edu.cmu.tetradapp.editor.IndependenceFactsEditor 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.editor;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.search.IndependenceTest;
import edu.cmu.tetrad.search.test.IndependenceResult;
import edu.cmu.tetrad.search.test.MsepTest;
import edu.cmu.tetrad.util.ChoiceGenerator;
import edu.cmu.tetrad.util.SublistGenerator;
import edu.cmu.tetradapp.model.IndTestModel;
import edu.cmu.tetradapp.model.IndTestProducer;
import edu.cmu.tetradapp.model.IndependenceResultIndFacts;
import edu.cmu.tetradapp.util.IntTextField;
import javax.swing.*;
import javax.swing.border.EmptyBorder;
import javax.swing.table.AbstractTableModel;
import javax.swing.table.DefaultTableCellRenderer;
import javax.swing.table.JTableHeader;
import java.awt.*;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.List;
import java.util.*;
import java.util.prefs.Preferences;
/**
* Lists independence facts specified by user and allows the list to be sorted by independence fact or by p value.
*
* @author josephramsey
*/
public class IndependenceFactsEditor extends JPanel {
private final NumberFormat nf = new DecimalFormat("0.0000");
private IndTestModel model;
private LinkedList vars;
private JTextField textField;
private List indTestProducers;
private List> results = new ArrayList<>();
private AbstractTableModel tableModel;
private int sortDir;
private int lastSortCol;
private boolean showPs;
public IndependenceFactsEditor(IndTestModel model) {
this.indTestProducers = model.getIndTestProducers();
this.model = model;
this.vars = new LinkedList<>();
this.textField = new JTextField(40);
this.textField.setEditable(false);
this.textField.setFont(new Font("Serif", Font.BOLD, 14));
this.textField.setBackground(new Color(250, 250, 250));
this.vars = model.getVars();
this.results = model.getResults();
if (this.results == null) {
this.results = new ArrayList<>();
}
resetText();
if (this.indTestProducers.isEmpty()) {
throw new IllegalArgumentException("At least one source must be specified");
}
List names = this.indTestProducers.get(0).getIndependenceTest().getVariableNames();
for (int i = 1; i < this.indTestProducers.size(); i++) {
List _names = this.indTestProducers.get(i).getIndependenceTest().getVariableNames();
if (!new HashSet<>(names).equals(new HashSet<>(_names))) {
throw new IllegalArgumentException("All sources must have the same variable names.");
}
}
buildGui();
}
//========================PUBLIC METHODS==========================//
public IndependenceFactsEditor(LayoutManager layout, boolean isDoubleBuffered) {
super(layout, isDoubleBuffered);
}
//=============================PRIVATE METHODS=======================//
private static List asList(int[] indices, List nodes) {
List list = new LinkedList<>();
for (int i : indices) {
list.add(nodes.get(i));
}
return list;
}
private static String factString(Node x, Node y, Set condSet) {
StringBuilder sb = new StringBuilder();
sb.append(x.getName());
sb.append(" _||_ ");
sb.append(y.getName());
Iterator it = condSet.iterator();
if (it.hasNext()) {
sb.append(" | ");
sb.append(it.next());
}
while (it.hasNext()) {
sb.append(", ");
sb.append(it.next());
}
return sb.toString();
}
/**
* Performs the action of opening a session from a file.
*/
private void buildGui() {
// this.independenceTest = getIndTestProducer().getIndependenceTest();
List varNames = new ArrayList<>();
varNames.add("VAR");
varNames.addAll(getDataVars());
varNames.add("?");
varNames.add("+");
JComboBox variableBox = new JComboBox<>();
DefaultComboBoxModel aModel1 = new DefaultComboBoxModel<>(varNames.toArray(new String[0]));
aModel1.setSelectedItem("VAR");
variableBox.setModel(aModel1);
variableBox.addActionListener(e -> {
JComboBox box = (JComboBox) e.getSource();
String var = (String) box.getSelectedItem();
LinkedList vars = getVars();
int size = vars.size();
if ("VAR".equals(var)) {
return;
}
if ("?".equals(var)) {
if (!vars.contains("+")) {
vars.addLast(var);
}
} else if ("+".equals(var)) {
if (size >= 2) {
vars.addLast(var);
}
} else if ((vars.indexOf("?") < 2) && !(vars.contains("+")) &&
!(vars.contains(var))) {
vars.add(var);
}
resetText();
// This is a workaround to an introduced bug in the JDK whereby
// repeated selections of the same item send out just one
// action event.
