edu.cmu.tetradapp.model.TabularComparison 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.statistic.*;
import edu.cmu.tetrad.data.*;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.session.DoNotAddOldModel;
import edu.cmu.tetrad.session.SessionModel;
import edu.cmu.tetrad.session.SimulationParamsSource;
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.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)
*/
public final class TabularComparison implements SessionModel, SimulationParamsSource,
DoNotAddOldModel {
private static final long serialVersionUID = 23L;
private final Graph targetGraph;
private final Graph referenceGraph;
private final Parameters params;
private final DataModel dataModel = null;
private String name;
private Map allParamSettings;
private DataSet dataSet;
private ArrayList statistics;
private String targetName;
private String referenceName;
//=============================CONSTRUCTORS==========================//
public TabularComparison(GraphSource model1, GraphSource model2,
Parameters params) {
this(model1, model2, null, params);
}
/**
* Compares the results of a PC to a reference workbench by counting errors of omission and commission. The counts
* can be retrieved using the methods
* countOmissionErrors and countCommissionErrors.
*/
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>");
}
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();
// addRecord();
TetradLogger.getInstance().log("info", "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);
}
}
/**
* Generates a simple exemplar of this class to test serialization.
*
* @see TetradSerializableUtils
*/
// public static TabularComparison serializableInstance() {
// return new TabularComparison(DagWrapper.serializableInstance(),
// DagWrapper.serializableInstance(),
// new Parameters());
// }
//==============================PUBLIC METHODS========================//
public DataSet getDataSet() {
return this.dataSet;
}
public String getName() {
return this.name;
}
public void setName(String name) {
this.name = name;
}
//============================PRIVATE METHODS=========================//
/**
* 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();
}
@Override
public Map getParamSettings() {
return new HashMap<>();
}
@Override
public Map getAllParamSettings() {
return this.allParamSettings;
}
@Override
public void setAllParamSettings(Map paramSettings) {
this.allParamSettings = new LinkedHashMap<>(paramSettings);
}
public Graph getReferenceGraph() {
return this.referenceGraph;
}
public Graph getTargetGraph() {
return this.targetGraph;
}
public String getTargetName() {
return this.targetName;
}
public void setTargetName(String targetName) {
this.targetName = targetName;
}
public String getReferenceName() {
return this.referenceName;
}
public void setReferenceName(String referenceName) {
this.referenceName = referenceName;
}
public Parameters getParams() {
return this.params;
}
public DataModel getDataModel() {
return this.dataModel;
}
}
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