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

Example 1 with SemPm

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

the class SemEstimatorEditor method reestimate.

private void reestimate() {
    SemOptimizer optimizer;
    String type = wrapper.getSemOptimizerType();
    switch(type) {
        case "Regression":
            optimizer = new SemOptimizerRegression();
            break;
        case "EM":
            optimizer = new SemOptimizerEm();
            break;
        case "Powell":
            optimizer = new SemOptimizerPowell();
            break;
        case "Random Search":
            optimizer = new SemOptimizerScattershot();
            break;
        case "RICF":
            optimizer = new SemOptimizerRicf();
            break;
        default:
            throw new IllegalArgumentException("Unexpected optimizer type: " + type);
    }
    int numRestarts = wrapper.getNumRestarts();
    optimizer.setNumRestarts(numRestarts);
    java.util.List<SemEstimator> estimators = wrapper.getMultipleResultList();
    java.util.List<SemEstimator> newEstimators = new ArrayList<>();
    estimators.forEach(estimator -> {
        SemPm semPm = estimator.getSemPm();
        DataSet dataSet = estimator.getDataSet();
        ICovarianceMatrix covMatrix = estimator.getCovMatrix();
        SemEstimator newEstimator;
        if (dataSet != null) {
            newEstimator = new SemEstimator(dataSet, semPm, optimizer);
            newEstimator.setNumRestarts(numRestarts);
            newEstimator.setScoreType(wrapper.getScoreType());
        } else if (covMatrix != null) {
            newEstimator = new SemEstimator(covMatrix, semPm, optimizer);
            newEstimator.setNumRestarts(numRestarts);
            newEstimator.setScoreType(wrapper.getScoreType());
        } else {
            throw new IllegalStateException("Only continuous rectangular" + " data sets and covariance matrices can be processed.");
        }
        newEstimator.estimate();
        newEstimators.add(newEstimator);
    });
    wrapper.setSemEstimator(newEstimators.get(0));
    wrapper.setMultipleResultList(newEstimators);
    resetSemImEditor();
}

Example 2 with SemPm

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

the class PatternFitEditor method setup.

// ============================ Private Methods =========================//
private void setup() {
    JTabbedPane pane = new JTabbedPane(JTabbedPane.LEFT);
    DataModelList data = comparison.getDataModelList();
    List<BayesIm> bayesIms = comparison.getBayesIms();
    List<SemPm> semPms = comparison.getSemPms();
    if (bayesIms != null && semPms != null) {
        throw new IllegalArgumentException("That's weird; both Bayes and SEM estimations were done. Please complain.");
    }
    if (bayesIms != null) {
        for (int i = 0; i < bayesIms.size(); i++) {
            BayesEstimatorEditor editor = new BayesEstimatorEditor(bayesIms.get(i), (DataSet) data.get(i));
            JPanel panel = new JPanel();
            JScrollPane scroll = new JScrollPane(editor);
            scroll.setPreferredSize(new Dimension(900, 600));
            panel.add(Box.createVerticalStrut(10));
            Box box = Box.createHorizontalBox();
            panel.add(box);
            panel.add(Box.createVerticalStrut(10));
            Box box1 = Box.createHorizontalBox();
            box1.add(new JLabel("Graph Comparison: "));
            box1.add(Box.createHorizontalGlue());
            add(box1);
            setLayout(new BorderLayout());
            pane.add("" + (i + 1), scroll);
        }
    }
    if (semPms != null) {
        for (int i = 0; i < semPms.size(); i++) {
            SemEstimatorEditor editor = new SemEstimatorEditor(semPms.get(i), (DataSet) data.get(i));
            pane.add("" + (i + 1), editor);
        }
    }
    add(pane);
}

Example 3 with SemPm

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

the class TestDM method test2.

@Test
public void test2() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    Graph graph = emptyGraph(8);
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X2"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X2"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X4"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X4"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X5"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X5"), new ContinuousVariable("X7"));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(100000, false);
    DMSearch search = new DMSearch();
    search.setInputs(new int[] { 0, 1, 4, 5 });
    search.setOutputs(new int[] { 2, 3, 6, 7 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    Graph foundGraph = search.search();
    print("Test Case 2");
    Graph trueGraph = new EdgeListGraph();
    trueGraph.addNode(new ContinuousVariable("X0"));
    trueGraph.addNode(new ContinuousVariable("X1"));
    trueGraph.addNode(new ContinuousVariable("X2"));
    trueGraph.addNode(new ContinuousVariable("X3"));
    trueGraph.addNode(new ContinuousVariable("X4"));
    trueGraph.addNode(new ContinuousVariable("X5"));
    trueGraph.addNode(new ContinuousVariable("X6"));
    trueGraph.addNode(new ContinuousVariable("X7"));
    trueGraph.addNode(new ContinuousVariable("L0"));
    trueGraph.addNode(new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X3"));
    // trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X4"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X5"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L1"), new ContinuousVariable("X6"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L1"), new ContinuousVariable("X7"));
    assertTrue(foundGraph.equals(trueGraph));
}

Example 4 with SemPm

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

the class TestDM method rtest13.

