/*
* 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.
*/
/*
* NominalToBinary.java
* Copyright (C) 1999 Eibe Frank
*
*/
package weka.filters.supervised.attribute;
import weka.filters.*;
import java.io.*;
import java.util.*;
import weka.core.*;
/**
* Converts all nominal attributes into binary numeric attributes. An
* attribute with k values is transformed into k binary attributes if
* the class is nominal (using the one-attribute-per-value approach).
* Binary attributes are left binary.
*
* If the class is numeric, k - 1 new binary attributes are generated
* (in the manner described in "Classification and Regression
* Trees").<p>
*
* Valid filter-specific options are: <p>
*
* -N <br>
* If binary attributes are to be coded as nominal ones.<p>
*
* @author Eibe Frank (eibe@cs.waikato.ac.nz)
* @version $Revision: 1.1.1.1 $
*/
public class NominalToBinary extends Filter implements SupervisedFilter,
OptionHandler {
/** The sorted indices of the attribute values. */
private int[][] m_Indices = null;
/** Are the new attributes going to be nominal or numeric ones? */
private boolean m_Numeric = true;
/**
* 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
* @exception Exception if the input format can't be set
* successfully
*/
public boolean setInputFormat(Instances instanceInfo)
throws Exception {
super.setInputFormat(instanceInfo);
if (instanceInfo.classIndex() < 0) {
throw new UnassignedClassException("No class has been assigned to the instances");
}
setOutputFormat();
m_Indices = null;
if (instanceInfo.classAttribute().isNominal()) {
return true;
} else {
return false;
}
}
/**
* Input an instance for filtering. Filter requires all
* training instances be read before producing output.
*
* @param instance the input instance
* @return true if the filtered instance may now be
* collected with output().
* @exception IllegalStateException if no input format has been set
*/
public boolean input(Instance instance) {
if (getInputFormat() == null) {
throw new IllegalStateException("No input instance format defined");
}
if (m_NewBatch) {
resetQueue();
m_NewBatch = false;
}
if ((m_Indices != null) ||
(getInputFormat().classAttribute().isNominal())) {
convertInstance(instance);
return true;
}
bufferInput(instance);
return false;
}
/**
* Signify that this batch of input to the filter is finished.
* If the filter requires all instances prior to filtering,
* output() may now be called to retrieve the filtered instances.
*
* @return true if there are instances pending output
* @exception IllegalStateException if no input structure has been defined
*/
public boolean batchFinished() {
if (getInputFormat() == null) {
throw new IllegalStateException("No input instance format defined");
}
if ((m_Indices == null) &&
(getInputFormat().classAttribute().isNumeric())) {
computeAverageClassValues();
setOutputFormat();
// Convert pending input instances
for(int i = 0; i < getInputFormat().numInstances(); i++) {
convertInstance(getInputFormat().instance(i));
}
}
flushInput();
m_NewBatch = true;
return (numPendingOutput() != 0);
}
/**
* 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(
"\tSets if binary attributes are to be coded as nominal ones.",
"N", 0, "-N"));
return newVector.elements();
}
/**
* Parses the options for this object. Valid options are: <p>
*
* -N <br>
* If binary attributes are to be coded as nominal ones.<p>
*
* @param options the list of options as an array of strings
* @exception Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
setBinaryAttributesNominal(Utils.getFlag('N', options));
if (getInputFormat() != null)
setInputFormat(getInputFormat());
}
/**
* Gets the current settings of the filter.
*
* @return an array of strings suitable for passing to setOptions
*/
public String [] getOptions() {
String [] options = new String [1];
int current = 0;
if (getBinaryAttributesNominal()) {
options[current++] = "-N";
}
while (current < options.length) {
options[current++] = "";
}
return options;
}
/**
* Gets if binary attributes are to be treated as nominal ones.
*
* @return true if binary attributes are to be treated as nominal ones
*/
public boolean getBinaryAttributesNominal() {
return !m_Numeric;
}
/**
* Sets if binary attributes are to be treates as nominal ones.
