Examples with TestType edu.cmu.tetrad.search.TestType used on opensource projects

Example 1 with TestType

use of edu.cmu.tetrad.search.TestType in project tetrad by cmu-phil.

the class PurifyParamsEditor method setup.

public void setup() {
    DoubleTextField alphaField = new DoubleTextField(params.getDouble("alpha", 0.001), 4, NumberFormatUtil.getInstance().getNumberFormat());
    alphaField.setFilter(new DoubleTextField.Filter() {

        public double filter(double value, double oldValue) {
            try {
                getParams().set("alpha", 0.001);
                return value;
            } catch (Exception e) {
                return oldValue;
            }
        }
    });
    final TestType[] descriptions = TestType.getTestDescriptions();
    JComboBox testSelector = new JComboBox(descriptions);
    testSelector.setSelectedItem(params.get("tetradTestType", TestType.TETRAD_WISHART));
    testSelector.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            JComboBox combo = (JComboBox) e.getSource();
            TestType testType = (TestType) combo.getSelectedItem();
            getParams().set("tetradTestType", testType);
        }
    });
    boolean discreteModel = setVarNames(parentModels, params);
    editClusters = new JButton("Edit");
    editClusters.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            openClusterEditor();
        }
    });
    Box b = Box.createVerticalBox();
    Box b1 = Box.createHorizontalBox();
    b1.add(new JLabel("Alpha:"));
    b1.add(Box.createHorizontalGlue());
    b1.add(alphaField);
    b.add(b1);
    Box b2 = Box.createHorizontalBox();
    b2.add(new JLabel("search_for_structure_over_latents Assignments:"));
    b2.add(Box.createHorizontalGlue());
    b2.add(editClusters);
    b.add(b2);
    if (!discreteModel) {
        Box b3 = Box.createHorizontalBox();
        b3.add(new JLabel("Statistical Test:"));
        b3.add(Box.createHorizontalGlue());
        b3.add(testSelector);
        b.add(b3);
    } else {
        this.params.set("tetradTestType", TestType.DISCRETE_LRT);
    }
    setLayout(new BorderLayout());
    add(b, BorderLayout.CENTER);
}

Example 2 with TestType

use of edu.cmu.tetrad.search.TestType in project tetrad by cmu-phil.

the class Bpc method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        ICovarianceMatrix cov = DataUtils.getCovMatrix(dataSet);
        double alpha = parameters.getDouble("alpha");
        boolean wishart = parameters.getBoolean("useWishart", true);
        TestType testType;
        if (wishart) {
            testType = TestType.TETRAD_WISHART;
        } else {
            testType = TestType.TETRAD_DELTA;
        }
        TestType purifyType = TestType.TETRAD_BASED;
        BuildPureClusters bpc = new BuildPureClusters(cov, alpha, testType, purifyType);
        bpc.setVerbose(parameters.getBoolean("verbose"));
        return bpc.search();
    } else {
        Bpc algorithm = new Bpc();
        // algorithm.setKnowledge(knowledge);
        // if (initialGraph != null) {
        // algorithm.setInitialGraph(initialGraph);
        // }
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, algorithm, parameters.getInt("bootstrapSampleSize"));
        search.setKnowledge(knowledge);
        BootstrapEdgeEnsemble edgeEnsemble = BootstrapEdgeEnsemble.Highest;
        switch(parameters.getInt("bootstrapEnsemble", 1)) {
            case 0:
                edgeEnsemble = BootstrapEdgeEnsemble.Preserved;
                break;
            case 1:
                edgeEnsemble = BootstrapEdgeEnsemble.Highest;
                break;
            case 2:
                edgeEnsemble = BootstrapEdgeEnsemble.Majority;
        }
        search.setEdgeEnsemble(edgeEnsemble);
        search.setParameters(parameters);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    }
}

Example 3 with TestType

use of edu.cmu.tetrad.search.TestType in project tetrad by cmu-phil.

the class FofcRunner method execute.

