/*
* 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., 675 Mass Ave, Cambridge, MA 02139, USA.
*/
/*
* AttributeSelectionPanel.java
* Copyright (C) 1999 University of Waikato, Hamilton, New Zealand
*
*/
package weka.gui.explorer;
import java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.GridLayout;
import java.awt.Insets;
import java.awt.Point;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.InputEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.Random;
import java.util.Vector;
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
import javax.swing.DefaultComboBoxModel;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.JViewport;
import javax.swing.SwingConstants;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import weka.attributeSelection.ASEvaluation;
import weka.attributeSelection.ASSearch;
import weka.attributeSelection.AttributeEvaluator;
import weka.attributeSelection.AttributeSelection;
import weka.attributeSelection.AttributeTransformer;
import weka.attributeSelection.Ranker;
import weka.core.Attribute;
import weka.core.Capabilities;
import weka.core.CapabilitiesHandler;
import weka.core.FastVector;
import weka.core.Instances;
import weka.core.OptionHandler;
import weka.core.Utils;
import weka.gui.ExtensionFileFilter;
import weka.gui.GenericObjectEditor;
import weka.gui.Logger;
import weka.gui.PropertyPanel;
import weka.gui.ResultHistoryPanel;
import weka.gui.SaveBuffer;
import weka.gui.SysErrLog;
import weka.gui.TaskLogger;
import weka.gui.explorer.Explorer.CapabilitiesFilterChangeEvent;
import weka.gui.explorer.Explorer.CapabilitiesFilterChangeListener;
import weka.gui.explorer.Explorer.ExplorerPanel;
import weka.gui.explorer.Explorer.LogHandler;
import weka.gui.visualize.MatrixPanel;
/**
* This panel allows the user to select and configure an attribute
* evaluator and a search method, set the
* attribute of the current dataset to be used as the class, and perform
* attribute selection using one of two selection modes (select using all the
* training data or perform a n-fold cross validation---on each trial
* selecting features using n-1 folds of the data).
* The results of attribute selection runs are stored in a results history
* so that previous results are accessible.
*
* @author Mark Hall (mhall@cs.waikato.ac.nz)
* @version $Revision: 7099 $
*/
public class AttributeSelectionPanel
extends JPanel
implements CapabilitiesFilterChangeListener, ExplorerPanel, LogHandler {
/** for serialization */
static final long serialVersionUID = 5627185966993476142L;
/** the parent frame */
protected Explorer m_Explorer = null;
/** Lets the user configure the attribute evaluator */
protected GenericObjectEditor m_AttributeEvaluatorEditor =
new GenericObjectEditor();
/** Lets the user configure the search method */
protected GenericObjectEditor m_AttributeSearchEditor =
new GenericObjectEditor();
/** The panel showing the current attribute evaluation method */
protected PropertyPanel m_AEEPanel =
new PropertyPanel(m_AttributeEvaluatorEditor);
/** The panel showing the current search method */
protected PropertyPanel m_ASEPanel =
new PropertyPanel(m_AttributeSearchEditor);
/** The output area for attribute selection results */
protected JTextArea m_OutText = new JTextArea(20, 40);
/** The destination for log/status messages */
protected Logger m_Log = new SysErrLog();
/** The buffer saving object for saving output */
SaveBuffer m_SaveOut = new SaveBuffer(m_Log, this);
/** A panel controlling results viewing */
protected ResultHistoryPanel m_History = new ResultHistoryPanel(m_OutText);
/** Lets the user select the class column */
protected JComboBox m_ClassCombo = new JComboBox();
/** Click to set evaluation mode to cross-validation */
protected JRadioButton m_CVBut = new JRadioButton("Cross-validation");
/** Click to set test mode to test on training data */
protected JRadioButton m_TrainBut =
new JRadioButton("Use full training set");
/** Label by where the cv folds are entered */
protected JLabel m_CVLab = new JLabel("Folds", SwingConstants.RIGHT);
/** The field where the cv folds are entered */
protected JTextField m_CVText = new JTextField("10");
/** Label by where cv random seed is entered */
protected JLabel m_SeedLab = new JLabel("Seed",SwingConstants.RIGHT);
/** The field where the seed value is entered */
protected JTextField m_SeedText = new JTextField("1");
/**
* Alters the enabled/disabled status of elements associated with each
* radio button
*/
ActionListener m_RadioListener = new ActionListener() {
public void actionPerformed(ActionEvent e) {
updateRadioLinks();
}
};
/** Click to start running the attribute selector */
protected JButton m_StartBut = new JButton("Start");
/** Click to stop a running classifier */
protected JButton m_StopBut = new JButton("Stop");
/** Stop the class combo from taking up to much space */
private Dimension COMBO_SIZE = new Dimension(150, m_StartBut
.getPreferredSize().height);
/** The main set of instances we're playing with */
protected Instances m_Instances;
/** A thread that attribute selection runs in */
protected Thread m_RunThread;
/* Register the property editors we need */
static {
GenericObjectEditor.registerEditors();
}
/**
* Creates the classifier panel
*/
public AttributeSelectionPanel() {
// Connect / configure the components
m_OutText.setEditable(false);
m_OutText.setFont(new Font("Monospaced", Font.PLAIN, 12));
m_OutText.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
m_OutText.addMouseListener(new MouseAdapter() {
public void mouseClicked(MouseEvent e) {
if ((e.getModifiers() & InputEvent.BUTTON1_MASK)
!= InputEvent.BUTTON1_MASK) {
m_OutText.selectAll();
}
}
});
m_History.setBorder(BorderFactory.createTitledBorder("Result list (right-click for options)"));
m_AttributeEvaluatorEditor.setClassType(ASEvaluation.class);
m_AttributeEvaluatorEditor.setValue(ExplorerDefaults.getASEvaluator());
m_AttributeEvaluatorEditor.
