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authorAndrej Shadura <andrewsh@debian.org>2019-03-09 22:30:28 +0000
committerAndrej Shadura <andrewsh@debian.org>2019-03-09 22:30:28 +0000
commitcde76aeb42240f7270bc6605c606ae07d2dc5a7d (patch)
treec3ebf1d7745224f524da31dbabc5d76b9ea75916 /src/de/lmu/ifi/dbs/elki/index/preprocessed/subspaceproj/AbstractSubspaceProjectionIndex.java
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+package de.lmu.ifi.dbs.elki.index.preprocessed.subspaceproj;
+/*
+This file is part of ELKI:
+Environment for Developing KDD-Applications Supported by Index-Structures
+
+Copyright (C) 2011
+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.List;
+
+import de.lmu.ifi.dbs.elki.algorithm.clustering.AbstractProjectedDBSCAN;
+import de.lmu.ifi.dbs.elki.data.NumberVector;
+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.datastore.DataStoreFactory;
+import de.lmu.ifi.dbs.elki.database.datastore.DataStoreUtil;
+import de.lmu.ifi.dbs.elki.database.ids.DBID;
+import de.lmu.ifi.dbs.elki.database.query.DistanceResultPair;
+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.distance.distancefunction.EuclideanDistanceFunction;
+import de.lmu.ifi.dbs.elki.distance.distancevalue.Distance;
+import de.lmu.ifi.dbs.elki.index.preprocessed.AbstractPreprocessorIndex;
+import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress;
+import de.lmu.ifi.dbs.elki.math.linearalgebra.ProjectionResult;
+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.ExceptionMessages;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.Parameterizable;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.GreaterConstraint;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DistanceParameter;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter;
+
+/**
+ * Abstract base class for a local PCA based index.
+ *
+ * @author Elke Achtert
+ * @author Erich Schubert
+ *
+ * @apiviz.has DistanceFunction
+ *
+ * @param <NV> Vector type
+ */
+@Title("Local PCA Preprocessor")
+@Description("Materializes the local PCA and the locally weighted matrix of objects of a database.")
+public abstract class AbstractSubspaceProjectionIndex<NV extends NumberVector<?, ?>, D extends Distance<D>, P extends ProjectionResult> extends AbstractPreprocessorIndex<NV, P> implements SubspaceProjectionIndex<NV, P> {
+ /**
+ * Contains the value of parameter epsilon;
+ */
+ protected D epsilon;
+
+ /**
+ * The distance function for the variance analysis.
+ */
+ protected DistanceFunction<NV, D> rangeQueryDistanceFunction;
+
+ /**
+ * Holds the value of parameter minpts.
+ */
+ protected int minpts;
+
+ /**
+ * Constructor.
+ *
+ * @param relation Relation
+ * @param epsilon Maximum Epsilon
+ * @param rangeQueryDistanceFunction range query
+ * @param minpts Minpts
+ */
+ public AbstractSubspaceProjectionIndex(Relation<NV> relation, D epsilon, DistanceFunction<NV, D> rangeQueryDistanceFunction, int minpts) {
+ super(relation);
+ this.epsilon = epsilon;
+ this.rangeQueryDistanceFunction = rangeQueryDistanceFunction;
+ this.minpts = minpts;
+ }
+
+ /**
+ * Preprocessing step.
+ */
+ protected void preprocess() {
+ if(relation == null || relation.size() <= 0) {
+ throw new IllegalArgumentException(ExceptionMessages.DATABASE_EMPTY);
+ }
+ if(storage != null) {
+ // Preprocessor was already run.
+ return;
+ }
+ storage = DataStoreUtil.makeStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, ProjectionResult.class);
+
+ long start = System.currentTimeMillis();
+ RangeQuery<NV, D> rangeQuery = QueryUtil.getRangeQuery(relation, rangeQueryDistanceFunction);
+
+ FiniteProgress progress = getLogger().isVerbose() ? new FiniteProgress(this.getClass().getName(), relation.size(), getLogger()) : null;
+ for(DBID id : relation.iterDBIDs()) {
+ List<DistanceResultPair<D>> neighbors = rangeQuery.getRangeForDBID(id, epsilon);
+
+ final P pres;
+ if(neighbors.size() >= minpts) {
+ pres = computeProjection(id, neighbors, relation);
+ }
+ else {
+ DistanceResultPair<D> firstQR = neighbors.get(0);
+ neighbors = new ArrayList<DistanceResultPair<D>>();
+ neighbors.add(firstQR);
+ pres = computeProjection(id, neighbors, relation);
+ }
+ storage.put(id, pres);
+
+ if(progress != null) {
+ progress.incrementProcessed(getLogger());
+ }
+ }
+ if(progress != null) {
+ progress.ensureCompleted(getLogger());
+ }
+
+ long end = System.currentTimeMillis();
+ // TODO: re-add timing code!
