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diff --git a/src/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestSumPointsInitialMeans.java b/src/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/initialization/FarthestSumPointsInitialMeans.java
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+package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization;
+
+/*
+ This file is part of ELKI:
+ Environment for Developing KDD-Applications Supported by Index-Structures
+
+ Copyright (C) 2014
+ 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.List;
+
+import de.lmu.ifi.dbs.elki.data.NumberVector;
+import de.lmu.ifi.dbs.elki.database.Database;
+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.datastore.WritableDoubleDataStore;
+import de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs;
+import de.lmu.ifi.dbs.elki.database.ids.DBIDIter;
+import de.lmu.ifi.dbs.elki.database.ids.DBIDRef;
+import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil;
+import de.lmu.ifi.dbs.elki.database.ids.DBIDVar;
+import de.lmu.ifi.dbs.elki.database.ids.DBIDs;
+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.PrimitiveDistanceFunction;
+import de.lmu.ifi.dbs.elki.math.random.RandomFactory;
+
+/**
+ * K-Means initialization by repeatedly choosing the farthest point (by the
+ * <em>sum</em> of distances to previous objects).
+ *
+ * Note: this is less random than other initializations, so running multiple
+ * times will be more likely to return the same local minima.
+ *
+ * @author Erich Schubert
+ *
+ * @param <O> Object type for kmedoids and kmedians
+ */
+public class FarthestSumPointsInitialMeans<O> extends FarthestPointsInitialMeans<O> {
+ /**
+ * Constructor.
+ *
+ * @param rnd Random generator.
+ * @param dropfirst Flag to discard the first vector.
+ */
+ public FarthestSumPointsInitialMeans(RandomFactory rnd, boolean dropfirst) {
+ super(rnd, dropfirst);
+ }
+
+ @Override
+ public <T extends NumberVector, V extends NumberVector> List<V> chooseInitialMeans(Database database, Relation<T> relation, int k, PrimitiveDistanceFunction<? super T> distanceFunction, NumberVector.Factory<V> factory) {
+ // Get a distance query
+ DistanceQuery<T> distQ = database.getDistanceQuery(relation, distanceFunction);
+
+ DBIDs ids = relation.getDBIDs();
+ WritableDoubleDataStore store = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, 0.);
+
+ // Chose first mean
+ List<V> means = new ArrayList<>(k);
+
+ DBIDRef first = DBIDUtil.randomSample(ids, 1, rnd).iter();
+ T prevmean = relation.get(first);
+ means.add(factory.newNumberVector(prevmean));
+
+ // Find farthest object each.
+ DBIDVar best = DBIDUtil.newVar(first);
+ for(int i = (dropfirst ? 0 : 1); i < k; i++) {
+ double maxdist = Double.NEGATIVE_INFINITY;
+ for(DBIDIter it = ids.iter(); it.valid(); it.advance()) {
+ final double prev = store.doubleValue(it);
+ if(prev != prev) {
+ continue; // NaN: already chosen!
+ }
+ double dsum = prev + distQ.distance(prevmean, it);
+ // Don't store distance to first mean, when it will be dropped below.
+ if(i > 0) {
+ store.putDouble(it, dsum);
+ }
+ if(dsum > maxdist) {
+ maxdist = dsum;
+ best.set(it);
+ }
+ }
+ // Add new mean (and drop the initial mean when desired)
+ if(i == 0) {
+ means.clear(); // Remove temporary first element.
+ }
+ store.putDouble(best, Double.NaN); // So it won't be chosen twice.
+ prevmean = relation.get(best);
+ means.add(factory.newNumberVector(prevmean));
+ }
+
+ // Explicitly destroy temporary data.
+ store.destroy();
+ return means;
+ }
+
+ @Override
+ public DBIDs chooseInitialMedoids(int k, DBIDs ids, DistanceQuery<? super O> distQ) {
+ @SuppressWarnings("unchecked")
+ final Relation<O> relation = (Relation<O>) distQ.getRelation();
+
+ WritableDoubleDataStore store = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, 0.);
+
+ ArrayModifiableDBIDs means = DBIDUtil.newArray(k);
+
+ DBIDRef first = DBIDUtil.randomSample(ids, 1, rnd).iter();
+ means.add(first);
+ O prevmean = relation.get(first);
+
+ DBIDVar best = DBIDUtil.newVar(first);
+ for(int i = (dropfirst ? 0 : 1); i < k; i++) {
+ // Find farthest object:
+ double maxdist = Double.NEGATIVE_INFINITY;
+ for(DBIDIter it = relation.iterDBIDs(); it.valid(); it.advance()) {
+ final double prev = store.doubleValue(it);
+ if(prev != prev) {
+ continue; // NaN: already chosen!
+ }
+ double dsum = prev + distQ.distance(prevmean, it);
+ // Don't store distance to first mean, when it will be dropped below.
+ if(i > 0) {
+ store.putDouble(it, dsum);
+ }
+ if(dsum > maxdist) {
+ maxdist = dsum;
+ best.set(it);
+ }
+ }
+ // Add new mean:
+ if(k == 0) {
+ means.clear(); // Remove temporary first element.
+ }
+ store.putDouble(best, Double.NaN); // So it won't be chosen twice.
+ prevmean = relation.get(best);
+ means.add(best);
+ }
+
+ return means;
+ }
+
+ /**
+ * Parameterization class.
+ *
+ * @author Erich Schubert
+ *
+ * @apiviz.exclude
+ */
+ public static class Parameterizer<V> extends FarthestPointsInitialMeans.Parameterizer<V> {
+ /**
+ * Flag for discarding the first object chosen.
+ */
+ protected boolean keepfirst = false;
+
+ @Override
+ protected FarthestSumPointsInitialMeans<V> makeInstance() {
+ return new FarthestSumPointsInitialMeans<>(rnd, !keepfirst);
+ }
+ }
+}