Examples with KnowledgeEdge edu.cmu.tetrad.data.KnowledgeEdge used on opensource projects

Example 11 with KnowledgeEdge

use of edu.cmu.tetrad.data.KnowledgeEdge in project tetrad by cmu-phil.

the class KnowledgeBoxEditor method resetEdgeDisplayOld.

/**
 * This is an old method that needs to be removed when cleaning up code.
 */
private void resetEdgeDisplayOld() {
    List<String> varNames = getVarNames();
    IKnowledge knowledge = getKnowledge();
    for (String name : varNames) {
        knowledge.addVariable(name);
    }
    KnowledgeGraph graph = new KnowledgeGraph(getKnowledge());
    for (String varName : varNames) {
        graph.addNode(new KnowledgeModelNode(varName));
    }
    if (this.showRequiredByGroups) {
        for (Iterator<KnowledgeEdge> i = knowledge.requiredEdgesIterator(); i.hasNext(); ) {
            KnowledgeEdge edge = i.next();
            String from = edge.getFrom();
            String to = edge.getTo();
            if (knowledge.isRequiredByGroups(from, to)) {
                KnowledgeModelNode fromNode = (KnowledgeModelNode) graph.getNode(from);
                KnowledgeModelNode toNode = (KnowledgeModelNode) graph.getNode(to);
                graph.addEdge(new KnowledgeModelEdge(fromNode, toNode, KnowledgeModelEdge.REQUIRED_BY_GROUPS));
            }
        }
    }
    if (this.showForbiddenByGroups) {
        for (Iterator<KnowledgeEdge> i = knowledge.forbiddenEdgesIterator(); i.hasNext(); ) {
            KnowledgeEdge edge = i.next();
            String from = edge.getFrom();
            String to = edge.getTo();
            if (knowledge.isForbiddenByGroups(from, to)) {
                KnowledgeModelNode fromNode = (KnowledgeModelNode) graph.getNode(from);
                KnowledgeModelNode toNode = (KnowledgeModelNode) graph.getNode(to);
                graph.addEdge(new KnowledgeModelEdge(fromNode, toNode, KnowledgeModelEdge.FORBIDDEN_BY_GROUPS));
            }
        }
    }
    if (showRequired) {
        for (Iterator<KnowledgeEdge> i = knowledge.explicitlyRequiredEdgesIterator(); i.hasNext(); ) {
            KnowledgeEdge pair = i.next();
            String from = pair.getFrom();
            String to = pair.getTo();
            KnowledgeModelNode fromNode = (KnowledgeModelNode) graph.getNode(from);
            KnowledgeModelNode toNode = (KnowledgeModelNode) graph.getNode(to);
            if (fromNode == null || toNode == null) {
                continue;
            }
            graph.addEdge(new KnowledgeModelEdge(fromNode, toNode, KnowledgeModelEdge.REQUIRED));
        }
    }
    if (showForbiddenByTiers) {
        for (Iterator<KnowledgeEdge> i = knowledge.forbiddenEdgesIterator(); i.hasNext(); ) {
            KnowledgeEdge pair = i.next();
            String from = pair.getFrom();
            String to = pair.getTo();
            if (!knowledge.isForbiddenByTiers(from, to)) {
                continue;
            }
            KnowledgeModelNode fromNode = (KnowledgeModelNode) graph.getNode(from);
            KnowledgeModelNode toNode = (KnowledgeModelNode) graph.getNode(to);
            if (fromNode == null) {
                graph.addNode(new KnowledgeModelNode(from));
                fromNode = (KnowledgeModelNode) graph.getNode(from);
            }
            if (toNode == null) {
                graph.addNode(new KnowledgeModelNode(to));
                toNode = (KnowledgeModelNode) graph.getNode(to);
            }
            KnowledgeModelEdge knowledgeModelEdge = new KnowledgeModelEdge(fromNode, toNode, KnowledgeModelEdge.FORBIDDEN_BY_TIERS);
            graph.addEdge(knowledgeModelEdge);
        // Hacked fix. Jdramsey.
        // if (!graph.containsEdge(knowledgeModelEdge)) {
        // graph.addEdge(knowledgeModelEdge);
        // }
        }
    }
    if (showForbiddenExplicitly) {
        for (Iterator<KnowledgeEdge> i = knowledge.explicitlyForbiddenEdgesIterator(); i.hasNext(); ) {
            KnowledgeEdge pair = i.next();
            String from = pair.getFrom();
            String to = pair.getTo();
            KnowledgeModelNode fromNode = (KnowledgeModelNode) graph.getNode(from);
            KnowledgeModelNode toNode = (KnowledgeModelNode) graph.getNode(to);
            KnowledgeModelEdge edge = new KnowledgeModelEdge(fromNode, toNode, KnowledgeModelEdge.FORBIDDEN_EXPLICITLY);
            if (!graph.containsEdge(edge)) {
                graph.addEdge(edge);
            }
        }
    }
    boolean arrangedAll = GraphUtils.arrangeBySourceGraph(graph, edgeWorkbench.getGraph());
    if (!arrangedAll) {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
    edgeWorkbench.setGraph(graph);
    if (knowledgeBoxModel != null) {
        notifyKnowledge();
    }
}

Example 12 with KnowledgeEdge

use of edu.cmu.tetrad.data.KnowledgeEdge in project tetrad by cmu-phil.

the class TsFci method fciOrientbk.

