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

Example 31 with DataModel

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

the class SubsetContinuousVariablesAction 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;
        List variables = dataSet.getVariables();
        int n = 0;
        for (Object variable : variables) {
            if (variable instanceof ContinuousVariable) {
                n++;
            }
        }
        if (n == 0) {
            JOptionPane.showMessageDialog(getDataEditor(), "There are no continuous variables in this data set.");
            return;
        }
        int[] indices = new int[n];
        int m = -1;
        for (int i = 0; i < variables.size(); i++) {
            if (variables.get(i) instanceof ContinuousVariable) {
                indices[++m] = i;
            }
        }
        dataSet = dataSet.subsetColumns(indices);
        DataModelList list = new DataModelList();
        list.add(dataSet);
        getDataEditor().reset(list);
        getDataEditor().selectFirstTab();
    } else {
        JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "Requires a tabular data set.");
    }
}

Example 32 with DataModel

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

the class SplitCasesParamsEditor method setParentModels.

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 33 with DataModel

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

the class SearchParamEditor 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 it = graph.getNodes().iterator();
        varNames = new ArrayList();
        Node temp;
        while (it.hasNext()) {
            temp = (Node) 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);
                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 {
                    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 b0 = Box.createHorizontalBox();
        b0.add(new JLabel("Alpha Value:"));
        b0.add(Box.createGlue());
        b0.add(alphaField);
        add(b0);
        add(Box.createVerticalStrut(10));
    }
    Box b1 = Box.createHorizontalBox();
    b1.add(new JLabel("Search Depth:"));
    b1.add(Box.createGlue());
    b1.add(depthField);
    add(b1);
    add(Box.createVerticalStrut(10));
}

Example 34 with DataModel

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

the class TimeoutComparison method doRun.

