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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.calculator.expression.Expression;
import edu.cmu.tetrad.calculator.expression.VariableExpression;
import edu.cmu.tetrad.graph.*;
import edu.cmu.tetrad.search.IndependenceTest;
import edu.cmu.tetrad.search.test.MsepTest;
import edu.cmu.tetrad.sem.GeneralizedSemIm;
import edu.cmu.tetrad.sem.GeneralizedSemPm;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.TetradLogger;
import edu.cmu.tetrad.util.TetradSerializableUtils;
import edu.cmu.tetradapp.session.SimulationParamsSource;
import edu.cmu.tetradapp.util.IonInput;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serial;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Holds a tetrad-style graph with all of the constructors necessary for it to serve as a model for the tetrad
* application.
*
* @author josephramsey
* @version $Id: $Id
*/
public class GraphWrapper implements KnowledgeBoxInput, IonInput, IndTestProducer,
SimulationParamsSource, GraphSettable, MultipleGraphSource {
@Serial
private static final long serialVersionUID = 23L;
/**
* The number of models.
*/
private int numModels = 1;
/**
* The index of the model.
*/
private int modelIndex;
/**
* The name of the model source.
*/
private String modelSourceName;
/**
* The name of the model.
*/
private String name;
/**
* The graphs.
*/
private List graphs;
/**
* The parameters settings.
*/
private Map allParamSettings;
/**
* The parameters.
*/
private Parameters parameters;
//=============================CONSTRUCTORS==========================//
private GraphWrapper() {
}
/**
* Constructor for GraphWrapper.
*
* @param graphSource a {@link edu.cmu.tetradapp.model.GraphSource} object
* @param parameters a {@link edu.cmu.tetrad.util.Parameters} object
*/
public GraphWrapper(GraphSource graphSource, Parameters parameters) {
this.parameters = parameters;
if (graphSource instanceof Simulation simulation) {
this.graphs = simulation.getGraphs();
this.numModels = this.graphs.size();
this.modelIndex = 0;
this.modelSourceName = simulation.getName();
} else {
setGraph(new EdgeListGraph(graphSource.getGraph()));
}
// log();
}
/**
* Constructor for GraphWrapper.
*
* @param graph a {@link edu.cmu.tetrad.graph.Graph} object
*/
public GraphWrapper(Graph graph) {
if (graph == null) {
throw new NullPointerException("Graph must not be null.");
}
setGraph(graph);
// log();
}
/**
* Constructor for GraphWrapper.
*
* @param graph a {@link edu.cmu.tetrad.graph.Graph} object
* @param message a {@link java.lang.String} object
*/
public GraphWrapper(Graph graph, String message) {
TetradLogger.getInstance().log(message);
if (graph == null) {
throw new NullPointerException("Graph must not be null.");
}
setGraph(graph);
}
/**
* Constructor for GraphWrapper.
*
* @param parameters a {@link edu.cmu.tetrad.util.Parameters} object
*/
public GraphWrapper(Parameters parameters) {
this.parameters = parameters;
setGraph(new EdgeListGraph());
// log();
}
/**
* Constructor for GraphWrapper.
*
* @param simulation a {@link edu.cmu.tetradapp.model.Simulation} object
* @param parameters a {@link edu.cmu.tetrad.util.Parameters} object
*/
public GraphWrapper(Simulation simulation, Parameters parameters) {
this.parameters = parameters;
this.graphs = simulation.getGraphs();
this.numModels = this.graphs.size();
this.modelIndex = 0;
this.modelSourceName = simulation.getName();
// log();
}
/**
* Constructor for GraphWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.DataWrapper} object
*/
public GraphWrapper(DataWrapper wrapper) {
if (wrapper instanceof Simulation simulation) {
this.graphs = simulation.getGraphs();
this.numModels = this.graphs.size();
this.modelIndex = 0;
this.modelSourceName = simulation.getName();
} else {
setGraph(new EdgeListGraph(wrapper.getVariables()));
}
LayoutUtil.defaultLayout(getGraph());
}
/**
* Constructor for GraphWrapper.
*
* @param wrapper a {@link edu.cmu.tetradapp.model.GeneralizedSemImWrapper} object
*/
public GraphWrapper(GeneralizedSemImWrapper wrapper) {
this(GraphWrapper.getStrongestInfluenceGraph(wrapper.getSemIms().get(0)));
if (wrapper.getSemIms() == null || wrapper.getSemIms().size() > 1) {
throw new IllegalArgumentException("I'm sorry; this editor can only edit a single generalized SEM IM.");
}
}
/**
* Generates a simple exemplar of this class to test serialization.
