/*
* 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/>.
*/
/*
* PartitionedMultiFilter.java
* Copyright (C) 2006-2012 University of Waikato, Hamilton, New Zealand
*
*/
package weka.filters.unsupervised.attribute;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Vector;
import weka.core.Attribute;
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.AllFilter;
import weka.filters.Filter;
import weka.filters.SimpleBatchFilter;
/**
<!-- globalinfo-start -->
* A filter that applies filters on subsets of attributes and assembles the output into a new dataset. Attributes that are not covered by any of the ranges can be either retained or removed from the output.
* <p/>
<!-- globalinfo-end -->
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -D
* Turns on output of debugging information.</pre>
*
* <pre> -F <classname [options]>
* A filter to apply (can be specified multiple times).</pre>
*
* <pre> -R <range>
* An attribute range (can be specified multiple times).
* For each filter a range must be supplied. 'first' and 'last'
* are valid indices. 'inv(...)' around the range denotes an
* inverted range.</pre>
*
* <pre> -U
* Flag for leaving unused attributes out of the output, by default
* these are included in the filter output.</pre>
*
<!-- options-end -->
*
* @author FracPete (fracpete at waikato dot ac dot nz)
* @version $Revision: 8034 $
* @see weka.filters.StreamableFilter
*/
public class PartitionedMultiFilter
extends SimpleBatchFilter {
/** for serialization. */
private static final long serialVersionUID = -6293720886005713120L;
/** The filters. */
protected Filter m_Filters[] = {new AllFilter()};
/** The attribute ranges. */
protected Range m_Ranges[] = {new Range("first-last")};
/** Whether unused attributes are left out of the output. */
protected boolean m_RemoveUnused = false;
/** the indices of the unused attributes. */
protected int[] m_IndicesUnused = new int[0];
/**
* 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 applies filters on subsets of attributes and "
+ "assembles the output into a new dataset. Attributes that are "
+ "not covered by any of the ranges can be either retained or removed "
+ "from the output.";
}
/**
* Returns an enumeration describing the available options.
*
* @return an enumeration of all the available options.
*/
public Enumeration listOptions() {
Vector result = new Vector();
Enumeration enm = super.listOptions();
while (enm.hasMoreElements())
result.add(enm.nextElement());
result.addElement(new Option(
"\tA filter to apply (can be specified multiple times).",
"F", 1, "-F <classname [options]>"));
result.addElement(new Option(
"\tAn attribute range (can be specified multiple times).\n"
+ "\tFor each filter a range must be supplied. 'first' and 'last'\n"
+ "\tare valid indices. 'inv(...)' around the range denotes an\n"
+ "\tinverted range.",
"R", 1, "-R <range>"));
result.addElement(new Option(
"\tFlag for leaving unused attributes out of the output, by default\n"
+ "\tthese are included in the filter output.",
"U", 0, "-U"));
return result.elements();
}
/**
* Parses a list of options for this object. <p/>
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -D
* Turns on output of debugging information.</pre>
*
* <pre> -F <classname [options]>
* A filter to apply (can be specified multiple times).</pre>
*
* <pre> -R <range>
* An attribute range (can be specified multiple times).
* For each filter a range must be supplied. 'first' and 'last'
* are valid indices. 'inv(...)' around the range denotes an
* inverted range.</pre>
*
* <pre> -U
* Flag for leaving unused attributes out of the output, by default
* these are included in the filter output.</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 tmpStr;
String classname;
String[] options2;
Vector objects;
Range range;
super.setOptions(options);
setRemoveUnused(Utils.getFlag("U", options));
objects = new Vector();
while ((tmpStr = Utils.getOption("F", options)).length() != 0) {
options2 = Utils.splitOptions(tmpStr);
classname = options2[0];
options2[0] = "";
objects.add(Utils.forName(Filter.class, classname, options2));
}
// at least one filter
if (objects.size() == 0)
objects.add(new AllFilter());
setFilters((Filter[]) objects.toArray(new Filter[objects.size()]));
objects = new Vector();
while ((tmpStr = Utils.getOption("R", options)).length() != 0) {
if (tmpStr.startsWith("inv(") && tmpStr.endsWith(")")) {
range = new Range(tmpStr.substring(4, tmpStr.length() - 1));
range.setInvert(true);
}
else {
range = new Range(tmpStr);
}
objects.add(range);
}
// at least one Range
if (objects.size() == 0)
objects.add(new Range("first-last"));
setRanges((Range[]) objects.toArray(new Range[objects.size()]));
// is number of filters the same as ranges?
checkDimensions();
}
/**
* Gets the current settings of the filter.
