Examples with UndirectedGraph org.gephi.graph.api.UndirectedGraph used on opensource projects

Example 31 with UndirectedGraph

use of org.gephi.graph.api.UndirectedGraph in project gephi by gephi.

the class PageRankNGTest method testUndirectedWeightedGraphPageRank.

@Test
public void testUndirectedWeightedGraphPageRank() {
    pc.newProject();
    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");
    undirectedGraph.addNode(node1);
    undirectedGraph.addNode(node2);
    undirectedGraph.addNode(node3);
    undirectedGraph.addNode(node4);
    undirectedGraph.addNode(node5);
    undirectedGraph.addNode(node6);
    Edge edge12 = graphModel.factory().newEdge(node1, node2, false);
    Edge edge23 = graphModel.factory().newEdge(node2, node3, 0, 10, false);
    Edge edge34 = graphModel.factory().newEdge(node3, node4, false);
    Edge edge45 = graphModel.factory().newEdge(node4, node5, false);
    Edge edge56 = graphModel.factory().newEdge(node5, node6, false);
    Edge edge61 = graphModel.factory().newEdge(node6, node1, false);
    undirectedGraph.addEdge(edge12);
    undirectedGraph.addEdge(edge23);
    undirectedGraph.addEdge(edge34);
    undirectedGraph.addEdge(edge45);
    undirectedGraph.addEdge(edge56);
    undirectedGraph.addEdge(edge61);
    UndirectedGraph graph = graphModel.getUndirectedGraph();
    PageRank pr = new PageRank();
    double[] pageRank;
    HashMap<Node, Integer> indicies = pr.createIndiciesMap(graph);
    pageRank = pr.calculatePagerank(graph, indicies, false, true, 0.001, 0.85);
    int index1 = indicies.get(node1);
    int index2 = indicies.get(node2);
    int index3 = indicies.get(node3);
    int index6 = indicies.get(node6);
    double diff = 0.01;
    double pr1 = pageRank[index1];
    double pr2 = pageRank[index2];
    double pr3 = pageRank[index3];
    double pr6 = pageRank[index6];
    assertTrue(Math.abs(pr2 - pr3) < diff);
    assertTrue(pr1 < pr2);
    assertTrue(pr1 < pr6);
}

Example 32 with UndirectedGraph

use of org.gephi.graph.api.UndirectedGraph in project gephi by gephi.

the class ModularityNGTest method testCyclicWithWeightsGraphModularity.

@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);
}

Example 33 with UndirectedGraph

use of org.gephi.graph.api.UndirectedGraph in project gephi by gephi.

the class ModularityNGTest method testComputeBarbellGraphModularityHasHighWeight.

@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);
}

Example 34 with UndirectedGraph

use of org.gephi.graph.api.UndirectedGraph in project gephi by gephi.

the class ModularityNGTest method testTwoConnectedNodesModularity.

@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);
}

Example 35 with UndirectedGraph

use of org.gephi.graph.api.UndirectedGraph in project gephi by gephi.

the class PageRankNGTest method testCyclicGraphPageRank.

@Test
public void testCyclicGraphPageRank() {
    pc.newProject();
    GraphModel graphModel = GraphGenerator.generateCyclicUndirectedGraph(6);
    UndirectedGraph graph = graphModel.getUndirectedGraph();
    PageRank pr = new PageRank();
    double[] pageRank;
    HashMap<Node, Integer> indicies = pr.createIndiciesMap(graph);
    pageRank = pr.calculatePagerank(graph, indicies, false, false, 0.001, 0.6);
    Node n4 = graph.getNode("3");
    int index4 = indicies.get(n4);
    double pr4 = pageRank[index4];
    double res = 0.1667;
    double diff4 = Math.abs(pr4 - res);
    assertTrue(diff4 < 0.01);
}