7 @@ de.lmu.ifi.dbs.elki.algorithm.outlier.anglebased.ABOD de.lmu.ifi.dbs.elki.algorithm.outlier.ABOD abod de.lmu.ifi.dbs.elki.algorithm.outlier.anglebased.FastABOD de.lmu.ifi.dbs.elki.algorithm.outlier.FastABOD fastabod de.lmu.ifi.dbs.elki.algorithm.outlier.anglebased.LBABOD de.lmu.ifi.dbs.elki.algorithm.outlier.LBABOD lb-abod -de.lmu.ifi.dbs.elki.algorithm.outlier.clustering.EMOutlier +de.lmu.ifi.dbs.elki.algorithm.outlier.clustering.EMOutlier de.lmu.ifi.dbs.elki.algorithm.outlier.EMOutlier de.lmu.ifi.dbs.elki.algorithm.outlier.clustering.KMeansOutlierDetection de.lmu.ifi.dbs.elki.algorithm.outlier.clustering.SilhouetteOutlierDetection de.lmu.ifi.dbs.elki.algorithm.outlier.COP @@ -20,27 +20,27 @@ de.lmu.ifi.dbs.elki.algorithm.outlier.GaussianModel de.lmu.ifi.dbs.elki.algorithm.outlier.GaussianUniformMixture de.lmu.ifi.dbs.elki.algorithm.outlier.OPTICSOF de.lmu.ifi.dbs.elki.algorithm.outlier.SimpleCOP -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LOF de.lmu.ifi.dbs.elki.algorithm.outlier.LOF LOF +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LOF de.lmu.ifi.dbs.elki.algorithm.outlier.LOF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.parallel.ParallelLOF -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.ALOCI +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.ALOCI de.lmu.ifi.dbs.elki.algorithm.outlier.ALOCI de.lmu.ifi.dbs.elki.algorithm.outlier.lof.COF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.FlexibleLOF -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.INFLO +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.INFLO de.lmu.ifi.dbs.elki.algorithm.outlier.INFLO de.lmu.ifi.dbs.elki.algorithm.outlier.lof.KDEOS -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LDF +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LDF de.lmu.ifi.dbs.elki.algorithm.outlier.LDF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LDOF de.lmu.ifi.dbs.elki.algorithm.outlier.LDOF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LOCI de.lmu.ifi.dbs.elki.algorithm.outlier.LOCI -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LoOP de.lmu.ifi.dbs.elki.algorithm.outlier.LoOP LoOP -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.OnlineLOF -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.SimplifiedLOF SimplifiedLOF outlier.SimplifiedLOF de.lmu.ifi.dbs.elki.algorithm.outlier.SimplifiedLOF +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LoOP de.lmu.ifi.dbs.elki.algorithm.outlier.LoOP +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.OnlineLOF de.lmu.ifi.dbs.elki.algorithm.outlier.OnlineLOF +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.SimplifiedLOF de.lmu.ifi.dbs.elki.algorithm.outlier.SimpleLOF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.parallel.ParallelSimplifiedLOF -de.lmu.ifi.dbs.elki.algorithm.outlier.lof.SimpleKernelDensityLOF +de.lmu.ifi.dbs.elki.algorithm.outlier.lof.SimpleKernelDensityLOF de.lmu.ifi.dbs.elki.algorithm.outlier.SimpleKernelDensityLOF de.lmu.ifi.dbs.elki.algorithm.outlier.lof.VarianceOfVolume -de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.AggarwalYuEvolutionary -de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.AggarwalYuNaive +de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.AggarwalYuEvolutionary de.lmu.ifi.dbs.elki.algorithm.outlier.AggarwalYuEvolutionary +de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.AggarwalYuNaive de.lmu.ifi.dbs.elki.algorithm.outlier.AggarwalYuNaive de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.OUTRES de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.OutRankS1 -de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.SOD +de.lmu.ifi.dbs.elki.algorithm.outlier.subspace.SOD de.lmu.ifi.dbs.elki.algorithm.outlier.SOD de.lmu.ifi.dbs.elki.algorithm.outlier.spatial.CTLuGLSBackwardSearchAlgorithm de.lmu.ifi.dbs.elki.algorithm.outlier.spatial.CTLuMeanMultipleAttributes de.lmu.ifi.dbs.elki.algorithm.outlier.spatial.CTLuMedianAlgorithm diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.DatabaseConnection b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.DatabaseConnection index 6c4c8ebf..6293505c 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.DatabaseConnection +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.DatabaseConnection @@ -1,4 +1,4 @@ -de.lmu.ifi.dbs.elki.datasource.FileBasedDatabaseConnection +de.lmu.ifi.dbs.elki.datasource.FileBasedDatabaseConnection de.lmu.ifi.dbs.elki.database.connection.FileBasedDatabaseConnection de.lmu.ifi.dbs.elki.datasource.BundleDatabaseConnection de.lmu.ifi.dbs.elki.datasource.GeneratorXMLDatabaseConnection de.lmu.ifi.dbs.elki.datasource.RandomDoubleVectorDatabaseConnection @@ -6,7 +6,7 @@ de.lmu.ifi.dbs.elki.datasource.DBIDRangeDatabaseConnection de.lmu.ifi.dbs.elki.datasource.ExternalIDJoinDatabaseConnection de.lmu.ifi.dbs.elki.datasource.LabelJoinDatabaseConnection de.lmu.ifi.dbs.elki.datasource.ConcatenateFilesDatabaseConnection -de.lmu.ifi.dbs.elki.datasource.EmptyDatabaseConnection +de.lmu.ifi.dbs.elki.datasource.EmptyDatabaseConnection de.lmu.ifi.dbs.elki.database.connection.EmptyDatabaseConnection de.lmu.ifi.dbs.elki.datasource.PresortedBlindJoinDatabaseConnection # de.lmu.ifi.dbs.elki.datasource.InputStreamDatabaseConnection # de.lmu.ifi.dbs.elki.datasource.ArrayAdapterDatabaseConnection diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.filter.ObjectFilter b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.filter.ObjectFilter index e4ee565e..7ff816b2 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.filter.ObjectFilter +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.filter.ObjectFilter @@ -1,38 +1,38 @@ de.lmu.ifi.dbs.elki.datasource.filter.FixedDBIDsFilter de.lmu.ifi.dbs.elki.datasource.filter.NoOpFilter -de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.ClassLabelFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.ClassLabelFilter -de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.ClassLabelFromPatternFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.ClassLabelFromPatternFilter -de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.ExternalIDFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.ExternalIDFilter +de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.ClassLabelFilter de.lmu.ifi.dbs.elki.datasource.filter.ClassLabelFilter +de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.ClassLabelFromPatternFilter de.lmu.ifi.dbs.elki.datasource.filter.ClassLabelFromPatternFilter +de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.ExternalIDFilter de.lmu.ifi.dbs.elki.datasource.filter.ExternalIDFilter de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.MultivariateTimeSeriesFilter de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.SparseVectorFieldFilter de.lmu.ifi.dbs.elki.datasource.filter.SparseVectorFieldFilter -de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.SplitNumberVectorFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.SplitNumberVectorFilter +de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.SplitNumberVectorFilter de.lmu.ifi.dbs.elki.datasource.filter.SplitNumberVectorFilter de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.UncertainSplitFilter de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.WeightedUncertainSplitFilter de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.UncertainifyFilter -de.lmu.ifi.dbs.elki.datasource.filter.selection.ByLabelFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.ByLabelFilter -de.lmu.ifi.dbs.elki.datasource.filter.selection.RandomSamplingStreamFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.RandomSamplingStreamFilter +de.lmu.ifi.dbs.elki.datasource.filter.selection.ByLabelFilter de.lmu.ifi.dbs.elki.datasource.filter.ByLabelFilter de.lmu.ifi.dbs.elki.datasource.filter.FilterByLabelFilter +de.lmu.ifi.dbs.elki.datasource.filter.selection.RandomSamplingStreamFilter de.lmu.ifi.dbs.elki.datasource.filter.RandomSamplingStreamFilter de.lmu.ifi.dbs.elki.datasource.filter.selection.ShuffleObjectsFilter de.lmu.ifi.dbs.elki.datasource.filter.ShuffleObjectsFilter -de.lmu.ifi.dbs.elki.datasource.filter.selection.SortByLabelFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.SortByLabelFilter -de.lmu.ifi.dbs.elki.datasource.filter.cleaning.DropNaNFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.DropNaNFilter -de.lmu.ifi.dbs.elki.datasource.filter.cleaning.ReplaceNaNWithRandomFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.ReplaceNaNWithRandomFilter -de.lmu.ifi.dbs.elki.datasource.filter.cleaning.NoMissingValuesFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.NoMissingValuesFilter -de.lmu.ifi.dbs.elki.datasource.filter.cleaning.VectorDimensionalityFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.VectorDimensionalityFilter -de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.AttributeWiseMinMaxNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseMinMaxNormalization -de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.AttributeWiseVarianceNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseVarianceNormalization z -de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.AttributeWiseMeanNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseMeanNormalization +de.lmu.ifi.dbs.elki.datasource.filter.selection.SortByLabelFilter de.lmu.ifi.dbs.elki.datasource.filter.SortByLabelFilter +de.lmu.ifi.dbs.elki.datasource.filter.cleaning.DropNaNFilter de.lmu.ifi.dbs.elki.datasource.filter.DropNaNFilter +de.lmu.ifi.dbs.elki.datasource.filter.cleaning.ReplaceNaNWithRandomFilter de.lmu.ifi.dbs.elki.datasource.filter.ReplaceNaNWithRandomFilter +de.lmu.ifi.dbs.elki.datasource.filter.cleaning.NoMissingValuesFilter de.lmu.ifi.dbs.elki.datasource.filter.FilterNoMissingValuesFilter de.lmu.ifi.dbs.elki.datasource.filter.NoMissingValuesFilter +de.lmu.ifi.dbs.elki.datasource.filter.cleaning.VectorDimensionalityFilter +de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.AttributeWiseMinMaxNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseMinMaxNormalization de.lmu.ifi.dbs.elki.datasource.filter.AttributeWiseMinMaxNormalization +de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.AttributeWiseVarianceNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseVarianceNormalization z de.lmu.ifi.dbs.elki.datasource.filter.AttributeWiseVarianceNormalization +de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.AttributeWiseMeanNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.AttributeWiseMADNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseMADNormalization -de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.AttributeWiseErfNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseErfNormalization +de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.AttributeWiseErfNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseErfNormalization de.lmu.ifi.dbs.elki.datasource.filter.AttributeWiseErfNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.AttributeWiseCDFNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseCDFNormalization -de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.AttributeWiseBetaNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.AttributeWiseBetaNormalization -de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.InverseDocumentFrequencyNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.InverseDocumentFrequencyNormalization -de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.IntegerRankTieNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.IntegerRankTieNormalization +de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.AttributeWiseBetaNormalization +de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.InverseDocumentFrequencyNormalization de.lmu.ifi.dbs.elki.datasource.filter.InverseDocumentFrequencyNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.InverseDocumentFrequencyNormalization +de.lmu.ifi.dbs.elki.datasource.filter.normalization.columnwise.IntegerRankTieNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.RankTieNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.LengthNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.LengthNormalization -de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.HellingerHistogramNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.HellingerHistogramNormalization +de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.HellingerHistogramNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.InstanceMeanVarianceNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.InstanceMinMaxNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.InstanceRankNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.InstanceLogRankNormalization -de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.Log1PlusNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.Log1PlusNormalization +de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.Log1PlusNormalization de.lmu.ifi.dbs.elki.datasource.filter.transform.GlobalPrincipalComponentAnalysisTransform whiten whitening pca de.lmu.ifi.dbs.elki.datasource.filter.transform.FastMultidimensionalScalingTransform fastmds de.lmu.ifi.dbs.elki.datasource.filter.transform.ClassicMultidimensionalScalingTransform mds @@ -43,4 +43,4 @@ de.lmu.ifi.dbs.elki.datasource.filter.transform.LatLngToECEFFilter de.lmu.ifi.dbs.elki.datasource.filter.transform.LngLatToECEFFilter de.lmu.ifi.dbs.elki.datasource.filter.transform.PerturbationFilter de.lmu.ifi.dbs.elki.datasource.filter.transform.ProjectionFilter -de.lmu.ifi.dbs.elki.datasource.filter.transform.HistogramJitterFilter +de.lmu.ifi.dbs.elki.datasource.filter.transform.HistogramJitterFilter de.lmu.ifi.dbs.elki.datasource.filter.HistogramJitterFilter diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.filter.StreamFilter b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.filter.StreamFilter index efa92740..b995c871 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.filter.StreamFilter +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.filter.StreamFilter @@ -1,22 +1,22 @@ de.lmu.ifi.dbs.elki.datasource.filter.NoOpFilter -de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.ClassLabelFromPatternFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.ClassLabelFromPatternFilter +de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.ClassLabelFromPatternFilter de.lmu.ifi.dbs.elki.datasource.filter.ClassLabelFromPatternFilter de.lmu.ifi.dbs.elki.datasource.filter.typeconversions.MultivariateTimeSeriesFilter -de.lmu.ifi.dbs.elki.datasource.filter.selection.ByLabelFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.ByLabelFilter -de.lmu.ifi.dbs.elki.datasource.filter.selection.RandomSamplingStreamFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.RandomSamplingStreamFilter -de.lmu.ifi.dbs.elki.datasource.filter.cleaning.VectorDimensionalityFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.VectorDimensionalityFilter -de.lmu.ifi.dbs.elki.datasource.filter.cleaning.DropNaNFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.DropNaNFilter -de.lmu.ifi.dbs.elki.datasource.filter.cleaning.ReplaceNaNWithRandomFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.ReplaceNaNWithRandomFilter -de.lmu.ifi.dbs.elki.datasource.filter.cleaning.NoMissingValuesFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.NoMissingValuesFilter +de.lmu.ifi.dbs.elki.datasource.filter.selection.ByLabelFilter de.lmu.ifi.dbs.elki.datasource.filter.ByLabelFilter de.lmu.ifi.dbs.elki.datasource.filter.FilterByLabelFilter +de.lmu.ifi.dbs.elki.datasource.filter.selection.RandomSamplingStreamFilter de.lmu.ifi.dbs.elki.datasource.filter.RandomSamplingStreamFilter +de.lmu.ifi.dbs.elki.datasource.filter.cleaning.VectorDimensionalityFilter +de.lmu.ifi.dbs.elki.datasource.filter.cleaning.DropNaNFilter de.lmu.ifi.dbs.elki.datasource.filter.DropNaNFilter +de.lmu.ifi.dbs.elki.datasource.filter.cleaning.ReplaceNaNWithRandomFilter de.lmu.ifi.dbs.elki.datasource.filter.ReplaceNaNWithRandomFilter +de.lmu.ifi.dbs.elki.datasource.filter.cleaning.NoMissingValuesFilter de.lmu.ifi.dbs.elki.datasource.filter.FilterNoMissingValuesFilter de.lmu.ifi.dbs.elki.datasource.filter.NoMissingValuesFilter de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.LengthNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.LengthNormalization -de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.HellingerHistogramNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.HellingerHistogramNormalization +de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.HellingerHistogramNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.InstanceMeanVarianceNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.InstanceMinMaxNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.InstanceRankNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.InstanceLogRankNormalization -de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.Log1PlusNormalization de.lmu.ifi.dbs.elki.datasource.filter.normalization.Log1PlusNormalization +de.lmu.ifi.dbs.elki.datasource.filter.normalization.instancewise.Log1PlusNormalization de.lmu.ifi.dbs.elki.datasource.filter.transform.NumberVectorFeatureSelectionFilter de.lmu.ifi.dbs.elki.datasource.filter.transform.NumberVectorRandomFeatureSelectionFilter de.lmu.ifi.dbs.elki.datasource.filter.transform.LatLngToECEFFilter de.lmu.ifi.dbs.elki.datasource.filter.transform.LngLatToECEFFilter de.lmu.ifi.dbs.elki.datasource.filter.transform.ProjectionFilter -de.lmu.ifi.dbs.elki.datasource.filter.transform.HistogramJitterFilter +de.lmu.ifi.dbs.elki.datasource.filter.transform.HistogramJitterFilter de.lmu.ifi.dbs.elki.datasource.filter.HistogramJitterFilter diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.parser.Parser b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.parser.Parser index 74d45151..ca42b0b5 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.parser.Parser +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.datasource.parser.Parser @@ -1,10 +1,10 @@ -de.lmu.ifi.dbs.elki.datasource.parser.NumberVectorLabelParser +de.lmu.ifi.dbs.elki.datasource.parser.NumberVectorLabelParser de.lmu.ifi.dbs.elki.parser.NumberVectorLabelParser de.lmu.ifi.dbs.elki.parser.RealVectorLabelParser de.lmu.ifi.dbs.elki.datasource.parser.ArffParser de.lmu.ifi.dbs.elki.datasource.parser.SparseNumberVectorLabelParser de.lmu.ifi.dbs.elki.datasource.parser.LibSVMFormatParser de.lmu.ifi.dbs.elki.datasource.parser.CategorialDataAsNumberVectorParser de.lmu.ifi.dbs.elki.datasource.parser.TermFrequencyParser -de.lmu.ifi.dbs.elki.datasource.parser.BitVectorLabelParser +de.lmu.ifi.dbs.elki.datasource.parser.BitVectorLabelParser de.lmu.ifi.dbs.elki.parser.BitVectorLabelParser de.lmu.ifi.dbs.elki.datasource.parser.SimplePolygonParser de.lmu.ifi.dbs.elki.datasource.parser.StringParser de.lmu.ifi.dbs.elki.datasource.parser.SimpleTransactionParser diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction index 5569c7df..d98773ce 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction @@ -1,5 +1,5 @@ -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction euclidean euclid l2 EuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.EuclideanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.ManhattanDistanceFunction taxicab cityblock l1 ManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.ManhattanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction euclidean euclid l2 de.lmu.ifi.dbs.elki.distance.distancefunction.EuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.ManhattanDistanceFunction taxicab cityblock l1 de.lmu.ifi.dbs.elki.distance.distancefunction.ManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPNormDistanceFunction lp minkowski p de.lmu.ifi.dbs.elki.distance.distancefunction.LPNormDistanceFunction # de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPIntegerNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.MaximumDistanceFunction maximum max chebyshev de.lmu.ifi.dbs.elki.distance.distancefunction.MaximumDistanceFunction @@ -16,18 +16,18 @@ de.lmu.ifi.dbs.elki.distance.distancefunction.Kulczynski1DistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.LorentzianDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.SharedNearestNeighborJaccardDistanceFunction # de.lmu.ifi.dbs.elki.distance.distancefunction.MatrixWeightedDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedLPNormDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedMaximumDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedSquaredEuclideanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseEuclideanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseManhattanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseLPNormDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseMaximumDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.adapter.ArccosSimilarityAdapter -de.lmu.ifi.dbs.elki.distance.distancefunction.adapter.LinearAdapterLinear -de.lmu.ifi.dbs.elki.distance.distancefunction.adapter.LnSimilarityAdapter +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedSquaredEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedSquaredEuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.SparseEuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.SparseManhattanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.SparseLPNormDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseMaximumDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.SparseMaximumDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.adapter.ArccosSimilarityAdapter de.lmu.ifi.dbs.elki.distance.distancefunction.adapter.SimilarityAdapterArccos +de.lmu.ifi.dbs.elki.distance.distancefunction.adapter.LinearAdapterLinear de.lmu.ifi.dbs.elki.distance.distancefunction.adapter.SimilarityAdapterLinear +de.lmu.ifi.dbs.elki.distance.distancefunction.adapter.LnSimilarityAdapter de.lmu.ifi.dbs.elki.distance.distancefunction.adapter.SimilarityAdapterLn de.lmu.ifi.dbs.elki.distance.distancefunction.colorhistogram.HSBHistogramQuadraticDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.colorhistogram.HistogramIntersectionDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.colorhistogram.RGBHistogramQuadraticDistanceFunction @@ -52,14 +52,14 @@ de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic.KullbackLeiblerDiver de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic.KullbackLeiblerDivergenceReverseAsymmetricDistanceFunction kli de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic.SqrtJensenShannonDivergenceDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.set.HammingDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.set.JaccardSimilarityDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.set.JaccardSimilarityDistanceFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.JaccardPrimitiveSimilarityFunction de.lmu.ifi.dbs.elki.distance.distancefunction.strings.LevenshteinDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.strings.NormalizedLevenshteinDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceEuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionsSelectingEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceMaximumDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.OnedimensionalDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.OnedimensionalDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionSelectingDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.timeseries.DTWDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.timeseries.EDRDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.timeseries.ERPDistanceFunction diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.Norm b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.Norm index 2bfb112e..ba7bc172 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.Norm +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.Norm @@ -1,22 +1,22 @@ -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction euclidean euclid l2 EuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.EuclideanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.ManhattanDistanceFunction taxicab cityblock l1 ManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.ManhattanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction euclidean euclid l2 de.lmu.ifi.dbs.elki.distance.distancefunction.EuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.ManhattanDistanceFunction taxicab cityblock l1 de.lmu.ifi.dbs.elki.distance.distancefunction.ManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.MaximumDistanceFunction maximum max chebyshev de.lmu.ifi.dbs.elki.distance.distancefunction.MaximumDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.MinimumDistanceFunction minimum min de.lmu.ifi.dbs.elki.distance.distancefunction.MinimumDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPNormDistanceFunction lp minkowski p de.lmu.ifi.dbs.elki.distance.distancefunction.LPNormDistanceFunction # de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPIntegerNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SquaredEuclideanDistanceFunction squaredeuclidean de.lmu.ifi.dbs.elki.distance.distancefunction.SquaredEuclideanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedLPNormDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedMaximumDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedSquaredEuclideanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseEuclideanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseManhattanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseLPNormDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseMaximumDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceEuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedSquaredEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedSquaredEuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.SparseEuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.SparseManhattanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.SparseLPNormDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseMaximumDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.SparseMaximumDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionsSelectingEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceMaximumDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.OnedimensionalDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.OnedimensionalDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionSelectingDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.LorentzianDistanceFunction diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunction b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunction index 22ac6cef..f94a9e62 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunction +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunction @@ -1,5 +1,5 @@ -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction euclidean euclid l2 EuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.EuclideanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.ManhattanDistanceFunction taxicab cityblock l1 ManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.ManhattanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction euclidean euclid l2 de.lmu.ifi.dbs.elki.distance.distancefunction.EuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.ManhattanDistanceFunction taxicab cityblock l1 de.lmu.ifi.dbs.elki.distance.distancefunction.ManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPNormDistanceFunction lp minkowski p de.lmu.ifi.dbs.elki.distance.distancefunction.LPNormDistanceFunction # de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPIntegerNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.MaximumDistanceFunction maximum max chebyshev de.lmu.ifi.dbs.elki.distance.distancefunction.MaximumDistanceFunction @@ -14,11 +14,11 @@ de.lmu.ifi.dbs.elki.distance.distancefunction.ClarkDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.Kulczynski1DistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.LorentzianDistanceFunction # de.lmu.ifi.dbs.elki.distance.distancefunction.MatrixWeightedDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedLPNormDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedMaximumDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedSquaredEuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedSquaredEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedSquaredEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.colorhistogram.HSBHistogramQuadraticDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.colorhistogram.HistogramIntersectionDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.colorhistogram.RGBHistogramQuadraticDistanceFunction @@ -43,12 +43,12 @@ de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic.KullbackLeiblerDiver de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic.KullbackLeiblerDivergenceReverseAsymmetricDistanceFunction kli de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic.SqrtJensenShannonDivergenceDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.set.HammingDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.set.JaccardSimilarityDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceEuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.set.JaccardSimilarityDistanceFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.JaccardPrimitiveSimilarityFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionsSelectingEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceMaximumDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.OnedimensionalDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.OnedimensionalDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionSelectingDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.timeseries.DTWDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.timeseries.EDRDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.timeseries.ERPDistanceFunction diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.PrimitiveDistanceFunction b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.PrimitiveDistanceFunction index 20669ef2..6671866d 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.PrimitiveDistanceFunction +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.PrimitiveDistanceFunction @@ -1,5 +1,5 @@ -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction euclidean euclid l2 EuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.EuclideanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.ManhattanDistanceFunction taxicab cityblock l1 ManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.ManhattanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction euclidean euclid l2 de.lmu.ifi.dbs.elki.distance.distancefunction.EuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.ManhattanDistanceFunction taxicab cityblock l1 de.lmu.ifi.dbs.elki.distance.distancefunction.ManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPNormDistanceFunction lp minkowski p de.lmu.ifi.dbs.elki.distance.distancefunction.LPNormDistanceFunction # de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPIntegerNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.ArcCosineDistanceFunction arccos @@ -14,15 +14,15 @@ de.lmu.ifi.dbs.elki.distance.distancefunction.ClarkDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.Kulczynski1DistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.LorentzianDistanceFunction # de.lmu.ifi.dbs.elki.distance.distancefunction.MatrixWeightedDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedLPNormDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedMaximumDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedSquaredEuclideanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseEuclideanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseManhattanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseLPNormDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseMaximumDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedSquaredEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedSquaredEuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.SparseEuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.SparseManhattanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.SparseLPNormDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SparseMaximumDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.SparseMaximumDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.colorhistogram.HSBHistogramQuadraticDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.colorhistogram.HistogramIntersectionDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.colorhistogram.RGBHistogramQuadraticDistanceFunction @@ -47,14 +47,14 @@ de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic.KullbackLeiblerDiver de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic.KullbackLeiblerDivergenceReverseAsymmetricDistanceFunction kli de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic.SqrtJensenShannonDivergenceDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.set.HammingDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.set.JaccardSimilarityDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.set.JaccardSimilarityDistanceFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.JaccardPrimitiveSimilarityFunction de.lmu.ifi.dbs.elki.distance.distancefunction.strings.LevenshteinDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.strings.NormalizedLevenshteinDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceEuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionsSelectingEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceMaximumDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.OnedimensionalDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.OnedimensionalDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionSelectingDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.timeseries.DTWDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.timeseries.EDRDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.timeseries.ERPDistanceFunction diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.SpatialPrimitiveDistanceFunction b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.SpatialPrimitiveDistanceFunction index cc284275..9777ec5b 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.SpatialPrimitiveDistanceFunction +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.SpatialPrimitiveDistanceFunction @@ -1,5 +1,5 @@ -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction euclidean euclid l2 EuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.EuclideanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.ManhattanDistanceFunction taxicab cityblock l1 ManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.ManhattanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction euclidean euclid l2 de.lmu.ifi.dbs.elki.distance.distancefunction.EuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.ManhattanDistanceFunction taxicab cityblock l1 de.lmu.ifi.dbs.elki.distance.distancefunction.ManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPNormDistanceFunction lp minkowski p de.lmu.ifi.dbs.elki.distance.distancefunction.LPNormDistanceFunction # de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPIntegerNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.MaximumDistanceFunction maximum max chebyshev de.lmu.ifi.dbs.elki.distance.distancefunction.MaximumDistanceFunction @@ -13,11 +13,11 @@ de.lmu.ifi.dbs.elki.distance.distancefunction.ClarkDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.Kulczynski1DistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.LorentzianDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.SquaredEuclideanDistanceFunction squaredeuclidean de.lmu.ifi.dbs.elki.distance.distancefunction.SquaredEuclideanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedLPNormDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedMaximumDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedSquaredEuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedSquaredEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedSquaredEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.colorhistogram.HistogramIntersectionDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.geo.LatLngDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.geo.LngLatDistanceFunction @@ -26,8 +26,8 @@ de.lmu.ifi.dbs.elki.distance.distancefunction.histogram.HistogramMatchDistanceFu de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic.ChiSquaredDistanceFunction chisq de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic.JeffreyDivergenceDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic.JensenShannonDivergenceDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceEuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionsSelectingEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceMaximumDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.OnedimensionalDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.OnedimensionalDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionSelectingDistanceFunction diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedNumberVectorDistanceFunction b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedNumberVectorDistanceFunction index b7022678..eb4d4134 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedNumberVectorDistanceFunction +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedNumberVectorDistanceFunction @@ -1,8 +1,8 @@ de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedCanberraDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedLPNormDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedMaximumDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedSquaredEuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedSquaredEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedSquaredEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.correlation.WeightedPearsonCorrelationDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.correlation.WeightedSquaredPearsonCorrelationDistanceFunction diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.external.DistanceParser b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.external.DistanceParser index 46b4fa03..f4ea4764 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.external.DistanceParser +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.external.DistanceParser @@ -1 +1 @@ -de.lmu.ifi.dbs.elki.distance.distancefunction.external.AsciiDistanceParser
