/*
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
or only the GPL Version 3, indicate your decision by adding
"[Contributor] elects to include this software in this distribution
under the [CDDL or GPL Version 3] license." If you do not indicate a
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your version of this file under either the CDDL, the GPL Version 3 or
to extend the choice of license to its licensees as provided above.
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.ArrayList;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
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.HierarchicalUndirectedGraph;
import org.gephi.graph.api.Node;
import org.gephi.graph.api.NodeIterable;
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";
private boolean isDirected;
private ProgressTicket progress;
private boolean isCanceled;
private int componentCount;
private int stronglyCount;
private int[] componentsSize;
int count;
public ConnectedComponents() {
GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
if (graphController != null && graphController.getModel() != null) {
isDirected = graphController.getModel().isDirected();
}
}
public void execute(GraphModel graphModel, AttributeModel attributeModel) {
HierarchicalUndirectedGraph undirectedGraph = graphModel.getHierarchicalUndirectedGraphVisible();
weaklyConnected(undirectedGraph, attributeModel);
if (isDirected) {
HierarchicalDirectedGraph directedGraph = graphModel.getHierarchicalDirectedGraphVisible();
top_tarjans(directedGraph, attributeModel);
}
}
public void weaklyConnected(HierarchicalUndirectedGraph hgraph, AttributeModel attributeModel) {
isCanceled = false;
componentCount = 0;
AttributeTable nodeTable = attributeModel.getNodeTable();
AttributeColumn componentCol = nodeTable.getColumn(WEAKLY);
if (componentCol == null) {
componentCol = nodeTable.addColumn(WEAKLY, "Component ID", AttributeType.INT, AttributeOrigin.COMPUTED, new Integer(0));
}
List<Integer> sizeList = new ArrayList<Integer>();
hgraph.readLock();
HashMap<Node, Integer> indicies = new HashMap<Node, Integer>();
int index = 0;
for (Node s : hgraph.getNodes()) {
indicies.put(s, index);
index++;
}
int N = hgraph.getNodeCount();
//Keep track of which nodes have been seen
int[] color = new int[N];
Progress.start(progress, hgraph.getNodeCount());
int seenCount = 0;
while (seenCount < N) {
//The search Q
LinkedList<Node> Q = new LinkedList<Node>();
//The component-list
LinkedList<Node> component = new LinkedList<Node>();
//Seed the seach Q
NodeIterable iter = hgraph.getNodes();
for (Node first : iter) {
if (color[indicies.get(first)] == 0) {
Q.add(first);
iter.doBreak();
break;
}
}
//While there are more nodes to search
while (!Q.isEmpty()) {
if (isCanceled) {
hgraph.readUnlock();
return;
}
//Get the next Node and add it to the component list
Node u = Q.removeFirst();
component.add(u);
//Iterate over all of u's neighbors
EdgeIterable edgeIter = hgraph.getEdgesAndMetaEdges(u);
//For each neighbor
for (Edge edge : edgeIter) {
Node reachable = hgraph.getOpposite(u, edge);
int id = indicies.get(reachable);
//If this neighbor is unvisited
if (color[id] == 0) {
color[id] = 1;
//Add it to the search Q
Q.addLast(reachable);
//Mark it as used
Progress.progress(progress, seenCount);
}
}
color[indicies.get(u)] = 2;
seenCount++;
}
for (Node s : component) {
AttributeRow row = (AttributeRow) s.getNodeData().getAttributes();
row.setValue(componentCol, componentCount);
}
sizeList.add(component.size());
componentCount++;
}
hgraph.readUnlock();
componentsSize = new int[sizeList.size()];
for (int i = 0; i < sizeList.size(); i++) {
componentsSize[i] = sizeList.get(i);
}
}
public void top_tarjans(HierarchicalDirectedGraph hgraph, AttributeModel attributeModel) {
count = 1;
stronglyCount = 0;
AttributeTable nodeTable = attributeModel.getNodeTable();
AttributeColumn componentCol = nodeTable.getColumn(STRONG);
if (componentCol == null) {
componentCol = nodeTable.addColumn(STRONG, "Strongly-Connected ID", AttributeType.INT, AttributeOrigin.COMPUTED, new Integer(0));
}
hgraph.readLock();
HashMap<Node, Integer> indicies = new HashMap<Node, Integer>();
int v = 0;
for (Node s : hgraph.getNodes()) {
indicies.put(s, v);
v++;
}
int N = hgraph.getNodeCount();
int[] index = new int[N];
int[] low_index = new int[N];
while (true) {
//The search Q
LinkedList<Node> S = new LinkedList<Node>();
//The component-list
//LinkedList<Node> component = new LinkedList<Node>();
//Seed the seach Q
Node first = null;
NodeIterable iter = hgraph.getNodes();
for (Node u : iter) {
if (index[indicies.get(u)] == 0) {
first = u;
iter.doBreak();
break;
}
}
if (first == null) {
hgraph.readUnlockAll();
return;
}
tarjans(componentCol, S, hgraph, first, index, low_index, indicies);
}
}
private void tarjans(AttributeColumn col, LinkedList<Node> S, HierarchicalDirectedGraph hgraph, Node f, int[] index, int[] low_index, HashMap<Node, Integer> indicies) {
int id = indicies.get(f);
index[id] = count;
low_index[id] = count;
count++;
S.addFirst(f);
EdgeIterable edgeIter = hgraph.getOutEdgesAndMetaOutEdges(f);
for (Edge e : edgeIter) {
Node u = hgraph.getOpposite(f, e);
int x = indicies.get(u);
if (index[x] == 0) {
tarjans(col, S, hgraph, u, index, low_index, indicies);
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]);
}
}
if (low_index[id] == index[id]) {
Node v = null;
while (v != f) {
v = S.removeFirst();
AttributeRow row = (AttributeRow) v.getNodeData().getAttributes();
row.setValue(col, stronglyCount);
}
stronglyCount++;
}
}
public int getConnectedComponentsCount() {
return componentCount;
}
public void setDirected(boolean isDirected) {
this.isDirected = isDirected;
}
public boolean isDirected() {
return isDirected;
}
public int[] getComponentsSize() {
return componentsSize;
}
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 String getReport() {
Map<Integer, Integer> sizeDist = new HashMap<Integer, Integer>();
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 = "<HTML> <BODY> <h1>Connected Components Report </h1> "
+ "<hr>"
+ "<br>"
+ "<h2> Parameters: </h2>"
+ "Network Interpretation: " + (isDirected ? "directed" : "undirected") + "<br>"
+ "<br> <h2> Results: </h2>"
+ "Number of Weakly Connected Components: " + componentCount + "<br>"
+ (isDirected ? "Number of Stronlgy Connected Components: " + stronglyCount + "<br>" : "")
+ "<br /><br />"+imageFile
+ "<br />" + "<h2> Algorithm: </h2>"
+ "Robert Tarjan, <i>Depth-First Search and Linear Graph Algorithms</i>, in SIAM Journal on Computing 1 (2): 146–160 (1972)<br />"
+ "</BODY> </HTML>";
return report;
}
public boolean cancel() {
isCanceled = true;
return true;
}
public void setProgressTicket(ProgressTicket progressTicket) {
progress = progressTicket;
}
}