private void doRun(List<AlgorithmSimulationWrapper> algorithmSimulationWrappers, List<AlgorithmWrapper> algorithmWrappers, List<SimulationWrapper> simulationWrappers, Statistics statistics, int numGraphTypes, double[][][][] allStats, Run run) {
    System.out.println();
    System.out.println("Run " + (run.getRunIndex() + 1));
    System.out.println();
    AlgorithmSimulationWrapper algorithmSimulationWrapper = algorithmSimulationWrappers.get(run.getAlgSimIndex());
    AlgorithmWrapper algorithmWrapper = algorithmSimulationWrapper.getAlgorithmWrapper();
    SimulationWrapper simulationWrapper = algorithmSimulationWrapper.getSimulationWrapper();
    DataModel data = simulationWrapper.getDataModel(run.getRunIndex());
    Graph trueGraph = simulationWrapper.getTrueGraph(run.getRunIndex());
    System.out.println((run.getAlgSimIndex() + 1) + ". " + algorithmWrapper.getDescription() + " simulationWrapper: " + simulationWrapper.getDescription());
    long start = System.currentTimeMillis();
    Graph out;
    try {
        Algorithm algorithm = algorithmWrapper.getAlgorithm();
        Simulation simulation = simulationWrapper.getSimulation();
        if (algorithm instanceof HasKnowledge && simulation instanceof HasKnowledge) {
            ((HasKnowledge) algorithm).setKnowledge(((HasKnowledge) simulation).getKnowledge());
        }
        if (algorithmWrapper.getAlgorithm() instanceof ExternalAlgorithm) {
            ExternalAlgorithm external = (ExternalAlgorithm) algorithmWrapper.getAlgorithm();
            external.setSimulation(simulationWrapper.getSimulation());
            external.setPath(resultsPath);
            external.setSimIndex(simulationWrappers.indexOf(simulationWrapper));
        }
        if (algorithm instanceof MultiDataSetAlgorithm) {
            List<Integer> indices = new ArrayList<>();
            int numDataModels = simulationWrapper.getSimulation().getNumDataModels();
            for (int i = 0; i < numDataModels; i++) {
                indices.add(i);
            }
            Collections.shuffle(indices);
            List<DataModel> dataModels = new ArrayList<>();
            int randomSelectionSize = algorithmWrapper.getAlgorithmSpecificParameters().getInt("randomSelectionSize");
            for (int i = 0; i < Math.min(numDataModels, randomSelectionSize); i++) {
                dataModels.add(simulationWrapper.getSimulation().getDataModel(indices.get(i)));
            }
            Parameters _params = algorithmWrapper.getAlgorithmSpecificParameters();
            out = ((MultiDataSetAlgorithm) algorithm).search(dataModels, _params);
        } else {
            DataModel dataModel = copyData ? data.copy() : data;
            Parameters _params = algorithmWrapper.getAlgorithmSpecificParameters();
            out = algorithm.search(dataModel, _params);
        }
    } catch (Exception e) {
        System.out.println("Could not run " + algorithmWrapper.getDescription());
        e.printStackTrace();
        return;
    }
    int simIndex = simulationWrappers.indexOf(simulationWrapper) + 1;
    int algIndex = algorithmWrappers.indexOf(algorithmWrapper) + 1;
    long stop = System.currentTimeMillis();
    long elapsed = stop - start;
    saveGraph(resultsPath, out, run.getRunIndex(), simIndex, algIndex, algorithmWrapper, elapsed);
    if (trueGraph != null) {
        out = GraphUtils.replaceNodes(out, trueGraph.getNodes());
    }
    if (algorithmWrapper.getAlgorithm() instanceof ExternalAlgorithm) {
        ExternalAlgorithm extAlg = (ExternalAlgorithm) algorithmWrapper.getAlgorithm();
        extAlg.setSimIndex(simulationWrappers.indexOf(simulationWrapper));
        extAlg.setSimulation(simulationWrapper.getSimulation());
        extAlg.setPath(resultsPath);
        elapsed = extAlg.getElapsedTime(data, simulationWrapper.getSimulationSpecificParameters());
    }
    Graph[] est = new Graph[numGraphTypes];
    Graph comparisonGraph;
    if (this.comparisonGraph == ComparisonGraph.true_DAG) {
        comparisonGraph = new EdgeListGraph(trueGraph);
    } else if (this.comparisonGraph == ComparisonGraph.Pattern_of_the_true_DAG) {
        comparisonGraph = SearchGraphUtils.patternForDag(new EdgeListGraph(trueGraph));
    } else if (this.comparisonGraph == ComparisonGraph.PAG_of_the_true_DAG) {
        comparisonGraph = new DagToPag(new EdgeListGraph(trueGraph)).convert();
    } else {
        throw new IllegalArgumentException("Unrecognized graph type.");
    }
    // Graph comparisonGraph = trueGraph == null ? null : algorithmSimulationWrapper.getComparisonGraph(trueGraph);
    est[0] = out;
    graphTypeUsed[0] = true;
    if (data.isMixed()) {
        est[1] = getSubgraph(out, true, true, data);
        est[2] = getSubgraph(out, true, false, data);
        est[3] = getSubgraph(out, false, false, data);
        graphTypeUsed[1] = true;
        graphTypeUsed[2] = true;
        graphTypeUsed[3] = true;
    }
    Graph[] truth = new Graph[numGraphTypes];
    truth[0] = comparisonGraph;
    if (data.isMixed() && comparisonGraph != null) {
        truth[1] = getSubgraph(comparisonGraph, true, true, data);
        truth[2] = getSubgraph(comparisonGraph, true, false, data);
        truth[3] = getSubgraph(comparisonGraph, false, false, data);
    }
    if (comparisonGraph != null) {
        for (int u = 0; u < numGraphTypes; u++) {
            if (!graphTypeUsed[u]) {
                continue;
            }
            int statIndex = -1;
            for (Statistic _stat : statistics.getStatistics()) {
                statIndex++;
                if (_stat instanceof ParameterColumn) {
                    continue;
                }
                double stat;
                if (_stat instanceof ElapsedTime) {
                    stat = elapsed / 1000.0;
                } else {
                    stat = _stat.getValue(truth[u], est[u]);
                }
                allStats[u][run.getAlgSimIndex()][statIndex][run.getRunIndex()] = stat;
            }
        }
    }
}

Example 35 with DataModel

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

the class GeneralAlgorithmEditor method doRemoteCompute.

