Examples with SemIm edu.cmu.tetrad.sem.SemIm used on opensource projects

Example 36 with SemIm

use of edu.cmu.tetrad.sem.SemIm in project tetrad by cmu-phil.

the class TestSemXml method testRoundtrip2.

public void testRoundtrip2() {
    SemIm semIm = sampleSemIm1();
    Element element = SemXmlRenderer.getElement(semIm);
    SemXmlParser parser = new SemXmlParser();
    SemIm semIm2 = parser.getSemIm(element);
}

Example 37 with SemIm

use of edu.cmu.tetrad.sem.SemIm in project tetrad by cmu-phil.

the class TestMatrixUtils method testImpiedCovar.

@Test
public void testImpiedCovar() {
    List<Node> nodes = new ArrayList<>();
    for (int i = 0; i < 10; i++) {
        nodes.add(new ContinuousVariable("X" + (i + 1)));
    }
    Graph graph = new Dag(GraphUtils.randomGraph(nodes, 0, 10, 30, 15, 15, false));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    TetradMatrix err = im.getErrCovar();
    TetradMatrix coef = im.getEdgeCoef();
    TetradMatrix implied = MatrixUtils.impliedCovar(coef, err);
    assertTrue(MatrixUtils.isPositiveDefinite(implied));
    TetradMatrix corr = MatrixUtils.convertCovToCorr(new TetradMatrix(implied));
    assertTrue(MatrixUtils.isPositiveDefinite(corr));
}

Example 38 with SemIm

use of edu.cmu.tetrad.sem.SemIm in project tetrad by cmu-phil.

the class TestMimbuild2 method test1.

@Test
public void test1() {
    RandomUtil.getInstance().setSeed(49283494L);
    for (int r = 0; r < 1; r++) {
        Graph mim = DataGraphUtils.randomSingleFactorModel(5, 5, 6, 0, 0, 0);
        Graph mimStructure = structure(mim);
        Parameters params = new Parameters();
        params.set("coefLow", .5);
        params.set("coefHigh", 1.5);
        SemPm pm = new SemPm(mim);
        SemIm im = new SemIm(pm, params);
        DataSet data = im.simulateData(300, false);
        String algorithm = "FOFC";
        Graph searchGraph;
        List<List<Node>> partition;
        if (algorithm.equals("FOFC")) {
            FindOneFactorClusters fofc = new FindOneFactorClusters(data, TestType.TETRAD_WISHART, FindOneFactorClusters.Algorithm.GAP, 0.001);
            searchGraph = fofc.search();
            partition = fofc.getClusters();
        } else if (algorithm.equals("BPC")) {
            TestType testType = TestType.TETRAD_WISHART;
            TestType purifyType = TestType.TETRAD_BASED;
            BuildPureClusters bpc = new BuildPureClusters(data, 0.001, testType, purifyType);
            searchGraph = bpc.search();
            partition = MimUtils.convertToClusters2(searchGraph);
        } else {
            throw new IllegalStateException();
        }
        List<String> latentVarList = reidentifyVariables(mim, data, partition, 2);
        // System.out.println(partition);
        // System.out.println(latentVarList);
        // 
        // System.out.println("True\n" + mimStructure);
        Graph mimbuildStructure;
        for (int mimbuildMethod : new int[] { 2 }) {
            if (mimbuildMethod == 2) {
                Mimbuild2 mimbuild = new Mimbuild2();
                mimbuild.setAlpha(0.001);
                mimbuild.setMinClusterSize(3);
                mimbuildStructure = mimbuild.search(partition, latentVarList, new CovarianceMatrix(data));
                int shd = SearchGraphUtils.structuralHammingDistance(mimStructure, mimbuildStructure);
                assertEquals(7, shd);
            } else if (mimbuildMethod == 3) {
                // System.out.println("Mimbuild Trek\n");
                MimbuildTrek mimbuild = new MimbuildTrek();
                mimbuild.setAlpha(0.1);
                mimbuild.setMinClusterSize(3);
                mimbuildStructure = mimbuild.search(partition, latentVarList, new CovarianceMatrix(data));
                // ICovarianceMatrix latentcov = mimbuild.getLatentsCov();
                // System.out.println("\nCovariance over the latents");
                // System.out.println(latentcov);
                // System.out.println("Estimated\n" + mimbuildStructure);
                int shd = SearchGraphUtils.structuralHammingDistance(mimStructure, mimbuildStructure);
                // System.out.println("SHD = " + shd);
                // System.out.println();
                assertEquals(3, shd);
            } else {
                throw new IllegalStateException();
            }
        }
    }
}

