/*
* 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/>.
*/
/*
* NumericTransform.java
* Copyright (C) 1999-2012 University of Waikato, Hamilton, New Zealand
*
*/
package weka.filters.unsupervised.attribute;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.util.Enumeration;
import java.util.Vector;
import weka.core.Capabilities;
import weka.core.Capabilities.Capability;
import weka.core.DenseInstance;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.Range;
import weka.core.RevisionUtils;
import weka.core.SparseInstance;
import weka.core.Utils;
import weka.filters.Filter;
import weka.filters.StreamableFilter;
import weka.filters.UnsupervisedFilter;
/**
<!-- globalinfo-start -->
* Transforms numeric attributes using a given transformation method.
* <p/>
<!-- globalinfo-end -->
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -R <index1,index2-index4,...>
* Specify list of columns to transform. First and last are
* valid indexes (default none). Non-numeric columns are
* skipped.</pre>
*
* <pre> -V
* Invert matching sense.</pre>
*
* <pre> -C <string>
* Sets the class containing transformation method.
* (default java.lang.Math)</pre>
*
* <pre> -M <string>
* Sets the method. (default abs)</pre>
*
<!-- options-end -->
*
* @author Eibe Frank (eibe@cs.waikato.ac.nz)
* @version $Revision: 8034 $
*/
public class NumericTransform
extends Filter
implements UnsupervisedFilter, StreamableFilter, OptionHandler {
/** for serialization */
static final long serialVersionUID = -8561413333351366934L;
/** Stores which columns to transform. */
private Range m_Cols = new Range();
/** Class containing transformation method. */
private String m_Class;
/** Transformation method. */
private String m_Method;
/**
* Returns a string describing this filter
*
* @return a description of the filter suitable for
* displaying in the explorer/experimenter gui
*/
public String globalInfo() {
return "Transforms numeric attributes using a given transformation method.";
}
/**
* Default constructor -- sets the default transform method
* to java.lang.Math.abs().
*/
public NumericTransform() {
m_Class = "java.lang.Math";
m_Method = "abs";
}
/**
* Returns the Capabilities of this filter.
*
* @return the capabilities of this object
* @see Capabilities
*/
public Capabilities getCapabilities() {
Capabilities result = super.getCapabilities();
result.disableAll();
// attributes
result.enableAllAttributes();
result.enable(Capability.MISSING_VALUES);
// class
result.enableAllClasses();
result.enable(Capability.MISSING_CLASS_VALUES);
result.enable(Capability.NO_CLASS);
return result;
}
/**
* 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 input format can't be set
* successfully
*/
public boolean setInputFormat(Instances instanceInfo)
throws Exception {
if (m_Class == null) {
throw new IllegalStateException("No class has been set.");
}
if (m_Method == null) {
throw new IllegalStateException("No method has been set.");
}
super.setInputFormat(instanceInfo);
m_Cols.setUpper(instanceInfo.numAttributes() - 1);
setOutputFormat(instanceInfo);
return true;
}
/**
* Input an instance for filtering. The instance is processed
* and made available for output immediately.
*
* @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 set.
* @throws InvocationTargetException if there is a problem applying
* the configured transform method.
*/
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;
}
Method m = (Class.forName(m_Class)).getMethod(m_Method, new Class[] {Double.TYPE});
double []vals = new double[instance.numAttributes()];
Double []params = new Double[1];
Double newVal;
for(int i = 0; i < instance.numAttributes(); i++) {
if (instance.isMissing(i)) {
vals[i] = Utils.missingValue();
} else {
if (m_Cols.isInRange(i) &&
instance.attribute(i).isNumeric()) {
params[0] = new Double(instance.value(i));
newVal = (Double) m.invoke(null, (Object[])params);
if (newVal.isNaN() || newVal.isInfinite()) {
vals[i] = Utils.missingValue();
} else {
vals[i] = newVal.doubleValue();
}
} else {
vals[i] = instance.value(i);
}
}
}
Instance inst = null;
if (instance instanceof SparseInstance) {
inst = new SparseInstance(instance.weight(), vals);
} else {
inst = new DenseInstance(instance.weight(), vals);
}
inst.setDataset(instance.dataset());
push(inst);
return true;
}
/**
* Returns an enumeration describing the available options.
*
* @return an enumeration of all the available options.