addPropertyChangeListener(new PropertyChangeListener() {
public void propertyChange(PropertyChangeEvent e) {
if (m_AttributeEvaluatorEditor.getValue() instanceof AttributeEvaluator) {
if (!(m_AttributeSearchEditor.getValue() instanceof Ranker)) {
Object backup = m_AttributeEvaluatorEditor.getBackup();
int result =
JOptionPane.showConfirmDialog(null, "You must use use the Ranker search method "
+"in order to use\n"
+m_AttributeEvaluatorEditor.getValue().getClass().getName()
+".\nShould I select the Ranker search method for you?",
"Alert!", JOptionPane.YES_NO_OPTION);
if (result == JOptionPane.YES_OPTION) {
m_AttributeSearchEditor.setValue(new Ranker());
} else {
// restore to what was there previously (if possible)
if (backup != null) {
m_AttributeEvaluatorEditor.setValue(backup);
}
}
}
} else {
if (m_AttributeSearchEditor.getValue() instanceof Ranker) {
Object backup = m_AttributeEvaluatorEditor.getBackup();
int result =
JOptionPane.showConfirmDialog(null, "You must use use a search method that explores \n"
+"the space of attribute subsets (such as GreedyStepwise) in "
+"order to use\n"
+m_AttributeEvaluatorEditor.getValue().getClass().getName()
+".\nShould I select the GreedyStepwise search method for "
+"you?\n(you can always switch to a different method afterwards)",
"Alert!", JOptionPane.YES_NO_OPTION);
if (result == JOptionPane.YES_OPTION) {
m_AttributeSearchEditor.setValue(new weka.attributeSelection.GreedyStepwise());
} else {
// restore to what was there previously (if possible)
if (backup != null) {
m_AttributeEvaluatorEditor.setValue(backup);
}
}
}
}
updateRadioLinks();
m_StartBut.setEnabled(true);
// check capabilities...
Capabilities currentFilter = m_AttributeEvaluatorEditor.getCapabilitiesFilter();
ASEvaluation evaluator = (ASEvaluation) m_AttributeEvaluatorEditor.getValue();
Capabilities currentSchemeCapabilities = null;
if (evaluator != null && currentFilter != null &&
(evaluator instanceof CapabilitiesHandler)) {
currentSchemeCapabilities = ((CapabilitiesHandler)evaluator).getCapabilities();
if (!currentSchemeCapabilities.supportsMaybe(currentFilter) &&
!currentSchemeCapabilities.supports(currentFilter)) {
m_StartBut.setEnabled(false);
}
}
repaint();
}
});
m_AttributeSearchEditor.setClassType(ASSearch.class);
m_AttributeSearchEditor.setValue(ExplorerDefaults.getASSearch());
m_AttributeSearchEditor.
