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

Example 26 with DataModel

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

the class GeneralBootstrapSearch method search.

public List<Graph> search() {
    PAGs.clear();
    parameters.set("bootstrapSampleSize", 0);
    long start, stop;
    if (!this.runParallel) {
        // Running in the sequential form
        if (verbose) {
            out.println("Running Bootstraps in Sequential Mode, numBoostrap = " + numBootstrap);
        }
        for (int i1 = 0; i1 < this.numBootstrap; i1++) {
            start = System.currentTimeMillis();
            GeneralBootstrapSearchRunnable task = null;
            if (data != null) {
                DataSet dataSet = DataUtils.getBootstrapSample(data, data.getNumRows());
                task = new GeneralBootstrapSearchRunnable(dataSet, algorithm, parameters, this, verbose);
            // GeneralBootstrapSearchAction task = new GeneralBootstrapSearchAction(i1, 1, algorithm, parameters, this, verbose);
            } else {
                List<DataModel> dataModels = new ArrayList<>();
                for (DataSet data : dataSets) {
                    DataSet dataSet = DataUtils.getBootstrapSample(data, data.getNumRows());
                    dataModels.add(dataSet);
                }
                task = new GeneralBootstrapSearchRunnable(dataModels, multiDataSetAlgorithm, parameters, this, verbose);
            }
            if (initialGraph != null) {
                task.setInitialGraph(initialGraph);
            }
            task.setKnowledge(knowledge);
            task.run();
            // task.compute();
            stop = System.currentTimeMillis();
            if (verbose) {
                out.println("processing time of bootstrap : " + (stop - start) / 1000.0 + " sec");
            }
        }
    } else {
        // Running in the parallel multiThread form
        if (verbose) {
            out.println("Running Bootstraps in Parallel Mode, numBoostrap = " + numBootstrap);
        }
        for (int i1 = 0; i1 < this.numBootstrap; i1++) {
            GeneralBootstrapSearchRunnable task = null;
            if (data != null) {
                DataSet dataSet = DataUtils.getBootstrapSample(data, data.getNumRows());
                task = new GeneralBootstrapSearchRunnable(dataSet, algorithm, parameters, this, verbose);
            } else {
                List<DataModel> dataModels = new ArrayList<>();
                for (DataSet data : dataSets) {
                    DataSet dataSet = DataUtils.getBootstrapSample(data, data.getNumRows());
                    dataModels.add(dataSet);
                }
                task = new GeneralBootstrapSearchRunnable(dataModels, multiDataSetAlgorithm, parameters, this, verbose);
            }
            task.setKnowledge(knowledge);
            pool.submit(task);
        }
        pool.shutdown();
        while (!pool.isTerminated()) {
            try {
                Thread.sleep(1000);
            // out.println("Waiting...");
            } catch (InterruptedException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }
        }
    // out.println("Is terminated: " + pool.isTerminated());
    }
    parameters.set("bootstrapping", true);
    return PAGs;
}

Example 27 with DataModel

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

the class GeneralAlgorithmRunner method execute.

