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, 92 insertions, 104 deletions

diff --git a/src/de/lmu/ifi/dbs/elki/index/preprocessed/preference/DiSHPreferenceVectorIndex.java b/src/de/lmu/ifi/dbs/elki/index/preprocessed/preference/DiSHPreferenceVectorIndex.java
index 416a5ffb..2b02e7d6 100644
--- a/src/de/lmu/ifi/dbs/elki/index/preprocessed/preference/DiSHPreferenceVectorIndex.java
+++ b/src/de/lmu/ifi/dbs/elki/index/preprocessed/preference/DiSHPreferenceVectorIndex.java
@@ -40,31 +40,28 @@ import de.lmu.ifi.dbs.elki.database.HashmapDatabase;
 import de.lmu.ifi.dbs.elki.database.UpdatableDatabase;
 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.DBIDUtil;
 import de.lmu.ifi.dbs.elki.database.ids.DBIDs;
 import de.lmu.ifi.dbs.elki.database.ids.ModifiableDBIDs;
-import de.lmu.ifi.dbs.elki.database.query.DistanceDBIDResult;
-import de.lmu.ifi.dbs.elki.database.query.DistanceResultPair;
 import de.lmu.ifi.dbs.elki.database.query.distance.PrimitiveDistanceQuery;
 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.database.relation.RelationUtil;
 import de.lmu.ifi.dbs.elki.datasource.bundle.SingleObjectBundle;
 import de.lmu.ifi.dbs.elki.distance.distancefunction.subspace.DimensionSelectingDistanceFunction;
+import de.lmu.ifi.dbs.elki.distance.distanceresultlist.DistanceDBIDResult;
 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.result.AprioriResult;
 import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil;
-import de.lmu.ifi.dbs.elki.utilities.DatabaseUtil;
 import de.lmu.ifi.dbs.elki.utilities.FormatUtil;
 import de.lmu.ifi.dbs.elki.utilities.documentation.Description;
 import de.lmu.ifi.dbs.elki.utilities.exceptions.ExceptionMessages;
 import de.lmu.ifi.dbs.elki.utilities.exceptions.UnableToComplyException;
 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.ParameterException;
 import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException;
 import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.GreaterConstraint;
 import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization;
@@ -77,13 +74,15 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter;
  * database.
  * 
  * @author Elke Achtert
+ * 
+ * @param <V> Vector type
  */
 @Description("Computes the preference vector of objects of a certain database according to the DiSH algorithm.")
-public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends AbstractPreferenceVectorIndex<V> implements PreferenceVectorIndex<V> {
+public class DiSHPreferenceVectorIndex<V extends NumberVector<?>> extends AbstractPreferenceVectorIndex<V> implements PreferenceVectorIndex<V> {
   /**
-   * Logger to use
+   * Logger to use.
    */
-  protected static final Logging logger = Logging.getLogger(DiSHPreferenceVectorIndex.class);
+  private static final Logging LOG = Logging.getLogger(DiSHPreferenceVectorIndex.class);
 
   /**
    * Available strategies for determination of the preference vector.
@@ -92,17 +91,17 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
    */
   public enum Strategy {
     /**
-     * Apriori strategy
+     * Apriori strategy.
      */
     APRIORI,
     /**
-     * Max intersection strategy
+     * Max intersection strategy.
      */
     MAX_INTERSECTION
   }
 
   /**
-   * The epsilon value for each dimension;
+   * The epsilon value for each dimension.
    */
   protected DoubleDistance[] epsilon;
 
@@ -139,84 +138,76 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
 
     storage = DataStoreUtil.makeStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, BitSet.class);
 
-    if(logger.isDebugging()) {
-      StringBuffer msg = new StringBuffer();
+    if(LOG.isDebugging()) {
+      StringBuilder msg = new StringBuilder();
       msg.append("\n eps ").append(Arrays.asList(epsilon));
       msg.append("\n minpts ").append(minpts);
       msg.append("\n strategy ").append(strategy);
-      logger.debugFine(msg.toString());
+      LOG.debugFine(msg.toString());
     }
 