DefaultComboBoxModel aModel = new DefaultComboBoxModel<>(
varNames.toArray(new String[0]));
aModel.setSelectedItem("VAR");
variableBox.setModel(aModel);
});
JButton delete = new JButton("Delete");
delete.addActionListener(e -> {
if (!getVars().isEmpty()) {
getVars().removeLast();
resetText();
}
});
this.textField.addKeyListener(new KeyAdapter() {
public void keyTyped(KeyEvent e) {
if ('?' == e.getKeyChar()) {
variableBox.setSelectedItem("?");
} else if ('+' == e.getKeyChar()) {
variableBox.setSelectedItem("+");
} else if ('\b' == e.getKeyChar()) {
IndependenceFactsEditor.this.vars.removeLast();
resetText();
}
e.consume();
}
});
delete.addKeyListener(new KeyAdapter() {
public void keyTyped(KeyEvent e) {
if ('?' == e.getKeyChar()) {
variableBox.setSelectedItem("?");
} else if ('+' == e.getKeyChar()) {
variableBox.setSelectedItem("+");
} else if ('\b' == e.getKeyChar()) {
IndependenceFactsEditor.this.vars.removeLast();
resetText();
}
}
});
variableBox.addKeyListener(new KeyAdapter() {
public void keyTyped(KeyEvent e) {
super.keyTyped(e);
if ('\b' == e.getKeyChar()) {
IndependenceFactsEditor.this.vars.removeLast();
resetText();
}
}
});
JButton list = new JButton("LIST");
list.setFont(new Font("Dialog", Font.BOLD, 14));
list.addActionListener(e -> generateResults());
Box b1 = Box.createVerticalBox();
Box b2 = Box.createHorizontalBox();
b2.add(new JLabel("Compares conditional independence tests from the given sources: "));
b2.add(Box.createHorizontalGlue());
b1.add(b2);
for (int i = 0; i < this.indTestProducers.size(); i++) {
Box b2a = Box.createHorizontalBox();
b2a.add(new JLabel(this.indTestProducers.get(i).getName() + ": " + getIndependenceTest(i).toString()));
b2a.add(Box.createHorizontalGlue());
b1.add(b2a);
}
b1.add(Box.createVerticalStrut(5));
Box b3 = Box.createHorizontalBox();
b3.add(getTextField());
b3.add(variableBox);
b3.add(delete);
b1.add(b3);
b1.add(Box.createVerticalStrut(10));
this.tableModel = new AbstractTableModel() {
public String getColumnName(int column) {
if (column == 0) {
return "Index";
}
if (column == 1) {
return "Fact";
} else if (column >= 2) {
return IndependenceFactsEditor.this.indTestProducers.get(column - 2).getName();// "Judgment";
}
return null;
}
public int getColumnCount() {
return 2 + IndependenceFactsEditor.this.indTestProducers.size();
}
public int getRowCount() {
return IndependenceFactsEditor.this.results.size();
}
public Object getValueAt(int rowIndex, int columnIndex) {
if (rowIndex > IndependenceFactsEditor.this.results.size()) return null;
if (columnIndex == 0) {
return IndependenceFactsEditor.this.results.get(rowIndex).get(0).getIndex();
}
if (columnIndex == 1) {
return IndependenceFactsEditor.this.results.get(rowIndex).get(0).getFact();
}
IndependenceResultIndFacts independenceResult = IndependenceFactsEditor.this.results.get(rowIndex).get(columnIndex - 2);
for (int i = 0; i < IndependenceFactsEditor.this.indTestProducers.size(); i++) {
if (columnIndex == i + 2) {
if (getIndependenceTest(i) instanceof MsepTest) {
if (independenceResult.getType() == IndependenceResultIndFacts.Type.INDEPENDENT) {
return "D-SEPARATED";
} else if (independenceResult.getType() == IndependenceResultIndFacts.Type.DEPENDENT) {
return "d-connected";
} else if (independenceResult.getType() == IndependenceResultIndFacts.Type.UNDETERMINED) {
return "*";
