/*
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. 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
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"[Contributor] elects to include this software in this distribution
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However, if you add GPL Version 3 code and therefore, elected the GPL
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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 java.util.LinkedList;
import java.util.ListIterator;
import java.util.Map;
import java.util.Stack;
import org.gephi.graph.api.*;
import org.gephi.statistics.spi.Statistics;
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
* @author Jonny Wray
*/
public class GraphDistance implements Statistics, LongTask {
public static final String BETWEENNESS = "betweenesscentrality";
public static final String CLOSENESS = "closnesscentrality";
public static final String HARMONIC_CLOSENESS = "harmonicclosnesscentrality";
public static final String ECCENTRICITY = "eccentricity";
/**
*
*/
private double[] betweenness;
/**
*
*/
private double[] closeness;
private double[] harmonicCloseness;
/**
*
*/
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 boolean isNormalized;
/**
* Gets the average shortest path length in the network
*
* @return average shortest path length for all nodes
*/
public double getPathLength() {
return avgDist;
}
/**
* @return the diameter of the network
*/
public double getDiameter() {
return diameter;
}
/**
* @return the radius of the network
*/
public double getRadius() {
return radius;
}
/**
* Construct a GraphDistance calculator for the current graph model
*/
public GraphDistance() {
GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
if (graphController != null && graphController.getGraphModel() != null) {
isDirected = graphController.getGraphModel().isDirected();
}
}
/**
*
* @param graphModel
*/
@Override
public void execute(GraphModel graphModel) {
isDirected = graphModel.isDirected();
Graph graph;
if (isDirected) {
graph = graphModel.getDirectedGraphVisible();
} else {
graph = graphModel.getUndirectedGraphVisible();
}
execute(graph);
}
public void execute(Graph graph) {
isCanceled = false;
initializeAttributeColunms(graph.getModel());
graph.readLock();
try {
N = graph.getNodeCount();
initializeStartValues();
HashMap<Node, Integer> indicies = createIndiciesMap(graph);
Map<String, double[]> metrics = calculateDistanceMetrics(graph, indicies, isDirected, isNormalized);
eccentricity = metrics.get(ECCENTRICITY);
closeness = metrics.get(CLOSENESS);
harmonicCloseness = metrics.get(HARMONIC_CLOSENESS);
betweenness = metrics.get(BETWEENNESS);
saveCalculatedValues(graph, indicies, eccentricity, betweenness, closeness, harmonicCloseness);
} finally {
graph.readUnlock();
}
}
public Map<String, double[]> calculateDistanceMetrics(Graph graph, HashMap<Node, Integer> indicies, boolean directed, boolean normalized) {
int n = graph.getNodeCount();
HashMap<String, double[]> metrics = new HashMap<>();
double[] nodeEccentricity = new double[n];
double[] nodeBetweenness = new double[n];
double[] nodeCloseness = new double[n];
double[] nodeHarmonicCloseness = new double[n];
metrics.put(ECCENTRICITY, nodeEccentricity);
metrics.put(CLOSENESS, nodeCloseness);
metrics.put(HARMONIC_CLOSENESS, nodeHarmonicCloseness);
metrics.put(BETWEENNESS, nodeBetweenness);
Progress.start(progress, graph.getNodeCount());
int count = 0;
int totalPaths = 0;
for (Node s : graph.getNodes()) {
Stack<Node> S = new Stack<>();
LinkedList<Node>[] P = new LinkedList[n];
double[] theta = new double[n];
int[] d = new int[n];
int s_index = indicies.get(s);
setInitParametetrsForNode(s, P, theta, d, s_index, n);
LinkedList<Node> Q = new LinkedList<>();
Q.addLast(s);
while (!Q.isEmpty()) {
Node v = Q.removeFirst();
S.push(v);
int v_index = indicies.get(v);
EdgeIterable edgeIter = getEdgeIter(graph, v, directed);
for (Edge edge : edgeIter) {
Node reachable = graph.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];
