Import Upstream version 0.6.5~20141030

1 files changed, 65 insertions, 72 deletions

diff --git a/src/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedDoubleDistanceFunction.java b/src/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedDoubleDistanceFunction.java
index 29546401..055d5d75 100644
--- a/src/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedDoubleDistanceFunction.java
+++ b/src/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedDoubleDistanceFunction.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction.external;
  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
@@ -23,63 +23,44 @@ package de.lmu.ifi.dbs.elki.distance.distancefunction.external;
  along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
+import gnu.trove.map.TLongDoubleMap;
+import gnu.trove.map.hash.TLongDoubleHashMap;
+
 import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.util.Map;
 
-import de.lmu.ifi.dbs.elki.database.ids.DBIDPair;
-import de.lmu.ifi.dbs.elki.database.ids.DBIDRef;
-import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil;
-import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractDBIDDistanceFunction;
-import de.lmu.ifi.dbs.elki.distance.distancevalue.DoubleDistance;
+import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractDBIDRangeDistanceFunction;
 import de.lmu.ifi.dbs.elki.utilities.FileUtil;
 import de.lmu.ifi.dbs.elki.utilities.documentation.Description;
 import de.lmu.ifi.dbs.elki.utilities.documentation.Title;
 import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException;
 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.FileParameter;
 import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter;
 
 /**
- * Provides a DistanceFunction that is based on double distances given by a
- * distance matrix of an external file.
+ * Distance function that is based on double distances given by a distance
+ * matrix of an external ascii file.
+ * 
+ * See {@link AsciiDistanceParser} for the default input format.
  * 
- * See {@link NumberDistanceParser} for the default input format.
+ * TODO: use a {@code double[]} instead of the hash map.
  * 
  * @author Elke Achtert
+ * @author Erich Schubert
  */
 @Title("File based double distance for database objects.")
 @Description("Loads double distance values from an external text file.")
-public class FileBasedDoubleDistanceFunction extends AbstractDBIDDistanceFunction<DoubleDistance> {
-  /**
-   * Parameter that specifies the name of the distance matrix file.
-   * <p>
-   * Key: {@code -distance.matrix}
-   * </p>
-   */
-  public static final OptionID MATRIX_ID = new OptionID("distance.matrix", "The name of the file containing the distance matrix.");
-
-  /**
-   * Optional parameter to specify the parsers to provide a database, must
-   * extend {@link DistanceParser}. If this parameter is not set,
-   * {@link NumberDistanceParser} is used as parser for all input files.
-   * <p>
-   * Key: {@code -distance.parser}
-   * </p>
-   */
-  public static final OptionID PARSER_ID = new OptionID("distance.parser", "Parser used to load the distance matrix.");
-
+public class FileBasedDoubleDistanceFunction extends AbstractDBIDRangeDistanceFunction {
   /**
    * The distance cache
    */
-  private Map<DBIDPair, DoubleDistance> cache;
+  private TLongDoubleMap cache;
 
   /**
    * Constructor.
@@ -87,7 +68,7 @@ public class FileBasedDoubleDistanceFunction extends AbstractDBIDDistanceFunctio
    * @param parser Parser
    * @param matrixfile input file
    */
-  public FileBasedDoubleDistanceFunction(DistanceParser<DoubleDistance> parser, File matrixfile) {
+  public FileBasedDoubleDistanceFunction(DistanceParser parser, File matrixfile) {
     super();
     try {
       loadCache(parser, matrixfile);
@@ -97,45 +78,41 @@ public class FileBasedDoubleDistanceFunction extends AbstractDBIDDistanceFunctio
     }
   }
 
