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weka.filters.unsupervised.attribute.Copy 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 .
 */

/*
 *    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.*;
import weka.core.Capabilities.Capability;
import weka.filters.Filter;
import weka.filters.StreamableFilter;
import weka.filters.UnsupervisedFilter;

/**
 *  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.
 * 

 * 
 * 
 *  Valid options are:
 * 

 * 
 * 
 * -R <index1,index2-index4,...>
 *  Specify list of columns to copy. First and last are valid
 *  indexes. (default none)
 * 
 * 
 * 
 * -V
 *  Invert matching sense (i.e. copy all non-specified columns)
 * 
 * 
 * 
 * 
 * @author Len Trigg ([email protected])
 * @version $Revision: 14508 $
 */
public class Copy extends Filter implements UnsupervisedFilter,
  StreamableFilter, OptionHandler, WeightedInstancesHandler, WeightedAttributesHandler {

  /** 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.
   */
  @Override
  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 "));
    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.
   * 

   * 
   *  Valid options are:
   * 

   * 
   * 
   * -R <index1,index2-index4,...>
   *  Specify list of columns to copy. First and last are valid
   *  indexes. (default none)
   * 
   * 
   * 
   * -V
   *  Invert matching sense (i.e. copy all non-specified columns)
   * 
   * 
   * 
   * 
   * @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 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
   */
  @Override
  public String[] getOptions() {

    Vector options = new Vector();

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

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

  /**
   * Returns the Capabilities of this filter.
   * 
   * @return the capabilities of this object
   * @see Capabilities
   */
  @Override
  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
   */
  @Override
  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 current : m_SelectedAttributes) {
      // Create a copy of the attribute with a different name
      Attribute origAttribute = instanceInfo.attribute(current);
      outputFormat.insertAttributeAt(
        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.
   */
  @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 < 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);
    }

    copyValues(inst, false, instance.dataset(), outputFormatPeek());

    push(inst); // No need to copy instance
    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. 

   * Note: use this method before you call
   * setInputFormat(Instances), 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. 

   *          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 {

    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.

   *          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: 14508 $");
  }

  /**
   * 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);
  }
}