edu.cmu.tetradapp.editor.EvidenceWizardMultipleObs Maven / Gradle / Ivy
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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. //
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// 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 //
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package edu.cmu.tetradapp.editor;
import edu.cmu.tetrad.bayes.BayesIm;
import edu.cmu.tetrad.bayes.BayesPm;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.graph.NodeType;
import edu.cmu.tetrad.util.NumberFormatUtil;
import edu.cmu.tetradapp.model.UpdaterWrapper;
import edu.cmu.tetradapp.workbench.DisplayNode;
import edu.cmu.tetradapp.workbench.GraphWorkbench;
import org.apache.commons.math3.util.FastMath;
import javax.swing.*;
import javax.swing.border.MatteBorder;
import java.text.NumberFormat;
import java.util.LinkedList;
import java.util.List;
/**
* Lets the user visually add and remove evidence, perform updates, and view Bayes updating results.
*
* @author William Taysom -- Jun 14, 2003
* @author josephramsey
*/
class EvidenceWizardMultipleObs extends JPanel {
private final UpdaterWrapper updaterWrapper;
private final GraphWorkbench workbench;
private final EvidenceEditorObs evidenceEditor;
private JTextArea textArea = new JTextArea("Nothing to display");
/**
* This is the wizard for the BayesUpdateEditor class. It allows you to add and remove evidence, and to updater
* based on it.
*
* @param updaterWrapper a {@link edu.cmu.tetradapp.model.UpdaterWrapper} object
* @param workbench a {@link edu.cmu.tetradapp.workbench.GraphWorkbench} object
*/
public EvidenceWizardMultipleObs(UpdaterWrapper updaterWrapper,
GraphWorkbench workbench) {
if (updaterWrapper == null) {
throw new NullPointerException();
}
if (workbench == null) {
throw new NullPointerException();
}
// Components.
this.updaterWrapper = updaterWrapper;
this.workbench = workbench;
workbench.setAllowDoubleClickActions(false);
setBorder(new MatteBorder(10, 10, 10, 10, getBackground()));
setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
JButton calcMarginalsAndJointButton =
new JButton("Calculate Marginals and Joint");
// Do Layout.
Box b0 = Box.createHorizontalBox();
b0.add(new JLabel("" +
"Select a set of nodes (by holding down the shift key) whose" +
"
marginals you would like to see given the evidence indicated" +
"
above. Click the 'Calculate Marginals' button to view" +
"
marginals and log odds results."));
b0.add(Box.createHorizontalGlue());
add(b0);
add(Box.createVerticalStrut(10));
this.evidenceEditor = new EvidenceEditorObs(updaterWrapper.getBayesUpdater().getEvidence());
getUpdaterWrapper().getParams().set("evidence", this.evidenceEditor.getEvidence());
add(this.evidenceEditor);
add(Box.createVerticalStrut(10));
Box b2 = Box.createHorizontalBox();
b2.add(Box.createHorizontalGlue());
b2.add(calcMarginalsAndJointButton);
add(b2);
add(Box.createVerticalGlue());
// Add listeners.
