1 files changed, 220 insertions, 0 deletions
diff --git a/src/de/lmu/ifi/dbs/elki/application/cache/CacheFloatDistanceInOnDiskMatrix.java b/src/de/lmu/ifi/dbs/elki/application/cache/CacheFloatDistanceInOnDiskMatrix.java
new file mode 100644
index 00000000..67fdcb9a
--- /dev/null
+++ b/src/de/lmu/ifi/dbs/elki/application/cache/CacheFloatDistanceInOnDiskMatrix.java
@@ -0,0 +1,220 @@
+package de.lmu.ifi.dbs.elki.application.cache;
+/*
+This file is part of ELKI:
+Environment for Developing KDD-Applications Supported by Index-Structures
+
+Copyright (C) 2011
+Ludwig-Maximilians-Universität München
+Lehr- und Forschungseinheit für Datenbanksysteme
+ELKI Development Team
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU Affero General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Affero General Public License for more details.
+
+You should have received a copy of the GNU Affero General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+import java.io.File;
+import java.io.IOException;
+
+import de.lmu.ifi.dbs.elki.application.AbstractApplication;
+import de.lmu.ifi.dbs.elki.database.Database;
+import de.lmu.ifi.dbs.elki.database.StaticArrayDatabase;
+import de.lmu.ifi.dbs.elki.database.ids.DBID;
+import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery;
+import de.lmu.ifi.dbs.elki.database.relation.Relation;
+import de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction;
+import de.lmu.ifi.dbs.elki.distance.distancefunction.external.DiskCacheBasedFloatDistanceFunction;
+import de.lmu.ifi.dbs.elki.distance.distancevalue.NumberDistance;
+import de.lmu.ifi.dbs.elki.logging.Logging;
+import de.lmu.ifi.dbs.elki.persistent.OnDiskUpperTriangleMatrix;
+import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID;
+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;
+
+/**
+ * Wrapper to convert a traditional text-serialized result into a on-disk matrix
+ * for random access.
+ * 
+ * @author Erich Schubert
+ * 
+ * @apiviz.has OnDiskUpperTriangleMatrix
+ * @apiviz.has DistanceFunction
+ * 
+ * @param <O> Object type
+ * @param <D> Distance type
+ */
+public class CacheFloatDistanceInOnDiskMatrix<O, D extends NumberDistance<D, ?>> extends AbstractApplication {
+  /**
+   * The logger for this class.
+   */
+  private static final Logging logger = Logging.getLogger(CacheFloatDistanceInOnDiskMatrix.class);
+
+  /**
+   * Parameter that specifies the name of the directory to be re-parsed.
+   * <p>
+   * Key: {@code -loader.diskcache}
+   * </p>
+   */
+  public static final OptionID CACHE_ID = OptionID.getOrCreateOptionID("loader.diskcache", "File name of the disk cache to create.");
+
+  /**
+   * Parameter that specifies the name of the directory to be re-parsed.
+   * <p>
+   * Key: {@code -loader.distance}
+   * </p>
+   */
+  public static final OptionID DISTANCE_ID = OptionID.getOrCreateOptionID("loader.distance", "Distance function to cache.");
+
+  /**
+   * Debug flag, to double-check all write operations.
+   */
+  private static final boolean debugExtraCheckSymmetry = false;
+
+  /**
+   * Storage size: 4 bytes floats
+   */
+  private static final int FLOAT_SIZE = 4;
+
+  /**
+   * Holds the database connection to have the algorithm run with.
+   */
+  private Database database;
+
+  /**
+   * Distance function that is to be cached.
+   */
+  private DistanceFunction<O, D> distance;
+
+  /**
+   * Output file.
+   */
+  private File out;
+
+  /**
+   * Constructor.
