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

Example 11 with NodeIterable

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

the class WeightedDegree method calculateAverageWeightedDegree.

public double calculateAverageWeightedDegree(Graph graph, boolean isDirected, boolean updateAttributes) {
    double averageWeightedDegree = 0;
    DirectedGraph directedGraph = null;
    if (isDirected) {
        directedGraph = (DirectedGraph) graph;
    }
    Progress.start(progress, graph.getNodeCount());
    NodeIterable nodesIterable = graph.getNodes();
    for (Node n : nodesIterable) {
        double totalWeight = 0;
        if (isDirected) {
            double totalInWeight = 0;
            double totalOutWeight = 0;
            for (Edge e : directedGraph.getEdges(n)) {
                if (e.getSource().equals(n)) {
                    totalOutWeight += e.getWeight();
                }
                if (e.getTarget().equals(n)) {
                    totalInWeight += e.getWeight();
                }
            }
            totalWeight = totalInWeight + totalOutWeight;
            n.setAttribute(WINDEGREE, totalInWeight);
            n.setAttribute(WOUTDEGREE, totalOutWeight);
            n.setAttribute(WDEGREE, totalWeight);
            updateDegreeDists(totalInWeight, totalOutWeight, totalWeight);
        } else {
            for (Edge e : graph.getEdges(n)) {
                totalWeight += (e.isSelfLoop() ? 2 : 1) * e.getWeight();
            }
            n.setAttribute(WDEGREE, totalWeight);
            updateDegreeDists(totalWeight);
        }
        averageWeightedDegree += totalWeight;
        if (isCanceled) {
            nodesIterable.doBreak();
            break;
        }
        Progress.progress(progress);
    }
    averageWeightedDegree /= (isDirected ? 2.0 : 1.0) * graph.getNodeCount();
    return averageWeightedDegree;
}

Example 12 with NodeIterable

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

the class ExporterGML method exportData.

private void exportData(Graph graph) throws IOException {
    printOpen("graph");
    printTag("Creator \"Gephi\"");
    if (graph.isDirected() || graph.isMixed()) {
        printTag("directed 1");
    } else if (graph.isUndirected()) {
        printTag("directed 0");
    }
    NodeIterable nodeIterable = graph.getNodes();
    for (Node node : nodeIterable) {
        if (cancel) {
            nodeIterable.doBreak();
            return;
        }
        printNode(node, graph);
    }
    EdgeIterable edgeIterable = graph.getEdges();
    for (Edge edge : edgeIterable) {
        if (cancel) {
            edgeIterable.doBreak();
            return;
        }
        printEdge(edge, graph);
    }
    printClose();
}

Example 13 with NodeIterable

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

the class ExporterGraphML method createNodes.

private void createNodes(Document document, Element parentE, Graph graph) throws Exception {
    NodeIterable nodeIterable = graph.getNodes();
    for (Node n : nodeIterable) {
        if (cancel) {
            nodeIterable.doBreak();
            break;
        }
        Element nodeE = createNode(document, graph, n);
        parentE.appendChild(nodeE);
    }
}

Example 14 with NodeIterable

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

the class AbstractLayout method ensureSafeLayoutNodePositions.

/**
 * See https://github.com/gephi/gephi/issues/603 Nodes position to NaN on applied layout
 *
 * @param graphModel
 */
public static void ensureSafeLayoutNodePositions(GraphModel graphModel) {
    Graph graph = graphModel.getGraph();
    NodeIterable nodesIterable = graph.getNodes();
    for (Node node : nodesIterable) {
        if (node.x() != 0 || node.y() != 0) {
            nodesIterable.doBreak();
            return;
        }
    }
    // All at 0.0, init some random positions
    nodesIterable = graph.getNodes();
    for (Node node : nodesIterable) {
        node.setX((float) ((0.01 + Math.random()) * 1000) - 500);
        node.setY((float) ((0.01 + Math.random()) * 1000) - 500);
    }
}

Example 15 with NodeIterable

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

the class ClusteringCoefficient method computeTriangles.

private HashMap<String, Double> computeTriangles(Graph graph, ArrayWrapper[] currentNetwork, int[] currentTriangles, double[] nodeClustering, boolean directed) {
    HashMap<String, Double> resultValues = new HashMap<>();
    int ProgressCount = 0;
    Progress.start(progress, 7 * graph.getNodeCount());
    graph.readLock();
    try {
        int n = graph.getNodeCount();
        /**
         * Create network for processing
         */
        /**
         */
        HashMap<Node, Integer> indicies = new HashMap<>();
        ProgressCount = createIndiciesMapAndInitNetwork(graph, indicies, currentNetwork, ProgressCount);
        int index = 0;
        NodeIterable nodesIterable = graph.getNodes();
        for (Node node : nodesIterable) {
            HashMap<Node, EdgeWrapper> neighborTable = createNeighbourTable(graph, node, indicies, currentNetwork, directed);
            EdgeWrapper[] edges = getEdges(neighborTable);
            currentNetwork[index].node = node;
            currentNetwork[index].setArray(edges);
            index++;
            Progress.progress(progress, ++ProgressCount);
            if (isCanceled) {
                nodesIterable.doBreak();
                return resultValues;
            }
        }
        ProgressCount = processNetwork(currentNetwork, ProgressCount);
        int k = (int) Math.sqrt(n);
        for (int v = 0; v < k && v < n; v++) {
            newVertex(currentNetwork, currentTriangles, v, n);
            Progress.progress(progress, ++ProgressCount);
        }
        /* remaining links */
        ProgressCount = computeRemainingTrianles(graph, currentNetwork, currentTriangles, ProgressCount);
        resultValues = computeResultValues(graph, currentNetwork, currentTriangles, nodeClustering, directed, ProgressCount);
    } finally {
        graph.readUnlock();
    }
    return resultValues;
}