Examples with DataModel edu.cmu.tetrad.data.DataModel used on opensource projects

Example 6 with DataModel

use of edu.cmu.tetrad.data.DataModel in project tetrad by cmu-phil.

the class MimSearchEditor2 method getIndTestParamBox.

/**
 * Factory to return the correct param editor for independence test params.
 * This will go in a little box in the search editor.
 */
private JComponent getIndTestParamBox(Parameters params) {
    if (params == null) {
        throw new NullPointerException();
    }
    if (params instanceof Parameters) {
        MimRunner runner = getMimRunner();
        params.set("varNames", runner.getParams().get("varNames", null));
        DataModel dataModel = runner.getData();
        if (dataModel instanceof DataSet) {
            DataSet data = (DataSet) runner.getData();
            boolean discrete = data.isDiscrete();
            return new BuildPureClustersIndTestParamsEditor2(params, discrete);
        } else if (dataModel instanceof ICovarianceMatrix) {
            return new BuildPureClustersIndTestParamsEditor2(params, false);
        }
    }
    if (params instanceof Parameters) {
        MimRunner runner = getMimRunner();
        params.set("varNames", runner.getParams().get("varNames", null));
        boolean discreteData = false;
        if (runner.getData() instanceof DataSet) {
            discreteData = ((DataSet) runner.getData()).isDiscrete();
        }
        return new PurifyIndTestParamsEditor(params, discreteData);
    }
    if (params instanceof Parameters) {
        MimRunner runner = getMimRunner();
        params.set("varNames", runner.getParams().get("varNames", null));
        return new MimBuildIndTestParamsEditor(params);
    }
    throw new IllegalArgumentException("Unrecognized Parameters: " + params.getClass());
}

Example 7 with DataModel

use of edu.cmu.tetrad.data.DataModel in project tetrad by cmu-phil.

the class MbSearchEditor method addSpecialMenus.

protected void addSpecialMenus(JMenuBar menuBar) {
    JMenu test = new JMenu("Independence");
    menuBar.add(test);
    IndTestMenuItems.addIndependenceTestChoices(test, this);
    if (getAlgorithmRunner() instanceof MbfsRunner) {
        JMenu graph = new JMenu("Graph");
        JMenuItem showDags = new JMenuItem("Show DAG's Consistent with forbid_latent_common_causes");
        // JMenuItem meekOrient = new JMenuItem("Meek Orientation");
        JMenuItem gesOrient = new JMenuItem("Global Score-based Reorientation");
        JMenuItem nextGraph = new JMenuItem("Next Graph");
        JMenuItem previousGraph = new JMenuItem("Previous Graph");
        graph.add(new GraphPropertiesAction(getWorkbench()));
        graph.add(new PathsAction(getWorkbench()));
        // graph.add(new DirectedPathsAction(getWorkbench()));
        // graph.add(new TreksAction(getWorkbench()));
        // graph.add(new AllPathsAction(getWorkbench()));
        // graph.add(new NeighborhoodsAction(getWorkbench()));
        graph.addSeparator();
        // graph.add(meekOrient);
        graph.add(gesOrient);
        graph.addSeparator();
        graph.add(previousGraph);
        graph.add(nextGraph);
        graph.addSeparator();
        graph.add(showDags);
        menuBar.add(graph);
        showDags.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                AlgorithmRunner runner = getAlgorithmRunner();
                if (!(runner instanceof MbfsRunner)) {
                    return;
                }
                MbfsRunner mbRunner = (MbfsRunner) runner;
                final Mbfs search = mbRunner.getMbFanSearch();
                if (search == null) {
                    JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "The search was not stored.");
                    return;
                }
                MbPatternDisplay display = new MbPatternDisplay(search);
                JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), display, "MB DAG's Consistent with forbid_latent_common_causes", JOptionPane.PLAIN_MESSAGE);
            }
        });
        // meekOrient.addActionListener(new ActionListener() {
        // public void actionPerformed(ActionEvent e) {
        // ImpliedOrientation rules = getAlgorithmRunner().getMeekRules();
        // rules.setKnowledge((IKnowledge) getAlgorithmRunner().getParams().get("knowledge", new Knowledge2()));
        // rules.orientImplied(getGraph());
        // getWorkbench().setGraph(getGraph());
        // }
        // });
        gesOrient.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                DataModel dataModel = getAlgorithmRunner().getDataModel();
                final Graph graph = SearchGraphUtils.reorient(getGraph(), dataModel, getKnowledge());
                getGraphHistory().add(graph);
                getWorkbench().setGraph(graph);
                firePropertyChange("modelChanged", null, null);
            }
        });
    }
    // if (getAlgorithmRunner().supportsKnowledge()) {
    // menuBar.add(new Knowledge2Menu(this));
    // }
    menuBar.add(new LayoutMenu(this));
}

Example 8 with DataModel

use of edu.cmu.tetrad.data.DataModel in project tetrad by cmu-phil.

the class PcSearchParamEditor method setup.

