Examples with ChoiceGenerator edu.cmu.tetrad.util.ChoiceGenerator used on opensource projects

Example 16 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class FciOrientT method ruleR3.

/**
 * Implements the double-triangle orientation rule, which states that if D*-oB, A*->B<-*C and A*-oDo-*C, then
 * D*->B.
 * <p>
 * This is Zhang's rule R3.
 */
public void ruleR3(Graph graph) {
    List<Node> nodes = graph.getNodes();
    for (Node B : nodes) {
        List<Node> intoBArrows = graph.getNodesInTo(B, Endpoint.ARROW);
        List<Node> intoBCircles = graph.getNodesInTo(B, Endpoint.CIRCLE);
        for (Node D : intoBCircles) {
            if (intoBArrows.size() < 2) {
                continue;
            }
            ChoiceGenerator gen = new ChoiceGenerator(intoBArrows.size(), 2);
            int[] choice;
            while ((choice = gen.next()) != null) {
                Node A = intoBArrows.get(choice[0]);
                Node C = intoBArrows.get(choice[1]);
                if (graph.isAdjacentTo(A, C)) {
                    continue;
                }
                if (!graph.isAdjacentTo(A, D) || !graph.isAdjacentTo(C, D)) {
                    continue;
                }
                if (graph.getEndpoint(A, D) != Endpoint.CIRCLE) {
                    continue;
                }
                if (graph.getEndpoint(C, D) != Endpoint.CIRCLE) {
                    continue;
                }
                if (!isArrowpointAllowed(D, B, graph)) {
                    continue;
                }
                graph.setEndpoint(D, B, Endpoint.ARROW);
                logger.log("impliedOrientations", SearchLogUtils.edgeOrientedMsg("Double triangle", graph.getEdge(D, B)));
                System.out.println(SearchLogUtils.edgeOrientedMsg("Double triangle", graph.getEdge(D, B)));
                changeFlag = true;
            }
        }
    }
}

Example 17 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator 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 18 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class TsFciOrient method ruleR3.

// /**
// * Implements the double-triangle orientation rule, which states that if D*-oB, A*->B<-*C and A*-oDo-*C, then
// * D*->B.
// * <p/>
// * This is Zhang's rule R3.
// */
// private void ruleR3(Graph graph) {
// List<Node> nodes = graph.getNodes();
// 
// for (Node d : nodes) {
// final List<Node> adjacentNodes = graph.getAdjacentNodes(d);
// 
// if (adjacentNodes.size() < 3) {
// continue;
// }
// 
// ChoiceGenerator gen = new ChoiceGenerator(adjacentNodes.size(), 3);
// int[] choice;
// 
// while ((choice = gen.next()) != null) {
// List<Node> adj = DataGraphUtils.asList(choice, adjacentNodes);
// 
// Node a = adj.get(0);
// Node b = adj.get(1);
// Node c = adj.get(2);
// 
// if (graph.getEndpoint(a, b) == Endpoint.ARROW && graph.getEndpoint(c, b) == Endpoint.ARROW
// && graph.getEndpoint(a, d) == Endpoint.CIRCLE && graph.getEndpoint(c, d) == Endpoint.ARROW
// && !graph.isAdjacentTo(a, c) && graph.getEndpoint(d, b) == Endpoint.CIRCLE) {
// graph.setEndpoint(d, b, Endpoint.ARROW);
// }
// }
// }
// }
/**
 * Implements the double-triangle orientation rule, which states that if D*-oB, A*->B<-*C and A*-oDo-*C, then
 * D*->B.
 * <p>
 * This is Zhang's rule R3.
 */
public void ruleR3(Graph graph) {
    List<Node> nodes = graph.getNodes();
    for (Node B : nodes) {
        List<Node> intoBArrows = graph.getNodesInTo(B, Endpoint.ARROW);
        List<Node> intoBCircles = graph.getNodesInTo(B, Endpoint.CIRCLE);
        for (Node D : intoBCircles) {
            if (intoBArrows.size() < 2) {
                continue;
            }
            ChoiceGenerator gen = new ChoiceGenerator(intoBArrows.size(), 2);
            int[] choice;
            while ((choice = gen.next()) != null) {
                Node A = intoBArrows.get(choice[0]);
                Node C = intoBArrows.get(choice[1]);
                if (graph.isAdjacentTo(A, C)) {
                    continue;
                }
                if (!graph.isAdjacentTo(A, D) || !graph.isAdjacentTo(C, D)) {
                    continue;
                }
                if (graph.getEndpoint(A, D) != Endpoint.CIRCLE) {
                    continue;
                }
                if (graph.getEndpoint(C, D) != Endpoint.CIRCLE) {
                    continue;
                }
                if (!isArrowpointAllowed(D, B, graph)) {
                    continue;
                }
                graph.setEndpoint(D, B, Endpoint.ARROW);
                this.orientSimilarPairs(graph, this.getKnowledge(), D, B, Endpoint.ARROW);
                if (verbose) {
                    logger.log("impliedOrientations", SearchLogUtils.edgeOrientedMsg("Double triangle", graph.getEdge(D, B)));
                    System.out.println(SearchLogUtils.edgeOrientedMsg("Double triangle", graph.getEdge(D, B)));
                }
                changeFlag = true;
            }
        }
    }
}

