/*
* 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/>.
*/
/*
* Copy.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.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 -->
* An instance filter that copies a range of attributes in the dataset. This is used in conjunction with other filters that overwrite attribute values during the course of their operation -- this filter allows the original attributes to be kept as well as the new attributes.
* <p/>
<!-- globalinfo-end -->
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -R <index1,index2-index4,...>
* Specify list of columns to copy. First and last are valid
* indexes. (default none)</pre>
*
* <pre> -V
* Invert matching sense (i.e. copy all non-specified columns)</pre>
*
<!-- options-end -->
*
* @author Len Trigg (trigg@cs.waikato.ac.nz)
* @version $Revision: 8034 $
*/
public class Copy
extends Filter
implements UnsupervisedFilter, StreamableFilter, OptionHandler {
/** for serialization */
static final long serialVersionUID = -8543707493627441566L;
/** Stores which columns to copy */
protected Range m_CopyCols = new Range();
/**
* Stores the indexes of the selected attributes in order, once the
* dataset is seen
*/
protected int [] m_SelectedAttributes;
/**
* Returns an enumeration describing the available options.
*
* @return an enumeration of all the available options.
*/
public Enumeration listOptions() {
Vector newVector = new Vector(2);
newVector.addElement(new Option(
"\tSpecify list of columns to copy. First and last are valid\n"
+"\tindexes. (default none)",
"R", 1, "-R <index1,index2-index4,...>"));
newVector.addElement(new Option(
"\tInvert matching sense (i.e. copy all non-specified columns)",
"V", 0, "-V"));
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 copy. First and last are valid
* indexes. (default none)</pre>
*
* <pre> -V
* Invert matching sense (i.e. copy all non-specified columns)</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 copyList = Utils.getOption('R', options);
if (copyList.length() != 0) {
setAttributeIndices(copyList);
}
setInvertSelection(Utils.getFlag('V', 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 [3];
int current = 0;
if (getInvertSelection()) {
options[current++] = "-V";
}
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 Exception if a problem occurs setting the input format
*/
public boolean setInputFormat(Instances instanceInfo) throws Exception {
super.setInputFormat(instanceInfo);
m_CopyCols.setUpper(instanceInfo.numAttributes() - 1);
// Create the output buffer
Instances outputFormat = new Instances(instanceInfo, 0);
m_SelectedAttributes = m_CopyCols.getSelection();
for (int i = 0; i < m_SelectedAttributes.length; i++) {
int current = m_SelectedAttributes[i];
// Create a copy of the attribute with a different name
Attribute origAttribute = instanceInfo.attribute(current);
outputFormat.insertAttributeAt((Attribute)origAttribute.copy("Copy of " + origAttribute.name()),
outputFormat.numAttributes());
}
// adapt locators
int[] newIndices = new int[instanceInfo.numAttributes() + m_SelectedAttributes.length];
for (int i = 0; i < instanceInfo.numAttributes(); i++)
newIndices[i] = i;
for (int i = 0; i < m_SelectedAttributes.length; i++)
newIndices[instanceInfo.numAttributes() + i] = m_SelectedAttributes[i];
initInputLocators(instanceInfo, newIndices);
setOutputFormat(outputFormat);
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;
}
double[] vals = new double[outputFormatPeek().numAttributes()];
for(int i = 0; i < getInputFormat().numAttributes(); i++) {
vals[i] = instance.value(i);
}
int j = getInputFormat().numAttributes();
for (int i = 0; i < m_SelectedAttributes.length; i++) {
int current = m_SelectedAttributes[i];
vals[i + j] = instance.value(current);
}
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 a string describing this filter
*
* @return a description of the filter suitable for
* displaying in the explorer/experimenter gui
*/
public String globalInfo() {
return "An instance filter that copies a range of attributes in the"
+ " dataset. This is used in conjunction with other filters that"
+ " overwrite attribute values during the course of their operation --"
+ " this filter allows the original attributes to be kept as well"
+ " as the new attributes.";
}
/**
* 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 "Sets copy selected vs unselected action."
+ " If set to false, only the specified attributes will be copied;"
+ " If set to true, non-specified attributes will be copied.";
}
/**
* Get whether the supplied columns are to be removed or kept
*
* @return true if the supplied columns will be kept
*/
public boolean getInvertSelection() {
return m_CopyCols.getInvert();
}
/**
* Set whether selected columns should be removed or kept. If true the
* selected columns are kept and unselected columns are copied. If false
* selected columns are copied and unselected columns are kept. <br>
* Note: use this method before you call
* <code>setInputFormat(Instances)</code>, since the output format is
* determined in that method.
*
* @param invert the new invert setting
*/
public void setInvertSelection(boolean invert) {
m_CopyCols.setInvert(invert);
}
/**
* Get the current range selection
*
* @return a string containing a comma separated list of ranges
*/
public String getAttributeIndices() {
return m_CopyCols.getRanges();
}
/**
* 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\".";
}
/**
* Set which attributes are to be copied (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<br>
* Note: use this method before you call
* <code>setInputFormat(Instances)</code>, since the output format is
* determined in that method.
* @throws Exception if an invalid range list is supplied
*/
public void setAttributeIndices(String rangeList) throws Exception {
m_CopyCols.setRanges(rangeList);
}
/**
* Set which attributes are to be copied (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.<br>
* Note: use this method before you call
* <code>setInputFormat(Instances)</code>, since the output format is
* determined in that method.
* @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 Copy(), argv);
}
}