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/*
Copyright 2008-2011 Gephi
Authors : Patick J. McSweeney , Sebastien Heymann
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
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"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
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;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.Map;
import org.gephi.graph.api.Column;
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.graph.api.NodeIterable;
import org.gephi.graph.api.Table;
import org.gephi.graph.api.UndirectedGraph;
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 ConnectedComponents implements Statistics, LongTask {
public static final String WEAKLY = "componentnumber";
public static final String STRONG = "strongcompnum";
int count;
private boolean isDirected;
private ProgressTicket progress;
private boolean isCanceled;
private int componentCount;
private int stronglyCount;
private int[] componentsSize;
public ConnectedComponents() {
GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
if (graphController != null && graphController.getGraphModel() != null) {
isDirected = graphController.getGraphModel().isDirected();
}
}
@Override
public void execute(GraphModel graphModel) {
isCanceled = false;
UndirectedGraph undirectedGraph = graphModel.getUndirectedGraphVisible();
Column weaklyConnectedColumn = initializeWeaklyConnectedColumn(graphModel);
Column stronglyConnectedColumn = null;
if (isDirected) {
stronglyConnectedColumn = initializeStronglyConnectedColumn(graphModel);
}
undirectedGraph.readLock();
try {
weaklyConnected(undirectedGraph, weaklyConnectedColumn);
if (isDirected) {
DirectedGraph directedGraph = graphModel.getDirectedGraphVisible();
stronglyConnected(directedGraph, graphModel, stronglyConnectedColumn);
}
} finally {
undirectedGraph.readUnlock();
}
}
public void weaklyConnected(UndirectedGraph graph, Column componentCol) {
isCanceled = false;
HashMap indices = createIndicesMap(graph);
LinkedList> components = computeWeaklyConnectedComponents(graph, indices);
saveComputedComponents(components, componentCol);
fillComponentSizeList(components);
componentCount = components.size();
}
public LinkedList> computeWeaklyConnectedComponents(Graph graph, HashMap indices) {
int N = graph.getNodeCount();
//Keep track of which nodes have been seen
int[] color = new int[N];
Progress.start(progress, N);
int seenCount = 0;
LinkedList> components = new LinkedList<>();
while (seenCount < N) {
//The search Q
LinkedList Q = new LinkedList<>();
//The component-list
LinkedList component = new LinkedList<>();
//Seed the search Q
NodeIterable iter = graph.getNodes();
for (Node next : iter) {
if (color[indices.get(next)] == 0) {
Q.add(next);
iter.doBreak();
break;
}
}
//While there are more nodes to search
while (!Q.isEmpty()) {
if (isCanceled) {
return new LinkedList<>();
}
//Get the next Node and add it to the component list
Node u = Q.removeFirst();
component.add(u);
color[indices.get(u)] = 2;
//Iterate over all of u's neighbors
EdgeIterable edgeIter = graph.getEdges(u);
//For each neighbor
for (Edge edge : edgeIter) {
Node reachable = graph.getOpposite(u, edge);
int id = indices.get(reachable);
//If this neighbor is unvisited
if (color[id] == 0) {
//Mark it as used
color[id] = 1;
//Add it to the search Q
Q.addLast(reachable);
}
}
seenCount++;
Progress.progress(progress, seenCount);
}
components.add(component);
}
return components;
}
private Column initializeWeaklyConnectedColumn(GraphModel graphModel) {
Table nodeTable = graphModel.getNodeTable();
ColumnUtils.cleanUpColumns(nodeTable, new String[] {WEAKLY}, Integer.class);
Column componentCol = nodeTable.getColumn(WEAKLY);
if (componentCol == null) {
componentCol = nodeTable.addColumn(WEAKLY, "Component ID", Integer.class, 0);
}
return componentCol;
}
public HashMap createIndicesMap(Graph graph) {
HashMap indices = new HashMap<>();
int index = 0;
for (Node s : graph.getNodes()) {
indices.put(s, index);
index++;
}
return indices;
}
private void saveComputedComponents(LinkedList> components, Column componentCol) {
int i = 0;
for (LinkedList component : components) {
for (Node s : component) {
s.setAttribute(componentCol, i);
}
i++;
}
}
void fillComponentSizeList(LinkedList> components) {
componentsSize = new int[components.size()];
for (int i = 0; i < components.size(); i++) {
componentsSize[i] = components.get(i).size();
}
}
private Column initializeStronglyConnectedColumn(GraphModel graphModel) {
