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

Example 21 with GraphNode

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

the class IndependenceFactsModel method loadFacts.

public static IndependenceFactsModel loadFacts(Reader reader) throws IOException {
    IndependenceFactsModel facts = new IndependenceFactsModel();
    Set<String> names = new HashSet<>();
    Map<String, Node> nodes = new HashMap<>();
    BufferedReader in = new BufferedReader(reader);
    String line;
    while ((line = in.readLine()) != null) {
        String[] tokens = line.split("[ ,;_|]+");
        if (tokens.length == 0)
            continue;
        if (tokens.length < 2)
            throw new IllegalArgumentException("Must specify at least two variables--e.g. X1 X2, for X1 _||_ X2.");
        for (String token : tokens) {
            names.add(token);
            if (!nodes.containsKey(token)) {
                nodes.put(token, new GraphNode(token));
            }
        }
        List<Node> z = new ArrayList<>();
        for (int i = 2; i < tokens.length; i++) {
            z.add(nodes.get(tokens[i]));
        }
        facts.add(new IndependenceFact(nodes.get(tokens[0]), nodes.get(tokens[1]), z));
    }
    return facts;
}

Example 22 with GraphNode

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

the class SemEstimatorGibbsParams method serializableInstance.

/**
 * Generates a simple exemplar of this class to test serialization.
 */
public static SemEstimatorGibbsParams serializableInstance() {
    SemGraph graph = new SemGraph();
    graph.addNode(new GraphNode("X"));
    return new SemEstimatorGibbsParams(new SemIm(new SemPm(graph)), false, 0.0d, 1);
}

Example 23 with GraphNode

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

the class XdslXmlParser method buildIM.

private BayesIm buildIM(Element element0, Map<String, String> displayNames) {
    Elements elements = element0.getChildElements();
    for (int i = 0; i < elements.size(); i++) {
        if (!"cpt".equals(elements.get(i).getQualifiedName())) {
            throw new IllegalArgumentException("Expecting cpt element.");
        }
    }
    Dag dag = new Dag();
    // Get the nodes.
    for (int i = 0; i < elements.size(); i++) {
        Element cpt = elements.get(i);
        String name = cpt.getAttribute(0).getValue();
        if (displayNames == null) {
            dag.addNode(new GraphNode(name));
        } else {
            dag.addNode(new GraphNode(displayNames.get(name)));
        }
    }
    // Get the edges.
    for (int i = 0; i < elements.size(); i++) {
        Element cpt = elements.get(i);
        Elements cptElements = cpt.getChildElements();
        for (int j = 0; j < cptElements.size(); j++) {
            Element cptElement = cptElements.get(j);
            if (cptElement.getQualifiedName().equals("parents")) {
                String list = cptElement.getValue();
                String[] parentNames = list.split(" ");
                for (String name : parentNames) {
                    if (displayNames == null) {
                        edu.cmu.tetrad.graph.Node parent = dag.getNode(name);
                        edu.cmu.tetrad.graph.Node child = dag.getNode(cpt.getAttribute(0).getValue());
                        dag.addDirectedEdge(parent, child);
                    } else {
                        edu.cmu.tetrad.graph.Node parent = dag.getNode(displayNames.get(name));
                        edu.cmu.tetrad.graph.Node child = dag.getNode(displayNames.get(cpt.getAttribute(0).getValue()));
                        dag.addDirectedEdge(parent, child);
                    }
                }
            }
        }
        String name;
        if (displayNames == null) {
            name = cpt.getAttribute(0).getValue();
        } else {
            name = displayNames.get(cpt.getAttribute(0).getValue());
        }
        dag.addNode(new GraphNode(name));
    }
    // PM
    BayesPm pm = new BayesPm(dag);
    for (int i = 0; i < elements.size(); i++) {
        Element cpt = elements.get(i);
        String varName = cpt.getAttribute(0).getValue();
        Node node;
        if (displayNames == null) {
            node = dag.getNode(varName);
        } else {
            node = dag.getNode(displayNames.get(varName));
        }
        Elements cptElements = cpt.getChildElements();
        List<String> stateNames = new ArrayList<>();
        for (int j = 0; j < cptElements.size(); j++) {
            Element cptElement = cptElements.get(j);
            if (cptElement.getQualifiedName().equals("state")) {
                Attribute attribute = cptElement.getAttribute(0);
                String stateName = attribute.getValue();
                stateNames.add(stateName);
            }
        }
        pm.setCategories(node, stateNames);
    }
    // IM
    BayesIm im = new MlBayesIm(pm);
    for (int nodeIndex = 0; nodeIndex < elements.size(); nodeIndex++) {
        Element cpt = elements.get(nodeIndex);
        Elements cptElements = cpt.getChildElements();
        for (int j = 0; j < cptElements.size(); j++) {
            Element cptElement = cptElements.get(j);
            if (cptElement.getQualifiedName().equals("probabilities")) {
                String list = cptElement.getValue();
                String[] probsStrings = list.split(" ");
                List<Double> probs = new ArrayList<>();
                for (String probString : probsStrings) {
                    probs.add(Double.parseDouble(probString));
                }
                int count = -1;
                for (int row = 0; row < im.getNumRows(nodeIndex); row++) {
                    for (int col = 0; col < im.getNumColumns(nodeIndex); col++) {
                        im.setProbability(nodeIndex, row, col, probs.get(++count));
                    }
                }
            }
        }
    }
    return im;
}

