/*
* 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.
*/
/*
* ClustererPanel.java
* Copyright (C) 1999 University of Waikato, Hamilton, New Zealand
*
*/
package weka.gui.explorer;
import weka.clusterers.ClusterEvaluation;
import weka.clusterers.Clusterer;
import weka.core.Attribute;
import weka.core.Capabilities;
import weka.core.CapabilitiesHandler;
import weka.core.Drawable;
import weka.core.FastVector;
import weka.core.Instances;
import weka.core.OptionHandler;
import weka.core.SerializedObject;
import weka.core.Utils;
import weka.core.Version;
import weka.filters.Filter;
import weka.filters.unsupervised.attribute.Remove;
import weka.gui.ExtensionFileFilter;
import weka.gui.GenericObjectEditor;
import weka.gui.InstancesSummaryPanel;
import weka.gui.ListSelectorDialog;
import weka.gui.Logger;
import weka.gui.PropertyPanel;
import weka.gui.ResultHistoryPanel;
import weka.gui.SaveBuffer;
import weka.gui.SetInstancesPanel;
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.treevisualizer.PlaceNode2;
import weka.gui.treevisualizer.TreeVisualizer;
import weka.gui.visualize.VisualizePanel;
import weka.gui.visualize.plugins.TreeVisualizePlugin;
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.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.InputStream;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.OutputStream;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.Random;
import java.util.Vector;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
import javax.swing.DefaultComboBoxModel;
import javax.swing.DefaultListModel;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JMenu;
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 javax.swing.filechooser.FileFilter;
import weka.gui.hierarchyvisualizer.HierarchyVisualizer;
/**
* This panel allows the user to select and configure a clusterer, and evaluate
* the clusterer using a number of testing modes (test on the training data,
* train/test on a percentage split, test on a
* separate split). The results of clustering runs are stored in a result
* history so that previous results are accessible.
*
* @author Mark Hall (mhall@cs.waikato.ac.nz)
* @author Richard Kirkby (rkirkby@cs.waikato.ac.nz)
* @version $Revision: 6889 $
*/
public class ClustererPanel
extends JPanel
implements CapabilitiesFilterChangeListener, ExplorerPanel, LogHandler {
/** for serialization */
static final long serialVersionUID = -2474932792950820990L;
/** the parent frame */
protected Explorer m_Explorer = null;
/** The filename extension that should be used for model files */
public static String MODEL_FILE_EXTENSION = ".model";
/** Lets the user configure the clusterer */
protected GenericObjectEditor m_ClustererEditor =
new GenericObjectEditor();
/** The panel showing the current clusterer selection */
protected PropertyPanel m_CLPanel = new PropertyPanel(m_ClustererEditor);
/** The output area for classification 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);
/** Click to set test mode to generate a % split */
protected JRadioButton m_PercentBut = new JRadioButton("Percentage split");
/** Click to set test mode to test on training data */
protected JRadioButton m_TrainBut = new JRadioButton("Use training set");
/** Click to set test mode to a user-specified test set */
protected JRadioButton m_TestSplitBut =
new JRadioButton("Supplied test set");
/** Click to set test mode to classes to clusters based evaluation */
protected JRadioButton m_ClassesToClustersBut =
new JRadioButton("Classes to clusters evaluation");
/** Lets the user select the class column for classes to clusters based
evaluation */
protected JComboBox m_ClassCombo = new JComboBox();
/** Label by where the % split is entered */
protected JLabel m_PercentLab = new JLabel("%", SwingConstants.RIGHT);
/** The field where the % split is entered */
protected JTextField m_PercentText = new JTextField("66");
/** The button used to open a separate test dataset */
protected JButton m_SetTestBut = new JButton("Set...");
/** The frame used to show the test set selection panel */
protected JFrame m_SetTestFrame;
/** The button used to popup a list for choosing attributes to ignore while
clustering */
protected JButton m_ignoreBut = new JButton("Ignore attributes");
protected DefaultListModel m_ignoreKeyModel = new DefaultListModel();
protected JList m_ignoreKeyList = new JList(m_ignoreKeyModel);
// protected Remove m_ignoreFilter = null;
/**
* 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 clusterer */
protected JButton m_StartBut = new JButton("Start");
/** Stop the class combo from taking up to much space */
private Dimension COMBO_SIZE = new Dimension(250, m_StartBut
.getPreferredSize().height);
/** Click to stop a running clusterer */
protected JButton m_StopBut = new JButton("Stop");
/** The main set of instances we're playing with */
protected Instances m_Instances;
/** The user-supplied test set (if any) */
protected Instances m_TestInstances;
/** The current visualization object */
protected VisualizePanel m_CurrentVis = null;
/** Check to save the predictions in the results list for visualizing
later on */
protected JCheckBox m_StorePredictionsBut =
new JCheckBox("Store clusters for visualization");
/** A thread that clustering runs in */
protected Thread m_RunThread;
/** The instances summary panel displayed by m_SetTestFrame */
protected InstancesSummaryPanel m_Summary;
/** Filter to ensure only model files are selected */
protected FileFilter m_ModelFilter =
new ExtensionFileFilter(MODEL_FILE_EXTENSION, "Model object files");
/** The file chooser for selecting model files */
protected JFileChooser m_FileChooser
= new JFileChooser(new File(System.getProperty("user.dir")));
/* Register the property editors we need */
static {
GenericObjectEditor.registerEditors();
}
/**
* Creates the clusterer panel
*/
public ClustererPanel() {
// 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_ClustererEditor.setClassType(Clusterer.class);
m_ClustererEditor.setValue(ExplorerDefaults.getClusterer());
m_ClustererEditor.addPropertyChangeListener(new PropertyChangeListener() {
public void propertyChange(PropertyChangeEvent e) {
m_StartBut.setEnabled(true);
Capabilities currentFilter = m_ClustererEditor.getCapabilitiesFilter();
Clusterer clusterer = (Clusterer) m_ClustererEditor.getValue();
Capabilities currentSchemeCapabilities = null;
if (clusterer != null && currentFilter != null &&
(clusterer instanceof CapabilitiesHandler)) {
currentSchemeCapabilities = ((CapabilitiesHandler)clusterer).getCapabilities();
if (!currentSchemeCapabilities.supportsMaybe(currentFilter) &&
!currentSchemeCapabilities.supports(currentFilter)) {
m_StartBut.setEnabled(false);
}
}
repaint();
}
});
m_TrainBut.setToolTipText("Cluster the same set that the clusterer"
+ " is trained on");
m_PercentBut.setToolTipText("Train on a percentage of the data and"
+ " cluster the remainder");
m_TestSplitBut.setToolTipText("Cluster a user-specified dataset");
m_ClassesToClustersBut.setToolTipText("Evaluate clusters with respect to a"
+" class");
m_ClassCombo.setToolTipText("Select the class attribute for class based"
+" evaluation");
m_StartBut.setToolTipText("Starts the clustering");
m_StopBut.setToolTipText("Stops a running clusterer");
m_StorePredictionsBut.
