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The Waikato Environment for Knowledge Analysis (WEKA), a machine
learning workbench. This version represents the developer version, the
"bleeding edge" of development, you could say. New functionality gets added
to this version.
/*
* 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 m_listenees = new Hashtable();
/**
* Objects listening for batch clusterer events
*/
private final Vector m_batchClustererListeners = new Vector();
/**
* Objects listening for graph events
*/
private final Vector m_graphListeners = new Vector();
/**
* Objects listening for text events
*/
private final Vector m_textListeners = new Vector();
/**
* Holds training instances for batch training.
*/
private Instances m_trainingSet;
private transient Instances m_testingSet;
private weka.clusterers.Clusterer m_Clusterer = new EM();
private transient Logger m_log = null;
@SuppressWarnings("unused")
private final Double m_dummy = new Double(0.0);
private transient WekaFileChooser m_fileChooser = null;
/**
* Global info (if it exists) for the wrapped classifier
*
* @return the global info
*/
public String globalInfo() {
return m_globalInfo;
}
/**
* Creates a new Clusterer instance.
*/
public Clusterer() {
setLayout(new BorderLayout());
add(m_visual, BorderLayout.CENTER);
setClusterer(m_Clusterer);
}
/**
* Set a custom (descriptive) name for this bean
*
* @param name the name to use
*/
@Override
public void setCustomName(String name) {
m_visual.setText(name);
}
/**
* Get the custom (descriptive) name for this bean (if one has been set)
*
* @return the custom name (or the default name)
*/
@Override
public String getCustomName() {
return m_visual.getText();
}
/**
* Set the clusterer for this wrapper
*
* @param c a weka.clusterers.Clusterer value
*/
public void setClusterer(weka.clusterers.Clusterer c) {
boolean loadImages = true;
if (c.getClass().getName().compareTo(m_Clusterer.getClass().getName()) == 0) {
loadImages = false;
} else {
// clusterer has changed so any batch training status is now
// invalid
m_trainingSet = null;
}
m_Clusterer = c;
String clustererName = c.getClass().toString();
clustererName = clustererName.substring(clustererName.lastIndexOf('.') + 1,
clustererName.length());
if (loadImages) {
if (!m_visual.loadIcons(BeanVisual.ICON_PATH + clustererName + ".gif",
BeanVisual.ICON_PATH + clustererName + "_animated.gif")) {
useDefaultVisual();
}
}
m_visual.setText(clustererName);
// get global info
m_globalInfo = KnowledgeFlowApp.getGlobalInfo(m_Clusterer);
}
/**
* Returns true if this clusterer has an incoming connection that is a batch
* set of instances
*
* @return a boolean value
*/
public boolean hasIncomingBatchInstances() {
if (m_listenees.size() == 0) {
return false;
}
if (m_listenees.containsKey("trainingSet")
|| m_listenees.containsKey("testSet")
|| m_listenees.containsKey("dataSet")) {
return true;
}
return false;
}
/**
* Get the clusterer currently set for this wrapper
*
* @return a weka.clusterers.Clusterer value
*/
public weka.clusterers.Clusterer getClusterer() {
return m_Clusterer;
}
/**
* Sets the algorithm (clusterer) for this bean
*
* @param algorithm an Object value
* @exception IllegalArgumentException if an error occurs
*/
@Override
public void setWrappedAlgorithm(Object algorithm) {
if (!(algorithm instanceof weka.clusterers.Clusterer)) {
throw new IllegalArgumentException(algorithm.getClass() + " : incorrect "
+ "type of algorithm (Clusterer)");
}
setClusterer((weka.clusterers.Clusterer) algorithm);
}
/**
* Returns the wrapped clusterer
*
* @return an Object value
*/
@Override
public Object getWrappedAlgorithm() {
return getClusterer();
}
/**
* Accepts a training set and builds batch clusterer
*
* @param e a TrainingSetEvent value
*/
@Override
public void acceptTrainingSet(final TrainingSetEvent e) {
if (e.isStructureOnly()) {
