/*
* 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/>.
*/
/*
* FirstOrder.java
* Copyright (C) 1999-2012 University of Waikato, Hamilton, New Zealand
*
*/
package weka.filters.unsupervised.attribute;
import java.util.Enumeration;
import java.util.Vector;
import weka.core.Attribute;
import weka.core.Capabilities;
import weka.core.Capabilities.Capability;
import weka.core.DenseInstance;
import weka.core.FastVector;
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.UnsupportedAttributeTypeException;
import weka.core.Utils;
import weka.filters.Filter;
import weka.filters.StreamableFilter;
import weka.filters.UnsupervisedFilter;
/**
<!-- globalinfo-start -->
* This instance filter takes a range of N numeric attributes and replaces them with N-1 numeric attributes, the values of which are the difference between consecutive attribute values from the original instance. eg: <br/>
* <br/>
* Original attribute values<br/>
* <br/>
* 0.1, 0.2, 0.3, 0.1, 0.3<br/>
* <br/>
* New attribute values<br/>
* <br/>
* 0.1, 0.1, -0.2, 0.2<br/>
* <br/>
* The range of attributes used is taken in numeric order. That is, a range spec of 7-11,3-5 will use the attribute ordering 3,4,5,7,8,9,10,11 for the differences, NOT 7,8,9,10,11,3,4,5.
* <p/>
<!-- globalinfo-end -->
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -R <index1,index2-index4,...>
* Specify list of columns to take the differences between.
* First and last are valid indexes.
* (default none)</pre>
*
<!-- options-end -->
*
* @author Len Trigg (trigg@cs.waikato.ac.nz)
* @version $Revision: 8034 $
*/
public class FirstOrder
extends Filter
implements UnsupervisedFilter, StreamableFilter, OptionHandler {
/** for serialization */
static final long serialVersionUID = -7500464545400454179L;
/** Stores which columns to take differences between */
protected Range m_DeltaCols = new Range();
/**
* Returns a string describing this filter
*
* @return a description of the filter suitable for
* displaying in the explorer/experimenter gui
*/
public String globalInfo() {
return "This instance filter takes a range of N numeric attributes and replaces "
+ "them with N-1 numeric attributes, the values of which are the difference "
+ "between consecutive attribute values from the original instance. eg: \n\n"
+ "Original attribute values\n\n"
+ " 0.1, 0.2, 0.3, 0.1, 0.3\n\n"
+ "New attribute values\n\n"
+ " 0.1, 0.1, -0.2, 0.2\n\n"
+ "The range of attributes used is taken in numeric order. That is, a range "
+ "spec of 7-11,3-5 will use the attribute ordering 3,4,5,7,8,9,10,11 for the "
+ "differences, NOT 7,8,9,10,11,3,4,5.";
}
/**
* 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(
"\tSpecify list of columns to take the differences between.\n"
+ "\tFirst and last are valid indexes.\n"
+ "\t(default none)",
"R", 1, "-R <index1,index2-index4,...>"));
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 take the differences between.
* First and last are valid indexes.
* (default none)</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 {
String deltaList = Utils.getOption('R', options);
if (deltaList.length() != 0) {
setAttributeIndices(deltaList);
} else {
setAttributeIndices("");
}
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 [2];
int current = 0;
if (!getAttributeIndices().equals("")) {
options[current++] = "-R"; options[current++] = getAttributeIndices();
}
while (current < options.length) {
options[current++] = "";
}
return options;
}
/**
* 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 UnsupportedAttributeTypeException if any of the
* selected attributes are not numeric
* @throws Exception if only one attribute has been selected.
*/
public boolean setInputFormat(Instances instanceInfo) throws Exception {
super.setInputFormat(instanceInfo);
m_DeltaCols.setUpper(getInputFormat().numAttributes() - 1);
int selectedCount = 0;
for (int i = getInputFormat().numAttributes() - 1; i >= 0; i--) {
if (m_DeltaCols.isInRange(i)) {
selectedCount++;
if (!getInputFormat().attribute(i).isNumeric()) {
throw new UnsupportedAttributeTypeException("Selected attributes must be all numeric");
}
}
}
if (selectedCount == 1) {
throw new Exception("Cannot select only one attribute.");
}
// Create the output buffer
FastVector newAtts = new FastVector();
boolean inRange = false;
String foName = null;
int clsIndex = -1;
for(int i = 0; i < instanceInfo.numAttributes(); i++) {
if (m_DeltaCols.isInRange(i) && (i != instanceInfo.classIndex())) {
if (inRange) {
Attribute newAttrib = new Attribute(foName);
newAtts.addElement(newAttrib);
}
foName = instanceInfo.attribute(i).name();
foName = "'FO " + foName.replace('\'', ' ').trim() + '\'';
inRange = true;
} else {
newAtts.addElement((Attribute)instanceInfo.attribute(i).copy());
if ((i == instanceInfo.classIndex()))
clsIndex = newAtts.size() - 1;
}
}
Instances data = new Instances(instanceInfo.relationName(), newAtts, 0);
data.setClassIndex(clsIndex);
setOutputFormat(data);
return true;
}
/**
* 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) {
if (getInputFormat() == null) {
throw new IllegalStateException("No input instance format defined");
}
if (m_NewBatch) {
resetQueue();
m_NewBatch = false;
}
Instances outputFormat = outputFormatPeek();
double[] vals = new double[outputFormat.numAttributes()];
boolean inRange = false;
double lastVal = Utils.missingValue();
int i, j;
for(i = 0, j = 0; j < outputFormat.numAttributes(); i++) {
if (m_DeltaCols.isInRange(i) && (i != instance.classIndex())) {
if (inRange) {
if (Utils.isMissingValue(lastVal) || instance.isMissing(i)) {
vals[j++] = Utils.missingValue();
} else {
vals[j++] = instance.value(i) - lastVal;
}
} else {
inRange = true;
}
lastVal = instance.value(i);
} else {
vals[j++] = 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(getOutputFormat());
copyValues(inst, false, instance.dataset(), getOutputFormat());
inst.setDataset(getOutputFormat());
push(inst);
return true;
}
/**
* 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_DeltaCols.getRanges();
}
/**
* Set which attributes are to be deleted (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 Exception if an invalid range list is supplied
*/
public void setAttributeIndices(String rangeList) throws Exception {
m_DeltaCols.setRanges(rangeList);
}
/**
* Set which attributes are to be deleted (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 Exception if an invalid set of ranges is supplied
*/
public void setAttributeIndicesArray(int [] attributes) throws Exception {
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 FirstOrder(), argv);
}
}