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

Example 11 with Knowledge2

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

the class CpcLocalRunner method getMeekRules.

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

Example 12 with Knowledge2

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

the class CpcLocalRunner method execute.

// ===================PUBLIC METHODS OVERRIDING ABSTRACT================//
public void execute() {
    IKnowledge knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    IndependenceTest independenceTest = getIndependenceTest();
    Parameters testParams = getParams();
    CpcLocal search = new CpcLocal(independenceTest);
    search.setAggressivelyPreventCycles(isAggressivelyPreventCycles());
    search.setKnowledge(knowledge);
    Graph graph = search.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);
}

Example 13 with Knowledge2

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

the class AbstractSearchEditor method execute.

/**
 * Executes the algorithm. The execution takes place inside a thread, so one
 * cannot count on a result graph having been found when the method
 */
void execute() {
    Window owner = (Window) getTopLevelAncestor();
    final WatchedProcess process = new WatchedProcess(owner) {

        public void watch() {
            try {
                getExecuteButton().setEnabled(false);
            } catch (Exception e) {
                throw new RuntimeException(e);
            }
            setErrorMessage(null);
            if (!knowledgeMessageShown) {
                Parameters searchParams = getAlgorithmRunner().getParams();
                if (searchParams != null) {
                    IKnowledge knowledge = (IKnowledge) searchParams.get("knowledge", new Knowledge2());
                    if (!knowledge.isEmpty()) {
                        JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "Using previously set knowledge. (To edit, use " + "the Knowledge menu.)");
                        knowledgeMessageShown = true;
                    }
                }
            }
            try {
                storeLatestWorkbenchGraph();
                getAlgorithmRunner().execute();
            } catch (Exception e) {
                CharArrayWriter writer1 = new CharArrayWriter();
                PrintWriter writer2 = new PrintWriter(writer1);
                e.printStackTrace(writer2);
                String message = writer1.toString();
                writer2.close();
                e.printStackTrace(System.out);
                TetradLogger.getInstance().error(message);
                String messageString = e.getMessage();
                if (e.getCause() != null) {
                    messageString = e.getCause().getMessage();
                }
                if (messageString == null) {
                    messageString = message;
                }
                setErrorMessage(messageString);
                TetradLogger.getInstance().error("************Algorithm stopped!");
                getExecuteButton().setEnabled(true);
                throw new RuntimeException(e);
            }
            // getWorkbenchScroll().setBorder(
            // new TitledBorder(getResultLabel()));
            Graph resultGraph = resultGraph();
            doDefaultArrangement(resultGraph);
            getWorkbench().setBackground(Color.WHITE);
            getWorkbench().setGraph(resultGraph);
            getGraphHistory().clear();
            getGraphHistory().add(resultGraph);
            getWorkbench().repaint();
            // For Mimbuild, e.g., that need to do a second stage.
            firePropertyChange("algorithmFinished", null, null);
            getExecuteButton().setEnabled(true);
            firePropertyChange("modelChanged", null, null);
        }
    };
    Thread watcher = new Thread() {

        public void run() {
            while (true) {
                try {
                    sleep(300);
                    if (!process.isAlive()) {
                        getExecuteButton().setEnabled(true);
                        return;
                    }
                } catch (InterruptedException e) {
                    getExecuteButton().setEnabled(true);
                    return;
                }
            }
        }
    };
    watcher.start();
}

Example 14 with Knowledge2

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

the class LingSearchEditor 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 15 with Knowledge2

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

the class LingSearchEditor method execute.

/**
 * Executes the algorithm. The execution takes place inside a thread, so one
 * cannot count on a result graph having been found when the method
 */
public void execute() {
    Window owner = (Window) getTopLevelAncestor();
    final WatchedProcess process = new WatchedProcess(owner) {

        public void watch() {
            getExecuteButton().setEnabled(false);
            setErrorMessage(null);
            if (!knowledgeMessageShown) {
                IKnowledge knowledge = (IKnowledge) getAlgorithmRunner().getParams().get("knowledge", new Knowledge2());
                if (!knowledge.isEmpty()) {
                    JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "Using previously set knowledge. (To edit, use " + "the Knowledge menu.)");
                    knowledgeMessageShown = true;
                }
            }
            try {
                storeLatestWorkbenchGraph();
                getAlgorithmRunner().execute();
                LingRunner runner = (LingRunner) getAlgorithmRunner();
                arrangeGraphs();
                lingDisplay.resetGraphs(runner.getStoredGraphs());
            } catch (Exception e) {
                CharArrayWriter writer1 = new CharArrayWriter();
                PrintWriter writer2 = new PrintWriter(writer1);
                e.printStackTrace(writer2);
                String message = writer1.toString();
                writer2.close();
                e.printStackTrace(System.out);
                TetradLogger.getInstance().error(message);
                String messageString = e.getMessage();
                if (e.getCause() != null) {
                    messageString = e.getCause().getMessage();
                }
                if (messageString == null) {
                    messageString = message;
                }
                setErrorMessage(messageString);
                TetradLogger.getInstance().error("************Algorithm stopped!");
                getExecuteButton().setEnabled(true);
                throw new RuntimeException(e);
            }
            getWorkbenchScroll().setBorder(new TitledBorder(getResultLabel()));
            Graph resultGraph = resultGraph();
            doDefaultArrangement(resultGraph);
            getWorkbench().setBackground(Color.WHITE);
            getWorkbench().setGraph(resultGraph);
            getGraphHistory().clear();
            getGraphHistory().add(resultGraph);
            getWorkbench().repaint();
            // For Mimbuild, e.g., that need to do a second stage.
            firePropertyChange("algorithmFinished", null, null);
            getExecuteButton().setEnabled(true);
            firePropertyChange("modelChanged", null, null);
        }
    };
    Thread watcher = new Thread() {

        public void run() {
            while (true) {
                try {
                    sleep(300);
                    if (!process.isAlive()) {
                        getExecuteButton().setEnabled(true);
                        return;
                    }
                } catch (InterruptedException e) {
                    getExecuteButton().setEnabled(true);
                    return;
                }
            }
        }
    };
    watcher.start();
}