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authorAndrej Shadura <andrewsh@debian.org>2019-03-09 22:30:28 +0000
committerAndrej Shadura <andrewsh@debian.org>2019-03-09 22:30:28 +0000
commitcde76aeb42240f7270bc6605c606ae07d2dc5a7d (patch)
treec3ebf1d7745224f524da31dbabc5d76b9ea75916 /src/de/lmu/ifi/dbs/elki/algorithm/MaterializeDistances.java
Import Upstream version 0.4.0~beta1
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+package de.lmu.ifi.dbs.elki.algorithm;
+/*
+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.util.ArrayList;
+import java.util.Collection;
+
+import de.lmu.ifi.dbs.elki.data.type.TypeInformation;
+import de.lmu.ifi.dbs.elki.data.type.TypeUtil;
+import de.lmu.ifi.dbs.elki.database.Database;
+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.distancevalue.NumberDistance;
+import de.lmu.ifi.dbs.elki.logging.Logging;
+import de.lmu.ifi.dbs.elki.result.CollectionResult;
+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.pairs.CTriple;
+
+/**
+ * Algorithm to materialize all the distances in a data set.
+ *
+ * The result can then be used with the DoubleDistanceParser and
+ * MultipleFileInput to use cached distances.
+ *
+ * Symmetry is assumed.
+ *
+ * @param <O> Object type
+ * @param <D> Distance type
+ */
+@Title("MaterializeDistances")
+@Description("Materialize all distances in the data set to use as cached/precalculated data.")
+public class MaterializeDistances<O, D extends NumberDistance<D, ?>> extends AbstractDistanceBasedAlgorithm<O, D, CollectionResult<CTriple<DBID, DBID, Double>>> {
+ /**
+ * The logger for this class.
+ */
+ private static final Logging logger = Logging.getLogger(MaterializeDistances.class);
+
+ /**
+ * Constructor.
+ *
+ * @param distanceFunction Parameterization
+ */
+ public MaterializeDistances(DistanceFunction<? super O, D> distanceFunction) {
+ super(distanceFunction);
+ }
+
+ /**
+ * Iterates over all points in the database.
+ */
+ public CollectionResult<CTriple<DBID, DBID, Double>> run(Database database, Relation<O> relation) {
+ DistanceQuery<O, D> distFunc = database.getDistanceQuery(relation, getDistanceFunction());
+ final int size = relation.size();
+
+ Collection<CTriple<DBID, DBID, Double>> r = new ArrayList<CTriple<DBID, DBID, Double>>(size * (size + 1) / 2);
+
+ for(DBID id1 : relation.iterDBIDs()) {
+ for(DBID id2 : relation.iterDBIDs()) {
+ // skip inverted pairs
+ if(id2.compareTo(id1) > 0) {
+ continue;
+ }
+ double d = distFunc.distance(id1, id2).doubleValue();
+ r.add(new CTriple<DBID, DBID, Double>(id1, id2, d));
+ }
+ }
+ return new CollectionResult<CTriple<DBID, DBID, Double>>("Distance Matrix", "distance-matrix", r);
+ }
+
+ @Override
+ protected Logging getLogger() {
+ return logger;
+ }
+
+ @Override
+ public TypeInformation[] getInputTypeRestriction() {
+ return TypeUtil.array(getDistanceFunction().getInputTypeRestriction());
+ }
+
+ /**
+ * Parameterization class.
+ *
+ * @author Erich Schubert
+ *
+ * @apiviz.exclude
+ */
+ public static class Parameterizer<O, D extends NumberDistance<D, ?>> extends AbstractDistanceBasedAlgorithm.Parameterizer<O, D> {
+ @Override
+ protected MaterializeDistances<O, D> makeInstance() {
+ return new MaterializeDistances<O, D>(distanceFunction);
+ }
+ }
+} \ No newline at end of file