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

Example 11 with Node

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

the class Modularity method saveValues.

private void saveValues(int[] struct, Graph graph, CommunityStructure theStructure) {
    Table nodeTable = graph.getModel().getNodeTable();
    Column modCol = nodeTable.getColumn(MODULARITY_CLASS);
    if (modCol == null) {
        modCol = nodeTable.addColumn(MODULARITY_CLASS, "Modularity Class", Integer.class, 0);
    }
    for (Node n : graph.getNodes()) {
        int n_index = theStructure.map.get(n);
        n.setAttribute(modCol, struct[n_index]);
    }
}

Example 12 with Node

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

the class PageRank method setInitialValues.

private void setInitialValues(Graph graph, double[] pagerankValues, double[] weights, boolean directed, boolean useWeights) {
    int N = graph.getNodeCount();
    int index = 0;
    for (Node s : graph.getNodes()) {
        pagerankValues[index] = 1.0f / N;
        if (useWeights) {
            double sum = 0;
            EdgeIterable eIter;
            if (directed) {
                eIter = ((DirectedGraph) graph).getOutEdges(s);
            } else {
                eIter = ((UndirectedGraph) graph).getEdges(s);
            }
            for (Edge edge : eIter) {
                sum += edge.getWeight();
            }
            weights[index] = sum;
        }
        index++;
    }
}

Example 13 with Node

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

the class DynamicDegree method loop.

@Override
public void loop(GraphView window, Interval interval) {
    Graph graph = graphModel.getGraph(window);
    DirectedGraph directedGraph = null;
    if (isDirected) {
        directedGraph = graphModel.getDirectedGraph(window);
    }
    TimeRepresentation tr = graphModel.getConfiguration().getTimeRepresentation();
    long sum = 0;
    for (Node n : graph.getNodes().toArray()) {
        int degree = graph.getDegree(n);
        if (!averageOnly) {
            switch(tr) {
                case INTERVAL:
                    n.setAttribute(dynamicDegreeColumn, degree, new Interval(interval.getLow(), interval.getLow() + tick));
                    break;
                case TIMESTAMP:
                    n.setAttribute(dynamicDegreeColumn, degree, interval.getLow());
                    n.setAttribute(dynamicDegreeColumn, degree, interval.getHigh());
                    break;
            }
            if (isDirected) {
                int indegree = directedGraph.getInDegree(n);
                int outdegree = directedGraph.getOutDegree(n);
                switch(tr) {
                    case INTERVAL:
                        n.setAttribute(dynamicInDegreeColumn, indegree, new Interval(interval.getLow(), interval.getLow() + tick));
                        n.setAttribute(dynamicOutDegreeColumn, outdegree, new Interval(interval.getLow(), interval.getLow() + tick));
                        break;
                    case TIMESTAMP:
                        n.setAttribute(dynamicInDegreeColumn, indegree, interval.getLow());
                        n.setAttribute(dynamicInDegreeColumn, indegree, interval.getHigh());
                        n.setAttribute(dynamicOutDegreeColumn, outdegree, interval.getLow());
                        n.setAttribute(dynamicOutDegreeColumn, outdegree, interval.getHigh());
                        break;
                }
            }
        }
        sum += degree;
        if (cancel) {
            break;
        }
    }
    double avg = sum / (double) graph.getNodeCount();
    averages.put(interval.getLow(), avg);
    averages.put(interval.getHigh(), avg);
    graphModel.getGraphVisible().setAttribute(DYNAMIC_AVGDEGREE, avg, interval.getLow());
    graphModel.getGraphVisible().setAttribute(DYNAMIC_AVGDEGREE, avg, interval.getHigh());
}

Example 14 with Node

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

the class ClusteringCoefficientNGTest method testTriangleNonCompleteDirectedGraphClusteringCoefficient.

@Test
public void testTriangleNonCompleteDirectedGraphClusteringCoefficient() {
    GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
    DirectedGraph directedGraph = graphModel.getDirectedGraph();
    Node node1 = graphModel.factory().newNode("0");
    Node node2 = graphModel.factory().newNode("1");
    Node node3 = graphModel.factory().newNode("2");
    directedGraph.addNode(node1);
    directedGraph.addNode(node2);
    directedGraph.addNode(node3);
    Edge edge12 = graphModel.factory().newEdge(node1, node2);
    Edge edge21 = graphModel.factory().newEdge(node2, node1);
    Edge edge23 = graphModel.factory().newEdge(node2, node3);
    Edge edge32 = graphModel.factory().newEdge(node3, node2);
    Edge edge13 = graphModel.factory().newEdge(node1, node3);
    directedGraph.addEdge(edge12);
    directedGraph.addEdge(edge21);
    directedGraph.addEdge(edge23);
    directedGraph.addEdge(edge32);
    directedGraph.addEdge(edge13);
    DirectedGraph graph = graphModel.getDirectedGraph();
    ClusteringCoefficient cc = new ClusteringCoefficient();
    ArrayWrapper[] network = new ArrayWrapper[3];
    int[] triangles = new int[3];
    double[] nodeClustering = new double[3];
    HashMap<String, Double> results = cc.computeClusteringCoefficient(graph, network, triangles, nodeClustering, true);
    double avClusteringCoefficient = results.get("clusteringCoefficient");
    double res = 0.833;
    double diff = 0.01;
    assertTrue(Math.abs(avClusteringCoefficient - res) < diff);
}

Example 15 with Node

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

the class ClusteringCoefficientNGTest method testSpecial3UndirectedGraphClusteringCoefficient.

@Test
public void testSpecial3UndirectedGraphClusteringCoefficient() {
    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, false);
    Edge edge31 = graphModel.factory().newEdge(node3, node1, false);
    Edge edge14 = graphModel.factory().newEdge(node1, node4, false);
    Edge edge25 = graphModel.factory().newEdge(node2, node5, false);
    Edge edge36 = graphModel.factory().newEdge(node3, node6, false);
    undirectedGraph.addEdge(edge12);
    undirectedGraph.addEdge(edge23);
    undirectedGraph.addEdge(edge31);
    undirectedGraph.addEdge(edge14);
    undirectedGraph.addEdge(edge25);
    undirectedGraph.addEdge(edge36);
    Graph graph = graphModel.getGraph();
    ClusteringCoefficient cc = new ClusteringCoefficient();
    ArrayWrapper[] network = new ArrayWrapper[6];
    int[] triangles = new int[6];
    double[] nodeClustering = new double[6];
    HashMap<String, Double> results = cc.computeClusteringCoefficient(graph, network, triangles, nodeClustering, false);
    double cl1 = nodeClustering[0];
    double res1 = 0.333;
    double diff = 0.01;
    assertTrue(Math.abs(cl1 - res1) < diff);
}