// ===================PUBLIC METHODS OVERRIDING ABSTRACT================//
/**
 * Executes the algorithm, producing (at least) a result workbench. Must be
 * implemented in the extending class.
 */
public void execute() {
    Graph searchGraph;
    FindOneFactorClusters fofc;
    Object source = getData();
    TestType tetradTestType = (TestType) getParams().get("tetradTestType", TestType.TETRAD_WISHART);
    if (tetradTestType == null || (!(tetradTestType == TestType.TETRAD_DELTA || tetradTestType == TestType.TETRAD_WISHART))) {
        tetradTestType = TestType.TETRAD_DELTA;
        getParams().set("tetradTestType", tetradTestType);
    }
    FindOneFactorClusters.Algorithm algorithm = (FindOneFactorClusters.Algorithm) getParams().get("fofcAlgorithm", FindOneFactorClusters.Algorithm.GAP);
    if (source instanceof DataSet) {
        fofc = new FindOneFactorClusters((DataSet) source, tetradTestType, algorithm, getParams().getDouble("alpha", 0.001));
        searchGraph = fofc.search();
    } else if (source instanceof CovarianceMatrix) {
        fofc = new FindOneFactorClusters((CovarianceMatrix) source, tetradTestType, algorithm, getParams().getDouble("alpha", 0.001));
        searchGraph = fofc.search();
    } else {
        throw new IllegalArgumentException("Unrecognized data type.");
    }
    if (semIm != null) {
        List<List<Node>> partition = MimUtils.convertToClusters2(searchGraph);
        List<String> variableNames = ReidentifyVariables.reidentifyVariables2(partition, trueGraph, (DataSet) getData());
        rename(searchGraph, partition, variableNames);
    // searchGraph = reidentifyVariables2(searchGraph, semIm);
    } else if (trueGraph != null) {
        List<List<Node>> partition = MimUtils.convertToClusters2(searchGraph);
        List<String> variableNames = ReidentifyVariables.reidentifyVariables1(partition, trueGraph);
        rename(searchGraph, partition, variableNames);
    // searchGraph = reidentifyVariables(searchGraph, trueGraph);
    }
    System.out.println("Search Graph " + searchGraph);
    try {
        Graph graph = new MarshalledObject<>(searchGraph).get();
        GraphUtils.circleLayout(graph, 200, 200, 150);
        GraphUtils.fruchtermanReingoldLayout(graph);
        setResultGraph(graph);
        setClusters(MimUtils.convertToClusters(graph, getData().getVariables()));
    } catch (Exception e) {
        e.printStackTrace();
        throw new RuntimeException(e);
    }
}

Example 4 with TestType

use of edu.cmu.tetrad.search.TestType in project tetrad by cmu-phil.

the class FtfcRunner method execute.

// ===================PUBLIC METHODS OVERRIDING ABSTRACT================//
/**
 * Executes the algorithm, producing (at least) a result workbench. Must be
 * implemented in the extending class.
 */
public void execute() {
    Graph searchGraph;
    FindTwoFactorClusters ftfc;
    Object source = getData();
    TestType tetradTestType = (TestType) getParams().get("tetradTestType", TestType.TETRAD_WISHART);
    if (tetradTestType == null || (!(tetradTestType == TestType.TETRAD_DELTA || tetradTestType == TestType.TETRAD_WISHART))) {
        tetradTestType = TestType.TETRAD_DELTA;
        getParams().set("tetradTestType", tetradTestType);
    }
    FindTwoFactorClusters.Algorithm algorithm = (FindTwoFactorClusters.Algorithm) getParams().get("ftfcAlgorithm", FindTwoFactorClusters.Algorithm.GAP);
    if (source instanceof DataSet) {
        ftfc = new FindTwoFactorClusters((DataSet) source, algorithm, getParams().getDouble("alpha", 0.001));
        ftfc.setVerbose(true);
        searchGraph = ftfc.search();
    } else if (source instanceof CovarianceMatrix) {
        ftfc = new FindTwoFactorClusters((CovarianceMatrix) source, algorithm, getParams().getDouble("alpha", 0.001));
        ftfc.setVerbose(true);
        searchGraph = ftfc.search();
    } else {
        throw new IllegalArgumentException("Unrecognized data type.");
    }
    if (semIm != null) {
        List<List<Node>> partition = MimUtils.convertToClusters2(searchGraph);
        List<String> variableNames = ReidentifyVariables.reidentifyVariables2(partition, trueGraph, (DataSet) getData());
        rename(searchGraph, partition, variableNames);
    // searchGraph = reidentifyVariables2(searchGraph, semIm);
    } else if (trueGraph != null) {
        List<List<Node>> partition = MimUtils.convertToClusters2(searchGraph);
        List<String> variableNames = ReidentifyVariables.reidentifyVariables1(partition, trueGraph);
        rename(searchGraph, partition, variableNames);
    // searchGraph = reidentifyVariables(searchGraph, trueGraph);
    }
    System.out.println("Search Graph " + searchGraph);
    try {
        Graph graph = new MarshalledObject<>(searchGraph).get();
        GraphUtils.circleLayout(graph, 200, 200, 150);
        GraphUtils.fruchtermanReingoldLayout(graph);
        setResultGraph(graph);
        setClusters(MimUtils.convertToClusters(graph, getData().getVariables()));
    } catch (Exception e) {
        e.printStackTrace();
        throw new RuntimeException(e);
    }
}