// ============================PUBLIC METHODS==========================//
@Override
public void execute() {
    List<Graph> graphList = new ArrayList<>();
    int i = 0;
    if (getDataModelList().isEmpty()) {
        if (getSourceGraph() != null) {
            Algorithm algo = getAlgorithm();
            if (algo instanceof HasKnowledge) {
                ((HasKnowledge) algo).setKnowledge(getKnowledge());
            }
            graphList.add(algo.search(null, parameters));
        } else {
            throw new IllegalArgumentException("The parent boxes did not include any datasets or graphs. Try opening\n" + "the editors for those boxes and loading or simulating them.");
        }
    } else {
        if (getAlgorithm() instanceof MultiDataSetAlgorithm) {
            for (int k = 0; k < parameters.getInt("numRuns"); k++) {
                List<DataSet> dataSets = getDataModelList().stream().map(e -> (DataSet) e).collect(Collectors.toCollection(ArrayList::new));
                if (dataSets.size() < parameters.getInt("randomSelectionSize")) {
                    throw new IllegalArgumentException("Sorry, the 'random selection size' is greater than " + "the number of data sets.");
                }
                Collections.shuffle(dataSets);
                List<DataModel> sub = new ArrayList<>();
                for (int j = 0; j < parameters.getInt("randomSelectionSize"); j++) {
                    sub.add(dataSets.get(j));
                }
                Algorithm algo = getAlgorithm();
                if (algo instanceof HasKnowledge) {
                    ((HasKnowledge) algo).setKnowledge(getKnowledge());
                }
                graphList.add(((MultiDataSetAlgorithm) algo).search(sub, parameters));
            }
        } else if (getAlgorithm() instanceof ClusterAlgorithm) {
            for (int k = 0; k < parameters.getInt("numRuns"); k++) {
                getDataModelList().forEach(dataModel -> {
                    if (dataModel instanceof ICovarianceMatrix) {
                        ICovarianceMatrix dataSet = (ICovarianceMatrix) dataModel;
                        graphList.add(algorithm.search(dataSet, parameters));
                    } else if (dataModel instanceof DataSet) {
                        DataSet dataSet = (DataSet) dataModel;
                        if (!dataSet.isContinuous()) {
                            throw new IllegalArgumentException("Sorry, you need a continuous dataset for a cluster algorithm.");
                        }
                        graphList.add(algorithm.search(dataSet, parameters));
                    }
                });
            }
        } else {
            getDataModelList().forEach(data -> {
                IKnowledge knowledgeFromData = data.getKnowledge();
                if (!(knowledgeFromData == null || knowledgeFromData.getVariables().isEmpty())) {
                    this.knowledge = knowledgeFromData;
                }
                Algorithm algo = getAlgorithm();
                if (algo instanceof HasKnowledge) {
                    ((HasKnowledge) algo).setKnowledge(getKnowledge());
                }
                DataType algDataType = algo.getDataType();
                if (data.isContinuous() && (algDataType == DataType.Continuous || algDataType == DataType.Mixed)) {
                    graphList.add(algo.search(data, parameters));
                } else if (data.isDiscrete() && (algDataType == DataType.Discrete || algDataType == DataType.Mixed)) {
                    graphList.add(algo.search(data, parameters));
                } else if (data.isMixed() && algDataType == DataType.Mixed) {
                    graphList.add(algo.search(data, parameters));
                } else {
                    throw new IllegalArgumentException("The type of data changed; try opening up the search editor and " + "running the algorithm there.");
                }
            });
        }
    }
    if (getKnowledge().getVariablesNotInTiers().size() < getKnowledge().getVariables().size()) {
        for (Graph graph : graphList) {
            SearchGraphUtils.arrangeByKnowledgeTiers(graph, getKnowledge());
        }
    } else {
        for (Graph graph : graphList) {
            GraphUtils.circleLayout(graph, 225, 200, 150);
        }
    }
    this.graphList = graphList;
}

Example 28 with DataModel

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

the class SubsetDiscreteVariablesAction method actionPerformed.

/**
 * Performs the action of loading a session from a file.
 */
public void actionPerformed(ActionEvent e) {
    DataModel selectedDataModel = getDataEditor().getSelectedDataModel();
    if (selectedDataModel instanceof DataSet) {
        DataSet dataSet = (DataSet) selectedDataModel;
        for (int i = dataSet.getNumColumns(); i >= 0; i--) {
            if (dataSet.getVariable(i) instanceof DiscreteVariable) {
                dataSet.removeColumn(i);
            }
        }
        DataModelList list = new DataModelList();
        list.add(dataSet);
        getDataEditor().reset(list);
        getDataEditor().selectFirstTab();
    } else {
        JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "Requires a tabular data set.");
    }
}

Example 29 with DataModel

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

the class ShiftDataParamsEditor method setup.

/**
 * Builds the panel.
 */
public void setup() {
    DataModelList dataModelList = null;
    for (Object parentModel : parentModels) {
        if (parentModel instanceof DataWrapper) {
            DataWrapper dataWrapper = (DataWrapper) parentModel;
            dataModelList = dataWrapper.getDataModelList();
        }
    }
    if (dataModelList == null) {
        throw new NullPointerException("Null data model list.");
    }
    for (DataModel model : dataModelList) {
        if (!(model instanceof DataSet)) {
            JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "For the shift search, all of the data in the data box must be in the form of data sets.");
            return;
        }
    }
    final List<DataModel> dataSets = new ArrayList<>();
    for (Object aDataModelList : dataModelList) {
        dataSets.add((DataSet) aDataModelList);
    }
    SpinnerModel maxVarsModel = new SpinnerNumberModel(Preferences.userRoot().getInt("shiftSearchMaxNumShifts", 3), 1, 50, 1);
    JSpinner maxVarsSpinner = new JSpinner(maxVarsModel);
    maxVarsSpinner.setMaximumSize(maxVarsSpinner.getPreferredSize());
    maxVarsSpinner.addChangeListener(new ChangeListener() {

        public void stateChanged(ChangeEvent e) {
            JSpinner spinner = (JSpinner) e.getSource();
            SpinnerNumberModel model = (SpinnerNumberModel) spinner.getModel();
            int value = (Integer) model.getValue();
            Preferences.userRoot().putInt("shiftSearchMaxNumShifts", value);
        }
    });
    SpinnerModel maxShiftModel = new SpinnerNumberModel(Preferences.userRoot().getInt("shiftSearchMaxShift", 2), 1, 50, 1);
    JSpinner maxShiftSpinner = new JSpinner(maxShiftModel);
    maxShiftSpinner.setMaximumSize(maxShiftSpinner.getPreferredSize());
    maxShiftSpinner.addChangeListener(new ChangeListener() {