/**
 * Orients according to background knowledge
 */
private void fciOrientbk(IKnowledge bk, Graph graph, List<Node> variables) {
    logger.log("info", "Starting BK Orientation.");
    for (Iterator<KnowledgeEdge> it = bk.forbiddenEdgesIterator(); it.hasNext(); ) {
        if (Thread.currentThread().isInterrupted()) {
            break;
        }
        KnowledgeEdge edge = it.next();
        // match strings to variables in the graph.
        Node from = SearchGraphUtils.translate(edge.getFrom(), variables);
        Node to = SearchGraphUtils.translate(edge.getTo(), variables);
        if (from == null || to == null) {
            continue;
        }
        if (graph.getEdge(from, to) == null) {
            continue;
        }
        // Orient to*->from
        graph.setEndpoint(to, from, Endpoint.ARROW);
        graph.setEndpoint(from, to, Endpoint.CIRCLE);
        logger.log("knowledgeOrientation", SearchLogUtils.edgeOrientedMsg("Knowledge", graph.getEdge(from, to)));
    }
    for (Iterator<KnowledgeEdge> it = bk.requiredEdgesIterator(); it.hasNext(); ) {
        if (Thread.currentThread().isInterrupted()) {
            break;
        }
        KnowledgeEdge edge = it.next();
        // match strings to variables in this graph
        Node from = SearchGraphUtils.translate(edge.getFrom(), variables);
        Node to = SearchGraphUtils.translate(edge.getTo(), variables);
        if (from == null || to == null) {
            continue;
        }
        if (graph.getEdge(from, to) == null) {
            continue;
        }
        graph.setEndpoint(to, from, Endpoint.TAIL);
        graph.setEndpoint(from, to, Endpoint.ARROW);
        logger.log("knowledgeOrientation", SearchLogUtils.edgeOrientedMsg("Knowledge", graph.getEdge(from, to)));
    }
    logger.log("info", "Finishing BK Orientation.");
}

Example 13 with KnowledgeEdge

use of edu.cmu.tetrad.data.KnowledgeEdge in project tetrad by cmu-phil.

the class TsFges2 method addRequiredEdges.

// Adds edges required by knowledge.
private void addRequiredEdges(Graph graph) {
    if (!existsKnowledge())
        return;
    for (Iterator<KnowledgeEdge> it = getKnowledge().requiredEdgesIterator(); it.hasNext(); ) {
        if (Thread.currentThread().isInterrupted()) {
            break;
        }
        KnowledgeEdge next = it.next();
        Node nodeA = graph.getNode(next.getFrom());
        Node nodeB = graph.getNode(next.getTo());
        if (!graph.isAncestorOf(nodeB, nodeA)) {
            graph.removeEdges(nodeA, nodeB);
            graph.addDirectedEdge(nodeA, nodeB);
            TetradLogger.getInstance().log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeA, nodeB));
        }
    }
    for (Edge edge : graph.getEdges()) {
        if (Thread.currentThread().isInterrupted()) {
            break;
        }
        final String A = edge.getNode1().getName();
        final String B = edge.getNode2().getName();
        if (knowledge.isForbidden(A, B)) {
            Node nodeA = edge.getNode1();
            Node nodeB = edge.getNode2();
            if (nodeA == null || nodeB == null)
                throw new NullPointerException();
            if (graph.isAdjacentTo(nodeA, nodeB) && !graph.isChildOf(nodeA, nodeB)) {
                if (!graph.isAncestorOf(nodeA, nodeB)) {
                    graph.removeEdges(nodeA, nodeB);
                    graph.addDirectedEdge(nodeB, nodeA);
                    TetradLogger.getInstance().log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
                }
            }
            if (!graph.isChildOf(nodeA, nodeB) && getKnowledge().isForbidden(nodeA.getName(), nodeB.getName())) {
                if (!graph.isAncestorOf(nodeA, nodeB)) {
                    graph.removeEdges(nodeA, nodeB);
                    graph.addDirectedEdge(nodeB, nodeA);
                    TetradLogger.getInstance().log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
                }
            }
        } else if (knowledge.isForbidden(B, A)) {
            Node nodeA = edge.getNode2();
            Node nodeB = edge.getNode1();
            if (nodeA == null || nodeB == null)
                throw new NullPointerException();
            if (graph.isAdjacentTo(nodeA, nodeB) && !graph.isChildOf(nodeA, nodeB)) {
                if (!graph.isAncestorOf(nodeA, nodeB)) {
                    graph.removeEdges(nodeA, nodeB);
                    graph.addDirectedEdge(nodeB, nodeA);
                    TetradLogger.getInstance().log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
                }
            }
            if (!graph.isChildOf(nodeA, nodeB) && getKnowledge().isForbidden(nodeA.getName(), nodeB.getName())) {
                if (!graph.isAncestorOf(nodeA, nodeB)) {
                    graph.removeEdges(nodeA, nodeB);
                    graph.addDirectedEdge(nodeB, nodeA);
                    TetradLogger.getInstance().log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
                }
            }
        }
    }
}

