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

Example 16 with DataModel

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

the class FciSearchParamEditor method setup.

public void setup() {
    /*
      The variable names from the object being searched over (usually data).
     */
    List varNames = (List<String>) params.get("varNames", null);
    DataModel dataModel1 = null;
    Graph graph = null;
    for (Object parentModel1 : 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).");
    }
    params.set("varNames", varNames);
    IntTextField depthField = new IntTextField(params.getInt("depth", -1), 4);
    depthField.setFilter(new IntTextField.Filter() {

        public int filter(int value, int oldValue) {
            try {
                params.set("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 {
                    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));
    Box b1 = Box.createHorizontalBox();
    b1.add(new JLabel("Knowledge:"));
    b1.add(Box.createGlue());
    add(b1);
    add(Box.createVerticalStrut(10));
    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 17 with DataModel

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

the class TimeoutComparison method saveToFiles.

/**
 * Saves simulationWrapper data.
 *
 * @param dataPath The path to the directory where the simulationWrapper
 * data should be saved.
 * @param simulation The simulate used to generate the graphs and data.
 * @param parameters The parameters to be used in the simulationWrapper.
 */
public void saveToFiles(String dataPath, Simulation simulation, Parameters parameters) {
    List<SimulationWrapper> simulationWrappers = getSimulationWrappers(simulation, parameters);
    File dir0 = new File(dataPath);
    File dir;
    int i = 0;
    dir = new File(dir0, "save");
    // 
    // do {
    // dir = new File(dir0, "Simulation" + (++i));
    // } while (dir.exists());
    // if (dir.exists()) {
    // JOptionPane.showMessageDialog(JOptionUtils.centeringComp(),
    // "A file already exists named 'Simulation' in directory '" + dir0.getPath() + "'; \n" +
    // "please remove it first or move it out of the way.");
    // }
    deleteFilesThenDirectory(dir);
    try {
        int index = 0;
        for (SimulationWrapper simulationWrapper : simulationWrappers) {
            for (String param : simulationWrapper.getParameters()) {
                parameters.set(param, simulationWrapper.getValue(param));
            }
            simulationWrapper.createData(simulationWrapper.getSimulationSpecificParameters());
            index++;
            File subdir = new File(dir, "" + index);
            subdir.mkdirs();
            File dir1 = new File(subdir, "graph");
            File dir2 = new File(subdir, "data");
            dir1.mkdirs();
            dir2.mkdirs();
            File dir3 = null;
            if (isSavePatterns()) {
                dir3 = new File(subdir, "patterns");
                dir3.mkdirs();
            }
            File dir4 = null;
            if (isSavePags()) {
                dir4 = new File(subdir, "pags");
                dir4.mkdirs();
            }
            for (int j = 0; j < simulationWrapper.getNumDataModels(); j++) {
                File file2 = new File(dir1, "graph." + (j + 1) + ".txt");
                Graph graph = simulationWrapper.getTrueGraph(j);
                GraphUtils.saveGraph(graph, file2, false);
                File file = new File(dir2, "data." + (j + 1) + ".txt");
                Writer out = new FileWriter(file);
                DataModel dataModel = (DataModel) simulationWrapper.getDataModel(j);
                DataWriter.writeRectangularData((DataSet) dataModel, out, '\t');
                out.close();
                if (isSavePatterns()) {
                    File file3 = new File(dir3, "pattern." + (j + 1) + ".txt");
                    GraphUtils.saveGraph(SearchGraphUtils.patternForDag(graph), file3, false);
                }
                if (isSavePags()) {
                    File file4 = new File(dir4, "pag." + (j + 1) + ".txt");
                    GraphUtils.saveGraph(new DagToPag2(graph).convert(), file4, false);
                }
            }
            PrintStream out = new PrintStream(new FileOutputStream(new File(subdir, "parameters.txt")));
            out.println(simulationWrapper.getDescription());
            // out.println();
            out.println(simulationWrapper.getSimulationSpecificParameters());
            out.close();
        }
    } catch (IOException e) {
        e.printStackTrace();
    }
}

Example 18 with DataModel

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

the class ConcatenateDatasetsWrapper method construct.

private void construct(DataWrapper... dataWrappers) {
    for (DataWrapper wrapper : dataWrappers) {
        if (wrapper == null) {
            throw new NullPointerException("The given data must not be null");
        }
    }
    List<DataSet> dataSets = new ArrayList<>();
    for (DataWrapper wrapper : dataWrappers) {
        for (DataModel model : wrapper.getDataModelList()) {
            if (!(model instanceof DataSet)) {
                throw new IllegalArgumentException("Sorry, I am only willing to concatenate tabular datasets.");
            }
            DataSet dataSet = (DataSet) model;
            dataSets.add(dataSet);
        }
    }
    DataSet concatenated = DataUtils.concatenate(dataSets);
    concatenated.setName("Concatenated");
    this.setDataModel(concatenated);
    LogDataUtils.logDataModelList("Parent data in which constant columns have been removed.", getDataModelList());
}

Example 19 with DataModel

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

the class LoadDataDialog method loadAllFiles.

/**
 * Add all files to model once all can be loaded successfully
 */
private void loadAllFiles() throws IOException {
    // Try to load each file and store the file name for failed loading
    for (int i = 0; i < loadedFiles.size(); i++) {
        DataModel dataModel = dataLoaderSettings.loadDataWithSettings(loadedFiles.get(i));
        // Add to dataModelList for further use
        if (dataModel != null) {
            // Must setName() here, file names will be used by the spreadsheet - Zhou
            dataModel.setName(loadedFiles.get(i).getName());
            dataModelList.add(dataModel);
            System.out.println("File index = " + i + " has been loaded successfully");
        }
    }
}

Example 20 with DataModel

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

the class LofsSearchEditor 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));
}