addPropertyChangeListener(new PropertyChangeListener() {
public void propertyChange(PropertyChangeEvent e) {
if (m_AttributeSearchEditor.getValue() instanceof Ranker) {
if (!(m_AttributeEvaluatorEditor.getValue() instanceof AttributeEvaluator)) {
Object backup = m_AttributeSearchEditor.getBackup();
int result =
JOptionPane.showConfirmDialog(null, "You must use use an evaluator that evaluates\n"
+"single attributes (such as InfoGain) in order to use\n"
+"the Ranker. Should I select the InfoGain evaluator "
+"for you?\n"
+"(You can always switch to a different method afterwards)" ,
"Alert!", JOptionPane.YES_NO_OPTION);
if (result == JOptionPane.YES_OPTION) {
m_AttributeEvaluatorEditor.setValue(new weka.attributeSelection.InfoGainAttributeEval());
} else {
// restore to what was there previously (if possible)
if (backup != null) {
m_AttributeSearchEditor.setValue(backup);
}
}
}
} else {
if (m_AttributeEvaluatorEditor.getValue() instanceof AttributeEvaluator) {
Object backup = m_AttributeSearchEditor.getBackup();
int result =
JOptionPane.showConfirmDialog(null, "You must use use an evaluator that evaluates\n"
+"subsets of attributes (such as CFS) in order to use\n"
+m_AttributeEvaluatorEditor.getValue().getClass().getName()
+".\nShould I select the CFS subset evaluator for you?"
+"\n(you can always switch to a different method afterwards)",
"Alert!", JOptionPane.YES_NO_OPTION);
if (result == JOptionPane.YES_OPTION) {
m_AttributeEvaluatorEditor.setValue(new weka.attributeSelection.CfsSubsetEval());
} else {
// restore to what was there previously (if possible)
if (backup != null) {
m_AttributeSearchEditor.setValue(backup);
}
}
}
}
repaint();
}
});
m_ClassCombo.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
updateCapabilitiesFilter(m_AttributeEvaluatorEditor.getCapabilitiesFilter());
}
});
m_ClassCombo.setToolTipText("Select the attribute to use as the class");
m_TrainBut.setToolTipText("select attributes using the full training "
+ "dataset");
m_CVBut.setToolTipText("Perform a n-fold cross-validation");
m_StartBut.setToolTipText("Starts attribute selection");
m_StopBut.setToolTipText("Stops a attribute selection task");
m_ClassCombo.setPreferredSize(COMBO_SIZE);
m_ClassCombo.setMaximumSize(COMBO_SIZE);
m_ClassCombo.setMinimumSize(COMBO_SIZE);
m_History.setPreferredSize(COMBO_SIZE);
m_History.setMaximumSize(COMBO_SIZE);
m_History.setMinimumSize(COMBO_SIZE);
m_ClassCombo.setEnabled(false);
m_TrainBut.setSelected(ExplorerDefaults.getASTestMode() == 0);
m_CVBut.setSelected(ExplorerDefaults.getASTestMode() == 1);
updateRadioLinks();
ButtonGroup bg = new ButtonGroup();
bg.add(m_TrainBut);
bg.add(m_CVBut);
m_TrainBut.addActionListener(m_RadioListener);
m_CVBut.addActionListener(m_RadioListener);
m_CVText.setText("" + ExplorerDefaults.getASCrossvalidationFolds());
m_SeedText.setText("" + ExplorerDefaults.getASRandomSeed());
m_StartBut.setEnabled(false);
m_StopBut.setEnabled(false);
m_StartBut.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
startAttributeSelection();
}
});
m_StopBut.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
stopAttributeSelection();
}
});
m_History.setHandleRightClicks(false);
// see if we can popup a menu for the selected result
m_History.getList().addMouseListener(new MouseAdapter() {
public void mouseClicked(MouseEvent e) {
if (((e.getModifiers() & InputEvent.BUTTON1_MASK)
!= InputEvent.BUTTON1_MASK) || e.isAltDown()) {
int index = m_History.getList().locationToIndex(e.getPoint());
if (index != -1) {
String name = m_History.getNameAtIndex(index);
visualize(name, e.getX(), e.getY());
} else {
visualize(null, e.getX(), e.getY());
}
}
}
});
// Layout the GUI
JPanel p1 = new JPanel();
p1.setBorder(BorderFactory.createCompoundBorder(
BorderFactory.createTitledBorder("Attribute Evaluator"),
BorderFactory.createEmptyBorder(0, 5, 5, 5)
));
p1.setLayout(new BorderLayout());
