/*
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.
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or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
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*/
package org.gephi.statistics.plugin;
import java.util.HashMap;
import org.gephi.graph.api.Edge;
import org.gephi.graph.api.GraphController;
import org.gephi.graph.api.GraphModel;
import org.gephi.graph.api.Node;
import org.gephi.graph.api.UndirectedGraph;
import org.gephi.project.api.ProjectController;
import org.gephi.project.impl.ProjectControllerImpl;
import org.openide.util.Lookup;
import static org.testng.Assert.*;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
/**
*
* @author Anna
*/
public class ModularityNGTest {
private ProjectController pc;
@BeforeClass
public void setUp() {
pc = Lookup.getDefault().lookup(ProjectControllerImpl.class);
}
@BeforeMethod
public void initialize() {
pc.newProject();
}
@AfterMethod
public void clean() {
pc.closeCurrentProject();
}
@Test
public void testTwoConnectedNodesModularity() {
GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(2);
UndirectedGraph graph = graphModel.getUndirectedGraph();
Modularity mod = new Modularity();
Modularity.CommunityStructure theStructure = mod.new CommunityStructure(graph);
int[] comStructure = new int[graph.getNodeCount()];
HashMap<String, Double> modularityValues = mod.computeModularity(graph, theStructure, comStructure,
1., true, false);
double modValue = modularityValues.get("modularity");
int class1 = comStructure[0];
int class2 = comStructure[1];
assertEquals(modValue, 0.0);
assertEquals(class1, class2);
}
@Test
public void testGraphWithouLinksModularity() {
GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(5);
UndirectedGraph graph = graphModel.getUndirectedGraph();
Modularity mod = new Modularity();
Modularity.CommunityStructure theStructure = mod.new CommunityStructure(graph);
int[] comStructure = new int[graph.getNodeCount()];
HashMap<String, Double> modularityValues = mod.computeModularity(graph, theStructure, comStructure,
1., true, false);
double modValue = modularityValues.get("modularity");
assertEquals(modValue, Double.NaN);
}
@Test
public void testComputeBarbellGraphModularityNormalResolution() {
GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(4);
UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
Node[] nodes = new Node[4];
for (int i = 0; i < 4; i++) {
Node currentNode = graphModel.factory().newNode(((Integer) (i + 4)).toString());
nodes[i] = currentNode;
undirectedGraph.addNode(currentNode);
}
for (int i = 0; i < 3; i++) {
for (int j = i + 1; j < 4; j++) {
Edge currentEdge = graphModel.factory().newEdge(nodes[i], nodes[j], false);
undirectedGraph.addEdge(currentEdge);
}
}
Edge currentEdge = graphModel.factory().newEdge(undirectedGraph.getNode("0"), undirectedGraph.getNode("5"), false);
undirectedGraph.addEdge(currentEdge);
UndirectedGraph graph = graphModel.getUndirectedGraph();
Modularity mod = new Modularity();
Modularity.CommunityStructure theStructure = mod.new CommunityStructure(graph);
int[] comStructure = new int[graph.getNodeCount()];
HashMap<String, Double> modularityValues = mod.computeModularity(graph, theStructure, comStructure,
1., true, false);
double modValue = modularityValues.get("modularity");
int class4 = comStructure[0];
int class5 = comStructure[5];
boolean correctResult = (class4 != class5 || modValue == 0.);
assertTrue(correctResult);
}
@Test
public void testComputeBarbellGraphHighResolution() {
GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(4);
UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
Node[] nodes = new Node[4];
for (int i = 0; i < 4; i++) {
Node currentNode = graphModel.factory().newNode(((Integer) (i + 4)).toString());
nodes[i] = currentNode;
undirectedGraph.addNode(currentNode);
}
for (int i = 0; i < 3; i++) {
for (int j = i + 1; j < 4; j++) {
Edge currentEdge = graphModel.factory().newEdge(nodes[i], nodes[j], false);
undirectedGraph.addEdge(currentEdge);
}
}
Edge currentEdge = graphModel.factory().newEdge(undirectedGraph.getNode("0"), undirectedGraph.getNode("5"), false);
undirectedGraph.addEdge(currentEdge);
UndirectedGraph graph = graphModel.getUndirectedGraph();
Modularity mod = new Modularity();
Modularity.CommunityStructure theStructure = mod.new CommunityStructure(graph);
