DynamicClusteringCoefficient.java

/*
Copyright 2008-2010 Gephi
Authors : Mathieu Bastian <mathieu.bastian@gephi.org>
Website : http://www.gephi.org

This file is part of Gephi.

DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.

Copyright 2011 Gephi Consortium. All rights reserved.

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General Public License Version 3 only ("GPL") or the Common
Development and Distribution License("CDDL") (collectively, the
"License"). You may not use this file except in compliance with the
License. You can obtain a copy of the License at
http://gephi.org/about/legal/license-notice/
or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
specific language governing permissions and limitations under the
License.  When distributing the software, include this License Header
Notice in each file and include the License files at
/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
License Header, with the fields enclosed by brackets [] replaced by
your own identifying information:
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"[Contributor] elects to include this software in this distribution
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 */
package org.gephi.statistics.plugin.dynamic;

import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.HashMap;
import java.util.Map;
import org.gephi.graph.api.Column;
import org.gephi.graph.api.Graph;
import org.gephi.graph.api.GraphController;
import org.gephi.graph.api.GraphModel;
import org.gephi.graph.api.GraphView;
import org.gephi.graph.api.Interval;
import org.gephi.graph.api.Node;
import org.gephi.graph.api.Table;
import org.gephi.graph.api.TimeRepresentation;
import org.gephi.graph.api.types.IntervalDoubleMap;
import org.gephi.graph.api.types.TimestampDoubleMap;
import org.gephi.statistics.plugin.ChartUtils;
import org.gephi.statistics.plugin.ClusteringCoefficient;
import org.gephi.statistics.spi.DynamicStatistics;
import org.gephi.utils.longtask.spi.LongTask;
import org.gephi.utils.progress.ProgressTicket;
import org.jfree.chart.ChartFactory;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.data.xy.XYSeries;
import org.jfree.data.xy.XYSeriesCollection;
import org.openide.util.Lookup;
import org.openide.util.NbBundle;

/**
 *
 * @author Mathieu Bastian
 */
public class DynamicClusteringCoefficient implements DynamicStatistics, LongTask {

    public static final String DYNAMIC_AVG_CLUSTERING_COEFFICIENT = "dynamic_avg_clustering";
    public static final String DYNAMIC_CLUSTERING_COEFFICIENT = "dynamic_clustering";
    //Data
    private GraphModel graphModel;
    private double window;
    private double tick;
    private Interval bounds;
    private boolean isDirected;
    private boolean averageOnly;
    private boolean cancel = false;
    private ClusteringCoefficient clusteringCoefficientStat;
    //Cols
    private Column dynamicCoefficientColumn;
    //Average
    private Column dynamicAverageCoefficientColumn;
    private Map<Double, Double> averages;

    public DynamicClusteringCoefficient() {
        GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
        if (graphController != null && graphController.getGraphModel() != null) {
            isDirected = graphController.getGraphModel().isDirected();
        }
    }

    @Override
    public void execute(GraphModel graphModel) {
        this.graphModel = graphModel;
        this.isDirected = graphModel.isDirected();
        this.averages = new HashMap<>();

        //Attributes cols
        if (!averageOnly) {
            TimeRepresentation tr = graphModel.getConfiguration().getTimeRepresentation();

            Table nodeTable = graphModel.getNodeTable();
            dynamicCoefficientColumn = nodeTable.getColumn(DYNAMIC_CLUSTERING_COEFFICIENT);
            if (dynamicCoefficientColumn == null) {
                dynamicCoefficientColumn = nodeTable.addColumn(DYNAMIC_CLUSTERING_COEFFICIENT, NbBundle.getMessage(DynamicClusteringCoefficient.class, "DynamicClusteringCoefficient.nodecolumn.ClusteringCoefficient"), tr.equals(TimeRepresentation.INTERVAL) ? IntervalDoubleMap.class : TimestampDoubleMap.class, null);
            }
        }
    }

    @Override
    public String getReport() {
        //Time series
        XYSeries dSeries = ChartUtils.createXYSeries(averages, "Clustering Coefficient Time Series");