-    try {
-      long start = System.currentTimeMillis();
-      FiniteProgress progress = logger.isVerbose() ? new FiniteProgress("Preprocessing preference vector", relation.size(), logger) : null;
-
-      // only one epsilon value specified
-      int dim = DatabaseUtil.dimensionality(relation);
-      if(epsilon.length == 1 && dim != 1) {
-        DoubleDistance eps = epsilon[0];
-        epsilon = new DoubleDistance[dim];
-        Arrays.fill(epsilon, eps);
-      }
-
-      // epsilons as string
-      RangeQuery<V, DoubleDistance>[] rangeQueries = initRangeQueries(relation, dim);
+    long start = System.currentTimeMillis();
+    FiniteProgress progress = LOG.isVerbose() ? new FiniteProgress("Preprocessing preference vector", relation.size(), LOG) : null;
 
-      for(DBIDIter it = relation.iterDBIDs(); it.valid(); it.advance()) {
-        StringBuffer msg = new StringBuffer();
-        final DBID id = it.getDBID();
+    // only one epsilon value specified
+    int dim = RelationUtil.dimensionality(relation);
+    if(epsilon.length == 1 && dim != 1) {
+      DoubleDistance eps = epsilon[0];
+      epsilon = new DoubleDistance[dim];
+      Arrays.fill(epsilon, eps);
+    }
 
-        if(logger.isDebugging()) {
-          msg.append("\nid = ").append(id);
-          // msg.append(" ").append(database.get(id));
-          //msg.append(" ").append(database.getObjectLabelQuery().get(id));
-        }
+    // epsilons as string
+    RangeQuery<V, DoubleDistance>[] rangeQueries = initRangeQueries(relation, dim);
 
-        // determine neighbors in each dimension
-        ModifiableDBIDs[] allNeighbors = ClassGenericsUtil.newArrayOfNull(dim, ModifiableDBIDs.class);
-        for(int d = 0; d < dim; d++) {
-          DistanceDBIDResult<DoubleDistance> qrList = rangeQueries[d].getRangeForDBID(id, epsilon[d]);
-          allNeighbors[d] = DBIDUtil.newHashSet(qrList.size());
-          for(DistanceResultPair<DoubleDistance> qr : qrList) {
-            allNeighbors[d].add(qr.getDBID());
-          }
-        }
+    for(DBIDIter it = relation.iterDBIDs(); it.valid(); it.advance()) {
+      StringBuilder msg = new StringBuilder();
 
-        if(logger.isDebugging()) {
-          for(int d = 0; d < dim; d++) {
-            msg.append("\n neighbors [").append(d).append("]");
-            msg.append(" (").append(allNeighbors[d].size()).append(") = ");
-            msg.append(allNeighbors[d]);
-          }
-        }
+      if(LOG.isDebugging()) {
+        msg.append("\nid = ").append(DBIDUtil.toString(it));
+        // msg.append(" ").append(database.get(id));
+        // msg.append(" ").append(database.getObjectLabelQuery().get(id));
+      }
 
-        BitSet preferenceVector = determinePreferenceVector(relation, allNeighbors, msg);
-        storage.put(id, preferenceVector);
+      // determine neighbors in each dimension
+      ModifiableDBIDs[] allNeighbors = new ModifiableDBIDs[dim];
+      for(int d = 0; d < dim; d++) {
+        DistanceDBIDResult<DoubleDistance> qrList = rangeQueries[d].getRangeForDBID(it, epsilon[d]);
+        allNeighbors[d] = DBIDUtil.newHashSet(qrList);
+      }
 
-        if(logger.isDebugging()) {
-          logger.debugFine(msg.toString());
+      if(LOG.isDebugging()) {
+        for(int d = 0; d < dim; d++) {
+          msg.append("\n neighbors [").append(d).append(']');
+          msg.append(" (").append(allNeighbors[d].size()).append(") = ");
+          msg.append(allNeighbors[d]);
         }
+      }
 
