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

Example 41 with Edge

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

the class ExploreAutisticsNeurotypicals method getAllTrekEdges.

public static List<Edge> getAllTrekEdges(List<List<Graph>> graphs, int maxLength) {
    List<Node> nodes = graphs.get(0).get(0).getNodes();
    ContinuousVariable group = new ContinuousVariable("Group");
    nodes.add(group);
    graphs = reconcileNodes(graphs);
    int numGraphs = getNumGraphs(graphs);
    DataSet dataSet = new BoxDataSet(new VerticalDoubleDataBox(numGraphs, nodes.size()), nodes);
    for (int i = 0; i < dataSet.getNumRows(); i++) {
        for (int j = 0; j < dataSet.getNumColumns(); j++) {
            dataSet.setDouble(i, j, 0);
        }
    }
    Node fusiformLeft = graphs.get(0).get(0).getNode("Fusiform_L");
    Node fusiformRight = graphs.get(0).get(0).getNode("Fusiform_R");
    Set<Edge> trekEdges = new HashSet<>();
    for (int _group = 0; _group < graphs.size(); _group++) {
        List<Graph> __graphs = graphs.get(_group);
        for (Graph graph : __graphs) {
            List<List<Node>> treks = GraphUtils.treks(graph, fusiformLeft, fusiformRight, maxLength);
            for (List<Node> trek : treks) {
                for (int i = 0; i < trek.size() - 2; i++) {
                    trekEdges.add(graph.getEdge(trek.get(i), trek.get(i + 1)));
                }
            }
        }
    }
    return new ArrayList<>(trekEdges);
}

Example 42 with Edge

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

the class TestAutisticClassification method trainTest.

private void trainTest(FaskGraphs train, FaskGraphs test) {
    int numTp = 0;
    int numFp = 0;
    int numMeh = 0;
    List<Edge> allEdges = getAllEdges(train.getGraphs(), train.getTypes(), train.getGraphs());
    List<List<Edge>> ret = train(train.getGraphs(), allEdges, train.getTypes());
    printFiles(train.getGraphs(), train.getTypes(), -1, ret);
    for (int i = 0; i < test.getGraphs().size(); i++) {
        int _class = test(i, test.getFilenames(), test.getGraphs(), test.getTypes(), ret);
        if (_class == 1)
            numTp++;
        if (_class == -1)
            numFp++;
        if (_class == 0)
            numMeh++;
    }
    System.out.println();
    System.out.println("# TP = " + numTp);
    System.out.println("# FP = " + numFp);
    System.out.println("# Unclassified = " + numMeh);
    NumberFormat nf = new DecimalFormat("0.00");
    System.out.println("Precision = " + nf.format((numTp / (double) (numTp + numFp))));
    System.out.println();
}

Example 43 with Edge

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

the class TestAutisticClassification method test.

private int test(int i, List<String> filenames, List<Graph> graphs, List<Boolean> types, List<List<Edge>> ret) {
    Graph testGraph = graphs.get(i);
    List<Edge> forAutisismIfPresent = ret.get(0);
    List<Edge> forAutisismIfAbsent = ret.get(1);
    List<Edge> forTypicalIfPresent = ret.get(2);
    List<Edge> forTypicalIfAbsent = ret.get(3);
    List<Edge> presentAutistic = new ArrayList<>();
    List<Edge> absentAutistic = new ArrayList<>();
    List<Edge> presentTypical = new ArrayList<>();
    List<Edge> absentTypical = new ArrayList<>();
    for (Edge edge : forAutisismIfPresent) {
        if (testGraph.containsEdge(edge)) {
            presentAutistic.add(edge);
        }
    }
    for (Edge edge : forAutisismIfAbsent) {
        if (!testGraph.containsEdge(edge)) {
            absentAutistic.add(edge);
        }
    }
    for (Edge edge : forTypicalIfPresent) {
        if (testGraph.containsEdge(edge)) {
            presentTypical.add(edge);
        }
    }
    for (Edge edge : forTypicalIfAbsent) {
        if (!testGraph.containsEdge(edge)) {
            absentTypical.add(edge);
        }
    }
    boolean autistic = false;
    boolean typical = false;
    if (!absentAutistic.isEmpty()) {
        autistic = true;
    }
    if (!presentAutistic.isEmpty()) {
        autistic = true;
    }
    if (!presentTypical.isEmpty()) {
        typical = true;
    }
    if (!absentTypical.isEmpty()) {
        typical = true;
    }
    String name = "" + (i + 1) + ". " + filenames.get(i) + ". ";
    if (autistic && !typical) {
        System.out.println(name + ". Autistic");
    } else if (typical && !autistic) {
        System.out.println(name + ". Typical");
    }
    if (autistic && !typical) {
        for (Edge aPresent : presentAutistic) {
            System.out.println("..... present autistic " + aPresent);
        }
        for (Edge anAbsent : absentAutistic) {
            System.out.println("..... absent autistic " + anAbsent);
        }
    }
    if (typical && !autistic) {
        for (Edge aPresent : presentTypical) {
            System.out.println("..... present typical " + aPresent);
        }
        for (Edge anAbsent : absentTypical) {
            System.out.println("..... absent typical " + anAbsent);
        }
    }
    if (autistic && !typical) {
        if (types.get(i)) {
            return 1;
        } else {
            return -1;
        }
    }
    if (typical && !autistic) {
        if (!types.get(i)) {
            return 1;
        } else {
            return -1;
        }
    }
    return 0;
}