\ No newline at end of file +de.lmu.ifi.dbs.elki.distance.distancefunction.external.AsciiDistanceParser de.lmu.ifi.dbs.elki.datasource.parser.NumberDistanceParser de.lmu.ifi.dbs.elki.distance.distancefunction.external.NumberDistanceParser de.lmu.ifi.dbs.elki.parser.NumberDistanceParser
\ No newline at end of file diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPNormDistanceFunction b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPNormDistanceFunction index 056db729..2594300b 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPNormDistanceFunction +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPNormDistanceFunction @@ -1,9 +1,9 @@ -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction euclidean euclid l2 EuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.EuclideanDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.ManhattanDistanceFunction taxicab cityblock l1 ManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.ManhattanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction euclidean euclid l2 de.lmu.ifi.dbs.elki.distance.distancefunction.EuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.ManhattanDistanceFunction taxicab cityblock l1 de.lmu.ifi.dbs.elki.distance.distancefunction.ManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPNormDistanceFunction lp minkowski p de.lmu.ifi.dbs.elki.distance.distancefunction.LPNormDistanceFunction # de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.LPIntegerNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.MaximumDistanceFunction maximum max chebyshev de.lmu.ifi.dbs.elki.distance.distancefunction.MaximumDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedLPNormDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.WeightedLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.WeightedMaximumDistanceFunction diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionSelectingSubspaceDistanceFunction b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionSelectingSubspaceDistanceFunction index 3467fa9c..a2a6e7a8 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionSelectingSubspaceDistanceFunction +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionSelectingSubspaceDistanceFunction @@ -1,5 +1,5 @@ -de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceEuclideanDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionsSelectingEuclideanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceLPNormDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceManhattanDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.SubspaceMaximumDistanceFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.OnedimensionalDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.OnedimensionalDistanceFunction de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionSelectingDistanceFunction diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.similarityfunction.NormalizedSimilarityFunction b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.similarityfunction.NormalizedSimilarityFunction index 23761a5e..4e804e80 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.similarityfunction.NormalizedSimilarityFunction +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.similarityfunction.NormalizedSimilarityFunction @@ -1,5 +1,5 @@ de.lmu.ifi.dbs.elki.distance.similarityfunction.FractionalSharedNearestNeighborSimilarityFunction -de.lmu.ifi.dbs.elki.distance.distancefunction.set.JaccardSimilarityDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.set.JaccardSimilarityDistanceFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.JaccardPrimitiveSimilarityFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.cluster.ClusteringAdjustedRandIndexSimilarityFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.cluster.ClusteringBCubedF1SimilarityFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.cluster.ClusteringFowlkesMallowsSimilarityFunction diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.similarityfunction.PrimitiveSimilarityFunction b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.similarityfunction.PrimitiveSimilarityFunction index 57331dd2..67d82042 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.similarityfunction.PrimitiveSimilarityFunction +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.similarityfunction.PrimitiveSimilarityFunction @@ -4,7 +4,7 @@ de.lmu.ifi.dbs.elki.distance.similarityfunction.Kulczynski2SimilarityFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel.LinearKernelFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel.PolynomialKernelFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel.RadialBasisFunctionKernelFunction rbf -de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel.SigmoidKernelFunction +de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel.SigmoidKernelFunction sigmoid de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel.LaplaceKernelFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel.RationalQuadraticKernelFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.cluster.ClusterIntersectionSimilarityFunction @@ -14,4 +14,4 @@ de.lmu.ifi.dbs.elki.distance.similarityfunction.cluster.ClusteringRandIndexSimil de.lmu.ifi.dbs.elki.distance.similarityfunction.cluster.ClusteringBCubedF1SimilarityFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.cluster.ClusteringFowlkesMallowsSimilarityFunction de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic.HellingerDistanceFunction hellinger bhattacharyya -de.lmu.ifi.dbs.elki.distance.distancefunction.set.JaccardSimilarityDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.set.JaccardSimilarityDistanceFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.JaccardPrimitiveSimilarityFunction diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.similarityfunction.SimilarityFunction b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.similarityfunction.SimilarityFunction index f1ce1f1a..59cb902d 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.similarityfunction.SimilarityFunction +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.distance.similarityfunction.SimilarityFunction @@ -6,7 +6,7 @@ de.lmu.ifi.dbs.elki.distance.similarityfunction.InvertedDistanceSimilarityFuncti de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel.LinearKernelFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel.PolynomialKernelFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel.RadialBasisFunctionKernelFunction rbf -de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel.SigmoidKernelFunction +de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel.SigmoidKernelFunction sigmoid de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel.LaplaceKernelFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel.RationalQuadraticKernelFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.cluster.ClusterIntersectionSimilarityFunction @@ -16,4 +16,4 @@ de.lmu.ifi.dbs.elki.distance.similarityfunction.cluster.ClusteringRandIndexSimil de.lmu.ifi.dbs.elki.distance.similarityfunction.cluster.ClusteringBCubedF1SimilarityFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.cluster.ClusteringFowlkesMallowsSimilarityFunction de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic.HellingerDistanceFunction hellinger bhattacharyya -de.lmu.ifi.dbs.elki.distance.distancefunction.set.JaccardSimilarityDistanceFunction +de.lmu.ifi.dbs.elki.distance.distancefunction.set.JaccardSimilarityDistanceFunction de.lmu.ifi.dbs.elki.distance.similarityfunction.JaccardPrimitiveSimilarityFunction diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.evaluation.Evaluator b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.evaluation.Evaluator index 8afd9f4a..9c836bbd 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.evaluation.Evaluator +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.evaluation.Evaluator @@ -1,6 +1,6 @@ de.lmu.ifi.dbs.elki.evaluation.AutomaticEvaluation de.lmu.ifi.dbs.elki.evaluation.NoAutomaticEvaluation -de.lmu.ifi.dbs.elki.evaluation.clustering.EvaluateClustering +de.lmu.ifi.dbs.elki.evaluation.clustering.EvaluateClustering de.lmu.ifi.dbs.elki.evaluation.paircounting.EvaluatePairCountingFMeasure de.lmu.ifi.dbs.elki.evaluation.clustering.LogClusterSizes de.lmu.ifi.dbs.elki.evaluation.clustering.internal.EvaluateSilhouette de.lmu.ifi.dbs.elki.evaluation.clustering.internal.EvaluateSimplifiedSilhouette @@ -18,7 +18,7 @@ de.lmu.ifi.dbs.elki.evaluation.histogram.ComputeOutlierHistogram de.lmu.ifi.dbs.elki.evaluation.index.IndexPurity de.lmu.ifi.dbs.elki.evaluation.index.IndexStatistics de.lmu.ifi.dbs.elki.evaluation.outlier.OutlierRankingEvaluation -de.lmu.ifi.dbs.elki.evaluation.outlier.OutlierROCCurve ComputeROCCurve de.lmu.ifi.dbs.elki.evaluation.roc.ComputeROCCurve +de.lmu.ifi.dbs.elki.evaluation.outlier.OutlierROCCurve de.lmu.ifi.dbs.elki.evaluation.roc.ComputeROCCurve de.lmu.ifi.dbs.elki.evaluation.ComputeROCCurve de.lmu.ifi.dbs.elki.evaluation.outlier.OutlierThresholdClustering de.lmu.ifi.dbs.elki.evaluation.outlier.OutlierPrecisionAtKCurve de.lmu.ifi.dbs.elki.evaluation.outlier.OutlierPrecisionRecallCurve diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.preprocessed.knn.MaterializeKNNPreprocessor b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.preprocessed.knn.MaterializeKNNPreprocessor index 293dd23a..969c994b 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.preprocessed.knn.MaterializeKNNPreprocessor +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.preprocessed.knn.MaterializeKNNPreprocessor @@ -1,2 +1,2 @@ -de.lmu.ifi.dbs.elki.index.preprocessed.knn.MaterializeKNNPreprocessor +de.lmu.ifi.dbs.elki.index.preprocessed.knn.MaterializeKNNPreprocessor de.lmu.ifi.dbs.elki.preprocessing.MaterializeKNNPreprocessor de.lmu.ifi.dbs.elki.index.preprocessed.knn.MaterializeKNNAndRKNNPreprocessor diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.strategies.split.MTreeSplit b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.strategies.split.MTreeSplit index 2e49d269..ab8c255c 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.strategies.split.MTreeSplit +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.strategies.split.MTreeSplit @@ -1,4 +1,4 @@ de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.strategies.split.MMRadSplit -de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.strategies.split.MLBDistSplit -de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.strategies.split.MRadSplit +de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.strategies.split.MLBDistSplit de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.split.MLBDistSplit +de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.strategies.split.MRadSplit de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.split.MRadSplit de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.strategies.split.RandomSplit
\ No newline at end of file diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.BulkSplit b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.BulkSplit index c1ce58c7..ed08bf68 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.BulkSplit +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.BulkSplit @@ -1,7 +1,7 @@ de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.SortTileRecursiveBulkSplit str STR de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.AdaptiveSortTileRecursiveBulkSplit de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.SpatialSortBulkSplit -de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.MaxExtensionBulkSplit +de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.MaxExtensionBulkSplit de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.bulk.MaxExtensionBulkSplit de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.OneDimSortBulkSplit de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.FileOrderBulkSplit de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.MaxExtensionSortTileRecursiveBulkSplit diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.split.SplitStrategy b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.split.SplitStrategy index 46523b64..838ae341 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.split.SplitStrategy +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.split.SplitStrategy @@ -1,4 +1,4 @@ -de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.split.TopologicalSplitter +de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.split.TopologicalSplitter de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.util.TopologicalSplitter de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.split.RTreeQuadraticSplit de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.split.RTreeLinearSplit de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.split.AngTanLinearSplit diff --git a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.math.statistics.distribution.Distribution b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.math.statistics.distribution.Distribution index c193b5ae..72a16b2b 100644 --- a/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.math.statistics.distribution.Distribution +++ b/elki/src/main/resources/META-INF/elki/de.lmu.ifi.dbs.elki.math.statistics.distribution.Distribution @@ -1,7 +1,7 @@ -de.lmu.ifi.dbs.elki.math.statistics.distribution.UniformDistribution +de.lmu.ifi.dbs.elki.math.statistics.distribution.UniformDistribution de.lmu.ifi.dbs.elki.data.synthetic.bymodel.distribution.UniformDistribution de.lmu.ifi.dbs.elki.math.statistics.distribution.NormalDistribution GaussianDistribution normal gauss de.lmu.ifi.dbs.elki.math.statistics.distribution.ExponentialDistribution -de.lmu.ifi.dbs.elki.math.statistics.distribution.GammaDistribution +de.lmu.ifi.dbs.elki.math.statistics.distribution.GammaDistribution de.lmu.ifi.dbs.elki.data.synthetic.bymodel.distribution.GammaDistribution de.lmu.ifi.dbs.elki.math.statistics.distribution.BetaDistribution de.lmu.ifi.dbs.elki.math.statistics.distribution.CauchyDistribution de.lmu.ifi.dbs.elki.math.statistics.distribution.ChiDistribution diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/AllTests.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/AllTestsTestSuite.java index e4490bba..8809528e 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/AllTests.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/AllTestsTestSuite.java @@ -22,6 +22,8 @@ package de.lmu.ifi.dbs.elki; along with this program. If not, see <http://www.gnu.org/licenses/>. */ +import org.junit.Ignore; + import de.lmu.ifi.dbs.elki.utilities.ELKIServiceRegistry; import junit.framework.JUnit4TestAdapter; import junit.framework.Test; @@ -32,8 +34,9 @@ import junit.framework.TestSuite; * Build a test suite with all tests included with ELKI * * @author Erich Schubert + * @since 0.2 */ -public class AllTests extends TestSuite { +public class AllTestsTestSuite extends TestSuite { /** * Build a test suite with all tests included in ELKI. * @@ -42,7 +45,10 @@ public class AllTests extends TestSuite { public static Test suite() { TestSuite suite = new TestSuite(); for(Class<?> cls : ELKIServiceRegistry.findAllImplementations(TestCase.class, false, false)) { - if(cls == AllTests.class) { + if(cls == AllTestsTestSuite.class) { + continue; + } + if (cls.isAnnotationPresent(Ignore.class)) { continue; } Test test = new JUnit4TestAdapter(cls); @@ -51,7 +57,10 @@ public class AllTests extends TestSuite { } } for(Class<?> cls : ELKIServiceRegistry.findAllImplementations(JUnit4Test.class, false, false)) { - if(cls == AllTests.class) { + if(cls == AllTestsTestSuite.class) { + continue; + } + if (cls.isAnnotationPresent(Ignore.class)) { continue; } Test test = new JUnit4TestAdapter(cls); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/JUnit4Test.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/JUnit4Test.java index 86f72fe0..db347eea 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/JUnit4Test.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/JUnit4Test.java @@ -27,9 +27,10 @@ import org.junit.runner.RunWith; import org.junit.runners.JUnit4; /** - * This interface is used for test-discovery by the {@link AllTests} TestSuite. + * This interface is used for test-discovery by the {@link AllTestsTestSuite} TestSuite. * * @author Erich Schubert + * @since 0.2 */ @RunWith(JUnit4.class) public interface JUnit4Test { diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/AbstractSimpleAlgorithmTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/AbstractSimpleAlgorithmTest.java index 4f92a350..b3911c52 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/AbstractSimpleAlgorithmTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/AbstractSimpleAlgorithmTest.java @@ -60,6 +60,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Abstract base class useful for testing various algorithms. * * @author Erich Schubert + * @since 0.4.0 */ public abstract class AbstractSimpleAlgorithmTest { /** diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/TestKNNJoin.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/KNNJoinTest.java index cf2ca7e0..c30896c3 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/TestKNNJoin.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/KNNJoinTest.java @@ -57,7 +57,13 @@ import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; -public class TestKNNJoin implements JUnit4Test { +/** + * Unit test for kNN joins. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class KNNJoinTest implements JUnit4Test { // the following values depend on the data set used! String dataset = "data/testdata/unittests/uebungsblatt-2d-mini.csv"; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/TestDBSCAN.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/DBSCANTest.java index d457600f..7c2b0bce 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/TestDBSCAN.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/DBSCANTest.java @@ -44,8 +44,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * @author Elke Achtert * @author Erich Schubert * @author Katharina Rausch + * @since 0.3 */ -public class TestDBSCAN extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class DBSCANTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run DBSCAN with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/GriDBSCANTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/GriDBSCANTest.java new file mode 100644 index 00000000..4afd3096 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/GriDBSCANTest.java @@ -0,0 +1,118 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.data.model.Model; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Test GriDBSCAN. + * + * @author Erich Schubert + * @since 0.3 + */ +public class GriDBSCANTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run DBSCAN with fixed parameters and compare the result to a golden + * standard. + * + * @throws ParameterException + */ + @Test + public void testGriDBSCANResults() { + Database db = makeSimpleDatabase(UNITTEST + "3clusters-and-noise-2d.csv", 330); + + // setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(DBSCAN.Parameterizer.EPSILON_ID, 0.04); + params.addParameter(DBSCAN.Parameterizer.MINPTS_ID, 20); + params.addParameter(GriDBSCAN.Parameterizer.GRID_ID, 0.08); + GriDBSCAN<DoubleVector> dbscan = ClassGenericsUtil.parameterizeOrAbort(GriDBSCAN.class, params); + testParameterizationOk(params); + + // run DBSCAN on database + Clustering<Model> result = dbscan.run(db); + + testFMeasure(db, result, 0.996413); + testClusterSizes(result, new int[] { 29, 50, 101, 150 }); + } + + /** + * Run DBSCAN with fixed parameters and compare the result to a golden + * standard, with larger grid width (fewer cells, less redundancy). + * + * @throws ParameterException + */ + @Test + public void testGriDBSCANWide() { + Database db = makeSimpleDatabase(UNITTEST + "3clusters-and-noise-2d.csv", 330); + + // setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(DBSCAN.Parameterizer.EPSILON_ID, 0.04); + params.addParameter(DBSCAN.Parameterizer.MINPTS_ID, 20); + params.addParameter(GriDBSCAN.Parameterizer.GRID_ID, 0.4); + GriDBSCAN<DoubleVector> dbscan = ClassGenericsUtil.parameterizeOrAbort(GriDBSCAN.class, params); + testParameterizationOk(params); + + // run DBSCAN on database + Clustering<Model> result = dbscan.run(db); + + testFMeasure(db, result, 0.996413); + testClusterSizes(result, new int[] { 29, 50, 101, 150 }); + } + + /** + * Run DBSCAN with fixed parameters and compare the result to a golden + * standard. + * + * @throws ParameterException + */ + @Test + public void testDBSCANOnSingleLinkDataset() { + Database db = makeSimpleDatabase(UNITTEST + "single-link-effect.ascii", 638); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(DBSCAN.Parameterizer.EPSILON_ID, 11.5); + params.addParameter(DBSCAN.Parameterizer.MINPTS_ID, 120); + params.addParameter(GriDBSCAN.Parameterizer.GRID_ID, 25.); + GriDBSCAN<DoubleVector> dbscan = ClassGenericsUtil.parameterizeOrAbort(GriDBSCAN.class, params); + testParameterizationOk(params); + + // run DBSCAN on database + Clustering<Model> result = dbscan.run(db); + testFMeasure(db, result, 0.954382); + testClusterSizes(result, new int[] { 11, 200, 203, 224 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/TestSNNClusteringResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/SNNClusteringTest.java index ca47b2e2..ecdb8a90 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/TestSNNClusteringResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/SNNClusteringTest.java @@ -44,8 +44,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * * @author Katharina Rausch * @author Erich Schubert + * @since 0.4.0 */ -public class TestSNNClusteringResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class SNNClusteringTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run SNNClustering with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/AffinityPropagationClusteringAlgorithmTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/AffinityPropagationClusteringAlgorithmTest.java new file mode 100644 index 00000000..41a4d7d4 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/affinitypropagation/AffinityPropagationClusteringAlgorithmTest.java @@ -0,0 +1,111 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.affinitypropagation; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.data.model.MedoidModel; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel.PolynomialKernelFunction; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Test Affinity Propagation + * + * @author Erich Schubert + * @since 0.7.1 + */ +public class AffinityPropagationClusteringAlgorithmTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run AffinityPropagationClusteringAlgorithm with fixed parameters and + * compare the result to a golden standard. + * + * @throws ParameterException + */ + @Test + public void testAffinityPropagationClusteringAlgorithmResults() { + Database db = makeSimpleDatabase(UNITTEST + "3clusters-and-noise-2d.csv", 330); + + // setup algorithm + ListParameterization params = new ListParameterization(); + AffinityPropagationClusteringAlgorithm<DoubleVector> apc = ClassGenericsUtil.parameterizeOrAbort(AffinityPropagationClusteringAlgorithm.class, params); + testParameterizationOk(params); + + // run AffinityPropagationClusteringAlgorithm on database + Clustering<MedoidModel> result = apc.run(db); + + testFMeasure(db, result, 0.957227259); + testClusterSizes(result, new int[] { 5, 5, 7, 55, 105, 153 }); + } + + /** + * Run AffinityPropagationClusteringAlgorithm with fixed parameters and + * compare the result to a golden standard. + * + * @throws ParameterException + */ + @Test + public void testAffinityPropagationClusteringAlgorithmOnSingleLinkDataset() { + Database db = makeSimpleDatabase(UNITTEST + "single-link-effect.ascii", 638); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + AffinityPropagationClusteringAlgorithm<DoubleVector> apc = ClassGenericsUtil.parameterizeOrAbort(AffinityPropagationClusteringAlgorithm.class, params); + testParameterizationOk(params); + + // run AffinityPropagationClusteringAlgorithm on database + Clustering<MedoidModel> result = apc.run(db); + testFMeasure(db, result, 0.351689882); + testClusterSizes(result, new int[] { 24, 27, 29, 34, 36, 36, 37, 38, 41, 43, 43, 44, 46, 47, 56, 57 }); + } + + /** + * Run AffinityPropagationClusteringAlgorithm with fixed parameters and + * compare the result to a golden standard. + * + * @throws ParameterException + */ + @Test + public void testAffinityPropagationSimilarity() { + Database db = makeSimpleDatabase(UNITTEST + "single-link-effect.ascii", 638); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(AffinityPropagationClusteringAlgorithm.Parameterizer.INITIALIZATION_ID, SimilarityBasedInitializationWithMedian.class); + params.addParameter(SimilarityBasedInitializationWithMedian.Parameterizer.SIMILARITY_ID, PolynomialKernelFunction.class); + AffinityPropagationClusteringAlgorithm<DoubleVector> apc = ClassGenericsUtil.parameterizeOrAbort(AffinityPropagationClusteringAlgorithm.class, params); + testParameterizationOk(params); + + // run AffinityPropagationClusteringAlgorithm on database + Clustering<MedoidModel> result = apc.run(db); + testFMeasure(db, result, 0.352103); + testClusterSizes(result, new int[] { 20, 30, 32, 33, 34, 35, 36, 39, 39, 40, 43, 45, 45, 49, 49, 69 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/TestCASHResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/CASHTest.java index e9f9f228..b0c225bf 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/TestCASHResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/CASHTest.java @@ -39,11 +39,12 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * from the data set labels. This test ensures that CASH performance doesn't * unexpectedly drop on this data set (and also ensures that the algorithms * work, as a side effect). - * + * * @author Erich Schubert * @author Katharina Rausch + * @since 0.2 */ -public class TestCASHResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class CASHTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run CASH with fixed parameters and compare the result to a golden standard. */ @@ -54,10 +55,10 @@ public class TestCASHResults extends AbstractSimpleAlgorithmTest implements JUni // CASH parameters ListParameterization params = new ListParameterization(); - params.addParameter(CASH.JITTER_ID, 0.7); - params.addParameter(CASH.MINPTS_ID, 50); - params.addParameter(CASH.MAXLEVEL_ID, 25); - params.addFlag(CASH.ADJUST_ID); + params.addParameter(CASH.Parameterizer.JITTER_ID, 0.7); + params.addParameter(CASH.Parameterizer.MINPTS_ID, 50); + params.addParameter(CASH.Parameterizer.MAXLEVEL_ID, 25); + params.addFlag(CASH.Parameterizer.ADJUST_ID); // setup algorithm CASH<DoubleVector> cash = ClassGenericsUtil.parameterizeOrAbort(CASH.class, params); @@ -80,9 +81,9 @@ public class TestCASHResults extends AbstractSimpleAlgorithmTest implements JUni // CASH parameters ListParameterization params = new ListParameterization(); - params.addParameter(CASH.JITTER_ID, 0.7); - params.addParameter(CASH.MINPTS_ID, 160); - params.addParameter(CASH.MAXLEVEL_ID, 40); + params.addParameter(CASH.Parameterizer.JITTER_ID, 0.7); + params.addParameter(CASH.Parameterizer.MINPTS_ID, 160); + params.addParameter(CASH.Parameterizer.MAXLEVEL_ID, 40); // setup algorithm CASH<DoubleVector> cash = ClassGenericsUtil.parameterizeOrAbort(CASH.class, params); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/TestCOPACResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/COPACTest.java index f3b06c81..95503656 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/TestCOPACResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/COPACTest.java @@ -46,15 +46,16 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * from the data set labels. This test ensures that COPAC performance doesn't * unexpectedly drop on this data set (and also ensures that the algorithms * work, as a side effect). - * + * * @author Erich Schubert * @author Katharina Rausch + * @since 0.3 */ -public class TestCOPACResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class COPACTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run COPAC with fixed parameters and compare the result to a golden * standard. - * + * * @throws ParameterException on errors. */ @Test @@ -80,7 +81,7 @@ public class TestCOPACResults extends AbstractSimpleAlgorithmTest implements JUn /** * Run COPAC with fixed parameters and compare the result to a golden * standard. - * + * * @throws ParameterException on errors. */ @Test @@ -93,10 +94,10 @@ public class TestCOPACResults extends AbstractSimpleAlgorithmTest implements JUn params.addParameter(DBSCAN.Parameterizer.MINPTS_ID, 20); params.addParameter(COPAC.Settings.Parameterizer.K_ID, 45); // PCA - params.addParameter(PCARunner.PCA_COVARIANCE_MATRIX, WeightedCovarianceMatrixBuilder.class); - params.addParameter(WeightedCovarianceMatrixBuilder.WEIGHT_ID, ErfcWeight.class); + params.addParameter(PCARunner.Parameterizer.PCA_COVARIANCE_MATRIX, WeightedCovarianceMatrixBuilder.class); + params.addParameter(WeightedCovarianceMatrixBuilder.Parameterizer.WEIGHT_ID, ErfcWeight.class); params.addParameter(PCAFilteredRunner.Parameterizer.PCA_EIGENPAIR_FILTER, PercentageEigenPairFilter.class); - params.addParameter(PercentageEigenPairFilter.ALPHA_ID, 0.8); + params.addParameter(PercentageEigenPairFilter.Parameterizer.ALPHA_ID, 0.8); COPAC<DoubleVector> copac = ClassGenericsUtil.parameterizeOrAbort(COPAC.class, params); testParameterizationOk(params); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/TestERiCResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/ERiCTest.java index 7f2fb737..268fc827 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/TestERiCResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/ERiCTest.java @@ -47,14 +47,15 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * from the data set labels. This test ensures that ERiC performance doesn't * unexpectedly drop on this data set (and also ensures that the algorithms * work, as a side effect). - * + * * @author Erich Schubert * @author Katharina Rausch + * @since 0.2 */ -public class TestERiCResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class ERiCTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run ERiC with fixed parameters and compare the result to a golden standard. - * + * * @throws ParameterException on errors. */ @Test @@ -69,10 +70,10 @@ public class TestERiCResults extends AbstractSimpleAlgorithmTest implements JUni params.addParameter(ERiC.Settings.Parameterizer.TAU_ID, 0.04); params.addParameter(ERiC.Settings.Parameterizer.K_ID, 50); // PCA - params.addParameter(PCARunner.PCA_COVARIANCE_MATRIX, WeightedCovarianceMatrixBuilder.class); - params.addParameter(WeightedCovarianceMatrixBuilder.WEIGHT_ID, ErfcWeight.class); + params.addParameter(PCARunner.Parameterizer.PCA_COVARIANCE_MATRIX, WeightedCovarianceMatrixBuilder.class); + params.addParameter(WeightedCovarianceMatrixBuilder.Parameterizer.WEIGHT_ID, ErfcWeight.class); params.addParameter(PCAFilteredRunner.Parameterizer.PCA_EIGENPAIR_FILTER, RelativeEigenPairFilter.class); - params.addParameter(RelativeEigenPairFilter.EIGENPAIR_FILTER_RALPHA, 1.60); + params.addParameter(RelativeEigenPairFilter.Parameterizer.EIGENPAIR_FILTER_RALPHA, 1.60); ERiC<DoubleVector> eric = ClassGenericsUtil.parameterizeOrAbort(ERiC.class, params); testParameterizationOk(params); @@ -86,7 +87,7 @@ public class TestERiCResults extends AbstractSimpleAlgorithmTest implements JUni /** * Run ERiC with fixed parameters and compare the result to a golden standard. - * + * * @throws ParameterException on errors. */ @Test @@ -102,10 +103,10 @@ public class TestERiCResults extends AbstractSimpleAlgorithmTest implements JUni params.addParameter(ERiC.Settings.Parameterizer.TAU_ID, 1.0); params.addParameter(ERiC.Settings.Parameterizer.K_ID, 45); // PCA - params.addParameter(PCARunner.PCA_COVARIANCE_MATRIX, WeightedCovarianceMatrixBuilder.class); - params.addParameter(WeightedCovarianceMatrixBuilder.WEIGHT_ID, ErfcWeight.class); + params.addParameter(PCARunner.Parameterizer.PCA_COVARIANCE_MATRIX, WeightedCovarianceMatrixBuilder.class); + params.addParameter(WeightedCovarianceMatrixBuilder.Parameterizer.WEIGHT_ID, ErfcWeight.class); params.addParameter(PCAFilteredRunner.Parameterizer.PCA_EIGENPAIR_FILTER, PercentageEigenPairFilter.class); - params.addParameter(PercentageEigenPairFilter.ALPHA_ID, 0.6); + params.addParameter(PercentageEigenPairFilter.Parameterizer.ALPHA_ID, 0.6); ERiC<DoubleVector> eric = ClassGenericsUtil.parameterizeOrAbort(ERiC.class, params); testParameterizationOk(params); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/TestFourCResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/FourCTest.java