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.io.IOException; import java.util.HashMap; import org.gephi.statistics.spi.Statistics; import org.gephi.graph.api.*; import java.util.LinkedList; import java.util.ListIterator; import java.util.Map; import java.util.Stack; import org.gephi.data.attributes.api.AttributeTable; 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.AttributeType; import org.gephi.utils.TempDirUtils; import org.gephi.utils.TempDirUtils.TempDir; 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.Exceptions; import org.openide.util.Lookup; /** * Ref: Ulrik Brandes, A Faster Algorithm for Betweenness Centrality, * in Journal of Mathematical Sociology 25(2):163-177, (2001) * * @author pjmcswee */ public class GraphDistance implements Statistics, LongTask { public static final String BETWEENNESS = "betweenesscentrality"; public static final String CLOSENESS = "closnesscentrality"; public static final String ECCENTRICITY = "eccentricity"; /** */ private double[] betweenness; /** */ private double[] closeness; /** */ private double[] eccentricity; /** */ private int diameter; private int radius; /** */ private double avgDist; /** */ private int N; /** */ private boolean isDirected; /** */ private ProgressTicket progress; /** */ private boolean isCanceled; private int shortestPaths; private boolean isNormalized; public GraphDistance() { GraphController graphController = Lookup.getDefault().lookup(GraphController.class); if (graphController != null && graphController.getModel() != null) { isDirected = graphController.getModel().isDirected(); } } public double getPathLength() { return avgDist; } /** * * @return */ public double getDiameter() { return diameter; } /** * * @param graphModel */ 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) { isCanceled = false; AttributeTable nodeTable = attributeModel.getNodeTable(); AttributeColumn eccentricityCol = nodeTable.getColumn(ECCENTRICITY); AttributeColumn closenessCol = nodeTable.getColumn(CLOSENESS); AttributeColumn betweenessCol = nodeTable.getColumn(BETWEENNESS); if (eccentricityCol == null) { eccentricityCol = nodeTable.addColumn(ECCENTRICITY, "Eccentricity", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0)); } if (closenessCol == null) { closenessCol = nodeTable.addColumn(CLOSENESS, "Closeness Centrality", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0)); } if (betweenessCol == null) { betweenessCol = nodeTable.addColumn(BETWEENNESS, "Betweenness Centrality", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0)); } hgraph.readLock(); N = hgraph.getNodeCount(); betweenness = new double[N]; eccentricity = new double[N]; closeness = new double[N]; diameter = 0; avgDist = 0; shortestPaths = 0; radius = Integer.MAX_VALUE; HashMap<Node, Integer> indicies = new HashMap<Node, Integer>(); int index = 0; for (Node s : hgraph.getNodes()) { indicies.put(s, index); index++; } Progress.start(progress, hgraph.getNodeCount()); int count = 0; for (Node s : hgraph.getNodes()) { Stack<Node> S = new Stack<Node>(); LinkedList<Node>[] P = new LinkedList[N]; double[] theta = new double[N]; int[] d = new int[N]; for (int j = 0; j < N; j++) { P[j] = new LinkedList<Node>(); theta[j] = 0; d[j] = -1; } int s_index = indicies.get(s); theta[s_index] = 1; d[s_index] = 0; LinkedList<Node> Q = new LinkedList<Node>(); Q.addLast(s); while (!Q.isEmpty()) { Node v = Q.removeFirst(); S.push(v); int v_index = indicies.get(v); EdgeIterable edgeIter = null; if (isDirected) { edgeIter = ((HierarchicalDirectedGraph) hgraph).getOutEdgesAndMetaOutEdges(v); } else { edgeIter = hgraph.getEdgesAndMetaEdges(v); } for (Edge edge : edgeIter) { Node reachable = hgraph.getOpposite(v, edge); int r_index = indicies.get(reachable); if (d[r_index] < 0) { Q.addLast(reachable); d[r_index] = d[v_index] + 1; } if (d[r_index] == (d[v_index] + 