@Ignore
public void rtest13() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    Graph graph = emptyGraph(12);
    Node X0 = graph.getNode("X0");
    Node X1 = graph.getNode("X1");
    Node X2 = graph.getNode("X2");
    Node X3 = graph.getNode("X3");
    Node X4 = graph.getNode("X4");
    Node X5 = graph.getNode("X5");
    Node X6 = graph.getNode("X6");
    Node X7 = graph.getNode("X7");
    Node X8 = graph.getNode("X8");
    Node X9 = graph.getNode("X9");
    Node X10 = graph.getNode("X10");
    Node X11 = graph.getNode("X11");
    graph.addDirectedEdge(X0, X6);
    graph.addDirectedEdge(X1, X6);
    graph.addDirectedEdge(X1, X7);
    graph.addDirectedEdge(X1, X8);
    graph.addDirectedEdge(X2, X8);
    graph.addDirectedEdge(X3, X8);
    graph.addDirectedEdge(X3, X9);
    graph.addDirectedEdge(X3, X10);
    graph.addDirectedEdge(X3, X9);
    graph.addDirectedEdge(X4, X10);
    graph.addDirectedEdge(X4, X11);
    graph.addDirectedEdge(X5, X11);
    // 
    // graph.addDirectedEdge(X1, X8);
    // graph.addDirectedEdge(X2, X6);
    // graph.addDirectedEdge(X2, X7);
    // graph.addDirectedEdge(X2, X8);
    // 
    // 
    // graph.addDirectedEdge(X3, X8);
    // graph.addDirectedEdge(X3, X7);
    // graph.addDirectedEdge(X4, X8);
    // graph.addDirectedEdge(X4, X7);
    // 
    // 
    // graph.addDirectedEdge(X5, X8);
    RandomUtil.getInstance().setSeed(29483818483L);
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(100000, false);
    DMSearch search = new DMSearch();
    search.setInputs(new int[] { 0, 1, 2, 3, 4, 5 });
    search.setOutputs(new int[] { 6, 7, 8, 9, 10, 11 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    search.search();
    print("");
    print("" + search.getDmStructure());
    print("graph.existsDirectedCycle: " + search.getDmStructure().latentStructToEdgeListGraph(search.getDmStructure()).existsDirectedCycle());
    print("Graph structure: " + search);
    assertTrue(true);
}

Example 5 with SemPm

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

the class TestDM method rtest12.

@Ignore
public void rtest12() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    Graph graph = emptyGraph(9);
    Node X0 = graph.getNode("X0");
    Node X1 = graph.getNode("X1");
    Node X2 = graph.getNode("X2");
    Node X3 = graph.getNode("X3");
    Node X4 = graph.getNode("X4");
    Node X5 = graph.getNode("X5");
    Node X6 = graph.getNode("X6");
    Node X7 = graph.getNode("X7");
    Node X8 = graph.getNode("X8");
    graph.addDirectedEdge(X0, X6);
    graph.addDirectedEdge(X0, X7);
    graph.addDirectedEdge(X0, X8);
    graph.addDirectedEdge(X1, X6);
    graph.addDirectedEdge(X1, X7);
    graph.addDirectedEdge(X1, X8);
    graph.addDirectedEdge(X2, X6);
    graph.addDirectedEdge(X2, X7);
    graph.addDirectedEdge(X2, X8);
    graph.addDirectedEdge(X3, X8);
    graph.addDirectedEdge(X3, X7);
    graph.addDirectedEdge(X4, X8);
    graph.addDirectedEdge(X4, X7);
    graph.addDirectedEdge(X5, X8);
    RandomUtil.getInstance().setSeed(29483818483L);
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(100000, false);
    DMSearch search = new DMSearch();
    search.setInputs(new int[] { 0, 1, 2, 3, 4, 5 });
    search.setOutputs(new int[] { 6, 7, 8 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    search.search();
    print("");
    print("" + search.getDmStructure());
    print("graph.existsDirectedCycle: " + search.getDmStructure().latentStructToEdgeListGraph(search.getDmStructure()).existsDirectedCycle());
    print("Graph structure: " + search);
    assertTrue(true);
}