probcog.clustering.SimpleClusterer.java Source code

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Here is the source code for probcog.clustering.SimpleClusterer.java

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/*******************************************************************************
 * Copyright (C) 2006-2012 Dominik Jain.
 * 
 * This file is part of ProbCog.
 * 
 * ProbCog is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * ProbCog 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 General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with ProbCog. If not, see <http://www.gnu.org/licenses/>.
 ******************************************************************************/
package probcog.clustering;

import java.util.Arrays;

import weka.clusterers.SimpleKMeans;

/**
 * The K-Means clusterer as implemented in WEKA with some additional functionality.
 * @author Dominik Jain
 */
public class SimpleClusterer extends BasicClusterer<SimpleKMeans> {

    int[] clusterIndex2sortedClusterIndex;

    public SimpleClusterer(SimpleKMeans clusterer) {
        super(clusterer);
    }

    public SimpleClusterer() {
        this(new SimpleKMeans());
    }

    public void buildClusterer(int numClusters) throws Exception {
        if (numClusters != 0)
            setNumClusters(numClusters);
        buildClusterer();
    }

    @Override
    public void buildClusterer() throws Exception {
        super.buildClusterer();
        clusterIndex2sortedClusterIndex = getSortedCentroidIndices();
    }

    public void setNumClusters(int n) throws Exception {
        clusterer.setNumClusters(n);
    }

    public double[] getCentroids() {
        return clusterer.getClusterCentroids().attributeToDoubleArray(0);
    }

    public double[] getStdDevs() {
        return clusterer.getClusterStandardDevs().attributeToDoubleArray(0);
    }

    /**
     * classifies the given value
     * @return *not* the index of the actual cluster but the index into a list of clusters sorted in ascending order of centroid mean 
     * @throws Exception 
     */
    @Override
    public int classify(double value) throws Exception {
        int i = super.classify(value);
        return clusterIndex2sortedClusterIndex[i];
    }

    /**
     * 
     * @return an array of indices that maps the index of a centroid to its position in the sorted
     * list of centroids  
     */
    protected int[] getSortedCentroidIndices() {
        // get an unsorted and a sorted version of the centroids array
        int numClusters = clusterer.getNumClusters();
        double[] values = getCentroids();
        double[] sorted_values = (double[]) values.clone();
        Arrays.sort(sorted_values);
        // get an array of indices that corresponds to the sort order
        int[] indices = new int[numClusters];
        for (int i = 0; i < numClusters; i++)
            for (int j = 0; j < numClusters; j++)
                if (sorted_values[i] == values[j])
                    indices[j] = i;
        return indices;
    }
}