Examples with Edge edu.cmu.tetrad.graph.Edge used on opensource projects

Example 31 with Edge

use of edu.cmu.tetrad.graph.Edge in project tetrad by cmu-phil.

the class PngWriter method writePng.

public static void writePng(Graph graph, File file) {
    // circleLayout(graph, 200, 200, 175);
    JPanel panel = new JPanel();
    panel.setLayout(new BorderLayout());
    // Remove self-loops.
    graph = new EdgeListGraph(graph);
    for (Node node : graph.getNodes()) {
        for (Edge edge : new ArrayList<>(graph.getEdges(node, node))) {
            graph.removeEdge(edge);
        }
    }
    final GraphWorkbench workbench = new GraphWorkbench(graph);
    int maxx = 0;
    int maxy = 0;
    for (Node node : graph.getNodes()) {
        if (node.getCenterX() > maxx) {
            maxx = node.getCenterX();
        }
        if (node.getCenterY() > maxy) {
            maxy = node.getCenterY();
        }
    }
    workbench.setSize(new Dimension(maxx + 50, maxy + 50));
    panel.add(workbench, BorderLayout.CENTER);
    JDialog dialog = new JDialog();
    dialog.add(workbench);
    dialog.pack();
    Dimension size = workbench.getSize();
    BufferedImage image = new BufferedImage(size.width, size.height, BufferedImage.TYPE_BYTE_INDEXED);
    Graphics2D graphics = image.createGraphics();
    workbench.paint(graphics);
    image.flush();
    // Write the image to resultFile.
    try {
        ImageIO.write(image, "PNG", file);
    } catch (IOException e1) {
        throw new RuntimeException("Could not write to " + file, e1);
    }
}

Example 32 with Edge

use of edu.cmu.tetrad.graph.Edge in project tetrad by cmu-phil.

the class MixedFgesDiscretingContinuousVariables method convertBack.

private Graph convertBack(DataSet Dk, Graph p) {
    Graph p2 = new EdgeListGraph(Dk.getVariables());
    for (int i = 0; i < p.getNodes().size(); i++) {
        for (int j = i + 1; j < p.getNodes().size(); j++) {
            Node v1 = p.getNodes().get(i);
            Node v2 = p.getNodes().get(j);
            Edge e = p.getEdge(v1, v2);
            if (e != null) {
                Node w1 = Dk.getVariable(e.getNode1().getName());
                Node w2 = Dk.getVariable(e.getNode2().getName());
                Edge e2 = new Edge(w1, w2, e.getEndpoint1(), e.getEndpoint2());
                p2.addEdge(e2);
            }
        }
    }
    return p2;
}

Example 33 with Edge

use of edu.cmu.tetrad.graph.Edge in project tetrad by cmu-phil.

the class MixedFgesTreatingDiscreteAsContinuous method convertBack.

private Graph convertBack(DataSet Dk, Graph p) {
    Graph p2 = new EdgeListGraph(Dk.getVariables());
    for (int i = 0; i < p.getNodes().size(); i++) {
        for (int j = i + 1; j < p.getNodes().size(); j++) {
            Node v1 = p.getNodes().get(i);
            Node v2 = p.getNodes().get(j);
            Edge e = p.getEdge(v1, v2);
            if (e != null) {
                Node w1 = Dk.getVariable(e.getNode1().getName());
                Node w2 = Dk.getVariable(e.getNode2().getName());
                Edge e2 = new Edge(w1, w2, e.getEndpoint1(), e.getEndpoint2());
                p2.addEdge(e2);
            }
        }
    }
    return p2;
}

Example 34 with Edge

use of edu.cmu.tetrad.graph.Edge in project tetrad by cmu-phil.

the class TsFci method search.