// no need to build a clusterer, instead just generate a dummy
// BatchClustererEvent in order to pass on instance structure to
// any listeners
BatchClustererEvent ce = new BatchClustererEvent(this, m_Clusterer,
new DataSetEvent(this, e.getTrainingSet()), e.getSetNumber(),
e.getMaxSetNumber(), 1);
notifyBatchClustererListeners(ce);
return;
}
if (m_buildThread == null) {
try {
if (m_state == IDLE) {
synchronized (this) {
m_state = BUILDING_MODEL;
}
m_trainingSet = e.getTrainingSet();
// final String oldText = m_visual.getText();
m_buildThread = new Thread() {
@SuppressWarnings("deprecation")
@Override
public void run() {
try {
if (m_trainingSet != null) {
m_visual.setAnimated();
// m_visual.setText("Building clusters...");
if (m_log != null) {
m_log.statusMessage(statusMessagePrefix()
+ "Building clusters...");
}
buildClusterer();
if (m_batchClustererListeners.size() > 0) {
BatchClustererEvent ce = new BatchClustererEvent(this,
m_Clusterer, new DataSetEvent(this, e.getTrainingSet()),
e.getSetNumber(), e.getMaxSetNumber(), 1);
notifyBatchClustererListeners(ce);
}
if (m_Clusterer instanceof weka.core.Drawable
&& m_graphListeners.size() > 0) {
String grphString = ((weka.core.Drawable) m_Clusterer)
.graph();
int grphType = ((weka.core.Drawable) m_Clusterer)
.graphType();
String grphTitle = m_Clusterer.getClass().getName();
grphTitle = grphTitle.substring(
grphTitle.lastIndexOf('.') + 1, grphTitle.length());
grphTitle = "Set " + e.getSetNumber() + " ("
+ e.getTrainingSet().relationName() + ") " + grphTitle;
GraphEvent ge = new GraphEvent(Clusterer.this, grphString,
grphTitle, grphType);
notifyGraphListeners(ge);
}
if (m_textListeners.size() > 0) {
String modelString = m_Clusterer.toString();
String titleString = m_Clusterer.getClass().getName();
titleString = titleString.substring(
titleString.lastIndexOf('.') + 1, titleString.length());
modelString = "=== Clusterer model ===\n\n"
+ "Scheme: "
+ titleString
+ "\n"
+ "Relation: "
+ m_trainingSet.relationName()
+ ((e.getMaxSetNumber() > 1) ? "\nTraining Fold: "
+ e.getSetNumber() : "") + "\n\n" + modelString;
titleString = "Model: " + titleString;
TextEvent nt = new TextEvent(Clusterer.this, modelString,
titleString);
notifyTextListeners(nt);
}
}
} catch (Exception ex) {
Clusterer.this.stop(); // stop processing
if (m_log != null) {
m_log.statusMessage(statusMessagePrefix()
+ "ERROR (See log for details");
m_log.logMessage("[Clusterer] " + statusMessagePrefix()
+ " problem training clusterer. " + ex.getMessage());
}
ex.printStackTrace();
} finally {
// m_visual.setText(oldText);
m_visual.setStatic();
m_state = IDLE;
if (isInterrupted()) {
// prevent any clusterer events from being fired
m_trainingSet = null;
if (m_log != null) {
m_log.logMessage("[Clusterer]" + statusMessagePrefix()
+ " Build clusterer interrupted!");
m_log.statusMessage(statusMessagePrefix() + "INTERRUPTED");
}
} else {
// save header
m_trainingSet = new Instances(m_trainingSet, 0);
if (m_log != null) {
m_log.statusMessage(statusMessagePrefix() + "Finished.");
}
}
block(false);
}
}
};
m_buildThread.setPriority(Thread.MIN_PRIORITY);
m_buildThread.start();
// make sure the thread is still running before we block
// if (m_buildThread.isAlive()) {
block(true);
// }
m_buildThread = null;
m_state = IDLE;
}
} catch (Exception ex) {
ex.printStackTrace();
}
}
}
/**
* Accepts a test set for a batch trained clusterer
*
* @param e a TestSetEvent value
*/
@Override
public void acceptTestSet(TestSetEvent e) {
if (m_trainingSet != null) {
try {
if (m_state == IDLE) {
synchronized (this) {
m_state = CLUSTERING;
}
m_testingSet = e.getTestSet();
if (m_trainingSet.equalHeaders(m_testingSet)) {
BatchClustererEvent ce = new BatchClustererEvent(this, m_Clusterer,
new DataSetEvent(this, e.getTestSet()), e.getSetNumber(),
e.getMaxSetNumber(), 0);
notifyBatchClustererListeners(ce);
}
m_state = IDLE;
}
} catch (Exception ex) {