public void setup() {
    /*
      The variable names from the object being searched over (usually data).
     */
    List<String> varNames = (List<String>) params.get("varNames", null);
    DataModel dataModel1 = null;
    Graph graph = null;
    for (Object parentModel1 : this.parentModels) {
        if (parentModel1 instanceof DataWrapper) {
            DataWrapper dataWrapper = (DataWrapper) parentModel1;
            dataModel1 = dataWrapper.getSelectedDataModel();
        }
        if (parentModel1 instanceof GraphWrapper) {
            GraphWrapper graphWrapper = (GraphWrapper) parentModel1;
            graph = graphWrapper.getGraph();
        }
        if (parentModel1 instanceof DagWrapper) {
            DagWrapper dagWrapper = (DagWrapper) parentModel1;
            graph = dagWrapper.getDag();
        }
        if (parentModel1 instanceof SemGraphWrapper) {
            SemGraphWrapper semGraphWrapper = (SemGraphWrapper) parentModel1;
            graph = semGraphWrapper.getGraph();
        }
    }
    if (dataModel1 != null) {
        varNames = new ArrayList<>(dataModel1.getVariableNames());
    } else if (graph != null) {
        Iterator<Node> it = graph.getNodes().iterator();
        varNames = new ArrayList();
        Node temp;
        while (it.hasNext()) {
            temp = it.next();
            if (temp.getNodeType() == NodeType.MEASURED) {
                varNames.add(temp.getName());
            }
        }
    } else {
        throw new NullPointerException("Null model (no graph or data model " + "passed to the search).");
    }
    this.params.set("varNames", varNames);
    IntTextField depthField = new IntTextField(this.params.getInt("depth", -1), 4);
    depthField.setFilter(new IntTextField.Filter() {

        public int filter(int value, int oldValue) {
            try {
                PcSearchParamEditor.this.params.set("depth", value);
                Preferences.userRoot().putInt("depth", value);
                return value;
            } catch (Exception e) {
                return oldValue;
            }
        }
    });
    double alpha = params.getDouble("alpha", 0.001);
    if (!Double.isNaN(alpha)) {
        alphaField = new DoubleTextField(alpha, 4, NumberFormatUtil.getInstance().getNumberFormat());
        alphaField.setFilter(new DoubleTextField.Filter() {

            public double filter(double value, double oldValue) {
                try {
                    PcSearchParamEditor.this.params.set("alpha", 0.001);
                    Preferences.userRoot().putDouble("alpha", value);
                    return value;
                } catch (Exception e) {
                    return oldValue;
                }
            }
        });
    }
    setBorder(new MatteBorder(10, 10, 10, 10, super.getBackground()));
    setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
    if (!Double.isNaN(alpha)) {
        Box b2 = Box.createHorizontalBox();
        b2.add(new JLabel("Alpha Value:"));
        b2.add(Box.createGlue());
        b2.add(alphaField);
        add(b2);
        add(Box.createVerticalStrut(10));
    }
    Box b3 = Box.createHorizontalBox();
    b3.add(new JLabel("Search Depth:"));
    b3.add(Box.createGlue());
    b3.add(depthField);
    add(b3);
    add(Box.createVerticalStrut(10));
}

Example 9 with DataModel

use of edu.cmu.tetrad.data.DataModel in project tetrad by cmu-phil.

the class TsImages method search.

@Override
public Graph search(List<DataModel> dataSets, Parameters parameters) {
    List<DataModel> dataModels = new ArrayList<>();
    for (DataModel dataSet : dataSets) {
        dataModels.add(dataSet);
    }
    TsGFci search;
    if (score instanceof SemBicScore) {
        SemBicScoreImages gesScore = new SemBicScoreImages(dataModels);
        gesScore.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
        IndependenceTest test = new IndTestScore(gesScore);
        search = new TsGFci(test, gesScore);
    } else if (score instanceof BdeuScore) {
        double samplePrior = parameters.getDouble("samplePrior", 1);
        double structurePrior = parameters.getDouble("structurePrior", 1);
        BdeuScoreImages score = new BdeuScoreImages(dataModels);
        score.setSamplePrior(samplePrior);
        score.setStructurePrior(structurePrior);
        IndependenceTest test = new IndTestScore(score);
        search = new TsGFci(test, score);
    } else {
        throw new IllegalStateException("Sorry, data must either be all continuous or all discrete.");
    }
    IKnowledge knowledge = dataModels.get(0).getKnowledge();
    search.setKnowledge(knowledge);
    return search.search();
}

Example 10 with DataModel

use of edu.cmu.tetrad.data.DataModel in project tetrad by cmu-phil.

the class LingamStructureRunner method execute.

// ============================PUBLIC METHODS==========================//
/**
 * Executes the algorithm, producing (at least) a result workbench. Must be
 * implemented in the extending class.
 */
public void execute() {
    DataModel source = getDataModel();
    if (!(source instanceof DataSet)) {
        throw new IllegalArgumentException("Expecting a rectangular data set.");
    }
    DataSet data = (DataSet) source;
    if (!data.isContinuous()) {
        throw new IllegalArgumentException("Expecting a continuous data set.");
    }
    // Lingam_old lingam = new Lingam_old();
    // lingam.setAlternativePenalty(getParameters().getAlternativePenalty());
    // lingam.setPruningDone(true);
    // lingam.setAlternativePenalty(getParameters().getAlternativePenalty());
    // GraphWithParameters result = lingam.lingam(data);
    // Graph graph = result.getGraph();
    Lingam lingam = new Lingam();
    Parameters params = getParams();
    Graph graph = lingam.search(data);
    setResultGraph(graph);
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
    } else {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
}