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

Example 1 with Edge

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

the class YifanHuLayout method getAverageEdgeLength.

public float getAverageEdgeLength(Graph graph) {
    float edgeLength = 0;
    int count = 1;
    for (Edge e : graph.getEdges()) {
        edgeLength += ForceVectorUtils.distance(e.getSource(), e.getTarget());
        count++;
    }
    return edgeLength / count;
}

Example 2 with Edge

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

the class FruchtermanReingold method goAlgo.

@Override
public void goAlgo() {
    this.graph = graphModel.getGraphVisible();
    graph.readLock();
    try {
        Node[] nodes = graph.getNodes().toArray();
        Edge[] edges = graph.getEdges().toArray();
        for (Node n : nodes) {
            if (n.getLayoutData() == null || !(n.getLayoutData() instanceof ForceVectorNodeLayoutData)) {
                n.setLayoutData(new ForceVectorNodeLayoutData());
            }
            ForceVectorNodeLayoutData layoutData = n.getLayoutData();
            layoutData.dx = 0;
            layoutData.dy = 0;
        }
        // Déplacement limite : on peut le calibrer...
        float maxDisplace = (float) (Math.sqrt(AREA_MULTIPLICATOR * area) / 10f);
        // La variable k, l'idée principale du layout.
        float k = (float) Math.sqrt((AREA_MULTIPLICATOR * area) / (1f + nodes.length));
        for (Node N1 : nodes) {
            for (Node N2 : nodes) {
                // On fait toutes les paires de noeuds
                if (N1 != N2) {
                    // distance en x entre les deux noeuds
                    float xDist = N1.x() - N2.x();
                    float yDist = N1.y() - N2.y();
                    // distance tout court
                    float dist = (float) Math.sqrt(xDist * xDist + yDist * yDist);
                    if (dist > 0) {
                        // Force de répulsion
                        float repulsiveF = k * k / dist;
                        ForceVectorNodeLayoutData layoutData = N1.getLayoutData();
                        // on l'applique...
                        layoutData.dx += xDist / dist * repulsiveF;
                        layoutData.dy += yDist / dist * repulsiveF;
                    }
                }
            }
        }
        for (Edge E : edges) {
            // Idem, pour tous les noeuds on applique la force d'attraction
            Node Nf = E.getSource();
            Node Nt = E.getTarget();
            float xDist = Nf.x() - Nt.x();
            float yDist = Nf.y() - Nt.y();
            float dist = (float) Math.sqrt(xDist * xDist + yDist * yDist);
            float attractiveF = dist * dist / k;
            if (dist > 0) {
                ForceVectorNodeLayoutData sourceLayoutData = Nf.getLayoutData();
                ForceVectorNodeLayoutData targetLayoutData = Nt.getLayoutData();
                sourceLayoutData.dx -= xDist / dist * attractiveF;
                sourceLayoutData.dy -= yDist / dist * attractiveF;
                targetLayoutData.dx += xDist / dist * attractiveF;
                targetLayoutData.dy += yDist / dist * attractiveF;
            }
        }
        // gravity
        for (Node n : nodes) {
            ForceVectorNodeLayoutData layoutData = n.getLayoutData();
            float d = (float) Math.sqrt(n.x() * n.x() + n.y() * n.y());
            float gf = 0.01f * k * (float) gravity * d;
            layoutData.dx -= gf * n.x() / d;
            layoutData.dy -= gf * n.y() / d;
        }
        // speed
        for (Node n : nodes) {
            ForceVectorNodeLayoutData layoutData = n.getLayoutData();
            layoutData.dx *= speed / SPEED_DIVISOR;
            layoutData.dy *= speed / SPEED_DIVISOR;
        }
        for (Node n : nodes) {
            // Maintenant on applique le déplacement calculé sur les noeuds.
            // nb : le déplacement à chaque passe "instantanné" correspond à la force : c'est une sorte d'accélération.
            ForceVectorNodeLayoutData layoutData = n.getLayoutData();
            float xDist = layoutData.dx;
            float yDist = layoutData.dy;
            float dist = (float) Math.sqrt(layoutData.dx * layoutData.dx + layoutData.dy * layoutData.dy);
            if (dist > 0 && !n.isFixed()) {
                float limitedDist = Math.min(maxDisplace * ((float) speed / SPEED_DIVISOR), dist);
                n.setX(n.x() + xDist / dist * limitedDist);
                n.setY(n.y() + yDist / dist * limitedDist);
            }
        }
    } finally {
        graph.readUnlockAll();
    }
}

Example 3 with Edge

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

the class EdgeWeightRankingImpl method refresh.

@Override
protected void refresh() {
    if (graph.getEdgeCount() > 0) {
        double minV = Double.MAX_VALUE;
        double maxV = Double.MIN_VALUE;
        for (Edge e : graph.getEdges()) {
            if (e.hasDynamicWeight()) {
                TimeMap timeMap = (TimeMap) e.getAttribute("weight");
                if (timeMap != null) {
                    Double numMin = (Double) timeMap.get(graph.getView().getTimeInterval(), Estimator.MIN);
                    Double numMax = (Double) timeMap.get(graph.getView().getTimeInterval(), Estimator.MAX);
                    minV = Math.min(numMin, minV);
                    maxV = Math.max(numMax, maxV);
                }
            } else {
                minV = Math.min(e.getWeight(), minV);
                maxV = Math.max(e.getWeight(), maxV);
            }
        }
        min = minV;
        max = maxV;
    }
}

Example 4 with Edge

use of org.gephi.graph.api.Edge 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 5 with Edge

use of org.gephi.graph.api.Edge 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);
}