Example 5 with TestType

use of edu.cmu.tetrad.search.TestType in project tetrad by cmu-phil.

the class BuildPureClustersParamsEditor method setup.

public void setup() {
    DoubleTextField alphaField = new DoubleTextField(params.getDouble("alpha", 0.001), 4, NumberFormatUtil.getInstance().getNumberFormat());
    alphaField.setFilter(new DoubleTextField.Filter() {

        public double filter(double value, double oldValue) {
            try {
                getParams().set("alpha", 0.001);
                return value;
            } catch (Exception e) {
                return oldValue;
            }
        }
    });
    final TestType[] descriptions = TestType.getTestDescriptions();
    JComboBox testSelector = new JComboBox(descriptions);
    testSelector.setSelectedItem(getParams().get("tetradTestType", TestType.TETRAD_WISHART));
    testSelector.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            JComboBox combo = (JComboBox) e.getSource();
            TestType testType = (TestType) combo.getSelectedItem();
            getParams().set("tetradTestType", testType);
        }
    });
    final TestType[] purifyDescriptions = TestType.getPurifyTestDescriptions();
    JComboBox purifySelector = new JComboBox(purifyDescriptions);
    purifySelector.setSelectedItem(getParams().get("purifyTestType", TestType.NONE));
    purifySelector.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            JComboBox combo = (JComboBox) e.getSource();
            TestType testType = (TestType) combo.getSelectedItem();
            getParams().set("purifyTestType", testType);
        }
    });
    // Where is it setting the appropriate knowledge for the search?
    DataModel dataModel = null;
    for (Object parentModel : this.parentModels) {
        if (parentModel instanceof DataWrapper) {
            DataWrapper dataWrapper = (DataWrapper) parentModel;
            dataModel = dataWrapper.getSelectedDataModel();
        }
    }
    if (dataModel == null) {
        throw new IllegalStateException("Null data model.");
    }
    List<String> varNames = new ArrayList<>(dataModel.getVariableNames());
    boolean isDiscreteModel;
    if (dataModel instanceof ICovarianceMatrix) {
        isDiscreteModel = false;
    } else {
        DataSet dataSet = (DataSet) dataModel;
        isDiscreteModel = dataSet.isDiscrete();
    // try {
    // new DataSet((DataSet) dataModel);
    // isDiscreteModel = true;
    // }
    // catch (IllegalArgumentException e) {
    // isDiscreteModel = false;
    // }
    }
    params.set("varNames", varNames);
    alphaField.setValue(params.getDouble("alpha", 0.001));
    Box b = Box.createVerticalBox();
    Box b1 = Box.createHorizontalBox();
    b1.add(new JLabel("Alpha:"));
    b1.add(Box.createHorizontalGlue());
    b1.add(alphaField);
    b.add(b1);
    if (!isDiscreteModel) {
        Box b2 = Box.createHorizontalBox();
        b2.add(new JLabel("Statistical Test:"));
        b2.add(Box.createHorizontalGlue());
        b2.add(testSelector);
        b.add(b2);
        Box b3 = Box.createHorizontalBox();
        b3.add(new JLabel("Purify Test:"));
        b3.add(Box.createHorizontalGlue());
        b3.add(purifySelector);
        b.add(b3);
    } else {
        this.params.set("purifyTestType", TestType.DISCRETE_LRT);
        this.params.set("tetradTestType", TestType.DISCRETE);
    }
    setLayout(new BorderLayout());
    add(b, BorderLayout.CENTER);
}