*/
public Enumeration listOptions() {
Vector newVector = new Vector(4);
newVector.addElement(new Option(
"\tSpecify list of columns to transform. First and last are\n"
+ "\tvalid indexes (default none). Non-numeric columns are \n"
+ "\tskipped.",
"R", 1, "-R <index1,index2-index4,...>"));
newVector.addElement(new Option(
"\tInvert matching sense.",
"V", 0, "-V"));
newVector.addElement(new Option(
"\tSets the class containing transformation method.\n"+
"\t(default java.lang.Math)",
"C", 1, "-C <string>"));
newVector.addElement(new Option(
"\tSets the method. (default abs)",
"M", 1, "-M <string>"));
return newVector.elements();
}
/**
* Parses a given list of options. <p/>
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -R <index1,index2-index4,...>
* Specify list of columns to transform. First and last are
* valid indexes (default none). Non-numeric columns are
* skipped.</pre>
*
* <pre> -V
* Invert matching sense.</pre>
*
* <pre> -C <string>
* Sets the class containing transformation method.
* (default java.lang.Math)</pre>
*
* <pre> -M <string>
* Sets the method. (default abs)</pre>
*
<!-- options-end -->
*
* @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 {
setAttributeIndices(Utils.getOption('R', options));
setInvertSelection(Utils.getFlag('V', options));
String classString = Utils.getOption('C', options);
if (classString.length() != 0) {
setClassName(classString);
}
String methodString = Utils.getOption('M', options);
if (methodString.length() != 0) {
setMethodName(methodString);
}
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 [7];
int current = 0;
if (getInvertSelection()) {
options[current++] = "-V";
}
if (!getAttributeIndices().equals("")) {
options[current++] = "-R"; options[current++] = getAttributeIndices();
}
if (m_Class != null) {
options[current++] = "-C"; options[current++] = getClassName();
}
if (m_Method != null) {
options[current++] = "-M"; options[current++] = getMethodName();
}
while (current < options.length) {
options[current++] = "";
}
return options;
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String classNameTipText() {
return "Name of the class containing the method used for the transformation.";
}
/**
* Get the class containing the transformation method.
*
* @return string describing the class
*/
public String getClassName() {
return m_Class;
}
/**
* Sets the class containing the transformation method.
*
* @param name the name of the class
* @throws ClassNotFoundException if class can't be found
*/
public void setClassName(String name) throws ClassNotFoundException {
m_Class = name;
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String methodNameTipText() {
return "Name of the method used for the transformation.";
}
/**
* Get the transformation method.
*
* @return string describing the transformation method.
*/
public String getMethodName() {
return m_Method;
}
/**
* Set the transformation method.
*
* @param name the name of the method
* @throws NoSuchMethodException if method can't be found in class
*/
public void setMethodName(String name) throws NoSuchMethodException {
m_Method = name;
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String invertSelectionTipText() {
return "Whether to process the inverse of the given attribute ranges.";
}
/**
* Get whether the supplied columns are to be transformed or not
*
* @return true if the supplied columns will be kept
*/
public boolean getInvertSelection() {
return m_Cols.getInvert();
}
/**
* Set whether selected columns should be transformed or not.
*
* @param invert the new invert setting
*/
public void setInvertSelection(boolean invert) {
m_Cols.setInvert(invert);
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String attributeIndicesTipText() {
return "Specify range of attributes to act on."
+ " This is a comma separated list of attribute indices, with"
+ " \"first\" and \"last\" valid values. Specify an inclusive"
+ " range with \"-\". E.g: \"first-3,5,6-10,last\".";
}
/**
* Get the current range selection
*
* @return a string containing a comma separated list of ranges
*/
public String getAttributeIndices() {
return m_Cols.getRanges();
}
/**
* Set which attributes are to be transformed (or kept if invert is true).
*
* @param rangeList a string representing the list of attributes. Since
* the string will typically come from a user, attributes are indexed from
* 1. <br> eg:
* first-3,5,6-last
* @throws InvalidArgumentException if an invalid range list is supplied
*/
public void setAttributeIndices(String rangeList) {
m_Cols.setRanges(rangeList);
}
/**
* Set which attributes are to be transformed (or kept if invert is true)
*
* @param attributes an array containing indexes of attributes to select.
* Since the array will typically come from a program, attributes are indexed
* from 0.
* @throws InvalidArgumentException if an invalid set of ranges is supplied
*/
public void setAttributeIndicesArray(int [] attributes) {
setAttributeIndices(Range.indicesToRangeList(attributes));
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 8034 $");
}
/**
* 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 NumericTransform(), argv);
}
}