*
* @return an array of strings suitable for passing to setOptions
*/
public String[] getOptions() {
Vector result;
String[] options;
int i;
String tmpStr;
result = new Vector();
options = super.getOptions();
for (i = 0; i < options.length; i++)
result.add(options[i]);
if (getRemoveUnused())
result.add("-U");
for (i = 0; i < getFilters().length; i++) {
result.add("-F");
result.add(getFilterSpec(getFilter(i)));
}
for (i = 0; i < getRanges().length; i++) {
tmpStr = getRange(i).getRanges();
if (getRange(i).getInvert())
tmpStr = "inv(" + tmpStr + ")";
result.add("-R");
result.add(tmpStr);
}
return (String[]) result.toArray(new String[result.size()]);
}
/**
* checks whether the dimensions of filters and ranges fit together.
*
* @throws Exception if dimensions differ
*/
protected void checkDimensions() throws Exception {
if (getFilters().length != getRanges().length)
throw new IllegalArgumentException(
"Number of filters (= " + getFilters().length + ") "
+ "and ranges (= " + getRanges().length + ") don't match!");
}
/**
* 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 {
for (int i = 0; i < getRanges().length; i++) {
Instances newi = new Instances(instanceInfo, 0);
if (instanceInfo.size() > 0){
newi.add((Instance)instanceInfo.get(0).copy());
}
Range range = getRanges()[i];
range.setUpper(instanceInfo.numAttributes() - 1);
Instances subset = generateSubset(newi, range);
getFilters()[i].setInputFormat(subset);
}
}
/**
* Sets whether unused attributes (ones that are not covered by any of the
* ranges) are removed from the output.
*
* @param value if true then the unused attributes get removed
*/
public void setRemoveUnused(boolean value) {
m_RemoveUnused = value;
}
/**
* Gets whether unused attributes (ones that are not covered by any of the
* ranges) are removed from the output.
*
* @return true if unused attributes are removed
*/
public boolean getRemoveUnused() {
return m_RemoveUnused;
}
/**
* Returns the tip text for this property.
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String removeUnusedTipText() {
return
"If true then unused attributes (ones that are not covered by any "
+ "of the ranges) will be removed from the output.";
}
/**
* Sets the list of possible filters to choose from.
* Also resets the state of the filter (this reset doesn't affect the
* options).
*
* @param filters an array of filters with all options set.
* @see #reset()
*/
public void setFilters(Filter[] filters) {
m_Filters = filters;
reset();
}
/**
* Gets the list of possible filters to choose from.
*
* @return the array of Filters
*/
public Filter[] getFilters() {
return m_Filters;
}
/**
* Returns the tip text for this property.
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String filtersTipText() {
return "The base filters to be used.";
}
/**
* Gets a single filter from the set of available filters.
*
* @param index the index of the filter wanted
* @return the Filter
*/
public Filter getFilter(int index) {
return m_Filters[index];
}
/**
* returns the filter classname and the options as one string.
*
* @param filter the filter to get the specs for
* @return the classname plus options
*/
protected String getFilterSpec(Filter filter) {
String result;
if (filter == null) {
result = "";
}
else {
result = filter.getClass().getName();
if (filter instanceof OptionHandler)
result += " "
+ Utils.joinOptions(((OptionHandler) filter).getOptions());
}
return result;
}
/**
* Sets the list of possible Ranges to choose from.
* Also resets the state of the Range (this reset doesn't affect the
* options).
*
* @param Ranges an array of Ranges with all options set.
* @see #reset()
*/
public void setRanges(Range[] Ranges) {
m_Ranges = Ranges;
reset();
}
/**
* Gets the list of possible Ranges to choose from.
*
* @return the array of Ranges
*/
public Range[] getRanges() {
return m_Ranges;
}
/**
* Returns the tip text for this property.
