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, 53 insertions, 48 deletions

diff --git a/src/de/lmu/ifi/dbs/elki/index/preprocessed/preference/HiSCPreferenceVectorIndex.java b/src/de/lmu/ifi/dbs/elki/index/preprocessed/preference/HiSCPreferenceVectorIndex.java
index 65f5f61e..fd6aa0bf 100644
--- a/src/de/lmu/ifi/dbs/elki/index/preprocessed/preference/HiSCPreferenceVectorIndex.java
+++ b/src/de/lmu/ifi/dbs/elki/index/preprocessed/preference/HiSCPreferenceVectorIndex.java
@@ -30,13 +30,15 @@ import de.lmu.ifi.dbs.elki.data.NumberVector;
 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.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.query.knn.KNNQuery;
-import de.lmu.ifi.dbs.elki.database.query.knn.KNNResult;
 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.EuclideanDistanceFunction;
+import de.lmu.ifi.dbs.elki.distance.distanceresultlist.KNNResult;
 import de.lmu.ifi.dbs.elki.distance.distancevalue.DoubleDistance;
 import de.lmu.ifi.dbs.elki.logging.Logging;
 import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress;
@@ -48,7 +50,7 @@ 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.OptionID;
 import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.GreaterConstraint;
-import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.IntervalConstraint;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.LessConstraint;
 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;
@@ -60,14 +62,16 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter;
  * @author Elke Achtert
  * 
  * @see HiSC
+ * 
+ * @param <V> Vector type
  */
 @Title("HiSC Preprocessor")
 @Description("Computes the preference vector of objects of a certain database according to the HiSC algorithm.")
-public class HiSCPreferenceVectorIndex<V extends NumberVector<?, ?>> extends AbstractPreferenceVectorIndex<V> implements PreferenceVectorIndex<V> {
+public class HiSCPreferenceVectorIndex<V extends NumberVector<?>> extends AbstractPreferenceVectorIndex<V> implements PreferenceVectorIndex<V> {
   /**
-   * Logger to use
+   * Logger to use.
    */
-  protected static final Logging logger = Logging.getLogger(HiSCPreferenceVectorIndex.class);
+  private static final Logging LOG = Logging.getLogger(HiSCPreferenceVectorIndex.class);
 
   /**
    * Holds the value of parameter alpha.
@@ -94,49 +98,47 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
 
   @Override
   protected void preprocess() {
-    if(relation == null || relation.size() <= 0) {
+    if (relation == null || relation.size() <= 0) {
       throw new IllegalArgumentException(ExceptionMessages.DATABASE_EMPTY);
     }
 
     storage = DataStoreUtil.makeStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, BitSet.class);
 
-    StringBuffer msg = new StringBuffer();
+    StringBuilder msg = new StringBuilder();
 
     long start = System.currentTimeMillis();
-    FiniteProgress progress = logger.isVerbose() ? new FiniteProgress("Preprocessing preference vector", relation.size(), logger) : null;
+    FiniteProgress progress = LOG.isVerbose() ? new FiniteProgress("Preprocessing preference vector", relation.size(), LOG) : null;
 
     KNNQuery<V, DoubleDistance> knnQuery = QueryUtil.getKNNQuery(relation, EuclideanDistanceFunction.STATIC, k);
 
     for (DBIDIter it = relation.iterDBIDs(); it.valid(); it.advance()) {
-      DBID id = it.getDBID();
-
-      if(logger.isDebugging()) {
-        msg.append("\n\nid = ").append(id);
-        ///msg.append(" ").append(database.getObjectLabelQuery().get(id));
+      if (LOG.isDebugging()) {
+        msg.append("\n\nid = ").append(DBIDUtil.toString(it));
+        // /msg.append(" ").append(database.getObjectLabelQuery().get(id));
         msg.append("\n knns: ");
       }
 
-      KNNResult<DoubleDistance> knns = knnQuery.getKNNForDBID(id, k);
-      BitSet preferenceVector = determinePreferenceVector(relation, id, knns.asDBIDs(), msg);
-      storage.put(id, preferenceVector);
+      KNNResult<DoubleDistance> knns = knnQuery.getKNNForDBID(it, k);
+      BitSet preferenceVector = determinePreferenceVector(relation, it, knns, msg);
+      storage.put(it, preferenceVector);
 
-      if(progress != null) {
-        progress.incrementProcessed(logger);
+      if (progress != null) {
+        progress.incrementProcessed(LOG);
       }
     }
-    if(progress != null) {
-      progress.ensureCompleted(logger);
+    if (progress != null) {
+      progress.ensureCompleted(LOG);
     }
 
-    if(logger.isDebugging()) {
-      logger.debugFine(msg.toString());
+    if (LOG.isDebugging()) {
+      LOG.debugFine(msg.toString());
     }
 
     long end = System.currentTimeMillis();
     // TODO: re-add timing code!
-    if(logger.isVerbose()) {
+    if (LOG.isVerbose()) {
       long elapsedTime = end - start;
-      logger.verbose(this.getClass().getName() + " runtime: " + elapsedTime + " milliseconds.");
+      LOG.verbose(this.getClass().getName() + " runtime: " + elapsedTime + " milliseconds.");
     }
   }
 