p1.add(m_AEEPanel, BorderLayout.NORTH);
JPanel p1_1 = new JPanel();
p1_1.setBorder(BorderFactory.createCompoundBorder(
BorderFactory.createTitledBorder("Search Method"),
BorderFactory.createEmptyBorder(0, 5, 5, 5)
));
p1_1.setLayout(new BorderLayout());
p1_1.add(m_ASEPanel, BorderLayout.NORTH);
JPanel p_new = new JPanel();
p_new.setLayout(new BorderLayout());
p_new.add(p1, BorderLayout.NORTH);
p_new.add(p1_1, BorderLayout.CENTER);
JPanel p2 = new JPanel();
GridBagLayout gbL = new GridBagLayout();
p2.setLayout(gbL);
p2.setBorder(BorderFactory.createCompoundBorder(
BorderFactory.createTitledBorder("Attribute Selection Mode"),
BorderFactory.createEmptyBorder(0, 5, 5, 5)
));
GridBagConstraints gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.WEST;
gbC.gridy = 2; gbC.gridx = 0;
gbL.setConstraints(m_TrainBut, gbC);
p2.add(m_TrainBut);
gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.WEST;
gbC.gridy = 4; gbC.gridx = 0;
gbL.setConstraints(m_CVBut, gbC);
p2.add(m_CVBut);
gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.EAST;
gbC.fill = GridBagConstraints.HORIZONTAL;
gbC.gridy = 4; gbC.gridx = 1;
gbC.insets = new Insets(2, 10, 2, 10);
gbL.setConstraints(m_CVLab, gbC);
p2.add(m_CVLab);
gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.EAST;
gbC.fill = GridBagConstraints.HORIZONTAL;
gbC.gridy = 4; gbC.gridx = 2; gbC.weightx = 100;
gbC.ipadx = 20;
gbL.setConstraints(m_CVText, gbC);
p2.add(m_CVText);
gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.EAST;
gbC.fill = GridBagConstraints.HORIZONTAL;
gbC.gridy = 6; gbC.gridx = 1;
gbC.insets = new Insets(2, 10, 2, 10);
gbL.setConstraints(m_SeedLab, gbC);
p2.add(m_SeedLab);
gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.EAST;
gbC.fill = GridBagConstraints.HORIZONTAL;
gbC.gridy = 6; gbC.gridx = 2; gbC.weightx = 100;
gbC.ipadx = 20;
gbL.setConstraints(m_SeedText, gbC);
p2.add(m_SeedText);
JPanel buttons = new JPanel();
buttons.setLayout(new GridLayout(2, 2));
buttons.add(m_ClassCombo);
m_ClassCombo.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
JPanel ssButs = new JPanel();
ssButs.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
ssButs.setLayout(new GridLayout(1, 2, 5, 5));
ssButs.add(m_StartBut);
ssButs.add(m_StopBut);
buttons.add(ssButs);
JPanel p3 = new JPanel();
p3.setBorder(BorderFactory.
createTitledBorder("Attribute selection output"));
p3.setLayout(new BorderLayout());
final JScrollPane js = new JScrollPane(m_OutText);
p3.add(js, BorderLayout.CENTER);
js.getViewport().addChangeListener(new ChangeListener() {
private int lastHeight;
public void stateChanged(ChangeEvent e) {
JViewport vp = (JViewport)e.getSource();
int h = vp.getViewSize().height;
if (h != lastHeight) { // i.e. an addition not just a user scrolling
lastHeight = h;
int x = h - vp.getExtentSize().height;
vp.setViewPosition(new Point(0, x));
}
}
});
JPanel mondo = new JPanel();
gbL = new GridBagLayout();
mondo.setLayout(gbL);
gbC = new GridBagConstraints();
gbC.fill = GridBagConstraints.HORIZONTAL;
gbC.gridy = 0; gbC.gridx = 0; gbC.weightx = 0;
gbL.setConstraints(p2, gbC);
mondo.add(p2);
gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.NORTH;
gbC.fill = GridBagConstraints.HORIZONTAL;
gbC.gridy = 1; gbC.gridx = 0; gbC.weightx = 0;
gbL.setConstraints(buttons, gbC);
mondo.add(buttons);
gbC = new GridBagConstraints();
gbC.fill = GridBagConstraints.BOTH;
gbC.gridy = 2; gbC.gridx = 0; gbC.weightx = 0; gbC.weighty = 100;
gbL.setConstraints(m_History, gbC);
mondo.add(m_History);
gbC = new GridBagConstraints();
gbC.fill = GridBagConstraints.BOTH;
gbC.gridy = 0; gbC.gridx = 1;
gbC.gridheight = 3;
gbC.weightx = 100; gbC.weighty = 100;
gbL.setConstraints(p3, gbC);
mondo.add(p3);
setLayout(new BorderLayout());
add(p_new, BorderLayout.NORTH);
add(mondo, BorderLayout.CENTER);
}
/**
* Updates the enabled status of the input fields and labels.
