lu.lippmann.cdb.lab.mds.MDSResult.java Source code

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Here is the source code for lu.lippmann.cdb.lab.mds.MDSResult.java

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/**
 * Copyright 2014-2016 LIST (Luxembourg Institute of Science and Technology), all right reserved.
 * Authorship : Olivier PARISOT, Yoanne DIDRY
 * Licensed under GNU General Public License version 3
 */
package lu.lippmann.cdb.lab.mds;

import java.util.*;

import org.ejml.simple.SimpleMatrix;

import weka.core.*;

/**
 * 
 * @author didry
 *
 */
public class MDSResult {

    /** Distance matrix + correspondance maps etc **/
    private CollapsedInstances cInstances;

    /** MDS matrix result **/
    private SimpleMatrix coordinates;

    private boolean normalized;

    /**
     * 
     * @param distanceMDS
     * @param matrix
     */
    public MDSResult(final CollapsedInstances cInstances, final SimpleMatrix matrix, final boolean normalized) {
        this.cInstances = cInstances;
        this.coordinates = matrix;
        this.normalized = normalized;
    }

    /**
     * @return the distanceMDS
     */
    public CollapsedInstances getCInstances() {
        return cInstances;
    }

    /**
     * @return the matrix
     */
    public SimpleMatrix getCoordinates() {
        return coordinates;
    }

    /**
     * 
     * @return
     */
    public Instances buildInstancesFromMatrix() {
        final int nbInstances = coordinates.numRows();
        final ArrayList<Attribute> attrs = new ArrayList<Attribute>();
        attrs.add(new Attribute("X", 0));
        attrs.add(new Attribute("Y", 1));
        final Instances ds = new Instances("Projection dataset", attrs, nbInstances);
        for (int i = 0; i < nbInstances; i++) {
            final Instance inst = new DenseInstance(1.0d,
                    new double[] { coordinates.get(i, 0), coordinates.get(i, 1) });
            ds.add(inst);
        }
        return ds;
    }

    /**
     * 
     * @return
     */
    public Instances getCollapsedInstances() {
        if (cInstances.isCollapsed()) {
            final List<Instance> centroids = cInstances.getCentroidMap().getCentroids();
            final int nbCentroids = centroids.size();
            Instances collapsedInstances = new Instances(cInstances.getInstances(), 0);
            for (int i = 0; i < nbCentroids; i++) {
                collapsedInstances.add(centroids.get(i));
            }
            return collapsedInstances;
        } else {
            return cInstances.getInstances();
        }
    }

    /**
     * @return the normalized
     */
    public boolean isNormalized() {
        return normalized;
    }

}