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String rangesTipText() {
return "The attribute ranges to be used; 'inv(...)' denotes an inverted range.";
}
/**
* Gets a single Range from the set of available Ranges.
*
* @param index the index of the Range wanted
* @return the Range
*/
public Range getRange(int index) {
return m_Ranges[index];
}
/**
* determines the indices of unused attributes (ones that are not covered
* by any of the range).
*
* @param data the data to base the determination on
* @see #m_IndicesUnused
*/
protected void determineUnusedIndices(Instances data) {
Vector<Integer> indices;
int i;
int n;
boolean covered;
// traverse all ranges
indices = new Vector<Integer>();
for (i = 0; i < data.numAttributes(); i++) {
if (i == data.classIndex())
continue;
covered = false;
for (n = 0; n < getRanges().length; n++) {
if (getRanges()[n].isInRange(i)) {
covered = true;
break;
}
}
if (!covered)
indices.add(new Integer(i));
}
// create array
m_IndicesUnused = new int[indices.size()];
for (i = 0; i < indices.size(); i++)
m_IndicesUnused[i] = indices.get(i).intValue();
if (getDebug())
System.out.println(
"Unused indices: " + Utils.arrayToString(m_IndicesUnused));
}
/**
* generates a subset of the dataset with only the attributes from the range
* (class is always added if present).
*
* @param data the data to work on
* @param range the range of attribute to use
* @return the generated subset
* @throws Exception if creation fails
*/
protected Instances generateSubset(Instances data, Range range) throws Exception {
Remove filter;
StringBuilder atts;
Instances result;
int[] indices;
int i;
// determine attributes
indices = range.getSelection();
atts = new StringBuilder();
for (i = 0; i < indices.length; i++) {
if (i > 0)
atts.append(",");
atts.append("" + (indices[i] + 1));
}
if ((data.classIndex() > -1) && (!range.isInRange(data.classIndex())))
atts.append("," + (data.classIndex() + 1));
// setup filter
filter = new Remove();
filter.setAttributeIndices(atts.toString());
filter.setInvertSelection(true);
filter.setInputFormat(data);
// generate output
result = Filter.useFilter(data, filter);
return result;
}
/**
* renames all the attributes in the dataset (excluding the class if present)
* by adding the prefix to the name.
*
* @param data the data to work on
* @param prefix the prefix for the attributes
* @return a copy of the data with the attributes renamed
* @throws Exception if renaming fails
*/
protected Instances renameAttributes(Instances data, String prefix) throws Exception {
Instances result;
int i;
ArrayList<Attribute> atts;
// rename attributes
atts = new ArrayList<Attribute>();
for (i = 0; i < data.numAttributes(); i++) {
if (i == data.classIndex())
atts.add((Attribute) data.attribute(i).copy());
else
atts.add(data.attribute(i).copy(prefix + data.attribute(i).name()));
}
// create new dataset
result = new Instances(data.relationName(), atts, data.numInstances());
for (i = 0; i < data.numInstances(); i++) {
result.add((Instance) data.instance(i).copy());
}
// set class if present
if (data.classIndex() > -1)
result.setClassIndex(data.classIndex());
return result;
}
/**
* Determines the output format based only on the full input dataset and
* returns this otherwise null is returned. In case the output format cannot
* be returned immediately, i.e., immediateOutputFormat() returns false,
* then this method will be called from batchFinished().
