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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.algcomparison.simulation.GeneralSemSimulation;
import edu.cmu.tetrad.graph.*;
import edu.cmu.tetrad.sem.GeneralizedSemIm;
import edu.cmu.tetrad.sem.GeneralizedSemPm;
import edu.cmu.tetrad.sem.SemPm;
import edu.cmu.tetrad.sem.TemplateExpander;
import edu.cmu.tetrad.util.TetradLogger;
import edu.cmu.tetrad.util.TetradSerializableUtils;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serial;
import java.text.ParseException;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
/**
* Wraps a Bayes Pm for use in the Tetrad application.
*
* @author josephramsey
* @version $Id: $Id
*/
public class GeneralizedSemPmWrapper implements KnowledgeBoxInput {
@Serial
private static final long serialVersionUID = 23L;
/**
* The wrapped SemPm.
*/
private final GeneralizedSemPm semPm;
/**
* The name of the model.
*/
private String name;
/**
* True iff errors should be shown in teh editor.
*/
private boolean showErrors;
//==============================CONSTRUCTORS==========================//
/**
* Constructor for GeneralizedSemPmWrapper.
*
* @param simulation a {@link edu.cmu.tetradapp.model.Simulation} object
*/
public GeneralizedSemPmWrapper(Simulation simulation) {
GeneralizedSemPm semPm = null;
if (simulation == null) {
throw new NullPointerException("The Simulation box does not contain a simulation.");
}
edu.cmu.tetrad.algcomparison.simulation.Simulation _simulation = simulation.getSimulation();
if (_simulation == null) {
throw new NullPointerException("No data sets have been simulated.");
}
if (!(_simulation instanceof GeneralSemSimulation)) {
throw new IllegalArgumentException("That was not a Generalized SEM simulation.");
}
List ims = ((GeneralSemSimulation) _simulation).getIms();
if (ims == null || ims.size() == 0) {
throw new NullPointerException("It looks like you have not done a simulation.");
}
semPm = ims.get(0).getGeneralizedSemPm();
this.semPm = semPm;
}
/**
* Constructor for GeneralizedSemPmWrapper.
*
* @param graph a {@link edu.cmu.tetrad.graph.Graph} object
*/
public GeneralizedSemPmWrapper(Graph graph) {
if (graph == null) {
throw new NullPointerException("Graph must not be null.");
}
if (graph instanceof SemGraph) {
this.semPm = new GeneralizedSemPm(graph);
} else {
try {
this.semPm = new GeneralizedSemPm(new SemGraph(graph));
} catch (Exception e) {
e.printStackTrace();
throw new RuntimeException(e);
}
}
log(this.semPm);
}
/**
* Constructor for GeneralizedSemPmWrapper.
*
* @param graph a {@link edu.cmu.tetrad.graph.Graph} object
* @param oldPm a {@link edu.cmu.tetrad.sem.GeneralizedSemPm} object
*/
public GeneralizedSemPmWrapper(Graph graph, GeneralizedSemPm oldPm) {
this(graph);
// We can keep the old expression if the node exists in the old pm and all of the node expressions
// in the old expression are parents of the node in the new pm.