1)) { theta[r_index] = theta[r_index] + theta[v_index]; P[r_index].addLast(v); } } } double reachable = 0; for (int i = 0; i < N; i++) { if (d[i] > 0) { avgDist += d[i]; eccentricity[s_index] = (int) Math.max(eccentricity[s_index], d[i]); closeness[s_index] += d[i]; diameter = Math.max(diameter, d[i]); reachable++; } } radius = (int) Math.min(eccentricity[s_index], radius); if (reachable != 0) { closeness[s_index] /= reachable; } shortestPaths += reachable; double[] delta = new double[N]; while (!S.empty()) { Node w = S.pop(); int w_index = indicies.get(w); ListIterator<Node> iter1 = P[w_index].listIterator(); while (iter1.hasNext()) { Node u = iter1.next(); int u_index = indicies.get(u); delta[u_index] += (theta[u_index] / theta[w_index]) * (1 + delta[w_index]); } if (w != s) { betweenness[w_index] += delta[w_index]; } } count++; if (isCanceled) { hgraph.readUnlockAll(); return; } Progress.progress(progress, count); } avgDist /= shortestPaths;//mN * (mN - 1.0f); for (Node s : hgraph.getNodes()) { AttributeRow row = (AttributeRow) s.getNodeData().getAttributes(); int s_index = indicies.get(s); if (!isDirected) { betweenness[s_index] /= 2; } if (isNormalized) { closeness[s_index] = (closeness[s_index] == 0) ? 0 : 1.0 / closeness[s_index]; betweenness[s_index] /= isDirected ? (N - 1) * (N - 2) : (N - 1) * (N - 2) / 2; } row.setValue(eccentricityCol, eccentricity[s_index]); row.setValue(closenessCol, closeness[s_index]); row.setValue(betweenessCol, betweenness[s_index]); } hgraph.readUnlock(); } public void setNormalized(boolean isNormalized) { this.isNormalized = isNormalized; } public boolean isNormalized() { return isNormalized; } public void setDirected(boolean isDirected) { this.isDirected = isDirected; } public boolean isDirected() { return isDirected; } private String createImageFile(TempDir tempDir, double[] pVals, String pName, String pX, String pY) { //distribution of values Map<Double, Integer> dist = new HashMap<Double, Integer>(); for (int i = 0; i < N; i++) { Double d = pVals[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, pName); XYSeriesCollection dataset = new XYSeriesCollection(); dataset.addSeries(dSeries); JFreeChart chart = ChartFactory.createXYLineChart(pName, pX, pY, dataset, PlotOrientation.VERTICAL, true, false, false); chart.removeLegend(); ChartUtils.decorateChart(chart); ChartUtils.scaleChart(chart, dSeries, isNormalized); return ChartUtils.renderChart(chart, pName + ".png"); } /** * * @return */ public String getReport() { String htmlIMG1 = ""; String htmlIMG2 = ""; String htmlIMG3 = ""; try { TempDir tempDir = TempDirUtils.createTempDir(); htmlIMG1 = createImageFile(tempDir, betweenness, "Betweenness Centrality Distribution", "Value", "Count"); htmlIMG2 = createImageFile(tempDir, closeness, "Closeness Centrality Distribution", "Value", "Count"); htmlIMG3 = createImageFile(tempDir, eccentricity, "Eccentricity Distribution", "Value", "Count"); } catch (IOException ex) { Exceptions.printStackTrace(ex); } String report = "<HTML> <BODY> <h1>Graph Distance Report </h1> " + "<hr>" + "<br>" + "<h2> Parameters: </h2>" + "Network Interpretation: " + (isDirected ? "directed" : "undirected") + "<br />" + "<br /> <h2> Results: </h2>" + "Diameter: " + diameter + "<br />" + "Radius: " + radius + "<br />" + "Average Path length: " + avgDist + "<br />" + "Number of shortest paths: " + shortestPaths + "<br /><br />" + htmlIMG1 + "<br /><br />" + htmlIMG2 + "<br /><br />" + htmlIMG3 + "<br /><br />" + "<h2> Algorithm: </h2>" + "Ulrik Brandes, <i>A Faster Algorithm for Betweenness Centrality</i>, in Journal of Mathematical Sociology 25(2):163-177, (2001)<br />" + "</BODY> </HTML>"; return report; } /** * * @return */ public boolean cancel() { this.isCanceled = true; return true; } /** * * @param progressTicket */ public void setProgressTicket(ProgressTicket progressTicket) { this.progress = progressTicket; } }