Examples with Knowledge2 edu.cmu.tetrad.data.Knowledge2 used on opensource projects

Example 56 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class CpcRunner method getMeekRules.

public ImpliedOrientation getMeekRules() {
    MeekRules meekRules = new MeekRules();
    meekRules.setAggressivelyPreventCycles(this.isAggressivelyPreventCycles());
    meekRules.setKnowledge((IKnowledge) getParams().get("knowledge", new Knowledge2()));
    return meekRules;
}

Example 57 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class CpcRunner method execute.

// ===================PUBLIC METHODS OVERRIDING ABSTRACT================//
public void execute() {
    IKnowledge knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    if (trueGraph != null) {
        CpcOrienter orienter = new CpcOrienter(getIndependenceTest(), knowledge);
        Graph graph = GraphUtils.undirectedGraph(trueGraph);
        orienter.orient(graph);
        if (getSourceGraph() != null) {
            GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
        } else if (knowledge.isDefaultToKnowledgeLayout()) {
            SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
        } else {
            GraphUtils.circleLayout(graph, 200, 200, 150);
        }
        setResultGraph(graph);
    } else {
        Cpc cpc = new Cpc(getIndependenceTest());
        cpc.setKnowledge(knowledge);
        cpc.setAggressivelyPreventCycles(this.isAggressivelyPreventCycles());
        cpc.setDepth(getParams().getInt("depth", -1));
        Graph graph = cpc.search();
        if (getSourceGraph() != null) {
            GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
        } else if (knowledge.isDefaultToKnowledgeLayout()) {
            SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
        } else {
            GraphUtils.circleLayout(graph, 200, 200, 150);
        }
        setResultGraph(graph);
        setCpcFields(cpc);
    }
}

Example 58 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 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);
}

Example 59 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class GlassoSearchEditor method layoutByKnowledge.

public void layoutByKnowledge() {
    GraphWorkbench resultWorkbench = getWorkbench();
    Graph graph = resultWorkbench.getGraph();
    IKnowledge knowledge = (IKnowledge) getAlgorithmRunner().getParams().get("knowledge", new Knowledge2());
    SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
// resultWorkbench.setGraph(graph);
}

Example 60 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class TsFciRunner method execute.

// =================PUBLIC METHODS OVERRIDING ABSTRACT=================//
/**
 * Executes the algorithm, producing (at least) a result workbench. Must be
 * implemented in the extending class.
 */
public void execute() {
    if (this.knowledge == null) {
        knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    }
    /*else {knowledge = this.knowledge;}*/
    Parameters searchParams = getParams();
    Parameters params = searchParams;
    // Cfci fciSearch =
    // new Cfci(getIndependenceTest(), knowledge);
    // fciSearch.setMaxIndegree(params.depth());
    // Graph graph = fciSearch.search();
    // 
    // if (knowledge.isDefaultToKnowledgeLayout()) {
    // SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
    // }
    // 
    // setResultGraph(graph);
    Graph graph;
    if (params.getBoolean("rfciUsed", false)) {
        System.out.println("WARNING: there is no RFCI option for tsFCI! Just using tsFCI.");
        // Rfci fci = new Rfci(getIndependenceTest());
        TsFci fci = new TsFci(getIndependenceTest());
        fci.setKnowledge(knowledge);
        fci.setCompleteRuleSetUsed(true);
        fci.setMaxPathLength(params.getInt("maxReachablePathLength", -1));
        fci.setDepth(params.getInt("depth", -1));
        graph = fci.search();
    } else {
        TsFci fci = new TsFci(getIndependenceTest());
        fci.setKnowledge(knowledge);
        fci.setCompleteRuleSetUsed(true);
        fci.setPossibleDsepSearchDone(params.getBoolean("possibleDsepDone", true));
        fci.setMaxPathLength(params.getInt("maxReachablePathLength", -1));
        fci.setDepth(params.getInt("depth", -1));
        graph = fci.search();
    }
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
    } else if (knowledge.isDefaultToKnowledgeLayout()) {
        SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
    } else {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
    setResultGraph(graph);
}