Example 39 with SemIm

use of edu.cmu.tetrad.sem.SemIm in project tetrad by cmu-phil.

the class SemUpdaterEditor method getUpdatePanel.

private Box getUpdatePanel() {
    final SemEvidence evidence = semUpdater.getEvidence();
    focusTraversalOrder.clear();
    Box b = Box.createVerticalBox();
    Box b0 = Box.createHorizontalBox();
    b0.add(new JLabel("<html>" + "In the list below, specify values for variables you have evidence " + "<br>for. Click the 'Do Update Now' button to view updated model."));
    b0.add(Box.createHorizontalGlue());
    b.add(b0);
    b.add(Box.createVerticalStrut(10));
    Box d = Box.createHorizontalBox();
    d.add(new JLabel("Variable = value"));
    d.add(Box.createHorizontalGlue());
    d.add(new JLabel("Manipulated"));
    b.add(d);
    for (int i = 0; i < evidence.getNumNodes(); i++) {
        Box c = Box.createHorizontalBox();
        SemIm semIm = evidence.getSemIm();
        Node node = semIm.getVariableNodes().get(i);
        String name = node.getName();
        JLabel label = new JLabel(name + " =  ") {

            private static final long serialVersionUID = 820570350956700782L;

            @Override
            public Dimension getMaximumSize() {
                return getPreferredSize();
            }
        };
        c.add(label);
        double mean = evidence.getProposition().getValue(i);
        final DoubleTextField field = new DoubleTextField(mean, 5, NumberFormatUtil.getInstance().getNumberFormat());
        field.setFilter((value, oldValue) -> {
            try {
                final int nodeIndex = labels.get(field);
                if (Double.isNaN(value) && evidence.isManipulated(nodeIndex)) {
                    throw new IllegalArgumentException();
                }
                evidence.getProposition().setValue(nodeIndex, value);
                SemIm updatedSem = semUpdater.getUpdatedSemIm();
                semImEditor.displaySemIm(updatedSem, semImEditor.getTabSelectionIndex(), semImEditor.getMatrixSelection());
                return value;
            } catch (IllegalArgumentException e) {
                return oldValue;
            }
        });
        labels.put(field, i);
        variablesToTextFields.put(i, field);
        focusTraversalOrder.add(field);
        c.add(field);
        c.add(Box.createHorizontalStrut(2));
        c.add(Box.createHorizontalGlue());
        JCheckBox checkbox = new JCheckBox() {

            private static final long serialVersionUID = -3808843047563493212L;

            @Override
            public Dimension getMaximumSize() {
                return getPreferredSize();
            }
        };
        checkbox.setSelected(evidence.isManipulated(i));
        checkBoxesToVariables.put(checkbox, i);
        variablesToCheckboxes.put(i, checkbox);
        checkbox.addActionListener((e) -> {
            JCheckBox chkbox = (JCheckBox) e.getSource();
            boolean selected = chkbox.isSelected();
            Integer o = checkBoxesToVariables.get(chkbox);
            // If no value has been set for this variable, set it to
            // the mean.
            double value = evidence.getProposition().getValue(o);
            if (Double.isNaN(value)) {
                DoubleTextField dblTxtField = variablesToTextFields.get(o);
                SemIm semIM = semUpdater.getSemIm();
                Node varNode = semIM.getVariableNodes().get(o);
                double semIMMean = semIM.getMean(varNode);
                dblTxtField.setValue(semIMMean);
            }
            semUpdater.getEvidence().setManipulated(o, selected);
            SemIm updatedSem = semUpdater.getUpdatedSemIm();
            semImEditor.displaySemIm(updatedSem, semImEditor.getTabSelectionIndex(), semImEditor.getMatrixSelection());
        });
        checkbox.setBackground(Color.WHITE);
        checkbox.setBorder(null);
        c.add(checkbox);
        c.setMaximumSize(new Dimension(1000, 30));
        b.add(c);
    }
    b.add(Box.createVerticalGlue());
    Box b2 = Box.createHorizontalBox();
    b2.add(Box.createHorizontalGlue());
    JButton button = new JButton("Do Update Now");
    button.addActionListener((e) -> {
        SemIm updatedSem = semUpdater.getUpdatedSemIm();
        semImEditor.displaySemIm(updatedSem, semImEditor.getTabSelectionIndex(), semImEditor.getMatrixSelection());
        semUpdater.setEvidence(new SemEvidence(updatedSem));
    });
    b2.add(button);
    b.add(b2);
    b.setBorder(new EmptyBorder(5, 5, 5, 5));
    setFocusTraversalPolicy(new FocusTraversalPolicy() {