public Graph search(IFas fas) {
    logger.log("info", "Starting FCI algorithm.");
    logger.log("info", "Independence test = " + getIndependenceTest() + ".");
    fas.setKnowledge(getKnowledge());
    fas.setDepth(depth);
    fas.setVerbose(verbose);
    // fas.setInitialGraph(initialGraph);
    this.graph = fas.search();
    this.sepsets = fas.getSepsets();
    graph.reorientAllWith(Endpoint.CIRCLE);
    SepsetProducer sp = new SepsetsPossibleDsep(graph, independenceTest, knowledge, depth, maxPathLength);
    sp.setVerbose(verbose);
    // // Optional step: Possible Dsep. (Needed for correctness but very time consuming.)
    if (isPossibleDsepSearchDone()) {
        // long time1 = System.currentTimeMillis();
        TsFciOrient tsFciOrient = new TsFciOrient(new SepsetsSet(this.sepsets, independenceTest), independenceTest);
        tsFciOrient.setKnowledge(knowledge);
        tsFciOrient.ruleR0(graph);
        for (Edge edge : new ArrayList<>(graph.getEdges())) {
            Node x = edge.getNode1();
            Node y = edge.getNode2();
            List<Node> sepset = sp.getSepset(x, y);
            if (sepset != null) {
                graph.removeEdge(x, y);
                sepsets.set(x, y, sepset);
                System.out.println("Possible DSEP Removed " + x + "--- " + y + " sepset = " + sepset);
                // This is another added component to enforce repeating structure, specifically for possibleDsep
                // added 4.27.2016
                removeSimilarPairs(getIndependenceTest(), x, y, sepset);
            }
        }
        // long time2 = System.currentTimeMillis();
        // logger.log("info", "Step C: " + (time2 - time1) / 1000. + "s");
        // 
        // // Step FCI D.
        // long time3 = System.currentTimeMillis();
        // 
        // System.out.println("Starting possible dsep search");
        // PossibleDsepFci possibleDSep = new PossibleDsepFci(graph, independenceTest);
        // possibleDSep.setMaxDegree(getPossibleDsepDepth());
        // possibleDSep.setKnowledge(getKnowledge());
        // possibleDSep.setMaxPathLength(maxPathLength);
        // this.sepsets.addAll(possibleDSep.search());
        // long time4 = System.currentTimeMillis();
        // logger.log("info", "Step D: " + (time4 - time3) / 1000. + "s");
        // System.out.println("Starting possible dsep search");
        // Reorient all edges as o-o.
        graph.reorientAllWith(Endpoint.CIRCLE);
    }
    // Step CI C (Zhang's step F3.)
    long time5 = System.currentTimeMillis();
    // fciOrientbk(getKnowledge(), graph, independenceTest.getVariable());    - Robert Tillman 2008
    // fciOrientbk(getKnowledge(), graph, variables);
    // new FciOrient(graph, new Sepsets(this.sepsets)).ruleR0(new Sepsets(this.sepsets));
    long time6 = System.currentTimeMillis();
    logger.log("info", "Step CI C: " + (time6 - time5) / 1000. + "s");
    final TsFciOrient fciOrient = new TsFciOrient(new SepsetsSet(this.sepsets, independenceTest), independenceTest);
    fciOrient.setCompleteRuleSetUsed(completeRuleSetUsed);
    fciOrient.setMaxPathLength(maxPathLength);
    fciOrient.setKnowledge(knowledge);
    fciOrient.ruleR0(graph);
    fciOrient.doFinalOrientation(graph);
    graph.setPag(true);
    return graph;
}

Example 35 with Edge

use of edu.cmu.tetrad.graph.Edge in project tetrad by cmu-phil.

the class WFges method search.

public Graph search() {
    score.setPenaltyDiscount(penaltyDiscount);
    Graph g = fges.search();
    Graph out = new EdgeListGraph(searchVariables);
    for (int i = 0; i < searchVariables.size(); i++) {
        for (int j = i + 1; j < searchVariables.size(); j++) {
            Node x = searchVariables.get(i);
            Node y = searchVariables.get(j);
            List<Node> xNodes = variablesPerNode.get(x);
            List<Node> yNodes = variablesPerNode.get(y);
            int left = 0;
            int right = 0;
            int total = 0;
            for (int k = 0; k < xNodes.size(); k++) {
                for (int l = 0; l < yNodes.size(); l++) {
                    Edge e = g.getEdge(xNodes.get(k), yNodes.get(l));
                    if (e != null) {
                        total++;
                        if (e.pointsTowards(xNodes.get(k)))
                            left++;
                        if (e.pointsTowards(yNodes.get(l)))
                            right++;
                    }
                }
            }
            if (total > 0) {
                if (left == total)
                    out.addDirectedEdge(y, x);
                else if (right == total)
                    out.addDirectedEdge(x, y);
                else
                    out.addUndirectedEdge(x, y);
            }
        }
    }
    return out;
}