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

Example 91 with ChoiceGenerator

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

the class Purify method countCrossConstructPValues.

private List<Double> countCrossConstructPValues(List<int[]> partition, boolean[] eliminated, double cutoff) {
    List<Double> allPValues = new ArrayList<>();
    for (int p1 = 0; p1 < partition.size(); p1++) {
        for (int p2 = p1 + 1; p2 < partition.size(); p2++) {
            int[] cluster1 = partition.get(p1);
            int[] cluster2 = partition.get(p2);
            if (cluster1.length >= 3 && cluster2.length >= 1) {
                ChoiceGenerator gen1 = new ChoiceGenerator(cluster1.length, 3);
                ChoiceGenerator gen2 = new ChoiceGenerator(cluster2.length, 1);
                int[] choice1, choice2;
                while ((choice1 = gen1.next()) != null) {
                    while ((choice2 = gen2.next()) != null) {
                        List<Integer> crossCluster = new ArrayList<>();
                        for (int i : choice1) crossCluster.add(cluster1[i]);
                        for (int i : choice2) crossCluster.add(cluster2[i]);
                        allPValues.addAll(listPValues(crossCluster, eliminated, cutoff));
                    }
                }
            }
            if (cluster1.length >= 2 && cluster2.length >= 2) {
                ChoiceGenerator gen1 = new ChoiceGenerator(cluster1.length, 2);
                ChoiceGenerator gen2 = new ChoiceGenerator(cluster2.length, 2);
                int[] choice1, choice2;
                while ((choice1 = gen1.next()) != null) {
                    while ((choice2 = gen2.next()) != null) {
                        List<Integer> crossCluster = new ArrayList<>();
                        for (int i : choice1) crossCluster.add(cluster1[i]);
                        for (int i : choice2) crossCluster.add(cluster2[i]);
                        allPValues.addAll(listPValues(crossCluster, eliminated, cutoff));
                    }
                }
            }
        }
    }
    return allPValues;
}

Example 92 with ChoiceGenerator

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

the class PurifySextadBased method listCrossConstructSextads.

private Set<IntSextad> listCrossConstructSextads(List<List<Integer>> clustering, Set<Integer> eliminated, double cutoff) {
    Set<IntSextad> allSextads = new HashSet<>();
    boolean countable = false;
    for (int p1 = 0; p1 < clustering.size(); p1++) {
        for (int p2 = p1 + 1; p2 < clustering.size(); p2++) {
            List<Integer> cluster1 = clustering.get(p1);
            List<Integer> cluster2 = clustering.get(p2);
            if (cluster1.size() >= 5 && cluster2.size() >= 1) {
                ChoiceGenerator gen1 = new ChoiceGenerator(cluster1.size(), 5);
                int[] choice1;
                while ((choice1 = gen1.next()) != null) {
                    ChoiceGenerator gen2 = new ChoiceGenerator(cluster2.size(), 1);
                    int[] choice2;
                    while ((choice2 = gen2.next()) != null) {
                        List<Integer> crossCluster = new ArrayList<>();
                        for (int i : choice1) crossCluster.add(cluster1.get(i));
                        for (int i : choice2) crossCluster.add(cluster2.get(i));
                        Set<IntSextad> Sextads = listSextads(crossCluster, eliminated, cutoff);
                        if (Sextads != null) {
                            countable = true;
                            allSextads.addAll(Sextads);
                        }
                    }
                }
            }
            if (cluster2.size() >= 5 && cluster1.size() >= 1) {
                ChoiceGenerator gen1 = new ChoiceGenerator(cluster2.size(), 5);
                int[] choice1;
                while ((choice1 = gen1.next()) != null) {
                    ChoiceGenerator gen2 = new ChoiceGenerator(cluster1.size(), 1);
                    int[] choice2;
                    while ((choice2 = gen2.next()) != null) {
                        List<Integer> crossCluster = new ArrayList<>();
                        for (int i : choice1) crossCluster.add(cluster2.get(i));
                        for (int i : choice2) crossCluster.add(cluster1.get(i));
                        Set<IntSextad> Sextads = listSextads(crossCluster, eliminated, cutoff);
                        if (Sextads != null) {
                            countable = true;
                            allSextads.addAll(Sextads);
                        }
                    }
                }
            }
        // if (cluster1.size() >= 2 && cluster2.size() >= 2) {
        // ChoiceGenerator gen1 = new ChoiceGenerator(cluster1.size(), 2);
        // int[] choice1;
        // 
        // while ((choice1 = gen1.next()) != null) {
        // ChoiceGenerator gen2 = new ChoiceGenerator(cluster2.size(), 2);
        // int[] choice2;
        // 
        // while ((choice2 = gen2.next()) != null) {
        // List<Integer> crossCluster = new ArrayList<Integer>();
        // for (int i : choice1) crossCluster.add(cluster1.get(i));
        // for (int i : choice2) crossCluster.add(cluster2.get(i));
        // 
        // Set<IntSextad> Sextads = listSextads2By2(crossCluster, eliminated, cutoff);
        // 
        // if (Sextads != null) {
        // countable = true;
        // allSextads.addAll(Sextads);
        // }
        // }
        // }
        // }
        }
    }
    return countable ? allSextads : null;
}