setToolTipText("Store predictions in the result list for later "
+"visualization");
m_ignoreBut.setToolTipText("Ignore attributes during clustering");
m_FileChooser.setFileFilter(m_ModelFilter);
m_FileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
m_ClassCombo.setPreferredSize(COMBO_SIZE);
m_ClassCombo.setMaximumSize(COMBO_SIZE);
m_ClassCombo.setMinimumSize(COMBO_SIZE);
m_ClassCombo.setEnabled(false);
m_PercentBut.setSelected(ExplorerDefaults.getClustererTestMode() == 2);
m_TrainBut.setSelected(ExplorerDefaults.getClustererTestMode() == 3);
m_TestSplitBut.setSelected(ExplorerDefaults.getClustererTestMode() == 4);
m_ClassesToClustersBut.setSelected(ExplorerDefaults.getClustererTestMode() == 5);
m_StorePredictionsBut.setSelected(ExplorerDefaults.getClustererStoreClustersForVis());
updateRadioLinks();
ButtonGroup bg = new ButtonGroup();
bg.add(m_TrainBut);
bg.add(m_PercentBut);
bg.add(m_TestSplitBut);
bg.add(m_ClassesToClustersBut);
m_TrainBut.addActionListener(m_RadioListener);
m_PercentBut.addActionListener(m_RadioListener);
m_TestSplitBut.addActionListener(m_RadioListener);
m_ClassesToClustersBut.addActionListener(m_RadioListener);
m_SetTestBut.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
setTestSet();
}
});
m_StartBut.setEnabled(false);
m_StopBut.setEnabled(false);
m_ignoreBut.setEnabled(false);
m_StartBut.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
startClusterer();
}
});
m_StopBut.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
stopClusterer();
}
});
m_ignoreBut.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
setIgnoreColumns();
}
});
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);
visualizeClusterer(name, e.getX(), e.getY());
} else {
visualizeClusterer(null, e.getX(), e.getY());
}
}
}
});
m_ClassCombo.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
updateCapabilitiesFilter(m_ClustererEditor.getCapabilitiesFilter());
}
});
// Layout the GUI
JPanel p1 = new JPanel();
p1.setBorder(BorderFactory.createCompoundBorder(
BorderFactory.createTitledBorder("Clusterer"),
BorderFactory.createEmptyBorder(0, 5, 5, 5)
));
p1.setLayout(new BorderLayout());
p1.add(m_CLPanel, BorderLayout.NORTH);
JPanel p2 = new JPanel();
GridBagLayout gbL = new GridBagLayout();
p2.setLayout(gbL);
p2.setBorder(BorderFactory.createCompoundBorder(
BorderFactory.createTitledBorder("Cluster mode"),
BorderFactory.createEmptyBorder(0, 5, 5, 5)
));
GridBagConstraints gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.WEST;
gbC.gridy = 0; gbC.gridx = 0;
gbL.setConstraints(m_TrainBut, gbC);
p2.add(m_TrainBut);
gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.WEST;
gbC.gridy = 1; gbC.gridx = 0;
gbL.setConstraints(m_TestSplitBut, gbC);
p2.add(m_TestSplitBut);
gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.EAST;
gbC.fill = GridBagConstraints.HORIZONTAL;
gbC.gridy = 1; gbC.gridx = 1; gbC.gridwidth = 2;
gbC.insets = new Insets(2, 10, 2, 0);
gbL.setConstraints(m_SetTestBut, gbC);
p2.add(m_SetTestBut);
gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.WEST;
gbC.gridy = 2; gbC.gridx = 0;
gbL.setConstraints(m_PercentBut, gbC);
p2.add(m_PercentBut);
gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.EAST;
gbC.fill = GridBagConstraints.HORIZONTAL;
gbC.gridy = 2; gbC.gridx = 1;
gbC.insets = new Insets(2, 10, 2, 10);
gbL.setConstraints(m_PercentLab, gbC);
p2.add(m_PercentLab);
gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.EAST;
gbC.fill = GridBagConstraints.HORIZONTAL;
gbC.gridy = 2; gbC.gridx = 2; gbC.weightx = 100;
gbC.ipadx = 20;
gbL.setConstraints(m_PercentText, gbC);
p2.add(m_PercentText);
gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.WEST;
gbC.gridy = 3; gbC.gridx = 0; gbC.gridwidth = 2;
gbL.setConstraints(m_ClassesToClustersBut, gbC);
p2.add(m_ClassesToClustersBut);
m_ClassCombo.setBorder(BorderFactory.createEmptyBorder(0, 20, 0, 0));
gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.WEST;
gbC.gridy = 4; gbC.gridx = 0; gbC.gridwidth = 2;
gbL.setConstraints(m_ClassCombo, gbC);
p2.add(m_ClassCombo);
gbC = new GridBagConstraints();
gbC.anchor = GridBagConstraints.WEST;
gbC.gridy = 5; gbC.gridx = 0; gbC.gridwidth = 2;
gbL.setConstraints(m_StorePredictionsBut, gbC);
p2.add(m_StorePredictionsBut);
JPanel buttons = new JPanel();
buttons.setLayout(new GridLayout(2, 1));
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);
JPanel ib = new JPanel();
ib.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
ib.setLayout(new GridLayout(1, 1, 5, 5));
ib.add(m_ignoreBut);
buttons.add(ib);
buttons.add(ssButs);
JPanel p3 = new JPanel();
p3.setBorder(BorderFactory.createTitledBorder("Clusterer 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.anchor = GridBagConstraints.WEST;
gbC.fill = GridBagConstraints.HORIZONTAL;
gbC.gridy = 0; gbC.gridx = 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;
gbL.setConstraints(buttons, gbC);
mondo.add(buttons);
gbC = new GridBagConstraints();
//gbC.anchor = GridBagConstraints.NORTH;
gbC.fill = GridBagConstraints.BOTH;
gbC.gridy = 2; gbC.gridx = 0; gbC.weightx = 0;
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(p1, BorderLayout.NORTH);
add(mondo, BorderLayout.CENTER);
}
/**
* Updates the enabled status of the input fields and labels.
*/
protected void updateRadioLinks() {
m_SetTestBut.setEnabled(m_TestSplitBut.isSelected());
if ((m_SetTestFrame != null) && (!m_TestSplitBut.isSelected())) {
m_SetTestFrame.setVisible(false);
}
m_PercentText.setEnabled(m_PercentBut.isSelected());
m_PercentLab.setEnabled(m_PercentBut.isSelected());
m_ClassCombo.setEnabled(m_ClassesToClustersBut.isSelected());
}
/**
* 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;
m_ignoreKeyModel.removeAllElements();
String [] attribNames = new String [m_Instances.numAttributes()];
for (int i = 0; i < m_Instances.numAttributes(); i++) {
String name = m_Instances.attribute(i).name();
m_ignoreKeyModel.addElement(name);
String type = "(" + Attribute.typeToStringShort(m_Instances.attribute(i)) + ") ";
String attnm = m_Instances.attribute(i).name();
attribNames[i] = type + attnm;
}
m_StartBut.setEnabled(m_RunThread == null);
m_StopBut.setEnabled(m_RunThread != null);
m_ignoreBut.setEnabled(true);
m_ClassCombo.setModel(new DefaultComboBoxModel(attribNames));
if (inst.classIndex() == -1)
m_ClassCombo.setSelectedIndex(attribNames.length - 1);
else
m_ClassCombo.setSelectedIndex(inst.classIndex());
updateRadioLinks();
}
/**
* Sets the user test set. Information about the current test set
* is displayed in an InstanceSummaryPanel and the user is given the
* ability to load another set from a file or url.
*
*/
protected void setTestSet() {
if (m_SetTestFrame == null) {
final SetInstancesPanel sp = new SetInstancesPanel();
sp.setReadIncrementally(false);
m_Summary = sp.getSummary();
if (m_TestInstances != null) {
sp.setInstances(m_TestInstances);
}
sp.addPropertyChangeListener(new PropertyChangeListener() {
public void propertyChange(PropertyChangeEvent e) {
m_TestInstances = sp.getInstances();
m_TestInstances.setClassIndex(-1); // make sure that no class attribute is set!
}
});
// Add propertychangelistener to update m_TestInstances whenever
// it changes in the settestframe
m_SetTestFrame = new JFrame("Test Instances");
sp.setParentFrame(m_SetTestFrame); // enable Close-Button
m_SetTestFrame.getContentPane().setLayout(new BorderLayout());
m_SetTestFrame.getContentPane().add(sp, BorderLayout.CENTER);
m_SetTestFrame.pack();
}
m_SetTestFrame.setVisible(true);
}
/**
* Starts running the currently configured clusterer with the current
* settings. This is run in a separate thread, and will only start if
* there is no clusterer already running. The clusterer output is sent
* to the results history panel.
