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

Example 16 with Node

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

the class TestDM method rtest13.

@Ignore
public void rtest13() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    Graph graph = emptyGraph(12);
    Node X0 = graph.getNode("X0");
    Node X1 = graph.getNode("X1");
    Node X2 = graph.getNode("X2");
    Node X3 = graph.getNode("X3");
    Node X4 = graph.getNode("X4");
    Node X5 = graph.getNode("X5");
    Node X6 = graph.getNode("X6");
    Node X7 = graph.getNode("X7");
    Node X8 = graph.getNode("X8");
    Node X9 = graph.getNode("X9");
    Node X10 = graph.getNode("X10");
    Node X11 = graph.getNode("X11");
    graph.addDirectedEdge(X0, X6);
    graph.addDirectedEdge(X1, X6);
    graph.addDirectedEdge(X1, X7);
    graph.addDirectedEdge(X1, X8);
    graph.addDirectedEdge(X2, X8);
    graph.addDirectedEdge(X3, X8);
    graph.addDirectedEdge(X3, X9);
    graph.addDirectedEdge(X3, X10);
    graph.addDirectedEdge(X3, X9);
    graph.addDirectedEdge(X4, X10);
    graph.addDirectedEdge(X4, X11);
    graph.addDirectedEdge(X5, X11);
    // 
    // graph.addDirectedEdge(X1, X8);
    // graph.addDirectedEdge(X2, X6);
    // graph.addDirectedEdge(X2, X7);
    // graph.addDirectedEdge(X2, X8);
    // 
    // 
    // graph.addDirectedEdge(X3, X8);
    // graph.addDirectedEdge(X3, X7);
    // graph.addDirectedEdge(X4, X8);
    // graph.addDirectedEdge(X4, X7);
    // 
    // 
    // graph.addDirectedEdge(X5, X8);
    RandomUtil.getInstance().setSeed(29483818483L);
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(100000, false);
    DMSearch search = new DMSearch();
    search.setInputs(new int[] { 0, 1, 2, 3, 4, 5 });
    search.setOutputs(new int[] { 6, 7, 8, 9, 10, 11 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    search.search();
    print("");
    print("" + search.getDmStructure());
    print("graph.existsDirectedCycle: " + search.getDmStructure().latentStructToEdgeListGraph(search.getDmStructure()).existsDirectedCycle());
    print("Graph structure: " + search);
    assertTrue(true);
}

Example 17 with Node

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

the class TestDM method rtest12.

@Ignore
public void rtest12() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    Graph graph = emptyGraph(9);
    Node X0 = graph.getNode("X0");
    Node X1 = graph.getNode("X1");
    Node X2 = graph.getNode("X2");
    Node X3 = graph.getNode("X3");
    Node X4 = graph.getNode("X4");
    Node X5 = graph.getNode("X5");
    Node X6 = graph.getNode("X6");
    Node X7 = graph.getNode("X7");
    Node X8 = graph.getNode("X8");
    graph.addDirectedEdge(X0, X6);
    graph.addDirectedEdge(X0, X7);
    graph.addDirectedEdge(X0, X8);
    graph.addDirectedEdge(X1, X6);
    graph.addDirectedEdge(X1, X7);
    graph.addDirectedEdge(X1, X8);
    graph.addDirectedEdge(X2, X6);
    graph.addDirectedEdge(X2, X7);
    graph.addDirectedEdge(X2, X8);
    graph.addDirectedEdge(X3, X8);
    graph.addDirectedEdge(X3, X7);
    graph.addDirectedEdge(X4, X8);
    graph.addDirectedEdge(X4, X7);
    graph.addDirectedEdge(X5, X8);
    RandomUtil.getInstance().setSeed(29483818483L);
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(100000, false);
    DMSearch search = new DMSearch();
    search.setInputs(new int[] { 0, 1, 2, 3, 4, 5 });
    search.setOutputs(new int[] { 6, 7, 8 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    search.search();
    print("");
    print("" + search.getDmStructure());
    print("graph.existsDirectedCycle: " + search.getDmStructure().latentStructToEdgeListGraph(search.getDmStructure()).existsDirectedCycle());
    print("Graph structure: " + search);
    assertTrue(true);
}

Example 18 with Node

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

the class TestDM method cycleExists.

public boolean cycleExists(Graph graph, List<Node> adjacentNodes, List<Node> path, Node currentNode) {
    if (adjacentNodes.isEmpty() && path.isEmpty()) {
        for (Node node : graph.getNodes()) {
            adjacentNodes = graph.getAdjacentNodes(node);
            if (adjacentNodes.isEmpty()) {
                continue;
            }
            path.add(node);
            currentNode = node;
            print("RAN: " + adjacentNodes + " " + path + " " + currentNode);
            return (cycleExists(graph, adjacentNodes, path, currentNode));
        }
    } else {
        adjacentNodes = graph.getAdjacentNodes(currentNode);
        for (Node node : adjacentNodes) {
            if (path.lastIndexOf(node) == (path.size() - 1)) {
                continue;
            } else {
                path.add(node);
                currentNode = node;
                return (cycleExists(graph, adjacentNodes, path, currentNode));
            }
        }
        if (listHasDuplicates(path)) {
            return (true);
        }
    }
    return (false);
}

Example 19 with Node

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

the class ExploreAutisticsNeurotypicals method restrictDataRange.

private static DataSet restrictDataRange(DataSet dataSet, double lowerRange, double upperRange) {
    int total = dataSet.getNumRows();
    List<Node> nodes = dataSet.getVariables();
    for (Node node : new ArrayList<>(nodes)) {
        if ("Group".equals(node.getName())) {
            continue;
        }
        int col = dataSet.getColumn(node);
        int count = 0;
        for (int i = 0; i < total; i++) {
            if (dataSet.getDouble(i, col) > 0) {
                count++;
            }
        }
        if (count < lowerRange * total || count > upperRange * total) {
            nodes.remove(node);
        }
    }
    return dataSet.subsetColumns(nodes);
}

Example 20 with Node

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

the class ExploreAutisticsNeurotypicals method printDegreeData.

public void printDegreeData() {
    // String path = "/Users/jdramsey/Documents/LAB_NOTEBOOK.2012.04.20/data/Joe_108_Variable";
    String path = "/Users/jdramsey/Documents/LAB_NOTEBOOK.2012.04.20/data/USM_Datasets/all";
    List<List<DataSet>> allDatasets = loadData(path, "ROI_data_autistic", "ROI_data_typical");
    List<List<Graph>> allGraphs = runAlgorithm(path, allDatasets, 10);
    List<List<Graph>> graphs = reconcileNodes(allGraphs);
    List<Node> nodes = graphs.get(0).get(0).getNodes();
    System.out.print("Group\t");
    for (Node node : nodes) {
        System.out.print(node.getName() + "\t");
    }
    System.out.println();
    for (int i = 0; i < graphs.size(); i++) {
        List<Graph> _graphs = graphs.get(i);
        for (Graph _graph : _graphs) {
            System.out.print(i + "\t");
            for (Node node : nodes) {
                System.out.print(_graph.getAdjacentNodes(node).size() + "\t");
            }
            System.out.println();
        }
    }
}