stop(); // stop any processing
if (m_log != null) {
m_log.statusMessage(statusMessagePrefix()
+ "ERROR (see log for details");
m_log.logMessage("[Clusterer] " + statusMessagePrefix()
+ " problem during testing. " + ex.getMessage());
}
ex.printStackTrace();
}
}
}
/**
* Builds the clusters
*/
private void buildClusterer() throws Exception {
if (m_trainingSet.classIndex() < 0) {
m_Clusterer.buildClusterer(m_trainingSet);
} else { // class based evaluation if class attribute is set
Remove removeClass = new Remove();
removeClass.setAttributeIndices("" + (m_trainingSet.classIndex() + 1));
removeClass.setInvertSelection(false);
removeClass.setInputFormat(m_trainingSet);
Instances clusterTrain = Filter.useFilter(m_trainingSet, removeClass);
m_Clusterer.buildClusterer(clusterTrain);
}
}
/**
* Sets the visual appearance of this wrapper bean
*
* @param newVisual a BeanVisual value
*/
@Override
public void setVisual(BeanVisual newVisual) {
m_visual = newVisual;
}
/**
* Gets the visual appearance of this wrapper bean
*/
@Override
public BeanVisual getVisual() {
return m_visual;
}
/**
* Use the default visual appearance for this bean
*/
@Override
public void useDefaultVisual() {
m_visual.loadIcons(BeanVisual.ICON_PATH + "DefaultClusterer.gif",
BeanVisual.ICON_PATH + "DefaultClusterer_animated.gif");
}
/**
* Add a batch clusterer listener
*
* @param cl a BatchClustererListener value
*/
public synchronized void addBatchClustererListener(BatchClustererListener cl) {
m_batchClustererListeners.addElement(cl);
}
/**
* Remove a batch clusterer listener
*
* @param cl a BatchClustererListener value
*/
public synchronized void removeBatchClustererListener(
BatchClustererListener cl) {
m_batchClustererListeners.remove(cl);
}
/**
* Notify all batch clusterer listeners of a batch clusterer event
*
* @param ce a BatchClustererEvent value
*/
@SuppressWarnings("unchecked")
private void notifyBatchClustererListeners(BatchClustererEvent ce) {
Vector l;
synchronized (this) {
l = (Vector) m_batchClustererListeners.clone();
}
if (l.size() > 0) {
for (int i = 0; i < l.size(); i++) {
l.elementAt(i).acceptClusterer(ce);
}
}
}
/**
* Add a graph listener
*
* @param cl a GraphListener value
*/
public synchronized void addGraphListener(GraphListener cl) {
m_graphListeners.addElement(cl);
}
/**
* Remove a graph listener
*
* @param cl a GraphListener value
*/
public synchronized void removeGraphListener(GraphListener cl) {
m_graphListeners.remove(cl);
}
/**
* Notify all graph listeners of a graph event
*
* @param ge a GraphEvent value
*/
@SuppressWarnings("unchecked")
private void notifyGraphListeners(GraphEvent ge) {
Vector l;
synchronized (this) {
l = (Vector) m_graphListeners.clone();
}
if (l.size() > 0) {
for (int i = 0; i < l.size(); i++) {
l.elementAt(i).acceptGraph(ge);
}
}
}
/**
* Add a text listener
*
* @param cl a TextListener value
*/
public synchronized void addTextListener(TextListener cl) {
m_textListeners.addElement(cl);
}
/**
* Remove a text listener
*
* @param cl a TextListener value
*/
public synchronized void removeTextListener(TextListener cl) {
m_textListeners.remove(cl);
}
/**
* Notify all text listeners of a text event
*
* @param ge a TextEvent value
*/
@SuppressWarnings("unchecked")
private void notifyTextListeners(TextEvent ge) {
Vector l;
synchronized (this) {
l = (Vector) m_textListeners.clone();
}
if (l.size() > 0) {
for (int i = 0; i < l.size(); i++) {
l.elementAt(i).acceptText(ge);
}
}
}
/**
* We don't have to keep track of configuration listeners (see the
* documentation for ConfigurationListener/ConfigurationEvent).
*
* @param cl a ConfigurationListener.
*/
@Override
public synchronized void addConfigurationListener(ConfigurationListener cl) {
}
/**
* We don't have to keep track of configuration listeners (see the
* documentation for ConfigurationListener/ConfigurationEvent).
*
* @param cl a ConfigurationListener.