*/
protected void startClusterer() {
if (m_RunThread == null) {
m_StartBut.setEnabled(false);
m_StopBut.setEnabled(true);
m_ignoreBut.setEnabled(false);
m_RunThread = new Thread() {
public void run() {
// Copy the current state of things
m_Log.statusMessage("Setting up...");
Instances inst = new Instances(m_Instances);
inst.setClassIndex(-1);
Instances userTest = null;
ClustererAssignmentsPlotInstances plotInstances = ExplorerDefaults.getClustererAssignmentsPlotInstances();
plotInstances.setClusterer((Clusterer) m_ClustererEditor.getValue());
if (m_TestInstances != null) {
userTest = new Instances(m_TestInstances);
}
boolean saveVis = m_StorePredictionsBut.isSelected();
String grph = null;
int[] ignoredAtts = null;
int testMode = 0;
int percent = 66;
Clusterer clusterer = (Clusterer) m_ClustererEditor.getValue();
Clusterer fullClusterer = null;
StringBuffer outBuff = new StringBuffer();
String name = (new SimpleDateFormat("HH:mm:ss - ")).format(new Date());
String cname = clusterer.getClass().getName();
if (cname.startsWith("weka.clusterers.")) {
name += cname.substring("weka.clusterers.".length());
} else {
name += cname;
}
String cmd = m_ClustererEditor.getValue().getClass().getName();
if (m_ClustererEditor.getValue() instanceof OptionHandler)
cmd += " " + Utils.joinOptions(((OptionHandler) m_ClustererEditor.getValue()).getOptions());
try {
m_Log.logMessage("Started " + cname);
m_Log.logMessage("Command: " + cmd);
if (m_Log instanceof TaskLogger) {
((TaskLogger)m_Log).taskStarted();
}
if (m_PercentBut.isSelected()) {
testMode = 2;
percent = Integer.parseInt(m_PercentText.getText());
if ((percent <= 0) || (percent >= 100)) {
throw new Exception("Percentage must be between 0 and 100");
}
} else if (m_TrainBut.isSelected()) {
testMode = 3;
} else if (m_TestSplitBut.isSelected()) {
testMode = 4;
// Check the test instance compatibility
if (userTest == null) {
throw new Exception("No user test set has been opened");
}
if (!inst.equalHeaders(userTest)) {
throw new Exception("Train and test set are not compatible\n" + inst.equalHeadersMsg(userTest));
}
} else if (m_ClassesToClustersBut.isSelected()) {
testMode = 5;
} else {
throw new Exception("Unknown test mode");
}
Instances trainInst = new Instances(inst);
if (m_ClassesToClustersBut.isSelected()) {
trainInst.setClassIndex(m_ClassCombo.getSelectedIndex());
inst.setClassIndex(m_ClassCombo.getSelectedIndex());
if (inst.classAttribute().isNumeric()) {
throw new Exception("Class must be nominal for class based "
+"evaluation!");
}
}
if (!m_ignoreKeyList.isSelectionEmpty()) {
trainInst = removeIgnoreCols(trainInst);
}
// Output some header information
outBuff.append("=== Run information ===\n\n");
outBuff.append("Scheme: " + cname);
if (clusterer instanceof OptionHandler) {
String [] o = ((OptionHandler) clusterer).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) {
boolean [] selected = new boolean [inst.numAttributes()];
for (int i = 0; i < inst.numAttributes(); i++) {
selected[i] = true;
}
if (!m_ignoreKeyList.isSelectionEmpty()) {
int [] indices = m_ignoreKeyList.getSelectedIndices();
for (int i = 0; i < indices.length; i++) {
selected[indices[i]] = false;
}
}
if (m_ClassesToClustersBut.isSelected()) {
selected[m_ClassCombo.getSelectedIndex()] = false;
}
for (int i = 0; i < inst.numAttributes(); i++) {
if (selected[i]) {
outBuff.append(" " + inst.attribute(i).name()
+ '\n');
}
}
if (!m_ignoreKeyList.isSelectionEmpty()
|| m_ClassesToClustersBut.isSelected()) {
outBuff.append("Ignored:\n");
for (int i = 0; i < inst.numAttributes(); i++) {
if (!selected[i]) {
outBuff.append(" " + inst.attribute(i).name()
+ '\n');
}
}
}
} else {
outBuff.append(" [list of attributes omitted]\n");
}
if (!m_ignoreKeyList.isSelectionEmpty()) {
ignoredAtts = m_ignoreKeyList.getSelectedIndices();
}
if (m_ClassesToClustersBut.isSelected()) {
// add class to ignored list
if (ignoredAtts == null) {
ignoredAtts = new int[1];
ignoredAtts[0] = m_ClassCombo.getSelectedIndex();
} else {
int[] newIgnoredAtts = new int[ignoredAtts.length+1];
System.arraycopy(ignoredAtts, 0, newIgnoredAtts, 0, ignoredAtts.length);
newIgnoredAtts[ignoredAtts.length] = m_ClassCombo.getSelectedIndex();
ignoredAtts = newIgnoredAtts;
}
}
outBuff.append("Test mode: ");
switch (testMode) {
case 3: // Test on training
outBuff.append("evaluate on training data\n");
break;
case 2: // Percent split
outBuff.append("split " + percent
+ "% train, remainder test\n");
break;
case 4: // Test on user split
outBuff.append("user supplied test set: "
+ userTest.numInstances() + " instances\n");
break;
case 5: // Classes to clusters evaluation on training
outBuff.append("Classes to clusters evaluation on training data");
break;
}
outBuff.append("\n");
m_History.addResult(name, outBuff);
m_History.setSingle(name);
// Build the model and output it.