-        if(progress != null) {
-          progress.incrementProcessed(logger);
-        }
+      try {
+        storage.put(it, determinePreferenceVector(relation, allNeighbors, msg));
       }
-      if(progress != null) {
-        progress.ensureCompleted(logger);
+      catch(UnableToComplyException e) {
+        throw new IllegalStateException(e);
       }
 
-      long end = System.currentTimeMillis();
-      // TODO: re-add timing code!
-      if(logger.isVerbose()) {
-        long elapsedTime = end - start;
-        logger.verbose(this.getClass().getName() + " runtime: " + elapsedTime + " milliseconds.");
+      if(LOG.isDebugging()) {
+        LOG.debugFine(msg.toString());
+      }
+
+      if(progress != null) {
+        progress.incrementProcessed(LOG);
       }
     }
-    catch(ParameterException e) {
-      throw new IllegalStateException(e);
+    if(progress != null) {
+      progress.ensureCompleted(LOG);
     }
-    catch(UnableToComplyException e) {
-      throw new IllegalStateException(e);
+
+    long end = System.currentTimeMillis();
+    // TODO: re-add timing code!
+    if(LOG.isVerbose()) {
+      long elapsedTime = end - start;
+      LOG.verbose(this.getClass().getName() + " runtime: " + elapsedTime + " milliseconds.");
     }
   }
 
@@ -227,11 +218,10 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
    * @param neighborIDs the list of ids of the neighbors in each dimension
    * @param msg a string buffer for debug messages
    * @return the preference vector
-   * @throws de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException
    * 
    * @throws de.lmu.ifi.dbs.elki.utilities.exceptions.UnableToComplyException
    */
-  private BitSet determinePreferenceVector(Relation<V> relation, ModifiableDBIDs[] neighborIDs, StringBuffer msg) throws ParameterException, UnableToComplyException {
+  private BitSet determinePreferenceVector(Relation<V> relation, ModifiableDBIDs[] neighborIDs, StringBuilder msg) throws UnableToComplyException {
     if(strategy.equals(Strategy.APRIORI)) {
       return determinePreferenceVectorByApriori(relation, neighborIDs, msg);
     }
@@ -250,23 +240,21 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
    * @param neighborIDs the list of ids of the neighbors in each dimension
    * @param msg a string buffer for debug messages
    * @return the preference vector
-   * @throws de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException
    * 
    * @throws de.lmu.ifi.dbs.elki.utilities.exceptions.UnableToComplyException
    * 
    */
-  private BitSet determinePreferenceVectorByApriori(Relation<V> relation, ModifiableDBIDs[] neighborIDs, StringBuffer msg) throws ParameterException, UnableToComplyException {
+  private BitSet determinePreferenceVectorByApriori(Relation<V> relation, ModifiableDBIDs[] neighborIDs, StringBuilder msg) throws UnableToComplyException {
     int dimensionality = neighborIDs.length;
 
     // database for apriori
     UpdatableDatabase apriori_db = new HashmapDatabase();
-    SimpleTypeInformation<?> bitmeta = VectorFieldTypeInformation.get(BitVector.class, dimensionality);
+    SimpleTypeInformation<?> bitmeta = new VectorFieldTypeInformation<BitVector>(BitVector.class, dimensionality);
     for(DBIDIter it = relation.iterDBIDs(); it.valid(); it.advance()) {
-      DBID id = it.getDBID();
       Bit[] bits = new Bit[dimensionality];
       boolean allFalse = true;
       for(int d = 0; d < dimensionality; d++) {
-        if(neighborIDs[d].contains(id)) {
+        if(neighborIDs[d].contains(it)) {
           bits[d] = new Bit(true);
           allFalse = false;
         }
@@ -286,9 +274,9 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
     // result of apriori
     List<BitSet> frequentItemsets = aprioriResult.getSolution();
     Map<BitSet, Integer> supports = aprioriResult.getSupports();
-    if(logger.isDebugging()) {
-      msg.append("\n Frequent itemsets: " + frequentItemsets);
-      msg.append("\n All supports: " + supports);
+    if(LOG.isDebugging()) {
+      msg.append("\n Frequent itemsets: ").append(frequentItemsets);
+      msg.append("\n All supports: ").append(supports);
     }
     int maxSupport = 0;
     int maxCardinality = 0;
@@ -302,11 +290,11 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
       }
     }
 
