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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.LinearFisherModel;
import edu.cmu.tetrad.algcomparison.simulation.SemSimulation;
import edu.cmu.tetrad.graph.*;
import edu.cmu.tetrad.sem.SemIm;
import edu.cmu.tetrad.sem.SemPm;
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;
import java.rmi.MarshalledObject;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
/**
* Wraps a Bayes Pm for use in the Tetrad application.
*
* @author josephramsey
* @version $Id: $Id
*/
public class SemPmWrapper implements SessionModel {
@Serial
private static final long serialVersionUID = 23L;
/**
* The wrapped SemPm.
*/
private int numModels = 1;
/**
* The index of the model to display.
*/
private int modelIndex;
/**
* The name of the source of the model.
*/
private String modelSourceName;
/**
* The name of the wrapper.
*/
private String name;
/**
* The wrapped SemPm.
*/
private List semPms;
//==============================CONSTRUCTORS==========================//
/**
* Constructor for SemPmWrapper.
*
* @param graph a {@link edu.cmu.tetrad.graph.Graph} object
*/
public SemPmWrapper(Graph graph) {
if (graph == null) {
throw new NullPointerException("Graph must not be null.");
}
this.semPms = new ArrayList<>();
this.semPms.add(new SemPm(graph));
for (int i = 0; i < this.semPms.size(); i++) {
log(i, this.semPms.get(i));
}
}
/**
* Creates a new SemPm from the given workbench and uses it to construct a new BayesPm.
*
* @param simulation a {@link edu.cmu.tetradapp.model.Simulation} object
* @param parameters a {@link edu.cmu.tetrad.util.Parameters} object
*/
public SemPmWrapper(Simulation simulation, Parameters parameters) {
List semIms = 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 LinearFisherModel) {
throw new IllegalArgumentException("Large SEM simulations cannot be represented "
+ "using a SEM PM or IM box, sorry.");
}
if (!(_simulation instanceof SemSimulation)) {
throw new IllegalArgumentException("That was not a linear, Gaussian SEM simulation.");
}
this.semPms = new ArrayList<>();
this.numModels = simulation.getDataModelList().size();
this.modelIndex = 0;
this.modelSourceName = simulation.getName();
}
/**
* Creates a new SemPm from the given workbench and uses it to construct a new BayesPm.
*
* @param graphWrapper a {@link edu.cmu.tetradapp.model.GraphSource} object
* @param parameters a {@link edu.cmu.tetrad.util.Parameters} object
*/
public SemPmWrapper(GraphSource graphWrapper, Parameters parameters) {
this(graphWrapper.getGraph() instanceof TimeLagGraph
? new TimeLagGraph((TimeLagGraph) graphWrapper.getGraph())
: new EdgeListGraph(graphWrapper.getGraph()));
}
/**
* Constructor for SemPmWrapper.
*
* @param graphSource a {@link edu.cmu.tetradapp.model.GraphSource} object
* @param dataWrapper a {@link edu.cmu.tetradapp.model.DataWrapper} object
* @param parameters a {@link edu.cmu.tetrad.util.Parameters} object
*/
public SemPmWrapper(GraphSource graphSource, DataWrapper dataWrapper, Parameters parameters) {
this(new EdgeListGraph(graphSource.getGraph()));
}
/**
* Constructor for SemPmWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.SemEstimatorWrapper} object
* @param parameters a {@link edu.cmu.tetrad.util.Parameters} object
*/
public SemPmWrapper(SemEstimatorWrapper wrapper, Parameters parameters) {
SemPm oldSemPm = wrapper.getSemEstimator().getEstimatedSem()
.getSemPm();
setSemPm(oldSemPm);
}
/**
* Constructor for SemPmWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.SemImWrapper} object
*/
public SemPmWrapper(SemImWrapper wrapper) {
SemPm pm = wrapper.getSemIm().getSemPm();
setSemPm(pm);
}
/**
* Constructor for SemPmWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.MimBuildRunner} object
*/
public SemPmWrapper(MimBuildRunner wrapper) {
SemPm pm = wrapper.getSemPm();
setSemPm(pm);
}
/**
* Constructor for SemPmWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.BuildPureClustersRunner} object
*/
public SemPmWrapper(BuildPureClustersRunner wrapper) {
Graph graph = wrapper.getResultGraph();
if (graph == null) {
throw new IllegalArgumentException("No graph to display.");
}
SemPm pm = new SemPm(graph);
setSemPm(pm);
}
/**
* Constructor for SemPmWrapper.
*
* @param simulation a {@link edu.cmu.tetradapp.model.Simulation} object
*/
public SemPmWrapper(Simulation simulation) {
List graphs = simulation.getGraphs();
if (!(graphs.size() == 1)) {
throw new IllegalArgumentException("Simulation must contain exactly one graph/data pair.");
}
setSemPm(new SemPm(graphs.get(0)));
}
/**
* Constructor for SemPmWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.AlgorithmRunner} object
*/
public SemPmWrapper(AlgorithmRunner wrapper) {
this(new EdgeListGraph(wrapper.getGraph()));
}
/**
* Constructor for SemPmWrapper.
*
* @param wrapper a {@link DagFromCPDAGWrapper} object
*/
public SemPmWrapper(DagFromCPDAGWrapper wrapper) {
this(new EdgeListGraph(wrapper.getGraph()));
}
/**
* Constructor for SemPmWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.ScoredGraphsWrapper} object
*/
public SemPmWrapper(ScoredGraphsWrapper wrapper) {
this(new EdgeListGraph(wrapper.getGraph()));
}
/**
* Constructor for SemPmWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.PValueImproverWrapper} object
*/
public SemPmWrapper(PValueImproverWrapper wrapper) {
SemPm oldSemPm = wrapper.getNewSemIm().getSemPm();
log(0, oldSemPm);
}
/**
* Generates a simple exemplar of this class to test serialization.
*
* @return a {@link edu.cmu.tetradapp.model.SemPmWrapper} object
* @see TetradSerializableUtils
*/
public static SemPmWrapper serializableInstance() {
return new SemPmWrapper(Dag.serializableInstance());
}
//============================PUBLIC METHODS=========================//
/**
* getSemPm.
*
* @return a {@link edu.cmu.tetrad.sem.SemPm} object
*/
public SemPm getSemPm() {
return this.semPms.get(getModelIndex());
}
private void setSemPm(SemPm oldSemPm) {
try {
SemPm pm = (SemPm) new MarshalledObject(oldSemPm).get();
this.semPms = Collections.singletonList(pm);
} catch (IOException | ClassNotFoundException e) {
e.printStackTrace();
}
}
/**
* 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.semPms.get(this.modelIndex).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;
}
//======================= Private methods ====================//
private void log(int i, SemPm pm) {
TetradLogger.getInstance().log("Linear Structural Equation Parametric Model (SEM PM)");
TetradLogger.getInstance().log("PM # " + (i + 1));
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 getResultGraph();
}
/**
* 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();
}
/**
* Getter for the field numModels.
*
* @return a int
*/
public int getNumModels() {
return this.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;
}
/**
* The wrapped SemPm.
*
* @return a {@link java.util.List} object
* @serial Cannot be null.
*/
public List getSemPms() {
return this.semPms;
}
}
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