m_Log.statusMessage("Building model on training data...");
// remove the class attribute (if set) and build the clusterer
clusterer.buildClusterer(removeClass(trainInst));
if (testMode == 2) {
outBuff.append("\n=== Clustering model (full training set) ===\n\n");
outBuff.append(clusterer.toString() + '\n');
}
m_History.updateResult(name);
if (clusterer instanceof Drawable) {
try {
grph = ((Drawable)clusterer).graph();
} catch (Exception ex) {
}
}
// copy full model for output
SerializedObject so = new SerializedObject(clusterer);
fullClusterer = (Clusterer) so.getObject();
ClusterEvaluation eval = new ClusterEvaluation();
eval.setClusterer(clusterer);
switch (testMode) {
case 3: case 5: // Test on training
m_Log.statusMessage("Clustering training data...");
eval.evaluateClusterer(trainInst);
plotInstances.setInstances(inst);
plotInstances.setClusterEvaluation(eval);
outBuff.append("=== Model and evaluation on training set ===\n\n");
break;
case 2: // Percent split
m_Log.statusMessage("Randomizing instances...");
inst.randomize(new Random(1));
trainInst.randomize(new Random(1));
int trainSize = trainInst.numInstances() * percent / 100;
int testSize = trainInst.numInstances() - trainSize;
Instances train = new Instances(trainInst, 0, trainSize);
Instances test = new Instances(trainInst, trainSize, testSize);
Instances testVis = new Instances(inst, trainSize, testSize);
m_Log.statusMessage("Building model on training split...");
clusterer.buildClusterer(train);
m_Log.statusMessage("Evaluating on test split...");
eval.evaluateClusterer(test);
plotInstances.setInstances(testVis);
plotInstances.setClusterEvaluation(eval);
outBuff.append("=== Model and evaluation on test split ===\n");
break;
case 4: // Test on user split
m_Log.statusMessage("Evaluating on test data...");
Instances userTestT = new Instances(userTest);
if (!m_ignoreKeyList.isSelectionEmpty()) {
userTestT = removeIgnoreCols(userTestT);
}
eval.evaluateClusterer(userTestT);
plotInstances.setInstances(userTest);
plotInstances.setClusterEvaluation(eval);
outBuff.append("=== Model and evaluation on test set ===\n");
break;
default:
throw new Exception("Test mode not implemented");
}
outBuff.append(eval.clusterResultsToString());
outBuff.append("\n");
m_History.updateResult(name);
m_Log.logMessage("Finished " + cname);
m_Log.statusMessage("OK");
} catch (Exception ex) {
ex.printStackTrace();
m_Log.logMessage(ex.getMessage());
JOptionPane.showMessageDialog(ClustererPanel.this,
"Problem evaluating clusterer:\n"
+ ex.getMessage(),
"Evaluate clusterer",
JOptionPane.ERROR_MESSAGE);
m_Log.statusMessage("Problem evaluating clusterer");
} finally {
if (plotInstances != null) {
plotInstances.setUp();
m_CurrentVis = new VisualizePanel();
m_CurrentVis.setName(name+" ("+inst.relationName()+")");
m_CurrentVis.setLog(m_Log);
try {
m_CurrentVis.addPlot(plotInstances.getPlotData(name));
} catch (Exception ex) {
System.err.println(ex);
}
plotInstances.cleanUp();
FastVector vv = new FastVector();
vv.addElement(fullClusterer);
Instances trainHeader = new Instances(m_Instances, 0);
vv.addElement(trainHeader);
if (ignoredAtts != null) vv.addElement(ignoredAtts);
if (saveVis) {
vv.addElement(m_CurrentVis);
if (grph != null) {
vv.addElement(grph);
}
}
m_History.addObject(name, vv);
}
if (isInterrupted()) {
m_Log.logMessage("Interrupted " + cname);
m_Log.statusMessage("See error log");
}
m_RunThread = null;
m_StartBut.setEnabled(true);
m_StopBut.setEnabled(false);
m_ignoreBut.setEnabled(true);
if (m_Log instanceof TaskLogger) {
((TaskLogger)m_Log).taskFinished();
}
}
}
};
m_RunThread.setPriority(Thread.MIN_PRIORITY);
m_RunThread.start();
}
}
private Instances removeClass(Instances inst) {
Remove af = new Remove();
Instances retI = null;
try {
if (inst.classIndex() < 0) {
retI = inst;
} else {
af.setAttributeIndices(""+(inst.classIndex()+1));
af.setInvertSelection(false);
af.setInputFormat(inst);
retI = Filter.useFilter(inst, af);
}
} catch (Exception e) {
e.printStackTrace();
}
return retI;
}
private Instances removeIgnoreCols(Instances inst) {
// If the user is doing classes to clusters evaluation and
// they have opted to ignore the class, then unselect the class in
// the ignore list
if (m_ClassesToClustersBut.isSelected()) {
int classIndex = m_ClassCombo.getSelectedIndex();
if (m_ignoreKeyList.isSelectedIndex(classIndex)) {
m_ignoreKeyList.removeSelectionInterval(classIndex, classIndex);
}
}
int [] selected = m_ignoreKeyList.getSelectedIndices();
Remove af = new Remove();
Instances retI = null;
try {
af.setAttributeIndicesArray(selected);
af.setInvertSelection(false);
af.setInputFormat(inst);
retI = Filter.useFilter(inst, af);
} catch (Exception e) {
e.printStackTrace();
}
return retI;
}
private Instances removeIgnoreCols(Instances inst, int[] toIgnore) {
Remove af = new Remove();
Instances retI = null;
try {
af.setAttributeIndicesArray(toIgnore);
af.setInvertSelection(false);
af.setInputFormat(inst);
retI = Filter.useFilter(inst, af);
} catch (Exception e) {
e.printStackTrace();
}
return retI;
}
/**
* Stops the currently running clusterer (if any).
*/
protected void stopClusterer() {
if (m_RunThread != null) {
m_RunThread.interrupt();
// This is deprecated (and theoretically the interrupt should do).