index 8bfa5962..ddfe8218 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/TestFourCResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/FourCTest.java @@ -42,14 +42,15 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * the data set labels. This test ensures that 4C performance doesn't * unexpectedly drop on this data set (and also ensures that the algorithms * work, as a side effect). - * + * * @author Erich Schubert * @author Katharina Rausch + * @since 0.3 */ -public class TestFourCResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class FourCTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run 4F with fixed parameters and compare the result to a golden standard. - * + * * @throws ParameterException on errors. */ @Test @@ -60,7 +61,7 @@ public class TestFourCResults extends AbstractSimpleAlgorithmTest implements JUn ListParameterization params = new ListParameterization(); params.addParameter(DBSCAN.Parameterizer.EPSILON_ID, 0.30); params.addParameter(DBSCAN.Parameterizer.MINPTS_ID, 50); - params.addParameter(LimitEigenPairFilter.EIGENPAIR_FILTER_DELTA, 0.5); + params.addParameter(LimitEigenPairFilter.Parameterizer.EIGENPAIR_FILTER_DELTA, 0.5); params.addParameter(FourC.Settings.Parameterizer.LAMBDA_ID, 1); FourC<DoubleVector> fourc = ClassGenericsUtil.parameterizeOrAbort(FourC.class, params); @@ -75,7 +76,7 @@ public class TestFourCResults extends AbstractSimpleAlgorithmTest implements JUn /** * Run ERiC with fixed parameters and compare the result to a golden standard. - * + * * @throws ParameterException on errors. */ @Test @@ -87,7 +88,7 @@ public class TestFourCResults extends AbstractSimpleAlgorithmTest implements JUn // 4C params.addParameter(DBSCAN.Parameterizer.EPSILON_ID, 3); params.addParameter(DBSCAN.Parameterizer.MINPTS_ID, 50); - params.addParameter(LimitEigenPairFilter.EIGENPAIR_FILTER_DELTA, 0.5); + params.addParameter(LimitEigenPairFilter.Parameterizer.EIGENPAIR_FILTER_DELTA, 0.5); params.addParameter(FourC.Settings.Parameterizer.LAMBDA_ID, 3); FourC<DoubleVector> fourc = ClassGenericsUtil.parameterizeOrAbort(FourC.class, params); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/LMCLUSTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/LMCLUSTest.java new file mode 100644 index 00000000..e3744626 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/LMCLUSTest.java @@ -0,0 +1,87 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.correlation; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.model.Model; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Test the LMCLUS algorithm. + * + * @author Erich Schubert + * @since 0.3 + */ +public class LMCLUSTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run 4F with fixed parameters and compare the result to a golden standard. + * + * @throws ParameterException on errors. + */ + @Test + public void testLMCLUSResults() { + Database db = makeSimpleDatabase(UNITTEST + "hierarchical-3d2d1d.csv", 600); + + ListParameterization params = new ListParameterization(); + params.addParameter(LMCLUS.Parameterizer.MINSIZE_ID, 100); + params.addParameter(LMCLUS.Parameterizer.THRESHOLD_ID, 10); + params.addParameter(LMCLUS.Parameterizer.RANDOM_ID, 0); + + LMCLUS lmclus = ClassGenericsUtil.parameterizeOrAbort(LMCLUS.class, params); + testParameterizationOk(params); + + Clustering<Model> result = lmclus.run(db); + testFMeasure(db, result, 0.43327638); + testClusterSizes(result, new int[] { 201, 399 }); + } + + /** + * Run ERiC with fixed parameters and compare the result to a golden standard. + * + * @throws ParameterException on errors. + */ + @Test + public void testLMCLUSOverlap() { + Database db = makeSimpleDatabase(UNITTEST + "correlation-overlap-3-5d.ascii", 650); + + ListParameterization params = new ListParameterization(); + params.addParameter(LMCLUS.Parameterizer.MINSIZE_ID, 100); + params.addParameter(LMCLUS.Parameterizer.THRESHOLD_ID, 10); + params.addParameter(LMCLUS.Parameterizer.RANDOM_ID, 0); + + LMCLUS lmclus = ClassGenericsUtil.parameterizeOrAbort(LMCLUS.class, params); + testParameterizationOk(params); + + Clustering<Model> result = lmclus.run(db); + testClusterSizes(result, new int[] { 196, 454 }); + testFMeasure(db, result, 0.6547222); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/TestORCLUSResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/ORCLUSTest.java index cd6d4558..f71f863a 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/TestORCLUSResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/correlation/ORCLUSTest.java @@ -43,8 +43,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * * @author Elke Achtert * @author Katharina Rausch + * @since 0.3 */ -public class TestORCLUSResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class ORCLUSTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run ORCLUS with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/TestEMResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/EMTest.java index 629a78d5..0ede15bb 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/TestEMResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/em/EMTest.java @@ -32,7 +32,6 @@ import de.lmu.ifi.dbs.elki.data.Clustering; import de.lmu.ifi.dbs.elki.data.DoubleVector; import de.lmu.ifi.dbs.elki.database.Database; import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; /** @@ -40,15 +39,14 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * from the data set labels. This test ensures that EM's performance doesn't * unexpectedly drop on this data set (and also ensures that the algorithms * work, as a side effect). - * + * * @author Katharina Rausch * @author Erich Schubert + * @since 0.4.0 */ -public class TestEMResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class EMTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run EM with fixed parameters and compare the result to a golden standard. - * - * @throws ParameterException */ @Test public void testEMResults() { @@ -63,7 +61,49 @@ public class TestEMResults extends AbstractSimpleAlgorithmTest implements JUnit4 // run EM on database Clustering<?> result = em.run(db); - testFMeasure(db, result, 0.781737); - testClusterSizes(result, new int[] { 2, 5, 17, 175, 200, 311 }); + testFMeasure(db, result, 0.780036); + testClusterSizes(result, new int[] { 2, 5, 27, 171, 200, 305 }); + } + + /** + * Run EM with fixed parameters and compare the result to a golden standard. + */ + @Test + public void testEMResultsDiagonal() { + Database db = makeSimpleDatabase(UNITTEST + "hierarchical-2d.ascii", 710); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(KMeans.SEED_ID, 0); + params.addParameter(EM.Parameterizer.K_ID, 6); + params.addParameter(EM.Parameterizer.INIT_ID, DiagonalGaussianModelFactory.class); + EM<DoubleVector, ?> em = ClassGenericsUtil.parameterizeOrAbort(EM.class, params); + testParameterizationOk(params); + + // run EM on database + Clustering<?> result = em.run(db); + testFMeasure(db, result, 0.9302319); + testClusterSizes(result, new int[] { 7, 22, 93, 97, 200, 291 }); + } + + /** + * Run EM with fixed parameters and compare the result to a golden standard. + */ + @Test + public void testEMResultsSpherical() { + Database db = makeSimpleDatabase(UNITTEST + "hierarchical-2d.ascii", 710); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(KMeans.SEED_ID, 0); + params.addParameter(EM.Parameterizer.K_ID, 6); + params.addParameter(EM.Parameterizer.INIT_ID, SphericalGaussianModelFactory.class); + EM<DoubleVector, ?> em = ClassGenericsUtil.parameterizeOrAbort(EM.class, params); + testParameterizationOk(params); + + // run EM on database + Clustering<?> result = em.run(db); + testFMeasure(db, result, 0.514850); + testClusterSizes(result, new int[] { 0, 6, 53, 69, 191, 391 }); } }
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/TestGeneralizedDBSCAN.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/GeneralizedDBSCANTest.java index c5bb1c5e..3c77f029 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/TestGeneralizedDBSCAN.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/GeneralizedDBSCANTest.java @@ -44,8 +44,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * @author Elke Achtert * @author Erich Schubert * @author Katharina Rausch + * @since 0.3 */ -public class TestGeneralizedDBSCAN extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class GeneralizedDBSCANTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run Generalized DBSCAN with fixed parameters and compare the result to a * golden standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/LSDBCTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/LSDBCTest.java new file mode 100644 index 00000000..c33ba0e7 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/LSDBCTest.java @@ -0,0 +1,78 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.gdbscan; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.data.model.Model; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Regression test for LSDBC. + * + * @author Erich Schubert + * @since 0.3 + */ +public class LSDBCTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testLSDBCResults() { + Database db = makeSimpleDatabase(UNITTEST + "3clusters-and-noise-2d.csv", 330); + + // setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(LSDBC.Parameterizer.ALPHA_ID, 0.4); + params.addParameter(LSDBC.Parameterizer.K_ID, 20); + LSDBC<DoubleVector> dbscan = ClassGenericsUtil.parameterizeOrAbort(LSDBC.class, params); + testParameterizationOk(params); + + // run LSDBC on database + Clustering<Model> result = dbscan.run(db); + + testFMeasure(db, result, 0.44848979); + testClusterSizes(result, new int[] { 38, 38, 41, 54, 159 }); + } + + @Test + public void testLSDBCOnSingleLinkDataset() { + Database db = makeSimpleDatabase(UNITTEST + "single-link-effect.ascii", 638); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(LSDBC.Parameterizer.ALPHA_ID, 0.2); + params.addParameter(LSDBC.Parameterizer.K_ID, 120); + LSDBC<DoubleVector> dbscan = ClassGenericsUtil.parameterizeOrAbort(LSDBC.class, params); + testParameterizationOk(params); + + // run LSDBC on database + Clustering<Model> result = dbscan.run(db); + testFMeasure(db, result, 0.95681073); + testClusterSizes(result, new int[] { 32, 197, 203, 206 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/TestAGNES.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AGNESTest.java index f12ae73d..c0421a54 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/TestAGNES.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AGNESTest.java @@ -39,8 +39,9 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * Perform agglomerative hierarchical clustering, using the naive algorithm. * * @author Erich Schubert + * @since 0.6.0 */ -public class TestAGNES extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class AGNESTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { // TODO: add more data sets. /** diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/TestAnderbergHierarchicalClustering.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AnderbergHierarchicalClusteringTest.java index 6dd73ec6..c94557dd 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/TestAnderbergHierarchicalClustering.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AnderbergHierarchicalClusteringTest.java @@ -40,8 +40,9 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * algorithm. * * @author Erich Schubert + * @since 0.6.0 */ -public class TestAnderbergHierarchicalClustering extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class AnderbergHierarchicalClusteringTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { // TODO: add more data sets. /** diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/TestCLINKResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/CLINKTest.java index d9276c5b..b6ce8545 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/TestCLINKResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/CLINKTest.java @@ -42,8 +42,9 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * work, as a side effect). * * @author Erich Schubert + * @since 0.4.0 */ -public class TestCLINKResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class CLINKTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run CLINK with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/TestSLINKResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/SLINKTest.java index 22b143a4..bde1e243 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/TestSLINKResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/SLINKTest.java @@ -43,8 +43,9 @@ import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; * * @author Katharina Rausch * @author Erich Schubert + * @since 0.4.0 */ -public class TestSLINKResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class SLINKTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { // TODO: add a test for a non-single-link dataset? /** diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestCLARA.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/CLARATest.java index f9c0b779..89599bda 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestCLARA.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/CLARATest.java @@ -43,8 +43,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * * @author Katharina Rausch * @author Erich Schubert + * @since 0.4.0 */ -public class TestCLARA extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class CLARATest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run CLARA with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansBatchedLloydTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansBatchedLloydTest.java new file mode 100644 index 00000000..bab15c09 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansBatchedLloydTest.java @@ -0,0 +1,68 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Regression test for batched Lloyd k-means. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class KMeansBatchedLloydTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run KMeans with fixed parameters and compare the result to a golden + * standard. + * + * @throws ParameterException + */ + @Test + public void testKMeansBatchedLloyd() { + Database db = makeSimpleDatabase(UNITTEST + "different-densities-2d-no-noise.ascii", 1000); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(KMeans.K_ID, 5); + params.addParameter(KMeans.SEED_ID, 2); + params.addParameter(KMeansBatchedLloyd.Parameterizer.BLOCKS_ID, 10); + params.addParameter(KMeansBatchedLloyd.Parameterizer.RANDOM_ID, 0); + AbstractKMeans<DoubleVector, ?> kmeans = ClassGenericsUtil.parameterizeOrAbort(KMeansBatchedLloyd.class, params); + testParameterizationOk(params); + + // run KMeans on database + Clustering<?> result = kmeans.run(db); + testFMeasure(db, result, 0.998005); + testClusterSizes(result, new int[] { 199, 200, 200, 200, 201 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMeansBisecting.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansBisectingTest.java index 06d55028..cb407e28 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMeansBisecting.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansBisectingTest.java @@ -39,8 +39,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the KMeansBisecting * * @author Stephan Baier + * @since 0.6.0 */ -public class TestKMeansBisecting extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class KMeansBisectingTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run KMeansBisecting with fixed parameters and compare cluster size to * expected value. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansCompareTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansCompareTest.java new file mode 100644 index 00000000..fead9461 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansCompareTest.java @@ -0,0 +1,66 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Regression test for Compare k-means. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class KMeansCompareTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run KMeans with fixed parameters and compare the result to a golden + * standard. + * + * @throws ParameterException + */ + @Test + public void testKMeansCompare() { + Database db = makeSimpleDatabase(UNITTEST + "different-densities-2d-no-noise.ascii", 1000); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(KMeans.K_ID, 5); + params.addParameter(KMeans.SEED_ID, 2); + AbstractKMeans<DoubleVector, ?> kmeans = ClassGenericsUtil.parameterizeOrAbort(KMeansCompare.class, params); + testParameterizationOk(params); + + // run KMeans on database + Clustering<?> result = kmeans.run(db); + testFMeasure(db, result, 0.998005); + testClusterSizes(result, new int[] { 199, 200, 200, 200, 201 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMeansElkan.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansElkanTest.java index 95f28c5d..2d1cbe5a 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMeansElkan.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansElkanTest.java @@ -35,26 +35,27 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; /** - * Regression test for Hamerly k-means. - * + * Regression test for Elkan k-means. + * * @author Erich Schubert + * @since 0.4.0 */ -public class TestKMeansElkan extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class KMeansElkanTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run KMeans with fixed parameters and compare the result to a golden * standard. - * + * * @throws ParameterException */ @Test - public void testKMeansLloyd() { + public void testKMeansElkan() { Database db = makeSimpleDatabase(UNITTEST + "different-densities-2d-no-noise.ascii", 1000); // Setup algorithm ListParameterization params = new ListParameterization(); params.addParameter(KMeans.K_ID, 5); params.addParameter(KMeans.SEED_ID, 2); - AbstractKMeans<DoubleVector, ?> kmeans = ClassGenericsUtil.parameterizeOrAbort(KMeansHamerly.class, params); + AbstractKMeans<DoubleVector, ?> kmeans = ClassGenericsUtil.parameterizeOrAbort(KMeansElkan.class, params); testParameterizationOk(params); // run KMeans on database diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMeansHamerly.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansHamerlyTest.java index e709861e..328211fb 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMeansHamerly.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansHamerlyTest.java @@ -38,8 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Regression test for Hamerly k-means. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestKMeansHamerly extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class KMeansHamerlyTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run KMeans with fixed parameters and compare the result to a golden * standard. @@ -47,7 +48,7 @@ public class TestKMeansHamerly extends AbstractSimpleAlgorithmTest implements JU * @throws ParameterException */ @Test - public void testKMeansLloyd() { + public void testKMeansHamerly() { Database db = makeSimpleDatabase(UNITTEST + "different-densities-2d-no-noise.ascii", 1000); // Setup algorithm diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansHybridLloydMacQueenTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansHybridLloydMacQueenTest.java new file mode 100644 index 00000000..390f5c3d --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansHybridLloydMacQueenTest.java @@ -0,0 +1,70 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Performs a full KMeans run, and compares the result with a clustering derived + * from the data set labels. This test ensures that KMeans's performance doesn't + * unexpectedly drop on this data set (and also ensures that the algorithms + * work, as a side effect). + * + * @author Katharina Rausch + * @author Erich Schubert + * @since 0.4.0 + */ +public class KMeansHybridLloydMacQueenTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run KMeans with fixed parameters and compare the result to a golden + * standard. + * + * @throws ParameterException + */ + @Test + public void testKMeansHybridLloydMacQueen() { + Database db = makeSimpleDatabase(UNITTEST + "different-densities-2d-no-noise.ascii", 1000); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(KMeans.K_ID, 5); + params.addParameter(KMeans.SEED_ID, 2); + AbstractKMeans<DoubleVector, ?> kmeans = ClassGenericsUtil.parameterizeOrAbort(KMeansHybridLloydMacQueen.class, params); + testParameterizationOk(params); + + // run KMeans on database + Clustering<?> result = kmeans.run(db); + testFMeasure(db, result, 0.998005); + testClusterSizes(result, new int[] { 199, 200, 200, 200, 201 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMeansLloyd.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansLloydTest.java index 15d73657..a0edbe5e 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMeansLloyd.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansLloydTest.java @@ -42,8 +42,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * * @author Katharina Rausch * @author Erich Schubert + * @since 0.4.0 */ -public class TestKMeansLloyd extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class KMeansLloydTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run KMeans with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMeansMacQueen.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansMacQueenTest.java index b4289b9f..6271929d 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMeansMacQueen.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansMacQueenTest.java @@ -42,8 +42,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * * @author Katharina Rausch * @author Erich Schubert + * @since 0.4.0 */ -public class TestKMeansMacQueen extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class KMeansMacQueenTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run KMeans with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansSortTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansSortTest.java new file mode 100644 index 00000000..b7b20097 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMeansSortTest.java @@ -0,0 +1,66 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Regression test for Sort-means. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class KMeansSortTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run KMeans with fixed parameters and compare the result to a golden + * standard. + * + * @throws ParameterException + */ + @Test + public void testKMeansSort() { + Database db = makeSimpleDatabase(UNITTEST + "different-densities-2d-no-noise.ascii", 1000); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(KMeans.K_ID, 5); + params.addParameter(KMeans.SEED_ID, 2); + AbstractKMeans<DoubleVector, ?> kmeans = ClassGenericsUtil.parameterizeOrAbort(KMeansSort.class, params); + testParameterizationOk(params); + + // run KMeans on database + Clustering<?> result = kmeans.run(db); + testFMeasure(db, result, 0.998005); + testClusterSizes(result, new int[] { 199, 200, 200, 200, 201 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMediansLloyd.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMediansLloydTest.java index ab451cab..c7abf806 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMediansLloyd.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMediansLloydTest.java @@ -42,8 +42,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * * @author Katharina Rausch * @author Erich Schubert + * @since 0.4.0 */ -public class TestKMediansLloyd extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class KMediansLloydTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run KMedians with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMedoidsEM.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMedoidsEMTest.java index ecfafffe..eee1c799 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMedoidsEM.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMedoidsEMTest.java @@ -41,8 +41,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * * @author Katharina Rausch * @author Erich Schubert + * @since 0.4.0 */ -public class TestKMedoidsEM extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class KMedoidsEMTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run KMedoidsEM with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMedoidsPAM.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMedoidsPAMTest.java index 4bb98041..a7fe2712 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestKMedoidsPAM.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMedoidsPAMTest.java @@ -43,8 +43,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * * @author Katharina Rausch * @author Erich Schubert + * @since 0.4.0 */ -public class TestKMedoidsPAM extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class KMedoidsPAMTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run KMedians PAM with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/SingleAssignmentKMeansTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/SingleAssignmentKMeansTest.java new file mode 100644 index 00000000..c20790b9 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/SingleAssignmentKMeansTest.java @@ -0,0 +1,67 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Performs a full KMeans run, and compares the result with a clustering derived + * from the data set labels. This test ensures that KMeans's performance doesn't + * unexpectedly drop on this data set (and also ensures that the algorithms + * work, as a side effect). + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class SingleAssignmentKMeansTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run KMeans with fixed parameters and compare the result to a golden + * standard. + */ + @Test + public void testSingleAssignmentKMeans() { + Database db = makeSimpleDatabase(UNITTEST + "different-densities-2d-no-noise.ascii", 1000); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(KMeans.K_ID, 5); + params.addParameter(KMeans.SEED_ID, 3); + AbstractKMeans<DoubleVector, ?> kmeans = ClassGenericsUtil.parameterizeOrAbort(SingleAssignmentKMeans.class, params); + testParameterizationOk(params); + + // run KMeans on database + Clustering<?> result = kmeans.run(db); + // Unsurprisingly, these results are much worse than normal k-means + testFMeasure(db, result, 0.7936860577); + testClusterSizes(result, new int[] { 52, 151, 200, 201, 396 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestXMeans.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/XMeansTest.java index 58871f75..91ec25e2 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/TestXMeans.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/XMeansTest.java @@ -39,8 +39,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * * @author Tibor Goldschwendt * @author Erich Schubert + * @since 0.4.0 */ -public class TestXMeans extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class XMeansTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testXMeans() { Database db = makeSimpleDatabase(UNITTEST + "3clusters-and-noise-2d.csv", 330); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestPointsInitialMeansTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestPointsInitialMeansTest.java new file mode 100644 index 00000000..f077abf7 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestPointsInitialMeansTest.java @@ -0,0 +1,70 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2016 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.AbstractKMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.SingleAssignmentKMeans; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Performs a single assignment with different k-means initializations. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class FarthestPointsInitialMeansTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run KMeans with fixed parameters and compare the result to a golden + * standard. + * + * @throws ParameterException + */ + @Test + public void testFarthestPointsInitialMeans() { + Database db = makeSimpleDatabase(UNITTEST + "different-densities-2d-no-noise.ascii", 1000); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(KMeans.K_ID, 5); + params.addParameter(KMeans.SEED_ID, 3); + params.addParameter(KMeans.INIT_ID, FarthestPointsInitialMeans.class); + AbstractKMeans<DoubleVector, ?> kmeans = ClassGenericsUtil.parameterizeOrAbort(SingleAssignmentKMeans.class, params); + testParameterizationOk(params); + + // run KMeans on database + Clustering<?> result = kmeans.run(db); + testFMeasure(db, result, 0.88132453); + testClusterSizes(result, new int[] { 128, 199, 201, 201, 271 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestSumPointsInitialMeansTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestSumPointsInitialMeansTest.java new file mode 100644 index 00000000..2f592fb3 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestSumPointsInitialMeansTest.java @@ -0,0 +1,70 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2016 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.AbstractKMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.SingleAssignmentKMeans; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Performs a single assignment with different k-means initializations. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class FarthestSumPointsInitialMeansTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run KMeans with fixed parameters and compare the result to a golden + * standard. + * + * @throws ParameterException + */ + @Test + public void testFarthestSumPointsInitialMeans() { + Database db = makeSimpleDatabase(UNITTEST + "different-densities-2d-no-noise.ascii", 1000); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(KMeans.K_ID, 5); + params.addParameter(KMeans.SEED_ID, 3); + params.addParameter(KMeans.INIT_ID, FarthestSumPointsInitialMeans.class); + AbstractKMeans<DoubleVector, ?> kmeans = ClassGenericsUtil.parameterizeOrAbort(SingleAssignmentKMeans.class, params); + testParameterizationOk(params); + + // run KMeans on database + Clustering<?> result = kmeans.run(db); + testFMeasure(db, result, 0.80399668933); + testClusterSizes(result, new int[] { 32, 169, 199, 201, 399 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FirstKInitialMeansTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FirstKInitialMeansTest.java new file mode 100644 index 00000000..dbcd91da --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FirstKInitialMeansTest.java @@ -0,0 +1,69 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2016 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.AbstractKMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.SingleAssignmentKMeans; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Performs a single assignment with different k-means initializations. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class FirstKInitialMeansTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run KMeans with fixed parameters and compare the result to a golden + * standard. + * + * @throws ParameterException + */ + @Test + public void testFirstKInitialMeans() { + Database db = makeSimpleDatabase(UNITTEST + "different-densities-2d-no-noise.ascii", 1000); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(KMeans.K_ID, 5); + params.addParameter(KMeans.INIT_ID, FirstKInitialMeans.class); + AbstractKMeans<DoubleVector, ?> kmeans = ClassGenericsUtil.parameterizeOrAbort(SingleAssignmentKMeans.class, params); + testParameterizationOk(params); + + // run KMeans on database + Clustering<?> result = kmeans.run(db); + testFMeasure(db, result, 0.62025907); + testClusterSizes(result, new int[] { 23, 38, 226, 258, 455 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/KMeansPlusPlusInitialMeansTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/KMeansPlusPlusInitialMeansTest.java new file mode 100644 index 00000000..0b9355e3 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/KMeansPlusPlusInitialMeansTest.java @@ -0,0 +1,70 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.AbstractKMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.SingleAssignmentKMeans; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Performs a single assignment with different k-means initializations. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class KMeansPlusPlusInitialMeansTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run KMeans with fixed parameters and compare the result to a golden + * standard. + * + * @throws ParameterException + */ + @Test + public void testSingleAssignmentKMeansPlusPlus() { + Database db = makeSimpleDatabase(UNITTEST + "different-densities-2d-no-noise.ascii", 1000); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(KMeans.K_ID, 5); + params.addParameter(KMeans.SEED_ID, 3); + params.addParameter(KMeans.INIT_ID, KMeansPlusPlusInitialMeans.class); + AbstractKMeans<DoubleVector, ?> kmeans = ClassGenericsUtil.parameterizeOrAbort(SingleAssignmentKMeans.class, params); + testParameterizationOk(params); + + // run KMeans on database + Clustering<?> result = kmeans.run(db); + testFMeasure(db, result, 0.99800500); + testClusterSizes(result, new int[] { 199, 200, 200, 200, 201 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/PAMInitialMeansTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/PAMInitialMeansTest.java new file mode 100644 index 00000000..c0d2b46d --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/PAMInitialMeansTest.java @@ -0,0 +1,69 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2016 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.AbstractKMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.SingleAssignmentKMeans; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Performs a single assignment with different k-means initializations. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class PAMInitialMeansTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run KMeans with fixed parameters and compare the result to a golden + * standard. + * + * @throws ParameterException + */ + @Test + public void testPAMInitialMeans() { + Database db = makeSimpleDatabase(UNITTEST + "different-densities-2d-no-noise.ascii", 1000); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(KMeans.K_ID, 5); + params.addParameter(KMeans.INIT_ID, PAMInitialMeans.class); + AbstractKMeans<DoubleVector, ?> kmeans = ClassGenericsUtil.parameterizeOrAbort(SingleAssignmentKMeans.class, params); + testParameterizationOk(params); + + // run KMeans on database + Clustering<?> result = kmeans.run(db); + testFMeasure(db, result, 0.99800500); + testClusterSizes(result, new int[] { 199, 200, 200, 200, 201 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/RandomlyChosenInitialMeansTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/RandomlyChosenInitialMeansTest.java new file mode 100644 index 00000000..a1e36fde --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/RandomlyChosenInitialMeansTest.java @@ -0,0 +1,70 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2016 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.AbstractKMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.SingleAssignmentKMeans; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Performs a single assignment with different k-means initializations. