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The Waikato Environment for Knowledge Analysis (WEKA), a machine
learning workbench. This is the stable version. Apart from bugfixes, this version
does not receive any other updates.
/*
* 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 3 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, see .
*/
/*
* ClustererPanel.java
* Copyright (C) 1999-2013 University of Waikato, Hamilton, New Zealand
*
*/
package weka.gui.explorer;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.FlowLayout;
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.ArrayList;
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.clusterers.ClusterEvaluation;
import weka.clusterers.Clusterer;
import weka.clusterers.SimpleKMeans;
import weka.core.Attribute;
import weka.core.Capabilities;
import weka.core.CapabilitiesHandler;
import weka.core.Defaults;
import weka.core.Drawable;
import weka.core.Environment;
import weka.core.Instances;
import weka.core.OptionHandler;
import weka.core.SerializedObject;
import weka.core.Settings;
import weka.core.Utils;
import weka.core.Version;
import weka.filters.Filter;
import weka.filters.unsupervised.attribute.Remove;
import weka.gui.AbstractPerspective;
import weka.gui.ExtensionFileFilter;
import weka.gui.GenericObjectEditor;
import weka.gui.InstancesSummaryPanel;
import weka.gui.ListSelectorDialog;
import weka.gui.Logger;
import weka.gui.PerspectiveInfo;
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.hierarchyvisualizer.HierarchyVisualizer;
import weka.gui.treevisualizer.PlaceNode2;
import weka.gui.treevisualizer.TreeVisualizer;
import weka.gui.visualize.VisualizePanel;
import weka.gui.visualize.plugins.TreeVisualizePlugin;
/**
* 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 ([email protected])
* @author Richard Kirkby ([email protected])
* @version $Revision: 12722 $
*/
@PerspectiveInfo(ID = "weka.gui.explorer.clustererpanel", title = "Cluster",
toolTipText = "Cluster instances",
iconPath = "weka/gui/weka_icon_new_small.png")
public class ClustererPanel extends AbstractPerspective 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() {
@Override
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 final 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")));
/** Whether startup settings have been applied yet or not */
protected boolean m_initialSettingsSet;
/* 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() {
@Override
public void mouseClicked(MouseEvent e) {
if ((e.getModifiers() & InputEvent.BUTTON1_MASK) != InputEvent.BUTTON1_MASK) {
m_OutText.selectAll();
}
}
});
JPanel historyHolder = new JPanel(new BorderLayout());
historyHolder.setBorder(BorderFactory
.createTitledBorder("Result list (right-click for options)"));
historyHolder.add(m_History, BorderLayout.CENTER);
m_ClustererEditor.setClassType(Clusterer.class);
m_ClustererEditor.setValue(ExplorerDefaults.getClusterer());
m_ClustererEditor.addPropertyChangeListener(new PropertyChangeListener() {
@Override
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() {
@Override
public void actionPerformed(ActionEvent e) {
setTestSet();
}
});
m_StartBut.setEnabled(false);
m_StopBut.setEnabled(false);
m_ignoreBut.setEnabled(false);
m_StartBut.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
boolean proceed = true;
if (Explorer.m_Memory.memoryIsLow()) {
proceed = Explorer.m_Memory.showMemoryIsLow();
}
if (proceed) {
startClusterer();
}
}
});
m_StopBut.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
stopClusterer();
}
});
m_ignoreBut.addActionListener(new ActionListener() {
@Override
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() {
@Override
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() {
@Override
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);
// Any launcher plugins
Vector pluginsVector =
GenericObjectEditor.getClassnames(ClustererPanelLaunchHandlerPlugin.class
.getName());
JButton pluginBut = null;
if (pluginsVector.size() == 1) {
try {
// display a single button
String className = pluginsVector.elementAt(0);
final ClustererPanelLaunchHandlerPlugin plugin =
(ClustererPanelLaunchHandlerPlugin) Class.forName(className)
