1 files changed, 18 insertions, 25 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 8ead8458..843e4eda 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
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.index.preprocessed.preference;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2013
+ Copyright (C) 2014
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
@@ -23,8 +23,6 @@ package de.lmu.ifi.dbs.elki.index.preprocessed.preference;
  along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-import java.util.BitSet;
-
 import de.lmu.ifi.dbs.elki.algorithm.clustering.subspace.HiSC;
 import de.lmu.ifi.dbs.elki.data.NumberVector;
 import de.lmu.ifi.dbs.elki.database.QueryUtil;
@@ -34,15 +32,14 @@ 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.distance.KNNList;
+import de.lmu.ifi.dbs.elki.database.ids.KNNList;
 import de.lmu.ifi.dbs.elki.database.query.knn.KNNQuery;
 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.minkowski.EuclideanDistanceFunction;
-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;
-import de.lmu.ifi.dbs.elki.utilities.DatabaseUtil;
+import de.lmu.ifi.dbs.elki.utilities.BitsUtil;
 import de.lmu.ifi.dbs.elki.utilities.FormatUtil;
 import de.lmu.ifi.dbs.elki.utilities.documentation.Description;
 import de.lmu.ifi.dbs.elki.utilities.documentation.Title;
@@ -66,7 +63,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter;
  */
 @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.
    */
@@ -101,14 +98,14 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?>> extends Abstra
       throw new IllegalArgumentException(ExceptionMessages.DATABASE_EMPTY);
     }
 
-    storage = DataStoreUtil.makeStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, BitSet.class);
+    storage = DataStoreUtil.makeStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, long[].class);
 
     StringBuilder msg = new StringBuilder();
 
     long start = System.currentTimeMillis();
     FiniteProgress progress = LOG.isVerbose() ? new FiniteProgress("Preprocessing preference vector", relation.size(), LOG) : null;
 
-    KNNQuery<V, DoubleDistance> knnQuery = QueryUtil.getKNNQuery(relation, EuclideanDistanceFunction.STATIC, k);
+    KNNQuery<V> knnQuery = QueryUtil.getKNNQuery(relation, EuclideanDistanceFunction.STATIC, k);
 
     for(DBIDIter it = relation.iterDBIDs(); it.valid(); it.advance()) {
       if(LOG.isDebugging()) {
@@ -117,17 +114,13 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?>> extends Abstra
         msg.append("\n knns: ");
       }
 
-      KNNList<DoubleDistance> knns = knnQuery.getKNNForDBID(it, k);
-      BitSet preferenceVector = determinePreferenceVector(relation, it, knns, msg);
+      KNNList knns = knnQuery.getKNNForDBID(it, k);
+      long[] preferenceVector = determinePreferenceVector(relation, it, knns, msg);
       storage.put(it, preferenceVector);
 
-      if(progress != null) {
-        progress.incrementProcessed(LOG);
-      }
-    }
-    if(progress != null) {
-      progress.ensureCompleted(LOG);
+      LOG.incrementProcessed(progress);
     }
+    LOG.ensureCompleted(progress);
 
     if(LOG.isDebugging()) {
       LOG.debugFine(msg.toString());
@@ -151,24 +144,24 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?>> extends Abstra
    * @param msg a string buffer for debug messages
    * @return the preference vector
    */
-  private BitSet determinePreferenceVector(Relation<V> relation, DBIDRef id, DBIDs neighborIDs, StringBuilder msg) {
+  private long[] determinePreferenceVector(Relation<V> relation, DBIDRef id, DBIDs neighborIDs, StringBuilder msg) {
     // variances
-    double[] variances = DatabaseUtil.variances(relation, relation.get(id), neighborIDs);
+    double[] variances = RelationUtil.variances(relation, relation.get(id), neighborIDs);
 
     // preference vector
-    BitSet preferenceVector = new BitSet(variances.length);
+    long[] preferenceVector = BitsUtil.zero(variances.length);
     for(int d = 0; d < variances.length; d++) {
       if(variances[d] < alpha) {
-        preferenceVector.set(d);
+        BitsUtil.setI(preferenceVector, d);
       }
     }
 
     if(msg != null && LOG.isDebugging()) {
       msg.append("\nalpha ").append(alpha);
       msg.append("\nvariances ");
-      msg.append(FormatUtil.format(variances, ", ", 4));
+      msg.append(FormatUtil.format(variances, ", ", FormatUtil.NF4));
       msg.append("\npreference ");
-      msg.append(FormatUtil.format(variances.length, preferenceVector));
+      msg.append(BitsUtil.toStringLow(preferenceVector, variances.length));
     }
 
     return preferenceVector;
@@ -204,7 +197,7 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?>> extends Abstra
    * 
    * @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.
      */
@@ -276,7 +269,7 @@ public class HiSCPreferenceVectorIndex<V extends NumberVector<?>> extends Abstra
      * 
      * @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}.
        */