Java tutorial
/* Copyright 2008-2010 Gephi Authors : Mathieu Bastian <mathieu.bastian@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 edu.uic.cs.compbio.DyNSPK; import java.text.DecimalFormat; import java.text.NumberFormat; import java.util.HashMap; import java.util.Map; import org.gephi.data.attributes.api.AttributeModel; import org.gephi.data.attributes.type.Interval; import org.gephi.dynamic.api.DynamicController; import org.gephi.dynamic.api.DynamicModel; import org.gephi.graph.api.*; import org.gephi.statistics.plugin.ChartUtils; import org.gephi.statistics.spi.DynamicStatistics; import org.gephi.utils.longtask.spi.LongTask; 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 Mathieu Bastian */ public class DynamicEntropy implements DynamicStatistics, LongTask { //Data private GraphModel graphModel; private DynamicModel dynamicModel; private double window; private double tick; private Interval bounds; private boolean isDirected; private boolean averageOnly; private boolean cancel = false; //Result //private List<Interval<Double>> averages; private Map<Double, Double> degreeTs; private int first; private Node[] previousnodes; private Edge[] previousedges; private Map<Double, Double> nodedata; private Map<Double, Double> edgedata; private Map<Double, Double> sumdata; public DynamicEntropy() { GraphController graphController = Lookup.getDefault().lookup(GraphController.class); if (graphController != null && graphController.getModel() != null) { isDirected = graphController.getModel().isDirected(); } } public void execute(GraphModel graphModel, AttributeModel attributeModel) { this.graphModel = graphModel; //this.averages = new ArrayList<Interval<Double>>(); this.degreeTs = new HashMap<Double, Double>(); this.nodedata = new HashMap<Double, Double>(); this.edgedata = new HashMap<Double, Double>(); this.sumdata = new HashMap<Double, Double>(); this.isDirected = graphModel.isDirected(); this.dynamicModel = Lookup.getDefault().lookup(DynamicController.class).getModel(graphModel.getWorkspace()); } public String makeChart(Map<Double, Double> data, String filename, String Title, String XAxis, String YAxis) { //Time series XYSeries dSeries = ChartUtils.createXYSeries(data, Title); XYSeriesCollection dataset = new XYSeriesCollection(); dataset.addSeries(dSeries); JFreeChart chart = ChartFactory.createXYLineChart(Title, XAxis, YAxis, dataset, PlotOrientation.HORIZONTAL, true, false, false); chart.removeLegend(); ChartUtils.decorateChart(chart); ChartUtils.scaleChart(chart, dSeries, false); String degreeImageFile = ChartUtils.renderChart(chart, filename); return degreeImageFile; } public String getReport() { NumberFormat f = new DecimalFormat("#0.000000"); String report = "<HTML> <BODY> <h1>Dynamic Entropy Report </h1> " + "<hr>" + "<br> Bounds: from " + f.format(bounds.getLow()) + " to " + f.format(bounds.getHigh()) + "<br> Window: " + window + "<br> Tick: " + tick + "<br><br><h2> Average degrees over time: </h2>" + "<br /><br />" + makeChart(this.nodedata, "nodets.png", "Node Entropy Time Series", " Time", "Node Changes") + makeChart(this.edgedata, "edgets.png", "Edge Entropy Time Series", " Time", "Edge Changes") + makeChart(this.sumdata, "sumts.png", "Entropy Time Series", " Time", "Total Changes"); /* * private Map<Double, Double> nodedata; private Map<Double, Double> * edgedata; private Map<Double, Double> sumdata; */ /* * for (Interval<Double> average : averages) { report += * average.toString(dynamicModel.getTimeFormat().equals(DynamicModel.TimeFormat.DOUBLE)) * + "<br />"; } */ report += "<br /><br /></BODY></HTML>"; return report; } public void loop(GraphView window, Interval interval) { //Time complexity of this algorithm is the cost of visiting each window twice and seeing if there is a change of edges or nodes. HierarchicalGraph graph = graphModel.getHierarchicalGraph(window); HierarchicalDirectedGraph directedGraph = null; graph.readLock(); if (isDirected) { directedGraph = graphModel.getHierarchicalDirectedGraph(window); if (this.first == 0) { //Initialization. Since this is executed first we allow for the previous window to be accessed first++; previousedges = directedGraph.getEdges().toArray(); previousnodes = directedGraph.getNodes().toArray(); edgedata.put(interval.getHigh(), 0.0); nodedata.put(interval.getHigh(), 0.0); } else if (this.first == 1) { //Here we count the changes double edgedelta = 0.0; for (Edge prevedge : previousedges) { if (!directedGraph.contains(prevedge)) { edgedelta++; } for (Edge nextedge : directedGraph.getEdges()) if (!prevedge.equals(nextedge)) { edgedelta++; } } // edgedelta = edgedelta / Collections.max(edgedata.values()); edgedata.put(interval.getHigh(), edgedelta); double nodedelta = 0; for (Node prevnode : previousnodes) { if (!directedGraph.contains(prevnode)) { nodedelta++; } for (Node nextnode : directedGraph.getNodes()) if (!prevnode.equals(nextnode)) { edgedelta++; } } //nodedelta = nodedelta / Collections.max(edgedata.values()); nodedata.put(interval.getHigh(), nodedelta); Double sumdelta = (nodedelta + edgedelta); sumdata.put(interval.getHigh(), sumdelta); //Now we mutate previous edge and node so we can compare it in the next window previousedges = directedGraph.getEdges().toArray(); previousnodes = directedGraph.getNodes().toArray(); } } else { if (this.first == 0) { //Initialization. Since this is executed first we allow for the previous window to be accessed first++; previousedges = graph.getEdges().toArray(); previousnodes = graph.getNodes().toArray(); edgedata.put(interval.getHigh(), 0.0); nodedata.put(interval.getHigh(), 0.0); } else if (this.first == 1) { //Here we count the changes double edgedelta = 0.0; for (Edge prevedge : previousedges) { if (!graph.contains(prevedge)) { edgedelta++; } for (Edge nextedge : graph.getEdges()) if (!prevedge.equals(nextedge)) { edgedelta++; } } edgedata.put(interval.getHigh(), edgedelta); double nodedelta = 0; for (Node prevnode : previousnodes) { if (!graph.contains(prevnode)) { nodedelta++; } for (Node nextnode : graph.getNodes()) if (!prevnode.equals(nextnode)) { edgedelta++; } } nodedata.put(interval.getHigh(), nodedelta); Double sumdelta = nodedelta + edgedelta; sumdata.put(interval.getHigh(), sumdelta); //Now we mutate previous edge and node so we can compare it in the next window previousedges = graph.getEdges().toArray(); previousnodes = graph.getNodes().toArray(); } } graph.readUnlockAll(); } public void end() { } public void setBounds(Interval bounds) { this.bounds = bounds; } public void setWindow(double window) { this.window = window; } public void setTick(double tick) { this.tick = tick; } public double getWindow() { return window; } public double getTick() { return tick; } public Interval getBounds() { return bounds; } public void setDirected(boolean isDirected) { this.isDirected = isDirected; } public boolean isDirected() { return isDirected; } public void setAverageOnly(boolean averageOnly) { this.averageOnly = averageOnly; } public boolean isAverageOnly() { return averageOnly; } public boolean cancel() { cancel = true; return true; } public void setProgressTicket(ProgressTicket progressTicket) { } }