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///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, //
// 2007, 2008, 2009, 2010, 2014, 2015, 2022 by Peter Spirtes, Richard //
// Scheines, Joseph Ramsey, and Clark Glymour. //
// //
// This program is free software; you can redistribute it and/or modify //
// it under the terms of the GNU General Public License as published by //
// the Free Software Foundation; either version 2 of the License, or //
// (at your option) any later version. //
// //
// This program is distributed in the hope that it will be useful, //
// but WITHOUT ANY WARRANTY; without even the implied warranty of //
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the //
// GNU General Public License for more details. //
// //
// You should have received a copy of the GNU General Public License //
// along with this program; if not, write to the Free Software //
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA //
///////////////////////////////////////////////////////////////////////////////
package edu.cmu.tetradapp.model;
import edu.cmu.tetrad.data.Knowledge;
import edu.cmu.tetrad.graph.*;
import edu.cmu.tetrad.search.Fci;
import edu.cmu.tetrad.search.IndependenceTest;
import edu.cmu.tetrad.search.Rfci;
import edu.cmu.tetrad.search.utils.GraphSearchUtils;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.TetradSerializableUtils;
import edu.cmu.tetradapp.util.IndTestType;
import edu.cmu.tetradapp.util.IonInput;
import java.util.ArrayList;
import java.util.List;
/**
* Extends AbstractAlgorithmRunner to produce a wrapper for the FCI algorithm.
*
* @author josephramsey
* @version $Id: $Id
*/
public class FciRunner extends AbstractAlgorithmRunner
implements IndTestProducer, IonInput {
private static final long serialVersionUID = 23L;
//=========================CONSTRUCTORS================================//
/**
* Constructor for FciRunner.
*
* @param dataWrapper a {@link edu.cmu.tetradapp.model.DataWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public FciRunner(DataWrapper dataWrapper, Parameters params) {
super(dataWrapper, params, null);
}
/**
* Constucts a wrapper for the given EdgeListGraph.
*
* @param graphWrapper a {@link edu.cmu.tetradapp.model.GraphSource} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
* @param knowledgeBoxModel a {@link edu.cmu.tetradapp.model.KnowledgeBoxModel} object
*/
public FciRunner(GraphSource graphWrapper, Parameters params, KnowledgeBoxModel knowledgeBoxModel) {
super(graphWrapper.getGraph(), params, knowledgeBoxModel);
}
/**
* Constructor for FciRunner.
*
* @param dataWrapper a {@link edu.cmu.tetradapp.model.DataWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
* @param knowledgeBoxModel a {@link edu.cmu.tetradapp.model.KnowledgeBoxModel} object
*/
public FciRunner(DataWrapper dataWrapper, Parameters params, KnowledgeBoxModel knowledgeBoxModel) {
super(dataWrapper, params, knowledgeBoxModel);
}
/**
* Constructor for FciRunner.
*
* @param graph a {@link edu.cmu.tetrad.graph.Graph} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public FciRunner(Graph graph, Parameters params) {
super(graph, params);
}
/**
* Constructor for FciRunner.
*
* @param graph a {@link edu.cmu.tetrad.graph.Graph} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
* @param knowledgeBoxModel a {@link edu.cmu.tetradapp.model.KnowledgeBoxModel} object
*/
public FciRunner(Graph graph, Parameters params, KnowledgeBoxModel knowledgeBoxModel) {
super(graph, params, knowledgeBoxModel);
}
/**
* Constructor for FciRunner.
*
* @param graphWrapper a {@link edu.cmu.tetradapp.model.GraphWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public FciRunner(GraphWrapper graphWrapper, Parameters params) {
super(graphWrapper.getGraph(), params);
}
/**
* Constructor for FciRunner.
*
* @param dagWrapper a {@link edu.cmu.tetradapp.model.DagWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public FciRunner(DagWrapper dagWrapper, Parameters params) {
super(dagWrapper.getDag(), params);
}
/**
* Constructor for FciRunner.
