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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.graph.*;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.TetradLogger;
import edu.cmu.tetrad.util.TetradSerializableUtils;
import edu.cmu.tetradapp.session.DoNotAddOldModel;
import edu.cmu.tetradapp.session.SimulationParamsSource;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serial;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Holds a tetrad dag with all of the constructors necessary for it to serve as a model for the tetrad application.
*
* @author josephramsey
* @version $Id: $Id
*/
public class SemGraphWrapper implements GraphSource,
KnowledgeBoxInput, SimulationParamsSource, DoNotAddOldModel, MultipleGraphSource {
@Serial
private static final long serialVersionUID = 23L;
/**
* The number of models in this wrapper.
*/
private int numModels = 1;
/**
* The index of the current model.
*/
private int modelIndex;
/**
* The name of the model source.
*/
private String modelSourceName;
/**
* The name of the wrapper.
*/
private String name;
/**
* The graphs in the wrapper.
*/
private List graphs;
/**
* The parameter settings for the wrapper.
*/
private Map allParamSettings;
/**
* The parameters for the wrapper.
*/
private Parameters parameters = new Parameters();
// =============================CONSTRUCTORS==========================//
/**
* Constructor for SemGraphWrapper.
*
* @param graphSource a {@link edu.cmu.tetradapp.model.GraphSource} object
* @param parameters a {@link edu.cmu.tetrad.util.Parameters} object
*/
public SemGraphWrapper(GraphSource graphSource, Parameters parameters) {
if (graphSource instanceof Simulation simulation) {
List graphs = simulation.getGraphs();
this.graphs = new ArrayList<>();
for (Graph graph : graphs) {
this.graphs.add(new SemGraph(graph));
}
this.numModels = this.graphs.size();
this.modelIndex = 0;
this.modelSourceName = simulation.getName();
} else {
setGraph(new SemGraph(graphSource.getGraph()));
}
log();
}
/**
* Constructor for SemGraphWrapper.
*
* @param graph a {@link edu.cmu.tetrad.graph.SemGraph} object
*/
public SemGraphWrapper(SemGraph graph) {
if (graph == null) {
throw new NullPointerException("MAG must not be null.");
}
setSemGraph(graph);
getSemGraph().setShowErrorTerms(false);
this.parameters = new Parameters();
log();
}
// Do not, repeat not, get rid of these params. -jdramsey 7/4/2010
/**
* Constructor for SemGraphWrapper.
*
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public SemGraphWrapper(Parameters params) {
if (params.getString("newGraphInitializationMode", "manual").equals("manual")) {
SemGraph semGraph = new SemGraph();
semGraph.setShowErrorTerms(false);
setSemGraph(semGraph);
} else if (params.getString("newGraphInitializationMode", "manual").equals("random")) {
// RandomUtil.getInstance().setSeed(new Date().getTime());
setSemGraph(new SemGraph(edu.cmu.tetradapp.util.GraphUtils.makeRandomGraph(getGraph(), this.parameters)));
} else {
// RandomUtil.getInstance().setSeed(new Date().getTime());
setSemGraph(new SemGraph(edu.cmu.tetradapp.util.GraphUtils.makeRandomGraph(getGraph(), this.parameters)));
}
this.parameters = params;
log();
}
/**
* Constructor for SemGraphWrapper.
*
* @param graphWrapper a {@link edu.cmu.tetradapp.model.SemGraphWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public SemGraphWrapper(SemGraphWrapper graphWrapper, Parameters params) {
this.parameters = params;
if (params.getString("newGraphInitializationMode", "manual").equals("manual")) {
try {
SemGraph semGraph = new SemGraph(graphWrapper.getSemGraph());
semGraph.setShowErrorTerms(false);
setSemGraph(semGraph);
} catch (Exception e) {
e.printStackTrace();
SemGraph semGraph = new SemGraph();
semGraph.setShowErrorTerms(false);
setSemGraph(semGraph);
}
} else if (params.getString("newGraphInitializationMode", "manual").equals("random")) {
// RandomUtil.getInstance().setSeed(new Date().getTime());
setSemGraph(new SemGraph(edu.cmu.tetradapp.util.GraphUtils.makeRandomGraph(getGraph(), this.parameters)));
}
log();
}
/**
* Constructor for SemGraphWrapper.
*
* @param graphWrapper a {@link edu.cmu.tetradapp.model.DagWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public SemGraphWrapper(DagWrapper graphWrapper, Parameters params) {
this.parameters = params;
if (params.getString("newGraphInitializationMode", "manual").equals("manual")) {
SemGraph semGraph = new SemGraph(graphWrapper.getDag());
semGraph.setShowErrorTerms(false);
setSemGraph(semGraph);
} else if (params.getString("newGraphInitializationMode", "manual").equals("random")) {
// RandomUtil.getInstance().setSeed(new Date().getTime());
setSemGraph(new SemGraph(edu.cmu.tetradapp.util.GraphUtils.makeRandomGraph(getGraph(), this.parameters)));
}
log();
}
/**
* Constructor for SemGraphWrapper.