Example 93 with ChoiceGenerator

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

the class PurifySextadBased method listSextads.

private Set<IntSextad> listSextads(List<Integer> cluster, Set<Integer> eliminated, double cutoff) {
    if (cluster.size() < 6)
        return null;
    cluster = new ArrayList<>(cluster);
    boolean countable = false;
    Set<IntSextad> Sextads = new HashSet<>();
    ChoiceGenerator gen = new ChoiceGenerator(cluster.size(), 6);
    int[] choice;
    while ((choice = gen.next()) != null) {
        int _i = choice[0];
        int _j = choice[1];
        int _k = choice[2];
        int _l = choice[3];
        int _m = choice[4];
        int _n = choice[5];
        int m1 = cluster.get(_i);
        int m2 = cluster.get(_j);
        int m3 = cluster.get(_k);
        int m4 = cluster.get(_l);
        int m5 = cluster.get(_m);
        int m6 = cluster.get(_n);
        if (eliminated.contains(m1) || eliminated.contains(m2) || eliminated.contains(m3) || eliminated.contains(m4) || eliminated.contains(m5) || eliminated.contains(m6)) {
            continue;
        }
        countable = true;
        double p1, p2, p3, p4, p5, p6, p7, p8, p9, p10;
        IntSextad t1 = new IntSextad(m1, m2, m3, m4, m5, m6);
        IntSextad t2 = new IntSextad(m1, m2, m4, m3, m5, m6);
        IntSextad t3 = new IntSextad(m1, m2, m5, m3, m4, m6);
        IntSextad t4 = new IntSextad(m1, m2, m6, m3, m4, m5);
        IntSextad t5 = new IntSextad(m1, m3, m4, m2, m5, m6);
        IntSextad t6 = new IntSextad(m1, m3, m5, m2, m4, m6);
        IntSextad t7 = new IntSextad(m1, m3, m6, m2, m4, m5);
        IntSextad t8 = new IntSextad(m1, m4, m5, m2, m3, m6);
        IntSextad t9 = new IntSextad(m1, m4, m6, m2, m3, m5);
        IntSextad t10 = new IntSextad(m1, m5, m6, m2, m3, m4);
        p1 = sextadTest.getPValue(t1);
        p2 = sextadTest.getPValue(t2);
        p3 = sextadTest.getPValue(t3);
        p4 = sextadTest.getPValue(t4);
        p5 = sextadTest.getPValue(t5);
        p6 = sextadTest.getPValue(t6);
        p7 = sextadTest.getPValue(t7);
        p8 = sextadTest.getPValue(t8);
        p9 = sextadTest.getPValue(t9);
        p10 = sextadTest.getPValue(t10);
        if (p1 < cutoff) {
            Sextads.add(t1);
        }
        if (p2 < cutoff) {
            Sextads.add(t2);
        }
        if (p3 < cutoff) {
            Sextads.add(t3);
        }
        if (p4 < cutoff) {
            Sextads.add(t4);
        }
        if (p5 < cutoff) {
            Sextads.add(t5);
        }
        if (p6 < cutoff) {
            Sextads.add(t6);
        }
        if (p7 < cutoff) {
            Sextads.add(t7);
        }
        if (p8 < cutoff) {
            Sextads.add(t8);
        }
        if (p9 < cutoff) {
            Sextads.add(t9);
        }
        if (p10 < cutoff) {
            Sextads.add(t10);
        }
    }
    return countable ? Sextads : null;
}

