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weka.filters.unsupervised.attribute.Reorder Maven / Gradle / Ivy

/*
 *   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 .
 */

/*
 * Reorder.java
 * Copyright (C) 2005-2012 University of Waikato, Hamilton, New Zealand
 *
 */

package weka.filters.unsupervised.attribute;

import java.util.ArrayList;
import java.util.Enumeration;
import java.util.StringTokenizer;
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;

/**
 *  A filter that generates output with a new order of
 * the attributes. Useful if one wants to move an attribute to the end to use it
 * as class attribute (e.g. with using "-R 2-last,1").

 * But it's not only possible to change the order of all the attributes, but
 * also to leave out attributes. E.g. if you have 10 attributes, you can
 * generate the following output order: 1,3,5,7,9,10 or 10,1-5.

 * You can also duplicate attributes, e.g. for further processing later on: e.g.
 * 1,1,1,4,4,4,2,2,2 where the second and the third column of each attribute are
 * processed differently and the first one, i.e. the original one is kept.

 * One can simply inverse the order of the attributes via 'last-first'.

 * After appyling the filter, the index of the class attribute is the last
 * attribute.
 * 

 * 
 * 
 *  Valid options are:
 * 

 * 
 * 
 * -R <index1,index2-index4,...>
 *  Specify list of columns to copy. First and last are valid
 *  indexes. (default first-last)
 * 
 * 
 * 
 * 
 * @author FracPete (fracpete at waikato dot ac dot nz)
 * @version $Revision: 10215 $
 */
public class Reorder extends Filter implements UnsupervisedFilter,
  StreamableFilter, OptionHandler {

  /** for serialization */
  static final long serialVersionUID = -1135571321097202292L;

  /** Stores which columns to reorder */
  protected String m_NewOrderCols = "first-last";

  /**
   * Stores the indexes of the selected attributes in order, once the dataset is
   * seen
   */
  protected int[] m_SelectedAttributes;

  /**
   * Contains an index of string attributes in the input format that survive the
   * filtering process -- some entries may be duplicated
   */
  protected int[] m_InputStringIndex;

  /**
   * Returns an enumeration describing the available options.
   * 
   * @return an enumeration of all the available options.
   */
  @Override
  public Enumeration listOptions() {

    Vector newVector = new Vector();

    newVector.addElement(new Option(
      "\tSpecify list of columns to copy. First and last are valid\n"
        + "\tindexes. (default first-last)", "R", 1,
      "-R "));

    return newVector.elements();
  }

  /**
   * Parses a given list of options.
   * 

   * 
   *  Valid options are:
   * 

   * 
   * 
   * -R <index1,index2-index4,...>
   *  Specify list of columns to copy. First and last are valid
   *  indexes. (default first-last)
   * 
   * 
   * 
   * 
   * @param options the list of options as an array of strings
   * @throws Exception if an option is not supported
   */
  @Override
  public void setOptions(String[] options) throws Exception {

    String orderList = Utils.getOption('R', options);
    if (orderList.length() != 0) {
      setAttributeIndices(orderList);
    }

    if (getInputFormat() != null) {
      setInputFormat(getInputFormat());
    }

    Utils.checkForRemainingOptions(options);
  }

  /**
   * Gets the current settings of the filter.
   * 
   * @return an array of strings suitable for passing to setOptions
   */
  @Override
  public String[] getOptions() {

    Vector options = new Vector();

    if (!getAttributeIndices().equals("")) {
      options.add("-R");
      options.add(getAttributeIndices());
    }

    return options.toArray(new String[0]);
  }

  /**
   * parses the index string and returns the corresponding int index
   * 
   * @param s the index string to parse
   * @param numAttributes necessary for "last" and OutOfBounds checks
   * @return the int index determined form the index string
   * @throws Exception if index is not valid
   */
  protected int determineIndex(String s, int numAttributes) throws Exception {
    int result;

    if (s.equals("first")) {
      result = 0;
    } else if (s.equals("last")) {
      result = numAttributes - 1;
    } else {
      result = Integer.parseInt(s) - 1;
    }

