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

Example 41 with ChoiceGenerator

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

the class LayeredDrawing method numCrossings.

private int numCrossings(List<Node> tier1, List<Node> tier2, Graph graph) {
    if (tier2.size() < 2) {
        return 0;
    }
    ChoiceGenerator cg = new ChoiceGenerator(tier2.size(), 2);
    int[] choice;
    int numCrossings = 0;
    while ((choice = cg.next()) != null) {
        List<Node> list1 = graph.getAdjacentNodes(tier2.get(choice[0]));
        List<Node> list2 = graph.getAdjacentNodes(tier2.get(choice[1]));
        list1.retainAll(tier1);
        list2.retainAll(tier1);
        for (Node node0 : list1) {
            for (Node node1 : list2) {
                if (list1.indexOf(node0) > list1.indexOf(node1)) {
                    numCrossings++;
                }
            }
        }
    }
    return numCrossings;
}

Example 42 with ChoiceGenerator

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

the class TestFci method ancestral.

private boolean ancestral(Node n, Node q, Graph pag) {
    if (n == q)
        return false;
    if (pag.isAncestorOf(n, q)) {
        return true;
    } else {
        List<Node> adj = uncoveredPotentiallyDirectedPathStarts(n, q, pag, new LinkedList<Node>());
        if (adj.size() >= 2) {
            ChoiceGenerator gen = new ChoiceGenerator(adj.size(), 2);
            int[] choice;
            boolean found = false;
            while ((choice = gen.next()) != null) {
                List<Node> c = GraphUtils.asList(choice, adj);
                Node n1 = c.get(0);
                Node n2 = c.get(1);
                if (!pag.isAdjacentTo(n1, n2)) {
                    if (pag.isDefNoncollider(n1, n, n2)) {
                        found = true;
                    }
                }
            }
            if (found) {
                return true;
            }
        }
    }
    return false;
}

Example 43 with ChoiceGenerator

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

the class FasDeterministic method searchAtDepth.

private boolean searchAtDepth(List<Node> nodes, final IndependenceTest test, Map<Node, Set<Node>> adjacencies, int depth) {
    int numRemoved = 0;
    int count = 0;
    List<IndependenceFact> facts = new ArrayList<>();
    for (Node x : nodes) {
        if (verbose) {
            if (++count % 100 == 0)
                out.println("count " + count + " of " + nodes.size());
        }
        List<Node> adjx = new ArrayList<>(adjacencies.get(x));
        EDGE: for (Node y : adjx) {
            List<Node> _adjx = new ArrayList<>(adjacencies.get(x));
            _adjx.remove(y);
            List<Node> ppx = possibleParents(x, _adjx, knowledge);
            if (ppx.size() >= depth) {
                ChoiceGenerator cg = new ChoiceGenerator(ppx.size(), depth);
                int[] choice;
                while ((choice = cg.next()) != null) {
                    List<Node> condSet = GraphUtils.asList(choice, ppx);
                    IndependenceFact fact = new IndependenceFact(x, y, condSet);
                    if (facts.contains(fact))
                        continue;
                    facts.add(fact);
                    boolean independent;
                    try {
                        numIndependenceTests++;
                        independent = test.isIndependent(x, y, condSet);
                    // if (test.determines(condSet, x) || test.determines(condSet, y)) {
                    // continue;
                    // }
                    } catch (Exception e) {
                        independent = false;
                    }
                    if (independent) {
                        numIndependenceJudgements++;
                    } else {
                        numDependenceJudgement++;
                    }
                    boolean noEdgeRequired = knowledge.noEdgeRequired(x.getName(), y.getName());
                    if (independent && noEdgeRequired) {
                        adjacencies.get(x).remove(y);
                        adjacencies.get(y).remove(x);
                        numRemoved++;
                        getSepsets().set(x, y, condSet);
                        TetradLogger.getInstance().log("independencies", SearchLogUtils.independenceFact(x, y, condSet) + " p = " + nf.format(test.getPValue()));
                        if (verbose) {
                            out.println(SearchLogUtils.independenceFactMsg(x, y, condSet, test.getPValue()));
                        }
                        continue EDGE;
                    } else {
                    // if (verbose) {
                    // out.println(SearchLogUtils.dependenceFactMsg(x, y, condSet, test.getScore()));
                    // }
                    }
                }
            }
        }
    }
    return freeDegree(nodes, adjacencies) > depth;
}

Example 44 with ChoiceGenerator

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

the class FciOrient method rulesR1R2cycle.

// Does all 3 of these rules at once instead of going through all
// triples multiple times per iteration of doFinalOrientation.
public void rulesR1R2cycle(Graph graph) {
    List<Node> nodes = graph.getNodes();
    for (Node B : nodes) {
        if (Thread.currentThread().isInterrupted()) {
            break;
        }
        List<Node> adj = graph.getAdjacentNodes(B);
        if (adj.size() < 2) {
            continue;
        }
        ChoiceGenerator cg = new ChoiceGenerator(adj.size(), 2);
        int[] combination;
        while ((combination = cg.next()) != null && !Thread.currentThread().isInterrupted()) {
            if (Thread.currentThread().isInterrupted()) {
                break;
            }
            Node A = adj.get(combination[0]);
            Node C = adj.get(combination[1]);
            // choice gen doesnt do diff orders, so must switch A & C around.
            ruleR1(A, B, C, graph);
            ruleR1(C, B, A, graph);
            ruleR2(A, B, C, graph);
            ruleR2(C, B, A, graph);
        }
    }
}

Example 45 with ChoiceGenerator

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

the class FciOrient 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) {
        if (Thread.currentThread().isInterrupted()) {
            break;
        }
        List<Node> intoBArrows = graph.getNodesInTo(B, Endpoint.ARROW);
        List<Node> intoBCircles = graph.getNodesInTo(B, Endpoint.CIRCLE);
        for (Node D : intoBCircles) {
            if (Thread.currentThread().isInterrupted()) {
                break;
            }
            if (intoBArrows.size() < 2) {
                continue;
            }
            ChoiceGenerator gen = new ChoiceGenerator(intoBArrows.size(), 2);
            int[] choice;
            while ((choice = gen.next()) != null && !Thread.currentThread().isInterrupted()) {
                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 (!sepsets.isNoncollider(A, D, C)) {
                    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);
                if (verbose) {
                    logger.log("impliedOrientations", SearchLogUtils.edgeOrientedMsg("Double triangle", graph.getEdge(D, B)));
                    out.println(SearchLogUtils.edgeOrientedMsg("Double triangle", graph.getEdge(D, B)));
                }
                changeFlag = true;
            }
        }
    }
}