try {
this.semPm.setVariablesTemplate(oldPm.getVariablesTemplate());
this.semPm.setParametersTemplate(oldPm.getParametersTemplate());
this.semPm.setErrorsTemplate(oldPm.getErrorsTemplate());
for (Node node : this.semPm.getNodes()) {
Set parents = new HashSet<>();
for (Node parent : this.semPm.getParents(node)) {
parents.add(parent.getName());
}
Node _node = oldPm.getNode(node.getName());
Set oldReferencedNodes = oldPm.getReferencedNodes(_node);
Set oldReferencedNames = new HashSet<>();
for (Node node2 : oldReferencedNodes) {
oldReferencedNames.add(node2.getName());
}
String template;
if (this.semPm.getVariableNodes().contains(node)) {
template = this.semPm.getVariablesTemplate();
} else {
template = this.semPm.getErrorsTemplate();
}
String newExpression = "";
try {
newExpression = TemplateExpander.getInstance().expandTemplate(template, this.semPm, node);
} catch (ParseException e) {
//
}
this.semPm.setNodeExpression(node, newExpression);
if (_node == null || !parents.equals(oldReferencedNames)) {
this.semPm.setNodeExpression(node, newExpression);
setReferencedParameters(node, this.semPm, oldPm);
} else {
try {
this.semPm.setNodeExpression(node, oldPm.getNodeExpressionString(node));
} catch (Exception e) {
this.semPm.setNodeExpression(node, newExpression);
}
}
}
for (String startsWith : oldPm.startsWithPrefixes()) {
try {
this.semPm.setStartsWithParametersTemplate(startsWith, oldPm.getStartsWithParameterTemplate(startsWith));
} catch (ParseException e) {
throw new RuntimeException(e);
}
}
for (String parameter : this.semPm.getParameters()) {
boolean found = false;
Set prefixes = oldPm.startsWithPrefixes();
for (String startsWith : prefixes) {
if (parameter.startsWith(startsWith)) {
this.semPm.setParameterExpression(parameter, oldPm.getStartsWithParameterTemplate(startsWith));
found = true;
break;
}
}
if (!found) {
this.semPm.setParameterExpression(parameter, this.semPm.getParameterExpressionString(parameter));
}
}
} catch (ParseException e) {
throw new RuntimeException("Couldn't parse expression.", e);
}
}
/**
* Constructor for GeneralizedSemPmWrapper.
*
* @param pmWrapper a {@link edu.cmu.tetradapp.model.SemPmWrapper} object
*/
public GeneralizedSemPmWrapper(SemPmWrapper pmWrapper) {
if (pmWrapper == null) {
throw new NullPointerException();
}
this.semPm = new GeneralizedSemPm(pmWrapper.getSemPm());
}
/**
* Creates a new BayesPm from the given workbench and uses it to construct a new BayesPm.
*
* @param graphWrapper a {@link edu.cmu.tetradapp.model.GraphSource} object
*/
public GeneralizedSemPmWrapper(GraphSource graphWrapper) {
this(new EdgeListGraph(graphWrapper.getGraph()));
}
/**
* Constructor for GeneralizedSemPmWrapper.
*
* @param graphWrapper a {@link edu.cmu.tetradapp.model.GraphSource} object
* @param dataWrapper a {@link edu.cmu.tetradapp.model.DataWrapper} object
*/
public GeneralizedSemPmWrapper(GraphSource graphWrapper, DataWrapper dataWrapper) {
this(new EdgeListGraph(graphWrapper.getGraph()));
}
/**
* Creates a new BayesPm from the given workbench and uses it to construct a new BayesPm.
*
* @param graphWrapper a {@link edu.cmu.tetradapp.model.GraphSource} object
* @param wrapper a {@link edu.cmu.tetradapp.model.GeneralizedSemPmWrapper} object
*/
public GeneralizedSemPmWrapper(GraphSource graphWrapper, GeneralizedSemPmWrapper wrapper) {
this(new EdgeListGraph(graphWrapper.getGraph()), wrapper.getSemPm());
}
/**
* Creates a new BayesPm from the given workbench and uses it to construct a new BayesPm.
*
* @param dagWrapper a {@link edu.cmu.tetradapp.model.DagWrapper} object
* @param wrapper a {@link edu.cmu.tetradapp.model.GeneralizedSemPmWrapper} object
*/
public GeneralizedSemPmWrapper(DagWrapper dagWrapper, GeneralizedSemPmWrapper wrapper) {
this(new EdgeListGraph(dagWrapper.getDag()), wrapper.getSemPm());
}
/**
* Creates a new BayesPm from the given workbench and uses it to construct a new BayesPm.
*
* @param semGraphWrapper a {@link edu.cmu.tetradapp.model.SemGraphWrapper} object
* @param wrapper a {@link edu.cmu.tetradapp.model.GeneralizedSemPmWrapper} object
*/
public GeneralizedSemPmWrapper(SemGraphWrapper semGraphWrapper, GeneralizedSemPmWrapper wrapper) {
this(semGraphWrapper.getSemGraph(), wrapper.getSemPm());
}
/**
* Constructor for GeneralizedSemPmWrapper.