-    if(logger.isDebugging()) {
+    if(LOG.isDebugging()) {
       msg.append("\n preference ");
       msg.append(FormatUtil.format(dimensionality, preferenceVector));
-      msg.append("\n");
-      logger.debugFine(msg.toString());
+      msg.append('\n');
+      LOG.debugFine(msg.toString());
     }
 
     return preferenceVector;
@@ -319,7 +307,7 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
    * @param msg a string buffer for debug messages
    * @return the preference vector
    */
-  private BitSet determinePreferenceVectorByMaxIntersection(ModifiableDBIDs[] neighborIDs, StringBuffer msg) {
+  private BitSet determinePreferenceVectorByMaxIntersection(ModifiableDBIDs[] neighborIDs, StringBuilder msg) {
     int dimensionality = neighborIDs.length;
     BitSet preferenceVector = new BitSet(dimensionality);
 
@@ -330,8 +318,8 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
         candidates.put(i, s_i);
       }
     }
-    if(logger.isDebugging()) {
-      msg.append("\n candidates " + candidates.keySet());
+    if(LOG.isDebugging()) {
+      msg.append("\n candidates ").append(candidates.keySet());
     }
 
     if(!candidates.isEmpty()) {
@@ -355,11 +343,11 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
       }
     }
 
-    if(logger.isDebugging()) {
+    if(LOG.isDebugging()) {
       msg.append("\n preference ");
       msg.append(FormatUtil.format(dimensionality, preferenceVector));
-      msg.append("\n");
-      logger.debug(msg.toString());
+      msg.append('\n');
+      LOG.debug(msg.toString());
     }
 
     return preferenceVector;
@@ -416,20 +404,19 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
    * @param dimensionality the dimensionality of the objects
    * @return the dimension selecting distancefunctions to determine the
    *         preference vectors
-   * @throws ParameterException
    */
-  private RangeQuery<V, DoubleDistance>[] initRangeQueries(Relation<V> relation, int dimensionality) throws ParameterException {
+  private RangeQuery<V, DoubleDistance>[] initRangeQueries(Relation<V> relation, int dimensionality) {
     Class<RangeQuery<V, DoubleDistance>> rqcls = ClassGenericsUtil.uglyCastIntoSubclass(RangeQuery.class);
     RangeQuery<V, DoubleDistance>[] rangeQueries = ClassGenericsUtil.newArrayOfNull(dimensionality, rqcls);
     for(int d = 0; d < dimensionality; d++) {
-      rangeQueries[d] = relation.getDatabase().getRangeQuery(new PrimitiveDistanceQuery<V, DoubleDistance>(relation, new DimensionSelectingDistanceFunction(d + 1)));
+      rangeQueries[d] = relation.getDatabase().getRangeQuery(new PrimitiveDistanceQuery<V, DoubleDistance>(relation, new DimensionSelectingDistanceFunction(d)));
     }
     return rangeQueries;
   }
 
   @Override
   protected Logging getLogger() {
-    return logger;
+    return LOG;
   }
 
   @Override
@@ -443,7 +430,7 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
   }
 