*
* @param graphWrapper a {@link edu.cmu.tetradapp.model.GraphWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public SemGraphWrapper(GraphWrapper graphWrapper, Parameters params) {
if (params.getString("newGraphInitializationMode", "manual").equals("manual")) {
SemGraph semGraph = new SemGraph(graphWrapper.getGraph());
semGraph.setShowErrorTerms(false);
setSemGraph(semGraph);
} else if (params.getString("newGraphInitializationMode", "manual").equals("random")) {
// RandomUtil.getInstance().setSeed(new Date().getTime());
setSemGraph(new SemGraph(edu.cmu.tetradapp.util.GraphUtils.makeRandomGraph(getGraph(), this.parameters)));
}
this.parameters = params;
log();
}
/**
* Constructor for SemGraphWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.AbstractAlgorithmRunner} object
*/
public SemGraphWrapper(AbstractAlgorithmRunner wrapper) {
this(new SemGraph(wrapper.getResultGraph()));
}
/**
* Constructor for SemGraphWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.DataWrapper} object
*/
public SemGraphWrapper(DataWrapper wrapper) {
if (wrapper instanceof Simulation simulation) {
this.graphs = new ArrayList<>();
for (Graph graph : simulation.getGraphs()) {
SemGraph semGraph = new SemGraph(graph);
semGraph.setShowErrorTerms(false);
this.graphs.add(semGraph);
}
this.numModels = this.graphs.size();
this.modelIndex = 0;
this.modelSourceName = simulation.getName();
} else {
setGraph(new EdgeListGraph(wrapper.getVariables()));
}
LayoutUtil.defaultLayout(getGraph());
}
/**
* Constructor for SemGraphWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.BayesPmWrapper} object
*/
public SemGraphWrapper(BayesPmWrapper wrapper) {
this(new SemGraph(wrapper.getBayesPm().getDag()));
}
/**
* Constructor for SemGraphWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.BayesImWrapper} object
*/
public SemGraphWrapper(BayesImWrapper wrapper) {
this(new SemGraph(wrapper.getBayesIm().getBayesPm().getDag()));
}
/**
* Constructor for SemGraphWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.BayesEstimatorWrapper} object
*/
public SemGraphWrapper(BayesEstimatorWrapper wrapper) {
this(new SemGraph(wrapper.getEstimatedBayesIm().getBayesPm().getDag()));
}
/**
* Constructor for SemGraphWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.CptInvariantUpdaterWrapper} object
*/
public SemGraphWrapper(CptInvariantUpdaterWrapper wrapper) {
this(new SemGraph(wrapper.getBayesUpdater().getManipulatedGraph()));
}
/**
* Constructor for SemGraphWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.SemPmWrapper} object
*/
public SemGraphWrapper(SemPmWrapper wrapper) {
this(new SemGraph(wrapper.getSemPm().getGraph()));
}
/**
* Constructor for SemGraphWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.SemImWrapper} object
*/
public SemGraphWrapper(SemImWrapper wrapper) {
this(new SemGraph(wrapper.getSemIm().getSemPm().getGraph()));
}
/**
* Constructor for SemGraphWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.SemEstimatorWrapper} object
*/
public SemGraphWrapper(SemEstimatorWrapper wrapper) {
this(new SemGraph(wrapper.getSemEstimator().getEstimatedSem()
.getSemPm().getGraph()));
}
/**
* Constructor for SemGraphWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.RegressionRunner} object
*/
public SemGraphWrapper(RegressionRunner wrapper) {
this(new SemGraph(wrapper.getResultGraph()));
}
/**
* Constructor for SemGraphWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.BuildPureClustersRunner} object
*/
public SemGraphWrapper(BuildPureClustersRunner wrapper) {
this(new SemGraph(wrapper.getResultGraph()));
}
/**
* Constructor for SemGraphWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.MimBuildRunner} object
*/
public SemGraphWrapper(MimBuildRunner wrapper) {
this(new SemGraph(wrapper.getResultGraph()));
}
/**
* Generates a simple exemplar of this class to test serialization.
*
* @return a {@link edu.cmu.tetradapp.model.SemGraphWrapper} object
* @see TetradSerializableUtils
*/
public static SemGraphWrapper serializableInstance() {
return new SemGraphWrapper(SemGraph.serializableInstance());
}
// ================================PUBLIC METHODS=======================//
/**
* getSemGraph.
