Package org.gephi.graph.api

Examples of org.gephi.graph.api.UndirectedGraph

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    }

    @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);

        Edge edge12 = graphModel.factory().newEdge(node1, node2, 0, 10.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);
        Edge edge78 = graphModel.factory().newEdge(node7, node8, 0, 10.f, false);
        Edge edge81 = graphModel.factory().newEdge(node8, node1, false);

        undirectedGraph.addEdge(edge12);
        undirectedGraph.addEdge(edge23);
        undirectedGraph.addEdge(edge34);
        undirectedGraph.addEdge(edge45);
        undirectedGraph.addEdge(edge56);
        undirectedGraph.addEdge(edge67);
        undirectedGraph.addEdge(edge78);
        undirectedGraph.addEdge(edge81);

        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
        Modularity mod = new Modularity();

        Modularity.CommunityStructure theStructure = mod.new CommunityStructure(hgraph);
        int[] comStructure = new int[hgraph.getNodeCount()];

        HashMap<String, Double> modularityValues = mod.computeModularity(hgraph, theStructure, comStructure,
                1., true, true);

        int class1 = comStructure[0];
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    }

    @Test
    public void testOneNodeEigenvectorCentrality() {
        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(1);
        UndirectedGraph hgraph = graphModel.getUndirectedGraph();

        EigenvectorCentrality ec = new EigenvectorCentrality();

        double[] centralities = new double[1];

        HashMap<Integer, Node> indicies = new HashMap();
        HashMap<Node, Integer> invIndicies = new HashMap();

        ec.fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);

        ec.calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, false, 100);

        Node n1 = hgraph.getNode("0");
        int index = invIndicies.get(n1);
        double ec1 = centralities[index];

        assertEquals(ec1, 0.0);
    }
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    }

    @Test
    public void testTwoConnectedNodesEigenvectorCentrality() {
        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(2);
        UndirectedGraph hgraph = graphModel.getUndirectedGraph();

        EigenvectorCentrality ec = new EigenvectorCentrality();

        double[] centralities = new double[2];

        HashMap<Integer, Node> indicies = new HashMap();
        HashMap<Node, Integer> invIndicies = new HashMap();

        ec.fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);

        ec.calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, false, 100);

        Node n1 = hgraph.getNode("0");
        int index = invIndicies.get(n1);
        double ec1 = centralities[index];

        assertEquals(ec1, 1.0);
    }
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    }

    @Test
    public void testNullGraphEigenvectorCentrality() {
        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(5);
        UndirectedGraph hgraph = graphModel.getUndirectedGraph();

        EigenvectorCentrality ec = new EigenvectorCentrality();

        double[] centralities = new double[5];

        HashMap<Integer, Node> indicies = new HashMap();
        HashMap<Node, Integer> invIndicies = new HashMap();

        ec.fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);

        ec.calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, false, 100);

        Node n2 = hgraph.getNode("1");
        int index = invIndicies.get(n2);
        double ec2 = centralities[index];

        assertEquals(ec2, 0.0);
    }
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    }

    @Test
    public void testCompleteUndirectedGraphEigenvectorCentrality() {
        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(5);
        UndirectedGraph hgraph = graphModel.getUndirectedGraph();

        EigenvectorCentrality ec = new EigenvectorCentrality();

        double[] centralities = new double[5];

        HashMap<Integer, Node> indicies = new HashMap();
        HashMap<Node, Integer> invIndicies = new HashMap();

        ec.fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);

        ec.calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, false, 100);

        Node n1 = hgraph.getNode("0");
        Node n3 = hgraph.getNode("2");
        int index1 = invIndicies.get(n1);
        int index3 = invIndicies.get(n3);
        double ec1 = centralities[index1];
        double ec3 = centralities[index3];
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    }

    @Test
    public void testSpecial1UndirectedGraphEigenvectorCentrlity() {
        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");

        undirectedGraph.addNode(node1);
        undirectedGraph.addNode(node2);
        undirectedGraph.addNode(node3);
        undirectedGraph.addNode(node4);