private void doRemoteCompute(final GeneralAlgorithmRunner runner, final HpcAccount hpcAccount) throws Exception {
    // **********************
    // Show progress panel *
    // **********************
    Frame ancestor = (Frame) JOptionUtils.centeringComp().getTopLevelAncestor();
    final JDialog progressDialog = new JDialog(ancestor, "HPC Job Submission's Progress...", false);
    Dimension progressDim = new Dimension(500, 150);
    JTextArea progressTextArea = new JTextArea();
    progressTextArea.setPreferredSize(progressDim);
    progressTextArea.setEditable(false);
    JScrollPane progressScroller = new JScrollPane(progressTextArea);
    progressScroller.setAlignmentX(LEFT_ALIGNMENT);
    progressDialog.setLayout(new BorderLayout());
    progressDialog.getContentPane().add(progressScroller, BorderLayout.CENTER);
    progressDialog.pack();
    Dimension screenDim = Toolkit.getDefaultToolkit().getScreenSize();
    progressDialog.setLocation((screenDim.width - progressDim.width) / 2, (screenDim.height - progressDim.height) / 2);
    progressDialog.setVisible(true);
    int totalProcesses = 4;
    String newline = "\n";
    String tab = "\t";
    int progressTextLength = 0;
    DataModel dataModel = runner.getDataModel();
    // 1. Generate temp file
    Path file = null;
    Path prior = null;
    try {
        // ****************************
        // Data Preparation Progress *
        // ****************************
        String dataMessage = String.format("1/%1$d Data Preparation", totalProcesses);
        progressTextArea.append(dataMessage);
        progressTextArea.append(tab);
        progressTextLength = progressTextArea.getText().length();
        progressTextArea.append("Preparing...");
        progressTextArea.updateUI();
        file = Files.createTempFile("Tetrad-data-", ".txt");
        // LOGGER.info(file.toAbsolutePath().toString());
        List<String> tempLine = new ArrayList<>();
        // Header
        List<Node> variables = dataModel.getVariables();
        if ((variables == null || variables.isEmpty()) && runner.getSourceGraph() != null) {
            variables = runner.getSourceGraph().getNodes();
        }
        String vars = StringUtils.join(variables.toArray(), tab);
        tempLine.add(vars);
        // Data
        DataSet dataSet = (DataSet) dataModel;
        for (int i = 0; i < dataSet.getNumRows(); i++) {
            String line = null;
            for (int j = 0; j < dataSet.getNumColumns(); j++) {
                String cell = null;
                if (dataSet.isContinuous()) {
                    cell = String.valueOf(dataSet.getDouble(i, j));
                } else {
                    cell = String.valueOf(dataSet.getInt(i, j));
                }
                if (line == null) {
                    line = cell;
                } else {
                    line = line + "\t" + cell;
                }
            }
            tempLine.add(line);
        }
        // for (String line : tempLine) {
        // LOGGER.info(line);
        // }
        Files.write(file, tempLine);
        // Get file's MD5 hash and use it as its identifier
        String datasetMd5 = MessageDigestHash.computeMD5Hash(file);
        progressTextArea.replaceRange("Done", progressTextLength, progressTextArea.getText().length());
        progressTextArea.append(newline);
        progressTextArea.updateUI();
        // ***************************************
        // Prior Knowledge Preparation Progress *
        // ***************************************
        String priorMessage = String.format("2/%1$d Prior Knowledge Preparation", totalProcesses);
        progressTextArea.append(priorMessage);
        progressTextArea.append(tab);
        progressTextLength = progressTextArea.getText().length();
        progressTextArea.append("Preparing...");
        progressTextArea.updateUI();
        // 2. Generate temp prior knowledge file
        Knowledge2 knowledge = (Knowledge2) dataModel.getKnowledge();
        if (knowledge != null && !knowledge.isEmpty()) {
            prior = Files.createTempFile(file.getFileName().toString(), ".prior");
            knowledge.saveKnowledge(Files.newBufferedWriter(prior));
            progressTextArea.replaceRange("Done", progressTextLength, progressTextArea.getText().length());
            progressTextArea.append(newline);
            progressTextArea.updateUI();
        } else {
            progressTextArea.replaceRange("Skipped", progressTextLength, progressTextArea.getText().length());
            progressTextArea.append(newline);
            progressTextArea.updateUI();
        }
        // Get knowledge file's MD5 hash and use it as its identifier
        String priorKnowledgeMd5 = null;
        if (prior != null) {
            priorKnowledgeMd5 = MessageDigestHash.computeMD5Hash(prior);
        }
        // *******************************************
        // Algorithm Parameter Preparation Progress *
        // *******************************************
        String algorMessage = String.format("3/%1$d Algorithm Preparation", totalProcesses);
        progressTextArea.append(algorMessage);
        progressTextArea.append(tab);
        progressTextLength = progressTextArea.getText().length();
        progressTextArea.append("Preparing...");
        progressTextArea.updateUI();
        // 3.1 Algorithm Id, Independent Test Id, Score Id
        AlgorithmModel algoModel = algorithmList.getSelectedValue();
        String algoId = algoModel.getAlgorithm().getAnnotation().command();
        // Test
        String testId = null;
        if (indTestComboBox.isEnabled()) {