*
* @param pmWrapper a {@link edu.cmu.tetradapp.model.GeneralizedSemPmWrapper} object
*/
public GeneralizedSemPmWrapper(GeneralizedSemPmWrapper pmWrapper) {
this.semPm = new GeneralizedSemPm(pmWrapper.getSemPm());
}
/**
* Creates a new SemPm from the given workbench and uses it to construct a new BayesPm.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.TimeLagGraphWrapper} object
*/
public GeneralizedSemPmWrapper(TimeLagGraphWrapper wrapper) {
this(wrapper.getGraph());
}
/**
* Constructor for GeneralizedSemPmWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.SemEstimatorWrapper} object
*/
public GeneralizedSemPmWrapper(SemEstimatorWrapper wrapper) {
try {
SemPm oldSemPm = wrapper.getSemEstimator().getEstimatedSem()
.getSemPm();
this.semPm = new GeneralizedSemPm(oldSemPm);
} catch (Exception e) {
throw new RuntimeException("SemPm could not be deep cloned.", e);
}
log(this.semPm);
}
/**
* Constructor for GeneralizedSemPmWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.SemImWrapper} object
*/
public GeneralizedSemPmWrapper(SemImWrapper wrapper) {
SemPm oldSemPm = wrapper.getSemIm().getSemPm();
this.semPm = new GeneralizedSemPm(oldSemPm);
log(this.semPm);
}
/**
* Constructor for GeneralizedSemPmWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.MimBuildRunner} object
*/
public GeneralizedSemPmWrapper(MimBuildRunner wrapper) {
SemPm oldSemPm = wrapper.getSemPm();
this.semPm = new GeneralizedSemPm(oldSemPm);
log(this.semPm);
}
/**
* Constructor for GeneralizedSemPmWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.BuildPureClustersRunner} object
*/
public GeneralizedSemPmWrapper(BuildPureClustersRunner wrapper) {
Graph graph = wrapper.getResultGraph();
if (graph == null) {
throw new IllegalArgumentException("No graph to display.");
}
SemPm oldSemPm = new SemPm(graph);
this.semPm = new GeneralizedSemPm(oldSemPm);
log(this.semPm);
}
/**
* Constructor for GeneralizedSemPmWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.AlgorithmRunner} object
*/
public GeneralizedSemPmWrapper(AlgorithmRunner wrapper) {
this(new EdgeListGraph(wrapper.getGraph()));
}
/**
* Generates a simple exemplar of this class to test serialization.
*
* @return a {@link edu.cmu.tetradapp.model.GeneralizedSemPmWrapper} object
* @see TetradSerializableUtils
*/
public static GeneralizedSemPmWrapper serializableInstance() {
return new GeneralizedSemPmWrapper(Dag.serializableInstance());
}
/**
* setReferencedParameters.
*
* @param node a {@link edu.cmu.tetrad.graph.Node} object
* @param oldPm a {@link edu.cmu.tetrad.sem.GeneralizedSemPm} object
* @param newPm a {@link edu.cmu.tetrad.sem.GeneralizedSemPm} object
*/
public void setReferencedParameters(Node node, GeneralizedSemPm oldPm, GeneralizedSemPm newPm) {
Set parameters = this.semPm.getReferencedParameters(node);
for (String parameter : parameters) {
}
}
//============================PUBLIC METHODS=========================//
/**
* Getter for the field semPm.
*
* @return a {@link edu.cmu.tetrad.sem.GeneralizedSemPm} object
*/
public GeneralizedSemPm getSemPm() {
return this.semPm;
}
/**
* 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.semPm.getGraph();
}
/**
* 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;
}
/**
* isShowErrors.
*
* @return a boolean
*/
public boolean isShowErrors() {
return this.showErrors;
}
/**
* Setter for the field showErrors.
*
* @param showErrors a boolean
*/
public void setShowErrors(boolean showErrors) {
this.showErrors = showErrors;
}
//======================= Private methods ====================//
private void log(GeneralizedSemPm pm) {
TetradLogger.getInstance().log("Generalized Structural Equation Parameter Model (Generalized SEM PM)");
String message = pm.toString();
TetradLogger.getInstance().log(message);
}
/**
* 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();
}
}
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