*
* @param dagWrapper a {@link edu.cmu.tetradapp.model.SemGraphWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public FciRunner(SemGraphWrapper dagWrapper, Parameters params) {
super(dagWrapper.getGraph(), params);
}
/**
* Constructor for FciRunner.
*
* @param model a {@link edu.cmu.tetradapp.model.IndependenceFactsModel} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public FciRunner(IndependenceFactsModel model, Parameters params) {
super(model, params, null);
}
/**
* Constructor for FciRunner.
*
* @param model a {@link edu.cmu.tetradapp.model.IndependenceFactsModel} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
* @param knowledgeBoxModel a {@link edu.cmu.tetradapp.model.KnowledgeBoxModel} object
*/
public FciRunner(IndependenceFactsModel model, Parameters params, KnowledgeBoxModel knowledgeBoxModel) {
super(model, params, knowledgeBoxModel);
}
/**
* Generates a simple exemplar of this class to test serialization.
*
* @return a {@link edu.cmu.tetradapp.model.FciRunner} object
* @see TetradSerializableUtils
*/
public static FciRunner serializableInstance() {
return new FciRunner(Dag.serializableInstance(), new Parameters());
}
//=================PUBLIC METHODS OVERRIDING ABSTRACT=================//
/**
* Executes the algorithm, producing (at least) a result workbench. Must be implemented in the extending class.
*/
public void execute() {
Knowledge knowledge = (Knowledge) getParams().get("knowledge", new Knowledge());
Graph graph;
if (getParams().getBoolean("rfciUsed", false)) {
Rfci fci = new Rfci(getIndependenceTest());
fci.setKnowledge(knowledge);
fci.setMaxDiscriminatingPathLength(getParams().getInt("maxReachablePathLength", -1));
fci.setDepth(getParams().getInt("depth", -1));
try {
graph = fci.search();
} catch (InterruptedException e) {
throw new RuntimeException(e);
}
} else {
Fci fci = new Fci(getIndependenceTest());
fci.setKnowledge(knowledge);
fci.setCompleteRuleSetUsed(getParams().getBoolean("completeRuleSetUsed", false));
fci.setPossibleDsepSearchDone(getParams().getBoolean("possibleMsepDone", true));
fci.setMaxDiscriminatingPathLength(getParams().getInt("maxReachablePathLength", -1));
fci.setDepth(getParams().getInt("depth", -1));
try {
graph = fci.search();
} catch (InterruptedException e) {
throw new RuntimeException(e);
}
}
if (getSourceGraph() != null) {
LayoutUtil.arrangeBySourceGraph(graph, getSourceGraph());
} else if (knowledge.isDefaultToKnowledgeLayout()) {
GraphSearchUtils.arrangeByKnowledgeTiers(graph, knowledge);
} else {
LayoutUtil.defaultLayout(graph);
}
setResultGraph(graph);
}
/**
* getIndependenceTest.
*
* @return a {@link edu.cmu.tetrad.search.IndependenceTest} object
*/
public IndependenceTest getIndependenceTest() {
Object dataModel = getDataModel();
if (dataModel == null) {
dataModel = getSourceGraph();
}
Parameters params = getParams();
IndTestType testType;
testType = (IndTestType) params.get("indTestType", IndTestType.FISHER_Z);
return new IndTestChooser().getTest(dataModel, params, testType);
}
/**
* getGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getGraph() {
return getResultGraph();
}
/**
* getTriplesClassificationTypes.
*
* @return the names of the triple classifications. Coordinates with
*/
public List getTriplesClassificationTypes() {
return new ArrayList<>();
}
/**
* {@inheritDoc}
*/
public List> getTriplesLists(Node node) {
List> triplesList = new ArrayList<>();
Graph graph = getGraph();
return triplesList;
}
/**
* supportsKnowledge.
*
* @return a boolean
*/
public boolean supportsKnowledge() {
return true;
}
/**
* {@inheritDoc}
*/
@Override
public String getAlgorithmName() {
return "FCI";
}
}
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