*
* @return a {@link edu.cmu.tetradapp.model.GraphWrapper} object
* @see TetradSerializableUtils
*/
public static GraphWrapper serializableInstance() {
return new GraphWrapper(Dag.serializableInstance());
}
//==============================PUBLIC METHODS======================//
private static String findParameter(Expression expression, String name) {
List expressions = expression.getExpressions();
if (expression.getToken().equals("*")) {
Expression expression1 = expressions.get(1);
VariableExpression varExpr = (VariableExpression) expression1;
if (varExpr.getVariable().equals(name)) {
Expression expression2 = expressions.get(0);
VariableExpression constExpr = (VariableExpression) expression2;
return constExpr.getVariable();
}
}
for (Expression _expression : expressions) {
String param = GraphWrapper.findParameter(_expression, name);
if (param != null) {
return param;
}
}
return null;
}
private static Graph getStrongestInfluenceGraph(GeneralizedSemIm im) {
GeneralizedSemPm pm = im.getGeneralizedSemPm();
Graph imGraph = im.getGeneralizedSemPm().getGraph();
List nodes = new ArrayList<>();
for (Node node : imGraph.getNodes()) {
if (!(node.getNodeType() == NodeType.ERROR)) {
nodes.add(node);
}
}
Graph graph2 = new EdgeListGraph(nodes);
for (Edge edge : imGraph.getEdges()) {
Node node1 = edge.getNode1();
Node node2 = edge.getNode2();
if (!graph2.containsNode(node1)) continue;
if (!graph2.containsNode(node2)) continue;
if (graph2.isAdjacentTo(node1, node2)) {
continue;
}
List edges = imGraph.getEdges(node1, node2);
if (edges.size() == 1) {
graph2.addEdge(edges.iterator().next());
} else {
Expression expression1 = pm.getNodeExpression(node1);
Expression expression2 = pm.getNodeExpression(node2);
String param1 = GraphWrapper.findParameter(expression1, node2.getName());
String param2 = GraphWrapper.findParameter(expression2, node1.getName());
if (param1 == null || param2 == null) {
continue;
}
double value1 = im.getParameterValue(param1);
double value2 = im.getParameterValue(param2);
if (value2 > value1) {
graph2.addDirectedEdge(node1, node2);
} else if (value1 > value2) {
graph2.addDirectedEdge(node2, node1);
}
}
}
return graph2;
}
/**
* getGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getGraph() {
return this.graphs.get(getModelIndex());
}
/**
* {@inheritDoc}
*/
public void setGraph(Graph graph) {
this.graphs = new ArrayList<>();
this.graphs.add(graph);
// log();
}
/**
* allowRandomGraph.
*
* @return a boolean
*/
public boolean allowRandomGraph() {
return true;
}
/**
* {@inheritDoc}
*/
@Override
public IndependenceTest getIndependenceTest() {
return new MsepTest(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;
}
/**
* 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 getGraph();
}
/**
* 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();
}
/**
* {@inheritDoc}
*/
@Override
public Map getParamSettings() {
Map paramSettings = new HashMap<>();
paramSettings.put("# Vars", Integer.toString(getGraph().getNumNodes()));
paramSettings.put("# Edges", Integer.toString(getGraph().getNumEdges()));
if (getGraph().paths().existsDirectedCycle()) paramSettings.put("Cyclic", null);
return paramSettings;
}
/**
* {@inheritDoc}
*/
@Override
public Map getAllParamSettings() {
return this.allParamSettings;
}
//==========================PRIVATE METaHODS===========================//
/**
* {@inheritDoc}
*/
@Override
public void setAllParamSettings(Map paramSettings) {
this.allParamSettings = paramSettings;
}
/**
* Getter for the field parameters.
*
* @return a {@link edu.cmu.tetrad.util.Parameters} object
*/
public Parameters getParameters() {
return this.parameters;
}
// private void log() {
// TetradLogger.getInstance().log("info", "General Graph");
// TetradLogger.getInstance().log("graph", "" + getGraph());
// }
/**
* 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 numModels.
*
* @return a int
*/
public int getNumModels() {
return this.numModels;
}
/**
* Getter for the field modelIndex.
*
* @return a int
*/
public int getModelIndex() {
return this.modelIndex;
}
/**
* {@inheritDoc}
*/
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;
}
/**
* {@inheritDoc}
*/
@Override
public List getGraphs() {
return this.graphs;
}
}
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