calcMarginalsAndJointButton.addActionListener(e -> {
List selectedGraphNodes =
getWorkbench().getSelectedNodes();
getUpdaterWrapper().getBayesUpdater().setEvidence(EvidenceWizardMultipleObs.this.evidenceEditor.getEvidence());
Graph updatedGraph = getUpdaterWrapper().getBayesUpdater().getManipulatedGraph();
getWorkbench().setGraph(updatedGraph);
BayesIm manipulatedIm = getUpdaterWrapper()
.getBayesUpdater().getManipulatedBayesIm();
List selectedNodes = new LinkedList<>();
for (DisplayNode selectedGraphNode : selectedGraphNodes) {
Node tetradNode = selectedGraphNode.getModelNode();
String selectedNodeName = tetradNode.getName();
Node selectedNode = updatedGraph.getNode(selectedNodeName);
// skip latent variables
if (selectedNode.getNodeType() == NodeType.MEASURED) {
selectedNodes.add(selectedNode);
}
}
for (Node node : selectedNodes) {
getWorkbench().selectNode(node);
}
selectedNodes.sort((o1, o2) -> {
String name1 = o1.getName();
String name2 = o2.getName();
return name1.compareTo(name2);
});
JTextArea marginalsArea = new JTextArea();
marginalsArea.setEditable(false);
NumberFormat nf = NumberFormatUtil.getInstance().getNumberFormat();
if (selectedNodes.size() == 0) {
marginalsArea.append("\nNo nodes selected.");
} else {
appendMarginals(selectedNodes, marginalsArea, manipulatedIm,
nf);
appendJoint(selectedNodes, marginalsArea, manipulatedIm,
nf);
}
EvidenceWizardMultipleObs.this.textArea = marginalsArea;
firePropertyChange("updateButtonPressed", null, null);
});
}
private void appendMarginals(List selectedNodes,
JTextArea marginalsArea, BayesIm manipulatedIm, NumberFormat nf) {
BayesPm bayesPm = manipulatedIm.getBayesPm();
marginalsArea.append("MARGINALS FOR SELECTED VARIABLES:\n");
for (Node selectedNode : selectedNodes) {
marginalsArea.append(
"\nVariable " + selectedNode.getName() + ":\n");
int nodeIndex = manipulatedIm.getNodeIndex(selectedNode);
for (int j = 0; j < bayesPm.getNumCategories(selectedNode); j++) {
double prob = getUpdaterWrapper().getBayesUpdater().getMarginal(nodeIndex, j);
// identifiability returns -1 if the requested prob is unidentifiable
if (prob < 0.0) {
marginalsArea.append("Category " +
bayesPm.getCategory(selectedNode, j) + ": p = " +
"Unidentifiable" + ", log odds = " +
"*" + "\n");
} else {
double logOdds = FastMath.log(prob / (1. - prob));
marginalsArea.append("Category " +
bayesPm.getCategory(selectedNode, j) + ": p = " +
nf.format(prob) + ", log odds = " +
nf.format(logOdds) + "\n");
}
}
}
}
private void appendJoint(List selectedNodes, JTextArea marginalsArea,
BayesIm manipulatedIm, NumberFormat nf) {
if (!getUpdaterWrapper().getBayesUpdater().isJointMarginalSupported()) {
marginalsArea.append("\n\n(Calculation of joint not supported " +
"for this updater.)");
return;
}
BayesPm bayesPm = manipulatedIm.getBayesPm();
int numNodes = selectedNodes.size();
int[] dims = new int[numNodes];
int[] variables = new int[numNodes];
int numRows = 1;
for (int i = 0; i < numNodes; i++) {
Node node = selectedNodes.get(i);
int numCategories = bayesPm.getNumCategories(node);
variables[i] = manipulatedIm.getNodeIndex(node);
dims[i] = numCategories;
numRows *= numCategories;
}
marginalsArea.append("\n\nJOINT OVER SELECTED VARIABLES:\n\n");
for (Node selectedNode : selectedNodes) {
marginalsArea.append(selectedNode + "\t");
}
marginalsArea.append("Joint\tLog odds\n");
for (int row = 0; row < numRows; row++) {
int[] values = getCategories(row, dims);
double prob = getUpdaterWrapper().getBayesUpdater().getJointMarginal(variables, values);
marginalsArea.append("\n");
for (int j = 0; j < numNodes; j++) {
Node node = selectedNodes.get(j);
marginalsArea.append(bayesPm.getCategory(node, values[j]));
marginalsArea.append("\t");
}
// identifiability returns -1 if the requested prob is unidentifiable
if (prob < 0.0) {
marginalsArea.append("Unidentifiable" + "\t");
marginalsArea.append("*");
} else {
double logOdds = FastMath.log(prob / (1. - prob));
marginalsArea.append(nf.format(prob) + "\t");
marginalsArea.append(nf.format(logOdds));
}
}
}
private int[] getCategories(int row, int[] dims) {
int[] values = new int[dims.length];
for (int i = dims.length - 1; i >= 0; i--) {
values[i] = row % dims[i];
row /= dims[i];
}
return values;
}
private UpdaterWrapper getUpdaterWrapper() {
return this.updaterWrapper;
}
private GraphWorkbench getWorkbench() {
return this.workbench;
}
/**
* Getter for the field textArea.
*
* @return a {@link javax.swing.JTextArea} object
*/
public JTextArea getTextArea() {
return this.textArea;
}
}
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