            IndependenceTestModel indTestModel = indTestComboBox.getItemAt(indTestComboBox.getSelectedIndex());
            testId = indTestModel.getIndependenceTest().getAnnotation().command();
        }
        // Score
        String scoreId = null;
        if (scoreComboBox.isEnabled()) {
            ScoreModel scoreModel = scoreComboBox.getItemAt(scoreComboBox.getSelectedIndex());
            scoreId = scoreModel.getScore().getAnnotation().command();
        }
        // 3.2 Parameters
        AlgorithmParamRequest algorithmParamRequest = new AlgorithmParamRequest();
        // Test and score
        algorithmParamRequest.setTestId(testId);
        algorithmParamRequest.setScoreId(scoreId);
        // Dataset and Prior paths
        String datasetPath = file.toAbsolutePath().toString();
        LOGGER.info(datasetPath);
        algorithmParamRequest.setDatasetPath(datasetPath);
        algorithmParamRequest.setDatasetMd5(datasetMd5);
        if (prior != null) {
            String priorKnowledgePath = prior.toAbsolutePath().toString();
            LOGGER.info(priorKnowledgePath);
            algorithmParamRequest.setPriorKnowledgePath(priorKnowledgePath);
            algorithmParamRequest.setPriorKnowledgeMd5(priorKnowledgeMd5);
        }
        // VariableType
        if (dataModel.isContinuous()) {
            algorithmParamRequest.setVariableType("continuous");
        } else if (dataModel.isDiscrete()) {
            algorithmParamRequest.setVariableType("discrete");
        } else {
            algorithmParamRequest.setVariableType("mixed");
        }
        // FileDelimiter
        // Pre-determined
        String fileDelimiter = "tab";
        algorithmParamRequest.setFileDelimiter(fileDelimiter);
        Set<AlgorithmParameter> AlgorithmParameters = new HashSet<>();
        Parameters parameters = runner.getParameters();
        List<String> parameterNames = runner.getAlgorithm().getParameters();
        for (String parameter : parameterNames) {
            String value = parameters.get(parameter).toString();
            LOGGER.info("parameter: " + parameter + "\tvalue: " + value);
            if (value != null) {
                AlgorithmParameter algorParam = new AlgorithmParameter();
                algorParam.setParameter(parameter);
                algorParam.setValue(value);
                AlgorithmParameters.add(algorParam);
            }
        }
        algorithmParamRequest.setAlgorithmParameters(AlgorithmParameters);
        String maxHeapSize = null;
        do {
            maxHeapSize = JOptionPane.showInputDialog(progressDialog, "Enter Your Request Java Max Heap Size (GB):", "5");
        } while (maxHeapSize != null && !StringUtils.isNumeric(maxHeapSize));
        if (maxHeapSize != null) {
            JvmOptions jvmOptions = new JvmOptions();
            jvmOptions.setMaxHeapSize(Integer.parseInt(maxHeapSize));
            algorithmParamRequest.setJvmOptions(jvmOptions);
        }
        // Hpc parameters
        final HpcAccountManager hpcAccountManager = desktop.getHpcAccountManager();
        JsonWebToken jsonWebToken = HpcAccountUtils.getJsonWebToken(hpcAccountManager, hpcAccount);
        if (jsonWebToken.getWallTime() != null) {
            // User allowed to customize the job's wall time
            String[] wallTime = jsonWebToken.getWallTime();
            Object userwallTime = JOptionPane.showInputDialog(progressDialog, "Wall Time:", "Choose Your Wall Time (in Hour)", JOptionPane.QUESTION_MESSAGE, null, wallTime, wallTime[0]);
            if (wallTime != null && userwallTime != null) {
                HpcParameter hpcParameter = new HpcParameter();
                hpcParameter.setKey("walltime");
                hpcParameter.setValue(userwallTime.toString());
                LOGGER.info("walltime: " + userwallTime.toString());
                Set<HpcParameter> hpcParameters = new HashSet<>();
                hpcParameters.add(hpcParameter);
                algorithmParamRequest.setHpcParameters(hpcParameters);
            }
        }
        progressTextArea.replaceRange("Done", progressTextLength, progressTextArea.getText().length());
        progressTextArea.append(newline);
        progressTextArea.updateUI();
        // ********************************
        // Adding HPC Job Queue Progress *
        // ********************************
        String dbMessage = String.format("4/%1$d HPC Job Queue Submission", totalProcesses);
        progressTextArea.append(dbMessage);
        progressTextArea.append(tab);
        progressTextLength = progressTextArea.getText().length();
        progressTextArea.append("Preparing...");
        progressTextArea.updateUI();
        HpcJobManager hpcJobManager = desktop.getHpcJobManager();
        // 4.1 Save HpcJobInfo
        hpcJobInfo = new HpcJobInfo();
        hpcJobInfo.setAlgoId(algoId);
        hpcJobInfo.setAlgorithmParamRequest(algorithmParamRequest);
        hpcJobInfo.setStatus(-1);
        hpcJobInfo.setHpcAccount(hpcAccount);
        hpcJobManager.submitNewHpcJobToQueue(hpcJobInfo, this);
        progressTextArea.replaceRange("Done", progressTextLength, progressTextArea.getText().length());
        progressTextArea.append(newline);
        progressTextArea.updateUI();
        this.jsonResult = null;
        JOptionPane.showMessageDialog(ancestor, "The " + hpcJobInfo.getAlgoId() + " job on the " + hpcJobInfo.getHpcAccount().getConnectionName() + " node is in the queue successfully!");
    } catch (IOException exception) {
        LOGGER.error("", exception);
    } finally {
        progressDialog.setVisible(false);
        progressDialog.dispose();
    }
    (new HpcJobActivityAction("")).actionPerformed(null);
}