+   * 
+   * @param verbose Verbose flag
+   * @param database Database
+   * @param distance Distance function
+   * @param out Matrix output file
+   */
+  public CacheFloatDistanceInOnDiskMatrix(boolean verbose, Database database, DistanceFunction<O, D> distance, File out) {
+    super(verbose);
+    this.database = database;
+    this.distance = distance;
+    this.out = out;
+  }
+
+  @Override
+  public void run() {
+    database.initialize();
+    Relation<O> relation = database.getRelation(distance.getInputTypeRestriction());
+    DistanceQuery<O, D> distanceQuery = database.getDistanceQuery(relation, distance);
+
+    int matrixsize = 0;
+    for(DBID id : distanceQuery.getRelation().iterDBIDs()) {
+      matrixsize = Math.max(matrixsize, id.getIntegerID() + 1);
+      if(id.getIntegerID() < 0) {
+        throw new AbortException("OnDiskMatrixCache does not allow negative DBIDs.");
+      }
+    }
+
+    OnDiskUpperTriangleMatrix matrix;
+    try {
+      matrix = new OnDiskUpperTriangleMatrix(out, DiskCacheBasedFloatDistanceFunction.FLOAT_CACHE_MAGIC, 0, FLOAT_SIZE, matrixsize);
+    }
+    catch(IOException e) {
+      throw new AbortException("Error creating output matrix.", e);
+    }
+
+    for(DBID id1 : distanceQuery.getRelation().iterDBIDs()) {
+      for(DBID id2 : distanceQuery.getRelation().iterDBIDs()) {
+        if(id2.getIntegerID() >= id1.getIntegerID()) {
+          float d = distanceQuery.distance(id1, id2).floatValue();
+          if(debugExtraCheckSymmetry) {
+            float d2 = distanceQuery.distance(id2, id1).floatValue();
+            if(Math.abs(d - d2) > 0.0000001) {
+              logger.warning("Distance function doesn't appear to be symmetric!");
+            }
+          }
+          try {
+            matrix.getRecordBuffer(id1.getIntegerID(), id2.getIntegerID()).putFloat(d);
+          }
+          catch(IOException e) {
+            throw new AbortException("Error writing distance record " + id1 + "," + id2 + " to matrix.", e);
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * Parameterization class.
+   * 
+   * @author Erich Schubert
+   * 
+   * @apiviz.exclude
+   */
+  public static class Parameterizer<O, D extends NumberDistance<D, ?>> extends AbstractApplication.Parameterizer {
+    /**
+     * Holds the database connection to have the algorithm run with.
+     */
+    private Database database = null;
+
+    /**
+     * Distance function that is to be cached.
+     */
+    private DistanceFunction<O, D> distance = null;
+
+    /**
+     * Output file.
+     */
+    private File out = null;
+
+    @Override
+    protected void makeOptions(Parameterization config) {
+      super.makeOptions(config);
+      // Database connection parameter
+      final ObjectParameter<Database> dbpar = new ObjectParameter<Database>(OptionID.DATABASE_CONNECTION, Database.class, StaticArrayDatabase.class);
+      if(config.grab(dbpar)) {
+        database = dbpar.instantiateClass(config);
+      }
+      // Distance function parameter
+      final ObjectParameter<DistanceFunction<O, D>> dpar = new ObjectParameter<DistanceFunction<O, D>>(DISTANCE_ID, DistanceFunction.class);
+      if(config.grab(dpar)) {
+        distance = dpar.instantiateClass(config);
+      }
+      // Output file parameter
+      final FileParameter cpar = new FileParameter(CACHE_ID, FileParameter.FileType.OUTPUT_FILE);
+      if(config.grab(cpar)) {
+        out = cpar.getValue();
+      }
+
+    }
+
+    @Override
+    protected CacheFloatDistanceInOnDiskMatrix<O, D> makeInstance() {
+      return new CacheFloatDistanceInOnDiskMatrix<O, D>(verbose, database, distance, out);
+    }
+  }
+
+  /**
+   * Main method, delegate to super class.
+   * 
+   * @param args Command line arguments
+   */
+  public static void main(String[] args) {
+    runCLIApplication(CacheFloatDistanceInOnDiskMatrix.class, args);
+  }
+}