}
} else {
if (IndependenceFactsEditor.this.isShowPs()) {
return nf.format(independenceResult.getpValue());
} else {
if (independenceResult.getType() == IndependenceResultIndFacts.Type.INDEPENDENT) {
return "INDEPENDENT";
} else if (independenceResult.getType() == IndependenceResultIndFacts.Type.DEPENDENT) {
return "dependent";
} else if (independenceResult.getType() == IndependenceResultIndFacts.Type.UNDETERMINED) {
return "*";
}
}
}
}
}
return null;
}
public Class getColumnClass(int columnIndex) {
if (columnIndex == 0) {
return Number.class;
}
if (columnIndex == 1) {
return String.class;
} else if (columnIndex == 2) {
return Number.class;
} else {
return Number.class;
}
}
};
JTable table = new JTable(tableModel);
table.getColumnModel().getColumn(0).setMinWidth(40);
table.getColumnModel().getColumn(0).setMaxWidth(40);
table.getColumnModel().getColumn(1).setMinWidth(200);
table.getColumnModel().getColumn(1).setCellRenderer(new Renderer(this));
for (int i = 2; i < table.getColumnModel().getColumnCount(); i++) {
table.getColumnModel().getColumn(i).setMinWidth(100);
table.getColumnModel().getColumn(i).setMaxWidth(100);
table.getColumnModel().getColumn(i).setCellRenderer(new Renderer(this));
}
JTableHeader header = table.getTableHeader();
header.addMouseListener(new MouseAdapter() {
public void mouseClicked(MouseEvent e) {
JTableHeader header = (JTableHeader) e.getSource();
Point point = e.getPoint();
int col = header.columnAtPoint(point);
int sortCol = header.getTable().convertColumnIndexToModel(col);
IndependenceFactsEditor.this.sortByColumn(sortCol);
}
});
JScrollPane scroll = new JScrollPane(table);
scroll.setPreferredSize(new Dimension(400, 400));
b1.add(scroll);
Box b4 = Box.createHorizontalBox();
b4.add(new JLabel("Limit list to "));
IntTextField field = new IntTextField(this.getListLimit(), 7);
field.setFilter((value, oldValue) -> {
try {
this.setListLimit(value);
return value;
} catch (Exception e) {
return oldValue;
}
});
b4.add(field);
b4.add(new JLabel(" items."));
b4.add(Box.createHorizontalStrut(10));
JButton showPValues = new JButton("Show P Values");
showPValues.addMouseListener(new MouseAdapter() {
@Override
public void mouseClicked(MouseEvent e) {
IndependenceFactsEditor.this.toggleShowPs();
if (showPs) {
showPValues.setText("Show Independencies");
} else {
showPValues.setText("Show P Values or Scores");
}
}
});
b4.add(showPValues);
b4.add(Box.createHorizontalGlue());
b4.add(list);
b1.add(b4);
b1.add(Box.createVerticalStrut(10));
JPanel panel = this;
panel.setLayout(new BorderLayout());
panel.add(b1, BorderLayout.CENTER);
panel.setBorder(new EmptyBorder(10, 10, 10, 10));
}
private void sortByColumn(int sortCol) {
if (sortCol == this.getLastSortCol()) {
this.setSortDir(-1 * this.getSortDir());
} else {
this.setSortDir(1);
}
this.setLastSortCol(sortCol);
results.sort((r1, r2) -> {
switch (sortCol) {
case 0:
case 1:
return this.getSortDir() * (r1.get(0).getIndex() - r2.get(0).getIndex());
default:
int ind1;
int ind2;
int col = sortCol - 2;
if (r1.get(col).getType() == IndependenceResultIndFacts.Type.UNDETERMINED) {
ind1 = 0;
} else if (r1.get(col).getType() == IndependenceResultIndFacts.Type.DEPENDENT) {
ind1 = 1;
} else {
ind1 = 2;
}
if (r2.get(col).getType() == IndependenceResultIndFacts.Type.UNDETERMINED) {
ind2 = 0;