+ if(true) {
+ long elapsedTime = end - start;
+ getLogger().verbose(this.getClass().getName() + " runtime: " + elapsedTime + " milliseconds.");
+ }
+ }
+
+ @Override
+ public P getLocalProjection(DBID objid) {
+ if(storage == null) {
+ preprocess();
+ }
+ return storage.get(objid);
+ }
+
+ /**
+ * This method implements the type of variance analysis to be computed for a
+ * given point.
+ * <p/>
+ * Example1: for 4C, this method should implement a PCA for the given point.
+ * Example2: for PreDeCon, this method should implement a simple axis-parallel
+ * variance analysis.
+ *
+ * @param id the given point
+ * @param neighbors the neighbors as query results of the given point
+ * @param relation the database for which the preprocessing is performed
+ *
+ * @return local subspace projection
+ */
+ protected abstract P computeProjection(DBID id, List<DistanceResultPair<D>> neighbors, Relation<NV> relation);
+
+ /**
+ * Factory class
+ *
+ * @author Erich Schubert
+ *
+ * @apiviz.stereotype factory
+ * @apiviz.uses AbstractSubspaceProjectionIndex oneway - - «create»
+ */
+ public static abstract class Factory<NV extends NumberVector<?, ?>, D extends Distance<D>, I extends AbstractSubspaceProjectionIndex<NV, D, ?>> implements SubspaceProjectionIndex.Factory<NV, I>, Parameterizable {
+ /**
+ * Contains the value of parameter epsilon;
+ */
+ protected D epsilon;
+
+ /**
+ * The distance function for the variance analysis.
+ */
+ protected DistanceFunction<NV, D> rangeQueryDistanceFunction;
+
+ /**
+ * Holds the value of parameter minpts.
+ */
+ protected int minpts;
+
+ /**
+ * Constructor.
+ *
+ * @param epsilon
+ * @param rangeQueryDistanceFunction
+ * @param minpts
+ */
+ public Factory(D epsilon, DistanceFunction<NV, D> rangeQueryDistanceFunction, int minpts) {
+ super();
+ this.epsilon = epsilon;
+ this.rangeQueryDistanceFunction = rangeQueryDistanceFunction;
+ this.minpts = minpts;
+ }
+
+ @Override
+ public abstract I instantiate(Relation<NV> relation);
+
+ @Override
+ public TypeInformation getInputTypeRestriction() {
+ return TypeUtil.NUMBER_VECTOR_FIELD;
+ }
+
+ /**
+ * Parameterization class.
+ *
+ * @author Erich Schubert
+ *
+ * @apiviz.exclude
+ */
+ public static abstract class Parameterizer<NV extends NumberVector<?, ?>, D extends Distance<D>, C> extends AbstractParameterizer {
+ /**
+ * Contains the value of parameter epsilon;
+ */
+ protected D epsilon = null;
+
+ /**
+ * The distance function for the variance analysis.
+ */
+ protected DistanceFunction<NV, D> rangeQueryDistanceFunction = null;
+
+ /**
+ * Holds the value of parameter minpts.
+ */
+ protected int minpts = 0;
+
+ @Override
+ protected void makeOptions(Parameterization config) {
+ super.makeOptions(config);
+ configRangeQueryDistanceFunction(config);
+ configEpsilon(config, rangeQueryDistanceFunction);
+ configMinPts(config);
+ }
+
+ protected void configRangeQueryDistanceFunction(Parameterization config) {
+ ObjectParameter<DistanceFunction<NV, D>> rangeQueryDistanceP = new ObjectParameter<DistanceFunction<NV, D>>(AbstractProjectedDBSCAN.INNER_DISTANCE_FUNCTION_ID, DistanceFunction.class, EuclideanDistanceFunction.class);
+ if(config.grab(rangeQueryDistanceP)) {
+ rangeQueryDistanceFunction = rangeQueryDistanceP.instantiateClass(config);
+ }
+ }
+
+ protected void configEpsilon(Parameterization config, DistanceFunction<NV, D> rangeQueryDistanceFunction) {
+ D distanceParser = rangeQueryDistanceFunction != null ? rangeQueryDistanceFunction.getDistanceFactory() : null;
+ DistanceParameter<D> epsilonP = new DistanceParameter<D>(AbstractProjectedDBSCAN.EPSILON_ID, distanceParser);
+ // parameter epsilon
+ if(config.grab(epsilonP)) {
+ epsilon = epsilonP.getValue();
+ }
+ }
+
+ protected void configMinPts(Parameterization config) {
+ IntParameter minptsP = new IntParameter(AbstractProjectedDBSCAN.MINPTS_ID, new GreaterConstraint(0));
+ if(config.grab(minptsP)) {
+ minpts = minptsP.getValue();
+ }
+ }
+ }
+ }
+} \ No newline at end of file