int[] comStructure = new int[graph.getNodeCount()];
HashMap<String, Double> modularityValues = mod.computeModularity(graph, theStructure, comStructure,
100., true, false);
double modValue = modularityValues.get("modularity");
int class4 = comStructure[0];
int class5 = comStructure[5];
assertEquals(modValue, 0.0);
assertEquals(class4, class5);
}
@Test
public void testComputeBarbellGraphModularityHasHighWeight() {
GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(4);
UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
Node[] nodes = new Node[4];
for (int i = 0; i < 4; i++) {
Node currentNode = graphModel.factory().newNode(((Integer) (i + 4)).toString());
nodes[i] = currentNode;
undirectedGraph.addNode(currentNode);
}
for (int i = 0; i < 3; i++) {
for (int j = i + 1; j < 4; j++) {
Edge currentEdge = graphModel.factory().newEdge(nodes[i], nodes[j], false);
undirectedGraph.addEdge(currentEdge);
}
}
Edge currentEdge = graphModel.factory().newEdge(undirectedGraph.getNode("0"), undirectedGraph.getNode("5"), 0, 100.f, false);
undirectedGraph.addEdge(currentEdge);
UndirectedGraph graph = graphModel.getUndirectedGraph();
Modularity mod = new Modularity();
Modularity.CommunityStructure theStructure = mod.new CommunityStructure(graph);
int[] comStructure = new int[graph.getNodeCount()];
HashMap<String, Double> modularityValues = mod.computeModularity(graph, theStructure, comStructure,
1., true, true);
int class4 = comStructure[0];
int class5 = comStructure[5];
assertEquals(class4, class5);
}
@Test
public void testCyclicWithWeightsGraphModularity() {
GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
Node node1 = graphModel.factory().newNode("0");
Node node2 = graphModel.factory().newNode("1");
Node node3 = graphModel.factory().newNode("2");
Node node4 = graphModel.factory().newNode("3");
Node node5 = graphModel.factory().newNode("4");
Node node6 = graphModel.factory().newNode("5");
Node node7 = graphModel.factory().newNode("6");
Node node8 = graphModel.factory().newNode("7");
undirectedGraph.addNode(node1);
undirectedGraph.addNode(node2);
undirectedGraph.addNode(node3);
undirectedGraph.addNode(node4);
undirectedGraph.addNode(node5);
undirectedGraph.addNode(node6);
undirectedGraph.addNode(node7);
undirectedGraph.addNode(node8);
//Test 3 parallel edges summing weight = 10
//Related issues ==> #1419 Getting null pointer error when trying to calculate modularity; #1526 NullPointerException on Modularity Statistics with gexf with kind / parallel nodes
Edge edge12_1 = graphModel.factory().newEdge(node1, node2, 1, 2.f, false);
Edge edge12_2 = graphModel.factory().newEdge(node1, node2, 2, 5.f, false);
Edge edge12_3 = graphModel.factory().newEdge(node1, node2, 2, 3.f, false);
Edge edge23 = graphModel.factory().newEdge(node2, node3, false);
Edge edge34 = graphModel.factory().newEdge(node3, node4, 0, 10.f, false);
Edge edge45 = graphModel.factory().newEdge(node4, node5, false);
Edge edge56 = graphModel.factory().newEdge(node5, node6, 0, 10.f, false);
Edge edge67 = graphModel.factory().newEdge(node6, node7, false);
//Test 2 parallel edges summing weight = 10
Edge edge78_1= graphModel.factory().newEdge(node7, node8, 0, 5.f, false);
Edge edge78_2 = graphModel.factory().newEdge(node7, node8, 0, 5.f, false);
Edge edge81 = graphModel.factory().newEdge(node8, node1, false);
undirectedGraph.addEdge(edge12_1);
undirectedGraph.addEdge(edge12_2);
undirectedGraph.addEdge(edge12_3);
undirectedGraph.addEdge(edge23);
undirectedGraph.addEdge(edge34);
undirectedGraph.addEdge(edge45);
undirectedGraph.addEdge(edge56);
undirectedGraph.addEdge(edge67);
undirectedGraph.addEdge(edge78_1);
undirectedGraph.addEdge(edge78_2);
undirectedGraph.addEdge(edge81);
UndirectedGraph graph = graphModel.getUndirectedGraph();
Modularity mod = new Modularity();
Modularity.CommunityStructure theStructure = mod.new CommunityStructure(graph);
int[] comStructure = new int[graph.getNodeCount()];
HashMap<String, Double> modularityValues = mod.computeModularity(graph, theStructure, comStructure,
1., true, true);
int class1 = comStructure[0];
int class2 = comStructure[1];
int class4 = comStructure[3];
int class5 = comStructure[4];
int class7 = comStructure[6];
int class8 = comStructure[7];
assertEquals(class1, class2);
assertEquals(class7, class8);
assertNotEquals(class4, class5);
}
}