*
* @param bool true if binary attributes are to be treated as nominal ones
*/
public void setBinaryAttributesNominal(boolean bool) {
m_Numeric = !bool;
}
/** Computes average class values for each attribute and value */
private void computeAverageClassValues() {
double totalCounts, sum;
Instance instance;
double [] counts;
double [][] avgClassValues = new double[getInputFormat().numAttributes()][0];
m_Indices = new int[getInputFormat().numAttributes()][0];
for (int j = 0; j < getInputFormat().numAttributes(); j++) {
Attribute att = getInputFormat().attribute(j);
if (att.isNominal()) {
avgClassValues[j] = new double [att.numValues()];
counts = new double [att.numValues()];
for (int i = 0; i < getInputFormat().numInstances(); i++) {
instance = getInputFormat().instance(i);
if (!instance.classIsMissing() &&
(!instance.isMissing(j))) {
counts[(int)instance.value(j)] += instance.weight();
avgClassValues[j][(int)instance.value(j)] +=
instance.weight() * instance.classValue();
}
}
sum = Utils.sum(avgClassValues[j]);
totalCounts = Utils.sum(counts);
if (Utils.gr(totalCounts, 0)) {
for (int k = 0; k < att.numValues(); k++) {
if (Utils.gr(counts[k], 0)) {
avgClassValues[j][k] /= (double)counts[k];
} else {
avgClassValues[j][k] = sum / (double)totalCounts;
}
}
}
m_Indices[j] = Utils.sort(avgClassValues[j]);
}
}
}
/** Set the output format. */
private void setOutputFormat() {
if (getInputFormat().classAttribute().isNominal()) {
setOutputFormatNominal();
} else {
setOutputFormatNumeric();
}
}
/**
* Convert a single instance over. The converted instance is
* added to the end of the output queue.
*
* @param instance the instance to convert
*/
private void convertInstance(Instance inst) {
if (getInputFormat().classAttribute().isNominal()) {
convertInstanceNominal(inst);
} else {
convertInstanceNumeric(inst);
}
}
/**
* Set the output format if the class is nominal.
*/
private void setOutputFormatNominal() {
FastVector newAtts;
int newClassIndex;
StringBuffer attributeName;
Instances outputFormat;
FastVector vals;
// Compute new attributes
newClassIndex = getInputFormat().classIndex();
newAtts = new FastVector();
for (int j = 0; j < getInputFormat().numAttributes(); j++) {
Attribute att = getInputFormat().attribute(j);
if ((!att.isNominal()) ||
(j == getInputFormat().classIndex())) {
newAtts.addElement(att.copy());
} else {
if (att.numValues() <= 2) {
if (m_Numeric) {
newAtts.addElement(new Attribute(att.name()));
} else {
newAtts.addElement(att.copy());
}
} else {
if (j < getInputFormat().classIndex()) {
newClassIndex += att.numValues() - 1;
}
// Compute values for new attributes
for (int k = 0; k < att.numValues(); k++) {
attributeName =
new StringBuffer(att.name() + "=");
attributeName.append(att.value(k));
if (m_Numeric) {
newAtts.
addElement(new Attribute(attributeName.toString()));
} else {
vals = new FastVector(2);
vals.addElement("f"); vals.addElement("t");
newAtts.
addElement(new Attribute(attributeName.toString(), vals));
}
}
}
}
}
outputFormat = new Instances(getInputFormat().relationName(),
newAtts, 0);
outputFormat.setClassIndex(newClassIndex);
setOutputFormat(outputFormat);
}
/**
* Set the output format if the class is numeric.
*/
private void setOutputFormatNumeric() {
if (m_Indices == null) {
setOutputFormat(null);
return;
}
FastVector newAtts;
int newClassIndex;
StringBuffer attributeName;
Instances outputFormat;
FastVector vals;
// Compute new attributes
newClassIndex = getInputFormat().classIndex();
newAtts = new FastVector();
for (int j = 0; j < getInputFormat().numAttributes(); j++) {
Attribute att = getInputFormat().attribute(j);
if ((!att.isNominal()) ||
(j == getInputFormat().classIndex())) {
newAtts.addElement(att.copy());
} else {
if (j < getInputFormat().classIndex())
newClassIndex += att.numValues() - 2;
// Compute values for new attributes
for (int k = 1; k < att.numValues(); k++) {
attributeName =
new StringBuffer(att.name() + "=");
for (int l = k; l < att.numValues(); l++) {
if (l > k) {
attributeName.append(',');
}
attributeName.append(att.value(m_Indices[j][l]));
}
if (m_Numeric) {
newAtts.