*/
protected void updateRadioLinks() {
m_CVBut.setEnabled(true);
m_CVText.setEnabled(m_CVBut.isSelected());
m_CVLab.setEnabled(m_CVBut.isSelected());
m_SeedText.setEnabled(m_CVBut.isSelected());
m_SeedLab.setEnabled(m_CVBut.isSelected());
if (m_AttributeEvaluatorEditor.getValue()
instanceof AttributeTransformer) {
m_CVBut.setSelected(false);
m_CVBut.setEnabled(false);
m_CVText.setEnabled(false);
m_CVLab.setEnabled(false);
m_SeedText.setEnabled(false);
m_SeedLab.setEnabled(false);
m_TrainBut.setSelected(true);
}
}
/**
* Sets the Logger to receive informational messages
*
* @param newLog the Logger that will now get info messages
*/
public void setLog(Logger newLog) {
m_Log = newLog;
}
/**
* Tells the panel to use a new set of instances.
*
* @param inst a set of Instances
*/
public void setInstances(Instances inst) {
m_Instances = inst;
String [] attribNames = new String [m_Instances.numAttributes() + 1];
attribNames[0] = "No class";
for (int i = 0; i < inst.numAttributes(); i++) {
String type = "(" + Attribute.typeToStringShort(m_Instances.attribute(i)) + ") ";
String attnm = m_Instances.attribute(i).name();
attribNames[i + 1] = type + attnm;
}
m_StartBut.setEnabled(m_RunThread == null);
m_StopBut.setEnabled(m_RunThread != null);
m_ClassCombo.setModel(new DefaultComboBoxModel(attribNames));
if (inst.classIndex() == -1)
m_ClassCombo.setSelectedIndex(attribNames.length - 1);
else
m_ClassCombo.setSelectedIndex(inst.classIndex());
m_ClassCombo.setEnabled(true);
}
/**
* Starts running the currently configured attribute evaluator and
* search method. This is run in a separate thread, and will only start if
* there is no attribute selection already running. The attribute selection
* output is sent to the results history panel.
*/
protected void startAttributeSelection() {
if (m_RunThread == null) {
m_StartBut.setEnabled(false);
m_StopBut.setEnabled(true);
m_RunThread = new Thread() {
public void run() {
// Copy the current state of things
m_Log.statusMessage("Setting up...");
Instances inst = new Instances(m_Instances);
int testMode = 0;
int numFolds = 10;
int seed = 1;
int classIndex = m_ClassCombo.getSelectedIndex() - 1;
ASEvaluation evaluator =
(ASEvaluation) m_AttributeEvaluatorEditor.getValue();
ASSearch search = (ASSearch) m_AttributeSearchEditor.getValue();
StringBuffer outBuff = new StringBuffer();
String name = (new SimpleDateFormat("HH:mm:ss - "))
.format(new Date());
String sname = search.getClass().getName();
if (sname.startsWith("weka.attributeSelection.")) {
name += sname.substring("weka.attributeSelection.".length());
} else {
name += sname;
}
String ename = evaluator.getClass().getName();
if (ename.startsWith("weka.attributeSelection.")) {
name += (" + "
+ename.substring("weka.attributeSelection.".length()));
} else {
name += (" + "+ename);
}
// assemble commands
String cmd;
String cmdFilter;
String cmdClassifier;
// 1. attribute selection command
Vector<String> list = new Vector<String>();
list.add("-s");
if (search instanceof OptionHandler)
list.add(sname + " " + Utils.joinOptions(((OptionHandler) search).getOptions()));
else
list.add(sname);
if (evaluator instanceof OptionHandler) {
String[] opt = ((OptionHandler) evaluator).getOptions();
for (int i = 0; i < opt.length; i++)
list.add(opt[i]);
}
cmd = ename + " "
+ Utils.joinOptions(list.toArray(new String[list.size()]));
// 2. filter command
weka.filters.supervised.attribute.AttributeSelection filter =
new weka.filters.supervised.attribute.AttributeSelection();
filter.setEvaluator((ASEvaluation) m_AttributeEvaluatorEditor.getValue());
filter.setSearch((ASSearch) m_AttributeSearchEditor.getValue());
cmdFilter = filter.getClass().getName() + " "
+ Utils.joinOptions(((OptionHandler) filter).getOptions());
// 3. meta-classifier command
weka.classifiers.meta.AttributeSelectedClassifier cls =
new weka.classifiers.meta.AttributeSelectedClassifier();
cls.setEvaluator((ASEvaluation) m_AttributeEvaluatorEditor.getValue());
cls.setSearch((ASSearch) m_AttributeSearchEditor.getValue());
cmdClassifier = cls.getClass().getName() + " "
+ Utils.joinOptions(cls.getOptions());
AttributeSelection eval = null;
try {
