Java tutorial
/* 2 Copyright 2008-2011 Gephi 3 Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org> 4 Website : http://www.gephi.org 5 6 This file is part of Gephi. 7 8 DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER. 9 10 Copyright 2011 Gephi Consortium. All rights reserved. 11 12 The contents of this file are subject to the terms of either the GNU 13 General Public License Version 3 only ("GPL") or the Common 14 Development and Distribution License("CDDL") (collectively, the 15 "License"). You may not use this file except in compliance with the 16 License. You can obtain a copy of the License at 17 http://gephi.org/about/legal/license-notice/ 18 or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the 19 specific language governing permissions and limitations under the 20 License. When distributing the software, include this License Header 21 Notice in each file and include the License files at 22 /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the 23 License Header, with the fields enclosed by brackets [] replaced by 24 your own identifying information: 25 "Portions Copyrighted [year] [name of copyright owner]" 26 27 If you wish your version of this file to be governed by only the CDDL 28 or only the GPL Version 3, indicate your decision by adding 29 "[Contributor] elects to include this software in this distribution 30 under the [CDDL or GPL Version 3] license." If you do not indicate a 31 single choice of license, a recipient has the option to distribute 32 your version of this file under either the CDDL, the GPL Version 3 or 33 to extend the choice of license to its licensees as provided above. 34 However, if you add GPL Version 3 code and therefore, elected the GPL 35 Version 3 license, then the option applies only if the new code is 36 made subject to such option by the copyright holder. 37 38 Contributor(s): 39 40 Portions Copyrighted 2011 Gephi Consortium. 41 */ package org.gephi.statistics.plugin; import java.util.HashMap; import java.util.Map; import org.gephi.attribute.api.AttributeModel; import org.gephi.attribute.api.Column; import org.gephi.attribute.api.Table; import org.gephi.graph.api.DirectedGraph; import org.gephi.graph.api.Edge; import org.gephi.graph.api.EdgeIterable; import org.gephi.graph.api.Graph; import org.gephi.graph.api.GraphController; import org.gephi.graph.api.GraphModel; import org.gephi.graph.api.Node; import org.gephi.statistics.spi.Statistics; import org.gephi.utils.longtask.spi.LongTask; import org.gephi.utils.progress.Progress; 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; /** * * @author pjmcswee */ public class EigenvectorCentrality implements Statistics, LongTask { public static final String EIGENVECTOR = "eigencentrality"; private int numRuns = 100; private double[] centralities; private double sumChange; private ProgressTicket progress; /** * */ private boolean isCanceled; private boolean isDirected; public EigenvectorCentrality() { GraphController graphController = Lookup.getDefault().lookup(GraphController.class); if (graphController != null && graphController.getGraphModel() != null) { isDirected = graphController.getGraphModel().isDirected(); } } public void setNumRuns(int numRuns) { this.numRuns = numRuns; } /** * * @return */ public int getNumRuns() { return numRuns; } /** * * @return */ public boolean isDirected() { return isDirected; } /** * * @param isDirected */ public void setDirected(boolean isDirected) { this.isDirected = isDirected; } /** * * @param graphModel * @param attributeModel */ @Override public void execute(GraphModel graphModel, AttributeModel attributeModel) { isDirected = graphModel.isDirected(); isCanceled = false; Graph graph; if (isDirected) { graph = graphModel.getDirectedGraphVisible(); } else { graph = graphModel.getUndirectedGraphVisible(); } execute(graph, attributeModel); } public void execute(Graph hgraph, AttributeModel attributeModel) { Column column = initializeAttributeColunms(attributeModel); int N = hgraph.getNodeCount(); hgraph.readLock(); centralities = new double[N]; Progress.start(progress, numRuns); HashMap<Integer, Node> indicies = new HashMap<Integer, Node>(); HashMap<Node, Integer> invIndicies = new