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

Example 11 with DataModel

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

the class DataLoaderSettings method loadDataWithSettings.

/**
 * Kevin's fast data reader
 *
 * @param file
 * @return DataModel on success
 */
public DataModel loadDataWithSettings(File file) throws IOException {
    DataModel dataModel = null;
    Delimiter delimiter = getDelimiterType();
    boolean hasHeader = isVarNamesFirstRow();
    String commentMarker = getCommentMarker();
    String missingValueMarker = getMissingValueMarker();
    if (tabularRadioButton.isSelected()) {
        TabularDataReader dataReader = null;
        // Continuous, discrete, mixed
        if (contRadioButton.isSelected()) {
            dataReader = new ContinuousTabularDataFileReader(file, delimiter);
        } else if (discRadioButton.isSelected()) {
            dataReader = new VerticalDiscreteTabularDataReader(file, delimiter);
        } else if (mixedRadioButton.isSelected()) {
            dataReader = new MixedTabularDataFileReader(getMaxNumOfDiscCategories(), file, delimiter);
        } else {
            throw new UnsupportedOperationException("Unsupported data type!");
        }
        // Header in first row or not
        dataReader.setHasHeader(hasHeader);
        // Set comment marker
        dataReader.setCommentMarker(commentMarker);
        dataReader.setMissingValueMarker(missingValueMarker);
        // Set the quote character
        if (doubleQuoteRadioButton.isSelected()) {
            dataReader.setQuoteCharacter('"');
        }
        if (singleQuoteRadioButton.isSelected()) {
            dataReader.setQuoteCharacter('\'');
        }
        Dataset dataset;
        // Handle case ID column based on different selections
        if (idNoneRadioButton.isSelected()) {
            // No column exclusion
            dataset = dataReader.readInData();
        } else if (idUnlabeledFirstColRadioButton.isSelected()) {
            // Exclude the first column
            dataset = dataReader.readInData(new int[] { 1 });
        } else if (idLabeledColRadioButton.isSelected() && !idStringField.getText().isEmpty()) {
            // Exclude the specified labled column
            dataset = dataReader.readInData(new HashSet<>(Arrays.asList(new String[] { idStringField.getText() })));
        } else {
            throw new UnsupportedOperationException("Unexpected 'Case ID column to ignore' selection.");
        }
        // Box Dataset to DataModel
        dataModel = DataConvertUtils.toDataModel(dataset);
    } else if (covarianceRadioButton.isSelected()) {
        // Covariance data can only be continuous
        CovarianceDataReader dataReader = new LowerCovarianceDataReader(file, delimiter);
        // Set comment marker
        dataReader.setCommentMarker(commentMarker);
        // Set the quote character
        if (doubleQuoteRadioButton.isSelected()) {
            dataReader.setQuoteCharacter('"');
        }
        if (singleQuoteRadioButton.isSelected()) {
            dataReader.setQuoteCharacter('\'');
        }
        Dataset dataset = dataReader.readInData();
        // Box Dataset to DataModel
        dataModel = DataConvertUtils.toDataModel(dataset);
    } else {
        throw new UnsupportedOperationException("Unsupported selection of File Type!");
    }
    return dataModel;
}

Example 12 with DataModel

use of edu.cmu.tetrad.data.DataModel 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);
}

Example 13 with DataModel

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

the class CalculatorEditor method setParentModels.

/**
 * Grabs the data set that the calculator is working on.
 */
public void setParentModels(Object[] parentModels) {
    if (parentModels == null || parentModels.length == 0) {
        throw new IllegalArgumentException("There must be parent model");
    }
    DataWrapper data = null;
    for (Object parent : parentModels) {
        if (parent instanceof DataWrapper) {
            data = (DataWrapper) parent;
        }
    }
    if (data == null) {
        throw new IllegalArgumentException("Should have have a data wrapper as a parent");
    }
    DataModel model = data.getSelectedDataModel();
    if (!(model instanceof DataSet)) {
        throw new IllegalArgumentException("The data must be tabular");
    }
    this.dataSet = (DataSet) model;
}

Example 14 with DataModel

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

the class IonSearchEditor method addSpecialMenus.

