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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.statistic.*;
import edu.cmu.tetrad.data.*;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.TetradLogger;
import edu.cmu.tetradapp.session.DoNotAddOldModel;
import edu.cmu.tetradapp.session.SessionModel;
import edu.cmu.tetradapp.session.SimulationParamsSource;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serial;
import java.text.DecimalFormat;
import java.util.*;
/**
* 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 TabularComparison implements SessionModel, SimulationParamsSource,
DoNotAddOldModel {
@Serial
private static final long serialVersionUID = 23L;
/**
* The target graph.
*/
private final Graph targetGraph;
/**
* The reference graph.
*/
private final Graph referenceGraph;
/**
* The parameters for the comparison.
*/
private final Parameters params;
/**
* The data model.
*/
private final DataModel dataModel = null;
/**
* The elapsed time in milliseconds.
*/
private long elapsedTime = 0L;
/**
* The name of the comparison.
*/
private String name;
/**
* The parameters for the comparison.
*/
private Map allParamSettings;
/**
* The data set.
*/
private DataSet dataSet;
/**
* The statistics.
*/
private ArrayList statistics;
/**
* The name of the target graph.
*/
private String targetName;
/**
* The name of the reference graph.
*/
private String referenceName;
//=============================CONSTRUCTORS==========================//
/**
* Compares the results an algorithm run using various statistics.
*
* @param model1 the first model to compare; its graph is used.
* @param model2 the second model to compare; its graph is used.
* @param params the parameters for the comparison.
*/
public TabularComparison(GraphSource model1, GraphSource model2,
Parameters params) {
this(model1, model2, null, params);
}
/**
* Compares the results an algorithm run using various statistics.
*
* @param model1 the first model to compare; its graph is used.
* @param model2 the second model to compare; its graph is used.
* @param dataWrapper the data wrapper to use for the comparison. (Unused here.)
* @param params the parameters for the comparison.
*/
public TabularComparison(GraphSource model1, GraphSource model2,
DataWrapper dataWrapper, Parameters params) {
if (params == null) {
throw new NullPointerException("Parameters must not be null");
}
if (model1 == null || model2 == null) {
throw new NullPointerException("Null graph source>");
}
if (model1 instanceof GeneralAlgorithmRunner) {
this.elapsedTime = ((GeneralAlgorithmRunner) model1).getElapsedTime();
} else if (model2 instanceof GeneralAlgorithmRunner) {
this.elapsedTime = ((GeneralAlgorithmRunner) model2).getElapsedTime();
}
this.params = params;
this.referenceName = params.getString("referenceGraphName", null);
this.targetName = params.getString("targetGraphName", null);
String model1Name = model1.getName();
String model2Name = model2.getName();
if (this.referenceName.equals(model1Name)) {
this.referenceGraph = model1.getGraph();
this.targetGraph = model2.getGraph();
} else if (this.referenceName.equals(model2Name)) {
this.referenceGraph = model2.getGraph();
this.targetGraph = model1.getGraph();
} else {
this.referenceGraph = model1.getGraph();
this.targetGraph = model2.getGraph();
}
newExecution();
TetradLogger.getInstance().log("Graph Comparison");
}
private void newExecution() {
this.statistics = new ArrayList<>();
this.statistics.add(new AdjacencyPrecision());
this.statistics.add(new AdjacencyRecall());
this.statistics.add(new ArrowheadPrecision());
this.statistics.add(new ArrowheadRecall());
this.statistics.add(new TwoCyclePrecision());
this.statistics.add(new TwoCycleRecall());
this.statistics.add(new TwoCycleFalsePositive());
List variables = new ArrayList<>();
for (Statistic statistic : this.statistics) {
variables.add(new ContinuousVariable(statistic.getAbbreviation()));
}
this.dataSet = new BoxDataSet(new DoubleDataBox(0, variables.size()), variables);
this.dataSet.setNumberFormat(new DecimalFormat("0.00"));
}
private void addRecord() {
int newRow = this.dataSet.getNumRows();
for (int j = 0; j < this.statistics.size(); j++) {
Statistic statistic = this.statistics.get(j);
double value = statistic.getValue(this.referenceGraph, this.targetGraph, null);
this.dataSet.setDouble(newRow, j, value);
}
}
//==============================PUBLIC METHODS========================//
/**
* Getter for the field dataSet.
*
* @return a {@link edu.cmu.tetrad.data.DataSet} object
*/
public DataSet getDataSet() {
return this.dataSet;
}
/**
* 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=========================//
/**
* 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;
}
}
/**
* {@inheritDoc}
*/
@Override
public Map getParamSettings() {
return new HashMap<>();
}
/**
* {@inheritDoc}
*/
@Override
public Map getAllParamSettings() {
return this.allParamSettings;
}
/**
* {@inheritDoc}
*/
@Override
public void setAllParamSettings(Map paramSettings) {
this.allParamSettings = new LinkedHashMap<>(paramSettings);
}
/**
* Getter for the field referenceGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getReferenceGraph() {
return this.referenceGraph;
}
/**
* Getter for the field targetGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getTargetGraph() {
return this.targetGraph;
}
/**
* Getter for the field targetName.
*
* @return a {@link java.lang.String} object
*/
public String getTargetName() {
return this.targetName;
}
/**
* Setter for the field targetName.
*
* @param targetName a {@link java.lang.String} object
*/
public void setTargetName(String targetName) {
this.targetName = targetName;
}
/**
* Getter for the field referenceName.
*
* @return a {@link java.lang.String} object
*/
public String getReferenceName() {
return this.referenceName;
}
/**
* Setter for the field referenceName.
*
* @param referenceName a {@link java.lang.String} object
*/
public void setReferenceName(String referenceName) {
this.referenceName = referenceName;
}
/**
* Getter for the field params.
*
* @return a {@link edu.cmu.tetrad.util.Parameters} object
*/
public Parameters getParams() {
return this.params;
}
/**
* Getter for the field dataModel.
*
* @return a {@link edu.cmu.tetrad.data.DataModel} object
*/
public DataModel getDataModel() {
return this.dataModel;
}
/**
* Returns the elapsed time in milliseconds. If the elapsed time is not available, this method returns -1.
*
* @return the elapsed time in milliseconds.
*/
public long getElapsedTime() {
return elapsedTime;
}
}
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