.newInstance();
if (plugin != null) {
plugin.setClustererPanel(this);
pluginBut = new JButton(plugin.getLaunchCommand());
pluginBut.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
plugin.launch();
}
});
}
} catch (Exception ex) {
ex.printStackTrace();
}
} else if (pluginsVector.size() > 1) {
// make a popup menu
int okPluginCount = 0;
final java.awt.PopupMenu pluginPopup = new java.awt.PopupMenu();
for (int i = 0; i < pluginsVector.size(); i++) {
String className = (pluginsVector.elementAt(i));
try {
final ClustererPanelLaunchHandlerPlugin plugin =
(ClustererPanelLaunchHandlerPlugin) Class.forName(className)
.newInstance();
if (plugin == null) {
continue;
}
okPluginCount++;
plugin.setClustererPanel(this);
java.awt.MenuItem popI =
new java.awt.MenuItem(plugin.getLaunchCommand());
popI.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
// pluginPopup.setVisible(false);
plugin.launch();
}
});
pluginPopup.add(popI);
} catch (Exception ex) {
ex.printStackTrace();
}
}
if (okPluginCount > 0) {
pluginBut = new JButton("Launchers...");
final JButton copyB = pluginBut;
copyB.add(pluginPopup);
pluginBut.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
pluginPopup.show(copyB, 0, 0);
}
});
} else {
pluginBut = null;
}
}
JPanel buttons = new JPanel();
buttons.setLayout(new GridLayout(2, 1));
JPanel ssButs = new JPanel();
ssButs.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
if (pluginBut == null) {
ssButs.setLayout(new GridLayout(1, 2, 5, 5));
} else {
ssButs.setLayout(new FlowLayout(FlowLayout.LEFT));
}
ssButs.add(m_StartBut);
ssButs.add(m_StopBut);
if (pluginBut != null) {
ssButs.add(pluginBut);
}
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;
@Override
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(historyHolder, gbC);
mondo.add(historyHolder);
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());
updateCapabilitiesFilter(m_ClustererEditor.getCapabilitiesFilter());
}
/**
* Sets the Logger to receive informational messages
*
* @param newLog the Logger that will now get info messages
*/
@Override
public void setLog(Logger newLog) {
m_Log = newLog;
}
/**
* Tells the panel to use a new set of instances.
*
* @param inst a set of Instances
*/
@Override
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() {
@Override
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() {
@Override
public void run() {
m_CLPanel.addToHistory();
// for timing
long trainTimeStart = 0, trainTimeElapsed = 0;
// 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
trainTimeStart = System.currentTimeMillis();
clusterer.buildClusterer(removeClass(trainInst));
trainTimeElapsed = System.currentTimeMillis() - trainTimeStart;
// if (testMode == 2) {
outBuff
.append("\n=== Clustering model (full training set) ===\n\n");
outBuff.append(clusterer.toString() + '\n');
outBuff
.append("\nTime taken to build model (full training data) : "
+ Utils.doubleToString(trainTimeElapsed / 1000.0, 2)
+ " seconds\n\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, "", false);
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...");
trainTimeStart = System.currentTimeMillis();
clusterer.buildClusterer(train);
trainTimeElapsed = System.currentTimeMillis() - trainTimeStart;
m_Log.statusMessage("Evaluating on test split...");
eval.evaluateClusterer(test, "", false);
plotInstances.setInstances(testVis);
plotInstances.setClusterEvaluation(eval);
outBuff.append("=== Model and evaluation on test split ===\n");
outBuff.append(clusterer.toString() + "\n");
outBuff
.append("\nTime taken to build model (percentage split) : "
+ Utils.doubleToString(trainTimeElapsed / 1000.0, 2)
+ " seconds\n\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, "", false);
plotInstances.setInstances(userTest);
plotInstances.setClusterEvaluation(eval);
outBuff.append("=== 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.canPlot(true)) {
m_CurrentVis = new VisualizePanel();
if (getMainApplication() != null) {
Settings settings = getMainApplication().getApplicationSettings();
m_CurrentVis.applySettings(settings,
weka.gui.explorer.VisualizePanel.ScatterDefaults.ID);
}
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();
ArrayList