protected void addSpecialMenus(JMenuBar menuBar) {
    if (!(getAlgorithmRunner() instanceof IGesRunner)) {
        JMenu test = new JMenu("Independence");
        menuBar.add(test);
        IndTestMenuItems.addIndependenceTestChoices(test, this);
    // test.addSeparator();
    // 
    // AlgorithmRunner algorithmRunner = getAlgorithmRunner();
    // if (algorithmRunner instanceof IndTestProducer) {
    // IndTestProducer p = (IndTestProducer) algorithmRunner;
    // IndependenceFactsAction action =
    // new IndependenceFactsAction(this, p, "Independence Facts...");
    // test.add(action);
    // }
    }
    JMenu graph = new JMenu("Graph");
    JMenuItem showDags = new JMenuItem("Show DAGs in forbid_latent_common_causes");
    // JMenuItem meekOrient = new JMenuItem("Meek Orientation");
    JMenuItem dagInPattern = new JMenuItem("Choose DAG in forbid_latent_common_causes");
    JMenuItem gesOrient = new JMenuItem("Global Score-based Reorientation");
    JMenuItem nextGraph = new JMenuItem("Next Graph");
    JMenuItem previousGraph = new JMenuItem("Previous Graph");
    // graph.add(new LayoutMenu(this));
    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.add(new TriplesAction(getWorkbench().getGraph(), getAlgorithmRunner()));
    graph.addSeparator();
    // graph.add(meekOrient);
    graph.add(dagInPattern);
    graph.add(gesOrient);
    graph.addSeparator();
    graph.add(previousGraph);
    graph.add(nextGraph);
    graph.addSeparator();
    graph.add(showDags);
    graph.addSeparator();
    graph.add(new JMenuItem(new SelectBidirectedAction(getWorkbench())));
    graph.add(new JMenuItem(new SelectUndirectedAction(getWorkbench())));
    menuBar.add(graph);
    showDags.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            Window owner = (Window) getTopLevelAncestor();
            new WatchedProcess(owner) {

                public void watch() {
                    // Needs to be a pattern search; this isn't checked
                    // before running the algorithm because of allowable
                    // "slop"--e.g. bidirected edges.
                    AlgorithmRunner runner = getAlgorithmRunner();
                    Graph graph = runner.getGraph();
                    if (graph == null) {
                        JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "No result gaph.");
                        return;
                    }
                    // if (runner instanceof ImagesRunner) {
                    // GraphScorer scorer = ((ImagesRunner) runner).getGraphScorer();
                    // Graph _graph = ((ImagesRunner) runner).getTopGraphs().get(getIndex()).getGraph();
                    // 
                    // ScoredGraphsDisplay display = new ScoredGraphsDisplay(_graph, scorer);
                    // GraphWorkbench workbench = getWorkbench();
                    // 
                    // EditorWindow editorWindow =
                    // new EditorWindow(display, "Independence Facts",
                    // "Close", false, workbench);
                    // DesktopController.getInstance().addEditorWindow(editorWindow, JLayeredPane.PALETTE_LAYER);
                    // editorWindow.setVisible(true);
                    // }
                    // else {
                    PatternDisplay display = new PatternDisplay(graph);
                    GraphWorkbench workbench = getWorkbench();
                    EditorWindow editorWindow = new EditorWindow(display, "Independence Facts", "Close", false, workbench);
                    DesktopController.getInstance().addEditorWindow(editorWindow, JLayeredPane.PALETTE_LAYER);
                    editorWindow.setVisible(true);
                // }
                }
            };
        }
    });
    // 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());
    // getGraphHistory().add(getGraph());
    // getWorkbench().setGraph(getGraph());
    // firePropertyChange("modelChanged", null, null);
    // }
    // });
    dagInPattern.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            Graph graph = new EdgeListGraph(getGraph());
            // Removing bidirected edges from the pattern before selecting a DAG.                                   4
            for (Edge edge : graph.getEdges()) {
                if (Edges.isBidirectedEdge(edge)) {
                    graph.removeEdge(edge);
                }
            }
            PatternToDag search = new PatternToDag(new EdgeListGraphSingleConnections(graph));
            Graph dag = search.patternToDagMeek();
            getGraphHistory().add(dag);
            getWorkbench().setGraph(dag);
            ((AbstractAlgorithmRunner) getAlgorithmRunner()).setResultGraph(dag);
            firePropertyChange("modelChanged", null, null);
        }
    });
    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);
        }
    });
    nextGraph.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            Graph next = getGraphHistory().next();
            getWorkbench().setGraph(next);
            ((AbstractAlgorithmRunner) getAlgorithmRunner()).setResultGraph(next);
            firePropertyChange("modelChanged", null, null);
        }
    });
    previousGraph.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            Graph previous = getGraphHistory().previous();
            getWorkbench().setGraph(previous);
            ((AbstractAlgorithmRunner) getAlgorithmRunner()).setResultGraph(previous);
            firePropertyChange("modelChanged", null, null);
        }
    });
    // if (getAlgorithmRunner().supportsKnowledge()) {
    // menuBar.add(new Knowledge2Menu(this));
    // }
    menuBar.add(new LayoutMenu(this));
}

Example 15 with DataModel

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

the class FciCcdSearchEditor method addSpecialMenus.