Example 94 with ChoiceGenerator

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

the class PurifyTetradBased2 method listCrossConstructTetrads.

private Set<Tetrad> listCrossConstructTetrads(List<List<Node>> clustering, Set<Node> eliminated, double cutoff) {
    Set<Tetrad> allTetrads = new HashSet<>();
    boolean countable = false;
    for (int p1 = 0; p1 < clustering.size(); p1++) {
        for (int p2 = p1 + 1; p2 < clustering.size(); p2++) {
            List<Node> cluster1 = clustering.get(p1);
            List<Node> cluster2 = clustering.get(p2);
            if (cluster1.size() >= 3 && cluster2.size() >= 1) {
                ChoiceGenerator gen1 = new ChoiceGenerator(cluster1.size(), 3);
                int[] choice1;
                while ((choice1 = gen1.next()) != null) {
                    ChoiceGenerator gen2 = new ChoiceGenerator(cluster2.size(), 1);
                    int[] choice2;
                    while ((choice2 = gen2.next()) != null) {
                        List<Node> crossCluster = new ArrayList<>();
                        for (int i : choice1) crossCluster.add(cluster1.get(i));
                        for (int i : choice2) crossCluster.add(cluster2.get(i));
                        Set<Tetrad> tetrads = listTetrads(crossCluster, eliminated, cutoff);
                        if (tetrads != null) {
                            countable = true;
                            allTetrads.addAll(tetrads);
                        }
                    }
                }
            }
            if (cluster2.size() >= 3 && cluster1.size() >= 1) {
                ChoiceGenerator gen1 = new ChoiceGenerator(cluster2.size(), 3);
                int[] choice1;
                while ((choice1 = gen1.next()) != null) {
                    ChoiceGenerator gen2 = new ChoiceGenerator(cluster1.size(), 1);
                    int[] choice2;
                    while ((choice2 = gen2.next()) != null) {
                        List<Node> crossCluster = new ArrayList<>();
                        for (int i : choice1) crossCluster.add(cluster2.get(i));
                        for (int i : choice2) crossCluster.add(cluster1.get(i));
                        Set<Tetrad> tetrads = listTetrads(crossCluster, eliminated, cutoff);
                        if (tetrads != null) {
                            countable = true;
                            allTetrads.addAll(tetrads);
                        }
                    }
                }
            }
            if (cluster1.size() >= 2 && cluster2.size() >= 2) {
                ChoiceGenerator gen1 = new ChoiceGenerator(cluster1.size(), 2);
                int[] choice1;
                while ((choice1 = gen1.next()) != null) {
                    ChoiceGenerator gen2 = new ChoiceGenerator(cluster2.size(), 2);
                    int[] choice2;
                    while ((choice2 = gen2.next()) != null) {
                        List<Node> crossCluster = new ArrayList<>();
                        for (int i : choice1) crossCluster.add(cluster1.get(i));
                        for (int i : choice2) crossCluster.add(cluster2.get(i));
                        Set<Tetrad> tetrads = listTetrads2By2(crossCluster, eliminated, cutoff);
                        if (tetrads != null) {
                            countable = true;
                            allTetrads.addAll(tetrads);
                        }
                    }
                }
            }
        }
    }
    return countable ? allTetrads : null;
}

Example 95 with ChoiceGenerator

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

the class Rfci method getRTuples.

// //////////////////////////////////////////////
// collect in rTupleList all unshielded tuples
// //////////////////////////////////////////////
private List<Node[]> getRTuples() {
    List<Node[]> rTuples = new ArrayList<>();
    List<Node> nodes = graph.getNodes();
    for (Node j : nodes) {
        List<Node> adjacentNodes = graph.getAdjacentNodes(j);
        if (adjacentNodes.size() < 2) {
            continue;
        }
        ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
        int[] combination;
        while ((combination = cg.next()) != null) {
            if (Thread.currentThread().isInterrupted()) {
                break;
            }
            Node i = adjacentNodes.get(combination[0]);
            Node k = adjacentNodes.get(combination[1]);
            // Skip triples that are shielded.
            if (!graph.isAdjacentTo(i, k)) {
                Node[] newTuple = { i, j, k };
                rTuples.add(newTuple);
            }
        }
    }
    return (rTuples);
}