m_RunThread.stop();
}
}
/**
* Pops up a TreeVisualizer for the clusterer from the currently
* selected item in the results list
* @param graphString the description of the tree in dotty format
* @param treeName the title to assign to the display
*/
protected void visualizeTree(String graphString, String treeName) {
final javax.swing.JFrame jf =
new javax.swing.JFrame("Weka Classifier Tree Visualizer: "+treeName);
jf.setSize(500,400);
jf.getContentPane().setLayout(new BorderLayout());
if (graphString.contains("digraph")) {
TreeVisualizer tv = new TreeVisualizer(null,
graphString,
new PlaceNode2());
jf.getContentPane().add(tv, BorderLayout.CENTER);
jf.addWindowListener(new java.awt.event.WindowAdapter() {
public void windowClosing(java.awt.event.WindowEvent e) {
jf.dispose();
}
});
jf.setVisible(true);
tv.fitToScreen();
} else if (graphString.startsWith("Newick:")) {
HierarchyVisualizer tv = new HierarchyVisualizer(graphString.substring(7));
jf.getContentPane().add(tv, BorderLayout.CENTER);
jf.addWindowListener(new java.awt.event.WindowAdapter() {
public void windowClosing(java.awt.event.WindowEvent e) {
jf.dispose();
}
});
jf.setVisible(true);
tv.fitToScreen();
}
}
/**
* Pops up a visualize panel to display cluster assignments
* @param sp the visualize panel to display
*/
protected void visualizeClusterAssignments(VisualizePanel sp) {
if (sp != null) {
String plotName = sp.getName();
final javax.swing.JFrame jf =
new javax.swing.JFrame("Weka Clusterer Visualize: "+plotName);
jf.setSize(500,400);
jf.getContentPane().setLayout(new BorderLayout());
jf.getContentPane().add(sp, BorderLayout.CENTER);
jf.addWindowListener(new java.awt.event.WindowAdapter() {
public void windowClosing(java.awt.event.WindowEvent e) {
jf.dispose();
}
});
jf.setVisible(true);
}
}
/**
* 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 visualizeClusterer(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);
resultListMenu.addSeparator();
JMenuItem loadModel = new JMenuItem("Load model");
loadModel.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
loadClusterer();
}
});
resultListMenu.add(loadModel);
FastVector o = null;
if (selectedName != null) {
o = (FastVector)m_History.getNamedObject(selectedName);
}
VisualizePanel temp_vp = null;
String temp_grph = null;
Clusterer temp_clusterer = null;
Instances temp_trainHeader = null;
int[] temp_ignoreAtts = null;
if (o != null) {
for (int i = 0; i < o.size(); i++) {
Object temp = o.elementAt(i);
if (temp instanceof Clusterer) {
temp_clusterer = (Clusterer)temp;
} else if (temp instanceof Instances) { // training header
temp_trainHeader = (Instances)temp;
} else if (temp instanceof int[]) { // ignored attributes
temp_ignoreAtts = (int[])temp;
} else if (temp instanceof VisualizePanel) { // normal errors
temp_vp = (VisualizePanel)temp;
} else if (temp instanceof String) { // graphable output
temp_grph = (String)temp;
}
}
}
final VisualizePanel vp = temp_vp;
final String grph = temp_grph;
final Clusterer clusterer = temp_clusterer;
final Instances trainHeader = temp_trainHeader;
final int[] ignoreAtts = temp_ignoreAtts;
JMenuItem saveModel = new JMenuItem("Save model");
if (clusterer != null) {
saveModel.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
saveClusterer(selectedName, clusterer, trainHeader, ignoreAtts);
}
});
} else {
saveModel.setEnabled(false);
}
resultListMenu.add(saveModel);
JMenuItem reEvaluate =
new JMenuItem("Re-evaluate model on current test set");
if (clusterer != null && m_TestInstances != null) {
reEvaluate.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
reevaluateModel(selectedName, clusterer, trainHeader, ignoreAtts);
}
});
} else {
reEvaluate.setEnabled(false);
}
resultListMenu.add(reEvaluate);
resultListMenu.addSeparator();
JMenuItem visClusts = new JMenuItem("Visualize cluster assignments");
if (vp != null) {
visClusts.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
visualizeClusterAssignments(vp);
}
});
} else {
visClusts.setEnabled(false);
}
resultListMenu.add(visClusts);
JMenuItem visTree = new JMenuItem("Visualize tree");
if (grph != null) {
visTree.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
String title;
if (vp != null) title = vp.getName();
else title = selectedName;
visualizeTree(grph, title);
}
});
} else {
visTree.setEnabled(false);
}
resultListMenu.add(visTree);
// visualization plugins
JMenu visPlugins = new JMenu("Plugins");
boolean availablePlugins = false;
// trees
if (grph != null) {
// trees
Vector pluginsVector = GenericObjectEditor.getClassnames(TreeVisualizePlugin.class.getName());
for (int i = 0; i < pluginsVector.size(); i++) {
String className = (String) (pluginsVector.elementAt(i));
try {
TreeVisualizePlugin plugin = (TreeVisualizePlugin) Class.forName(className).newInstance();
if (plugin == null)
continue;
availablePlugins = true;
JMenuItem pluginMenuItem = plugin.getVisualizeMenuItem(grph, selectedName);
Version version = new Version();
if (pluginMenuItem != null) {
if (version.compareTo(plugin.getMinVersion()) < 0)
pluginMenuItem.setText(pluginMenuItem.getText() + " (weka outdated)");
if (version.compareTo(plugin.getMaxVersion()) >= 0)
pluginMenuItem.setText(pluginMenuItem.getText() + " (plugin outdated)");
visPlugins.add(pluginMenuItem);
}
}
catch (Exception e) {
//e.printStackTrace();
}
}
}
if (availablePlugins)
resultListMenu.add(visPlugins);
resultListMenu.show(m_History.getList(), x, y);
}
/**
* Save the currently selected clusterer output to a file.