nodeEccentricity[s_index] = (int) Math.max(nodeEccentricity[s_index], d[i]);
nodeCloseness[s_index] += d[i];
nodeHarmonicCloseness[s_index] += Double.isInfinite(d[i]) ? 0.0 : 1.0 / d[i];
diameter = Math.max(diameter, d[i]);
reachable++;
}
}
radius = (int) Math.min(nodeEccentricity[s_index], radius);
if (reachable != 0) {
nodeCloseness[s_index] = (nodeCloseness[s_index] == 0) ? 0 : reachable / nodeCloseness[s_index];
nodeHarmonicCloseness[s_index] = nodeHarmonicCloseness[s_index] / reachable;
}
totalPaths += 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) {
nodeBetweenness[w_index] += delta[w_index];
}
}
count++;
if (isCanceled) {
return metrics;
}
Progress.progress(progress, count);
}
avgDist /= totalPaths;//mN * (mN - 1.0f);
calculateCorrection(graph, indicies, nodeBetweenness, directed, normalized);
return metrics;
}
private void setInitParametetrsForNode(Node s, LinkedList<Node>[] P, double[] theta, int[] d, int index, int n) {
for (int j = 0; j < n; j++) {
P[j] = new LinkedList<>();
theta[j] = 0;
d[j] = -1;
}
theta[index] = 1;
d[index] = 0;
}
private EdgeIterable getEdgeIter(Graph graph, Node v, boolean directed) {
EdgeIterable edgeIter;
if (directed) {
edgeIter = ((DirectedGraph) graph).getOutEdges(v);
} else {
edgeIter = graph.getEdges(v);
}
return edgeIter;
}
private void initializeAttributeColunms(GraphModel graphModel) {
Table nodeTable = graphModel.getNodeTable();
if (!nodeTable.hasColumn(ECCENTRICITY)) {
nodeTable.addColumn(ECCENTRICITY, "Eccentricity", Double.class, new Double(0));
}
if (!nodeTable.hasColumn(CLOSENESS)) {
nodeTable.addColumn(CLOSENESS, "Closeness Centrality", Double.class, new Double(0));
}
if (!nodeTable.hasColumn(HARMONIC_CLOSENESS)) {
nodeTable.addColumn(HARMONIC_CLOSENESS, "Harmonic Closeness Centrality", Double.class, new Double(0));
}
if (!nodeTable.hasColumn(BETWEENNESS)) {
nodeTable.addColumn(BETWEENNESS, "Betweenness Centrality", Double.class, new Double(0));
}
}
public HashMap<Node, Integer> createIndiciesMap(Graph graph) {
HashMap<Node, Integer> indicies = new HashMap<>();
int index = 0;
for (Node s : graph.getNodes()) {
indicies.put(s, index);
index++;
}
return indicies;
}
public void initializeStartValues() {
betweenness = new double[N];
eccentricity = new double[N];
closeness = new double[N];
harmonicCloseness = new double[N];
diameter = 0;
avgDist = 0;
radius = Integer.MAX_VALUE;
}
private void calculateCorrection(Graph graph, HashMap<Node, Integer> indicies,
double[] nodeBetweenness, boolean directed, boolean normalized) {
int n = graph.getNodeCount();
for (Node s : graph.getNodes()) {
int s_index = indicies.get(s);
if (!directed) {
nodeBetweenness[s_index] /= 2;
}
if (normalized) {
nodeBetweenness[s_index] /= directed ? (n - 1) * (n - 2) : (n - 1) * (n - 2) / 2;
}
}
}
private void saveCalculatedValues(Graph graph, HashMap<Node, Integer> indicies,
double[] nodeEccentricity, double[] nodeBetweenness, double[] nodeCloseness, double[] nodeHarmonicCloseness) {
for (Node s : graph.getNodes()) {
int s_index = indicies.get(s);
s.setAttribute(ECCENTRICITY, nodeEccentricity[s_index]);
s.setAttribute(CLOSENESS, nodeCloseness[s_index]);
s.setAttribute(HARMONIC_CLOSENESS, nodeHarmonicCloseness[s_index]);
s.setAttribute(BETWEENNESS, nodeBetweenness[s_index]);
}
}
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<>();
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
*/
@Override
public String getReport() {
String htmlIMG1 = "";
String htmlIMG2 = "";
String htmlIMG3 = "";
String htmlIMG4 = "";
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, harmonicCloseness, "Harmonic Closeness Centrality Distribution", "Value", "Count");
htmlIMG4 = 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 />"
+ htmlIMG1 + "<br /><br />"
+ htmlIMG2 + "<br /><br />"
+ htmlIMG3 + "<br /><br />"
+ htmlIMG4
+ "<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
*/
@Override
public boolean cancel() {
this.isCanceled = true;
return true;
}
/**
*
* @param progressTicket
*/
@Override
public void setProgressTicket(ProgressTicket progressTicket) {
this.progress = progressTicket;
}
}