Import Debian changes 0.5.5-1

elki (0.5.5-1) unstable; urgency=low

  * New upstream release: 0.5.5 interim release.

1 files changed, 222 insertions, 0 deletions

diff --git a/src/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/SimpleOutlierEnsemble.java b/src/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/SimpleOutlierEnsemble.java
new file mode 100644
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+++ b/src/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/SimpleOutlierEnsemble.java
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+package de.lmu.ifi.dbs.elki.algorithm.outlier.meta;
+
+/*
+ This file is part of ELKI:
+ Environment for Developing KDD-Applications Supported by Index-Structures
+
+ Copyright (C) 2012
+ 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.AbstractAlgorithm;
+import de.lmu.ifi.dbs.elki.algorithm.Algorithm;
+import de.lmu.ifi.dbs.elki.algorithm.outlier.OutlierAlgorithm;
+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.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.WritableDoubleDataStore;
+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.ModifiableDBIDs;
+import de.lmu.ifi.dbs.elki.database.relation.MaterializedRelation;
+import de.lmu.ifi.dbs.elki.database.relation.Relation;
+import de.lmu.ifi.dbs.elki.logging.Logging;
+import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress;
+import de.lmu.ifi.dbs.elki.math.DoubleMinMax;
+import de.lmu.ifi.dbs.elki.result.Result;
+import de.lmu.ifi.dbs.elki.result.ResultUtil;
+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.ensemble.EnsembleVoting;
+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.ChainedParameterization;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectListParameter;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter;
+
+/**
+ * Simple outlier ensemble method.
+ * 
+ * @author Erich Schubert
+ * 
+ * @apiviz.composedOf EnsembleVoting
+ * @apiviz.uses OutlierResult oneway - - reads
+ * @apiviz.uses OutlierResult oneway - - «create»
+ */
+public class SimpleOutlierEnsemble extends AbstractAlgorithm<OutlierResult> implements OutlierAlgorithm {
+  /**
+   * The logger for this class.
+   */
+  private static final Logging LOG = Logging.getLogger(SimpleOutlierEnsemble.class);
+
+  /**
+   * The algorithms to run.
+   */
+  private List<OutlierAlgorithm> algorithms;
+
+  /**
+   * The voting in use.
+   */
+  private EnsembleVoting voting;
+
+  /**
+   * Constructor.
+   * 
+   * @param algorithms Algorithms to run
+   * @param voting Voting method
+   */
+  public SimpleOutlierEnsemble(List<OutlierAlgorithm> algorithms, EnsembleVoting voting) {
+    this.algorithms = algorithms;
+    this.voting = voting;
+  }
+
+  @Override
+  public OutlierResult run(Database database) throws IllegalStateException {
+    int num = algorithms.size();
+    // Run inner outlier algorithms
+    ModifiableDBIDs ids = DBIDUtil.newHashSet();
+    ArrayList<OutlierResult> results = new ArrayList<OutlierResult>(num);
+    {
+      FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Inner outlier algorithms", num, LOG) : null;
+      for (Algorithm alg : algorithms) {
+        Result res = alg.run(database);
+        List<OutlierResult> ors = ResultUtil.getOutlierResults(res);
+        for (OutlierResult or : ors) {
+          results.add(or);
+          ids.addDBIDs(or.getScores().getDBIDs());
+        }
+        if (prog != null) {
+          prog.incrementProcessed(LOG);
+        }
+      }
+      if (prog != null) {
+        prog.ensureCompleted(LOG);
+      }
+    }
+    // Combine
+    WritableDoubleDataStore sumscore = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_STATIC);
+    DoubleMinMax minmax = new DoubleMinMax();
+    {
+      FiniteProgress cprog = LOG.isVerbose() ? new FiniteProgress("Combining results", ids.size(), LOG) : null;
+      for (DBIDIter id = ids.iter(); id.valid(); id.advance()) {
+        double[] scores = new double[num];
+        int i = 0;
+        for (OutlierResult r : results) {
+          Double score = r.getScores().get(id);
+          if (score != null) {
+            scores[i] = score;
+            i++;
+          } else {
+            LOG.warning("DBID " + id + " was not given a score by result " + r);
+          }
+        }
+        if (i > 0) {
+          // Shrink array if necessary.
+          if (i < scores.length) {
+            scores = Arrays.copyOf(scores, i);
+          }
+          double combined = voting.combine(scores);
+          sumscore.putDouble(id, combined);
+          minmax.put(combined);
+        } else {
+          LOG.warning("DBID " + id + " was not given any score at all.");
+        }
+        if (cprog != null) {
+          cprog.incrementProcessed(LOG);
+        }
+      }
+      if (cprog != null) {
+        cprog.ensureCompleted(LOG);
+      }
+    }
+    OutlierScoreMeta meta = new BasicOutlierScoreMeta(minmax.getMin(), minmax.getMax());
+    Relation<Double> scores = new MaterializedRelation<Double>("Simple Outlier Ensemble", "ensemble-outlier", TypeUtil.DOUBLE, sumscore, ids);
+    return new OutlierResult(meta, scores);
+  }
+
+  @Override
+  protected Logging getLogger() {
+    return LOG;
+  }
+
+  @Override
+  public TypeInformation[] getInputTypeRestriction() {
+    TypeInformation[] trs = new TypeInformation[algorithms.size()];
+    for (int i = 0; i < trs.length; i++) {
+      // FIXME: what if an algorithm needs more than one input data source?
+      trs[i] = algorithms.get(i).getInputTypeRestriction()[0];
+    }
+    return TypeUtil.array(new CombinedTypeInformation(trs));
+  }
+
+  /**
+   * Parameterization class.
+   * 
+   * @author Erich Schubert
+   * 
+   * @apiviz.exclude
+   */
+  public static class Parameterizer extends AbstractParameterizer {
+    /**
+     * Voting strategy to use in the ensemble.
+     */
+    public static final OptionID VOTING_ID = new OptionID("ensemble.voting", "Voting strategy to use in the ensemble.");
+
+    /**
+     * The algorithms to run.
+     */
+    private List<OutlierAlgorithm> algorithms;
+
+    /**
+     * The voting in use.
+     */
+    private EnsembleVoting voting;
+
+    @Override
+    protected void makeOptions(Parameterization config) {
+      super.makeOptions(config);
+      ObjectListParameter<OutlierAlgorithm> algP = new ObjectListParameter<OutlierAlgorithm>(OptionID.ALGORITHM, OutlierAlgorithm.class);
+      if (config.grab(algP)) {
+        ListParameterization subconfig = new ListParameterization();
+        ChainedParameterization chain = new ChainedParameterization(subconfig, config);
+        chain.errorsTo(config);
+        algorithms = algP.instantiateClasses(chain);
+        subconfig.logAndClearReportedErrors();
+      }
+      ObjectParameter<EnsembleVoting> votingP = new ObjectParameter<EnsembleVoting>(VOTING_ID, EnsembleVoting.class);
+      if (config.grab(votingP)) {
+        voting = votingP.instantiateClass(config);
+      }
+    }
+
+    @Override
+    protected SimpleOutlierEnsemble makeInstance() {
+      return new SimpleOutlierEnsemble(algorithms, voting);
+    }
+  }
+}