*
* @param inputFormat the input format to base the output format on
* @return the output format
* @throws Exception in case the determination goes wrong
* @see #hasImmediateOutputFormat()
* @see #batchFinished()
*/
protected Instances determineOutputFormat(Instances inputFormat) throws Exception {
Instances result;
Instances processed;
int i;
int n;
ArrayList<Attribute> atts;
Attribute att;
if (!isFirstBatchDone()) {
// we need the full dataset here, see process(Instances)
if (inputFormat.numInstances() == 0)
return null;
checkDimensions();
// determine unused indices
determineUnusedIndices(inputFormat);
atts = new ArrayList<Attribute>();
for (i = 0; i < getFilters().length; i++) {
if (!isFirstBatchDone()) {
// generate subset
processed = generateSubset(inputFormat, getRange(i));
// set input format
if (!getFilter(i).setInputFormat(processed))
Filter.useFilter(processed, getFilter(i));
}
// get output format
processed = getFilter(i).getOutputFormat();
// rename attributes
processed = renameAttributes(processed, "filtered-" + i + "-");
// add attributes
for (n = 0; n < processed.numAttributes(); n++) {
if (n == processed.classIndex())
continue;
atts.add((Attribute) processed.attribute(n).copy());
}
}
// add unused attributes
if (!getRemoveUnused()) {
for (i = 0; i < m_IndicesUnused.length; i++) {
att = inputFormat.attribute(m_IndicesUnused[i]);
atts.add(att.copy("unfiltered-" + att.name()));
}
}
// add class if present
if (inputFormat.classIndex() > -1)
atts.add((Attribute) inputFormat.classAttribute().copy());
// generate new dataset
result = new Instances(inputFormat.relationName(), atts, 0);
if (inputFormat.classIndex() > -1)
result.setClassIndex(result.numAttributes() - 1);
}
else {
result = getOutputFormat();
}
return result;
}
/**
* Processes the given data (may change the provided dataset) and returns
* the modified version. This method is called in batchFinished().
*
* @param instances the data to process
* @return the modified data
* @throws Exception in case the processing goes wrong
* @see #batchFinished()
*/
public Instances process(Instances instances) throws Exception {
Instances result;
int i;
int n;
int m;
int index;
Instances[] processed;
Instance inst;
Instance newInst;
double[] values;
Vector errors;
if (!isFirstBatchDone()) {
checkDimensions();
// set upper limits
for (i = 0; i < m_Ranges.length; i++)
m_Ranges[i].setUpper(instances.numAttributes() - 1);
// determine unused indices
determineUnusedIndices(instances);
}
// pass data through all filters
processed = new Instances[getFilters().length];
for (i = 0; i < getFilters().length; i++) {
processed[i] = generateSubset(instances, getRange(i));
if (!isFirstBatchDone())
getFilter(i).setInputFormat(processed[i]);
processed[i] = Filter.useFilter(processed[i], getFilter(i));
}
// set output format (can only be determined with full dataset, hence here)
if (!isFirstBatchDone()) {
result = determineOutputFormat(instances);
setOutputFormat(result);
}
else {
result = getOutputFormat();
}
// check whether all filters didn't change the number of instances
errors = new Vector();
for (i = 0; i < processed.length; i++) {
if (processed[i].numInstances() != instances.numInstances())
errors.add(new Integer(i));
}
if (errors.size() > 0)
throw new IllegalStateException(
"The following filter(s) changed the number of instances: " + errors);
// assemble data
for (i = 0; i < instances.numInstances(); i++) {
inst = instances.instance(i);
values = new double[result.numAttributes()];
// filtered data
index = 0;
for (n = 0; n < processed.length; n++) {
for (m = 0; m < processed[n].numAttributes(); m++) {
if (m == processed[n].classIndex())
continue;
if (result.attribute(index).isString())
values[index] = result.attribute(index).addStringValue(processed[n].instance(i).stringValue(m));
else if (result.attribute(index).isRelationValued())
values[index] = result.attribute(index).addRelation(processed[n].instance(i).relationalValue(m));
else
values[index] = processed[n].instance(i).value(m);
index++;
}
}
// unused attributes
if (!getRemoveUnused()) {
for (n = 0; n < m_IndicesUnused.length; n++) {
if (result.attribute(index).isString())
values[index] = result.attribute(index).addStringValue(inst.stringValue(m_IndicesUnused[n]));
else if (result.attribute(index).isRelationValued())
values[index] = result.attribute(index).addRelation(inst.relationalValue(m_IndicesUnused[n]));
else
values[index] = inst.value(m_IndicesUnused[n]);
index++;
}
}
// class
if (instances.classIndex() > -1)
values[values.length - 1] = inst.value(instances.classIndex());
// generate and add instance
if (inst instanceof SparseInstance)
newInst = new SparseInstance(instances.instance(i).weight(), values);
else
newInst = new DenseInstance(instances.instance(i).weight(), values);
result.add(newInst);
}
return result;
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 8034 $");
}
/**
* Main method for executing this class.
*
* @param args should contain arguments for the filter: use -h for help
*/
public static void main(String[] args) {
runFilter(new PartitionedMultiFilter(), args);
}
}