/*
* 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 <http://www.gnu.org/licenses/>.
*/
/*
* PartitionMembership.java
* Copyright (C) 2012 Eibe Frank
*
*/
package weka.filters.supervised.attribute;
import weka.core.Attribute;
import weka.core.Capabilities;
import weka.core.FastVector;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.PartitionGenerator;
import weka.core.SparseInstance;
import weka.core.Utils;
import weka.filters.Filter;
import weka.filters.SupervisedFilter;
import weka.filters.UnsupervisedFilter;
import weka.classifiers.trees.J48;
import java.util.Enumeration;
import java.util.Vector;
import weka.core.RevisionHandler;
import weka.core.RevisionUtils;
/**
<!-- globalinfo-start -->
* A filter that uses a PartitionGenerator to generate partition membership values; filtered instances are composed of these values plus the class attribute (if set in the input data) and rendered as sparse instances.
* <p/>
<!-- globalinfo-end -->
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -W <name of partition generator>
* Full name of partition generator to use, e.g.:
* weka.classifiers.trees.J48
* Additional options after the '--'.
* (default: weka.classifiers.trees.J48)</pre>
*
<!-- options-end -->
*
* Options after the -- are passed on to the clusterer.
*
* @author Eibe Frank (eibe@cs.waikato.ac.nz)
* @author Mark Hall (mhall@cs.waikato.ac.nz)
* @version $Revision: 9910 $
*/
public class PartitionMembership extends Filter implements SupervisedFilter, OptionHandler, RevisionHandler {
/** for serialization */
static final long serialVersionUID = 333532554667754026L;
/** The partition generator */
protected PartitionGenerator m_partitionGenerator = new J48();
/**
* Returns the Capabilities of this filter.
*
* @return the capabilities of this object
* @see Capabilities
*/
public Capabilities getCapabilities() {
Capabilities result = m_partitionGenerator.getCapabilities();
result.setMinimumNumberInstances(0);
return result;
}
/**
* Tests the data whether the filter can actually handle it
*
* @param instanceInfo the data to test
* @throws Exception if the test fails
*/
protected void testInputFormat(Instances instanceInfo) throws Exception {
getCapabilities().testWithFail(instanceInfo);
}
/**
* Sets the format of the input instances.
*
* @param instanceInfo an Instances object containing the input instance
* structure (any instances contained in the object are ignored - only the
* structure is required).
* @return true if the outputFormat may be collected immediately
* @throws Exception if the inputFormat can't be set successfully
*/
public boolean setInputFormat(Instances instanceInfo) throws Exception {
super.setInputFormat(instanceInfo);
return false;
}
/**
* Signify that this batch of input to the filter is finished.
*
* @return true if there are instances pending output
* @throws IllegalStateException if no input structure has been defined
*/
public boolean batchFinished() throws Exception {
if (getInputFormat() == null) {
throw new IllegalStateException("No input instance format defined");
}
if (outputFormatPeek() == null) {
Instances toFilter = getInputFormat();
// Build the partition generator
m_partitionGenerator.generatePartition(toFilter);
// Create output dataset
FastVector attInfo = new FastVector();
for (int i = 0; i < m_partitionGenerator.numElements(); i++) {
attInfo.addElement(new Attribute("partition_" + i));
}
if (toFilter.classIndex() >= 0) {
attInfo.addElement(toFilter.classAttribute().copy());
}
attInfo.trimToSize();
Instances filtered = new Instances(toFilter.relationName() + "_partitionMembership",
attInfo, 0);
if (toFilter.classIndex() >= 0) {
filtered.setClassIndex(filtered.numAttributes() - 1);
}
setOutputFormat(filtered);
// build new dataset
for (int i = 0; i < toFilter.numInstances(); i++) {
convertInstance(toFilter.instance(i));
}
}
flushInput();
m_NewBatch = true;
return (numPendingOutput() != 0);
}
/**
* Input an instance for filtering. Ordinarily the instance is processed
* and made available for output immediately. Some filters require all
* instances be read before producing output.
*
* @param instance the input instance
* @return true if the filtered instance may now be
* collected with output().
* @throws IllegalStateException if no input format has been defined.