    // out of bounds?
    if ((result < 0) || (result > numAttributes - 1)) {
      throw new IllegalArgumentException("'" + s
        + "' is not a valid index for the range '1-" + numAttributes + "'!");
    }

    return result;
  }

  /**
   * parses the range string and returns an array with the indices
   * 
   * @param numAttributes necessary for "last" and OutOfBounds checks
   * @return the indices determined form the range string
   * @see #m_NewOrderCols
   * @throws Exception if range is not valid
   */
  protected int[] determineIndices(int numAttributes) throws Exception {
    int[] result;
    Vector list;
    int i;
    StringTokenizer tok;
    String token;
    String[] range;
    int from;
    int to;

    list = new Vector();

    // parse range
    tok = new StringTokenizer(m_NewOrderCols, ",");
    while (tok.hasMoreTokens()) {
      token = tok.nextToken();
      if (token.indexOf("-") > -1) {
        range = token.split("-");
        if (range.length != 2) {
          throw new IllegalArgumentException("'" + token
            + "' is not a valid range!");
        }
        from = determineIndex(range[0], numAttributes);
        to = determineIndex(range[1], numAttributes);

        if (from <= to) {
          for (i = from; i <= to; i++) {
            list.add(i);
          }
        } else {
          for (i = from; i >= to; i--) {
            list.add(i);
          }
        }
      } else {
        list.add(determineIndex(token, numAttributes));
      }
    }

    // turn vector into int array
    result = new int[list.size()];
    for (i = 0; i < list.size(); i++) {
      result[i] = list.get(i);
    }

    return result;
  }

  /**
   * Returns the Capabilities of this filter.
   * 
   * @return the capabilities of this object
   * @see Capabilities
   */
  @Override
  public Capabilities getCapabilities() {
    Capabilities result = super.getCapabilities();
    result.disableAll();

    // attribute
    result.enableAllAttributes();
    result.enable(Capability.MISSING_VALUES);

    // class
    result.enableAllClasses();
    result.enable(Capability.NO_CLASS);
    result.enable(Capability.MISSING_CLASS_VALUES);

    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
   */
  @Override
  public boolean setInputFormat(Instances instanceInfo) throws Exception {
    super.setInputFormat(instanceInfo);

    ArrayList attributes = new ArrayList();
    int outputClass = -1;
    m_SelectedAttributes = determineIndices(instanceInfo.numAttributes());
    for (int current : m_SelectedAttributes) {
      if (instanceInfo.classIndex() == current) {
        outputClass = attributes.size();
      }
      Attribute keep = (Attribute) instanceInfo.attribute(current).copy();
      attributes.add(keep);
    }

    initInputLocators(instanceInfo, m_SelectedAttributes);

    Instances outputFormat = new Instances(instanceInfo.relationName(),
      attributes, 0);
    outputFormat.setClassIndex(outputClass);
    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.
   */
  @Override
  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 < m_SelectedAttributes.length; i++) {
      int current = m_SelectedAttributes[i];
      vals[i] = 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 "A filter that generates output with a new order of the "
      + "attributes. Useful if one wants to move an attribute to the end to "
      + "use it as class attribute (e.g. with using \"-R 2-last,1\").\n"
      + "But it's not only possible to change the order of all the attributes, "
      + "but also to leave out attributes. E.g. if you have 10 attributes, you "
      + "can generate the following output order: 1,3,5,7,9,10 or 10,1-5.\n"
      + "You can also duplicate attributes, e.g. for further processing later "
      + "on: e.g. 1,1,1,4,4,4,2,2,2 where the second and the third column of "
      + "each attribute are processed differently and the first one, i.e. the "
      + "original one is kept.\n"
      + "One can simply inverse the order of the attributes via 'last-first'.\n"
      + "After appyling the filter, the index of the class attribute is the "
      + "last attribute.";
  }

  /**
   * Get the current range selection
   * 
   * @return a string containing a comma separated list of ranges
   */
  public String getAttributeIndices() {
    return m_NewOrderCols;
  }

  /**
   * 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. 

   *          eg: first-3,5,6-last

   *          Note: use this method before you call
   *          setInputFormat(Instances), 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 {
    // simple test
    if (rangeList.replaceAll("[afilrst0-9\\-,]*", "").length() != 0) {
      throw new IllegalArgumentException("Not a valid range string!");
    }

    m_NewOrderCols = 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.

   *          Note: use this method before you call
   *          setInputFormat(Instances), 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
   */
  @Override
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 10215 $");
  }

  /**
   * 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 Reorder(), argv);
  }
}