edu.uga.cs.fluxbuster.clustering.hierarchicalclustering.Dendrogram.java Source code

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Here is the source code for edu.uga.cs.fluxbuster.clustering.hierarchicalclustering.Dendrogram.java

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/*
 * Copyright (C) 2009 Roberto Perdisci
 * Author: Roberto Perdisci
 *
 * This program 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 2 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 General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package edu.uga.cs.fluxbuster.clustering.hierarchicalclustering;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serializable;
import java.util.Map;
import java.util.TreeMap;
import java.util.Vector;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

/**
 * This class represents the result of hierarchical clustering represented
 * as a dendrogram
 * 
 * @author Roberto Perdisci
 */
public class Dendrogram implements Serializable {

    static final long serialVersionUID = -1235809600124455376L;

    private Map<Double, Vector<HCluster>> heights = new TreeMap<Double, Vector<HCluster>>();

    private static Log log = LogFactory.getLog(Dendrogram.class);

    /**
     * Adds the clusters at a specific height in the dendrogram.
     *
     * @param height the height
     * @param clusters the clusters
     */
    @SuppressWarnings("unchecked")
    public void addClusters(double height, Vector<HCluster> clusters) {
        // Makes a deep copy
        Vector<HCluster> c = (Vector<HCluster>) deepCopy(clusters);
        getHeights().put(height, c);
    }

    /**
     * Creates a deep copy of any object.
     *
     * @param o the object to copy
     * @return the copy
     */
    public Object deepCopy(Object o) {
        try {
            ByteArrayOutputStream byteOut = new ByteArrayOutputStream();
            ObjectOutputStream out = new ObjectOutputStream(byteOut);
            out.writeObject(o);
            out.close();

            byte[] data = byteOut.toByteArray();
            ObjectInputStream in = new ObjectInputStream(new ByteArrayInputStream(data));
            Object copy = in.readObject();
            in.close();

            return copy;
        } catch (Exception e) {
            if (log.isErrorEnabled()) {
                log.error("Error performing deep copy.", e);
            }
        }

        return null;
    }

    /**
     * Gets the clusters at a particular cut height.
     *
     * @param cutHeight the cut height
     * @return the clusters
     */
    public Vector<HCluster> getClusters(double cutHeight) {
        double height = 0;
        for (double h : getHeights().keySet()) {
            if (h > cutHeight)
                break;

            height = h;
        }

        return getHeights().get(height);
    }

    /**
     * Prints the dendrogram to stdout.
     */
    public void print() {
        for (double h : getHeights().keySet()) {
            System.out.println("h=" + h + " ---> ");
            for (HCluster v : getHeights().get(h)) {
                System.out.println(" " + v);
            }
        }
    }

    /**
     * Prints the clusters at a cut height.
     *
     * @param h the cut height.
     */
    public void print(double h) {
        System.out.println("h=" + h + " ---> ");
        for (HCluster v : getHeights().get(h)) {
            System.out.print(" " + v + " ");
        }
        System.out.println("Num of clusters = " + getHeights().get(h).size());
    }

    /**
     * Sets the dendrogram with the list clusters at specific heights.
     *
     * @param heights the heights, clusters map
     */
    public void setHeights(Map<Double, Vector<HCluster>> heights) {
        this.heights = heights;
    }

    /**
     * Gets all of the clusters at each height.
     *
     * @return the heights, clusters map
     */
    public Map<Double, Vector<HCluster>> getHeights() {
        return heights;
    }
}