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004*/
005/**
006 * Copyright (c) 2011, The University of Southampton and the individual contributors.
007 * All rights reserved.
008 *
009 * Redistribution and use in source and binary forms, with or without modification,
010 * are permitted provided that the following conditions are met:
011 *
012 *   *  Redistributions of source code must retain the above copyright notice,
013 *      this list of conditions and the following disclaimer.
014 *
015 *   *  Redistributions in binary form must reproduce the above copyright notice,
016 *      this list of conditions and the following disclaimer in the documentation
017 *      and/or other materials provided with the distribution.
018 *
019 *   *  Neither the name of the University of Southampton nor the names of its
020 *      contributors may be used to endorse or promote products derived from this
021 *      software without specific prior written permission.
022 *
023 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
024 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
025 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
026 * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
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028 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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030 * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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032 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
033 */
034 package org.openimaj.ml.clustering.kmeans;
035
036import gnu.trove.list.array.TIntArrayList;
037import gnu.trove.map.hash.TIntObjectHashMap;
038
039import org.openimaj.citation.annotation.Reference;
040import org.openimaj.citation.annotation.ReferenceType;
041import org.openimaj.data.DataSource;
042import org.openimaj.data.IndexedViewDataSource;
043import org.openimaj.knn.ShortNearestNeighbours;
044import org.openimaj.ml.clustering.IndexClusters;
045import org.openimaj.ml.clustering.SpatialClusterer;
046import org.openimaj.ml.clustering.assignment.HardAssigner;
047import org.openimaj.ml.clustering.kmeans.HierarchicalShortKMeansResult.Node;
048import org.openimaj.util.pair.IntFloatPair;
049
050/** 
051 * Hierarchical Short K-Means clustering ({@link HierarchicalShortKMeans}) is a simple
052 * hierarchical version of ShortKMeans. The algorithm recursively applies 
053 * @{link ShortKMeans} to create more refined partitions of the data.
054 *
055 * @author Sina Samangooei (ss@ecs.soton.ac.uk)
056 * @author Jonathon Hare (jsh2@ecs.soton.ac.uk)
057 */
058@Reference(
059        type = ReferenceType.Inproceedings,
060        author = { "David. Nist\'er", "Henrik. Stew\'enius" },
061        title = "Scalable Recognition with a Vocabulary Tree",
062        year = "2006",
063        booktitle = "CVPR",
064        pages = { "2161", "", "2168" },
065        customData = {
066                "Date-Added", "2010-11-12 09:33:18 +0000",
067                "Date-Modified", "2010-11-22 15:11:22 +0000"
068        }
069)
070public class HierarchicalShortKMeans implements SpatialClusterer<HierarchicalShortKMeansResult, short[]> {
071        /** data dimensionality */
072        int M;
073
074        /** K clusters per node */
075        int K;
076
077        /** KMeans configuration */
078        KMeansConfiguration<ShortNearestNeighbours, short[]> conf;
079
080        /** Depth of the tree */
081        int depth;
082
083        /** 
084         * Construct a new {@link HierarchicalShortKMeans} with the given parameters.
085         *
086         * @param config configuration for the underlying kmeans clustering.
087         * @param M Data dimensionality.
088         * @param K Number of clusters per node.
089         * @param depth Tree depth.
090         */
091        public HierarchicalShortKMeans(KMeansConfiguration<ShortNearestNeighbours, short[]> config, int M, int K, int depth) {  
092                this.conf = config;
093                this.M = M;
094                this.K = K;
095                this.depth = depth;
096        }
097        
098        /** 
099         * Construct a new {@link HierarchicalShortKMeans} with the given parameters.
100         * Uses the default parameters of the {@link KMeansConfiguration}.
101         *
102         * @param M Data dimensionality.
103         * @param K Number of clusters per node.
104         * @param depth Tree depth.
105         */
106        public HierarchicalShortKMeans(int M, int K, int depth) {       
107                this(new KMeansConfiguration<ShortNearestNeighbours, short[]>(), M, K, depth);
108        }
109
110        /**
111         * Extract a subset of the data to a buffer
112         * 
113         * @param data Data
114         * @param ids Data labels
115         * @param id Label of data to copy
116         * 
117         * @return a new buffer with a copy of the selected data.