Example 24 with GraphNode

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

the class TestEvidence method sampleBayesIm2.

private static BayesIm sampleBayesIm2() {
    Node a = new GraphNode("a");
    Node b = new GraphNode("b");
    Node c = new GraphNode("c");
    Dag graph;
    graph = new Dag();
    graph.addNode(a);
    graph.addNode(b);
    graph.addNode(c);
    graph.addDirectedEdge(a, b);
    graph.addDirectedEdge(a, c);
    graph.addDirectedEdge(b, c);
    BayesPm bayesPm = new BayesPm(graph);
    bayesPm.setNumCategories(b, 3);
    BayesIm bayesIm1 = new MlBayesIm(bayesPm);
    bayesIm1.setProbability(0, 0, 0, .3);
    bayesIm1.setProbability(0, 0, 1, .7);
    bayesIm1.setProbability(1, 0, 0, .3);
    bayesIm1.setProbability(1, 0, 1, .4);
    bayesIm1.setProbability(1, 0, 2, .3);
    bayesIm1.setProbability(1, 1, 0, .6);
    bayesIm1.setProbability(1, 1, 1, .1);
    bayesIm1.setProbability(1, 1, 2, .3);
    bayesIm1.setProbability(2, 0, 0, .9);
    bayesIm1.setProbability(2, 0, 1, .1);
    bayesIm1.setProbability(2, 1, 0, .1);
    bayesIm1.setProbability(2, 1, 1, .9);
    bayesIm1.setProbability(2, 2, 0, .5);
    bayesIm1.setProbability(2, 2, 1, .5);
    bayesIm1.setProbability(2, 3, 0, .2);
    bayesIm1.setProbability(2, 3, 1, .8);
    bayesIm1.setProbability(2, 4, 0, .6);
    bayesIm1.setProbability(2, 4, 1, .4);
    bayesIm1.setProbability(2, 5, 0, .7);
    bayesIm1.setProbability(2, 5, 1, .3);
    return bayesIm1;
}

Example 25 with GraphNode

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

the class TestFruchtermanReingoldLayout method testLayout2.

@Test
public void testLayout2() {
    Dag dag = new Dag();
    GraphNode x1 = new GraphNode("X1");
    GraphNode x2 = new GraphNode("X2");
    x1.setCenter(40, 5);
    x2.setCenter(50, 5);
    dag.addNode(x1);
    dag.addNode(x2);
    dag.addDirectedEdge(x1, x2);
    Dag dag2 = new Dag(dag);
    FruchtermanReingoldLayout layout = new FruchtermanReingoldLayout(dag);
    layout.doLayout();
    assertEquals(dag, dag2);
}