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

Example 1 with Triple

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

the class FciOrientT method findCollidersUsingSepsets.

/**
 * Step C of PC; orients colliders using specified sepset. That is, orients x *-* y *-* z as x *-> y <-* z just in
 * case y is in Sepset({x, z}).
 */
public List<Triple> findCollidersUsingSepsets(SepsetProducer sepsetProducer, Graph graph, boolean verbose) {
    TetradLogger.getInstance().log("details", "Starting Collider Orientation:");
    List<Triple> colliders = new ArrayList<>();
    List<Node> nodes = graph.getNodes();
    for (Node b : nodes) {
        List<Node> adjacentNodes = graph.getAdjacentNodes(b);
        if (adjacentNodes.size() < 2) {
            continue;
        }
        ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
        int[] combination;
        while ((combination = cg.next()) != null) {
            Node a = adjacentNodes.get(combination[0]);
            Node c = adjacentNodes.get(combination[1]);
            // Skip triples that are shielded.
            if (graph.isAdjacentTo(a, c)) {
                continue;
            }
            List<Node> sepset = sepsetProducer.getSepset(a, c);
            // 
            if (sepset == null)
                continue;
            if (!sepset.contains(b)) {
                if (verbose) {
                    System.out.println("Collider orientation <" + a + ", " + b + ", " + c + "> sepset = " + sepset);
                }
                colliders.add(new Triple(a, b, c));
                TetradLogger.getInstance().log("colliderOrientations", SearchLogUtils.colliderOrientedMsg(a, b, c, sepset));
            }
        }
    }
    TetradLogger.getInstance().log("details", "Finishing Collider Orientation.");
    return colliders;
}

Example 2 with Triple

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

the class FciOrientT method addColliders.

private void addColliders(Graph graph, final SepsetProducer sepsetProducer, IKnowledge knowledge) {
    List<Triple> colliders = findCollidersUsingSepsets(sepsetProducer, graph, verbose);
    for (Triple collider : colliders) {
        Node a = collider.getX();
        Node b = collider.getY();
        Node c = collider.getZ();
        if (!(isArrowpointAllowed(a, b, graph) && isArrowpointAllowed(c, b, graph))) {
            continue;
        }
        graph.setEndpoint(a, b, Endpoint.ARROW);
        graph.setEndpoint(c, b, Endpoint.ARROW);
    }
}

Example 3 with Triple

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

the class TriplesAction method actionPerformed.

/**
 * Copies a parentally closed selection of session nodes in the frontmost
 * session editor to the clipboard.
 */
public void actionPerformed(ActionEvent e) {
    Box b = Box.createVerticalBox();
    JTextArea textArea = new JTextArea();
    JScrollPane scroll = new JScrollPane(textArea);
    scroll.setPreferredSize(new Dimension(600, 600));
    textArea.append("Underlinings:");
    boolean allEmpty = true;
    List<Node> nodes = graph.getNodes();
    Collections.sort(nodes, new Comparator<Node>() {

        public int compare(Node node1, Node node2) {
            return node1.getName().compareTo(node2.getName());
        }
    });
    for (int i = 0; i < nodes.size(); i++) {
        Node node = nodes.get(i);
        List<String> types = graph.getTriplesClassificationTypes();
        List<List<Triple>> triplesList = graph.getTriplesLists(node);
        boolean existsClassification = false;
        for (List<Triple> list : triplesList) {
            if (!list.isEmpty()) {
                existsClassification = true;
            }
        }
        if (!existsClassification) {
            continue;
        }
        textArea.append("\n\nNode " + node);
        for (int j = 0; j < types.size(); j++) {
            String type = types.get(j);
            List<Triple> triples = triplesList.get(j);
            if (!triples.isEmpty()) {
                textArea.append("\n\n    ");
                textArea.append(type + niceList(triples));
            }
        }
        allEmpty = false;
    }
    if (allEmpty) {
        textArea.append("\n\nAll triple classifications can be read from the graph.");
    }
    Box b2 = Box.createHorizontalBox();
    b2.add(scroll);
    textArea.setCaretPosition(0);
    b.add(b2);
    JPanel panel = new JPanel();
    panel.setLayout(new BorderLayout());
    panel.add(b);
    EditorWindow window = new EditorWindow(panel, "Underlinings", "Close", false, JOptionUtils.centeringComp());
    DesktopController.getInstance().addEditorWindow(window, JLayeredPane.PALETTE_LAYER);
    window.setVisible(true);
// JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), b,
// "Graph Properties", JOptionPane.PLAIN_MESSAGE);
}

Example 4 with Triple

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

the class JsonUtils method parseJSONObjectToTetradGraph.

public static Graph parseJSONObjectToTetradGraph(JSONObject jObj) {
    // Node
    List<Node> nodes = parseJSONArrayToTetradNodes(jObj.getJSONArray("nodes"));
    EdgeListGraphSingleConnections graph = new EdgeListGraphSingleConnections(nodes);
    // Edge
    Set<Edge> edges = parseJSONArrayToTetradEdges(graph, jObj.getJSONArray("edgesSet"));
    for (Edge edge : edges) {
        graph.addEdge(edge);
    }
    // ambiguousTriples
    Set<Triple> ambiguousTriples = parseJSONArrayToTetradTriples(jObj.getJSONArray("ambiguousTriples"));
    for (Triple triple : ambiguousTriples) {
        graph.addAmbiguousTriple(triple.getX(), triple.getY(), triple.getZ());
    }
    // underLineTriples
    Set<Triple> underLineTriples = parseJSONArrayToTetradTriples(jObj.getJSONArray("underLineTriples"));
    for (Triple triple : underLineTriples) {
        graph.addUnderlineTriple(triple.getX(), triple.getY(), triple.getZ());
    }
    // dottedUnderLineTriples
    Set<Triple> dottedUnderLineTriples = parseJSONArrayToTetradTriples(jObj.getJSONArray("dottedUnderLineTriples"));
    for (Triple triple : dottedUnderLineTriples) {
        graph.addDottedUnderlineTriple(triple.getX(), triple.getY(), triple.getZ());
    }
    // stuffRemovedSinceLastTripleAccess
    boolean stuffRemovedSinceLastTripleAccess = jObj.getBoolean("stuffRemovedSinceLastTripleAccess");
    graph.setStuffRemovedSinceLastTripleAccess(stuffRemovedSinceLastTripleAccess);
    // highlightedEdges
    Set<Edge> highlightedEdges = parseJSONArrayToTetradEdges(graph, jObj.getJSONArray("highlightedEdges"));
    for (Edge edge : highlightedEdges) {
        graph.setHighlighted(edge, true);
    }
    return graph;
}

Example 5 with Triple

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

the class JsonUtils method parseJSONArrayToTetradTriples.

public static Set<Triple> parseJSONArrayToTetradTriples(JSONArray jArray) {
    Set<Triple> triples = new HashSet<>();
    for (int i = 0; i < jArray.length(); i++) {
        Triple triple = parseJSONArrayToTetradTriple(jArray.getJSONObject(i));
        triples.add(triple);
    }
    return triples;
}