118         */
119        private short[][] extractSubset(final short[][] data, int[] ids, int id) {
120                int N = data.length;
121                int M = data[0].length;
122                int count = 0;
123
124                // count how many data points with this label there are
125                for (int i = 0; i < N; i++)
126                        if (ids[i] == id)
127                                count++;
128
129                // copy each datum to the buffer
130                short[][] newData = new short[count][M];
131                count = 0;
132                for (int i = 0; i < N; i++) {
133                        if (ids[i] == id) {
134                                System.arraycopy(data[i], 0, newData[count], 0, M);
135                                count++;
136                        }
137                }
138                return newData;
139        }
140
141        /** 
142         * Compute HierarchicalShortKMeans clustering.
143         * 
144         * @param data Data to cluster.
145         * @param K Number of clusters for this node.
146         * @param height Tree height.
147         * 
148         * @return a new HierarchicalShortKMeans node representing a sub-clustering.
149         **/
150        private Node trainLevel(final short[][] data, int K, int height) {
151                Node node = new Node();
152                node.children = (height == 1) ? null : new Node[K];
153                
154                ShortKMeans kmeans = newShortKMeans(K);
155                node.result = kmeans.cluster(data);
156                
157                HardAssigner<short[], float[], IntFloatPair> assigner = node.result.defaultHardAssigner();
158                
159                if (height > 1) {
160                        int[] ids = assigner.assign(data);
161                        
162                        for (int k = 0; k < K; k++) {
163                                short[][] partition = extractSubset(data, ids, k);
164
165                                int partitionK = Math.min(K, partition.length);
166
167                                node.children[k] = trainLevel(partition, partitionK, height - 1);
168                        }
169                }
170
171                return node;
172        }
173        
174        /** 
175         * Compute HierarchicalShortKMeans clustering.
176         * 
177         * @param data Data to cluster.
178         * @param K Number of clusters for this node.
179         * @param height Tree height.
180         * 
181         * @return a new HierarchicalShortKMeans node representing a sub-clustering.
182         **/
183        private Node trainLevel(final DataSource<short[]> data, int K, int height) {
184                Node node = new Node();
185                node.children = (height == 1) ? null : new Node[K];
186
187                ShortKMeans kmeans = newShortKMeans(K);
188                node.result = kmeans.cluster(data);
189                
190                HardAssigner<short[], float[], IntFloatPair> assigner = node.result.defaultHardAssigner();
191                
192                if (height > 1) {
193                        final TIntObjectHashMap<TIntArrayList> assignments = new TIntObjectHashMap<TIntArrayList>();
194
195                        final short[][] tmp = new short[1][M];
196                        for (int i = 0; i < data.size(); i++) {
197                                data.getData(i, i + 1, tmp);
198                                final int asgn = assigner.assign(tmp[0]);
199
200                                TIntArrayList ids = assignments.get(asgn);
201                                if (ids == null)
202                                        assignments.put(asgn, ids = new TIntArrayList());
203                                ids.add(i);
204                        }
205
206                        for (int k = 0; k < K; k++) {
207                                final int[] indexes = assignments.get(k).toArray();
208                                final DataSource<short[]> partition = new IndexedViewDataSource<short[]>(data, indexes);
209
210                                final int partitionK = Math.min(K, partition.size());
211
212                                node.children[k] = trainLevel(partition, partitionK, height - 1);
213                        }
214                }
215
216                return node;
217        }
218
219        @Override
220        public HierarchicalShortKMeansResult cluster(final short[][] data) {
221                HierarchicalShortKMeansResult result = new HierarchicalShortKMeansResult();
222                
223                result.K = K;
224                result.M = M;
225                result.depth = depth;
226                result.root = trainLevel(data, Math.min(K, data.length), depth);
227                
228                return result;
229        }
230        
231        @Override
232        public int[][] performClustering(short[][] data) {
233                HierarchicalShortKMeansResult clusters = this.cluster(data);
234                return new IndexClusters(clusters.defaultHardAssigner().assign(data)).clusters();
235        }
236        
237        @Override
238        public HierarchicalShortKMeansResult cluster(DataSource<short[]> data) {
239                HierarchicalShortKMeansResult result = new HierarchicalShortKMeansResult();
240                
241                result.K = K;
242                result.M = M;
243                result.depth = depth;
244                result.root = trainLevel(data, Math.min(K, data.size()), depth);
245                
246                return result;
247        }
248
249        private ShortKMeans newShortKMeans(int K) {
250                KMeansConfiguration<ShortNearestNeighbours, short[]> newConf = conf.clone();
251                newConf.setK(K);
252                return new ShortKMeans(newConf);
253        }
254}