HashMap<Node, Integer>(); fillIndiciesMaps(hgraph, centralities, indicies, invIndicies); sumChange = calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, isDirected, numRuns); saveCalculatedValues(hgraph, column, indicies, centralities); hgraph.readUnlock(); Progress.finish(progress); } private Column initializeAttributeColunms(AttributeModel attributeModel) { Table nodeTable = attributeModel.getNodeTable(); Column eigenCol = nodeTable.getColumn(EIGENVECTOR); if (eigenCol == null) { eigenCol = nodeTable.addColumn(EIGENVECTOR, "Eigenvector Centrality", Double.class, new Double(0)); } return eigenCol; } private void saveCalculatedValues(Graph hgraph, Column attributeColumn, HashMap<Integer, Node> indicies, double[] eigCenrtalities) { int N = hgraph.getNodeCount(); for (int i = 0; i < N; i++) { Node s = indicies.get(i); s.setAttribute(attributeColumn, eigCenrtalities[i]); } } public void fillIndiciesMaps(Graph hgraph, double[] eigCentralities, HashMap<Integer, Node> indicies, HashMap<Node, Integer> invIndicies) { if (indicies == null || invIndicies == null) { return; } int count = 0; for (Node u : hgraph.getNodes()) { indicies.put(count, u); invIndicies.put(u, count); eigCentralities[count] = 1; count++; } } private double computeMaxValueAndTempValues(Graph hgraph, HashMap<Integer, Node> indicies, HashMap<Node, Integer> invIndicies, double[] tempValues, double[] centralityValues, boolean directed) { double max = 0.; int N = hgraph.getNodeCount(); for (int i = 0; i < N; i++) { Node u = indicies.get(i); EdgeIterable iter = null; if (directed) { iter = ((DirectedGraph) hgraph).getInEdges(u); } else { iter = hgraph.getEdges(u); } for (Edge e : iter) { Node v = hgraph.getOpposite(u, e); Integer id = invIndicies.get(v); tempValues[i] += centralityValues[id]; } max = Math.max(max, tempValues[i]); if (isCanceled) { return max; } } return max; } private double updateValues(Graph hgraph, double[] tempValues, double[] centralityValues, double max) { double sumChanged = 0.; int N = hgraph.getNodeCount(); for (int k = 0; k < N; k++) { if (max != 0) { sumChanged += Math.abs(centralityValues[k] - (tempValues[k] / max)); centralityValues[k] = tempValues[k] / max; } if (isCanceled) { return sumChanged; } } return sumChanged; } public double calculateEigenvectorCentrality(Graph hgraph, double[] eigCentralities, HashMap<Integer, Node> indicies, HashMap<Node, Integer> invIndicies, boolean directed, int numIterations) { int N = hgraph.getNodeCount(); double sumChanged = 0.; double[] tmp = new double[N]; for (int s = 0; s < numIterations; s++) { double max = computeMaxValueAndTempValues(hgraph, indicies, invIndicies, tmp, eigCentralities, directed); sumChanged = updateValues(hgraph, tmp, eigCentralities, max); if (isCanceled) { return sumChanged; } Progress.progress(progress); } return sumChanged; } /** * * @return */ @Override public String getReport() { //distribution of values Map<Double, Integer> dist = new HashMap<Double, Integer>(); for (int i = 0; i < centralities.length; i++) { Double d = centralities[i]; if (dist.containsKey(d)) { Integer v = dist.get(d); dist.put(d, v + 1); } else { dist.put(d, 1); } } //Distribution series XYSeries dSeries = ChartUtils.createXYSeries(dist, "Eigenvector Centralities"); XYSeriesCollection dataset = new XYSeriesCollection(); dataset.addSeries(dSeries); JFreeChart chart = ChartFactory.createScatterPlot("Eigenvector Centrality Distribution", "Score", "Count", dataset, PlotOrientation.VERTICAL, true, false, false); chart.removeLegend(); ChartUtils.decorateChart(chart); ChartUtils.scaleChart(chart, dSeries, true); String imageFile = ChartUtils.renderChart(chart, "eigenvector-centralities.png"); String report = "<HTML> <BODY> <h1>Eigenvector Centrality Report</h1> " + "<hr>" + "<h2> Parameters: </h2>" + "Network Interpretation: " + (isDirected ? "directed" : "undirected") + "<br>" + "Number of iterations: " + numRuns + "<br>" + "Sum change: " + sumChange + "<br> <h2> Results: </h2>" + imageFile + "</BODY></HTML>"; return report; } @Override public boolean cancel() { this.isCanceled = true; return true; } @Override public void setProgressTicket(ProgressTicket progressTicket) { this.progress = progressTicket; } }