} else if (r2.get(col).getType() == IndependenceResultIndFacts.Type.DEPENDENT) {
ind2 = 1;
} else {
ind2 = 2;
}
return this.getSortDir() * (ind1 - ind2);
}
});
tableModel.fireTableDataChanged();
}
private boolean isShowPs() {
return showPs;
}
private void toggleShowPs() {
showPs = !showPs;
tableModel.fireTableDataChanged();
}
private List getDataVars() {
return this.getIndependenceTest(0).getVariableNames();
}
private void resetText() {
StringBuilder buf = new StringBuilder();
if (this.getVars().size() == 0) {
buf.append("Choose variables and wildcards from dropdown-->");
}
if (this.getVars().size() > 0) {
buf.append(" ").append(this.getVars().get(0));
buf.append(" _||_ ");
}
if (this.getVars().size() > 1) {
buf.append(this.getVars().get(1));
}
if (this.getVars().size() > 2) {
buf.append(" | ");
}
for (int i = 2; i < this.getVars().size() - 1; i++) {
buf.append(this.getVars().get(i));
buf.append(", ");
}
if (this.getVars().size() > 2) {
buf.append(this.getVars().get(this.getVars().size() - 1));
}
model.setVars(this.getVars());
textField.setText(buf.toString());
}
private void generateResults() {
results = new ArrayList<>();
List dataVars = this.getDataVars();
if (this.getVars().size() < 2) {
tableModel.fireTableDataChanged();
return;
}
// Need a choice generator over the ?'s, and a depth choice generator over the +'s. The +'s all have to come
// at the end at index >= 2.
int numQuestionMarksFirstTwo = 0;
int numQuestionMarksRest = 0;
int numPluses = 0;
int numFixed = 0;
for (int i = 0; i < vars.size(); i++) {
String var = vars.get(i);
if ("?".equals(var) && i < 2) numQuestionMarksFirstTwo++;
else if ("?".equals(var)) numQuestionMarksRest++;
else if ("+".equals(var)) numPluses++;
else numFixed++;
}
int[] questionMarkFirstTwoIndices = new int[numQuestionMarksFirstTwo];
int[] questionMarkRestIndices = new int[numQuestionMarksRest];
int[] plusIndices = new int[numPluses];
int[] fixedIndices = new int[numFixed];
String[] fixedVars = new String[numFixed];
int _i = -1;
int _j = -1;
int _k = -1;
int _l = -1;
for (int i = 0; i < vars.size(); i++) {
if ("?".equals(vars.get(i)) && i < 2) questionMarkFirstTwoIndices[++_i] = i;
else if ("?".equals(vars.get(i))) questionMarkRestIndices[++_j] = i;
else if ("+".equals(vars.get(i))) plusIndices[++_k] = i;
else {
fixedIndices[++_l] = i;
fixedVars[_l] = vars.get(i);
}
}
List vars1 = new ArrayList<>(dataVars);
vars1.removeAll(vars);
ChoiceGenerator gen1 = new ChoiceGenerator(vars1.size(), questionMarkFirstTwoIndices.length);
int[] choice1;
LOOP:
while ((choice1 = gen1.next()) != null) {
List s2 = asList(choice1, vars1);
List vars2 = new ArrayList<>(vars1);
vars2.removeAll(s2);
ChoiceGenerator gen2 = new ChoiceGenerator(vars2.size(), questionMarkRestIndices.length);
int[] choice2;
while ((choice2 = gen2.next()) != null) {
List s3 = asList(choice2, vars2);
List vars3 = new ArrayList<>(vars2);
vars3.removeAll(s3);
SublistGenerator gen3 = new SublistGenerator(vars3.size(), plusIndices.length);
int[] choice3;
while ((choice3 = gen3.next()) != null) {
results.add(new ArrayList<>());
for (int prod = 0; prod < indTestProducers.size(); prod++) {
String[] vars4 = new String[fixedIndices.length + questionMarkFirstTwoIndices.length
+ questionMarkRestIndices.length + choice3.length];
for (int i = 0; i < fixedIndices.length; i++) {
vars4[fixedIndices[i]] = fixedVars[i];
}
