edu.cmu.tetradapp.model.SemPmWrapper Maven / Gradle / Ivy
///////////////////////////////////////////////////////////////////////////////
// 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.session.SessionModel;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.TetradLogger;
import edu.cmu.tetrad.util.TetradSerializableUtils;
import java.io.IOException;
import java.io.ObjectInputStream;
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
*/
public class SemPmWrapper implements SessionModel {
private static final long serialVersionUID = 23L;
private int numModels = 1;
private int modelIndex;
private String modelSourceName;
/**
* @serial Can be null.
*/
private String name;
private List semPms;
//==============================CONSTRUCTORS==========================//
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.
*/
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.");
}
semIms = ((SemSimulation) _simulation).getSemIms();
if (semIms == null) {
throw new NullPointerException("It looks like you have not done a simulation.");
}
this.semPms = new ArrayList<>();
for (SemIm semIm : semIms) {
this.semPms.add(semIm.getSemPm());
}
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.
*/
public SemPmWrapper(GraphSource graphWrapper, Parameters parameters) {
this(graphWrapper.getGraph() instanceof TimeLagGraph
? new TimeLagGraph((TimeLagGraph) graphWrapper.getGraph())
: new EdgeListGraph(graphWrapper.getGraph()));
}
public SemPmWrapper(GraphSource graphSource, DataWrapper dataWrapper, Parameters parameters) {
this(new EdgeListGraph(graphSource.getGraph()));
}
public SemPmWrapper(SemEstimatorWrapper wrapper, Parameters parameters) {
SemPm oldSemPm = wrapper.getSemEstimator().getEstimatedSem()
.getSemPm();
setSemPm(oldSemPm);
}
public SemPmWrapper(SemImWrapper wrapper) {
SemPm pm = wrapper.getSemIm().getSemPm();
setSemPm(pm);
}
public SemPmWrapper(MimBuildRunner wrapper) {
SemPm pm = wrapper.getSemPm();
setSemPm(pm);
}
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);
}
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)));
}
public SemPmWrapper(AlgorithmRunner wrapper) {
this(new EdgeListGraph(wrapper.getGraph()));
}
public SemPmWrapper(DagFromCPDAGWrapper wrapper) {
this(new EdgeListGraph(wrapper.getGraph()));
}
public SemPmWrapper(ScoredGraphsWrapper wrapper) {
this(new EdgeListGraph(wrapper.getGraph()));
}
public SemPmWrapper(PValueImproverWrapper wrapper) {
SemPm oldSemPm = wrapper.getNewSemIm().getSemPm();
log(0, oldSemPm);
}
/**
* Generates a simple exemplar of this class to test serialization.
*
* @see TetradSerializableUtils
*/
public static SemPmWrapper serializableInstance() {
return new SemPmWrapper(Dag.serializableInstance());
}
//============================PUBLIC METHODS=========================//
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();
}
}
/**
* Adds semantic checks to the default deserialization method. This method must have the standard signature for a
* readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any
* semantic checks can be specified and do not need to stay the same from version to version. A readObject method of
* this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the
* class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for
* help.
*/
private void readObject(ObjectInputStream s)
throws IOException, ClassNotFoundException {
s.defaultReadObject();
}
public Graph getGraph() {
return this.semPms.get(this.modelIndex).getGraph();
}
public String getName() {
return this.name;
}
public void setName(String name) {
this.name = name;
}
//======================= Private methods ====================//
private void log(int i, SemPm pm) {
TetradLogger.getInstance().log("info", "Linear Structural Equation Parametric Model (SEM PM)");
TetradLogger.getInstance().log("info", "PM # " + (i + 1));
TetradLogger.getInstance().log("pm", pm.toString());
}
public Graph getSourceGraph() {
return getGraph();
}
public Graph getResultGraph() {
return getResultGraph();
}
public List getVariableNames() {
return getGraph().getNodeNames();
}
public List getVariables() {
return getGraph().getNodes();
}
public int getNumModels() {
return this.numModels;
}
public int getModelIndex() {
return this.modelIndex;
}
public void setModelIndex(int modelIndex) {
this.modelIndex = modelIndex;
}
public String getModelSourceName() {
return this.modelSourceName;
}
/**
* The wrapped SemPm.
*
* @serial Cannot be null.
*/
public List getSemPms() {
return this.semPms;
}
}
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