* @param name the name of the buffer to save
*/
protected void saveBuffer(String name) {
StringBuffer sb = m_History.getNamedBuffer(name);
if (sb != null) {
if (m_SaveOut.save(sb)) {
m_Log.logMessage("Save successful.");
}
}
}
private void setIgnoreColumns() {
ListSelectorDialog jd = new ListSelectorDialog(null, m_ignoreKeyList);
// Open the dialog
int result = jd.showDialog();
if (result != ListSelectorDialog.APPROVE_OPTION) {
// clear selected indices
m_ignoreKeyList.clearSelection();
}
updateCapabilitiesFilter(m_ClustererEditor.getCapabilitiesFilter());
}
/**
* Saves the currently selected clusterer
*/
protected void saveClusterer(String name, Clusterer clusterer,
Instances trainHeader, int[] ignoredAtts) {
File sFile = null;
boolean saveOK = true;
int returnVal = m_FileChooser.showSaveDialog(this);
if (returnVal == JFileChooser.APPROVE_OPTION) {
sFile = m_FileChooser.getSelectedFile();
if (!sFile.getName().toLowerCase().endsWith(MODEL_FILE_EXTENSION)) {
sFile = new File(sFile.getParent(), sFile.getName()
+ MODEL_FILE_EXTENSION);
}
m_Log.statusMessage("Saving model to file...");
try {
OutputStream os = new FileOutputStream(sFile);
if (sFile.getName().endsWith(".gz")) {
os = new GZIPOutputStream(os);
}
ObjectOutputStream objectOutputStream = new ObjectOutputStream(os);
objectOutputStream.writeObject(clusterer);
if (trainHeader != null) objectOutputStream.writeObject(trainHeader);
if (ignoredAtts != null) objectOutputStream.writeObject(ignoredAtts);
objectOutputStream.flush();
objectOutputStream.close();
} catch (Exception e) {
JOptionPane.showMessageDialog(null, e, "Save Failed",
JOptionPane.ERROR_MESSAGE);
saveOK = false;
}
if (saveOK)
m_Log.logMessage("Saved model (" + name
+ ") to file '" + sFile.getName() + "'");
m_Log.statusMessage("OK");
}
}
/**
* Loads a clusterer
*/
protected void loadClusterer() {
int returnVal = m_FileChooser.showOpenDialog(this);
if (returnVal == JFileChooser.APPROVE_OPTION) {
File selected = m_FileChooser.getSelectedFile();
Clusterer clusterer = null;
Instances trainHeader = null;
int[] ignoredAtts = null;
m_Log.statusMessage("Loading model from file...");
try {
InputStream is = new FileInputStream(selected);
if (selected.getName().endsWith(".gz")) {
is = new GZIPInputStream(is);
}
ObjectInputStream objectInputStream = new ObjectInputStream(is);
clusterer = (Clusterer) objectInputStream.readObject();
try { // see if we can load the header & ignored attribute info
trainHeader = (Instances) objectInputStream.readObject();
ignoredAtts = (int[]) objectInputStream.readObject();
} catch (Exception e) {} // don't fuss if we can't
objectInputStream.close();
} catch (Exception e) {
JOptionPane.showMessageDialog(null, e, "Load Failed",
JOptionPane.ERROR_MESSAGE);
}
m_Log.statusMessage("OK");
if (clusterer != null) {
m_Log.logMessage("Loaded model from file '" + selected.getName()+ "'");
String name = (new SimpleDateFormat("HH:mm:ss - ")).format(new Date());
String cname = clusterer.getClass().getName();
if (cname.startsWith("weka.clusterers."))
cname = cname.substring("weka.clusterers.".length());
name += cname + " from file '" + selected.getName() + "'";
StringBuffer outBuff = new StringBuffer();
outBuff.append("=== Model information ===\n\n");
outBuff.append("Filename: " + selected.getName() + "\n");
outBuff.append("Scheme: " + clusterer.getClass().getName());
if (clusterer instanceof OptionHandler) {
String [] o = ((OptionHandler) clusterer).getOptions();
outBuff.append(" " + Utils.joinOptions(o));
}
outBuff.append("\n");
if (trainHeader != null) {
outBuff.append("Relation: " + trainHeader.relationName() + '\n');
outBuff.append("Attributes: " + trainHeader.numAttributes() + '\n');
if (trainHeader.numAttributes() < 100) {
boolean [] selectedAtts = new boolean [trainHeader.numAttributes()];
for (int i = 0; i < trainHeader.numAttributes(); i++) {
selectedAtts[i] = true;
}
if (ignoredAtts != null)
for (int i=0; i<ignoredAtts.length; i++)
selectedAtts[ignoredAtts[i]] = false;
for (int i = 0; i < trainHeader.numAttributes(); i++) {
if (selectedAtts[i]) {
outBuff.append(" " + trainHeader.attribute(i).name()
+ '\n');
}
}
if (ignoredAtts != null) {
outBuff.append("Ignored:\n");
for (int i=0; i<ignoredAtts.length; i++)
outBuff.append(" "
+ trainHeader.attribute(ignoredAtts[i]).name()
+ '\n');
}
} else {
outBuff.append(" [list of attributes omitted]\n");
}
} else {
outBuff.append("\nTraining data unknown\n");
}
outBuff.append("\n=== Clustering model ===\n\n");
outBuff.append(clusterer.toString() + "\n");
m_History.addResult(name, outBuff);
m_History.setSingle(name);
FastVector vv = new FastVector();
vv.addElement(clusterer);
if (trainHeader != null) vv.addElement(trainHeader);
if (ignoredAtts != null) vv.addElement(ignoredAtts);
// allow visualization of graphable classifiers
String grph = null;
if (clusterer instanceof Drawable) {
try {
grph = ((Drawable)clusterer).graph();
} catch (Exception ex) {
}
}
if (grph != null) vv.addElement(grph);
m_History.addObject(name, vv);
}
}
}
/**
* Re-evaluates the named clusterer with the current test set. Unpredictable
* things will happen if the data set is not compatible with the clusterer.
