Java tutorial
/* Copyright 2008-2011 Gephi Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@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. 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Contributor(s): Portions Copyrighted 2011 Gephi Consortium. */ package org.gephi.statistics.plugin; 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.AttributeRow; import org.gephi.data.attributes.api.AttributeTable; import org.gephi.data.attributes.api.AttributeType; import org.gephi.graph.api.Edge; import org.gephi.graph.api.EdgeIterable; import org.gephi.graph.api.GraphController; import org.gephi.graph.api.GraphModel; import org.gephi.graph.api.HierarchicalDirectedGraph; import org.gephi.graph.api.HierarchicalGraph; import org.gephi.graph.api.HierarchicalUndirectedGraph; 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.getModel() != null) { isDirected = graphController.getModel().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 */ public void execute(GraphModel graphModel, AttributeModel attributeModel) { HierarchicalGraph graph = null; if (isDirected) { graph = graphModel.getHierarchicalDirectedGraphVisible(); } else { graph = graphModel.getHierarchicalUndirectedGraphVisible(); } execute(graph, attributeModel); } public void execute(HierarchicalGraph hgraph, AttributeModel attributeModel) { AttributeTable nodeTable = attributeModel.getNodeTable(); AttributeColumn eigenCol = nodeTable.getColumn(EIGENVECTOR); if (eigenCol == null) { eigenCol = nodeTable.addColumn(EIGENVECTOR, "Eigenvector Centrality", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0)); } int N = hgraph.getNodeCount(); hgraph.readLock(); double[] tmp = new double[N]; centralities = new double[N]; Progress.start(progress, numRuns); HashMap<Integer, Node> indicies = new HashMap<Integer, Node>(); HashMap<Node, Integer> invIndicies = new HashMap<Node, Integer>(); int count = 0; for (Node u : hgraph.getNodes()) { indicies.put(count, u); invIndicies.put(u, count); centralities[count] = 1; count++; } for (int s = 0; s < numRuns; s++) { double max = 0; for (int i = 0; i < N; i++) { Node u = indicies.get(i); EdgeIterable iter = null; if (isDirected) { iter = ((HierarchicalDirectedGraph) hgraph).getInEdgesAndMetaInEdges(u); } else { iter = ((HierarchicalUndirectedGraph) hgraph).getEdgesAndMetaEdges(u); } for (Edge e : iter) { Node v = hgraph.getOpposite(u, e); Integer id = invIndicies.get(v); tmp[i] += centralities[id]; } max = Math.max(max, tmp[i]); if (isCanceled) { return; } } sumChange = 0; for (int k = 0; k < N; k++) { if (max != 0) { sumChange += Math.abs(centralities[k] - (tmp[k] / max)); centralities[k] = tmp[k] / max; //tmp[k] = 0; } if (isCanceled) { return; } } if (isCanceled) { return; } Progress.progress(progress); } for (int i = 0; i < N; i++) { Node s = indicies.get(i); AttributeRow row = (AttributeRow) s.getNodeData().getAttributes(); row.setValue(eigenCol, centralities[i]); if (isCanceled) { return; } } hgraph.readUnlock(); Progress.finish(progress); } /** * * @return */ 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; } public boolean cancel() { this.isCanceled = true; return true; } public void setProgressTicket(ProgressTicket progressTicket) { this.progress = progressTicket; } }