-  /**
-   * Returns the distance between the two objects specified by their objects
-   * ids. If a cache is used, the distance value is looked up in the cache. If
-   * the distance does not yet exists in cache, it will be computed an put to
-   * cache. If no cache is used, the distance is computed.
-   * 
-   * @param id1 first object id
-   * @param id2 second object id
-   * @return the distance between the two objects specified by their objects ids
-   */
   @Override
-  public DoubleDistance distance(DBIDRef id1, DBIDRef id2) {
-    if(id1 == null) {
-      return getDistanceFactory().undefinedDistance();
-    }
-    if(id2 == null) {
-      return getDistanceFactory().undefinedDistance();
+  public double distance(int i1, int i2) {
+    if(i1 == i2) {
+      return 0.;
     }
-    // the smaller id is the first key
-    if(DBIDUtil.compare(id1, id2) > 0) {
-      return distance(id2, id1);
-    }
-
-    DoubleDistance ret = cache.get(DBIDUtil.newPair(id1, id2));
-    if (ret == null && DBIDUtil.equal(id1, id2)) {
-      return DoubleDistance.ZERO_DISTANCE;
-    }
-    return ret;
+    return cache.get(makeKey(i1, i2));
   }
 
-  private void loadCache(DistanceParser<DoubleDistance> parser, File matrixfile) throws IOException {
+  private void loadCache(DistanceParser parser, File matrixfile) throws IOException {
     InputStream in = new BufferedInputStream(FileUtil.tryGzipInput(new FileInputStream(matrixfile)));
-    DistanceParsingResult<DoubleDistance> res = parser.parse(in);
-    cache = res.getDistanceCache();
+    cache = new TLongDoubleHashMap();
+    parser.parse(in, new DistanceCacheWriter() {
+      @Override
+      public void put(int id1, int id2, double distance) {
+        cache.put(makeKey(id1, id2), distance);
+      }
+
+      @Override
+      public boolean containsKey(int id1, int id2) {
+        return cache.containsKey(makeKey(id1, id2));
+      }
+    });
   }
 
-  @Override
-  public DoubleDistance getDistanceFactory() {
-    return DoubleDistance.FACTORY;
+  /**
+   * Combine two integer ids into a long value.
+   * 
+   * @param i1 First id
+   * @param i2 Second id
+   * @return Combined value
+   */
+  protected static final long makeKey(int i1, int i2) {
+    return (i1 < i2) //
+    ? ((((long) i1) << 32) | i2)//
+    : ((((long) i2) << 32) | i1);
   }
 
   @Override
@@ -158,9 +135,29 @@ public class FileBasedDoubleDistanceFunction extends AbstractDBIDDistanceFunctio
    * @apiviz.exclude
    */
   public static class Parameterizer extends AbstractParameterizer {
+    /**
+     * Parameter that specifies the name of the distance matrix file.
+     * <p>
+     * Key: {@code -distance.matrix}
+     * </p>
+     */
+    public static final OptionID MATRIX_ID = new OptionID("distance.matrix", //
+    "The name of the file containing the distance matrix.");
+
+    /**
+     * Optional parameter to specify the parsers to provide a database, must
+     * extend {@link DistanceParser}. If this parameter is not set,
+     * {@link AsciiDistanceParser} is used as parser for all input files.
+     * <p>
+     * Key: {@code -distance.parser}
+     * </p>
+     */
+    public static final OptionID PARSER_ID = new OptionID("distance.parser", //
+    "Parser used to load the distance matrix.");
+
     protected File matrixfile = null;
 
-    protected DistanceParser<DoubleDistance> parser = null;
+    protected DistanceParser parser = null;
 
     @Override
     protected void makeOptions(Parameterization config) {
@@ -170,13 +167,9 @@ public class FileBasedDoubleDistanceFunction extends AbstractDBIDDistanceFunctio
         matrixfile = MATRIX_PARAM.getValue();
       }
 
-      final ObjectParameter<DistanceParser<DoubleDistance>> PARSER_PARAM = new ObjectParameter<>(PARSER_ID, DistanceParser.class, NumberDistanceParser.class);
+      final ObjectParameter<DistanceParser> PARSER_PARAM = new ObjectParameter<>(PARSER_ID, DistanceParser.class, AsciiDistanceParser.class);
       if(config.grab(PARSER_PARAM)) {
-        ListParameterization parserConfig = new ListParameterization();
-        parserConfig.addParameter(DistanceParser.DISTANCE_ID, DoubleDistance.class);
-        ChainedParameterization combinedConfig = new ChainedParameterization(parserConfig, config);
-        combinedConfig.errorsTo(config);
-        parser = PARSER_PARAM.instantiateClass(combinedConfig);
+        parser = PARSER_PARAM.instantiateClass(config);
       }
     }