1 files changed, 45 insertions, 74 deletions

diff --git a/src/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedFloatDistanceFunction.java b/src/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedFloatDistanceFunction.java
index 994d854d..f39e1fdc 100644
--- a/src/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedFloatDistanceFunction.java
+++ b/src/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedFloatDistanceFunction.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 +23,43 @@ 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.TLongFloatMap;
+import gnu.trove.map.hash.TLongFloatHashMap;
+
 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.FloatDistance;
+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 float distances given by a
- * distance matrix of an external file.
+ * Distance function that is based on float 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 float[]} instead of the hash map.
  * 
  * @author Elke Achtert
+ * @author Erich Schubert
  */
 @Title("File based float distance for database objects.")
 @Description("Loads float distance values from an external text file.")
-public class FileBasedFloatDistanceFunction extends AbstractDBIDDistanceFunction<FloatDistance> {
-  /**
-   * 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 FileBasedFloatDistanceFunction extends AbstractDBIDRangeDistanceFunction {
   /**
    * The distance cache
    */
-  private Map<DBIDPair, FloatDistance> cache;
+  private TLongFloatMap cache;
 
   /**
    * Constructor.
@@ -87,7 +67,7 @@ public class FileBasedFloatDistanceFunction extends AbstractDBIDDistanceFunction
    * @param parser Parser
    * @param matrixfile input file
    */
-  public FileBasedFloatDistanceFunction(DistanceParser<FloatDistance> parser, File matrixfile) {
+  public FileBasedFloatDistanceFunction(DistanceParser parser, File matrixfile) {
     super();
     try {
       loadCache(parser, matrixfile);
@@ -97,44 +77,38 @@ public class FileBasedFloatDistanceFunction extends AbstractDBIDDistanceFunction
     }
   }
 
-  /**
-   * 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 FloatDistance distance(DBIDRef id1, DBIDRef id2) {
-    if(id1 == null) {
-      return getDistanceFactory().undefinedDistance();
-    }
-    if(id2 == null) {
-      return getDistanceFactory().undefinedDistance();
-    }
-    // the smaller id is the first key
-    if(DBIDUtil.compare(id1, id2) > 0) {
-      return distance(id2, id1);
-    }
-    FloatDistance ret = cache.get(DBIDUtil.newPair(id1, id2));
-    if (ret == null && DBIDUtil.equal(id1, id2)) {
-      return FloatDistance.ZERO_DISTANCE;
-    }
-    return ret;
+  public double distance(int i1, int i2) {
+    return (i1 == i2) ? 0. : cache.get(makeKey(i1, i2));
   }
 
-  private void loadCache(DistanceParser<FloatDistance> parser, File matrixfile) throws IOException {
+  private void loadCache(DistanceParser parser, File matrixfile) throws IOException {
     InputStream in = new BufferedInputStream(FileUtil.tryGzipInput(new FileInputStream(matrixfile)));
-    DistanceParsingResult<FloatDistance> res = parser.parse(in);
-    cache = res.getDistanceCache();
+    cache = new TLongFloatHashMap();
+    parser.parse(in, new DistanceCacheWriter() {
+      @Override
+      public void put(int id1, int id2, double distance) {
+        cache.put(makeKey(id1, id2), (float) distance);
+      }
+
+      @Override
+      public boolean containsKey(int id1, int id2) {
+        return cache.containsKey(makeKey(id1, id2));
+      }
+    });
   }
 
-  @Override
-  public FloatDistance getDistanceFactory() {
-    return FloatDistance.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
@@ -159,22 +133,19 @@ public class FileBasedFloatDistanceFunction extends AbstractDBIDDistanceFunction
   public static class Parameterizer extends AbstractParameterizer {
     protected File matrixfile = null;
 
-    protected DistanceParser<FloatDistance> parser = null;
+    protected DistanceParser parser = null;
 
     @Override
     protected void makeOptions(Parameterization config) {
       super.makeOptions(config);
-      final FileParameter MATRIX_PARAM = new FileParameter(MATRIX_ID, FileParameter.FileType.INPUT_FILE);
+      final FileParameter MATRIX_PARAM = new FileParameter(FileBasedDoubleDistanceFunction.Parameterizer.MATRIX_ID, FileParameter.FileType.INPUT_FILE);
       if(config.grab(MATRIX_PARAM)) {
         matrixfile = MATRIX_PARAM.getValue();
       }
-      final ObjectParameter<DistanceParser<FloatDistance>> PARSER_PARAM = new ObjectParameter<>(PARSER_ID, DistanceParser.class, NumberDistanceParser.class);
+
+      final ObjectParameter<DistanceParser> PARSER_PARAM = new ObjectParameter<>(FileBasedDoubleDistanceFunction.Parameterizer.PARSER_ID, DistanceParser.class, AsciiDistanceParser.class);
       if(config.grab(PARSER_PARAM)) {
-        ListParameterization parserConfig = new ListParameterization();
-        parserConfig.addParameter(DistanceParser.DISTANCE_ID, FloatDistance.class);
-        ChainedParameterization combinedConfig = new ChainedParameterization(parserConfig, config);
-        combinedConfig.errorsTo(config);
-        parser = PARSER_PARAM.instantiateClass(combinedConfig);
+        parser = PARSER_PARAM.instantiateClass(config);
       }
     }