if (m_CVBut.isSelected()) {
testMode = 1;
numFolds = Integer.parseInt(m_CVText.getText());
seed = Integer.parseInt(m_SeedText.getText());
if (numFolds <= 1) {
throw new Exception("Number of folds must be greater than 1");
}
}
if (classIndex >= 0) {
inst.setClassIndex(classIndex);
}
// Output some header information
m_Log.logMessage("Started " + ename);
m_Log.logMessage("Command: " + cmd);
m_Log.logMessage("Filter command: " + cmdFilter);
m_Log.logMessage("Meta-classifier command: " + cmdClassifier);
if (m_Log instanceof TaskLogger) {
((TaskLogger)m_Log).taskStarted();
}
outBuff.append("=== Run information ===\n\n");
outBuff.append("Evaluator: " + ename);
if (evaluator instanceof OptionHandler) {
String [] o = ((OptionHandler) evaluator).getOptions();
outBuff.append(" " + Utils.joinOptions(o));
}
outBuff.append("\nSearch: " + sname);
if (search instanceof OptionHandler) {
String [] o = ((OptionHandler) search).getOptions();
outBuff.append(" " + Utils.joinOptions(o));
}
outBuff.append("\n");
outBuff.append("Relation: " + inst.relationName() + '\n');
outBuff.append("Instances: " + inst.numInstances() + '\n');
outBuff.append("Attributes: " + inst.numAttributes() + '\n');
if (inst.numAttributes() < 100) {
for (int i = 0; i < inst.numAttributes(); i++) {
outBuff.append(" " + inst.attribute(i).name()
+ '\n');
}
} else {
outBuff.append(" [list of attributes omitted]\n");
}
outBuff.append("Evaluation mode: ");
switch (testMode) {
case 0: // select using all training
outBuff.append("evaluate on all training data\n");
break;
case 1: // CV mode
outBuff.append("" + numFolds + "-fold cross-validation\n");
break;
}
outBuff.append("\n");
m_History.addResult(name, outBuff);
m_History.setSingle(name);
// Do the feature selection and output the results.
m_Log.statusMessage("Doing feature selection...");
m_History.updateResult(name);
eval = new AttributeSelection();
eval.setEvaluator(evaluator);
eval.setSearch(search);
eval.setFolds(numFolds);
eval.setSeed(seed);
if (testMode == 1) {
eval.setXval(true);
}
switch (testMode) {
case 0: // select using training
m_Log.statusMessage("Evaluating on training data...");
eval.SelectAttributes(inst);
break;
case 1: // CV mode
m_Log.statusMessage("Randomizing instances...");
Random random = new Random(seed);
inst.randomize(random);
if (inst.attribute(classIndex).isNominal()) {
m_Log.statusMessage("Stratifying instances...");
inst.stratify(numFolds);
}
for (int fold = 0; fold < numFolds;fold++) {
m_Log.statusMessage("Creating splits for fold "
+ (fold + 1) + "...");
Instances train = inst.trainCV(numFolds, fold, random);
m_Log.statusMessage("Selecting attributes using all but fold "
+ (fold + 1) + "...");
eval.selectAttributesCVSplit(train);
}
break;
default:
throw new Exception("Test mode not implemented");
}
if (testMode == 0) {
outBuff.append(eval.toResultsString());
} else {
outBuff.append(eval.CVResultsString());
}
outBuff.append("\n");
m_History.updateResult(name);
m_Log.logMessage("Finished " + ename+" "+sname);
m_Log.statusMessage("OK");
} catch (Exception ex) {
m_Log.logMessage(ex.getMessage());
m_Log.statusMessage("See error log");
} finally {
if (evaluator instanceof AttributeTransformer) {
try {
Instances transformed =
((AttributeTransformer)evaluator).transformedData(inst);
transformed.
setRelationName("AT: "+transformed.relationName());
FastVector vv = new FastVector();
vv.addElement(transformed);
m_History.addObject(name, vv);
} catch (Exception ex) {
System.err.println(ex);
ex.printStackTrace();
}
} else if (testMode == 0) {
try {
Instances reducedInst = eval.reduceDimensionality(inst);
FastVector vv = new FastVector();
vv.addElement(reducedInst);
m_History.addObject(name, vv);
} catch (Exception ex) {
ex.printStackTrace();
}
}
if (isInterrupted()) {
m_Log.logMessage("Interrupted " + ename+" "+sname);
m_Log.statusMessage("See error log");
}
m_RunThread = null;
m_StartBut.setEnabled(true);
m_StopBut.setEnabled(false);
if (m_Log instanceof TaskLogger) {
((TaskLogger)m_Log).taskFinished();
}
}
}
};
m_RunThread.setPriority(Thread.MIN_PRIORITY);
m_RunThread.start();
}
}
/**
* Stops the currently running attribute selection (if any).