addElement(new Attribute(attributeName.toString()));
} else {
vals = new FastVector(2);
vals.addElement("f"); vals.addElement("t");
newAtts.
addElement(new Attribute(attributeName.toString(), vals));
}
}
}
}
outputFormat = new Instances(getInputFormat().relationName(),
newAtts, 0);
outputFormat.setClassIndex(newClassIndex);
setOutputFormat(outputFormat);
}
/**
* Convert a single instance over if the class is nominal. The converted
* instance is added to the end of the output queue.
*
* @param instance the instance to convert
*/
private void convertInstanceNominal(Instance instance) {
double [] vals = new double [outputFormatPeek().numAttributes()];
int attSoFar = 0;
for(int j = 0; j < getInputFormat().numAttributes(); j++) {
Attribute att = getInputFormat().attribute(j);
if ((!att.isNominal()) || (j == getInputFormat().classIndex())) {
vals[attSoFar] = instance.value(j);
attSoFar++;
} else {
if (att.numValues() <= 2) {
vals[attSoFar] = instance.value(j);
attSoFar++;
} else {
if (instance.isMissing(j)) {
for (int k = 0; k < att.numValues(); k++) {
vals[attSoFar + k] = instance.value(j);
}
} else {
for (int k = 0; k < att.numValues(); k++) {
if (k == (int)instance.value(j)) {
vals[attSoFar + k] = 1;
} else {
vals[attSoFar + k] = 0;
}
}
}
attSoFar += att.numValues();
}
}
}
Instance inst = null;
if (instance instanceof SparseInstance) {
inst = new SparseInstance(instance.weight(), vals);
} else {
inst = new Instance(instance.weight(), vals);
}
copyStringValues(inst, false, instance.dataset(), getInputStringIndex(),
getOutputFormat(), getOutputStringIndex());
inst.setDataset(getOutputFormat());
push(inst);
}
/**
* Convert a single instance over if the class is numeric. The converted
* instance is added to the end of the output queue.
*
* @param instance the instance to convert
*/
private void convertInstanceNumeric(Instance instance) {
double [] vals = new double [outputFormatPeek().numAttributes()];
int attSoFar = 0;
for(int j = 0; j < getInputFormat().numAttributes(); j++) {
Attribute att = getInputFormat().attribute(j);
if ((!att.isNominal()) || (j == getInputFormat().classIndex())) {
vals[attSoFar] = instance.value(j);
attSoFar++;
} else {
if (instance.isMissing(j)) {
for (int k = 0; k < att.numValues() - 1; k++) {
vals[attSoFar + k] = instance.value(j);
}
} else {
int k = 0;
while ((int)instance.value(j) != m_Indices[j][k]) {
vals[attSoFar + k] = 1;
k++;
}
while (k < att.numValues() - 1) {
vals[attSoFar + k] = 0;
k++;
}
}
attSoFar += att.numValues() - 1;
}
}
Instance inst = null;
if (instance instanceof SparseInstance) {
inst = new SparseInstance(instance.weight(), vals);
} else {
inst = new Instance(instance.weight(), vals);
}
copyStringValues(inst, false, instance.dataset(), getInputStringIndex(),
getOutputFormat(), getOutputStringIndex());
inst.setDataset(getOutputFormat());
push(inst);
}
/**
* Main method for testing this class.
*
* @param argv should contain arguments to the filter:
* use -h for help
*/
public static void main(String [] argv) {
try {
if (Utils.getFlag('b', argv)) {
Filter.batchFilterFile(new NominalToBinary(), argv);
} else {
Filter.filterFile(new NominalToBinary(), argv);
}
} catch (Exception ex) {
System.out.println(ex.getMessage());
}
}
}