*/
public boolean input(Instance instance) throws Exception {
if (getInputFormat() == null) {
throw new IllegalStateException("No input instance format defined");
}
if (m_NewBatch) {
resetQueue();
m_NewBatch = false;
}
if (outputFormatPeek() != null) {
convertInstance(instance);
return true;
}
bufferInput(instance);
return false;
}
/**
* Convert a single instance over. The converted instance is added to
* the end of the output queue.
*
* @param instance the instance to convert
* @throws Exception if something goes wrong
*/
protected void convertInstance(Instance instance) throws Exception {
// Make copy and set weight to one
Instance cp = (Instance)instance.copy();
cp.setWeight(1.0);
// Set up values
double [] instanceVals = new double[outputFormatPeek().numAttributes()];
double [] vals = m_partitionGenerator.getMembershipValues(cp);
System.arraycopy(vals, 0, instanceVals, 0, vals.length);
if (instance.classIndex() >= 0) {
instanceVals[instanceVals.length - 1] = instance.classValue();
}
push(new SparseInstance(instance.weight(), instanceVals));
}
/**
* Returns an enumeration describing the available options.
*
* @return an enumeration of all the available options.
*/
public Enumeration listOptions() {
Vector newVector = new Vector(1);
newVector.
addElement(new Option("\tFull name of partition generator to use, e.g.:\n"
+ "\t\tweka.classifiers.trees.J48\n"
+ "\tAdditional options after the '--'.\n"
+ "\t(default: weka.classifiers.trees.J48)",
"W", 1, "-W <name of partition generator>"));
return newVector.elements();
}
/**
* Parses a given list of options. <p/>
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -W <name of partition generator>
* Full name of partition generator to use, e.g.:
* weka.classifiers.trees.J48
* Additional options after the '--'.
* (default: weka.classifiers.trees.J48)</pre>
*
<!-- options-end -->
*
* Options after the -- are passed on to the clusterer.
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String generatorString = Utils.getOption('W', options);
if (generatorString.length() == 0) {
generatorString = J48.class.getName();
}
setPartitionGenerator((PartitionGenerator)Utils.
forName(PartitionGenerator.class, generatorString,
Utils.partitionOptions(options)));
Utils.checkForRemainingOptions(options);
}
/**
* Gets the current settings of the filter.
*
* @return an array of strings suitable for passing to setOptions
*/
public String [] getOptions() {
String [] generatorOptions = new String [0];
if ((m_partitionGenerator != null) &&
(m_partitionGenerator instanceof OptionHandler)) {
generatorOptions = ((OptionHandler)m_partitionGenerator).getOptions();
}
String [] options = new String [generatorOptions.length + 3];
int current = 0;
if (m_partitionGenerator != null) {
options[current++] = "-W";
options[current++] = getPartitionGenerator().getClass().getName();
}
options[current++] = "--";
System.arraycopy(generatorOptions, 0, options, current,
generatorOptions.length);
current += generatorOptions.length;
while (current < options.length) {
options[current++] = "";
}
return options;
}
/**
* Returns a string describing this filter
*
* @return a description of the filter suitable for
* displaying in the explorer/experimenter gui
*/
public String globalInfo() {
return "A filter that uses a PartitionGenerator to generate partition "
+ "membership values; filtered instances are composed of these values "
+ "plus the class attribute (if set in the input data) and rendered "
+ "as sparse instances.";
}
/**
* Returns a description of this option suitable for display
* as a tip text in the gui.
*
* @return description of this option
*/
public String partitionGeneratorTipText() {
return "The partition generator that will generate membership values for the instances.";
}
/**
* Set the generator for use in filtering
*
* @param newPartitionGenerator the generator to use
*/
public void setPartitionGenerator(PartitionGenerator newPartitionGenerator) {
m_partitionGenerator = newPartitionGenerator;
}
/**
* Get the generator used by this filter
*
* @return the generator used
*/
public PartitionGenerator getPartitionGenerator() {
return m_partitionGenerator;
}
/**
* Main method for testing this class.
*
* @param argv should contain arguments to the filter: use -h for help
*/
public static void main(String [] argv) {
runFilter(new PartitionMembership(), argv);
}
public String getRevision() {
return RevisionUtils.extract("$Revision: 9910 $");
}
}