Examples with Parameters edu.cmu.tetrad.util.Parameters used on opensource projects

Example 56 with Parameters

use of edu.cmu.tetrad.util.Parameters in project tetrad by cmu-phil.

the class VcpcFastRunner method execute.

// ===================PUBLIC METHODS OVERRIDING ABSTRACT================//
public void execute() {
    IKnowledge knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    Parameters searchParams = getParams();
    Parameters params = searchParams;
    VcpcFast fvcpc = new VcpcFast(getIndependenceTest());
    fvcpc.setKnowledge(knowledge);
    fvcpc.setAggressivelyPreventCycles(this.isAggressivelyPreventCycles());
    fvcpc.setDepth(params.getInt("depth", -1));
    if (independenceFactsModel != null) {
        fvcpc.setFacts(independenceFactsModel.getFacts());
    }
    Graph graph = fvcpc.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);
    setVcpcFastFields(fvcpc);
}

Example 57 with Parameters

use of edu.cmu.tetrad.util.Parameters in project tetrad by cmu-phil.

the class WFgesRunner method getParamSettings.

@Override
public Map<String, String> getParamSettings() {
    super.getParamSettings();
    Parameters params = getParams();
    paramSettings.put("Penalty Discount", new DecimalFormat("0.0").format(params.getDouble("penaltyDiscount", 4)));
    return paramSettings;
}

Example 58 with Parameters

use of edu.cmu.tetrad.util.Parameters in project tetrad by cmu-phil.

the class WFgesRunner method execute.

// ============================PUBLIC METHODS==========================//
/**
 * Executes the algorithm, producing (at least) a result workbench. Must be
 * implemented in the extending class.
 */
public void execute() {
    System.out.println("A");
    DataSet dataSet = (DataSet) getDataModel();
    Parameters params = getParams();
    double penaltyDiscount = params.getDouble("penaltyDiscount", 4);
    WFges fges = new WFges(dataSet);
    fges.setPenaltyDiscount(penaltyDiscount);
    Graph graph = fges.search();
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
    } else if (((IKnowledge) getParams().get("knowledge", new Knowledge2())).isDefaultToKnowledgeLayout()) {
        SearchGraphUtils.arrangeByKnowledgeTiers(graph, (IKnowledge) getParams().get("knowledge", new Knowledge2()));
    } else {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
    setResultGraph(graph);
    this.topGraphs = new ArrayList<>();
    topGraphs.add(new ScoredGraph(getResultGraph(), Double.NaN));
    setIndex(topGraphs.size() - 1);
}

Example 59 with Parameters

use of edu.cmu.tetrad.util.Parameters in project tetrad by cmu-phil.

the class RequiredGraphModel method createKnowledge.

private void createKnowledge(Parameters params) {
    IKnowledge knwl = getKnowledge();
    if (knwl == null) {
        return;
    }
    knwl.clear();
    List<String> varNames = getVarNames();
    getKnowledgeBoxInput().getVariableNames().stream().filter(e -> !e.startsWith("E_")).forEach(e -> {
        varNames.add(e);
        knwl.addVariable(e);
    });
    if (resultGraph == null) {
        throw new NullPointerException("I couldn't find a parent graph.");
    }
    List<Node> nodes = resultGraph.getNodes();
    int numOfNodes = nodes.size();
    for (int i = 0; i < numOfNodes; i++) {
        for (int j = i + 1; j < numOfNodes; j++) {
            Node n1 = nodes.get(i);
            Node n2 = nodes.get(j);
            if (n1.getName().startsWith("E_") || n2.getName().startsWith("E_")) {
                continue;
            }
            Edge edge = resultGraph.getEdge(n1, n2);
            if (edge == null) {
                continue;
            } else if (edge.isDirected()) {
                knwl.setRequired(edge.getNode1().getName(), edge.getNode2().getName());
            } else if (Edges.isUndirectedEdge(edge)) {
                knwl.setRequired(n1.getName(), n2.getName());
                knwl.setRequired(n2.getName(), n1.getName());
            }
        }
    }
}

Example 60 with Parameters

use of edu.cmu.tetrad.util.Parameters in project tetrad by cmu-phil.

the class SampleVcpcRunner method execute.

// ===================PUBLIC METHODS OVERRIDING ABSTRACT================//
public void execute() {
    IKnowledge knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    Parameters searchParams = getParams();
    Parameters params = searchParams;
    SampleVcpc svcpc = new SampleVcpc(getIndependenceTest());
    svcpc.setKnowledge(knowledge);
    svcpc.setAggressivelyPreventCycles(this.isAggressivelyPreventCycles());
    svcpc.setDepth(params.getInt("depth", -1));
    if (independenceFactsModel != null) {
        svcpc.setFacts(independenceFactsModel.getFacts());
    }
    // vcpc.setSemPm(semPm);
    // 
    // if (semPm != null) {
    // vcpc.setSemPm(getSemPm());
    // }
    svcpc.setSemIm(semIm);
    if (semIm != null) {
        svcpc.setSemIm(this.semIm);
    }
    Graph graph = svcpc.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);
    setSvcpcFields(svcpc);
}