*
* @param name the name of the clusterer entry
* @param clusterer the clusterer to evaluate
* @param trainHeader the header of the training set
* @param ignoredAtts ignored attributes
*/
protected void reevaluateModel(final String name,
final Clusterer clusterer,
final Instances trainHeader,
final int[] ignoredAtts) {
if (m_RunThread == null) {
m_StartBut.setEnabled(false);
m_StopBut.setEnabled(true);
m_ignoreBut.setEnabled(false);
m_RunThread = new Thread() {
public void run() {
// Copy the current state of things
m_Log.statusMessage("Setting up...");
StringBuffer outBuff = m_History.getNamedBuffer(name);
Instances userTest = null;
ClustererAssignmentsPlotInstances plotInstances = ExplorerDefaults.getClustererAssignmentsPlotInstances();
plotInstances.setClusterer(clusterer);
if (m_TestInstances != null) {
userTest = new Instances(m_TestInstances);
}
boolean saveVis = m_StorePredictionsBut.isSelected();
String grph = null;
try {
if (userTest == null) {
throw new Exception("No user test set has been opened");
}
if (trainHeader != null && !trainHeader.equalHeaders(userTest)) {
throw new Exception("Train and test set are not compatible\n" + trainHeader.equalHeadersMsg(userTest));
}
m_Log.statusMessage("Evaluating on test data...");
m_Log.logMessage("Re-evaluating clusterer (" + name + ") on test set");
m_Log.logMessage("Started reevaluate model");
if (m_Log instanceof TaskLogger) {
((TaskLogger)m_Log).taskStarted();
}
ClusterEvaluation eval = new ClusterEvaluation();
eval.setClusterer(clusterer);
Instances userTestT = new Instances(userTest);
if (ignoredAtts != null) {
userTestT = removeIgnoreCols(userTestT, ignoredAtts);
}
eval.evaluateClusterer(userTestT);
plotInstances.setClusterEvaluation(eval);
plotInstances.setInstances(userTest);
plotInstances.setUp();
outBuff.append("\n=== Re-evaluation on test set ===\n\n");
outBuff.append("User supplied test set\n");
outBuff.append("Relation: " + userTest.relationName() + '\n');
outBuff.append("Instances: " + userTest.numInstances() + '\n');
outBuff.append("Attributes: " + userTest.numAttributes() + "\n\n");
if (trainHeader == null)
outBuff.append("NOTE - if test set is not compatible then results are "
+ "unpredictable\n\n");
outBuff.append(eval.clusterResultsToString());
outBuff.append("\n");
m_History.updateResult(name);
m_Log.logMessage("Finished re-evaluation");
m_Log.statusMessage("OK");
} catch (Exception ex) {
ex.printStackTrace();
m_Log.logMessage(ex.getMessage());
JOptionPane.showMessageDialog(ClustererPanel.this,
"Problem evaluating clusterer:\n"
+ ex.getMessage(),
"Evaluate clusterer",
JOptionPane.ERROR_MESSAGE);
m_Log.statusMessage("Problem evaluating clusterer");
} finally {
if (plotInstances != null) {
m_CurrentVis = new VisualizePanel();
m_CurrentVis.setName(name+" ("+userTest.relationName()+")");
m_CurrentVis.setLog(m_Log);
try {
m_CurrentVis.addPlot(plotInstances.getPlotData(name));
} catch (Exception ex) {
System.err.println(ex);
}
FastVector vv = new FastVector();
vv.addElement(clusterer);
if (trainHeader != null) vv.addElement(trainHeader);
if (ignoredAtts != null) vv.addElement(ignoredAtts);
if (saveVis) {
vv.addElement(m_CurrentVis);
if (grph != null) {
vv.addElement(grph);
}
}
m_History.addObject(name, vv);
}
if (isInterrupted()) {
m_Log.logMessage("Interrupted reevaluate model");
m_Log.statusMessage("See error log");
}
m_RunThread = null;
m_StartBut.setEnabled(true);
m_StopBut.setEnabled(false);
m_ignoreBut.setEnabled(true);
if (m_Log instanceof TaskLogger) {
((TaskLogger)m_Log).taskFinished();
}
}
}
};
m_RunThread.setPriority(Thread.MIN_PRIORITY);
m_RunThread.start();
}
}
/**
* 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_ClustererEditor.setCapabilitiesFilter(new Capabilities(null));
return;
}
if (!ExplorerDefaults.getInitGenericObjectEditorFilter())
tempInst = new Instances(m_Instances, 0);
else
tempInst = new Instances(m_Instances);
tempInst.setClassIndex(-1);
if (!m_ignoreKeyList.isSelectionEmpty()) {
tempInst = removeIgnoreCols(tempInst);
}
try {
filterClass = Capabilities.forInstances(tempInst);
}
catch (Exception e) {
filterClass = new Capabilities(null);
}
m_ClustererEditor.setCapabilitiesFilter(filterClass);
// check capabilities
m_StartBut.setEnabled(true);
Capabilities currentFilter = m_ClustererEditor.getCapabilitiesFilter();
Clusterer clusterer = (Clusterer) m_ClustererEditor.getValue();
Capabilities currentSchemeCapabilities = null;
if (clusterer != null && currentFilter != null &&
(clusterer instanceof CapabilitiesHandler)) {
currentSchemeCapabilities = ((CapabilitiesHandler)clusterer).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 "Cluster";
}
/**
* Returns the tooltip for the tab in the Explorer
*
* @return the tooltip of this tab
*/
public String getTabTitleToolTip() {
return "Identify instance clusters";
}
/**
* Tests out the clusterer 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: Cluster");
jf.getContentPane().setLayout(new BorderLayout());
final ClustererPanel sp = new ClustererPanel();
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.setSize(800, 600);
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());
}
}
}