Example 19 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class TsFciOrient method ruleR0.

/**
 * Orients colliders in the graph.  (FCI Step C)
 * <p>
 * Zhang's step F3, rule R0.
 */
public void ruleR0(Graph graph) {
    graph.reorientAllWith(Endpoint.CIRCLE);
    fciOrientbk(knowledge, graph, graph.getNodes());
    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;
            }
            if (graph.isDefCollider(a, b, c)) {
                continue;
            }
            if (sepsets.isCollider(a, b, c)) {
                if (!isArrowpointAllowed(a, b, graph)) {
                    continue;
                }
                if (!isArrowpointAllowed(c, b, graph)) {
                    continue;
                }
                graph.setEndpoint(a, b, Endpoint.ARROW);
                graph.setEndpoint(c, b, Endpoint.ARROW);
                if (verbose) {
                    logger.log("colliderOrientations", SearchLogUtils.colliderOrientedMsg(a, b, c));
                    System.out.println(SearchLogUtils.colliderOrientedMsg(a, b, c));
                    String location = "R0";
                    printWrongColliderMessage(a, b, c, location, graph);
                }
                this.orientSimilarPairs(graph, knowledge, a, b, Endpoint.ARROW);
                this.orientSimilarPairs(graph, knowledge, c, b, Endpoint.ARROW);
            }
        }
    }
}

Example 20 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class TsGFci method modifiedR0.

// Due to Spirtes.
public void modifiedR0(Graph fgesGraph) {
    graph.reorientAllWith(Endpoint.CIRCLE);
    fciOrientbk(knowledge, graph, graph.getNodes());
    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]);
            if (fgesGraph.isDefCollider(a, b, c)) {
                graph.setEndpoint(a, b, Endpoint.ARROW);
                graph.setEndpoint(c, b, Endpoint.ARROW);
                /**
                 * orienting similar pairs to enforce repeating structure *
                 */
                orientSimilarPairs(graph, knowledge, a, b, Endpoint.ARROW);
                orientSimilarPairs(graph, knowledge, c, b, Endpoint.ARROW);
            /**
             */
            } else if (fgesGraph.isAdjacentTo(a, c) && !graph.isAdjacentTo(a, c)) {
                List<Node> sepset = sepsets.getSepset(a, c);
                if (sepset != null && !sepset.contains(b)) {
                    graph.setEndpoint(a, b, Endpoint.ARROW);
                    graph.setEndpoint(c, b, Endpoint.ARROW);
                    /**
                     * orienting similar pairs to enforce repeating structure *
                     */
                    orientSimilarPairs(graph, knowledge, a, b, Endpoint.ARROW);
                    orientSimilarPairs(graph, knowledge, c, b, Endpoint.ARROW);
                /**
                 */
                }
            }
        }
    }
}