        XYSeriesCollection dataset = new XYSeriesCollection();
        dataset.addSeries(dSeries);

        JFreeChart chart = ChartFactory.createXYLineChart(
                "Clustering Coefficient",
                "Time",
                "Average Clustering Coefficient",
                dataset,
                PlotOrientation.VERTICAL,
                true,
                false,
                false);

        chart.removeLegend();
        ChartUtils.decorateChart(chart);
        ChartUtils.scaleChart(chart, dSeries, false);
        String coefficientImageFile = ChartUtils.renderChart(chart, "coefficient-ts.png");

        NumberFormat f = new DecimalFormat("#0.000000");

        String report = "<HTML> <BODY> <h1>Dynamic Clustering Coefficient Report </h1> "
                + "<hr>"
                + "<br> Bounds: from " + f.format(bounds.getLow()) + " to " + f.format(bounds.getHigh())
                + "<br> Window: " + window
                + "<br> Tick: " + tick
                + "<br><br><h2> Average clustering cloefficient over time: </h2>"
                + "<br /><br />" + coefficientImageFile;

        /*for (Interval<Double> average : averages) {
        report += average.toString(dynamicModel.getTimeFormat().equals(DynamicModel.TimeFormat.DOUBLE)) + "<br />";
        }*/
        report += "<br /><br /></BODY></HTML>";
        return report;
    }

    @Override
    public void loop(GraphView window, Interval interval) {
        Graph graph;
        if (isDirected) {
            graph = graphModel.getDirectedGraph(window);
        } else {
            graph = graphModel.getUndirectedGraph(window);
        }
        TimeRepresentation tr = graphModel.getConfiguration().getTimeRepresentation();

        graph.readLock();
        
        try {
            clusteringCoefficientStat = new ClusteringCoefficient();
            clusteringCoefficientStat.setDirected(isDirected);
            clusteringCoefficientStat.triangles(graph);

            //Columns
            if (!averageOnly) {
                double[] coefficients = clusteringCoefficientStat.getCoefficientReuslts();
                int i = 0;
                for (Node n : graph.getNodes()) {
                    double coef = coefficients[i++];

                    switch (tr) {
                        case INTERVAL:
                            n.setAttribute(dynamicCoefficientColumn, coef, new Interval(interval.getLow(), interval.getLow() + tick));
                            break;
                        case TIMESTAMP:
                            n.setAttribute(dynamicCoefficientColumn, coef, interval.getLow());
                            n.setAttribute(dynamicCoefficientColumn, coef, interval.getHigh());
                            break;
                    }

                    if (cancel) {
                        break;
                    }
                }
            }
        } finally {
            graph.readUnlockAll();
        }

        //Average
        double avg = clusteringCoefficientStat.getAverageClusteringCoefficient();
        graphModel.getGraphVisible().setAttribute(DYNAMIC_AVG_CLUSTERING_COEFFICIENT, avg, interval.getLow());
        graphModel.getGraphVisible().setAttribute(DYNAMIC_AVG_CLUSTERING_COEFFICIENT, avg, interval.getHigh());

        averages.put(interval.getLow(), avg);
        averages.put(interval.getHigh(), avg);
    }

    @Override
    public void end() {
        clusteringCoefficientStat = null;
    }

    @Override
    public void setBounds(Interval bounds) {
        this.bounds = bounds;
    }

    @Override
    public void setWindow(double window) {
        this.window = window;
    }

    @Override
    public void setTick(double tick) {
        this.tick = tick;
    }

    @Override
    public double getWindow() {
        return window;
    }

    @Override
    public double getTick() {
        return tick;
    }

    @Override
    public Interval getBounds() {
        return bounds;
    }

    public void setDirected(boolean isDirected) {
        this.isDirected = isDirected;
    }

    public boolean isDirected() {
        return isDirected;
    }

    public void setAverageOnly(boolean averageOnly) {
        this.averageOnly = averageOnly;
    }

    public boolean isAverageOnly() {
        return averageOnly;
    }

    @Override
    public boolean cancel() {
        cancel = true;
        return true;
    }

    @Override
    public void setProgressTicket(ProgressTicket progressTicket) {
    }
}