@@ -150,20 +152,20 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
    * @param msg a string buffer for debug messages
    * @return the preference vector
    */
-  private BitSet determinePreferenceVector(Relation<V> relation, DBID id, DBIDs neighborIDs, StringBuffer msg) {
+  private BitSet determinePreferenceVector(Relation<V> relation, DBIDRef id, DBIDs neighborIDs, StringBuilder msg) {
     // variances
     double[] variances = DatabaseUtil.variances(relation, relation.get(id), neighborIDs);
 
     // preference vector
     BitSet preferenceVector = new BitSet(variances.length);
-    for(int d = 0; d < variances.length; d++) {
-      if(variances[d] < alpha) {
+    for (int d = 0; d < variances.length; d++) {
+      if (variances[d] < alpha) {
         preferenceVector.set(d);
       }
     }
 
-    if(msg != null && logger.isDebugging()) {
-      msg.append("\nalpha " + alpha);
+    if (msg != null && LOG.isDebugging()) {
+      msg.append("\nalpha ").append(alpha);
       msg.append("\nvariances ");
       msg.append(FormatUtil.format(variances, ", ", 4));
       msg.append("\npreference ");
@@ -175,7 +177,7 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
 
   @Override
   protected Logging getLogger() {
-    return logger;
+    return LOG;
   }
 
   @Override
@@ -189,7 +191,7 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
   }
 
   /**
-   * Factory class
+   * Factory class.
    * 
    * @author Erich Schubert
    * 
@@ -198,7 +200,7 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
    * 
    * @param <V> Vector type
    */
-  public static class Factory<V extends NumberVector<?, ?>> extends AbstractPreferenceVectorIndex.Factory<V, HiSCPreferenceVectorIndex<V>> {
+  public static class Factory<V extends NumberVector<?>> extends AbstractPreferenceVectorIndex.Factory<V, HiSCPreferenceVectorIndex<V>> {
     /**
      * The default value for alpha.
      */
@@ -214,7 +216,7 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
      * Key: {@code -hisc.alpha}
      * </p>
      */
-    public static final OptionID ALPHA_ID = OptionID.getOrCreateOptionID("hisc.alpha", "The maximum absolute variance along a coordinate axis.");
+    public static final OptionID ALPHA_ID = new OptionID("hisc.alpha", "The maximum absolute variance along a coordinate axis.");
 
     /**
      * The number of nearest neighbors considered to determine the preference
@@ -227,7 +229,7 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
      * Default value: three times of the dimensionality of the database objects
      * </p>
      */
-    public static final OptionID K_ID = OptionID.getOrCreateOptionID("hisc.k", "The number of nearest neighbors considered to determine the preference vector. If this value is not defined, k ist set to three times of the dimensionality of the database objects.");
+    public static final OptionID K_ID = new OptionID("hisc.k", "The number of nearest neighbors considered to determine the preference vector. If this value is not defined, k ist set to three times of the dimensionality of the database objects.");
 
     /**
      * Holds the value of parameter {@link #ALPHA_ID}.
@@ -254,10 +256,9 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
     @Override
     public HiSCPreferenceVectorIndex<V> instantiate(Relation<V> relation) {
       final int usek;
-      if(k == null) {
-        usek = 3 * DatabaseUtil.dimensionality(relation);
-      }
-      else {
+      if (k == null) {
+        usek = 3 * RelationUtil.dimensionality(relation);
+      } else {
         usek = k;
       }
       return new HiSCPreferenceVectorIndex<V>(relation, alpha, usek);
@@ -270,7 +271,7 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
      * 
      * @apiviz.exclude
      */
-    public static class Parameterizer<V extends NumberVector<?, ?>> extends AbstractParameterizer {
+    public static class Parameterizer<V extends NumberVector<?>> extends AbstractParameterizer {
       /**
        * Holds the value of parameter {@link #ALPHA_ID}.
        */
@@ -281,17 +282,21 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
        */
       protected Integer k;
 
-     @Override
+      @Override
       protected void makeOptions(Parameterization config) {
         super.makeOptions(config);
-        final DoubleParameter ALPHA_PARAM = new DoubleParameter(ALPHA_ID, new IntervalConstraint(0.0, IntervalConstraint.IntervalBoundary.OPEN, 1.0, IntervalConstraint.IntervalBoundary.OPEN), DEFAULT_ALPHA);
-        if(config.grab(ALPHA_PARAM)) {
-          alpha = ALPHA_PARAM.getValue();
+        final DoubleParameter alphaP = new DoubleParameter(ALPHA_ID, DEFAULT_ALPHA);
+        alphaP.addConstraint(new GreaterConstraint(0.0));
+        alphaP.addConstraint(new LessConstraint(1.0));
+        if (config.grab(alphaP)) {
+          alpha = alphaP.doubleValue();
         }
 
-        final IntParameter K_PARAM = new IntParameter(K_ID, new GreaterConstraint(0), true);
-        if(config.grab(K_PARAM)) {
-          k = K_PARAM.getValue();
+        final IntParameter kP = new IntParameter(K_ID);
+        kP.addConstraint(new GreaterConstraint(0));
+        kP.setOptional(true);
+        if (config.grab(kP)) {
+          k = kP.intValue();
         }
       }
 
@@ -301,4 +306,4 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
       }
     }
   }
-}
\ No newline at end of file
+}