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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.tetrad.search.utils;
import edu.cmu.tetrad.bayes.BayesIm;
import edu.cmu.tetrad.bayes.BayesPm;
import edu.cmu.tetrad.bayes.MlBayesIm;
import edu.cmu.tetrad.graph.Dag;
import edu.cmu.tetrad.graph.GraphNode;
import edu.cmu.tetrad.graph.Node;
import nu.xom.Attribute;
import nu.xom.Element;
import nu.xom.Elements;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Takes an xml element representing a bayes im and converts it to a BayesIM
*
* @author mattheweasterday
*/
public class BayesImParser {
private boolean useDisplayNames;
/**
* Creates a new BayesImParser.
*/
public BayesImParser() {
}
/**
* Sets whether to use display names.
*
* @param useDisplayNames True, if so.
*/
public void setUseDisplayNames(boolean useDisplayNames) {
this.useDisplayNames = useDisplayNames;
}
/**
* Takes an xml representation of a Bayes IM and reinstantiates the IM
*
* @param element the xml of the IM
* @return the BayesIM
*/
public BayesIm getBayesIm(Element element) {
if (!"smile".equals(element.getQualifiedName())) {
throw new IllegalArgumentException("Expecting " +
"smile" + " element.");
}
Elements elements = element.getChildElements();
Element element0 = null, element1 = null;
for (int i = 0; i < elements.size(); i++) {
Element _element = elements.get(i);
if ("nodes".equals(_element.getQualifiedName())) {
element0 = _element;
}
if ("extensions".equals(_element.getQualifiedName())) {
element1 = _element.getFirstChildElement("genie");
}
}
Map displayNames = mapDisplayNames(element1, this.useDisplayNames);
assert element0 != null;
return buildIM(element0, displayNames);
}
private BayesIm buildIM(Element element0, Map displayNames) {
Elements elements = element0.getChildElements();
for (int i = 0; i < elements.size(); i++) {
if (!"cpt".equals(elements.get(i).getQualifiedName())) {
throw new IllegalArgumentException("Expecting cpt element.");
}
}
Dag dag = new Dag();
// Get the nodes.
for (int i = 0; i < elements.size(); i++) {
Element cpt = elements.get(i);
String name = cpt.getAttribute(0).getValue();
if (displayNames == null) {
dag.addNode(new GraphNode(name));
} else {
dag.addNode(new GraphNode(displayNames.get(name)));
}
}
// Get the edges.
for (int i = 0; i < elements.size(); i++) {
Element cpt = elements.get(i);
Elements cptElements = cpt.getChildElements();
for (int j = 0; j < cptElements.size(); j++) {
Element cptElement = cptElements.get(j);
if (cptElement.getQualifiedName().equals("parents")) {
String list = cptElement.getValue();
String[] parentNames = list.split(" ");
for (String name : parentNames) {
Node parent;
Node child;
if (displayNames == null) {
parent = dag.getNode(name);
child = dag.getNode(cpt.getAttribute(0).getValue());
} else {
parent = dag.getNode(displayNames.get(name));
child = dag.getNode(displayNames.get(cpt.getAttribute(0).getValue()));
}
dag.addDirectedEdge(parent, child);
}
}
}
String name;
if (displayNames == null) {
name = cpt.getAttribute(0).getValue();
} else {
name = displayNames.get(cpt.getAttribute(0).getValue());
}
dag.addNode(new GraphNode(name));
}
// PM
BayesPm pm = new BayesPm(dag);
for (int i = 0; i < elements.size(); i++) {
Element cpt = elements.get(i);
String varName = cpt.getAttribute(0).getValue();
Node node;
if (displayNames == null) {
node = dag.getNode(varName);
} else {
node = dag.getNode(displayNames.get(varName));
}
Elements cptElements = cpt.getChildElements();
List stateNames = new ArrayList<>();
for (int j = 0; j < cptElements.size(); j++) {
Element cptElement = cptElements.get(j);
if (cptElement.getQualifiedName().equals("state")) {
Attribute attribute = cptElement.getAttribute(0);
String stateName = attribute.getValue();
stateNames.add(stateName);
}
}
pm.setCategories(node, stateNames);
}
// IM
BayesIm im = new MlBayesIm(pm);
for (int nodeIndex = 0; nodeIndex < elements.size(); nodeIndex++) {
Element cpt = elements.get(nodeIndex);
Elements cptElements = cpt.getChildElements();
for (int j = 0; j < cptElements.size(); j++) {
Element cptElement = cptElements.get(j);
if (cptElement.getQualifiedName().equals("probabilities")) {
String list = cptElement.getValue();
String[] probsStrings = list.split(" ");
List probs = new ArrayList<>();
for (String probString : probsStrings) {
probs.add(Double.parseDouble(probString));
}
int count = -1;
for (int row = 0; row < im.getNumRows(nodeIndex); row++) {
for (int col = 0; col < im.getNumColumns(nodeIndex); col++) {
im.setProbability(nodeIndex, row, col, probs.get(++count));
}
}
}
}
}
return im;
}
private Map mapDisplayNames(Element element1, boolean useDisplayNames) {
if (useDisplayNames) {
Map displayNames = new HashMap<>();
Elements elements = element1.getChildElements();
for (int i = 0; i < elements.size(); i++) {
Element nodeElement = elements.get(i);
if (nodeElement.getLocalName().equals("textbox")) continue;
String varName = nodeElement.getAttribute(0).getValue();
Elements nodeElements = nodeElement.getChildElements();
String displayName = null;
for (int j = 0; j < nodeElements.size(); j++) {
Element e = nodeElements.get(j);
if (e.getQualifiedName().equals("name")) {
String value = e.getValue();
value = value.replace(" ", "_");
displayName = value;
break;
}
}
displayNames.put(varName, displayName);
}
return displayNames;
} else {
return null;
}
}
}
