Import Debian changes 0.6.0~beta2-1

elki (0.6.0~beta2-1) unstable; urgency=low

  * New upstream beta release.
  * 3DPC extension is not yet included.

1 files changed, 120 insertions, 0 deletions

diff --git a/src/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/SqrtJensenShannonDivergenceDistanceFunction.java b/src/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/SqrtJensenShannonDivergenceDistanceFunction.java
new file mode 100644
index 00000000..af0590fc
--- /dev/null
+++ b/src/de/lmu/ifi/dbs/elki/distance/distancefunction/probabilistic/SqrtJensenShannonDivergenceDistanceFunction.java
@@ -0,0 +1,120 @@
+package de.lmu.ifi.dbs.elki.distance.distancefunction.probabilistic;
+
+/*
+ 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 de.lmu.ifi.dbs.elki.data.NumberVector;
+import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractVectorDoubleDistanceFunction;
+import de.lmu.ifi.dbs.elki.utilities.documentation.Reference;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer;
+
+/**
+ * The square root of Jensen-Shannon divergence is metric.
+ * 
+ * Reference (proof of triangle inequality, distance called D_PQ):
+ * <p>
+ * D. M. Endres, J. E. Schindelin<br />
+ * A new metric for probability distributions<br />
+ * IEEE Transactions on Information Theory, 49(7).
+ * </p>
+ * 
+ * @author Erich Schubert
+ */
+@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 AbstractVectorDoubleDistanceFunction {
+  /**
+   * Static instance. Use this!
+   */
+  public static final SqrtJensenShannonDivergenceDistanceFunction STATIC = new SqrtJensenShannonDivergenceDistanceFunction();
+
+  /**
+   * Constructor for sqrt Jensen Shannon divergence.
+   * 
+   * @deprecated Use static instance!
+   */
+  @Deprecated
+  public SqrtJensenShannonDivergenceDistanceFunction() {
+    super();
+  }
+
+  @Override
+  public double doubleDistance(NumberVector<?> v1, NumberVector<?> v2) {
+    final int dim = dimensionality(v1, v2);
+    double agg = 0.;
+    for(int d = 0; d < dim; d++) {
+      final double xd = v1.doubleValue(d), yd = v2.doubleValue(d);
+      if(xd == yd) {
+        continue;
+      }
+      final double md = .5 * (xd + yd);
+      if(!(md > 0. || md < 0.)) {
+        continue;
+      }
+      if(xd > 0.) {
+        agg += xd * Math.log(xd / md);
+      }
+      if(yd > 0.) {
+        agg += yd * Math.log(yd / md);
+      }
+    }
+    return Math.sqrt(agg);
+  }
+
+  @Override
+  public boolean isMetric() {
+    return true;
+  }
+
+  @Override
+  public String toString() {
+    return "SqrtJensenShannonDivergenceDistance";
+  }
+
+  @Override
+  public boolean equals(Object obj) {
+    if(obj == null) {
+      return false;
+    }
+    if(obj == this) {
+      return true;
+    }
+    if(this.getClass().equals(obj.getClass())) {
+      return true;
+    }
+    return super.equals(obj);
+  }
+
+  /**
+   * Parameterization class, using the static instance.
+   * 
+   * @author Erich Schubert
+   * 
+   * @apiviz.exclude
+   */
+  public static class Parameterizer extends AbstractParameterizer {
+    @Override
+    protected SqrtJensenShannonDivergenceDistanceFunction makeInstance() {
+      return STATIC;
+    }
+  }
+}