        Edge edge12 = graphModel.factory().newEdge(node1, node2, false);
        Edge edge23 = graphModel.factory().newEdge(node2, node3, false);
        Edge edge34 = graphModel.factory().newEdge(node3, node4, false);
        Edge edge13 = graphModel.factory().newEdge(node1, node3, false);
        Edge edge24 = graphModel.factory().newEdge(node2, node4, false);

        undirectedGraph.addEdge(edge12);
        undirectedGraph.addEdge(edge23);
        undirectedGraph.addEdge(edge34);
        undirectedGraph.addEdge(edge13);
        undirectedGraph.addEdge(edge24);

        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
        EigenvectorCentrality ec = new EigenvectorCentrality();

        double[] centralities = new double[4];

        HashMap<Integer, Node> indicies = new HashMap();
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    }

    @Test
    public void testSpecial2UndirectedGraphEigenvectorCentrlity() {
        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");

        undirectedGraph.addNode(node1);
        undirectedGraph.addNode(node2);
        undirectedGraph.addNode(node3);
        undirectedGraph.addNode(node4);
        undirectedGraph.addNode(node5);

        Edge edge13 = graphModel.factory().newEdge(node1, node3, false);
        Edge edge23 = graphModel.factory().newEdge(node2, node3, false);
        Edge edge34 = graphModel.factory().newEdge(node3, node4, false);
        Edge edge45 = graphModel.factory().newEdge(node4, node5, false);

        undirectedGraph.addEdge(edge13);
        undirectedGraph.addEdge(edge23);
        undirectedGraph.addEdge(edge34);
        undirectedGraph.addEdge(edge45);

        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
        EigenvectorCentrality ec = new EigenvectorCentrality();

        double[] centralities = new double[5];

        HashMap<Integer, Node> indicies = new HashMap();
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    }

    @Test
    public void testSpecial3UndirectedGraphEigenvectorCentrlity() {
        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");

        undirectedGraph.addNode(node1);
        undirectedGraph.addNode(node2);
        undirectedGraph.addNode(node3);

        Edge edge11 = graphModel.factory().newEdge(node1, node1, false);
        Edge edge12 = graphModel.factory().newEdge(node1, node2, false);
        Edge edge23 = graphModel.factory().newEdge(node2, node3, false);
        Edge edge33 = graphModel.factory().newEdge(node3, node3, false);

        undirectedGraph.addEdge(edge11);
        undirectedGraph.addEdge(edge12);
        undirectedGraph.addEdge(edge23);
        undirectedGraph.addEdge(edge33);

        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
        EigenvectorCentrality ec = new EigenvectorCentrality();

        double[] centralities = new double[3];

        HashMap<Integer, Node> indicies = new HashMap();
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    public void testOneNodeAvPathLength() {
        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(1);

        GraphDistance d = new GraphDistance();
        d.initializeStartValues();
        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
        HashMap<Node, Integer> indicies = d.createIndiciesMap(undirectedGraph);

        d.calculateDistanceMetrics(graphModel.getGraph(), indicies, false, false);

        double averageDegree = d.getPathLength();
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    public void testTwoConnectedNodesAvPathLength() {
        GraphModel graphModel = GraphGenerator.generatePathUndirectedGraph(2);

        GraphDistance d = new GraphDistance();
        d.initializeStartValues();
        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
        HashMap<Node, Integer> indicies = d.createIndiciesMap(undirectedGraph);

        d.calculateDistanceMetrics(graphModel.getGraph(), indicies, false, false);

        double averageDegree = d.getPathLength();
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Related Classes of org.gephi.graph.api.UndirectedGraph

  • org.gephi.io.exporter.plugin.ExporterCSV
  • org.gephi.statistics.plugin.ClusteringCoefficientNGTest
  • org.gephi.statistics.plugin.ConnectedComponents
  • org.gephi.statistics.plugin.ConnectedComponentsNGTest
  • org.gephi.statistics.plugin.EigenvectorCentralityNGTest
  • org.gephi.statistics.plugin.GraphDensityNGTest
  • org.gephi.statistics.plugin.GraphDistanceNGTest
  • org.gephi.statistics.plugin.GraphGenerator
  • org.gephi.statistics.plugin.HitsNGTest
  • org.gephi.statistics.plugin.ModularityNGTest
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