        @Override
        public Component getComponentAfter(Container focusCycleRoot, Component aComponent) {
            int index = focusTraversalOrder.indexOf(aComponent);
            int size = focusTraversalOrder.size();
            if (index != -1) {
                return focusTraversalOrder.get((index + 1) % size);
            } else {
                return getFirstComponent(focusCycleRoot);
            }
        }

        @Override
        public Component getComponentBefore(Container focusCycleRoot, Component aComponent) {
            int index = focusTraversalOrder.indexOf(aComponent);
            int size = focusTraversalOrder.size();
            if (index != -1) {
                return focusTraversalOrder.get((index - 1) % size);
            } else {
                return getFirstComponent(focusCycleRoot);
            }
        }

        @Override
        public Component getFirstComponent(Container focusCycleRoot) {
            return focusTraversalOrder.getFirst();
        }

        @Override
        public Component getLastComponent(Container focusCycleRoot) {
            return focusTraversalOrder.getLast();
        }

        @Override
        public Component getDefaultComponent(Container focusCycleRoot) {
            return getFirstComponent(focusCycleRoot);
        }
    });
    setFocusCycleRoot(true);
    return b;
}

Example 40 with SemIm

use of edu.cmu.tetrad.sem.SemIm in project tetrad by cmu-phil.

the class PurifyScoreBased method gaussianEM.

private double gaussianEM(SemGraph semdag, SemIm initialSemIm) {
    double score, newScore = -Double.MAX_VALUE, bestScore = -Double.MAX_VALUE;
    SemPm semPm = new SemPm(semdag);
    semdag.setShowErrorTerms(true);
    for (int p = 0; p < numObserved; p++) {
        for (int q = 0; q < numObserved; q++) {
            this.bestCyy[p][q] = this.Cyy[p][q];
        }
        if (this.Cyz != null) {
            for (int q = 0; q < numLatent; q++) {
                this.bestCyz[p][q] = this.Cyz[p][q];
            }
        }
    }
    if (this.Czz != null) {
        for (int p = 0; p < numLatent; p++) {
            for (int q = 0; q < numLatent; q++) {
                this.bestCzz[p][q] = this.Czz[p][q];
            }
        }
    }
    initializeGaussianEM(semdag);
    for (int i = 0; i < 3; i++) {
        System.out.println("--Trial " + i);
        SemIm semIm;
        if (i == 0 && initialSemIm != null) {
            semIm = initialSemIm;
        } else {
            semIm = new SemIm(semPm);
            semIm.setCovMatrix(this.covarianceMatrix);
        }
        do {
            score = newScore;
            gaussianExpectation(semIm);
            newScore = gaussianMaximization(semIm);
            if (newScore == -Double.MAX_VALUE) {
                break;
            }
        } while (Math.abs(score - newScore) > 1.E-3);
        System.out.println(newScore);
        if (newScore > bestScore && !Double.isInfinite(newScore)) {
            bestScore = newScore;
            for (int p = 0; p < numObserved; p++) {
                for (int q = 0; q < numObserved; q++) {
                    this.bestCyy[p][q] = this.Cyy[p][q];
                }
                for (int q = 0; q < numLatent; q++) {
                    this.bestCyz[p][q] = this.Cyz[p][q];
                }
            }
            for (int p = 0; p < numLatent; p++) {
                for (int q = 0; q < numLatent; q++) {
                    this.bestCzz[p][q] = this.Czz[p][q];
                }
            }
        }
    }
    for (int p = 0; p < numObserved; p++) {
        for (int q = 0; q < numObserved; q++) {
            this.Cyy[p][q] = this.bestCyy[p][q];
        }
        for (int q = 0; q < numLatent; q++) {
            this.Cyz[p][q] = this.bestCyz[p][q];
        }
    }
    for (int p = 0; p < numLatent; p++) {
        for (int q = 0; q < numLatent; q++) {
            this.Czz[p][q] = this.bestCzz[p][q];
        }
    }
    if (Double.isInfinite(bestScore)) {
        System.out.println("* * Warning: Heywood case in this step");
        return -Double.MAX_VALUE;
    }
    // System.exit(0);
    return bestScore;
}