biomine.bmvis2.pipeline.KMedoidsHighlight.java Source code

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Here is the source code for biomine.bmvis2.pipeline.KMedoidsHighlight.java

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

package biomine.bmvis2.pipeline;

import java.awt.Color;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map.Entry;

import javax.swing.Box;
import javax.swing.BoxLayout;
import javax.swing.JCheckBox;
import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JSpinner;
import javax.swing.SpinnerNumberModel;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;

import org.json.simple.JSONObject;

import biomine.bmvis2.GraphCache;
import biomine.bmvis2.SimpleVisualGraph;
import biomine.bmvis2.VisualGraph;
import biomine.bmvis2.VisualNode;
import biomine.bmvis2.VisualGraph.Change;
import biomine.bmvis2.algorithms.KMedoids;
import biomine.bmvis2.algorithms.KMedoids.KMedoidsResult;
import biomine.bmvis2.color.ColorPalette;

/**
 * Implements visualisation for k-medoids algorithm. Can color either just medoids
 * or clusters.
 * 
 * TODO: k-medoids grouper
 * 
 * @author alhartik
 *
 */
public class KMedoidsHighlight implements GraphOperation {

    private Color hlColor = Color.RED;
    private boolean showClusters = false;
    private GraphCache<ArrayList<VisualNode>> cache = new GraphCache<ArrayList<VisualNode>>(
            Change.POINTS_OF_INTEREST, Change.STRUCTURE);
    private GraphCache<HashMap<VisualNode, Integer>> clusterCache = new GraphCache<HashMap<VisualNode, Integer>>(
            Change.POINTS_OF_INTEREST, Change.STRUCTURE);
    private int k = 3;

    public int getK() {
        return k;
    }

    public void setK(int k) {
        this.k = k;
        cache.clear();
    }

    @Override
    public void doOperation(VisualGraph g) throws GraphOperationException {
        ArrayList<VisualNode> rlist = cache.get(g);
        HashMap<VisualNode, Integer> clusters = clusterCache.get(g);
        if (rlist == null) {
            rlist = new ArrayList<VisualNode>();
            SimpleVisualGraph sg = new SimpleVisualGraph(g);
            KMedoidsResult r = KMedoids.runKMedoids(sg, k);
            int[] meds = r.medoids;
            for (int i = 0; i < k; i++)
                rlist.add(sg.getVisualNode(meds[i]));
            cache.put(g, rlist);
            clusters = new HashMap<VisualNode, Integer>();
            for (int i = 0; i < sg.n; i++) {
                clusters.put(sg.getVisualNode(i), r.clusters[i]);
            }
            clusterCache.put(g, clusters);
        }

        assert (rlist.size() == k);
        if (showClusters && k < ColorPalette.pastelShades.length) {
            for (Entry<VisualNode, Integer> ent : clusters.entrySet()) {
                ent.getKey().setBaseColor(ColorPalette.pastelShades[ent.getValue()]);
            }
        }
        for (int i = 0; i < rlist.size(); i++) {
            rlist.get(i).setBaseColor(hlColor);
            //System.out.println(rlist.get(i));
            int c = i + 1;
            //rlist.get(i).addExtraLabel(""+c+". representative");
        }
    }

    @Override
    public JComponent getSettingsComponent(final SettingsChangeCallback v, VisualGraph graph) {
        Box ret = new Box(BoxLayout.X_AXIS);
        ret.add(new JLabel("k:"));

        final JSpinner spin = new JSpinner(new SpinnerNumberModel(3, 1, 1000, 1));

        spin.addChangeListener(new ChangeListener() {
            public void stateChanged(ChangeEvent arg0) {
                setK(((Number) spin.getValue()).intValue());
                v.settingsChanged(false);
            }
        });
        ret.add(spin);

        final JCheckBox showClustersBox = new JCheckBox("Color clusters");
        ret.add(showClustersBox);
        showClustersBox.addChangeListener(new ChangeListener() {
            @Override
            public void stateChanged(ChangeEvent arg0) {
                showClusters = showClustersBox.isSelected();
                v.settingsChanged(false);
            }
        });
        return ret;
    }

    @Override
    public String getTitle() {
        return "k-medoids hilight";
    }

    @Override
    public String getToolTip() {
        return null;
    }

    @Override
    public void fromJSON(JSONObject o) throws Exception {
        setK(((Number) o.get("k")).intValue());
        Object b = o.get("colorClusters");
        if (b != null && b instanceof Boolean) {
            Boolean bb = (Boolean) b;
            showClusters = bb;
        }
    }

    @Override
    public JSONObject toJSON() {
        JSONObject ret = new JSONObject();
        ret.put("k", getK());
        ret.put("colorClusters", showClusters);
        return ret;
    }
}