edu.cmu.tetradapp.editor.FactorAnalysisAction 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.data.ContinuousVariable;
import edu.cmu.tetrad.data.CovarianceMatrix;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.data.ICovarianceMatrix;
import edu.cmu.tetrad.graph.*;
import edu.cmu.tetrad.search.FactorAnalysis;
import edu.cmu.tetrad.sem.SemIm;
import edu.cmu.tetrad.sem.SemPm;
import edu.cmu.tetrad.util.Matrix;
import edu.cmu.tetrad.util.NumberFormatUtil;
import edu.cmu.tetrad.util.TextTable;
import edu.cmu.tetradapp.util.DesktopController;
import edu.cmu.tetradapp.workbench.GraphWorkbench;
import org.apache.commons.math3.util.FastMath;
import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.Vector;
/**
* Created by IntelliJ IDEA.
*
* @author Mike Freenor
*/
public class FactorAnalysisAction extends AbstractAction {
/**
* The data edtitor that action is attached to.
*/
private final DataEditor dataEditor;
/**
* Constructs the HistogramAction given the DataEditor that its attached to.
*/
public FactorAnalysisAction(DataEditor editor) {
super("Factor Analysis...");
this.dataEditor = editor;
}
public static void main(String[] args) {
java.util.List nodes = new ArrayList<>();
for (int i = 0; i < 9; i++) {
nodes.add(new ContinuousVariable("X" + (i + 1)));
}
Graph graph = new Dag(RandomGraph.randomGraph(nodes, 0, 9,
30, 15, 15, false));
SemPm pm = new SemPm(graph);
SemIm im = new SemIm(pm);
DataSet data = im.simulateData(500, false);
ICovarianceMatrix cov = new CovarianceMatrix(data);
FactorAnalysis factorAnalysis = new FactorAnalysis(cov);
//factorAnalysis.centroidUnity();
factorAnalysis.successiveResidual();
}
public void actionPerformed(ActionEvent e) {
DataSet dataSet = (DataSet) this.dataEditor.getSelectedDataModel();
if (dataSet == null || dataSet.getNumColumns() == 0) {
JOptionPane.showMessageDialog(findOwner(), "Cannot perform factor analysis on an empty data set.");
return;
}
FactorAnalysis factorAnalysis = new FactorAnalysis(dataSet);
//factorAnalysis.centroidUnity();
JPanel panel = createDialog(factorAnalysis);
EditorWindow window = new EditorWindow(panel,
"Factor Loading Matrices", "Close", false, this.dataEditor);
DesktopController.getInstance().addEditorWindow(window, JLayeredPane.PALETTE_LAYER);
window.setVisible(true);
}
private JPanel createDialog(FactorAnalysis analysis) {
final double threshold = .2;
Matrix unrotatedSolution = analysis.successiveResidual();
Matrix rotatedSolution = analysis.successiveFactorVarimax(unrotatedSolution);
DataSet dataSet = (DataSet) this.dataEditor.getSelectedDataModel();
NumberFormat nf = NumberFormatUtil.getInstance().getNumberFormat();
String output = "Unrotated Factor Loading Matrix:\n";
output += tableString(unrotatedSolution, nf, Double.POSITIVE_INFINITY);
if (unrotatedSolution.getNumColumns() != 1) {
output += "\n\nRotated Matrix (using sequential varimax):\n";
output += tableString(rotatedSolution, nf, threshold);
}
JTextArea display = new JTextArea(output);
JScrollPane scrollPane = new JScrollPane(display);
scrollPane.setPreferredSize(new Dimension(500, 400));
display.setEditable(false);
display.setFont(new Font("Monospaced", Font.PLAIN, 12));
//editorPanel.addPropertyChangeListener(new NormalityTestListener(display));
SemGraph graph = new SemGraph();
Vector observedVariables = new Vector<>();
assert dataSet != null;
for (Node a : dataSet.getVariables()) {
graph.addNode(a);
observedVariables.add(a);
}
Vector factors = new Vector<>();
for (int i = 0; i < rotatedSolution.getNumColumns(); i++) {
ContinuousVariable factor = new ContinuousVariable("Factor" + (i + 1));
factor.setNodeType(NodeType.LATENT);
graph.addNode(factor);
factors.add(factor);
}
for (int i = 0; i < rotatedSolution.getNumRows(); i++) {
for (int j = 0; j < rotatedSolution.getNumColumns(); j++) {
if (FastMath.abs(rotatedSolution.get(i, j)) > threshold) {
graph.addDirectedEdge(factors.get(j), observedVariables.get(i));
//HEY JOE -- rotatedSolution.get(i, j) is the edge coeficient
}
}
}
LayoutUtil.defaultLayout(graph);
LayoutUtil.fruchtermanReingoldLayout(graph);
GraphWorkbench workbench = new GraphWorkbench(graph);
JScrollPane graphPane = new JScrollPane(workbench);
graphPane.setPreferredSize(new Dimension(500, 400));
Box box = Box.createHorizontalBox();
box.add(scrollPane);
box.add(Box.createHorizontalStrut(3));
//box.add(editorPanel);
box.add(Box.createHorizontalStrut(5));
box.add(Box.createHorizontalGlue());
Box vBox = Box.createVerticalBox();
vBox.add(Box.createVerticalStrut(15));
vBox.add(box);
vBox.add(Box.createVerticalStrut(5));
box.add(graphPane);
JPanel panel = new JPanel();
panel.setLayout(new BorderLayout());
panel.add(vBox, BorderLayout.CENTER);
return panel;
}
//============================== Private methods ============================//
private String tableString(Matrix matrix, NumberFormat nf, double threshold) {
TextTable table = new TextTable(matrix.getNumRows() + 1, matrix.getNumColumns() + 1);
for (int i = 0; i < matrix.getNumRows() + 1; i++) {
for (int j = 0; j < matrix.getNumColumns() + 1; j++) {
if (i > 0 && j == 0) {
table.setToken(i, 0, "X" + i);
} else if (i == 0 && j > 0) {
table.setToken(0, j, "Factor " + j);
} else if (i > 0) {
double coefficient = matrix.get(i - 1, j - 1);
String token = !Double.isNaN(coefficient) ? nf.format(coefficient) : "Undefined";
token += FastMath.abs(coefficient) > threshold ? "*" : " ";
table.setToken(i, j, token);
}
}
}
return "\n" + table;
}
private JFrame findOwner() {
return (JFrame) SwingUtilities.getAncestorOfClass(
JFrame.class, this.dataEditor);
}
}
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