   /**
-   * Factory class
+   * Factory class.
    * 
    * @author Erich Schubert
    * 
@@ -452,7 +439,7 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
    * 
    * @param <V> Vector type
    */
-  public static class Factory<V extends NumberVector<?, ?>> extends AbstractPreferenceVectorIndex.Factory<V, DiSHPreferenceVectorIndex<V>> {
+  public static class Factory<V extends NumberVector<?>> extends AbstractPreferenceVectorIndex.Factory<V, DiSHPreferenceVectorIndex<V>> {
     /**
      * The default value for epsilon.
      */
@@ -472,7 +459,7 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
      * Default value: {@link #DEFAULT_EPSILON}
      * </p>
      */
-    public static final OptionID EPSILON_ID = OptionID.getOrCreateOptionID("dish.epsilon", "A comma separated list of positive doubles specifying the " + "maximum radius of the neighborhood to be " + "considered in each dimension for determination of " + "the preference vector " + "(default is " + DEFAULT_EPSILON + " in each dimension). " + "If only one value is specified, this value " + "will be used for each dimension.");
+    public static final OptionID EPSILON_ID = new OptionID("dish.epsilon", "A comma separated list of positive doubles specifying the " + "maximum radius of the neighborhood to be " + "considered in each dimension for determination of " + "the preference vector " + "(default is " + DEFAULT_EPSILON + " in each dimension). " + "If only one value is specified, this value " + "will be used for each dimension.");
 
     /**
      * Option name for {@link #MINPTS_ID}.
@@ -493,12 +480,12 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
      * Key: {@code -dish.minpts}
      * </p>
      */
-    public static final OptionID MINPTS_ID = OptionID.getOrCreateOptionID(MINPTS_P, "Positive threshold for minumum numbers of points in the epsilon-" + "neighborhood of a point. " + CONDITION);
+    public static final OptionID MINPTS_ID = new OptionID(MINPTS_P, "Positive threshold for minumum numbers of points in the epsilon-" + "neighborhood of a point. " + CONDITION);
 
     /**
      * Default strategy.
      */
-    public static Strategy DEFAULT_STRATEGY = Strategy.MAX_INTERSECTION;
+    public static final Strategy DEFAULT_STRATEGY = Strategy.MAX_INTERSECTION;
 
     /**
      * The strategy for determination of the preference vector, available
@@ -512,10 +499,10 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
      * Default value: {@link #DEFAULT_STRATEGY}
      * </p>
      */
-    public static final OptionID STRATEGY_ID = OptionID.getOrCreateOptionID("dish.strategy", "The strategy for determination of the preference vector, " + "available strategies are: [" + Strategy.APRIORI + "| " + Strategy.MAX_INTERSECTION + "]" + "(default is " + DEFAULT_STRATEGY + ")");
+    public static final OptionID STRATEGY_ID = new OptionID("dish.strategy", "The strategy for determination of the preference vector, " + "available strategies are: [" + Strategy.APRIORI + "| " + Strategy.MAX_INTERSECTION + "]" + "(default is " + DEFAULT_STRATEGY + ")");
 
     /**
-     * The epsilon value for each dimension;
+     * The epsilon value for each dimension.
      */
     protected DoubleDistance[] epsilon;
 
@@ -549,7 +536,7 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
     }
 
     /**
-     * Return the minpts value
+     * Return the minpts value.
      * 
      * @return minpts
      */
@@ -564,9 +551,9 @@ public class DiSHPreferenceVectorIndex<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 {
       /**
-       * The epsilon value for each dimension;
+       * The epsilon value for each dimension.
        */
       protected DoubleDistance[] epsilon;
 
@@ -583,7 +570,8 @@ public class DiSHPreferenceVectorIndex<V extends NumberVector<?, ?>> extends Abs
       @Override
       protected void makeOptions(Parameterization config) {
         super.makeOptions(config);
-        final IntParameter minptsP = new IntParameter(MINPTS_ID, new GreaterConstraint(0));
+        final IntParameter minptsP = new IntParameter(MINPTS_ID);
+        minptsP.addConstraint(new GreaterConstraint(0));
         if(config.grab(minptsP)) {
           minpts = minptsP.getValue();
         }