Java tutorial
/* 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. The contents of this file are subject to the terms of either the GNU 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: "Portions Copyrighted [year] [name of copyright owner]" If you wish your version of this file to be governed by only the CDDL or only the GPL Version 3, indicate your decision by adding "[Contributor] elects to include this software in this distribution under the [CDDL or GPL Version 3] license." If you do not indicate a single choice of license, a recipient has the option to distribute your version of this file under either the CDDL, the GPL Version 3 or to extend the choice of license to its licensees as provided above. However, if you add GPL Version 3 code and therefore, elected the GPL Version 3 license, then the option applies only if the new code is made subject to such option by the copyright holder. Contributor(s): Portions Copyrighted 2011 Gephi Consortium. */ 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.data.attributes.api.AttributeColumn; import org.gephi.data.attributes.api.AttributeModel; import org.gephi.data.attributes.api.AttributeOrigin; import org.gephi.data.attributes.api.AttributeTable; import org.gephi.data.attributes.api.AttributeType; import org.gephi.data.attributes.type.DynamicDouble; import org.gephi.data.attributes.type.Interval; import org.gephi.dynamic.api.DynamicController; import org.gephi.dynamic.api.DynamicModel; import org.gephi.graph.api.GraphController; import org.gephi.graph.api.GraphModel; import org.gephi.graph.api.GraphView; import org.gephi.graph.api.HierarchicalGraph; import org.gephi.graph.api.Node; 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 AttributeColumn dynamicCoefficientColumn; //Average private AttributeColumn dynamicAverageCoefficientColumn; private DynamicDouble averages; public DynamicClusteringCoefficient() { GraphController graphController = Lookup.getDefault().lookup(GraphController.class); if (graphController != null && graphController.getModel() != null) { isDirected = graphController.getModel().isDirected(); } } public void execute(GraphModel graphModel, AttributeModel attributeModel) { this.graphModel = graphModel; this.isDirected = graphModel.isDirected(); //Attributes cols if (!averageOnly) { AttributeTable nodeTable = attributeModel.getNodeTable(); dynamicCoefficientColumn = nodeTable.getColumn(DYNAMIC_CLUSTERING_COEFFICIENT); if (dynamicCoefficientColumn == null) { dynamicCoefficientColumn = nodeTable.addColumn(DYNAMIC_CLUSTERING_COEFFICIENT, NbBundle.getMessage(DynamicClusteringCoefficient.class, "DynamicClusteringCoefficient.nodecolumn.ClusteringCoefficient"), AttributeType.DYNAMIC_DOUBLE, AttributeOrigin.COMPUTED, new DynamicDouble()); } } //Column AttributeTable graphTable = attributeModel.getGraphTable(); dynamicAverageCoefficientColumn = graphTable.getColumn(DYNAMIC_AVG_CLUSTERING_COEFFICIENT); if (dynamicAverageCoefficientColumn == null) { dynamicAverageCoefficientColumn = graphTable.addColumn(DYNAMIC_AVG_CLUSTERING_COEFFICIENT, NbBundle.getMessage(DynamicClusteringCoefficient.class, "DynamicClusteringCoefficient.graphcolumn.AvgClusteringCoefficient"), AttributeType.DYNAMIC_DOUBLE, AttributeOrigin.COMPUTED, new DynamicDouble()); } } public String getReport() { //Transform to Map Map<Double, Double> map = new HashMap<Double, Double>(); for (Interval<Double> interval : averages.getIntervals()) { map.put(interval.getLow(), interval.getValue()); } //Time series XYSeries dSeries = ChartUtils.createXYSeries(map, "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; } public void loop(GraphView window, Interval interval) { HierarchicalGraph graph = null; if (isDirected) { graph = graphModel.getHierarchicalDirectedGraph(window); } else { graph = graphModel.getHierarchicalUndirectedGraph(window); } graph.readLock(); 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++]; Interval<Double> valInterval = new Interval<Double>(interval, coef); DynamicDouble val = (DynamicDouble) n.getAttributes().getValue(dynamicCoefficientColumn.getIndex()); if (val == null) { val = new DynamicDouble(valInterval); } else { val = new DynamicDouble(val, valInterval); } n.getAttributes().setValue(dynamicCoefficientColumn.getIndex(), val); if (cancel) { break; } } } graph.readUnlockAll(); //Average double avg = clusteringCoefficientStat.getAverageClusteringCoefficient(); averages = new DynamicDouble(averages, new Interval<Double>(interval.getLow(), interval.getHigh(), false, true, avg)); } public void end() { clusteringCoefficientStat = null; graphModel.getGraphVisible().getAttributes().setValue(dynamicAverageCoefficientColumn.getIndex(), averages); } public void setBounds(Interval bounds) { this.bounds = bounds; } public void setWindow(double window) { this.window = window; } public void setTick(double tick) { this.tick = tick; } public double getWindow() { return window; } public double getTick() { return tick; } 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; } public boolean cancel() { cancel = true; return true; } public void setProgressTicket(ProgressTicket progressTicket) { } }