*
* @return a {@link edu.cmu.tetrad.graph.SemGraph} object
*/
public SemGraph getSemGraph() {
return (SemGraph) getGraph();
}
/**
* setSemGraph.
*
* @param graph a {@link edu.cmu.tetrad.graph.SemGraph} object
*/
public void setSemGraph(SemGraph graph) {
this.graphs = new ArrayList<>();
graph.setShowErrorTerms(false);
this.graphs.add(graph);
log();
}
// ============================PRIVATE METHODS========================//
private void log() {
TetradLogger.getInstance().log("Structural Equation Model (SEM) Graph");
String message = "" + getGraph();
TetradLogger.getInstance().log(message);
}
/**
* Writes the object to the specified ObjectOutputStream.
*
* @param out The ObjectOutputStream to write the object to.
* @throws IOException If an I/O error occurs.
*/
@Serial
private void writeObject(ObjectOutputStream out) throws IOException {
try {
out.defaultWriteObject();
} catch (IOException e) {
TetradLogger.getInstance().log("Failed to serialize object: " + getClass().getCanonicalName()
+ ", " + e.getMessage());
throw e;
}
}
/**
* Reads the object from the specified ObjectInputStream. This method is used during deserialization
* to restore the state of the object.
*
* @param in The ObjectInputStream to read the object from.
* @throws IOException If an I/O error occurs.
* @throws ClassNotFoundException If the class of the serialized object cannot be found.
*/
@Serial
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
try {
in.defaultReadObject();
} catch (IOException e) {
TetradLogger.getInstance().log("Failed to deserialize object: " + getClass().getCanonicalName()
+ ", " + e.getMessage());
throw e;
}
}
/**
* getGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getGraph() {
return this.graphs.get(getModelIndex());
}
/**
* setGraph.
*
* @param graph a {@link edu.cmu.tetrad.graph.Graph} object
*/
public void setGraph(Graph graph) {
this.graphs = new ArrayList<>();
if (graph instanceof SemGraph) {
this.graphs.add(graph);
} else {
this.graphs.add(new SemGraph(graph));
}
// this.graphs.add(new SemGraph(graph));
log();
}
/**
* Getter for the field name.
*
* @return a {@link java.lang.String} object
*/
public String getName() {
return this.name;
}
/**
* {@inheritDoc}
*/
public void setName(String name) {
this.name = name;
}
/**
* getSourceGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getSourceGraph() {
return getGraph();
}
/**
* getResultGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getResultGraph() {
return getGraph();
}
/**
* getVariableNames.
*
* @return a {@link java.util.List} object
*/
public List getVariableNames() {
return getGraph().getNodeNames();
}
/**
* getVariables.
*
* @return a {@link java.util.List} object
*/
public List getVariables() {
return getGraph().getNodes();
}
/**
* {@inheritDoc}
*/
@Override
public Map getParamSettings() {
Map paramSettings = new HashMap<>();
if (!paramSettings.containsKey("# Vars")) {
paramSettings.put("# Nodes", Integer.toString(getSemGraph().getNumNodes()));
}
paramSettings.put("# Edges", Integer.toString(getSemGraph().getNumEdges()));
if (getSemGraph().paths().existsDirectedCycle()) {
paramSettings.put("Cyclic", null);
}
return paramSettings;
}
/**
* {@inheritDoc}
*/
@Override
public Map getAllParamSettings() {
return this.allParamSettings;
}
/**
* {@inheritDoc}
*/
@Override
public void setAllParamSettings(Map paramSettings) {
this.allParamSettings = paramSettings;
}
/**
* Getter for the field parameters.
*
* @return a {@link edu.cmu.tetrad.util.Parameters} object
*/
public Parameters getParameters() {
return this.parameters;
}
/**
* Getter for the field numModels.
*
* @return a int
*/
public int getNumModels() {
return this.numModels;
}
/**
* Setter for the field numModels.
*
* @param numModels a int
*/
public void setNumModels(int numModels) {
this.numModels = numModels;
}
/**
* Getter for the field modelIndex.
*
* @return a int
*/
public int getModelIndex() {
return this.modelIndex;
}
/**
* Setter for the field modelIndex.
*
* @param modelIndex a int
*/
public void setModelIndex(int modelIndex) {
this.modelIndex = modelIndex;
}
/**
* Getter for the field modelSourceName.
*
* @return a {@link java.lang.String} object
*/
public String getModelSourceName() {
return this.modelSourceName;
}
/**
* Setter for the field modelSourceName.
*
* @param modelSourceName a {@link java.lang.String} object
*/
public void setModelSourceName(String modelSourceName) {
this.modelSourceName = modelSourceName;
}
/**
* Getter for the field graphs.
*
* @return a {@link java.util.List} object
*/
public List getGraphs() {
return this.graphs;
}
}
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