protected void addSpecialMenus(JMenuBar menuBar) {
    if (!(getAlgorithmRunner() instanceof IGesRunner)) {
        JMenu test = new JMenu("Independence");
        menuBar.add(test);
        IndTestMenuItems.addIndependenceTestChoices(test, this);
    // test.addSeparator();
    // 
    // AlgorithmRunner algorithmRunner = getAlgorithmRunner();
    // if (algorithmRunner instanceof IndTestProducer) {
    // IndTestProducer p = (IndTestProducer) algorithmRunner;
    // IndependenceFactsAction action =
    // new IndependenceFactsAction(this, p, "Independence Facts...");
    // test.add(action);
    // }
    }
    JMenu graph = new JMenu("Graph");
    JMenuItem showDags = new JMenuItem("Show DAGs in forbid_latent_common_causes");
    // JMenuItem meekOrient = new JMenuItem("Meek Orientation");
    JMenuItem dagInPattern = new JMenuItem("Choose DAG in forbid_latent_common_causes");
    JMenuItem gesOrient = new JMenuItem("Global Score-based Reorientation");
    JMenuItem nextGraph = new JMenuItem("Next Graph");
    JMenuItem previousGraph = new JMenuItem("Previous Graph");
    // graph.add(new LayoutMenu(this));
    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.add(new TriplesAction(getWorkbench().getGraph(), getAlgorithmRunner()));
    graph.addSeparator();
    // graph.add(meekOrient);
    graph.add(dagInPattern);
    graph.add(gesOrient);
    graph.addSeparator();
    graph.add(previousGraph);
    graph.add(nextGraph);
    graph.addSeparator();
    graph.add(showDags);
    graph.addSeparator();
    graph.add(new JMenuItem(new SelectBidirectedAction(getWorkbench())));
    graph.add(new JMenuItem(new SelectUndirectedAction(getWorkbench())));
    menuBar.add(graph);
    showDags.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            Window owner = (Window) getTopLevelAncestor();
            new WatchedProcess(owner) {

                public void watch() {
                    // Needs to be a pattern search; this isn't checked
                    // before running the algorithm because of allowable
                    // "slop"--e.g. bidirected edges.
                    AlgorithmRunner runner = getAlgorithmRunner();
                    Graph graph = runner.getGraph();
                    if (graph == null) {
                        JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "No result gaph.");
                        return;
                    }
                    // if (runner instanceof ImagesRunner) {
                    // GraphScorer scorer = ((ImagesRunner) runner).getGraphScorer();
                    // Graph _graph = ((ImagesRunner) runner).getTopGraphs().get(getIndex()).getGraph();
                    // 
                    // ScoredGraphsDisplay display = new ScoredGraphsDisplay(_graph, scorer);
                    // GraphWorkbench workbench = getWorkbench();
                    // 
                    // EditorWindow editorWindow =
                    // new EditorWindow(display, "Independence Facts",
                    // "Close", false, workbench);
                    // DesktopController.getInstance().addEditorWindow(editorWindow, JLayeredPane.PALETTE_LAYER);
                    // editorWindow.setVisible(true);
                    // }
                    // else {
                    PatternDisplay display = new PatternDisplay(graph);
                    GraphWorkbench workbench = getWorkbench();
                    EditorWindow editorWindow = new EditorWindow(display, "Independence Facts", "Close", false, workbench);
                    DesktopController.getInstance().addEditorWindow(editorWindow, JLayeredPane.PALETTE_LAYER);
                    editorWindow.setVisible(true);
                // }
                }
            };
        }
    });
    // 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());
    // getGraphHistory().add(getGraph());
    // getWorkbench().setGraph(getGraph());
    // firePropertyChange("modelChanged", null, null);
    // }
    // });
    dagInPattern.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            Graph graph = new EdgeListGraph(getGraph());
            // Removing bidirected edges from the pattern before selecting a DAG.                                   4
            for (Edge edge : graph.getEdges()) {
                if (Edges.isBidirectedEdge(edge)) {
                    graph.removeEdge(edge);
                }
            }
            PatternToDag search = new PatternToDag(new EdgeListGraphSingleConnections(graph));
            Graph dag = search.patternToDagMeek();
            getGraphHistory().add(dag);
            getWorkbench().setGraph(dag);
            ((AbstractAlgorithmRunner) getAlgorithmRunner()).setResultGraph(dag);
            firePropertyChange("modelChanged", null, null);
        }
    });
    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);
        }
    });
    nextGraph.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            Graph next = getGraphHistory().next();
            getWorkbench().setGraph(next);
            ((AbstractAlgorithmRunner) getAlgorithmRunner()).setResultGraph(next);
            firePropertyChange("modelChanged", null, null);
        }
    });
    previousGraph.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            Graph previous = getGraphHistory().previous();
            getWorkbench().setGraph(previous);
            ((AbstractAlgorithmRunner) getAlgorithmRunner()).setResultGraph(previous);
            firePropertyChange("modelChanged", null, null);
        }
    });
    // if (getAlgorithmRunner().supportsKnowledge()) {
    // menuBar.add(new Knowledge2Menu(this));
    // }
    menuBar.add(new LayoutMenu(this));
}