for (int i = 0; i < choice1.length; i++) {
vars4[questionMarkFirstTwoIndices[i]] = vars1.get(choice1[i]);
}
for (int i = 0; i < choice2.length; i++) {
vars4[questionMarkRestIndices[i]] = vars2.get(choice2[i]);
}
for (int i = 0; i < choice3.length; i++) {
vars4[plusIndices[i]] = vars3.get(choice3[i]);
}
IndependenceTest independenceTest = this.getIndependenceTest(prod);
Node x = independenceTest.getVariable(vars4[0]);
Node y = independenceTest.getVariable(vars4[1]);
Set z = new HashSet<>();
for (int i = 2; i < vars4.length; i++) {
z.add(independenceTest.getVariable(vars4[i]));
}
IndependenceResultIndFacts.Type indep;
double pValue;
try {
IndependenceResult result = independenceTest.checkIndependence(x, y, z);
indep = result.isIndependent()
? IndependenceResultIndFacts.Type.INDEPENDENT
: IndependenceResultIndFacts.Type.DEPENDENT;
pValue = result.getPValue();
} catch (Exception e) {
indep = IndependenceResultIndFacts.Type.UNDETERMINED;
pValue = Double.NaN;
}
this.results.get(this.results.size() - 1).add(new IndependenceResultIndFacts(this.results.size(),
IndependenceFactsEditor.factString(x, y, z), indep, pValue));
}
if (this.results.size() > getListLimit()) break LOOP;
}
}
}
this.model.setResults(this.results);
this.tableModel.fireTableDataChanged();
}
private LinkedList getVars() {
return this.vars;
}
private JTextField getTextField() {
return this.textField;
}
private IndependenceTest getIndependenceTest(int i) {
return this.indTestProducers.get(i).getIndependenceTest();
}
private int getLastSortCol() {
return this.lastSortCol;
}
private void setLastSortCol(int lastSortCol) {
if (lastSortCol < 0 || lastSortCol > 4) {
throw new IllegalArgumentException();
}
this.lastSortCol = lastSortCol;
}
private int getSortDir() {
return this.sortDir;
}
private void setSortDir(int sortDir) {
if (!(sortDir == 1 || sortDir == -1)) {
throw new IllegalArgumentException();
}
this.sortDir = sortDir;
}
private int getListLimit() {
return Preferences.userRoot().getInt("indFactsListLimit", 10000);
}
private void setListLimit(int listLimit) {
if (listLimit < 1) {
throw new IllegalArgumentException();
}
Preferences.userRoot().putInt("indFactsListLimit", listLimit);
}
static class Renderer extends DefaultTableCellRenderer {
private final IndependenceFactsEditor editor;
private JTable table;
private int row;
private boolean selected;
public Renderer(IndependenceFactsEditor editor) {
this.editor = editor;
}
public void setValue(Object value) {
int indep = 0;
int numCols = table.getModel().getColumnCount();
if (selected) {
setForeground(table.getSelectionForeground());
setBackground(table.getSelectionBackground());
} else {
for (int i = 2; i < numCols; i++) {
Object _value = table.getModel().getValueAt(row, i);
if ("INDEPENDENT".equals(_value) || "D-SEPARATED".equals(_value)) {
indep++;
}
}
this.setForeground(table.getForeground());
if (!editor.isShowPs()) {
if (!(indep == 0 || indep == numCols - 2)) {
this.setBackground(Color.YELLOW);
} else {
this.setBackground(table.getBackground());
}
} else {
this.setBackground(table.getBackground());
}
}
this.setText((String) value);
}
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
this.table = table;
this.row = row;
selected = isSelected;
return super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
}
}
}
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