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class RandomlyChosenInitialMeansTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run KMeans with fixed parameters and compare the result to a golden + * standard. + * + * @throws ParameterException + */ + @Test + public void testRandomlyChosenInitialMeans() { + Database db = makeSimpleDatabase(UNITTEST + "different-densities-2d-no-noise.ascii", 1000); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(KMeans.K_ID, 5); + params.addParameter(KMeans.SEED_ID, 3); + params.addParameter(KMeans.INIT_ID, RandomlyChosenInitialMeans.class); + AbstractKMeans<DoubleVector, ?> kmeans = ClassGenericsUtil.parameterizeOrAbort(SingleAssignmentKMeans.class, params); + testParameterizationOk(params); + + // run KMeans on database + Clustering<?> result = kmeans.run(db); + testFMeasure(db, result, 0.793686); + testClusterSizes(result, new int[] { 52, 151, 200, 201, 396 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/RandomlyGeneratedInitialMeansTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/RandomlyGeneratedInitialMeansTest.java new file mode 100644 index 00000000..045e6b4f --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/RandomlyGeneratedInitialMeansTest.java @@ -0,0 +1,70 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2016 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.AbstractKMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.SingleAssignmentKMeans; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Performs a single assignment with different k-means initializations. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class RandomlyGeneratedInitialMeansTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run KMeans with fixed parameters and compare the result to a golden + * standard. + * + * @throws ParameterException + */ + @Test + public void testRandomlyGeneratedInitialMeans() { + Database db = makeSimpleDatabase(UNITTEST + "different-densities-2d-no-noise.ascii", 1000); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(KMeans.K_ID, 5); + params.addParameter(KMeans.SEED_ID, 3); + params.addParameter(KMeans.INIT_ID, RandomlyGeneratedInitialMeans.class); + AbstractKMeans<DoubleVector, ?> kmeans = ClassGenericsUtil.parameterizeOrAbort(SingleAssignmentKMeans.class, params); + testParameterizationOk(params); + + // run KMeans on database + Clustering<?> result = kmeans.run(db); + testFMeasure(db, result, 0.7597720973); + testClusterSizes(result, new int[] { 66, 200, 200, 245, 289 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/SampleKMeansInitializationTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/SampleKMeansInitializationTest.java new file mode 100644 index 00000000..9d9e4a2a --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/SampleKMeansInitializationTest.java @@ -0,0 +1,74 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.AbstractKMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansHamerly; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.SingleAssignmentKMeans; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Performs a single assignment with different k-means initializations. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class SampleKMeansInitializationTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run KMeans with fixed parameters and compare the result to a golden + * standard. + * + * @throws ParameterException + */ + @Test + public void testSampleKMeansInitialization() { + Database db = makeSimpleDatabase(UNITTEST + "different-densities-2d-no-noise.ascii", 1000); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(KMeans.K_ID, 5); + params.addParameter(KMeans.SEED_ID, 3); + params.addParameter(KMeans.INIT_ID, SampleKMeansInitialization.class); + params.addParameter(SampleKMeansInitialization.Parameterizer.KMEANS_ID, KMeansHamerly.class); + params.addParameter(KMeans.SEED_ID, 3); + params.addParameter(SampleKMeansInitialization.Parameterizer.SAMPLE_ID, 100); + AbstractKMeans<DoubleVector, ?> kmeans = ClassGenericsUtil.parameterizeOrAbort(SingleAssignmentKMeans.class, params); + testParameterizationOk(params); + + // run KMeans on database + Clustering<?> result = kmeans.run(db); + testFMeasure(db, result, 0.780753320); + testClusterSizes(result, new int[] { 75, 125, 200, 205, 395 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/parallel/TestParallelLloydKMeans.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/parallel/ParallelLloydKMeansTest.java index a396cf73..cf6151cf 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/parallel/TestParallelLloydKMeans.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/parallel/ParallelLloydKMeansTest.java @@ -44,8 +44,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * * @author Katharina Rausch * @author Erich Schubert + * @since 0.4.0 */ -public class TestParallelLloydKMeans extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class ParallelLloydKMeansTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run KMeans with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/TestWithinClusterMeanDistanceQualityMeasure.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/WithinClusterMeanDistanceQualityMeasureTest.java index f4531305..d2f619e7 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/TestWithinClusterMeanDistanceQualityMeasure.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/WithinClusterMeanDistanceQualityMeasureTest.java @@ -47,8 +47,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Test cluster quality measure computations. * * @author Stephan Baier + * @since 0.6.0 */ -public class TestWithinClusterMeanDistanceQualityMeasure extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class WithinClusterMeanDistanceQualityMeasureTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Test cluster average overall distance. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/TestWithinClusterVarianceQualityMeasure.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/WithinClusterVarianceQualityMeasureTest.java index 57b6ba75..eee4bf74 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/TestWithinClusterVarianceQualityMeasure.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/quality/WithinClusterVarianceQualityMeasureTest.java @@ -47,8 +47,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Test cluster quality measure computations. * * @author Stephan Baier + * @since 0.6.0 */ -public class TestWithinClusterVarianceQualityMeasure extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class WithinClusterVarianceQualityMeasureTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Test cluster variance. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/TestDeLiCluResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/DeLiCluTest.java index 51879af4..2773a61e 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/TestDeLiCluResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/DeLiCluTest.java @@ -49,8 +49,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * * @author Katharina Rausch * @author Erich Schubert + * @since 0.4.0 */ -public class TestDeLiCluResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class DeLiCluTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run DeLiClu with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/FastOPTICSTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/FastOPTICSTest.java new file mode 100644 index 00000000..3b00856a --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/FastOPTICSTest.java @@ -0,0 +1,62 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.optics; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.index.preprocessed.fastoptics.RandomProjectedNeighborsAndDensities; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Simple regression test for FastOPTICS. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class FastOPTICSTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testFastOPTICS() { + Database db = makeSimpleDatabase(UNITTEST + "hierarchical-2d.ascii", 710); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(OPTICSList.Parameterizer.MINPTS_ID, 18); + params.addParameter(OPTICSXi.Parameterizer.XI_ID, 0.038); + params.addParameter(OPTICSXi.Parameterizer.XIALG_ID, FastOPTICS.class); + params.addParameter(RandomProjectedNeighborsAndDensities.Parameterizer.RANDOM_ID, 0); + OPTICSXi opticsxi = ClassGenericsUtil.parameterizeOrAbort(OPTICSXi.class, params); + testParameterizationOk(params); + + // run OPTICS on database + Clustering<?> clustering = opticsxi.run(db); + + testFMeasure(db, clustering, 0.7495221); + testClusterSizes(clustering, new int[] { 3, 4, 5, 6, 7, 8, 13, 18, 23, 26, 36, 40, 42, 95, 167, 217 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/TestOPTICSHeapResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSHeapTest.java index f318636d..d47e5ea2 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/TestOPTICSHeapResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSHeapTest.java @@ -41,8 +41,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * * @author Katharina Rausch * @author Erich Schubert + * @since 0.4.0 */ -public class TestOPTICSHeapResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class OPTICSHeapTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run OPTICS with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/TestOPTICSListResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSListTest.java index 249c3cad..27125ad9 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/TestOPTICSListResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/OPTICSListTest.java @@ -41,8 +41,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * * @author Katharina Rausch * @author Erich Schubert + * @since 0.4.0 */ -public class TestOPTICSListResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class OPTICSListTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run OPTICS with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/TestCLIQUEResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/CLIQUETest.java index 25019d7a..b71bd57b 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/TestCLIQUEResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/CLIQUETest.java @@ -40,16 +40,17 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * from the data set labels. This test ensures that CLIQUE performance doesn't * unexpectedly drop on this data set (and also ensures that the algorithms * work, as a side effect). - * + * * @author Elke Achtert * @author Katharina Rausch * @author Erich Schubert + * @since 0.3 */ -public class TestCLIQUEResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class CLIQUETest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run CLIQUE with fixed parameters and compare the result to a golden * standard. - * + * * @throws ParameterException */ @Test @@ -75,7 +76,7 @@ public class TestCLIQUEResults extends AbstractSimpleAlgorithmTest implements JU /** * Run CLIQUE with fixed parameters and compare the result to a golden * standard. - * + * * @throws ParameterException */ @Test @@ -95,4 +96,29 @@ public class TestCLIQUEResults extends AbstractSimpleAlgorithmTest implements JU // testFMeasure(db, result, 0.433661); testClusterSizes(result, new int[] { 255, 409, 458, 458, 480 }); } + + /** + * Run CLIQUE with fixed parameters and compare the result to a golden + * standard. + * + * @throws ParameterException + */ + @Test + public void testCLIQUESubspaceOverlappingPrune() { + Database db = makeSimpleDatabase(UNITTEST + "subspace-overlapping-3-4d.ascii", 850); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(CLIQUE.TAU_ID, 0.2); + params.addParameter(CLIQUE.XSI_ID, 6); + params.addFlag(CLIQUE.PRUNE_ID); + CLIQUE<DoubleVector> clique = ClassGenericsUtil.parameterizeOrAbort(CLIQUE.class, params); + testParameterizationOk(params); + + // run CLIQUE on database + Clustering<SubspaceModel> result = clique.run(db); + // PairCounting is not appropriate here: overlapping clusterings! + // testFMeasure(db, result, 0.433661); + testClusterSizes(result, new int[] { 255, 409, 458, 458, 480 }); + } }
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DOCTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DOCTest.java new file mode 100644 index 00000000..00fe42bf --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DOCTest.java @@ -0,0 +1,91 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.subspace; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Test DOC on a simple test data set. + * + * On the first set, its an all-or-nothing depending on the parameters. + * + * @author Erich Schubert + * @since 0.3 + */ +public class DOCTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + /** + * Run DOC with fixed parameters and compare the result to a golden standard. + */ + @Test + public void testDOCSimple() { + Database db = makeSimpleDatabase(UNITTEST + "subspace-simple.csv", 600); + + ListParameterization params = new ListParameterization(); + params.addParameter(DOC.Parameterizer.RANDOM_ID, 0); + params.addParameter(DOC.Parameterizer.ALPHA_ID, 0.4); + params.addParameter(DOC.Parameterizer.BETA_ID, 0.85); + + // setup algorithm + DOC<DoubleVector> doc = ClassGenericsUtil.parameterizeOrAbort(DOC.class, params); + testParameterizationOk(params); + + // run DOC on database + Clustering<?> result = doc.run(db); + + testClusterSizes(result, new int[] { 200, 400 }); + testFMeasure(db, result, 1.0); + } + + /** + * Run DOC with fixed parameters and compare the result to a golden standard. + */ + @Test + public void testDOCOverlapping() { + Database db = makeSimpleDatabase(UNITTEST + "subspace-overlapping-3-4d.ascii", 850); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(DOC.Parameterizer.RANDOM_ID, 0); + params.addParameter(DOC.Parameterizer.ALPHA_ID, 0.4); + params.addParameter(DOC.Parameterizer.BETA_ID, 0.95); + params.addFlag(DOC.Parameterizer.HEURISTICS_ID); + params.addParameter(DOC.Parameterizer.D_ZERO_ID, 1); + + DOC<DoubleVector> doc = ClassGenericsUtil.parameterizeOrAbort(DOC.class, params); + testParameterizationOk(params); + + // run DOC on database + Clustering<?> result = doc.run(db); + testFMeasure(db, result, .54271816); + testClusterSizes(result, new int[] { 1, 20, 33, 40, 56, 104, 274, 322 }); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/TestDiSHResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DiSHTest.java index 7d78b18f..87b38f1d 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/TestDiSHResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DiSHTest.java @@ -45,8 +45,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * @author Elke Achtert * @author Katharina Rausch * @author Erich Schubert + * @since 0.3 */ -public class TestDiSHResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class DiSHTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run DiSH with fixed parameters and compare the result to a golden standard. * diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/TestP3C.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/P3CTest.java index cc8d2e7c..f7a88a83 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/TestP3C.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/P3CTest.java @@ -43,8 +43,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * But from visual inspection, this might be a true positive. * * @author Erich Schubert + * @since 0.3 */ -public class TestP3C extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class P3CTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run P3C with fixed parameters and compare the result to a golden standard. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/TestPROCLUSResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUSTest.java index 61c716a6..75d42b07 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/TestPROCLUSResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUSTest.java @@ -43,8 +43,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * @author Elke Achtert * @author Katharina Rausch * @author Erich Schubert + * @since 0.3 */ -public class TestPROCLUSResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class PROCLUSTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run PROCLUS with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/TestPreDeConResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PreDeConTest.java index ecd43770..6c9de70a 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/TestPreDeConResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PreDeConTest.java @@ -45,8 +45,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * * @author Erich Schubert * @author Katharina Rausch + * @since 0.3 */ -public class TestPreDeConResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class PreDeConTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run PreDeCon with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/TestSUBCLUResults.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/SUBCLUTest.java index 7ae7ecaf..027f906f 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/TestSUBCLUResults.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/SUBCLUTest.java @@ -44,8 +44,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * @author Elke Achtert * @author Katharina Rausch * @author Erich Schubert + * @since 0.3 */ -public class TestSUBCLUResults extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class SUBCLUTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { /** * Run SUBCLU with fixed parameters and compare the result to a golden * standard. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/COPTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/COPTest.java new file mode 100644 index 00000000..e4d1aaf2 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/COPTest.java @@ -0,0 +1,108 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.math.linearalgebra.pca.PCAFilteredAutotuningRunner; +import de.lmu.ifi.dbs.elki.math.linearalgebra.pca.RANSACCovarianceMatrixBuilder; +import de.lmu.ifi.dbs.elki.math.linearalgebra.pca.WeightedCovarianceMatrixBuilder; +import de.lmu.ifi.dbs.elki.math.linearalgebra.pca.weightfunctions.ErfcWeight; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Tests the COP algorithm. + * + * @author Erich Schubert + * @since 0.7.1 + */ +public class COPTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testCOP() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-parabolic.ascii", 530); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(COP.Parameterizer.K_ID, 30); + + // setup Algorithm + COP<DoubleVector> cop = ClassGenericsUtil.parameterizeOrAbort(COP.class, params); + testParameterizationOk(params); + + OutlierResult result = cop.run(db); + + testAUC(db, "Noise", result, 0.89476666); + testSingleScore(result, 416, 0.26795866); + } + + @Test + public void testCOPRobust() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-parabolic.ascii", 530); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(COP.Parameterizer.K_ID, 30); + params.addParameter(COP.Parameterizer.PCARUNNER_ID, PCAFilteredAutotuningRunner.class); + params.addParameter(PCAFilteredAutotuningRunner.Parameterizer.PCA_COVARIANCE_MATRIX, WeightedCovarianceMatrixBuilder.class); + params.addParameter(WeightedCovarianceMatrixBuilder.Parameterizer.WEIGHT_ID, ErfcWeight.class); + + // setup Algorithm + COP<DoubleVector> cop = ClassGenericsUtil.parameterizeOrAbort(COP.class, params); + testParameterizationOk(params); + + OutlierResult result = cop.run(db); + + testAUC(db, "Noise", result, 0.90166666); + testSingleScore(result, 416, 0.25705955); + } + + + @Test + public void testCOPRANSAC() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-parabolic.ascii", 530); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(COP.Parameterizer.K_ID, 30); + params.addParameter(COP.Parameterizer.PCARUNNER_ID, PCAFilteredAutotuningRunner.class); + params.addParameter(PCAFilteredAutotuningRunner.Parameterizer.PCA_COVARIANCE_MATRIX, RANSACCovarianceMatrixBuilder.class); + params.addParameter(RANSACCovarianceMatrixBuilder.Parameterizer.ITER_ID, 25); + params.addParameter(RANSACCovarianceMatrixBuilder.Parameterizer.SEED_ID, 0); + + // setup Algorithm + COP<DoubleVector> cop = ClassGenericsUtil.parameterizeOrAbort(COP.class, params); + testParameterizationOk(params); + + OutlierResult result = cop.run(db); + + testAUC(db, "Noise", result, 0.89269999); + testSingleScore(result, 416, 0.38287932); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/DWOFTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/DWOFTest.java new file mode 100644 index 00000000..24bf71ca --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/DWOFTest.java @@ -0,0 +1,60 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Tests the DWOF algorithm. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class DWOFTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testDWOF() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-parabolic.ascii", 530); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(DWOF.Parameterizer.K_ID, 20); + + // setup Algorithm + DWOF<DoubleVector> cop = ClassGenericsUtil.parameterizeOrAbort(DWOF.class, params); + testParameterizationOk(params); + + OutlierResult result = cop.run(db); + + testAUC(db, "Noise", result, 0.8098666); + testSingleScore(result, 416, 6.95226128); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/TestGaussianModel.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/GaussianModelTest.java index 588222bd..53bb618c 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/TestGaussianModel.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/GaussianModelTest.java @@ -37,8 +37,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the GaussianModel algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestGaussianModel extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class GaussianModelTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testGaussianModel() { Database db = makeSimpleDatabase(UNITTEST + "outlier-fire.ascii", 1025); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/TestGaussianUniformMixture.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/GaussianUniformMixtureTest.java index 7c508b27..d42b4324 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/TestGaussianUniformMixture.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/GaussianUniformMixtureTest.java @@ -37,8 +37,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the GaussianUniformMixture algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestGaussianUniformMixture extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class GaussianUniformMixtureTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testGaussianUniformMixture() { Database db = makeSimpleDatabase(UNITTEST + "outlier-fire.ascii", 1025); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/TestOPTICSOF.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/OPTICSOFTest.java index 6e04129e..3feb2450 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/TestOPTICSOF.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/OPTICSOFTest.java @@ -38,8 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the OPTICS-OF algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestOPTICSOF extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class OPTICSOFTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testOPTICSOF() { Database db = makeSimpleDatabase(UNITTEST + "outlier-parabolic.ascii", 530); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/SimpleCOPTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/SimpleCOPTest.java new file mode 100644 index 00000000..effcd9b7 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/SimpleCOPTest.java @@ -0,0 +1,60 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Tests the SimpleCOP algorithm. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class SimpleCOPTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testSimpleCOP() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-parabolic.ascii", 530); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(SimpleCOP.Parameterizer.K_ID, 50); + + // setup Algorithm + SimpleCOP<DoubleVector> cop = ClassGenericsUtil.parameterizeOrAbort(SimpleCOP.class, params); + testParameterizationOk(params); + + OutlierResult result = cop.run(db); + + testAUC(db, "Noise", result, 0.833); + testSingleScore(result, 416, 0.); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/TestABOD.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/ABODTest.java index 00f93cfc..a216dade 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/TestABOD.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/ABODTest.java @@ -39,8 +39,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Note: we don't implement JUnit4Test, as this test is slow. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestABOD extends AbstractSimpleAlgorithmTest { +public class ABODTest extends AbstractSimpleAlgorithmTest { @Test public void testABOD() { Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/TestFastABOD.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/FastABODTest.java index 6598c70d..ede44a57 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/TestFastABOD.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/FastABODTest.java @@ -37,8 +37,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the ABOD algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestFastABOD extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class FastABODTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testFastABOD() { Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/TestLBABOD.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/LBABODTest.java index 4b5b6920..aa5dc9ba 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/TestLBABOD.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/anglebased/LBABODTest.java @@ -40,8 +40,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Note: we don't implement JUnit4Test, as this test is slow. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestLBABOD extends AbstractSimpleAlgorithmTest { +public class LBABODTest extends AbstractSimpleAlgorithmTest { @Test public void testLBABOD() { Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/EMOutlierTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/EMOutlierTest.java new file mode 100644 index 00000000..590a7c29 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/EMOutlierTest.java @@ -0,0 +1,63 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier.clustering; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.algorithm.clustering.em.EM; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Tests the EM outlier detection algorithm. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class EMOutlierTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testEMOutlierDetection() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-parabolic.ascii", 530); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(EM.Parameterizer.K_ID, 5); + params.addParameter(KMeans.SEED_ID, 0); + + // setup Algorithm + EMOutlier<DoubleVector> silout = ClassGenericsUtil.parameterizeOrAbort(EMOutlier.class, params); + testParameterizationOk(params); + + OutlierResult result = silout.run(db); + + testAUC(db, "Noise", result, 0.54073333); + testSingleScore(result, 416, 0.00240242); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/KMeansOutlierDetectionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/KMeansOutlierDetectionTest.java new file mode 100644 index 00000000..8a40130a --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/KMeansOutlierDetectionTest.java @@ -0,0 +1,64 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier.clustering; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansHamerly; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Tests the KMeans outlier detection algorithm. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class KMeansOutlierDetectionTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testKMeansOutlierDetection() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-parabolic.ascii", 530); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(KMeansOutlierDetection.Parameterizer.CLUSTERING_ID, KMeansHamerly.class); + params.addParameter(KMeans.K_ID, 10); + params.addParameter(KMeans.SEED_ID, 0); + + // setup Algorithm + KMeansOutlierDetection<DoubleVector> silout = ClassGenericsUtil.parameterizeOrAbort(KMeansOutlierDetection.class, params); + testParameterizationOk(params); + + OutlierResult result = silout.run(db); + + testAUC(db, "Noise", result, 0.86166666); + testSingleScore(result, 416, 0.01025466); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/SilhouetteOutlierDetectionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/SilhouetteOutlierDetectionTest.java new file mode 100644 index 00000000..0b43e532 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/SilhouetteOutlierDetectionTest.java @@ -0,0 +1,64 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier.clustering; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeans; +import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMeansHamerly; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Tests the Silhouette outlier detection algorithm. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class SilhouetteOutlierDetectionTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testSilhouetteOutlierDetection() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-parabolic.ascii", 530); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(SilhouetteOutlierDetection.Parameterizer.CLUSTERING_ID, KMeansHamerly.class); + params.addParameter(KMeans.K_ID, 10); + params.addParameter(KMeans.SEED_ID, 0); + + // setup Algorithm + SilhouetteOutlierDetection<DoubleVector> silout = ClassGenericsUtil.parameterizeOrAbort(SilhouetteOutlierDetection.class, params); + testParameterizationOk(params); + + OutlierResult result = silout.run(db); + + testAUC(db, "Noise", result, 0.71993333); + testSingleScore(result, 416, 0.47335776); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/TestDBOutlierDetection.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/DBOutlierDetectionTest.java index 1c19366c..69ffff7d 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/TestDBOutlierDetection.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/DBOutlierDetectionTest.java @@ -38,8 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the DBOutlierDetection algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestDBOutlierDetection extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class DBOutlierDetectionTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testDBOutlierDetection() { Database db = makeSimpleDatabase(UNITTEST + "outlier-fire.ascii", 1025); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/TestDBOutlierScore.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/DBOutlierScoreTest.java index 47fd73bf..cb70cabe 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/TestDBOutlierScore.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/DBOutlierScoreTest.java @@ -38,8 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the DBOutlierScore algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestDBOutlierScore extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class DBOutlierScoreTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testDBOutlierScore() { Database db = makeSimpleDatabase(UNITTEST + "outlier-fire.ascii", 1025); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/HilOutTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/HilOutTest.java new file mode 100644 index 00000000..e1cd3a53 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/HilOutTest.java @@ -0,0 +1,62 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier.distance; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Tests the KNNWeightOutlier algorithm. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class HilOutTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testHilOut() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(HilOut.Parameterizer.K_ID, 4); + params.addParameter(HilOut.Parameterizer.N_ID, 200); + + // setup Algorithm + HilOut<DoubleVector> hilout = ClassGenericsUtil.parameterizeOrAbort(HilOut.class, params); + testParameterizationOk(params); + + // run KNNWeightOutlier on database + OutlierResult result = hilout.run(db); + + testAUC(db, "Noise", result, 0.985398148); + testSingleScore(result, 945, 1.70927657); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/TestKNNOutlier.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/KNNOutlierTest.java index b7ac1bd8..2720ff28 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/TestKNNOutlier.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/KNNOutlierTest.java @@ -38,8 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the KNNOutlier algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestKNNOutlier extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class KNNOutlierTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testKNNOutlier() { Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/TestKNNWeightOutlier.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/KNNWeightOutlierTest.java index 73f5db45..cb72b9d7 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/TestKNNWeightOutlier.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/KNNWeightOutlierTest.java @@ -38,8 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the KNNWeightOutlier algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestKNNWeightOutlier extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class KNNWeightOutlierTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testKNNWeightOutlier() { Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/TestLocalIsolationCoefficient.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/LocalIsolationCoefficientTest.java index c49beb5f..f781ed28 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/TestLocalIsolationCoefficient.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/LocalIsolationCoefficientTest.java @@ -37,8 +37,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the LocalIsolationCoefficient algorithm. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestLocalIsolationCoefficient extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class LocalIsolationCoefficientTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testLocalIsolationCoefficient() { Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/ODINTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/ODINTest.java new file mode 100644 index 00000000..1186bcac --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/ODINTest.java @@ -0,0 +1,61 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier.distance; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Tests the ODIN algorithm. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class ODINTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testODIN() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(ODIN.Parameterizer.K_ID, 10); + + // setup Algorithm + ODIN<DoubleVector> odin = ClassGenericsUtil.parameterizeOrAbort(ODIN.class, params); + testParameterizationOk(params); + + // run KNNOutlier on database + OutlierResult result = odin.run(db); + + testSingleScore(result, 945, 0.7); + testAUC(db, "Noise", result, 0.9142037037); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/ReferenceBasedOutlierDetectionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/ReferenceBasedOutlierDetectionTest.java new file mode 100644 index 00000000..d9b96d09 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/ReferenceBasedOutlierDetectionTest.java @@ -0,0 +1,151 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier.distance; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; +import de.lmu.ifi.dbs.elki.utilities.referencepoints.AxisBasedReferencePoints; +import de.lmu.ifi.dbs.elki.utilities.referencepoints.GridBasedReferencePoints; +import de.lmu.ifi.dbs.elki.utilities.referencepoints.RandomGeneratedReferencePoints; +import de.lmu.ifi.dbs.elki.utilities.referencepoints.RandomSampleReferencePoints; +import de.lmu.ifi.dbs.elki.utilities.referencepoints.StarBasedReferencePoints; + +/** + * Tests the ReferenceBasedOutlierDetection algorithm. + * + * @author Lucia Cichella + * @author Erich Schubert + * @since 0.4.0 + */ +public class ReferenceBasedOutlierDetectionTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testReferenceBasedOutlierDetection() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(ReferenceBasedOutlierDetection.Parameterizer.K_ID, 11); + params.addParameter(GridBasedReferencePoints.Parameterizer.GRID_ID, 3); + + // setup Algorithm + ReferenceBasedOutlierDetection referenceBasedOutlierDetection = ClassGenericsUtil.parameterizeOrAbort(ReferenceBasedOutlierDetection.class, params); + testParameterizationOk(params); + + // run ReferenceBasedOutlierDetection on database + OutlierResult result = referenceBasedOutlierDetection.run(db); + + testAUC(db, "Noise", result, 0.9693703703703); + testSingleScore(result, 945, 0.933574455); + } + + @Test + public void testReferenceBasedOutlierDetectionStar() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(ReferenceBasedOutlierDetection.Parameterizer.K_ID, 11); + params.addParameter(ReferenceBasedOutlierDetection.Parameterizer.REFP_ID, StarBasedReferencePoints.class); + + // setup Algorithm + ReferenceBasedOutlierDetection referenceBasedOutlierDetection = ClassGenericsUtil.parameterizeOrAbort(ReferenceBasedOutlierDetection.class, params); + testParameterizationOk(params); + + // run ReferenceBasedOutlierDetection on database + OutlierResult result = referenceBasedOutlierDetection.run(db); + + testAUC(db, "Noise", result, 0.910722222); + testSingleScore(result, 945, 0.920950222); + } + + @Test + public void testReferenceBasedOutlierDetectionAxis() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(ReferenceBasedOutlierDetection.Parameterizer.K_ID, 11); + params.addParameter(ReferenceBasedOutlierDetection.Parameterizer.REFP_ID, AxisBasedReferencePoints.class); + + // setup Algorithm + ReferenceBasedOutlierDetection referenceBasedOutlierDetection = ClassGenericsUtil.parameterizeOrAbort(ReferenceBasedOutlierDetection.class, params); + testParameterizationOk(params); + + // run ReferenceBasedOutlierDetection on database + OutlierResult result = referenceBasedOutlierDetection.run(db); + + testAUC(db, "Noise", result, 0.8110555); + testSingleScore(result, 945, 0.9523053); + } + + @Test + public void testReferenceBasedOutlierDetectionGenerated() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(ReferenceBasedOutlierDetection.Parameterizer.K_ID, 11); + params.addParameter(ReferenceBasedOutlierDetection.Parameterizer.REFP_ID, RandomGeneratedReferencePoints.class); + params.addParameter(RandomGeneratedReferencePoints.Parameterizer.N_ID, 15); + params.addParameter(RandomGeneratedReferencePoints.Parameterizer.RANDOM_ID, 0); + + // setup Algorithm + ReferenceBasedOutlierDetection referenceBasedOutlierDetection = ClassGenericsUtil.parameterizeOrAbort(ReferenceBasedOutlierDetection.class, params); + testParameterizationOk(params); + + // run ReferenceBasedOutlierDetection on database + OutlierResult result = referenceBasedOutlierDetection.run(db); + + testAUC(db, "Noise", result, 0.817407407); + testSingleScore(result, 945, 0.911353060); + } + + @Test + public void testReferenceBasedOutlierDetectionSample() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(ReferenceBasedOutlierDetection.Parameterizer.K_ID, 11); + params.addParameter(ReferenceBasedOutlierDetection.Parameterizer.REFP_ID, RandomSampleReferencePoints.class); + params.addParameter(RandomSampleReferencePoints.Parameterizer.N_ID, 15); + params.addParameter(RandomSampleReferencePoints.Parameterizer.RANDOM_ID, 0); + + // setup Algorithm + ReferenceBasedOutlierDetection referenceBasedOutlierDetection = ClassGenericsUtil.parameterizeOrAbort(ReferenceBasedOutlierDetection.class, params); + testParameterizationOk(params); + + // run ReferenceBasedOutlierDetection on database + OutlierResult result = referenceBasedOutlierDetection.run(db); + + testAUC(db, "Noise", result, 0.848472222); + testSingleScore(result, 945, 0.894389944); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/TestReferenceBasedOutlierDetection.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/TestReferenceBasedOutlierDetection.java deleted file mode 100644 index de0991d0..00000000 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/TestReferenceBasedOutlierDetection.java +++ /dev/null @@ -1,61 +0,0 @@ -package de.lmu.ifi.dbs.elki.algorithm.outlier.distance; - -/* - This file is part of ELKI: - Environment for Developing KDD-Applications Supported by Index-Structures - - Copyright (C) 2015 - Ludwig-Maximilians-Universität München - Lehr- und Forschungseinheit für Datenbanksysteme - ELKI Development Team - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU Affero General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU Affero General Public License for more details. - - You should have received a copy of the GNU Affero General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -import org.junit.Test; - -import de.lmu.ifi.dbs.elki.JUnit4Test; -import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; -import de.lmu.ifi.dbs.elki.database.Database; -import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; -import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; -import de.lmu.ifi.dbs.elki.utilities.referencepoints.GridBasedReferencePoints; - -/** - * Tests the ReferenceBasedOutlierDetection algorithm. - * - * @author Lucia Cichella - */ -public class TestReferenceBasedOutlierDetection extends AbstractSimpleAlgorithmTest implements JUnit4Test { - @Test - public void testReferenceBasedOutlierDetection() { - Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); - - // Parameterization - ListParameterization params = new ListParameterization(); - params.addParameter(ReferenceBasedOutlierDetection.Parameterizer.K_ID, 11); - params.addParameter(GridBasedReferencePoints.Parameterizer.GRID_ID, 3); - - // setup Algorithm - ReferenceBasedOutlierDetection referenceBasedOutlierDetection = ClassGenericsUtil.parameterizeOrAbort(ReferenceBasedOutlierDetection.class, params); - testParameterizationOk(params); - - // run ReferenceBasedOutlierDetection on database - OutlierResult result = referenceBasedOutlierDetection.run(db); - - testAUC(db, "Noise", result, 0.9418148148); - testSingleScore(result, 945, 0.87173403699); - } -}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/TestParallelKNNOutlier.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/ParallelKNNOutlierTest.java index 3dfe5664..455f5730 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/TestParallelKNNOutlier.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/ParallelKNNOutlierTest.java @@ -38,8 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the KNNOutlier algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestParallelKNNOutlier extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class ParallelKNNOutlierTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testKNNOutlier() { Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/TestParallelKNNWeightOutlier.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/ParallelKNNWeightOutlierTest.java index 7391bfed..1c298214 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/TestParallelKNNWeightOutlier.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/distance/parallel/ParallelKNNWeightOutlierTest.java @@ -38,8 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the KNNWeightOutlier algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestParallelKNNWeightOutlier extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class ParallelKNNWeightOutlierTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testKNNWeightOutlier() { Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/ALOCITest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/ALOCITest.java new file mode 100644 index 00000000..378f8477 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/ALOCITest.java @@ -0,0 +1,62 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier.lof; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Tests the ALOCI algorithm. + * + * @author Lucia Cichella + * @since 0.4.0 + */ +public class ALOCITest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testLOCI() { + Database db = makeSimpleDatabase(UNITTEST + "3clusters-and-noise-2d.csv", 330); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(ALOCI.Parameterizer.SEED_ID, 0); + params.addParameter(ALOCI.Parameterizer.GRIDS_ID, 3); + + // setup Algorithm + ALOCI<DoubleVector> aloci = ClassGenericsUtil.parameterizeOrAbort(ALOCI.class, params); + testParameterizationOk(params); + + // run LOCI on database + OutlierResult result = aloci.run(db); + + testAUC(db, "Noise", result, 0.77011111); + testSingleScore(result, 146, 1.1242238186577); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/COFTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/COFTest.java new file mode 100644 index 00000000..eac2f982 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/COFTest.java @@ -0,0 +1,61 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier.lof; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Tests the COF algorithm. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class COFTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testCOF() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-axis-subspaces-6d.ascii", 1345); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(COF.Parameterizer.K_ID, 10); + + // setup Algorithm + COF<DoubleVector> cof = ClassGenericsUtil.parameterizeOrAbort(COF.class, params); + testParameterizationOk(params); + + // run COF on database + OutlierResult result = cof.run(db); + + testSingleScore(result, 1293, 1.415457); + testAUC(db, "Noise", result, 0.8696806); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/FlexibleLOFTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/FlexibleLOFTest.java new file mode 100644 index 00000000..c4165a00 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/FlexibleLOFTest.java @@ -0,0 +1,61 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier.lof; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Tests the LOF algorithm. + * + * @author Lucia Cichella + * @since 0.4.0 + */ +public class FlexibleLOFTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testFlexibleLOF() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-axis-subspaces-6d.ascii", 1345); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(FlexibleLOF.Parameterizer.KREF_ID, 10); + + // setup Algorithm + FlexibleLOF<DoubleVector> flof = ClassGenericsUtil.parameterizeOrAbort(FlexibleLOF.class, params); + testParameterizationOk(params); + + // run LOF on database + OutlierResult result = flof.run(db); + + testSingleScore(result, 1293, 1.1945314199156365); + testAUC(db, "Noise", result, 0.8921680672268908); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestINFLO.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/INFLOTest.java index 866effa6..d6c01b2a 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestINFLO.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/INFLOTest.java @@ -37,8 +37,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the INFLO algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestINFLO extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class INFLOTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testINFLO() { Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/KDEOSTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/KDEOSTest.java new file mode 100644 index 00000000..096e3aa6 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/KDEOSTest.java @@ -0,0 +1,65 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier.lof; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.math.statistics.kernelfunctions.EpanechnikovKernelDensityFunction; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Tests the KDEOS algorithm. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class KDEOSTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testKDEOS() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-axis-subspaces-6d.ascii", 1345); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(KDEOS.Parameterizer.KERNEL_ID, EpanechnikovKernelDensityFunction.class); + params.addParameter(KDEOS.Parameterizer.KMIN_ID, 5); + params.addParameter(KDEOS.Parameterizer.KMAX_ID, 20); + params.addParameter(KDEOS.Parameterizer.KERNEL_SCALE_ID, 1.0); + + // setup Algorithm + KDEOS<DoubleVector> kdeos = ClassGenericsUtil.parameterizeOrAbort(KDEOS.class, params); + testParameterizationOk(params); + + // run LOF on database + OutlierResult result = kdeos.run(db); + + testAUC(db, "Noise", result, 0.7983529411764); + testSingleScore(result, 1293, 0.8788346606616); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LDFTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LDFTest.java new file mode 100644 index 00000000..c724598b --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LDFTest.java @@ -0,0 +1,62 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier.lof; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Tests the LDF algorithm. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class LDFTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testLDF() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-axis-subspaces-6d.ascii", 1345); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(LDF.Parameterizer.K_ID, 10); + params.addParameter(LDF.Parameterizer.H_ID, 1); + + // setup Algorithm + LDF<DoubleVector> ldf = ClassGenericsUtil.parameterizeOrAbort(LDF.class, params); + testParameterizationOk(params); + + // run LDF on database + OutlierResult result = ldf.run(db); + + testSingleScore(result, 1293, 3.158819); + testAUC(db, "Noise", result, 0.9127619); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestLDOF.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LDOFTest.java index c728e38e..8eb45790 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestLDOF.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LDOFTest.java @@ -37,8 +37,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the LDOF algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestLDOF extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class LDOFTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testLDOF() { Database db = makeSimpleDatabase(UNITTEST + "outlier-fire.ascii", 1025); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestLOCI.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LOCITest.java index a2934701..2438f6cb 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestLOCI.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LOCITest.java @@ -35,17 +35,18 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet /** * Tests the LOCI algorithm. - * + * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestLOCI extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class LOCITest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testLOCI() { Database db = makeSimpleDatabase(UNITTEST + "3clusters-and-noise-2d.csv", 330); // Parameterization ListParameterization params = new ListParameterization(); - params.addParameter(LOCI.RMAX_ID, 0.5); + params.addParameter(LOCI.Parameterizer.RMAX_ID, 0.5); // setup Algorithm LOCI<DoubleVector> loci = ClassGenericsUtil.parameterizeOrAbort(LOCI.class, params); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestLOF.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LOFTest.java index d54d760e..33ab6d2d 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestLOF.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LOFTest.java @@ -37,8 +37,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the LOF algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestLOF extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class LOFTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testLOF() { Database db = makeSimpleDatabase(UNITTEST + "outlier-axis-subspaces-6d.ascii", 1345); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestLoOP.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LoOPTest.java index 60dddb5d..110c02bd 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestLoOP.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LoOPTest.java @@ -37,8 +37,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the LoOP algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestLoOP extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class LoOPTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testLoOP() { Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestOnlineLOF.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/OnlineLOFTest.java index f5fda922..947d6fcf 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestOnlineLOF.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/OnlineLOFTest.java @@ -63,9 +63,10 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * BUG: This currently does not appear to work correctly! * * @author Elke Achtert + * @since 0.4.0 */ @Ignore -public class TestOnlineLOF implements JUnit4Test { +public class OnlineLOFTest implements JUnit4Test { // the following values depend on the data set used! static String dataset = "data/testdata/unittests/3clusters-and-noise-2d.csv"; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/SimpleKernelDensityLOFTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/SimpleKernelDensityLOFTest.java new file mode 100644 index 00000000..19223930 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/SimpleKernelDensityLOFTest.java @@ -0,0 +1,63 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier.lof; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.math.statistics.kernelfunctions.BiweightKernelDensityFunction; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Tests the SimpleKernelDensityLOF algorithm. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class SimpleKernelDensityLOFTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testLDF() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-axis-subspaces-6d.ascii", 1345); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(LOF.Parameterizer.K_ID, 20); + params.addParameter(SimpleKernelDensityLOF.Parameterizer.KERNEL_ID, BiweightKernelDensityFunction.class); + + // setup Algorithm + SimpleKernelDensityLOF<DoubleVector> klof = ClassGenericsUtil.parameterizeOrAbort(SimpleKernelDensityLOF.class, params); + testParameterizationOk(params); + + // run LDF on database + OutlierResult result = klof.run(db); + + testAUC(db, "Noise", result, 0.87192156); + testSingleScore(result, 1293, 12.271188); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestSimplifiedLOF.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/SimplifiedLOFTest.java index 3ef40851..851bb5d6 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestSimplifiedLOF.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/SimplifiedLOFTest.java @@ -37,8 +37,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the LOF algorithm. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestSimplifiedLOF extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class SimplifiedLOFTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testSimplifiedLOF() { Database db = makeSimpleDatabase(UNITTEST + "outlier-axis-subspaces-6d.ascii", 1345); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestVarianceOfVolume.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/VarianceOfVolumeTest.java index 266e9f35..3cbe5b78 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/TestVarianceOfVolume.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/VarianceOfVolumeTest.java @@ -37,8 +37,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the Variance of Volume algorithm. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestVarianceOfVolume extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class VarianceOfVolumeTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testVOV() { Database db = makeSimpleDatabase(UNITTEST + "outlier-axis-subspaces-6d.ascii", 1345); @@ -54,7 +55,7 @@ public class TestVarianceOfVolume extends AbstractSimpleAlgorithmTest implements // run LOF on database OutlierResult result = lof.run(db); - testSingleScore(result, 1293, 848349.0186); - testAUC(db, "Noise", result, 0.936448179271); + testSingleScore(result, 1293, 2.0733100852601836e13); + testAUC(db, "Noise", result, 0.9306946778); } }
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/ParallelLOFTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/ParallelLOFTest.java new file mode 100644 index 00000000..7dcd568a --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/ParallelLOFTest.java @@ -0,0 +1,62 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier.lof.parallel; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LOF; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Regression tests the ParallelLOF algorithm. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class ParallelLOFTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testParallelLOF() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-axis-subspaces-6d.ascii", 1345); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(LOF.Parameterizer.K_ID, 10); + + // setup Algorithm + ParallelLOF<DoubleVector> lof = ClassGenericsUtil.parameterizeOrAbort(ParallelLOF.class, params); + testParameterizationOk(params); + + // run ParallelLOF on database + OutlierResult result = lof.run(db); + + testSingleScore(result, 1293, 1.1945314199156365); + testAUC(db, "Noise", result, 0.8921680672268908); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/ParallelSimplifiedLOFTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/ParallelSimplifiedLOFTest.java new file mode 100644 index 00000000..5bea31e9 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/parallel/ParallelSimplifiedLOFTest.java @@ -0,0 +1,62 @@ +package de.lmu.ifi.dbs.elki.algorithm.outlier.lof.parallel; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.algorithm.outlier.lof.LOF; +import de.lmu.ifi.dbs.elki.data.DoubleVector; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Regression tests the parallel SimplifiedLOF algorithm. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class ParallelSimplifiedLOFTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + @Test + public void testParallelSimplifiedLOF() { + Database db = makeSimpleDatabase(UNITTEST + "outlier-axis-subspaces-6d.ascii", 1345); + + // Parameterization + ListParameterization params = new ListParameterization(); + params.addParameter(LOF.Parameterizer.K_ID, 10); + + // setup Algorithm + ParallelSimplifiedLOF<DoubleVector> lof = ClassGenericsUtil.parameterizeOrAbort(ParallelSimplifiedLOF.class, params); + testParameterizationOk(params); + + // run LOF on database + OutlierResult result = lof.run(db); + + testAUC(db, "Noise", result, 0.8892549019); + testSingleScore(result, 1293, 1.3025894); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/TestFeatureBagging.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/FeatureBaggingTest.java index 91f20b28..b5fd84be 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/TestFeatureBagging.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/FeatureBaggingTest.java @@ -37,8 +37,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the Feature Bagging algorithm. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestFeatureBagging extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class FeatureBaggingTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testFeatureBaggingSum() { Database db = makeSimpleDatabase(UNITTEST + "outlier-axis-subspaces-6d.ascii", 1345); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/TestHiCS.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/HiCSTest.java index bb10269d..cfa904dc 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/TestHiCS.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/HiCSTest.java @@ -40,8 +40,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the HiCS algorithm. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestHiCS extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class HiCSTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testHiCSKS() { Database db = makeSimpleDatabase(UNITTEST + "outlier-axis-subspaces-6d.ascii", 1345); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/TestAggarwalYuEvolutionary.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AggarwalYuEvolutionaryTest.java index 67168d3f..2961d6e7 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/TestAggarwalYuEvolutionary.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AggarwalYuEvolutionaryTest.java @@ -38,8 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the AggarwalYuEvolutionary algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestAggarwalYuEvolutionary extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class AggarwalYuEvolutionaryTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testAggarwalYuEvolutionary() { Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/TestAggarwalYuNaive.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AggarwalYuNaiveTest.java index 8ecdbe26..6e3eeb5d 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/TestAggarwalYuNaive.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/AggarwalYuNaiveTest.java @@ -38,8 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the AggarwalYuNaive algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestAggarwalYuNaive extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class AggarwalYuNaiveTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testAggarwalYuNaive() { Database db = makeSimpleDatabase(UNITTEST + "outlier-3d-3clusters.ascii", 960); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/TestSOD.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/SODTest.java index d55f3f41..d7fee573 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/TestSOD.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/outlier/subspace/SODTest.java @@ -38,8 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Tests the SOD algorithm. * * @author Lucia Cichella + * @since 0.4.0 */ -public class TestSOD extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class SODTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test public void testSOD() { Database db = makeSimpleDatabase(UNITTEST + "outlier-axis-subspaces-6d.ascii", 1345); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/data/spatial/TestPolygon.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/data/spatial/PolygonTest.java index 59dfa986..61040c8e 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/data/spatial/TestPolygon.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/data/spatial/PolygonTest.java @@ -33,7 +33,13 @@ import org.junit.Test; import de.lmu.ifi.dbs.elki.JUnit4Test; import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; -public class TestPolygon implements JUnit4Test { +/** + * Test the polygon class. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class PolygonTest implements JUnit4Test { @Test public void testPolygonContainment() { final Polygon p1, p2, p3; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/database/TestRelationSorting.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/database/RelationSortingTest.java index c2a356e3..2735f6b1 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/database/TestRelationSorting.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/database/RelationSortingTest.java @@ -47,9 +47,10 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * the database and ID layers. * * @author Erich Schubert + * @since 0.5.5 * */ -public class TestRelationSorting implements JUnit4Test { +public class RelationSortingTest implements JUnit4Test { public static final String filename = "data/testdata/unittests/hierarchical-3d2d1d.csv"; @Test diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/database/TestSortingDuplicates.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/database/SortingDuplicatesTest.java index ab4d69b0..62ddbaf8 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/database/TestSortingDuplicates.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/database/SortingDuplicatesTest.java @@ -33,8 +33,9 @@ import de.lmu.ifi.dbs.elki.database.ids.ModifiableDoubleDBIDList; * Test a corner case when sorting: duplicate keys. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestSortingDuplicates implements JUnit4Test { +public class SortingDuplicatesTest implements JUnit4Test { @Test(timeout = 100) public void testDuplicateKeys() { // We need an ide, but no real data. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/datasource/parser/TestTermFrequencyParser.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/datasource/parser/TermFrequencyParserTest.java index 02b227ce..59d53f28 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/datasource/parser/TestTermFrequencyParser.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/datasource/parser/TermFrequencyParserTest.java @@ -52,8 +52,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * TODO: maybe also run an example algorithm? * * @author Erich Schubert + * @since 0.6.0 */ -public class TestTermFrequencyParser implements JUnit4Test { +public class TermFrequencyParserTest implements JUnit4Test { /** Test data set to use. */ public static String DBLP_DATA = "data/testdata/parsing/termfreq-dblp.ascii.gz"; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/datasource/parser/TestTokenizer.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/datasource/parser/TokenizerTest.java index c9e66400..d1e2e31e 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/datasource/parser/TestTokenizer.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/datasource/parser/TokenizerTest.java @@ -40,8 +40,9 @@ import de.lmu.ifi.dbs.elki.utilities.io.Tokenizer; * TODO: add more test cases, refactor into input, expected-output pattern. * * @author Erich Schubert + * @since 0.6.0 */ -public class TestTokenizer implements JUnit4Test { +public class TokenizerTest implements JUnit4Test { Tokenizer t = new Tokenizer(Pattern.compile("\\s"), "\"'"); @Test diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/SpatialPrimitiveDistanceFunctionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/SpatialPrimitiveDistanceFunctionTest.java index 0eb7f36f..19091cd9 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/SpatialPrimitiveDistanceFunctionTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/SpatialPrimitiveDistanceFunctionTest.java @@ -49,6 +49,7 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * random objects. * * @author Erich Schubert + * @since 0.5.0 * */ public class SpatialPrimitiveDistanceFunctionTest implements JUnit4Test { diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/TestAbsolutePearsonCorrelationDistanceFunctionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/AbsolutePearsonCorrelationDistanceFunctionTest.java index 50d2e213..dfd01522 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/TestAbsolutePearsonCorrelationDistanceFunctionTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/AbsolutePearsonCorrelationDistanceFunctionTest.java @@ -33,13 +33,14 @@ import de.lmu.ifi.dbs.elki.data.DoubleVector; * Unit test for Absolute Pearson correlation distance. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestAbsolutePearsonCorrelationDistanceFunctionTest implements JUnit4Test { +public class AbsolutePearsonCorrelationDistanceFunctionTest implements JUnit4Test { /** Test set */ - final static DoubleVector[] TESTS = TestPearsonCorrelationDistanceFunctionTest.TESTS; + final static DoubleVector[] TESTS = PearsonCorrelationDistanceFunctionTest.TESTS; /** Note, these are not yet adjusted */ - final static double[][] SCORES = TestPearsonCorrelationDistanceFunctionTest.SCORES; + final static double[][] SCORES = PearsonCorrelationDistanceFunctionTest.SCORES; @Test public void testAbsolutePearson() { diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/TestAbsoluteUncenteredCorrelationDistanceFunctionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/AbsoluteUncenteredCorrelationDistanceFunctionTest.java index ade6e19a..f8855e67 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/TestAbsoluteUncenteredCorrelationDistanceFunctionTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/AbsoluteUncenteredCorrelationDistanceFunctionTest.java @@ -33,13 +33,14 @@ import de.lmu.ifi.dbs.elki.data.DoubleVector; * Unit test for Absolute Pearson correlation distance. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestAbsoluteUncenteredCorrelationDistanceFunctionTest implements JUnit4Test { +public class AbsoluteUncenteredCorrelationDistanceFunctionTest implements JUnit4Test { /** Inherited test data */ - final static DoubleVector[] TESTS = TestUncenteredCorrelationDistanceFunctionTest.TESTS; + final static DoubleVector[] TESTS = UncenteredCorrelationDistanceFunctionTest.TESTS; /** Note, these are not yet adjusted */ - final static double[][] SCORES = TestUncenteredCorrelationDistanceFunctionTest.SCORES; + final static double[][] SCORES = UncenteredCorrelationDistanceFunctionTest.SCORES; @Test public void testAbsoluteUncenteredCorrelation() { diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/TestPearsonCorrelationDistanceFunctionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/PearsonCorrelationDistanceFunctionTest.java index eb80b8f8..bbe50452 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/TestPearsonCorrelationDistanceFunctionTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/PearsonCorrelationDistanceFunctionTest.java @@ -33,8 +33,9 @@ import de.lmu.ifi.dbs.elki.data.DoubleVector; * Unit test for Pearson correlation distance. * * @author Erich Schubert + * @since 0.7.0 */ -public class TestPearsonCorrelationDistanceFunctionTest implements JUnit4Test { +public class PearsonCorrelationDistanceFunctionTest implements JUnit4Test { /** * Some test series. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/TestSquaredPearsonCorrelationDistanceFunctionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/SquaredPearsonCorrelationDistanceFunctionTest.java index b541ec0f..5896a4e9 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/TestSquaredPearsonCorrelationDistanceFunctionTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/SquaredPearsonCorrelationDistanceFunctionTest.java @@ -33,13 +33,14 @@ import de.lmu.ifi.dbs.elki.data.DoubleVector; * Unit test for squared Pearson correlation distance. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestSquaredPearsonCorrelationDistanceFunctionTest implements JUnit4Test { +public class SquaredPearsonCorrelationDistanceFunctionTest implements JUnit4Test { /** Test set */ - final static DoubleVector[] TESTS = TestPearsonCorrelationDistanceFunctionTest.TESTS; + final static DoubleVector[] TESTS = PearsonCorrelationDistanceFunctionTest.TESTS; /** Note, these are not yet adjusted */ - final static double[][] SCORES = TestPearsonCorrelationDistanceFunctionTest.SCORES; + final static double[][] SCORES = PearsonCorrelationDistanceFunctionTest.SCORES; @Test public void testSquaredPearson() { diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/TestSquaredUncenteredCorrelationDistanceFunctionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/SquaredUncenteredCorrelationDistanceFunctionTest.java index 85b0d934..298616ed 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/TestSquaredUncenteredCorrelationDistanceFunctionTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/SquaredUncenteredCorrelationDistanceFunctionTest.java @@ -33,13 +33,14 @@ import de.lmu.ifi.dbs.elki.data.DoubleVector; * Unit test for Squared Pearson correlation distance. