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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.sem;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.graph.SemGraph;
import nu.xom.Attribute;
import nu.xom.Element;
import java.util.ArrayList;
import java.util.List;
/**
* This class converts a SemIm into xml.
*
* @author Matt Easterday
*/
public class SemXmlRenderer {
/**
* Converts a Sem Im into xml.
*
* @param semIm the instantiated structural equation model to convert
* @return xml representation
*/
public static Element getElement(SemIm semIm) {
Element semElement = new Element(SemXmlConstants.SEM);
semElement.appendChild(SemXmlRenderer.makeVariables(semIm));
semElement.appendChild(SemXmlRenderer.makeEdges(semIm));
semElement.appendChild(SemXmlRenderer.makeMarginalErrorDistribution(semIm));
semElement.appendChild(SemXmlRenderer.makeJointErrorDistribution(semIm));
return semElement;
}
private static Element makeVariables(SemIm semIm) {
Element variablesElement = new Element(SemXmlConstants.SEM_VARIABLES);
Element variable;
Node measuredNode, latentNode;
for (Node node1 : semIm.getSemPm().getMeasuredNodes()) {
measuredNode = node1;
variable = new Element(SemXmlConstants.CONTINUOUS_VARIABLE);
variable.addAttribute(new Attribute(SemXmlConstants.NAME, measuredNode.getName()));
variable.addAttribute(new Attribute(SemXmlConstants.IS_LATENT, "no"));
variable.addAttribute(new Attribute(SemXmlConstants.INTERCEPT, Double.toString(semIm.getIntercept(measuredNode))));
variable.addAttribute(new Attribute(SemXmlConstants.X, Integer.toString(measuredNode.getCenterX())));
variable.addAttribute(new Attribute(SemXmlConstants.Y, Integer.toString(measuredNode.getCenterY())));
variablesElement.appendChild(variable);
}
for (Node node : semIm.getSemPm().getLatentNodes()) {
latentNode = node;
variable = new Element(SemXmlConstants.CONTINUOUS_VARIABLE);
variable.addAttribute(new Attribute(SemXmlConstants.NAME, latentNode.getName()));
variable.addAttribute(new Attribute(SemXmlConstants.IS_LATENT, "yes"));
variable.addAttribute(new Attribute(SemXmlConstants.INTERCEPT, Double.toString(semIm.getIntercept(latentNode))));
variable.addAttribute(new Attribute(SemXmlConstants.X, Integer.toString(latentNode.getCenterX())));
variable.addAttribute(new Attribute(SemXmlConstants.Y, Integer.toString(latentNode.getCenterY())));
variablesElement.appendChild(variable);
}
return variablesElement;
}
private static Element makeEdges(SemIm semIm) {
Element edgesElement = new Element(SemXmlConstants.EDGES);
Parameter param;
Element edge;
for (Parameter parameter : semIm.getSemPm().getParameters()) {
param = parameter;
if (param.getType() == ParamType.COEF) {
edge = new Element(SemXmlConstants.EDGE);
edge.addAttribute(new Attribute(SemXmlConstants.CAUSE_NODE, param.getNodeA().getName()));
edge.addAttribute(new Attribute(SemXmlConstants.EFFECT_NODE, param.getNodeB().getName()));
edge.addAttribute(new Attribute(SemXmlConstants.COEF, Double.toString(semIm.getParamValue(param))));
edge.addAttribute(new Attribute(SemXmlConstants.FIXED, Boolean.valueOf(param.isFixed()).toString()));
edgesElement.appendChild(edge);
}
}
return edgesElement;
}
private static Element makeMarginalErrorDistribution(SemIm semIm) {
Element marginalErrorElement = new Element(SemXmlConstants.MARGINAL_ERROR_DISTRIBUTION);
Element normal;
SemGraph semGraph = semIm.getSemPm().getGraph();
semGraph.setShowErrorTerms(true);
for (Node node : SemXmlRenderer.getExogenousNodes(semGraph)) {
// Node graphNode = semGraph.getChildren(node).get(0);
normal = new Element(SemXmlConstants.NORMAL);
normal.addAttribute(new Attribute(SemXmlConstants.VARIABLE, node.getName()));
// normal.addAttribute(new Attribute(SemXmlConstants.INTERCEPT, Double.toString(semIm.getIntercept(graphNode))));
normal.addAttribute(new Attribute(SemXmlConstants.VARIANCE, Double.toString(semIm.getParamValue(node, node))));
marginalErrorElement.appendChild(normal);
}
return marginalErrorElement;
}
private static List getExogenousNodes(SemGraph graph) {
List exogenousNodes = new ArrayList<>();
for (Node node : graph.getNodes()) {
exogenousNodes.add(graph.getExogenous(node));
}
return exogenousNodes;
}
private static Element makeJointErrorDistribution(SemIm semIm) {
Element jointErrorElement = new Element(SemXmlConstants.JOINT_ERROR_DISTRIBUTION);
Element normal;
Parameter param;
for (Parameter parameter : semIm.getSemPm().getParameters()) {
param = parameter;
if (param.getType() == ParamType.COVAR) {
normal = new Element(SemXmlConstants.NORMAL);
normal.addAttribute(new Attribute(SemXmlConstants.NODE_1, param.getNodeA().getName()));
normal.addAttribute(new Attribute(SemXmlConstants.NODE_2, param.getNodeB().getName()));
normal.addAttribute(new Attribute(SemXmlConstants.COVARIANCE, Double.toString(param.getStartingValue())));
jointErrorElement.appendChild(normal);
}
}
return jointErrorElement;
}
}