*/
protected void stopAttributeSelection() {
if (m_RunThread != null) {
m_RunThread.interrupt();
// This is deprecated (and theoretically the interrupt should do).
m_RunThread.stop();
}
}
/**
* Save the named buffer to a file.
* @param name the name of the buffer to be saved.
*/
protected void saveBuffer(String name) {
StringBuffer sb = m_History.getNamedBuffer(name);
if (sb != null) {
if (m_SaveOut.save(sb)) {
m_Log.logMessage("Save succesful.");
}
}
}
/**
* Popup a visualize panel for viewing transformed data
*
* @param ti the Instances to display
*/
protected void visualizeTransformedData(Instances ti) {
if (ti != null) {
MatrixPanel mp = new MatrixPanel();
mp.setInstances(ti);
String plotName = ti.relationName();
final javax.swing.JFrame jf =
new javax.swing.JFrame("Weka Attribute Selection Visualize: "
+plotName);
jf.setSize(800,600);
jf.getContentPane().setLayout(new BorderLayout());
jf.getContentPane().add(mp, BorderLayout.CENTER);
jf.addWindowListener(new java.awt.event.WindowAdapter() {
public void windowClosing(java.awt.event.WindowEvent e) {
jf.dispose();
}
});
jf.setVisible(true);
}
}
/**
* Popup a SaveDialog for saving the transformed data
*
* @param ti the Instances to display
*/
protected void saveTransformedData(Instances ti) {
JFileChooser fc;
int retVal;
BufferedWriter writer;
ExtensionFileFilter filter;
fc = new JFileChooser();
filter = new ExtensionFileFilter(".arff", "ARFF data files");
fc.setFileFilter(filter);
retVal = fc.showSaveDialog(this);
if (retVal == JFileChooser.APPROVE_OPTION) {
try {
writer = new BufferedWriter(new FileWriter(fc.getSelectedFile()));
writer.write(ti.toString());
writer.flush();
writer.close();
}
catch (Exception e) {
e.printStackTrace();
m_Log.logMessage("Problem saving data: " + e.getMessage());
JOptionPane.showMessageDialog(
this,
"Problem saving data:\n" + e.getMessage(),
"Error",
JOptionPane.ERROR_MESSAGE);
}
}
}
/**
* Handles constructing a popup menu with visualization options
* @param name the name of the result history list entry clicked on by
* the user.
* @param x the x coordinate for popping up the menu
* @param y the y coordinate for popping up the menu
*/
protected void visualize(String name, int x, int y) {
final String selectedName = name;
JPopupMenu resultListMenu = new JPopupMenu();
JMenuItem visMainBuffer = new JMenuItem("View in main window");
if (selectedName != null) {
visMainBuffer.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
m_History.setSingle(selectedName);
}
});
} else {
visMainBuffer.setEnabled(false);
}
resultListMenu.add(visMainBuffer);
JMenuItem visSepBuffer = new JMenuItem("View in separate window");
if (selectedName != null) {
visSepBuffer.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
m_History.openFrame(selectedName);
}
});
} else {
visSepBuffer.setEnabled(false);
}
resultListMenu.add(visSepBuffer);
JMenuItem saveOutput = new JMenuItem("Save result buffer");
if (selectedName != null) {
saveOutput.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
saveBuffer(selectedName);
}
});
} else {
saveOutput.setEnabled(false);
}
resultListMenu.add(saveOutput);
JMenuItem deleteOutput = new JMenuItem("Delete result buffer");
if (selectedName != null) {
deleteOutput.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
m_History.removeResult(selectedName);
}
});
} else {
deleteOutput.setEnabled(false);
}
resultListMenu.add(deleteOutput);
FastVector o = null;
if (selectedName != null) {
o = (FastVector)m_History.getNamedObject(selectedName);
}
// VisualizePanel temp_vp = null;
Instances tempTransformed = null;
if (o != null) {
for (int i = 0; i < o.size(); i++) {
Object temp = o.elementAt(i);
// if (temp instanceof VisualizePanel) {
if (temp instanceof Instances) {
// temp_vp = (VisualizePanel)temp;
tempTransformed = (Instances) temp;
}
}
}
// final VisualizePanel vp = temp_vp;
final Instances ti = tempTransformed;
JMenuItem visTrans = null;
if (ti != null) {
if (ti.relationName().startsWith("AT:")) {
visTrans = new JMenuItem("Visualize transformed data");
} else {
visTrans = new JMenuItem("Visualize reduced data");
}
resultListMenu.addSeparator();
}