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestSquaredUncenteredCorrelationDistanceFunctionTest implements JUnit4Test { +public class SquaredUncenteredCorrelationDistanceFunctionTest implements JUnit4Test { /** Inherited test data */ - final static DoubleVector[] TESTS = TestUncenteredCorrelationDistanceFunctionTest.TESTS; + final static DoubleVector[] TESTS = UncenteredCorrelationDistanceFunctionTest.TESTS; /** Note, these are not yet adjusted */ - final static double[][] SCORES = TestUncenteredCorrelationDistanceFunctionTest.SCORES; + final static double[][] SCORES = UncenteredCorrelationDistanceFunctionTest.SCORES; @Test public void testSquaredUncenteredCorrelation() { diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/TestUncenteredCorrelationDistanceFunctionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/UncenteredCorrelationDistanceFunctionTest.java index 2f03eb81..e580dbda 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/TestUncenteredCorrelationDistanceFunctionTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/correlation/UncenteredCorrelationDistanceFunctionTest.java @@ -33,10 +33,11 @@ import de.lmu.ifi.dbs.elki.data.DoubleVector; * Unit test for Absolute Pearson correlation distance. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestUncenteredCorrelationDistanceFunctionTest implements JUnit4Test { +public class UncenteredCorrelationDistanceFunctionTest implements JUnit4Test { /** Inherited test data */ - final static DoubleVector[] TESTS = TestPearsonCorrelationDistanceFunctionTest.TESTS; + final static DoubleVector[] TESTS = PearsonCorrelationDistanceFunctionTest.TESTS; /** Dissimilarities */ static final double C1 = 1.3636363636363638, C2 = 0.23636363636363633, diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/TestFileBasedDoubleDistanceFunction.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedDoubleDistanceFunctionTest.java index 8091727c..0bde5412 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/TestFileBasedDoubleDistanceFunction.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedDoubleDistanceFunctionTest.java @@ -43,8 +43,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Unit test for external distances. * * @author Erich Schubert + * @since 0.7.0 */ -public class TestFileBasedDoubleDistanceFunction extends AbstractSimpleAlgorithmTest implements JUnit4Test { +public class FileBasedDoubleDistanceFunctionTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { final static String FILENAME = "data/testdata/unittests/distance/AsciiDistanceMatrix.ascii"; @Test diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/LevenshteinDistanceFunctionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/LevenshteinDistanceFunctionTest.java index dff58823..7342a30c 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/LevenshteinDistanceFunctionTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/LevenshteinDistanceFunctionTest.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Unit test for Levenshtein distance. * * @author Erich Schubert + * @since 0.4.0 */ public class LevenshteinDistanceFunctionTest implements JUnit4Test { /** diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/NormalizedLevenshteinDistanceFunctionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/NormalizedLevenshteinDistanceFunctionTest.java index fa99837e..dee74ff2 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/NormalizedLevenshteinDistanceFunctionTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/strings/NormalizedLevenshteinDistanceFunctionTest.java @@ -32,6 +32,7 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Unit test for Levenshtein distance. * * @author Erich Schubert + * @since 0.4.0 */ public class NormalizedLevenshteinDistanceFunctionTest implements JUnit4Test { /** diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DTWDistanceFunctionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DTWDistanceFunctionTest.java index 4855c1bf..d4edcc25 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DTWDistanceFunctionTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DTWDistanceFunctionTest.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.data.DoubleVector; * Unit test for dynamic time warping distance. * * @author Erich Schubert + * @since 0.7.0 */ public class DTWDistanceFunctionTest implements JUnit4Test { /** diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DerivativeDTWDistanceFunctionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DerivativeDTWDistanceFunctionTest.java index 8d6e9361..4f61136b 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DerivativeDTWDistanceFunctionTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/distancefunction/timeseries/DerivativeDTWDistanceFunctionTest.java @@ -33,6 +33,7 @@ import de.lmu.ifi.dbs.elki.data.DoubleVector; * Unit test for dynamic time warping distance. * * @author Erich Schubert + * @since 0.7.0 */ public class DerivativeDTWDistanceFunctionTest implements JUnit4Test { /** diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/LinearKernelFunctionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/LinearKernelFunctionTest.java new file mode 100644 index 00000000..b7e10b6d --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/LinearKernelFunctionTest.java @@ -0,0 +1,55 @@ +package de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import static org.junit.Assert.assertEquals; + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.data.DoubleVector; + +/** + * Unit test for Kernel implementation. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class LinearKernelFunctionTest implements JUnit4Test { + @Test + public void testToyExamples() { + DoubleVector v1 = new DoubleVector(new double[] { 1, 0, 0 }); + DoubleVector v2 = new DoubleVector(new double[] { 0, 1, 0 }); + DoubleVector v3 = new DoubleVector(new double[] { 1, 1, 1 }); + DoubleVector v4 = new DoubleVector(new double[] { .1, .2, .3 }); + + LinearKernelFunction kernel = LinearKernelFunction.STATIC; + assertEquals("Linear kernel not correct.", 0., kernel.similarity(v1, v2), 0.); + assertEquals("Linear kernel not correct.", 1., kernel.similarity(v1, v3), 0.); + assertEquals("Linear kernel not correct.", .1, kernel.similarity(v1, v4), 0.); + assertEquals("Linear kernel not correct.", 1., kernel.similarity(v2, v3), 0.); + assertEquals("Linear kernel not correct.", .2, kernel.similarity(v2, v4), 0.); + assertEquals("Linear kernel not correct.", .6, kernel.similarity(v3, v4), 1e-13); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/PolynomialKernelFunctionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/PolynomialKernelFunctionTest.java new file mode 100644 index 00000000..fd1e0d39 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/distance/similarityfunction/kernel/PolynomialKernelFunctionTest.java @@ -0,0 +1,71 @@ +package de.lmu.ifi.dbs.elki.distance.similarityfunction.kernel; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import static org.junit.Assert.assertEquals; + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.data.DoubleVector; + +/** + * Unit test for Kernel implementation. + * + * @author Erich Schubert + * @since 0.7.1 + */ +public class PolynomialKernelFunctionTest implements JUnit4Test { + @Test + public void testToyExamplesPoly2() { + DoubleVector v1 = new DoubleVector(new double[] { 1, 0, 0 }); + DoubleVector v2 = new DoubleVector(new double[] { 0, 1, 0 }); + DoubleVector v3 = new DoubleVector(new double[] { 1, 1, 1 }); + DoubleVector v4 = new DoubleVector(new double[] { .1, .2, .3 }); + + PolynomialKernelFunction kernel = new PolynomialKernelFunction(2); + assertEquals("Linear kernel not correct.", 0., kernel.similarity(v1, v2), 0.); + assertEquals("Linear kernel not correct.", 1., kernel.similarity(v1, v3), 0.); + assertEquals("Linear kernel not correct.", .01, kernel.similarity(v1, v4), 1e-13); + assertEquals("Linear kernel not correct.", 1., kernel.similarity(v2, v3), 0.); + assertEquals("Linear kernel not correct.", .04, kernel.similarity(v2, v4), 1e-13); + assertEquals("Linear kernel not correct.", .36, kernel.similarity(v3, v4), 1e-13); + } + + @Test + public void testToyExamplesPoly3() { + DoubleVector v1 = new DoubleVector(new double[] { 1, 0, 0 }); + DoubleVector v2 = new DoubleVector(new double[] { 0, 1, 0 }); + DoubleVector v3 = new DoubleVector(new double[] { 1, 1, 1 }); + DoubleVector v4 = new DoubleVector(new double[] { .1, .2, .3 }); + + PolynomialKernelFunction kernel = new PolynomialKernelFunction(3); + assertEquals("Linear kernel not correct.", 0., kernel.similarity(v1, v2), 0.); + assertEquals("Linear kernel not correct.", 1., kernel.similarity(v1, v3), 0.); + assertEquals("Linear kernel not correct.", .001, kernel.similarity(v1, v4), 1e-13); + assertEquals("Linear kernel not correct.", 1., kernel.similarity(v2, v3), 0.); + assertEquals("Linear kernel not correct.", .008, kernel.similarity(v2, v4), 1e-13); + assertEquals("Linear kernel not correct.", .216, kernel.similarity(v3, v4), 1e-13); + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/paircounting/TestClusterContingencyTable.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/paircounting/ClusterContingencyTableTest.java index 7e2fd526..6a594bd1 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/paircounting/TestClusterContingencyTable.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/paircounting/ClusterContingencyTableTest.java @@ -49,8 +49,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * data clusterings. * * @author Erich Schubert + * @since 0.2 */ -public class TestClusterContingencyTable implements JUnit4Test { +public class ClusterContingencyTableTest implements JUnit4Test { // the following values depend on the data set used! String dataset = "data/testdata/unittests/hierarchical-3d2d1d.csv"; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/TestAveragePrecisionEvaluation.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/AveragePrecisionEvaluationTest.java index c635d790..a92cea06 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/TestAveragePrecisionEvaluation.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/AveragePrecisionEvaluationTest.java @@ -36,8 +36,9 @@ import de.lmu.ifi.dbs.elki.database.ids.ModifiableDoubleDBIDList; * Test to validate ROC curve computation. * * @author Erich Schubert + * @since 0.7.0 */ -public class TestAveragePrecisionEvaluation implements JUnit4Test { +public class AveragePrecisionEvaluationTest implements JUnit4Test { /** * Test Average Precision score computation. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/TestMaximumF1Evaluation.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/MaximumF1EvaluationTest.java index 3e6757fe..9666d7c2 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/TestMaximumF1Evaluation.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/MaximumF1EvaluationTest.java @@ -36,8 +36,9 @@ import de.lmu.ifi.dbs.elki.database.ids.ModifiableDoubleDBIDList; * Validate evaluation based on F1 scores. * * @author Erich Schubert + * @since 0.7.0 */ -public class TestMaximumF1Evaluation implements JUnit4Test { +public class MaximumF1EvaluationTest implements JUnit4Test { /** * Test maximum F1 score computation */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/TestPrecisionAtKEvaluation.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/PrecisionAtKEvaluationTest.java index ca973196..2aac1f30 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/TestPrecisionAtKEvaluation.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/PrecisionAtKEvaluationTest.java @@ -36,8 +36,9 @@ import de.lmu.ifi.dbs.elki.database.ids.ModifiableDoubleDBIDList; * Test precision@k evaluation. * * @author Erich Schubert + * @since 0.7.0 */ -public class TestPrecisionAtKEvaluation implements JUnit4Test { +public class PrecisionAtKEvaluationTest implements JUnit4Test { /** * Test Precision@k score computation. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/TestROCEvaluation.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/ROCEvaluationTest.java index 34ab3b3a..31113d70 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/TestROCEvaluation.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/evaluation/scores/ROCEvaluationTest.java @@ -39,8 +39,9 @@ import de.lmu.ifi.dbs.elki.math.geometry.XYCurve; * Test to validate ROC curve computation. * * @author Erich Schubert + * @since 0.7.0 */ -public class TestROCEvaluation implements JUnit4Test { +public class ROCEvaluationTest implements JUnit4Test { /** * Test ROC curve generation, including curve simplification */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/AbstractTestIndexStructures.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/AbstractIndexStructureTest.java index c3dbf7e6..abe7aaf2 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/AbstractTestIndexStructures.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/AbstractIndexStructureTest.java @@ -52,8 +52,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * results. * * @author Erich Schubert + * @since 0.2 */ -public abstract class AbstractTestIndexStructures implements JUnit4Test { +public abstract class AbstractIndexStructureTest implements JUnit4Test { // the following values depend on the data set used! String dataset = "data/testdata/unittests/hierarchical-3d2d1d.csv"; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/TestLinearScanReference.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/LinearScanReferenceTest.java index 82640612..6e2e0abb 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/TestLinearScanReference.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/LinearScanReferenceTest.java @@ -33,8 +33,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * This unit test verifies that the linear scan produces the reference result. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestLinearScanReference extends AbstractTestIndexStructures { +public class LinearScanReferenceTest extends AbstractIndexStructureTest { /** * Test exact query, also to validate the test is correct. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/idistance/TestIDistance.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/idistance/IDistanceTest.java index 7280af84..de406ef0 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/idistance/TestIDistance.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/idistance/IDistanceTest.java @@ -28,15 +28,16 @@ import org.junit.Test; import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.FarthestPointsInitialMeans; import de.lmu.ifi.dbs.elki.database.StaticArrayDatabase; import de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction; -import de.lmu.ifi.dbs.elki.index.AbstractTestIndexStructures; +import de.lmu.ifi.dbs.elki.index.AbstractIndexStructureTest; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; /** * Unit test for the iDistance index. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestIDistance extends AbstractTestIndexStructures { +public class IDistanceTest extends AbstractIndexStructureTest { /** * Test {@link InMemoryIDistanceIndex}. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/invertedlist/TestInMemoryInvertedIndex.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/invertedlist/InMemoryInvertedIndexTest.java index ca325176..7882c4c1 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/invertedlist/TestInMemoryInvertedIndex.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/invertedlist/InMemoryInvertedIndexTest.java @@ -26,15 +26,16 @@ package de.lmu.ifi.dbs.elki.index.invertedlist; import org.junit.Test; import de.lmu.ifi.dbs.elki.database.StaticArrayDatabase; -import de.lmu.ifi.dbs.elki.index.AbstractTestIndexStructures; +import de.lmu.ifi.dbs.elki.index.AbstractIndexStructureTest; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; /** * Unit test for the iDistance index. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestInMemoryInvertedIndex extends AbstractTestIndexStructures { +public class InMemoryInvertedIndexTest extends AbstractIndexStructureTest { /** * Test {@link InMemoryInvertedIndex}. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/CosineHashFunctionFamilyTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/CosineHashFunctionFamilyTest.java index 13b6dfea..cbe7eefe 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/CosineHashFunctionFamilyTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/lsh/hashfamilies/CosineHashFunctionFamilyTest.java @@ -44,6 +44,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Unit test for random hyperplane / cosine distance. * * @author Evgeniy Faerman + * @since 0.7.0 */ public class CosineHashFunctionFamilyTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { @Test diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/preprocessed/TestMaterializedKNNAndRKNNPreprocessor.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/preprocessed/MaterializedKNNAndRKNNPreprocessorTest.java index cbe374f9..e5deb7fd 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/preprocessed/TestMaterializedKNNAndRKNNPreprocessor.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/preprocessed/MaterializedKNNAndRKNNPreprocessorTest.java @@ -72,8 +72,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * * * @author Elke Achtert + * @since 0.4.0 */ -public class TestMaterializedKNNAndRKNNPreprocessor implements JUnit4Test { +public class MaterializedKNNAndRKNNPreprocessorTest implements JUnit4Test { // the following values depend on the data set used! static String dataset = "data/testdata/unittests/3clusters-and-noise-2d.csv"; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/CoverTreeTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/CoverTreeTest.java new file mode 100644 index 00000000..9531d802 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/CoverTreeTest.java @@ -0,0 +1,50 @@ +package de.lmu.ifi.dbs.elki.index.tree.metrical.covertree; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.database.StaticArrayDatabase; +import de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction; +import de.lmu.ifi.dbs.elki.index.AbstractIndexStructureTest; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Unit test for the Cover-tree. + * + * @author Erich Schubert + * @since 0.7.0 + */ +public class CoverTreeTest extends AbstractIndexStructureTest { + /** + * Test {@link CoverTree} using a file based database connection. + */ + @Test + public void testCovertree() { + ListParameterization metparams = new ListParameterization(); + metparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, CoverTree.Factory.class); + metparams.addParameter(CoverTree.Factory.Parameterizer.DISTANCE_FUNCTION_ID, EuclideanDistanceFunction.class); + testExactEuclidean(metparams, CoverTree.CoverTreeKNNQuery.class, CoverTree.CoverTreeRangeQuery.class); + } +} diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/SimplifiedCoverTreeTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/SimplifiedCoverTreeTest.java new file mode 100644 index 00000000..d63a5ecc --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/metrical/covertree/SimplifiedCoverTreeTest.java @@ -0,0 +1,50 @@ +package de.lmu.ifi.dbs.elki.index.tree.metrical.covertree; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.database.StaticArrayDatabase; +import de.lmu.ifi.dbs.elki.distance.distancefunction.minkowski.EuclideanDistanceFunction; +import de.lmu.ifi.dbs.elki.index.AbstractIndexStructureTest; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Unit test for the Cover-tree. + * + * @author Erich Schubert + * @since 0.7.0 + */ +public class SimplifiedCoverTreeTest extends AbstractIndexStructureTest { + /** + * Test {@link SimplifiedCoverTree} using a file based database connection. + */ + @Test + public void testCovertree() { + ListParameterization metparams = new ListParameterization(); + metparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, SimplifiedCoverTree.Factory.class); + metparams.addParameter(SimplifiedCoverTree.Factory.Parameterizer.DISTANCE_FUNCTION_ID, EuclideanDistanceFunction.class); + testExactEuclidean(metparams, SimplifiedCoverTree.CoverTreeKNNQuery.class, SimplifiedCoverTree.CoverTreeRangeQuery.class); + } +} diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/TestMTree.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTreeTest.java index b4eb7bc9..f4188e91 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/TestMTree.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mtree/MTreeTest.java @@ -26,7 +26,7 @@ package de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.mtree; import org.junit.Test; import de.lmu.ifi.dbs.elki.database.StaticArrayDatabase; -import de.lmu.ifi.dbs.elki.index.AbstractTestIndexStructures; +import de.lmu.ifi.dbs.elki.index.AbstractIndexStructureTest; import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.query.MetricalIndexKNNQuery; import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.query.MetricalIndexRangeQuery; import de.lmu.ifi.dbs.elki.persistent.AbstractPageFileFactory; @@ -36,8 +36,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * Unit test for the M-tree. * * @author Erich Schubert + * @since 0.7.0 */ -public class TestMTree extends AbstractTestIndexStructures { +public class MTreeTest extends AbstractIndexStructureTest { /** * Test {@link MTree} using a file based database connection. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/TestMinimalisticMemoryKDTree.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/MinimalisticMemoryKDTreeTest.java index 70fef1c3..c612f44c 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/TestMinimalisticMemoryKDTree.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/MinimalisticMemoryKDTreeTest.java @@ -26,15 +26,16 @@ package de.lmu.ifi.dbs.elki.index.tree.spatial.kd; import org.junit.Test; import de.lmu.ifi.dbs.elki.database.StaticArrayDatabase; -import de.lmu.ifi.dbs.elki.index.AbstractTestIndexStructures; +import de.lmu.ifi.dbs.elki.index.AbstractIndexStructureTest; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; /** * Unit test for the k-d-tree index. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestMinimalisticMemoryKDTree extends AbstractTestIndexStructures { +public class MinimalisticMemoryKDTreeTest extends AbstractIndexStructureTest { /** * Test {@link MinimalisticMemoryKDTree} using a file based database connection. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/TestSmallMemoryKDTree.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/SmallMemoryKDTreeTest.java index c5939ec1..fe12335f 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/TestSmallMemoryKDTree.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/spatial/kd/SmallMemoryKDTreeTest.java @@ -26,15 +26,16 @@ package de.lmu.ifi.dbs.elki.index.tree.spatial.kd; import org.junit.Test; import de.lmu.ifi.dbs.elki.database.StaticArrayDatabase; -import de.lmu.ifi.dbs.elki.index.AbstractTestIndexStructures; +import de.lmu.ifi.dbs.elki.index.AbstractIndexStructureTest; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; /** * Unit test for the k-d-tree index. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestSmallMemoryKDTree extends AbstractTestIndexStructures { +public class SmallMemoryKDTreeTest extends AbstractIndexStructureTest { /** * Test {@link SmallMemoryKDTree} using a file based database connection. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTreeTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTreeTest.java new file mode 100644 index 00000000..3a1a64c0 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/RStarTreeTest.java @@ -0,0 +1,362 @@ +package de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.rstar; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.database.StaticArrayDatabase; +import de.lmu.ifi.dbs.elki.index.AbstractIndexStructureTest; +import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.AbstractRStarTreeFactory; +import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.query.RStarTreeKNNQuery; +import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.query.RStarTreeRangeQuery; +import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.AdaptiveSortTileRecursiveBulkSplit; +import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.FileOrderBulkSplit; +import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.MaxExtensionBulkSplit; +import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.MaxExtensionSortTileRecursiveBulkSplit; +import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.OneDimSortBulkSplit; +import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.SortTileRecursiveBulkSplit; +import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.SpatialSortBulkSplit; +import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.insert.ApproximativeLeastOverlapInsertionStrategy; +import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.split.AngTanLinearSplit; +import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.split.GreeneSplit; +import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.split.RTreeLinearSplit; +import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.split.RTreeQuadraticSplit; +import de.lmu.ifi.dbs.elki.math.spacefillingcurves.BinarySplitSpatialSorter; +import de.lmu.ifi.dbs.elki.math.spacefillingcurves.HilbertSpatialSorter; +import de.lmu.ifi.dbs.elki.math.spacefillingcurves.PeanoSpatialSorter; +import de.lmu.ifi.dbs.elki.math.spacefillingcurves.ZCurveSpatialSorter; +import de.lmu.ifi.dbs.elki.persistent.AbstractPageFileFactory; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; + +/** + * Unit test for the R*-tree index. + * + * @author Erich Schubert + * @since 0.7.0 + */ +public class RStarTreeTest extends AbstractIndexStructureTest { + /** + * Test {@link RStarTree} using a file based database connection. + */ + @Test + public void testRStarTree() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } + + /** + * Test {@link RStarTree} using a file based database connection. With "fast" + * mode enabled on an extreme level (since this should only reduce + * performance, not correctness!) + */ + @Test + public void testRStarTreeFast() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractRStarTreeFactory.Parameterizer.INSERTION_STRATEGY_ID, ApproximativeLeastOverlapInsertionStrategy.class); + spatparams.addParameter(ApproximativeLeastOverlapInsertionStrategy.Parameterizer.INSERTION_CANDIDATES_ID, 1); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractRStarTreeFactory.Parameterizer.INSERTION_STRATEGY_ID, ApproximativeLeastOverlapInsertionStrategy.class); + spatparams.addParameter(ApproximativeLeastOverlapInsertionStrategy.Parameterizer.INSERTION_CANDIDATES_ID, 1); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } + + /** + * Test {@link RStarTree} using {@link RTreeLinearSplit} + */ + @Test + public void testRTreeLinearSplit() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.SPLIT_STRATEGY_ID, RTreeLinearSplit.class); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.SPLIT_STRATEGY_ID, RTreeLinearSplit.class); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } + + /** + * Test {@link RStarTree} using {@link RTreeQuadraticSplit} + */ + @Test + public void testRTreeQuadraticSplit() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.SPLIT_STRATEGY_ID, RTreeQuadraticSplit.class); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.SPLIT_STRATEGY_ID, RTreeQuadraticSplit.class); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } + + /** + * Test {@link RStarTree} using {@link GreeneSplit} + */ + @Test + public void testRTreeGreeneSplit() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.SPLIT_STRATEGY_ID, GreeneSplit.class); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.SPLIT_STRATEGY_ID, GreeneSplit.class); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } + + /** + * Test {@link RStarTree} using {@link RTreeLinearSplit} + */ + @Test + public void testRTreeAngTanLinearSplit() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.SPLIT_STRATEGY_ID, AngTanLinearSplit.class); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.SPLIT_STRATEGY_ID, AngTanLinearSplit.class); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } + + /** + * Test {@link RStarTree} bulk loaded using {@link FileOrderBulkSplit} + */ + @Test + public void testFileOrderBulkSplit() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, FileOrderBulkSplit.class); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, FileOrderBulkSplit.class); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } + + /** + * Test {@link RStarTree} bulk loaded using {@link MaxExtensionBulkSplit} + */ + @Test + public void testMaxExtensionBulkSplit() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, MaxExtensionBulkSplit.class); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, MaxExtensionBulkSplit.class); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } + + /** + * Test {@link RStarTree} bulk loaded using {@link OneDimSortBulkSplit} + */ + @Test + public void testOneDimSortBulkSplit() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, OneDimSortBulkSplit.class); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, OneDimSortBulkSplit.class); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } + + /** + * Test {@link RStarTree} bulk loaded using {@link SpatialSortBulkSplit} with + * {@link ZCurveSpatialSorter} + */ + @Test + public void testZCurveSpatialSortBulkSplit() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, SpatialSortBulkSplit.class); + spatparams.addParameter(SpatialSortBulkSplit.Parameterizer.SORTER_ID, ZCurveSpatialSorter.class); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, SpatialSortBulkSplit.class); + spatparams.addParameter(SpatialSortBulkSplit.Parameterizer.SORTER_ID, ZCurveSpatialSorter.class); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } + + /** + * Test {@link RStarTree} bulk loaded using {@link SpatialSortBulkSplit} with + * {@link HilbertSpatialSorter} + */ + @Test + public void testHilbertSpatialSortBulkSplit() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, SpatialSortBulkSplit.class); + spatparams.addParameter(SpatialSortBulkSplit.Parameterizer.SORTER_ID, HilbertSpatialSorter.class); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, SpatialSortBulkSplit.class); + spatparams.addParameter(SpatialSortBulkSplit.Parameterizer.SORTER_ID, HilbertSpatialSorter.class); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } + + /** + * Test {@link RStarTree} bulk loaded using {@link SpatialSortBulkSplit} with + * {@link PeanoSpatialSorter} + */ + @Test + public void testPeanoSpatialSortBulkSplit() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, SpatialSortBulkSplit.class); + spatparams.addParameter(SpatialSortBulkSplit.Parameterizer.SORTER_ID, PeanoSpatialSorter.class); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, SpatialSortBulkSplit.class); + spatparams.addParameter(SpatialSortBulkSplit.Parameterizer.SORTER_ID, PeanoSpatialSorter.class); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } + + /** + * Test {@link RStarTree} bulk loaded using {@link SpatialSortBulkSplit} with + * {@link BinarySplitSpatialSorter} + */ + @Test + public void testBinarySplitSpatialSortBulkSplit() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, SpatialSortBulkSplit.class); + spatparams.addParameter(SpatialSortBulkSplit.Parameterizer.SORTER_ID, BinarySplitSpatialSorter.class); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, SpatialSortBulkSplit.class); + spatparams.addParameter(SpatialSortBulkSplit.Parameterizer.SORTER_ID, BinarySplitSpatialSorter.class); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } + + /** + * Test {@link RStarTree} bulk loaded using {@link SortTileRecursiveBulkSplit} + */ + @Test + public void testSortTileRecursiveBulkSplit() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, SortTileRecursiveBulkSplit.class); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, SortTileRecursiveBulkSplit.class); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } + + /** + * Test {@link RStarTree} bulk loaded using + * {@link MaxExtensionSortTileRecursiveBulkSplit} + */ + @Test + public void testMaxExtensionSortTileRecursiveBulkSplit() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, MaxExtensionSortTileRecursiveBulkSplit.class); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, MaxExtensionSortTileRecursiveBulkSplit.class); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } + + /** + * Test {@link RStarTree} bulk loaded using + * {@link AdaptiveSortTileRecursiveBulkSplit} + */ + @Test + public void testAdaptiveSortTileRecursiveBulkSplit() { + ListParameterization spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, AdaptiveSortTileRecursiveBulkSplit.class); + testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + // + spatparams = new ListParameterization(); + spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); + spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); + spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, AdaptiveSortTileRecursiveBulkSplit.class); + testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); + } +} diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/TestRStarTree.