Table nodeTable = graphModel.getNodeTable();
ColumnUtils.cleanUpColumns(nodeTable, new String[] {STRONG}, Integer.class);
Column componentCol = nodeTable.getColumn(STRONG);
if (componentCol == null) {
componentCol = nodeTable.addColumn(STRONG, "Strongly-Connected ID", Integer.class, 0);
}
return componentCol;
}
public void stronglyConnected(DirectedGraph graph, GraphModel graphModel, Column componentCol) {
count = 1;
stronglyCount = 0;
HashMap indices = createIndicesMap(graph);
LinkedList> components = top_tarjans(graph, indices);
saveComputedComponents(components, componentCol);
stronglyCount = components.size();
}
public LinkedList> top_tarjans(DirectedGraph graph, HashMap indices) {
LinkedList> allComponents = new LinkedList<>();
count = 1;
stronglyCount = 0;
int N = graph.getNodeCount();
int[] index = new int[N];
int[] low_index = new int[N];
while (true) {
//The search Q
LinkedList S = new LinkedList<>();
//The component-list
//LinkedList component = new LinkedList();
//Seed the seach Q
Node first = null;
NodeIterable iter = graph.getNodes();
for (Node u : iter) {
if (index[indices.get(u)] == 0) {
first = u;
iter.doBreak();
break;
}
}
if (first == null) {
return allComponents;
}
LinkedList> components = new LinkedList<>();
components = tarjans(components, S, graph, first, index, low_index, indices);
for (LinkedList component : components) {
allComponents.add(component);
}
}
}
private LinkedList> tarjans(LinkedList> components, LinkedList S,
DirectedGraph graph, Node f, int[] index, int[] low_index,
HashMap indices) {
int id = indices.get(f);
index[id] = count;
low_index[id] = count;
count++;
S.addFirst(f);
EdgeIterable edgeIter = graph.getOutEdges(f);
for (Edge e : edgeIter) {
Node u = graph.getOpposite(f, e);
int x = indices.get(u);
if (index[x] == 0) {
tarjans(components, S, graph, u, index, low_index, indices);
low_index[id] = Math.min(low_index[x], low_index[id]);
} else if (S.contains(u)) {
low_index[id] = Math.min(low_index[id], index[x]);
}
}
LinkedList currentComponent = new LinkedList<>();
if (low_index[id] == index[id]) {
Node v = null;
while (v != f) {
v = S.removeFirst();
currentComponent.add(v);
}
components.add(currentComponent);
}
return components;
}
public int getConnectedComponentsCount() {
return componentCount;
}
public boolean isDirected() {
return isDirected;
}
public void setDirected(boolean isDirected) {
this.isDirected = isDirected;
}
/**
* @return an unordered array of component sizes
*/
public int[] getComponentsSize() {
return componentsSize;
}
/**
* @return the index of the largest component in the array returned by getComponentSize()
*/
public int getGiantComponent() {
int[] sizes = getComponentsSize();
int max = Integer.MIN_VALUE;
int maxIndex = -1;
for (int i = 0; i < sizes.length; i++) {
if (sizes[i] > max) {
max = sizes[i];
maxIndex = i;
}
}
return maxIndex;
}
public int getComponentNumber(LinkedList> components, Node node) {
int i = 0;
for (LinkedList component : components) {
for (Node currentNode : component) {
if (currentNode.equals(node)) {
return i;
}
}
i++;
}
return 0;
}
@Override
public String getReport() {
Map sizeDist = new HashMap<>();
for (int v : componentsSize) {
if (!sizeDist.containsKey(v)) {
sizeDist.put(v, 0);
}
sizeDist.put(v, sizeDist.get(v) + 1);
}
//Distribution series
XYSeries dSeries = ChartUtils.createXYSeries(sizeDist, "Size Distribution");
XYSeriesCollection dataset1 = new XYSeriesCollection();
dataset1.addSeries(dSeries);
JFreeChart chart = ChartFactory.createXYLineChart(
"Size Distribution",
"Size (number of nodes)",
"Count",
dataset1,
PlotOrientation.VERTICAL,
true,
false,
false);
chart.removeLegend();
ChartUtils.decorateChart(chart);
ChartUtils.scaleChart(chart, dSeries, false);
String imageFile = ChartUtils.renderChart(chart, "cc-size-distribution.png");
NumberFormat f = new DecimalFormat("#0.000");
String report = " Connected Components Report
"
+ "
"
+ "
"
+ " Parameters:
"
+ "Network Interpretation: " + (isDirected ? "directed" : "undirected") + "
"
+ "
Results:
"
+ "Number of Weakly Connected Components: " + componentCount + "
"
+ (isDirected ? "Number of Strongly Connected Components: " + stronglyCount + "
" : "")
+ "
" + imageFile
+ "
" + " Algorithm:
"
+
"Robert Tarjan, Depth-First Search and Linear Graph Algorithms, in SIAM Journal on Computing 1 (2): 146–160 (1972)
"
+ " ";
return report;
}
@Override
public boolean cancel() {
isCanceled = true;
return true;
}
@Override
public void setProgressTicket(ProgressTicket progressTicket) {
progress = progressTicket;
}
}