// JMenuItem visTrans = new JMenuItem("Visualize transformed data");
if (ti != null && visTrans != null) {
visTrans.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
visualizeTransformedData(ti);
}
});
}
if (visTrans != null) {
resultListMenu.add(visTrans);
}
JMenuItem saveTrans = null;
if (ti != null) {
if (ti.relationName().startsWith("AT:"))
saveTrans = new JMenuItem("Save transformed data...");
else
saveTrans = new JMenuItem("Save reduced data...");
}
if (saveTrans != null) {
saveTrans.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
saveTransformedData(ti);
}
});
resultListMenu.add(saveTrans);
}
resultListMenu.show(m_History.getList(), x, y);
}
/**
* updates the capabilities filter of the GOE
*
* @param filter the new filter to use
*/
protected void updateCapabilitiesFilter(Capabilities filter) {
Instances tempInst;
Capabilities filterClass;
if (filter == null) {
m_AttributeEvaluatorEditor.setCapabilitiesFilter(new Capabilities(null));
m_AttributeSearchEditor.setCapabilitiesFilter(new Capabilities(null));
return;
}
if (!ExplorerDefaults.getInitGenericObjectEditorFilter())
tempInst = new Instances(m_Instances, 0);
else
tempInst = new Instances(m_Instances);
int clIndex = m_ClassCombo.getSelectedIndex() - 1;
if (clIndex >= 0) {
tempInst.setClassIndex(clIndex);
}
try {
filterClass = Capabilities.forInstances(tempInst);
}
catch (Exception e) {
filterClass = new Capabilities(null);
}
// set new filter
m_AttributeEvaluatorEditor.setCapabilitiesFilter(filterClass);
m_AttributeSearchEditor.setCapabilitiesFilter(filterClass);
m_StartBut.setEnabled(true);
// check capabilities...
Capabilities currentFilter = m_AttributeEvaluatorEditor.getCapabilitiesFilter();
ASEvaluation evaluator = (ASEvaluation) m_AttributeEvaluatorEditor.getValue();
Capabilities currentSchemeCapabilities = null;
if (evaluator != null && currentFilter != null &&
(evaluator instanceof CapabilitiesHandler)) {
currentSchemeCapabilities = ((CapabilitiesHandler)evaluator).getCapabilities();
if (!currentSchemeCapabilities.supportsMaybe(currentFilter) &&
!currentSchemeCapabilities.supports(currentFilter)) {
m_StartBut.setEnabled(false);
}
}
}
/**
* method gets called in case of a change event
*
* @param e the associated change event
*/
public void capabilitiesFilterChanged(CapabilitiesFilterChangeEvent e) {
if (e.getFilter() == null)
updateCapabilitiesFilter(null);
else
updateCapabilitiesFilter((Capabilities) e.getFilter().clone());
}
/**
* Sets the Explorer to use as parent frame (used for sending notifications
* about changes in the data)
*
* @param parent the parent frame
*/
public void setExplorer(Explorer parent) {
m_Explorer = parent;
}
/**
* returns the parent Explorer frame
*
* @return the parent
*/
public Explorer getExplorer() {
return m_Explorer;
}
/**
* Returns the title for the tab in the Explorer
*
* @return the title of this tab
*/
public String getTabTitle() {
return "Select attributes";
}
/**
* Returns the tooltip for the tab in the Explorer
*
* @return the tooltip of this tab
*/
public String getTabTitleToolTip() {
return "Determine relevance of attributes";
}
/**
* Tests out the attribute selection panel from the command line.
*
* @param args may optionally contain the name of a dataset to load.
*/
public static void main(String [] args) {
try {
final javax.swing.JFrame jf =
new javax.swing.JFrame("Weka Explorer: Select attributes");
jf.getContentPane().setLayout(new BorderLayout());
final AttributeSelectionPanel sp = new AttributeSelectionPanel();
jf.getContentPane().add(sp, BorderLayout.CENTER);
weka.gui.LogPanel lp = new weka.gui.LogPanel();
sp.setLog(lp);
jf.getContentPane().add(lp, BorderLayout.SOUTH);
jf.addWindowListener(new java.awt.event.WindowAdapter() {
public void windowClosing(java.awt.event.WindowEvent e) {
jf.dispose();
System.exit(0);
}
});
jf.pack();
jf.setVisible(true);
if (args.length == 1) {
System.err.println("Loading instances from " + args[0]);
java.io.Reader r = new java.io.BufferedReader(
new java.io.FileReader(args[0]));
Instances i = new Instances(r);
sp.setInstances(i);
}
} catch (Exception ex) {
ex.printStackTrace();
System.err.println(ex.getMessage());
}
}
}