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/TestRStarTree.java deleted file mode 100644 index db88d600..00000000 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/rstar/TestRStarTree.java +++ /dev/null @@ -1,99 +0,0 @@ -package de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.rstar; - -/* - This file is part of ELKI: - Environment for Developing KDD-Applications Supported by Index-Structures - - Copyright (C) 2015 - Ludwig-Maximilians-Universität München - Lehr- und Forschungseinheit für Datenbanksysteme - ELKI Development Team - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU Affero General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU Affero General Public License for more details. - - You should have received a copy of the GNU Affero General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -import org.junit.Test; - -import de.lmu.ifi.dbs.elki.database.StaticArrayDatabase; -import de.lmu.ifi.dbs.elki.index.AbstractTestIndexStructures; -import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.AbstractRStarTreeFactory; -import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.query.RStarTreeKNNQuery; -import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.query.RStarTreeRangeQuery; -import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.bulk.SortTileRecursiveBulkSplit; -import de.lmu.ifi.dbs.elki.index.tree.spatial.rstarvariants.strategies.insert.ApproximativeLeastOverlapInsertionStrategy; -import de.lmu.ifi.dbs.elki.persistent.AbstractPageFileFactory; -import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; - -/** - * Unit test for the R*-tree index. - * - * @author Erich Schubert - */ -public class TestRStarTree extends AbstractTestIndexStructures { - /** - * Test {@link RStarTree} using a file based database connection. - */ - @Test - public void testRStarTree() { - ListParameterization spatparams = new ListParameterization(); - spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); - spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); - testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); - // - spatparams = new ListParameterization(); - spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); - spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); - testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); - } - - /** - * Test {@link RStarTree} using a file based database connection. With "fast" - * mode enabled on an extreme level (since this should only reduce - * performance, not correctness!) - */ - @Test - public void testRStarTreeFast() { - ListParameterization spatparams = new ListParameterization(); - spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); - spatparams.addParameter(AbstractRStarTreeFactory.Parameterizer.INSERTION_STRATEGY_ID, ApproximativeLeastOverlapInsertionStrategy.class); - spatparams.addParameter(ApproximativeLeastOverlapInsertionStrategy.Parameterizer.INSERTION_CANDIDATES_ID, 1); - spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); - testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); - // - spatparams = new ListParameterization(); - spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); - spatparams.addParameter(AbstractRStarTreeFactory.Parameterizer.INSERTION_STRATEGY_ID, ApproximativeLeastOverlapInsertionStrategy.class); - spatparams.addParameter(ApproximativeLeastOverlapInsertionStrategy.Parameterizer.INSERTION_CANDIDATES_ID, 1); - spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); - testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); - } - - /** - * Test {@link RStarTree} bulk loaded using {@link SortTileRecursiveBulkSplit} - */ - @Test - public void testSTRTree() { - ListParameterization spatparams = new ListParameterization(); - spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); - spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); - spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, SortTileRecursiveBulkSplit.class); - testExactEuclidean(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); - // - spatparams = new ListParameterization(); - spatparams.addParameter(StaticArrayDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class); - spatparams.addParameter(AbstractPageFileFactory.Parameterizer.PAGE_SIZE_ID, 300); - spatparams.addParameter(RStarTreeFactory.Parameterizer.BULK_SPLIT_ID, SortTileRecursiveBulkSplit.class); - testExactCosine(spatparams, RStarTreeKNNQuery.class, RStarTreeRangeQuery.class); - } -} diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/vafile/TestPartialVAFile.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/vafile/PartialVAFileTest.java index 4097256b..9060330c 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/vafile/TestPartialVAFile.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/vafile/PartialVAFileTest.java @@ -26,15 +26,16 @@ package de.lmu.ifi.dbs.elki.index.vafile; import org.junit.Test; import de.lmu.ifi.dbs.elki.database.StaticArrayDatabase; -import de.lmu.ifi.dbs.elki.index.AbstractTestIndexStructures; +import de.lmu.ifi.dbs.elki.index.AbstractIndexStructureTest; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; /** * Unit test for the partial VAfile index. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestPartialVAFile extends AbstractTestIndexStructures { +public class PartialVAFileTest extends AbstractIndexStructureTest { /** * Test {@link PartialVAFile} using a file based database connection. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/vafile/TestVAFile.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/vafile/VAFileTest.java index 7a49c685..a345b256 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/index/vafile/TestVAFile.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/index/vafile/VAFileTest.java @@ -26,15 +26,16 @@ package de.lmu.ifi.dbs.elki.index.vafile; import org.junit.Test; import de.lmu.ifi.dbs.elki.database.StaticArrayDatabase; -import de.lmu.ifi.dbs.elki.index.AbstractTestIndexStructures; +import de.lmu.ifi.dbs.elki.index.AbstractIndexStructureTest; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; /** * Unit test for the VAfile index. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestVAFile extends AbstractTestIndexStructures { +public class VAFileTest extends AbstractIndexStructureTest { /** * Test {@link VAFile} using a file based database connection. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/logging/TestOutputStreamLogger.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/logging/OutputStreamLoggerTest.java index bbde0e42..e5034d8d 100755 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/logging/TestOutputStreamLogger.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/logging/OutputStreamLoggerTest.java @@ -37,9 +37,10 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Small experiment to assert the console output logger works as expected. * * @author Erich Schubert + * @since 0.2 * */ -public class TestOutputStreamLogger implements JUnit4Test { +public class OutputStreamLoggerTest implements JUnit4Test { /** * Write a couple of messages to the console output writer and compare the * resulting characters. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestAffineTransformation.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/AffineTransformationTest.java index 7c39d691..e3e01d6d 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestAffineTransformation.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/AffineTransformationTest.java @@ -37,9 +37,10 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector; * JUnit Test for the class {@link AffineTransformation} * * @author Erich Schubert + * @since 0.2 * */ -public class TestAffineTransformation implements JUnit4Test { +public class AffineTransformationTest implements JUnit4Test { /** * Test identity transform */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestKernelDensityFitting.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/KernelDensityFittingTest.java index 3ec64c63..65c798f0 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestKernelDensityFitting.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/KernelDensityFittingTest.java @@ -51,8 +51,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParamet * JUnit test that does a complete Kernel and Levenberg-Marquadt fitting. * * @author Erich Schubert + * @since 0.2 */ -public class TestKernelDensityFitting implements JUnit4Test { +public class KernelDensityFittingTest implements JUnit4Test { // the following values depend on the data set used! String dataset = "data/testdata/unittests/gaussian-1d-for-fitting.csv"; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestLevenbergMarquardtGaussianFitting.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/LevenbergMarquardtGaussianFittingTest.java index 54b56b99..6bc171e1 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestLevenbergMarquardtGaussianFitting.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/LevenbergMarquardtGaussianFittingTest.java @@ -36,9 +36,10 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.fitting.LevenbergMarquardtMethod; * distribution. * * @author Erich Schubert + * @since 0.2 * */ -public class TestLevenbergMarquardtGaussianFitting implements JUnit4Test { +public class LevenbergMarquardtGaussianFittingTest implements JUnit4Test { /** * Evaluate on a symmetric Gaussian distribution. Traditional estimation * already has the mean quite good, but is far off on the stddev. The improved diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestMathUtil.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/MathUtilTest.java index 9f180ef9..bc5fb3b3 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestMathUtil.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/MathUtilTest.java @@ -34,10 +34,11 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; /** * Unit test for some basic math functions. - * + * * @author Erich Schubert + * @since 0.4.1 */ -public class TestMathUtil implements JUnit4Test { +public class MathUtilTest implements JUnit4Test { @Test public void testPearsonCorrelation() { final int size = 1000; @@ -48,7 +49,7 @@ public class TestMathUtil implements JUnit4Test { double[] weight2 = new double[size]; Random r = new Random(seed); - for (int i = 0; i < size; i++) { + for(int i = 0; i < size; i++) { data1[i] = r.nextDouble(); data2[i] = r.nextDouble(); weight1[i] = 1.0; @@ -88,7 +89,7 @@ public class TestMathUtil implements JUnit4Test { @Test public void testFloatToDouble() { Random r = new Random(1l); - for (int i = 0; i < 10000; i++) { + for(int i = 0; i < 10000; i++) { final double dbl = Double.longBitsToDouble(r.nextLong()); final float flt = (float) dbl; final double uppd = MathUtil.floatToDoubleUpper(flt); @@ -101,4 +102,12 @@ public class TestMathUtil implements JUnit4Test { assertTrue("Expected value to round to the same float.", flt == lowf || Double.isNaN(flt)); } } + + @Test + public void testPowi() { + assertEquals("Power incorrect", 0.01, MathUtil.powi(0.1, 2), 1e-13); + assertEquals("Power incorrect", 0.001, MathUtil.powi(0.1, 3), 1e-13); + assertEquals("Power incorrect", 0.0001, MathUtil.powi(0.1, 4), 1e-13); + assertEquals("Power incorrect", 0.00001, MathUtil.powi(0.1, 5), 1e-13); + } } diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestMatrix.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/MatrixTest.java index a7eab849..37876fef 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestMatrix.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/MatrixTest.java @@ -30,7 +30,13 @@ import org.junit.Test; import de.lmu.ifi.dbs.elki.JUnit4Test; import de.lmu.ifi.dbs.elki.math.linearalgebra.Matrix; -public class TestMatrix implements JUnit4Test { +/** + * Test some basic matrix operations. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class MatrixTest implements JUnit4Test { @Test public void testTransposedOperations() { diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestMean.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/MeanTest.java index eae531e4..a9783757 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestMean.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/MeanTest.java @@ -32,8 +32,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Test the Mean class. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestMean implements JUnit4Test { +public class MeanTest implements JUnit4Test { @Test public void testInfinity() { Mean m = new Mean(); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestSlidingVariance.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/MeanVarianceTest.java index 3b531f63..76ae56a1 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestSlidingVariance.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/MeanVarianceTest.java @@ -34,8 +34,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Unit test {@link MeanVariance} with negative weights. * * @author Erich Schubert + * @since 0.6.0 */ -public class TestSlidingVariance implements JUnit4Test { +public class MeanVarianceTest implements JUnit4Test { /** * Size of test data set. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestSinCosTable.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/SinCosTableTest.java index 4a346a4d..eaf9f1b4 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestSinCosTable.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/SinCosTableTest.java @@ -1,11 +1,4 @@ package de.lmu.ifi.dbs.elki.math; - -import static org.junit.Assert.assertEquals; - -import org.junit.Test; - -import de.lmu.ifi.dbs.elki.JUnit4Test; - /* This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures @@ -29,19 +22,30 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; along with this program. If not, see <http://www.gnu.org/licenses/>. */ -public class TestSinCosTable implements JUnit4Test { +import static org.junit.Assert.assertEquals; + +import org.junit.Test; +import de.lmu.ifi.dbs.elki.JUnit4Test; + +/** + * Test the sin-cos lookup table. + * + * @author Erich Schubert + * @since 0.4.0 + */ +public class SinCosTableTest implements JUnit4Test { @Test public void testSinCosTable() { - doTestSinCosTable(360); - doTestSinCosTable(142); // Divisible by two - doTestSinCosTable(17); - doTestSinCosTable(131); // Prime. + doSinCosTableTest(360); + doSinCosTableTest(142); // Divisible by two + doSinCosTableTest(17); + doSinCosTableTest(131); // Prime. } - protected void doTestSinCosTable(int steps) { + protected void doSinCosTableTest(int steps) { SinCosTable table = SinCosTable.make(steps); - for (int i = -steps; i < 2 * steps; i++) { + for(int i = -steps; i < 2 * steps; i++) { double angle = Math.toRadians(360. * i / steps); assertEquals("Cosine does not match at i=" + i + " a=" + angle, Math.cos(angle), table.cos(i), 1E-10); assertEquals("Sine does not match at i=" + i + " a=" + angle, Math.sin(angle), table.sin(i), 1E-10); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestStatisticalMoments.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/StatisticalMomentsTest.java index 976ec6b8..51106508 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestStatisticalMoments.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/StatisticalMomentsTest.java @@ -33,8 +33,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Unit test to check our statistical moments class for correctness. * * @author Erich Schubert + * @since 0.6.0 */ -public class TestStatisticalMoments implements JUnit4Test { +public class StatisticalMomentsTest implements JUnit4Test { @Test public void testTiny() { double[] data = new double[] { 222, 1122, 45444 }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/geodesy/TestEarthModels.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/geodesy/EarthModelsTest.java index 24f49f1f..1d72e521 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/geodesy/TestEarthModels.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/geodesy/EarthModelsTest.java @@ -37,8 +37,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * give different values. But in the end, it's always just an approximation. * * @author Erich Schubert + * @since 0.6.0 */ -public class TestEarthModels implements JUnit4Test { +public class EarthModelsTest implements JUnit4Test { // New York City final double[] NEW_YORK = new double[] { 40.67, -73.94 }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/geometry/TestPrimsMinimumSpanningTree.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/geometry/PrimsMinimumSpanningTreeTest.java index cb9f518e..6672fe29 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/geometry/TestPrimsMinimumSpanningTree.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/geometry/PrimsMinimumSpanningTreeTest.java @@ -34,8 +34,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Test class for Prim's minmum spanning tree algorithm. * * @author Erich Schubert + * @since 0.5.5 */ -public class TestPrimsMinimumSpanningTree implements JUnit4Test { +public class PrimsMinimumSpanningTreeTest implements JUnit4Test { @Test public void testSimple() { // A simple test. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/scales/TestLinearScale.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/scales/LinearScaleTest.java index 3e088b17..61988392 100755 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/scales/TestLinearScale.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/scales/LinearScaleTest.java @@ -34,9 +34,10 @@ import de.lmu.ifi.dbs.elki.math.scales.LinearScale; * Test class to test rounding of the linear scale. * * @author Erich Schubert + * @since 0.2 * */ -public class TestLinearScale implements JUnit4Test { +public class LinearScaleTest implements JUnit4Test { /** * Produces a simple linear scale and verifies the tick lines are placed as diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/TestAbstractDependenceMeasure.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/AbstractDependenceMeasureTest.java index 866f819a..4a938038 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/TestAbstractDependenceMeasure.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/AbstractDependenceMeasureTest.java @@ -34,8 +34,9 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayLikeUtil; * Validate jensen shannon dependence. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestAbstractDependenceMeasure implements JUnit4Test { +public class AbstractDependenceMeasureTest implements JUnit4Test { @Test public void testIndexing() { double[] data = { 1e-10, 1, 1e-5, 1, 2, 1 }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/TestCorrelationDependenceMeasure.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/CorrelationDependenceMeasureTest.java index 00e737c8..afe080c2 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/TestCorrelationDependenceMeasure.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/CorrelationDependenceMeasureTest.java @@ -36,8 +36,9 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayLikeUtil; * Validate correlation by comparing to the results of R. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestCorrelationDependenceMeasure implements JUnit4Test { +public class CorrelationDependenceMeasureTest implements JUnit4Test { double[][] data = { // { 1, 2, 3, 4 }, // { 1, 3, 5, 7 }, // diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/TestDistanceCorrelationDependenceMeasure.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/DistanceCorrelationDependenceMeasureTest.java index 8c000e30..bcf493be 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/TestDistanceCorrelationDependenceMeasure.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/DistanceCorrelationDependenceMeasureTest.java @@ -36,8 +36,9 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayLikeUtil; * Validate dCor by comparing to output of the official R version. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestDistanceCorrelationDependenceMeasure implements JUnit4Test { +public class DistanceCorrelationDependenceMeasureTest implements JUnit4Test { double[][] data = { // { 1, 2, 3, 4 }, // { 1, 3, 5, 7 }, // diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/TestJensenShannonEquiwidthDependenceMeasure.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/JensenShannonEquiwidthDependenceMeasureTest.java index 30019106..7d30b9a0 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/TestJensenShannonEquiwidthDependenceMeasure.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/JensenShannonEquiwidthDependenceMeasureTest.java @@ -37,8 +37,9 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayLikeUtil; * Validate jensen shannon dependence. * * @author Erich Schubert + * @since 0.7.0 */ -public class TestJensenShannonEquiwidthDependenceMeasure implements JUnit4Test { +public class JensenShannonEquiwidthDependenceMeasureTest implements JUnit4Test { double[][] data = { // { 1, 2, 3, 4 }, // { 1, 3, 5, 7 }, // diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/TestMutualInformationEquiwidthDependenceMeasure.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/MutualInformationEquiwidthDependenceMeasureTest.java index 07c2ee32..9807557b 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/TestMutualInformationEquiwidthDependenceMeasure.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/MutualInformationEquiwidthDependenceMeasureTest.java @@ -38,8 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayLikeUtil; * Validate correlation by comparing to manual computation. * * @author Erich Schubert + * @since 0.7.0 */ -public class TestMutualInformationEquiwidthDependenceMeasure implements JUnit4Test { +public class MutualInformationEquiwidthDependenceMeasureTest implements JUnit4Test { double[][] data = { // { 1, 2, 3, 4 }, // { 1, 3, 5, 7 }, // diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/TestSpearmanCorrelationDependenceMeasure.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SpearmanCorrelationDependenceMeasureTest.java index 11e347bb..ad056820 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/TestSpearmanCorrelationDependenceMeasure.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/dependence/SpearmanCorrelationDependenceMeasureTest.java @@ -36,8 +36,9 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayLikeUtil; * Validate correlation by comparing to the results of R. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestSpearmanCorrelationDependenceMeasure implements JUnit4Test { +public class SpearmanCorrelationDependenceMeasureTest implements JUnit4Test { double[][] data = { // { 1, 2, 3, 4 }, // { 1, 3, 5, 700 }, // diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/AbstractDistributionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/AbstractDistributionTest.java index 54ba4208..8b202e13 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/AbstractDistributionTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/AbstractDistributionTest.java @@ -29,6 +29,7 @@ import static org.junit.Assert.assertTrue; * Abstract base class for distribution unit testing. * * @author Erich Schubert + * @since 0.5.0 */ public class AbstractDistributionTest { public void checkPDF(Distribution d, double[] x, double[] expected, double err) { diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestBetaDistribution.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/BetaDistributionTest.java index dba4b8cb..3c95fc80 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestBetaDistribution.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/BetaDistributionTest.java @@ -32,8 +32,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * The reference values were computed using GNU R and SciPy. * * @author Erich Schubert + * @since 0.5.0 */ -public class TestBetaDistribution extends AbstractDistributionTest implements JUnit4Test { +public class BetaDistributionTest extends AbstractDistributionTest implements JUnit4Test { public static final double[] P_CDFPDF = { // 1e-10, 1e-05, 0.1, 0.1234567, 0.2, 0.271828182846, 0.3, 0.314159265359, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.71828182846, 3.14159265359 // }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestChiSquaredDistribution.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ChiSquaredDistributionTest.java index 2a9e9ae9..f2c0a85a 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestChiSquaredDistribution.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ChiSquaredDistributionTest.java @@ -32,8 +32,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * The reference values were computed using GNU R and SciPy. * * @author Erich Schubert + * @since 0.5.0 */ -public class TestChiSquaredDistribution extends AbstractDistributionTest implements JUnit4Test { +public class ChiSquaredDistributionTest extends AbstractDistributionTest implements JUnit4Test { public static final double[] P_CDFPDF = { // 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 1e-05, 1e-10, 0.1234567, 3.14159265359, 2.71828182846, 0.314159265359, 0.271828182846 // }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestExponentialDistribution.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ExponentialDistributionTest.java index e024eada..f5dc2e03 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestExponentialDistribution.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ExponentialDistributionTest.java @@ -32,8 +32,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * The reference values were computed using GNU R and SciPy. * * @author Erich Schubert + * @since 0.5.5 */ -public class TestExponentialDistribution extends AbstractDistributionTest implements JUnit4Test { +public class ExponentialDistributionTest extends AbstractDistributionTest implements JUnit4Test { public static final double[] P_CDFPDF = { // 1e-10, 1e-05, 0.1, 0.1234567, 0.2, 0.271828182846, 0.3, 0.314159265359, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.71828182846, 3.14159265359 // }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestExponentiallyModifiedGaussianDistribution.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ExponentiallyModifiedGaussianDistributionTest.java index 69c8443d..6012b548 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestExponentiallyModifiedGaussianDistribution.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/ExponentiallyModifiedGaussianDistributionTest.java @@ -32,8 +32,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * The reference values were computed using GNU R and SciPy. * * @author Erich Schubert + * @since 0.6.0 */ -public class TestExponentiallyModifiedGaussianDistribution extends AbstractDistributionTest implements JUnit4Test { +public class ExponentiallyModifiedGaussianDistributionTest extends AbstractDistributionTest implements JUnit4Test { public static final double[] P_CDFPDF = { // 1e-10, 1e-05, 0.1, 0.1234567, 0.2, 0.2718281828459045, 0.3, 0.3141592653589793, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.718281828459045, 3.141592653589793 // }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestGammaDistribution.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GammaDistributionTest.java index 9fa12068..fa1fe647 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestGammaDistribution.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GammaDistributionTest.java @@ -38,8 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayLikeUtil; * The reference values were computed using GNU R and SciPy. * * @author Erich Schubert + * @since 0.5.0 */ -public class TestGammaDistribution extends AbstractDistributionTest implements JUnit4Test { +public class GammaDistributionTest extends AbstractDistributionTest implements JUnit4Test { public static final double[] P_CDFPDF = { // 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 1e-05, 1e-10, 0.1234567, 3.14159265359, 2.71828182846, 0.314159265359, 0.271828182846 // }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestGeneralizedExtremeValueDistribution.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedExtremeValueDistributionTest.java index c4b0fce2..85ad93e3 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestGeneralizedExtremeValueDistribution.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedExtremeValueDistributionTest.java @@ -32,8 +32,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * The reference values were computed using SciPy. * * @author Erich Schubert + * @since 0.6.0 */ -public class TestGeneralizedExtremeValueDistribution extends AbstractDistributionTest implements JUnit4Test { +public class GeneralizedExtremeValueDistributionTest extends AbstractDistributionTest implements JUnit4Test { public static final double[] P_CDFPDF = { // 1e-10, 1e-05, 0.1, 0.1234567, 0.2, 0.271828182846, 0.3, 0.314159265359, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.71828182846, 3.14159265359 // }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestGeneralizedLogisticDistribution.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedLogisticDistributionTest.java index ca3d8fe9..c9b1baef 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestGeneralizedLogisticDistribution.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedLogisticDistributionTest.java @@ -32,8 +32,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * The reference values were computed using GNU R and SciPy. * * @author Erich Schubert + * @since 0.6.0 */ -public class TestGeneralizedLogisticDistribution extends AbstractDistributionTest implements JUnit4Test { +public class GeneralizedLogisticDistributionTest extends AbstractDistributionTest implements JUnit4Test { public static final double[] P_CDFPDF = { // 1e-10, 1e-05, 0.1, 0.1234567, 0.2, 0.271828182846, 0.3, 0.314159265359, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.71828182846, 3.14159265359 // }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestGeneralizedParetoDistribution.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedParetoDistributionTest.java index 23328e4d..83025a31 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestGeneralizedParetoDistribution.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GeneralizedParetoDistributionTest.java @@ -32,8 +32,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * The reference values were computed using SciPy. * * @author Erich Schubert + * @since 0.7.0 */ -public class TestGeneralizedParetoDistribution extends AbstractDistributionTest implements JUnit4Test { +public class GeneralizedParetoDistributionTest extends AbstractDistributionTest implements JUnit4Test { public static final double[] P_CDFPDF = { // 1e-10, 1e-05, 0.1, 0.1234567, 0.2, 0.271828182846, 0.3, 0.314159265359, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.71828182846, 3.14159265359 // }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestGumbelDistribution.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GumbelDistributionTest.java index 9efec3cf..9c7223f3 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestGumbelDistribution.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/GumbelDistributionTest.java @@ -32,8 +32,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * The reference values were computed using SciPy. * * @author Erich Schubert + * @since 0.6.0 */ -public class TestGumbelDistribution extends AbstractDistributionTest implements JUnit4Test { +public class GumbelDistributionTest extends AbstractDistributionTest implements JUnit4Test { public static final double[] P_CDFPDF = { // 1e-10, 1e-05, 0.1, 0.1234567, 0.2, 0.271828182846, 0.3, 0.314159265359, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.71828182846, 3.14159265359 // }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/HaltonUniformDistributionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/HaltonUniformDistributionTest.java new file mode 100644 index 00000000..2c70e509 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/HaltonUniformDistributionTest.java @@ -0,0 +1,91 @@ +package de.lmu.ifi.dbs.elki.math.statistics.distribution; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; + +/** + * Unit test for the Halton pseudo-Uniform distribution in ELKI. + * + * @author Erich Schubert + * @since 0.7.1 + */ +public class HaltonUniformDistributionTest extends AbstractDistributionTest implements JUnit4Test { + public static final double[] P_CDFPDF = { // + 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 1e-05, 1e-10, 0.1234567, 3.14159265359, 2.71828182846, 0.314159265359, 0.271828182846 // + }; + + public static final double[] P_PROBIT = { // + 0.0001, 0.001, 0.01, 0.1, 0.25, 0.5, 0.75, 0.9, 0.99, 0.999, 0.9999 // + }; + + @Test + public void testPDF() { + double[] buf = new double[P_CDFPDF.length]; + for(double l : new double[] { -1, 0, .1, 1 }) { + for(double h : new double[] { -1, 0, .1, 1, 2, 10 }) { + if(l < h) { + double w = h - l; + for(int i = 0; i < P_CDFPDF.length; i++) { + buf[i] = (P_CDFPDF[i] >= l && P_CDFPDF[i] < h) ? 1. / w : 0.; + } + checkPDF(new HaltonUniformDistribution(l, h), P_CDFPDF, buf, 1e-15); + } + } + } + } + + @Test + public void testCDF() { + double[] buf = new double[P_CDFPDF.length]; + for(double l : new double[] { -1, 0, .1, 1 }) { + for(double h : new double[] { -1, 0, .1, 1, 2, 10 }) { + if(l < h) { + double w = h - l; + for(int i = 0; i < P_CDFPDF.length; i++) { + buf[i] = P_CDFPDF[i] <= l ? 0. : P_CDFPDF[i] >= h ? 1. : (P_CDFPDF[i] - l) / w; + } + checkCDF(new HaltonUniformDistribution(l, h), P_CDFPDF, buf, 1e-15); + } + } + } + } + + @Test + public void testProbit() { + double[] buf = new double[P_PROBIT.length]; + for(double l : new double[] { -1, 0, .1, 1 }) { + for(double h : new double[] { -1, 0, .1, 1, 2, 10 }) { + if(l < h) { + double w = h - l; + for(int i = 0; i < P_PROBIT.length; i++) { + buf[i] = l + P_PROBIT[i] * w; + } + checkQuantile(new HaltonUniformDistribution(l, h), P_PROBIT, buf, 1e-15); + } + } + } + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestLogGammaAlternateDistribution.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogGammaAlternateDistributionTest.java index 436953cc..e3354f3f 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestLogGammaAlternateDistribution.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogGammaAlternateDistributionTest.java @@ -32,8 +32,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * The reference values were computed using GNU R and SciPy. * * @author Erich Schubert + * @since 0.6.0 */ -public class TestLogGammaAlternateDistribution extends AbstractDistributionTest implements JUnit4Test { +public class LogGammaAlternateDistributionTest extends AbstractDistributionTest implements JUnit4Test { public static final double[] P_CDFPDF = { // 1e-10, 1e-05, 0.1, 0.1234567, 0.2, 0.271828182846, 0.3, 0.314159265359, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.71828182846, 3.14159265359 // }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestLogNormalDistribution.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogNormalDistributionTest.java index 75284aae..c42ffe89 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestLogNormalDistribution.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogNormalDistributionTest.java @@ -32,8 +32,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * The reference values were computed using GNU R and SciPy. * * @author Erich Schubert + * @since 0.6.0 */ -public class TestLogNormalDistribution extends AbstractDistributionTest implements JUnit4Test { +public class LogNormalDistributionTest extends AbstractDistributionTest implements JUnit4Test { public static final double[] P_CDFPDF = { // 1e-10, 1e-05, 0.1, 0.1234567, 0.2, 0.271828182846, 0.3, 0.314159265359, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.71828182846, 3.14159265359 // }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestLogisticDistribution.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogisticDistributionTest.java index 54e90417..b6084401 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestLogisticDistribution.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/LogisticDistributionTest.java @@ -32,8 +32,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * The reference values were computed using GNU R and SciPy. * * @author Erich Schubert + * @since 0.6.0 */ -public class TestLogisticDistribution extends AbstractDistributionTest implements JUnit4Test { +public class LogisticDistributionTest extends AbstractDistributionTest implements JUnit4Test { public static final double[] P_CDFPDF = { // 1e-10, 1e-05, 0.1, 0.1234567, 0.2, 0.271828182846, 0.3, 0.314159265359, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.71828182846, 3.14159265359 // }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestNormalDistribution.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/NormalDistributionTest.java index 79693a60..1a301f3b 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestNormalDistribution.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/NormalDistributionTest.java @@ -32,8 +32,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * The reference values were computed using GNU R and SciPy. * * @author Erich Schubert + * @since 0.5.0 */ -public class TestNormalDistribution extends AbstractDistributionTest implements JUnit4Test { +public class NormalDistributionTest extends AbstractDistributionTest implements JUnit4Test { public static final double[] P_CDFPDF = { // 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 1e-05, 1e-10, 0.1234567, 3.14159265359, 2.71828182846, 0.314159265359, 0.271828182846 // }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/UniformDistributionTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/UniformDistributionTest.java new file mode 100644 index 00000000..84bff909 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/UniformDistributionTest.java @@ -0,0 +1,91 @@ +package de.lmu.ifi.dbs.elki.math.statistics.distribution; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; + +/** + * Unit test for the Uniform distribution in ELKI. + * + * @author Erich Schubert + * @since 0.7.1 + */ +public class UniformDistributionTest extends AbstractDistributionTest implements JUnit4Test { + public static final double[] P_CDFPDF = { // + 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 1e-05, 1e-10, 0.1234567, 3.14159265359, 2.71828182846, 0.314159265359, 0.271828182846 // + }; + + public static final double[] P_PROBIT = { // + 0.0001, 0.001, 0.01, 0.1, 0.25, 0.5, 0.75, 0.9, 0.99, 0.999, 0.9999 // + }; + + @Test + public void testPDF() { + double[] buf = new double[P_CDFPDF.length]; + for(double l : new double[] { -1, 0, .1, 1 }) { + for(double h : new double[] { -1, 0, .1, 1, 2, 10 }) { + if(l < h) { + double w = h - l; + for(int i = 0; i < P_CDFPDF.length; i++) { + buf[i] = (P_CDFPDF[i] >= l && P_CDFPDF[i] < h) ? 1. / w : 0.; + } + checkPDF(new UniformDistribution(l, h), P_CDFPDF, buf, 1e-15); + } + } + } + } + + @Test + public void testCDF() { + double[] buf = new double[P_CDFPDF.length]; + for(double l : new double[] { -1, 0, .1, 1 }) { + for(double h : new double[] { -1, 0, .1, 1, 2, 10 }) { + if(l < h) { + double w = h - l; + for(int i = 0; i < P_CDFPDF.length; i++) { + buf[i] = P_CDFPDF[i] <= l ? 0. : P_CDFPDF[i] >= h ? 1. : (P_CDFPDF[i] - l) / w; + } + checkCDF(new UniformDistribution(l, h), P_CDFPDF, buf, 1e-15); + } + } + } + } + + @Test + public void testProbit() { + double[] buf = new double[P_PROBIT.length]; + for(double l : new double[] { -1, 0, .1, 1 }) { + for(double h : new double[] { -1, 0, .1, 1, 2, 10 }) { + if(l < h) { + double w = h - l; + for(int i = 0; i < P_PROBIT.length; i++) { + buf[i] = l + P_PROBIT[i] * w; + } + checkQuantile(new UniformDistribution(l, h), P_PROBIT, buf, 1e-15); + } + } + } + } +}
