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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.bayes.BayesIm;
import edu.cmu.tetrad.bayes.BayesPm;
import edu.cmu.tetrad.bayes.FactoredBayesStructuralEM;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.TetradLogger;
import edu.cmu.tetrad.util.TetradSerializableUtils;
import edu.cmu.tetradapp.session.SessionModel;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serial;
/**
* Wraps a Bayes Pm for use in the Tetrad application.
*
* @author josephramsey
* @author Frank Wimberly adapted for EM Bayes estimator and structural EM Bayes search
* @version $Id: $Id
*/
public class StructEmBayesSearchRunner implements SessionModel, GraphSource {
private static final long serialVersionUID = 23L;
/**
* @serial Can be null.
*/
private String name;
/**
* The Bayes PM.
*/
private BayesPm bayesPm;
/**
* The data set.
*/
private DataSet dataSet;
/**
* The estimated Bayes IM.
*/
private BayesIm estimatedBayesIm;
//===============================CONSTRUCTORS============================//
private StructEmBayesSearchRunner(DataWrapper dataWrapper,
BayesPmWrapper bayesPmWrapper) {
if (dataWrapper == null) {
throw new NullPointerException(
"BayesDataWrapper must not be null.");
}
if (bayesPmWrapper == null) {
throw new NullPointerException("BayesPmWrapper must not be null");
}
this.dataSet = (DataSet) dataWrapper.getSelectedDataModel();
this.bayesPm = bayesPmWrapper.getBayesPm();
estimate(this.dataSet, this.bayesPm);
log();
}
/**
* Constructor for StructEmBayesSearchRunner.
*
* @param simulation a {@link edu.cmu.tetradapp.model.Simulation} object
* @param bayesPmWrapper a {@link edu.cmu.tetradapp.model.BayesPmWrapper} object
*/
public StructEmBayesSearchRunner(Simulation simulation,
BayesPmWrapper bayesPmWrapper) {
this((DataWrapper) simulation, bayesPmWrapper);
}
/**
* Constructor for StructEmBayesSearchRunner.
*
* @param dataWrapper a {@link edu.cmu.tetradapp.model.DataWrapper} object
* @param bayesPmWrapper a {@link edu.cmu.tetradapp.model.BayesPmWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public StructEmBayesSearchRunner(DataWrapper dataWrapper,
BayesPmWrapper bayesPmWrapper, Parameters params) {
if (dataWrapper == null) {
throw new NullPointerException();
}
if (bayesPmWrapper == null) {
throw new NullPointerException();
}
if (params == null) {
throw new NullPointerException();
}
DataSet dataSet =
(DataSet) dataWrapper.getSelectedDataModel();
FactoredBayesStructuralEM estimator = new FactoredBayesStructuralEM(
dataSet, bayesPmWrapper.getBayesPm());
this.dataSet = estimator.getDataSet();
try {
this.estimatedBayesIm =
estimator.maximization(params.getDouble("tolerance", 0.0001));
} catch (IllegalArgumentException e) {
throw new RuntimeException(e);
}
log();
}
/**
* Constructor for StructEmBayesSearchRunner.
*
* @param dataWrapper a {@link edu.cmu.tetradapp.model.DataWrapper} object
* @param bayesImWrapper a {@link edu.cmu.tetradapp.model.BayesImWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public StructEmBayesSearchRunner(DataWrapper dataWrapper,
BayesImWrapper bayesImWrapper, Parameters params) {
if (dataWrapper == null) {
throw new NullPointerException();
}
if (bayesImWrapper == null) {
throw new NullPointerException();
}
if (params == null) {
throw new NullPointerException();
}
DataSet dataSet =
(DataSet) dataWrapper.getSelectedDataModel();
this.bayesPm = bayesImWrapper.getBayesIm().getBayesPm();
FactoredBayesStructuralEM estimator =
new FactoredBayesStructuralEM(dataSet, this.bayesPm);
this.dataSet = estimator.getDataSet();
try {
this.estimatedBayesIm =
estimator.maximization(params.getDouble("tolerance", 0.0001));
} catch (IllegalArgumentException e) {
throw new RuntimeException(
"Please specify the search tolerance first.");
}
log();
}
/**
* Generates a simple exemplar of this class to test serialization.
*
* @return a {@link edu.cmu.tetradapp.model.PcRunner} object
* @see TetradSerializableUtils
*/
public static PcRunner serializableInstance() {
return PcRunner.serializableInstance();
}
//================================PUBLIC METHODS========================//
/**
* Getter for the field estimatedBayesIm.
*
* @return a {@link edu.cmu.tetrad.bayes.BayesIm} object
*/
public BayesIm getEstimatedBayesIm() {
return this.estimatedBayesIm;
}
private void estimate(DataSet DataSet, BayesPm bayesPm) {
final double thresh = 0.0001;
try {
FactoredBayesStructuralEM estimator =
new FactoredBayesStructuralEM(DataSet, bayesPm);
this.dataSet = estimator.getDataSet();
this.estimatedBayesIm = estimator.maximization(thresh);
} catch (ArrayIndexOutOfBoundsException e) {
e.printStackTrace();
throw new RuntimeException("Value assignments between Bayes PM " +
"and discrete data set do not match.");
}
}
/**
* Getter for the field dataSet.
*
* @return a {@link edu.cmu.tetrad.data.DataSet} object
*/
public DataSet getDataSet() {
return this.dataSet;
}
/**
* 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.estimatedBayesIm.getBayesPm().getDag();
}
/**
* 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;
}
private void log() {
TetradLogger.getInstance().log("EM-Estimated Bayes IM");
TetradLogger.getInstance().log("" + this.estimatedBayesIm);
}
}
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