Example 14 with KnowledgeEdge

use of edu.cmu.tetrad.data.KnowledgeEdge in project tetrad by cmu-phil.

the class Cfci method fciOrientbk.

/**
 * Orients according to background knowledge
 */
private void fciOrientbk(IKnowledge bk, Graph graph, List<Node> variables) {
    if (verbose) {
        logger.log("info", "Starting BK Orientation.");
    }
    for (Iterator<KnowledgeEdge> it = bk.forbiddenEdgesIterator(); it.hasNext(); ) {
        KnowledgeEdge edge = it.next();
        // match strings to variables in the graph.
        Node from = SearchGraphUtils.translate(edge.getFrom(), variables);
        Node to = SearchGraphUtils.translate(edge.getTo(), variables);
        if (from == null || to == null) {
            continue;
        }
        if (graph.getEdge(from, to) == null) {
            continue;
        }
        // Orient to*->from
        graph.setEndpoint(to, from, Endpoint.ARROW);
        if (verbose) {
            logger.log("knowledgeOrientation", SearchLogUtils.edgeOrientedMsg("Knowledge", graph.getEdge(from, to)));
        }
    }
    for (Iterator<KnowledgeEdge> it = bk.requiredEdgesIterator(); it.hasNext(); ) {
        KnowledgeEdge edge = it.next();
        // match strings to variables in this graph
        Node from = SearchGraphUtils.translate(edge.getFrom(), variables);
        Node to = SearchGraphUtils.translate(edge.getTo(), variables);
        if (from == null || to == null) {
            continue;
        }
        if (graph.getEdge(from, to) == null) {
            continue;
        }
        if (verbose) {
            System.out.println("Rule T3: Orienting " + from + "-->" + to);
        }
        graph.setEndpoint(to, from, Endpoint.TAIL);
        graph.setEndpoint(from, to, Endpoint.ARROW);
        if (verbose) {
            logger.log("knowledgeOrientation", SearchLogUtils.edgeOrientedMsg("Knowledge", graph.getEdge(from, to)));
        }
    }
    if (verbose) {
        logger.log("info", "Finishing BK Orientation.");
    }
}

Example 15 with KnowledgeEdge

use of edu.cmu.tetrad.data.KnowledgeEdge in project tetrad by cmu-phil.

the class FciMax method fciOrientbk.

// ===========================PRIVATE METHODS=========================//
/**
 * Orients according to background knowledge
 */
private void fciOrientbk(IKnowledge bk, Graph graph, List<Node> variables) {
    logger.log("info", "Starting BK Orientation.");
    for (Iterator<KnowledgeEdge> it = bk.forbiddenEdgesIterator(); it.hasNext(); ) {
        KnowledgeEdge edge = it.next();
        // match strings to variables in the graph.
        Node from = SearchGraphUtils.translate(edge.getFrom(), variables);
        Node to = SearchGraphUtils.translate(edge.getTo(), variables);
        if (from == null || to == null) {
            continue;
        }
        if (graph.getEdge(from, to) == null) {
            continue;
        }
        // Orient to*->from
        graph.setEndpoint(to, from, Endpoint.ARROW);
        graph.setEndpoint(from, to, Endpoint.CIRCLE);
        logger.log("knowledgeOrientation", SearchLogUtils.edgeOrientedMsg("Knowledge", graph.getEdge(from, to)));
    }
    for (Iterator<KnowledgeEdge> it = bk.requiredEdgesIterator(); it.hasNext(); ) {
        KnowledgeEdge edge = it.next();
        // match strings to variables in this graph
        Node from = SearchGraphUtils.translate(edge.getFrom(), variables);
        Node to = SearchGraphUtils.translate(edge.getTo(), variables);
        if (from == null || to == null) {
            continue;
        }
        if (graph.getEdge(from, to) == null) {
            continue;
        }
        graph.setEndpoint(to, from, Endpoint.TAIL);
        graph.setEndpoint(from, to, Endpoint.ARROW);
        logger.log("knowledgeOrientation", SearchLogUtils.edgeOrientedMsg("Knowledge", graph.getEdge(from, to)));
    }
    logger.log("info", "Finishing BK Orientation.");
}