        public void stateChanged(ChangeEvent e) {
            JSpinner spinner = (JSpinner) e.getSource();
            SpinnerNumberModel model = (SpinnerNumberModel) spinner.getModel();
            int value = (Integer) model.getValue();
            Preferences.userRoot().putInt("shiftSearchMaxShift", value);
        }
    });
    JButton searchButton = new JButton("Search");
    final JButton stopButton = new JButton("Stop");
    final JTextArea textArea = new JTextArea();
    JScrollPane textScroll = new JScrollPane(textArea);
    textScroll.setPreferredSize(new Dimension(500, 200));
    searchButton.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent actionEvent) {
            final Thread thread = new Thread() {

                public void run() {
                    textArea.setText("");
                    doShiftSearch(dataSets, textArea);
                }
            };
            thread.start();
        }
    });
    stopButton.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent actionEvent) {
            if (search != null) {
                search.stop();
                TaskManager.getInstance().setCanceled(true);
            }
        }
    });
    JComboBox directionBox = new JComboBox(new String[] { "forward", "backward" });
    directionBox.setSelectedItem(params.getBoolean("forwardSearch", true) ? "forward" : "backward");
    directionBox.setMaximumSize(directionBox.getPreferredSize());
    directionBox.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent actionEvent) {
            JComboBox source = (JComboBox) actionEvent.getSource();
            String selected = (String) source.getSelectedItem();
            params.set("forwardSearch", "forward".equals(selected));
        }
    });
    Box b1 = Box.createVerticalBox();
    Box b2 = Box.createHorizontalBox();
    b2.add(new JLabel("Maximum number of variables in shift set is: "));
    b2.add(maxVarsSpinner);
    b2.add(Box.createHorizontalGlue());
    b1.add(b2);
    Box b3 = Box.createHorizontalBox();
    b3.add(new JLabel("Maximum "));
    b3.add(directionBox);
    b3.add(new JLabel(" shift: "));
    b3.add(maxShiftSpinner);
    b3.add(Box.createHorizontalGlue());
    b1.add(b3);
    Box b4 = Box.createHorizontalBox();
    b4.add(new JLabel("Output:"));
    b4.add(Box.createHorizontalGlue());
    b1.add(b4);
    Box b5 = Box.createHorizontalBox();
    b5.add(textScroll);
    b1.add(b5);
    Box b6 = Box.createHorizontalBox();
    b6.add(searchButton);
    b6.add(stopButton);
    b1.add(b6);
    final Box a1 = Box.createVerticalBox();
    Box a2 = Box.createHorizontalBox();
    a2.add(new JLabel("Specify the shift (positive or negative) for each variable:"));
    a2.add(Box.createHorizontalGlue());
    a1.add(a2);
    a1.add(Box.createVerticalStrut(20));
    setUpA1(dataSets, a1);
    JTabbedPane tabbedPane = new JTabbedPane();
    tabbedPane.addTab("Shift", new JScrollPane(a1));
    tabbedPane.addTab("Search", new JScrollPane(b1));
    add(tabbedPane, BorderLayout.CENTER);
    tabbedPane.addChangeListener(new ChangeListener() {

        public void stateChanged(ChangeEvent changeEvent) {
            System.out.println("a1 shown");
            a1.removeAll();
            setUpA1(dataSets, a1);
        }
    });
}

Example 30 with DataModel

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

the class SplitCasesAction method actionPerformed.

/**
 * Performs the action of loading a session from a file.
 */
public void actionPerformed(ActionEvent e) {
    DataModel selectedDataModel = getDataEditor().getSelectedDataModel();
    if (!(selectedDataModel instanceof DataSet)) {
        JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "Requires a tabular data set.");
    }
    List<Node> selectedVariables = new LinkedList<>();
    DataSet dataSet = (DataSet) selectedDataModel;
    int numColumns = dataSet.getNumColumns();
    for (int i = 0; i < numColumns; i++) {
        Node variable = dataSet.getVariable(i);
        if (dataSet.isSelected(variable)) {
            selectedVariables.add(variable);
        }
    }
    if (dataSet.getNumRows() == 0) {
        JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "Data set is empty.");
        return;
    }
    if (selectedVariables.isEmpty()) {
        selectedVariables.addAll(dataSet.getVariables());
    }
// 
// ParamsEditor editor = new ParamsEditor(dataSet, 3);
// 
// int ret = JOptionPane.showOptionDialog(JOptionUtils.centeringComp(),
// editor, "Split Data by Cases", JOptionPane.OK_CANCEL_OPTION,
// JOptionPane.PLAIN_MESSAGE, null, null, null);
// 
// if (ret == JOptionPane.CANCEL_OPTION) {
// return;
// }
// 
// DataModelList list = editor.getSplits();
// getDataEditor().reset(list);
// getDataEditor().selectLastTab();
}