*/
@Override
public synchronized void removeConfigurationListener(ConfigurationListener cl) {
}
/**
* Returns true if, at this time, the object will accept a connection with
* respect to the named event
*
* @param eventName the event
* @return true if the object will accept a connection
*/
@Override
public boolean connectionAllowed(String eventName) {
/*
* if (eventName.compareTo("instance") == 0) { if (!(m_Clusterer instanceof
* weka.classifiers.UpdateableClassifier)) { return false; } }
*/
if (m_listenees.containsKey(eventName)) {
return false;
}
return true;
}
/**
* Returns true if, at this time, the object will accept a connection
* according to the supplied EventSetDescriptor
*
* @param esd the EventSetDescriptor
* @return true if the object will accept a connection
*/
@Override
public boolean connectionAllowed(EventSetDescriptor esd) {
return connectionAllowed(esd.getName());
}
/**
* Notify this object that it has been registered as a listener with a source
* with respect to the named event
*
* @param eventName the event
* @param source the source with which this object has been registered as a
* listener
*/
@Override
public synchronized void connectionNotification(String eventName,
Object source) {
if (connectionAllowed(eventName)) {
m_listenees.put(eventName, source);
/*
* if (eventName.compareTo("instance") == 0) { startIncrementalHandler();
* }
*/
}
}
/**
* Notify this object that it has been deregistered as a listener with a
* source with respect to the supplied event name
*
* @param eventName the event
* @param source the source with which this object has been registered as a
* listener
*/
@Override
public synchronized void disconnectionNotification(String eventName,
Object source) {
m_listenees.remove(eventName);
}
/**
* Function used to stop code that calls acceptTrainingSet. This is needed as
* clusterer construction is performed inside a separate thread of execution.
*
* @param tf a boolean value
*/
private synchronized void block(boolean tf) {
if (tf) {
try {
// only block if thread is still doing something useful!
if (m_buildThread.isAlive() && m_state != IDLE) {
wait();
}
} catch (InterruptedException ex) {
}
} else {
notifyAll();
}
}
/**
* Returns true if. at this time, the bean is busy with some (i.e. perhaps a
* worker thread is performing some calculation).
*
* @return true if the bean is busy.
*/
@Override
public boolean isBusy() {
return (m_buildThread != null);
}
/**
* Stop any clusterer action
*/
@SuppressWarnings("deprecation")
@Override
public void stop() {
// tell all listenees (upstream beans) to stop
Enumeration en = m_listenees.keys();
while (en.hasMoreElements()) {
Object tempO = m_listenees.get(en.nextElement());
if (tempO instanceof BeanCommon) {
((BeanCommon) tempO).stop();
}
}
// stop the build thread
if (m_buildThread != null) {
m_buildThread.interrupt();
m_buildThread.stop();
m_buildThread = null;
m_visual.setStatic();
}
}
/**
* Set a logger
*
* @param logger a Logger value
*/
@Override
public void setLog(Logger logger) {
m_log = logger;
}
public void saveModel() {
try {
if (m_fileChooser == null) {
// i.e. after de-serialization
m_fileChooser = new WekaFileChooser(new File(
System.getProperty("user.dir")));
ExtensionFileFilter ef = new ExtensionFileFilter("model",
"Serialized weka clusterer");
m_fileChooser.setFileFilter(ef);
}
int returnVal = m_fileChooser.showSaveDialog(this);
if (returnVal == JFileChooser.APPROVE_OPTION) {
File saveTo = m_fileChooser.getSelectedFile();
String fn = saveTo.getAbsolutePath();
if (!fn.endsWith(".model")) {
fn += ".model";
saveTo = new File(fn);
}
ObjectOutputStream os = new ObjectOutputStream(
new BufferedOutputStream(new FileOutputStream(saveTo)));
os.writeObject(m_Clusterer);
if (m_trainingSet != null) {
Instances header = m_trainingSet.stringFreeStructure();
os.writeObject(header);
}
os.close();
if (m_log != null) {
m_log.logMessage("[Clusterer] Saved clusterer " + getCustomName());
}
}
} catch (Exception ex) {
JOptionPane.showMessageDialog(Clusterer.this,
"Problem saving clusterer.\n", "Save Model", JOptionPane.ERROR_MESSAGE);
if (m_log != null) {
m_log.logMessage("[Clusterer] Problem saving clusterer. "
+ getCustomName() + ex.getMessage());
}
}
}
public void loadModel() {
try {
if (m_fileChooser == null) {
// i.e. after de-serialization
m_fileChooser = new WekaFileChooser(new File(