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestWeibullDistribution.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/WeibullDistributionTest.java index e7aadbf5..e97d1006 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/TestWeibullDistribution.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/distribution/WeibullDistributionTest.java @@ -32,8 +32,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * The reference values were computed using GNU R and SciPy. * * @author Erich Schubert + * @since 0.6.0 */ -public class TestWeibullDistribution extends AbstractDistributionTest implements JUnit4Test { +public class WeibullDistributionTest extends AbstractDistributionTest implements JUnit4Test { public static final double[] P_CDFPDF = { // 1e-10, 1e-05, 0.1, 0.1234567, 0.2, 0.271828182846, 0.3, 0.314159265359, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.71828182846, 3.14159265359 // }; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/tests/TestAndersonDarlingTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/tests/AndersonDarlingTestTest.java index 707d2093..09e8dd46 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/tests/TestAndersonDarlingTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/tests/AndersonDarlingTestTest.java @@ -33,8 +33,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Validate the Anderson Darling test. * * @author Erich Schubert + * @since 0.7.0 */ -public class TestAndersonDarlingTest implements JUnit4Test { +public class AndersonDarlingTestTest implements JUnit4Test { double[][] noncentral = { // { -1.877827740862672, -1.2459409569318343, -0.61175121460353787, -0.55626980422641181, // -0.35332777321703612, -0.24551480507545068, -0.23557108046219447, -0.080637593585376352, // diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/tests/TestStandardizedTwoSampleAndersonDarlingTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/tests/StandardizedTwoSampleAndersonDarlingTestTest.java index 5f9f76cf..f7cd0123 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/tests/TestStandardizedTwoSampleAndersonDarlingTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/statistics/tests/StandardizedTwoSampleAndersonDarlingTestTest.java @@ -33,8 +33,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Validate the two-sample anderson darling test. * * @author Erich Schubert + * @since 0.7.0 */ -public class TestStandardizedTwoSampleAndersonDarlingTest implements JUnit4Test { +public class StandardizedTwoSampleAndersonDarlingTestTest implements JUnit4Test { // Table 4, Scholz and Stephens (1987, p.922) double[][] pairs = { // { 38.7, 41.5, 43.8, 44.5, 45.5, 46.0, 47.7, 58.0 },// diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestWeightFunctions.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/weightfunctions/WeightFunctionsTest.java index 3866f35a..ceb00e8a 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/math/TestWeightFunctions.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/math/weightfunctions/WeightFunctionsTest.java @@ -1,4 +1,4 @@ -package de.lmu.ifi.dbs.elki.math; +package de.lmu.ifi.dbs.elki.math.weightfunctions; /* This file is part of ELKI: @@ -41,9 +41,10 @@ import de.lmu.ifi.dbs.elki.math.linearalgebra.pca.weightfunctions.WeightFunction * JUnit test to assert consistency of a couple of Weight functions * * @author Erich Schubert + * @since 0.2 * */ -public class TestWeightFunctions implements JUnit4Test { +public class WeightFunctionsTest implements JUnit4Test { /** * Just a 'boring' value test for completeness. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/persistent/TestByteArrayUtil.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/persistent/ByteArrayUtilTest.java index 80a4abf2..b85ce316 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/persistent/TestByteArrayUtil.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/persistent/ByteArrayUtilTest.java @@ -35,8 +35,9 @@ import de.lmu.ifi.dbs.elki.utilities.io.ByteArrayUtil; * Test some of the varint functions. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestByteArrayUtil implements JUnit4Test { +public class ByteArrayUtilTest implements JUnit4Test { /** * Test the Varint functions */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/persistent/TestOnDiskArray.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/persistent/OnDiskArrayTest.java index e0948ea8..a67ad5e6 100755 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/persistent/TestOnDiskArray.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/persistent/OnDiskArrayTest.java @@ -38,9 +38,10 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Test to validate proper OnDiskArray operation. * * @author Erich Schubert + * @since 0.2 */ // TODO: also test with a static sample file. -public class TestOnDiskArray implements JUnit4Test { +public class OnDiskArrayTest implements JUnit4Test { File file = new File("OnDiskArrayTestFile.test.dat"); /** diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/persistent/TestOnDiskUpperTriangleMatrix.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/persistent/OnDiskUpperTriangleMatrixTest.java index e87c1d47..ade4be8e 100755 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/persistent/TestOnDiskUpperTriangleMatrix.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/persistent/OnDiskUpperTriangleMatrixTest.java @@ -37,10 +37,11 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Test the on-disk OnDiskUpperTriangleMatrix class. * * @author Erich Schubert + * @since 0.2 * */ // TODO: also test with a static sample file. -public class TestOnDiskUpperTriangleMatrix implements JUnit4Test { +public class OnDiskUpperTriangleMatrixTest implements JUnit4Test { static File file = new File("UpperTriangleTestFile.test.dat"); /** diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/TestBitsUtil.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/BitsUtilTest.java index 274f5c30..879c4194 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/TestBitsUtil.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/BitsUtilTest.java @@ -34,7 +34,13 @@ import org.junit.Test; import de.lmu.ifi.dbs.elki.JUnit4Test; import de.lmu.ifi.dbs.elki.utilities.BitsUtil; -public class TestBitsUtil implements JUnit4Test { +/** + * Test bit manipulation code. + * + * @author Erich Schubert + * @since 0.5.0 + */ +public class BitsUtilTest implements JUnit4Test { @Test public void testAgainstBigInteger() { BigInteger bigint = new BigInteger("123"); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/TestFormatUtil.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/FormatUtilTest.java index fb0c9d37..7b1e3cae 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/TestFormatUtil.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/FormatUtilTest.java @@ -30,7 +30,13 @@ import org.junit.Test; import de.lmu.ifi.dbs.elki.JUnit4Test; -public class TestFormatUtil implements JUnit4Test { +/** + * Test output formatting. + * + * @author Erich Schubert + * @since 0.6.0 + */ +public class FormatUtilTest implements JUnit4Test { @Test public void testParseDouble() { assertEquals(0., FormatUtil.parseDouble("0"), 0.); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/TestQuickSelect.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/QuickSelectTest.java index eb921dc7..77061517 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/TestQuickSelect.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/QuickSelectTest.java @@ -24,8 +24,10 @@ package de.lmu.ifi.dbs.elki.utilities.datastructures; */ import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; import java.util.Arrays; +import java.util.List; import java.util.Random; import org.junit.Test; @@ -36,8 +38,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Test the QuickSelect math class. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestQuickSelect implements JUnit4Test { +public class QuickSelectTest implements JUnit4Test { /** * Array size to use. */ @@ -107,6 +110,11 @@ public class TestQuickSelect implements JUnit4Test { public void testTies() { double data[] = new double[] { 0.1, 0.1, 0.9, 0.9, 0.5, 0.9, 0.1, 0.1, 0.1, 0.9, 0.9, 0.9, 0.9, 0.1, 0.1 }; assertEquals("Full median incorrect.", 0.5, QuickSelect.median(data), Double.MIN_VALUE); + int half = data.length >> 1; + for (int i = 0; i < data.length; i++) { + assertTrue("Not partially sorted.", data[i] <= data[half] || i > half); + assertTrue("Not partially sorted.", data[i] >= data[half] || i < half); + } } @Test(timeout = 500) @@ -116,5 +124,35 @@ public class TestQuickSelect implements JUnit4Test { // Run QuickSelect QuickSelect.median(data); + int half = data.length >> 1; + for (int i = 0; i < data.length; i++) { + assertTrue("Not partially sorted.", data[i] <= data[half] || i > half); + assertTrue("Not partially sorted.", data[i] >= data[half] || i < half); + } + } + + @Test + public void testTiesInteger() { + int data[] = new int[] { 1, 1, 9, 9, 5, 9, 1, 1, 1, 9, 9, 9, 9, 1, 1 }; + final int half = data.length >> 1; + QuickSelect.quickSelect(data, QuickSelect.INTEGER_ADAPTER, 0, data.length, half); + for (int i = 0; i < data.length; i++) { + assertTrue("Not partially sorted.", data[i] <= data[half] || i > half); + assertTrue("Not partially sorted.", data[i] >= data[half] || i < half); + } + assertEquals("Full median incorrect.", 5, data[half]); } + + @Test + public void testTiesIntegerList() { + List<Integer> data = Arrays.asList(new Integer[] { 1, 1, 9, 9, 5, 9, 1, 1, 1, 9, 9, 9, 9, 1, 1 }); + final int half = data.size() >> 1; + QuickSelect.quickSelect(data, half); + for (int i = 0; i < data.size(); i++) { + assertTrue("Not partially sorted.", data.get(i) <= data.get(half) || i > half); + assertTrue("Not partially sorted.", data.get(i) >= data.get(half) || i < half); + } + assertEquals("Full median incorrect.", 5, data.get(half).intValue()); + } + }
\ No newline at end of file diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/DoubleArrayTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/DoubleArrayTest.java new file mode 100644 index 00000000..1ddea4f6 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/DoubleArrayTest.java @@ -0,0 +1,65 @@ +package de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike; +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2016 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; + +import java.util.Random; + +import org.junit.Test; + +/** + * Unit test for this arraylist of primitive doubles. + * + * @author Erich Schubert + * @since 0.7.1 + */ +public class DoubleArrayTest { + @Test + public void basicTest() { + DoubleArray arr = new DoubleArray(11); + assertTrue("Allocation does not match.", arr.data.length == 11); + assertTrue("Initial size is not empty.", arr.size() == 0); + + Random r = new Random(0L); + for(int i = 0; i < 11; i++) { + arr.add(r.nextDouble()); + } + assertTrue("Array is not full.", arr.data.length == arr.size()); + arr.add(r.nextDouble()); + assertEquals("Allocation does not match after resize.", 17, arr.data.length); + for(int i = 0; i < 81; i++) { + arr.add(r.nextDouble()); + } + assertEquals("Array does not have expected size.", 11 + 1 + 81, arr.size()); + arr.sort(); + assertEquals("Allocation does not match after resize.", 139, arr.data.length); + double prev = arr.get(0); + for(int i = 1; i < arr.size(); i++) { + double next = arr.get(i); + assertTrue("Array is not sorted.", prev <= next); + prev = next; + } + } +} diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/IntegerArrayTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/IntegerArrayTest.java new file mode 100644 index 00000000..a3949206 --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arraylike/IntegerArrayTest.java @@ -0,0 +1,65 @@ +package de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike; +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2016 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; + +import java.util.Random; + +import org.junit.Test; + +/** + * Unit test for this arraylist of primitive ints. + * + * @author Erich Schubert + * @since 0.7.1 + */ +public class IntegerArrayTest { + @Test + public void basicTest() { + IntegerArray arr = new IntegerArray(11); + assertTrue("Allocation does not match.", arr.data.length == 11); + assertTrue("Initial size is not empty.", arr.size() == 0); + + Random r = new Random(0L); + for(int i = 0; i < 11; i++) { + arr.add(r.nextInt()); + } + assertTrue("Array is not full.", arr.data.length == arr.size()); + arr.add(r.nextInt()); + assertEquals("Allocation does not match after resize.", 17, arr.data.length); + for(int i = 0; i < 81; i++) { + arr.add(r.nextInt()); + } + assertEquals("Array does not have expected size.", 11 + 1 + 81, arr.size()); + arr.sort(); + assertEquals("Allocation does not match after resize.", 139, arr.data.length); + int prev = arr.get(0); + for(int i = 1; i < arr.size(); i++) { + int next = arr.get(i); + assertTrue("Array is not sorted.", prev <= next); + prev = next; + } + } +} diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/TestDoubleIntegerArrayQuickSort.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/DoubleIntegerArrayQuickSortTest.java index 4db9b371..043e91dc 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/TestDoubleIntegerArrayQuickSort.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/DoubleIntegerArrayQuickSortTest.java @@ -35,8 +35,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Test the integer array (index array) quick sort. * * @author Erich Schubert + * @since 0.7.0 */ -public class TestDoubleIntegerArrayQuickSort implements JUnit4Test { +public class DoubleIntegerArrayQuickSortTest implements JUnit4Test { /** * Array size to use. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/TestIntegerArrayQuickSort.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/IntegerArrayQuickSortTest.java index f6dce701..0e5ee922 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/TestIntegerArrayQuickSort.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/IntegerArrayQuickSortTest.java @@ -35,8 +35,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Test the integer array (index array) quick sort. * * @author Erich Schubert + * @since 0.7.0 */ -public class TestIntegerArrayQuickSort implements JUnit4Test { +public class IntegerArrayQuickSortTest implements JUnit4Test { /** * Array size to use. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestDoubleHeap.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleHeapTest.java index 4e147faf..50fd4176 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestDoubleHeap.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleHeapTest.java @@ -35,8 +35,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Perform standard unit tests on the double-indexed heap structures. * * @author Erich Schubert + * @since 0.5.5 */ -public class TestDoubleHeap implements JUnit4Test { +public class DoubleHeapTest implements JUnit4Test { @Test public void testDoubleMinHeap() { Random r = new Random(); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestDoubleObjectHeaps.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleObjectHeapsTest.java index 31d3d7a5..03b069be 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestDoubleObjectHeaps.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/DoubleObjectHeapsTest.java @@ -35,8 +35,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * Perform standard unit tests on the double-object heap structures. * * @author Erich Schubert + * @since 0.5.5 */ -public class TestDoubleObjectHeaps implements JUnit4Test { +public class DoubleObjectHeapsTest implements JUnit4Test { @Test public void testDoubleObjMinHeap() { Random r = new Random(); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestHeapPerformance.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/HeapPerformanceTest.java index 554e61b5..87a61b39 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestHeapPerformance.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/HeapPerformanceTest.java @@ -33,23 +33,26 @@ import java.util.PriorityQueue; import java.util.Queue; import java.util.Random; +import org.junit.Ignore; import org.junit.Test; /** * Unit test to ensure that our heap is not significantly worse than SUN javas * regular PriorityQueue. - * + * * @author Erich Schubert + * @since 0.5.0 */ -public class TestHeapPerformance { +public class HeapPerformanceTest { final private int queueSize = 200000; final private int preiterations = 20; - + final private int iterations = 200; final private long seed = 123456L; + @Ignore @Test public void testRuntime() throws Exception { // prepare the data set @@ -93,8 +96,8 @@ public class TestHeapPerformance { long htime = System.nanoTime() - hstart; System.err.println("Heap performance test: us: " + htime*1E-9 + " java: " + pqtime*1E-9); - assertTrue("Heap performance regression - run test individually, since the hotspot optimizations may make the difference! " + htime + " >>= " + pqtime, htime < 1.05 * pqtime); - // 1.05 allows some difference in measuring + assertTrue("Heap performance regression - run test individually, since the hotspot optimizations may make the difference! " + htime + " >>= " + pqtime, htime < 1.1 * pqtime); + // 1.1 allows some difference in measuring, which can occur e.g. due to Jacoco instrumentation } private void testHeap(final List<Integer> elements, ComparableMinHeap<Integer> pq) { diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestHeap.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/HeapTest.java index f28750eb..40ab27c4 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestHeap.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/HeapTest.java @@ -34,8 +34,9 @@ import org.junit.Test; * Test the in-memory heap class. * * @author Erich Schubert + * @since 0.5.0 */ -public class TestHeap { +public class HeapTest { /** * Puts 10 integers into both an ascending and a descending heap and verifies * they come out in sequence. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestIntegerHeap.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerHeapTest.java index e5038142..3d24a247 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestIntegerHeap.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerHeapTest.java @@ -34,8 +34,9 @@ import org.junit.Test; * Test the in-memory heap class. * * @author Erich Schubert + * @since 0.5.0 */ -public class TestIntegerHeap { +public class IntegerHeapTest { /** * Puts 10 integers into both an ascending and a descending heap and verifies * they come out in sequence. diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestIntegerMinHeapPerformance.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerMinHeapPerformanceTest.java index 49a37330..89f21a2c 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestIntegerMinHeapPerformance.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/IntegerMinHeapPerformanceTest.java @@ -40,8 +40,9 @@ import org.junit.Test; * regular PriorityQueue. * * @author Erich Schubert + * @since 0.5.0 */ -public class TestIntegerMinHeapPerformance { +public class IntegerMinHeapPerformanceTest { final private int queueSize = 100000; final private int iterations = 20; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestTiedTopBoundedHeap.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TiedTopBoundedHeapTest.java index cab43e6e..7058e111 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestTiedTopBoundedHeap.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TiedTopBoundedHeapTest.java @@ -36,8 +36,9 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.heap.TiedTopBoundedHeap; * Test the in-memory bounded heap class. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestTiedTopBoundedHeap { +public class TiedTopBoundedHeapTest { /** * Test bounded heap */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestTiedTopBoundedUpdatableHeap.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TiedTopBoundedUpdatableHeapTest.java index 9b6a48d8..d1de52d6 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestTiedTopBoundedUpdatableHeap.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TiedTopBoundedUpdatableHeapTest.java @@ -34,7 +34,13 @@ import org.junit.Test; import de.lmu.ifi.dbs.elki.JUnit4Test; -public class TestTiedTopBoundedUpdatableHeap implements JUnit4Test { +/** + * Test the specialized heap structures. + * + * @author Erich Schubert + * @since 0.5.0 + */ +public class TiedTopBoundedUpdatableHeapTest implements JUnit4Test { @Test public void testTiedTopBoundedUpdatableHeap() { final int iters = 100; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestTopBoundedHeap.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TopBoundedHeapTest.java index 73271e44..c2305bcf 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestTopBoundedHeap.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TopBoundedHeapTest.java @@ -36,8 +36,9 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.heap.TopBoundedHeap; * Test the in-memory bounded heap class. * * @author Erich Schubert + * @since 0.4.0 */ -public class TestTopBoundedHeap { +public class TopBoundedHeapTest { /** * Test bounded heap */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestUpdatableHeap.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/UpdatableHeapTest.java index f1a68171..1c449781 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/TestUpdatableHeap.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/heap/UpdatableHeapTest.java @@ -33,7 +33,13 @@ import org.junit.Test; import de.lmu.ifi.dbs.elki.JUnit4Test; -public class TestUpdatableHeap implements JUnit4Test { +/** + * Test the updateable heap used by OPTICS. + * + * @author Erich Schubert + * @since 0.5.0 + */ +public class UpdatableHeapTest implements JUnit4Test { @Test public void testUpdatableHeap() { final int iters = 100; diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/TestHashMapHierarchy.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/HashMapHierarchyTest.java index 1f4beb40..ec273988 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/TestHashMapHierarchy.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/HashMapHierarchyTest.java @@ -38,8 +38,9 @@ import de.lmu.ifi.dbs.elki.utilities.datastructures.hierarchy.Hierarchy.Iter; * Test the main hierarchy implementation. * * @author Erich Schubert + * @since 0.6.0 */ -public class TestHashMapHierarchy implements JUnit4Test { +public class HashMapHierarchyTest implements JUnit4Test { @Test public void testEmpty() { HashMapHierarchy<Object> hier = new HashMapHierarchy<>(); diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/TestDoubleHistogram.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleHistogramTest.java index 8830fd9b..f558acaa 100755 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/TestDoubleHistogram.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/DoubleHistogramTest.java @@ -34,8 +34,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * JUnit test to test the {@link ReplacingHistogram} class. * * @author Erich Schubert + * @since 0.2 */ -public class TestDoubleHistogram implements JUnit4Test { +public class DoubleHistogramTest implements JUnit4Test { /** * Test that adds some data to the histogram and compares results. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/TestFlexiHistogram.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/FlexiHistogramTest.java index 3410ce69..b40413fd 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/TestFlexiHistogram.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/FlexiHistogramTest.java @@ -36,8 +36,9 @@ import de.lmu.ifi.dbs.elki.JUnit4Test; * JUnit test to test the {@link AbstractObjDynamicHistogram} class. * * @author Erich Schubert + * @since 0.5.5 */ -public class TestFlexiHistogram implements JUnit4Test { +public class FlexiHistogramTest implements JUnit4Test { /** * Test that adds some data to the histogram and compares results. */ diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionRangeDBIDsTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionRangeDBIDsTest.java index 242752a0..3405bbf6 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionRangeDBIDsTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionRangeDBIDsTest.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; * * @author Evgeniy Faerman * @author Erich Schubert + * @since 0.7.0 */ public class WeightedQuickUnionRangeDBIDsTest { @Test diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionStaticDBIDsTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionStaticDBIDsTest.java index d1778f6a..d2cb370f 100644 --- a/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionStaticDBIDsTest.java +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/utilities/datastructures/unionfind/WeightedQuickUnionStaticDBIDsTest.java @@ -40,6 +40,7 @@ import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; * * @author Evgeniy Faerman * @author Erich Schubert + * @since 0.7.0 */ public class WeightedQuickUnionStaticDBIDsTest { @Test diff --git a/elki/src/test/resources/de/lmu/ifi/dbs/elki/logging/logging.properties b/elki/src/test/resources/de/lmu/ifi/dbs/elki/logging/logging.properties new file mode 100644 index 00000000..ff2959c0 --- /dev/null +++ b/elki/src/test/resources/de/lmu/ifi/dbs/elki/logging/logging.properties @@ -0,0 +1,13 @@ +# +# Logging configuration for code coverage and unit testing +# +handlers = + +# Common values include: SEVERE, WARNING +# And for debugging: INFO, FINE, FINER, FINEST +# Configure debug levels: +.level = FINEST +de.lmu.ifi.dbs.elki.level = FINEST + +# general debugging flag +debug = true
\ No newline at end of file @@ -1,9 +1,10 @@ +<?xml version='1.0' encoding='UTF-8'?> <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> <modelVersion>4.0.0</modelVersion> <groupId>de.lmu.ifi.dbs.elki</groupId> - <version>0.7.0</version> + <version>0.7.1</version> <artifactId>elki-project</artifactId> <packaging>pom</packaging> @@ -23,13 +24,13 @@ <modules> <module>elki</module> - <module>addons/tutorial</module> <!-- Use PROFILES to enable further modules! --> </modules> <properties> <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> - <skipTests>true</skipTests> + <skipTests>false</skipTests> + <excludeTests>**/HeapPerformanceTest*</excludeTests> <elki.projdir>${basedir}</elki.projdir> <year>2015</year> </properties> @@ -38,9 +39,7 @@ <plugins> <!-- compilation --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-compiler-plugin</artifactId> - <version>3.0</version> <configuration> <useIncrementalCompilation>false</useIncrementalCompilation> <source>1.7</source> @@ -54,38 +53,37 @@ </plugin> <!-- unit tests --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-surefire-plugin</artifactId> - <version>2.7.2</version> <configuration> <!-- to have the desired paths to the data files --> <workingDirectory>${project.build.testOutputDirectory}</workingDirectory> <skipTests>${skipTests}</skipTests> + <failIfNoTests>false</failIfNoTests> + <excludes> + <exclude>${excludeTests}</exclude> + </excludes> </configuration> </plugin> - <!-- Include more metadata in the jar --> + <!-- Include more metadata in the jar, enable indexing. --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-jar-plugin</artifactId> - <version>2.4</version> <configuration> <archive> <manifestFile>${elki.projdir}/elki/src/main/resources/META-INF/MANIFEST.MF</manifestFile> <manifest> <addDefaultImplementationEntries>true</addDefaultImplementationEntries> </manifest> + <index>true</index> </archive> </configuration> </plugin> <!-- Dependencies --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-dependency-plugin</artifactId> - <version>2.8</version> <executions> <execution> <id>copy-dependencies</id> - <phase>process-sources</phase> + <phase>package</phase> <goals> <goal>copy-dependencies</goal> </goals> @@ -98,9 +96,7 @@ </plugin> <!-- Source code packaging --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-source-plugin</artifactId> - <version>2.2.1</version> <executions> <execution> <id>attach-sources</id> @@ -113,7 +109,6 @@ <!-- Additional JavaDoc resources to install --> <plugin> <artifactId>maven-resources-plugin</artifactId> - <version>2.7</version> <executions> <execution> <id>copy-resources</id> @@ -140,15 +135,13 @@ </plugin> <!-- JavaDoc generation --> <plugin> - <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-javadoc-plugin</artifactId> - <version>2.10.1</version> <executions> <execution> <id>attach-javadocs</id> <goals> <goal>aggregate</goal> - <goal>javadoc-no-fork</goal> + <goal>javadoc</goal> <goal>jar</goal> </goals> </execution> @@ -204,9 +197,10 @@ <packages>tutorial:tutorial.*</packages> </group> </groups> + <docencoding>UTF-8</docencoding> <header><![CDATA[<img src="{@docRoot}/figures/elki-logo-200.png" width="200">]]></header> <footer><![CDATA[ELKI Version ${project.version}]]></footer> - <bottom><![CDATA[Copyright © ${year} <a href="http://elki.dbs.ifi.lmu.de/">ELKI Development Team</a>, <a href="http://www.dbs.ifi.lmu.de/">Lehr- und Forschungseinheit für Datenbanksysteme</a>, <a href="http://www.lmu.de/">Ludwig-Maximilians-Universität München</a>. <a href="http://elki.dbs.ifi.lmu.de/wiki/License">License information.</a>]]></bottom> + <bottom><![CDATA[Copyright © ${year} <a href="http://elki.dbs.ifi.lmu.de/">ELKI Development Team</a>, <a href="http://www.dbs.ifi.lmu.de/">Lehr- und Forschungseinheit für Datenbanksysteme</a>, <a href="http://www.lmu.de/">Ludwig-Maximilians-Universität München</a>. <a href="http://elki.dbs.ifi.lmu.de/wiki/License">License information.</a>]]></bottom> <links> <!-- To link to related (external) JavaDoc --> <link>http://trove4j.sourceforge.net/javadocs/</link> @@ -216,6 +210,57 @@ </configuration> </plugin> </plugins> + <pluginManagement> + <!-- Plugin version configuration: --> + <plugins> + <!-- compilation --> + <plugin> + <artifactId>maven-compiler-plugin</artifactId> + <version>3.0</version> + </plugin> + <!-- unit tests --> + <plugin> + <artifactId>maven-surefire-plugin</artifactId> + <version>2.17</version> + </plugin> + <!-- Jar packaging --> + <plugin> + <artifactId>maven-jar-plugin</artifactId> + <version>2.4</version> + </plugin> + <!-- Dependencies --> + <plugin> + <artifactId>maven-dependency-plugin</artifactId> + <version>2.8</version> + </plugin> + <!-- Running of additional checks --> + <plugin> + <groupId>org.codehaus.mojo</groupId> + <artifactId>exec-maven-plugin</artifactId> + <version>1.3.2</version> + </plugin> + <!-- used for making a directory in batik visualization addon --> + <plugin> + <artifactId>maven-antrun-plugin</artifactId> + <version>1.7</version> + </plugin> + <!-- Source code packaging --> + <plugin> + <artifactId>maven-source-plugin</artifactId> + <version>2.2.1</version> + </plugin> + <!-- Additional resources installation --> + <plugin> + <artifactId>maven-resources-plugin</artifactId> + <version>2.7</version> + </plugin> + <!-- Javadoc --> + <plugin> + <artifactId>maven-javadoc-plugin</artifactId> + <version>2.10.1</version> + </plugin> + </plugins> + </pluginManagement> </build> <profiles> @@ -232,6 +277,21 @@ <modules> <module>addons/batikvis</module> </modules> + <activation> + <activeByDefault>true</activeByDefault> + </activation> + </profile> + <!-- Tutorial code profile --> + <profile> + <id>tutorial</id> + <modules> + <module>addons/tutorial</module> + <!-- since tutorial users will want to see visualizations: --> + <module>addons/batikvis</module> + </modules> + <activation> + <activeByDefault>true</activeByDefault> + </activation> </profile> <!-- LibSVM outlier detection --> <profile> @@ -239,6 +299,9 @@ <modules> <module>addons/libsvm</module> </modules> + <activation> + <activeByDefault>true</activeByDefault> + </activation> </profile> <!-- Image search --> <profile> @@ -282,7 +345,13 @@ </configuration> </plugin> <plugin> - <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-release-plugin</artifactId> + <version>2.3.2</version> + <configuration> + <mavenExecutorId>forked-path</mavenExecutorId> + </configuration> + </plugin> + <plugin> <artifactId>maven-gpg-plugin</artifactId> <version>1.5</version> <executions> @@ -302,6 +371,32 @@ </plugins> </build> </profile> + <profile> + <id>codecov</id> + <build> + <plugins> + <plugin> + <groupId>org.jacoco</groupId> + <artifactId>jacoco-maven-plugin</artifactId> + <version>0.7.5.201505241946</version> + <executions> + <execution> + <goals> + <goal>prepare-agent</goal> + </goals> + </execution> + <execution> + <id>report</id> + <phase>test</phase> + <goals> + <goal>report</goal> + </goals> + </execution> + </executions> + </plugin> + </plugins> + </build> + </profile> </profiles> <distributionManagement> @@ -339,6 +434,12 @@ <dependency> <groupId>org.apache.xmlgraphics</groupId> + <artifactId>batik-codec</artifactId> + <version>[1.7,1.9)</version> + </dependency> + + <dependency> + <groupId>org.apache.xmlgraphics</groupId> <artifactId>xmlgraphics-commons</artifactId> <version>[2,3)</version> </dependency> |