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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.data.Clusters;
import edu.cmu.tetrad.data.ContinuousVariable;
import edu.cmu.tetrad.data.DataModel;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.graph.NodeType;
import edu.cmu.tetrad.search.utils.ClusterUtils;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.TetradLogger;
import edu.cmu.tetradapp.session.ParamsResettable;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serial;
import java.util.ArrayList;
import java.util.List;
/**
* Compares a target workbench with a reference workbench by counting errors of omission and commission. (for edge
* presence only, not orientation).
*
* @author josephramsey
* @author Erin Korber (added remove latents functionality July 2004)
* @version $Id: $Id
*/
public final class MeasurementModelWrapper implements ParamsResettable,
KnowledgeBoxInput {
@Serial
private static final long serialVersionUID = 23L;
/**
* Clusters resulting from the last run of the algorithm.
*/
private Clusters clusters;
/**
* The names of the variables.
*/
private List varNames;
/**
* The data.
*/
private String name;
/**
* The source graph.
*/
private DataSet data;
/**
* The source graph.
*/
private Graph sourceGraph;
/**
* The parameters object, so the GUI can remember stuff for logging.
*/
private Parameters params;
//=============================CONSTRUCTORS==========================//
/**
* Constructor for MeasurementModelWrapper.
*
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public MeasurementModelWrapper(Parameters params) {
this.setVarNames(new ArrayList<>());
Clusters clusters = (Clusters) params.get("clusters", null);
if (clusters == null) clusters = new Clusters();
this.setClusters(clusters);
this.params = params;
}
/**
* Constructor for MeasurementModelWrapper.
*
* @param knowledgeInput a {@link KnowledgeBoxInput} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public MeasurementModelWrapper(KnowledgeBoxInput knowledgeInput, Parameters params) {
if (knowledgeInput instanceof GraphSource graphWrapper) {
Graph mim = graphWrapper.getGraph();
Clusters clusters = ClusterUtils.mimClusters(mim);
List nodeNames = new ArrayList<>();
for (Node node : mim.getNodes()) {
if (node.getNodeType() != NodeType.LATENT) {
nodeNames.add(node.getName());
}
}
this.setVarNames(nodeNames);
setClusters(clusters);
this.params = params;
getParams().set("clusters", clusters);
getParams().set("varNames", nodeNames);
} else {
this.setVarNames(knowledgeInput.getVariableNames());
this.setClusters((Clusters) params.get("clusters", null));
this.params = params;
}
}
/**
* Constructor for MeasurementModelWrapper.
*
* @param dataWrapper a {@link edu.cmu.tetradapp.model.DataWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public MeasurementModelWrapper(DataWrapper dataWrapper, Parameters params) {
this.setVarNames(dataWrapper.getVarNames());
this.setClusters(new Clusters());
DataModel selectedDataModel = dataWrapper.getSelectedDataModel();
if (!(selectedDataModel instanceof DataSet)) {
throw new IllegalArgumentException("That data box did not contain a dataset.");
}
this.data = (DataSet) selectedDataModel;
this.params = params;
}
/**
* serializableInstance.
*
* @return a {@link edu.cmu.tetradapp.model.PcRunner} object
*/
public static PcRunner serializableInstance() {
return PcRunner.serializableInstance();
}
/**
* 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;
}
/**
* 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;
}
}
/**
* Getter for the field clusters.
*
* @return a {@link edu.cmu.tetrad.data.Clusters} object
*/
public Clusters getClusters() {
return this.clusters;
}
private void setClusters(Clusters clusters) {
this.clusters = clusters;
}
/**
* Getter for the field varNames.
*
* @return a {@link java.util.List} object
*/
public List getVarNames() {
return this.varNames;
}
private void setVarNames(List varNames) {
this.varNames = varNames;
}
/**
* Getter for the field data.
*
* @return a {@link edu.cmu.tetrad.data.DataSet} object
*/
public DataSet getData() {
return this.data;
}
/**
* Getter for the field sourceGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getSourceGraph() {
return this.sourceGraph;
}
/**
* getResultGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getResultGraph() {
return this.sourceGraph;
}
private Parameters getParams() {
return this.params;
}
/**
* {@inheritDoc}
*/
public void resetParams(Object params) {
this.params = (Parameters) params;
}
/**
* getResettableParams.
*
* @return a {@link java.lang.Object} object
*/
public Object getResettableParams() {
return this.params;
}
/**
* getVariables.
*
* @return a {@link java.util.List} object
*/
public java.util.List getVariables() {
List latents = new ArrayList<>();
for (String name : getVariableNames()) {
Node node = new ContinuousVariable(name);
node.setNodeType(NodeType.LATENT);
latents.add(node);
}
return latents;
}
/**
* getVariableNames.
*
* @return a {@link java.util.List} object
*/
public List getVariableNames() {
List> partition = ClusterUtils.clustersToPartition(getClusters(),
getData().getVariables());
return ClusterUtils.generateLatentNames(partition.size());
}
}
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