System.getProperty("user.dir")));
ExtensionFileFilter ef = new ExtensionFileFilter("model",
"Serialized weka clusterer");
m_fileChooser.setFileFilter(ef);
}
int returnVal = m_fileChooser.showOpenDialog(this);
if (returnVal == JFileChooser.APPROVE_OPTION) {
File loadFrom = m_fileChooser.getSelectedFile();
ObjectInputStream is = new ObjectInputStream(new BufferedInputStream(
new FileInputStream(loadFrom)));
// try and read the model
weka.clusterers.Clusterer temp = (weka.clusterers.Clusterer) is
.readObject();
// Update name and icon
setClusterer(temp);
// try and read the header (if present)
try {
m_trainingSet = (Instances) is.readObject();
} catch (Exception ex) {
// quietly ignore
}
is.close();
if (m_log != null) {
m_log.logMessage("[Clusterer] Loaded clusterer: "
+ m_Clusterer.getClass().toString());
}
}
} catch (Exception ex) {
JOptionPane.showMessageDialog(Clusterer.this,
"Problem loading classifier.\n", "Load Model",
JOptionPane.ERROR_MESSAGE);
if (m_log != null) {
m_log.logMessage("[Clusterer] Problem loading classifier. "
+ ex.getMessage());
}
}
}
/**
* Return an enumeration of requests that can be made by the user
*
* @return an Enumeration value
*/
@Override
public Enumeration enumerateRequests() {
Vector newVector = new Vector(0);
if (m_buildThread != null) {
newVector.addElement("Stop");
}
if (m_buildThread == null && m_Clusterer != null) {
newVector.addElement("Save model");
}
if (m_buildThread == null) {
newVector.addElement("Load model");
}
return newVector.elements();
}
/**
* Perform a particular request
*
* @param request the request to perform
* @exception IllegalArgumentException if an error occurs
*/
@Override
public void performRequest(String request) {
if (request.compareTo("Stop") == 0) {
stop();
} else if (request.compareTo("Save model") == 0) {
saveModel();
} else if (request.compareTo("Load model") == 0) {
loadModel();
} else {
throw new IllegalArgumentException(request + " not supported (Clusterer)");
}
}
/**
* Returns true, if at the current time, the event described by the supplied
* event descriptor could be generated.
*
* @param esd an EventSetDescriptor value
* @return a boolean value
*/
public boolean eventGeneratable(EventSetDescriptor esd) {
String eventName = esd.getName();
return eventGeneratable(eventName);
}
/**
* Returns true, if at the current time, the named event could be generated.
* Assumes that the supplied event name is an event that could be generated by
* this bean
*
* @param eventName the name of the event in question
* @return true if the named event could be generated at this point in time
*/
@Override
public boolean eventGeneratable(String eventName) {
if (eventName.compareTo("graph") == 0) {
// can't generate a GraphEvent if clusterer is not drawable
if (!(m_Clusterer instanceof weka.core.Drawable)) {
return false;
}
// need to have a training set before the clusterer
// can generate a graph!
if (!m_listenees.containsKey("trainingSet")) {
return false;
}
// Source needs to be able to generate a trainingSet
// before we can generate a graph
Object source = m_listenees.get("trainingSet");
if (source instanceof EventConstraints) {
if (!((EventConstraints) source).eventGeneratable("trainingSet")) {
return false;
}
}
}
if (eventName.compareTo("batchClusterer") == 0) {
if (!m_listenees.containsKey("trainingSet")) {
return false;
}
Object source = m_listenees.get("trainingSet");
if (source != null && source instanceof EventConstraints) {
if (!((EventConstraints) source).eventGeneratable("trainingSet")) {
return false;
}
}
}
if (eventName.compareTo("text") == 0) {
if (!m_listenees.containsKey("trainingSet")) {
return false;
}
Object source = m_listenees.get("trainingSet");
if (source != null && source instanceof EventConstraints) {
if (!((EventConstraints) source).eventGeneratable("trainingSet")) {
return false;
}
}
}
if (eventName.compareTo("batchClassifier") == 0) {
return false;
}
if (eventName.compareTo("incrementalClassifier") == 0) {
return false;
}
return true;
}
private String statusMessagePrefix() {
return getCustomName()
+ "$"
+ hashCode()
+ "|"
+ ((m_Clusterer instanceof OptionHandler && Utils.joinOptions(
((OptionHandler) m_Clusterer).getOptions()).length() > 0) ? Utils
.joinOptions(((OptionHandler) m_Clusterer).getOptions()) + "|" : "");
}
}
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