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• Resample.java

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weka.filters.unsupervised.instance.Resample 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 .
 */

/*
 *    Resample.java
 *    Copyright (C) 2002-2012 University of Waikato, Hamilton, New Zealand
 *
 */

package weka.filters.unsupervised.instance;

import java.util.Collections;
import java.util.Enumeration;
import java.util.Random;
import java.util.Vector;

import weka.core.Capabilities;
import weka.core.Capabilities.Capability;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionUtils;
import weka.core.Utils;
import weka.filters.Filter;
import weka.filters.UnsupervisedFilter;

/**
 *  Produces a random subsample of a dataset using
 * either sampling with replacement or without replacement. The original dataset
 * must fit entirely in memory. The number of instances in the generated dataset
 * may be specified. When used in batch mode, subsequent batches are NOT
 * resampled.
 * 

 * 
 * 
 *  Valid options are:
 * 

 * 
 * 
 * -S <num>
 *  Specify the random number seed (default 1)
 * 
 * 
 * 
 * -Z <num>
 *  The size of the output dataset, as a percentage of
 *  the input dataset (default 100)
 * 
 * 
 * 
 * -no-replacement
 *  Disables replacement of instances
 *  (default: with replacement)
 * 
 * 
 * 
 * -V
 *  Inverts the selection - only available with '-no-replacement'.
 * 
 * 
 * 
 * 
 * @author Len Trigg ([email protected])
 * @author FracPete (fracpete at waikato dot ac dot nz)
 * @author Eibe Frank
 * @version $Revision: 12037 $
 */
public class Resample extends Filter implements UnsupervisedFilter,
OptionHandler {

  /** for serialization */
  static final long serialVersionUID = 3119607037607101160L;

  /** The subsample size, percent of original set, default 100% */
  protected double m_SampleSizePercent = 100;

  /** The random number generator seed */
  protected int m_RandomSeed = 1;

  /** Whether to perform sampling with replacement or without */
  protected boolean m_NoReplacement = false;

  /**
   * Whether to invert the selection (only if instances are drawn WITHOUT
   * replacement)
   * 
   * @see #m_NoReplacement
   */
  protected boolean m_InvertSelection = false;

  /**
   * Returns a string describing this classifier
   * 
   * @return a description of the classifier suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String globalInfo() {
    return "Produces a random subsample of a dataset using either sampling with "
      + "replacement or without replacement. The original dataset must fit "
      + "entirely in memory. The number of instances in the generated dataset "
      + "may be specified. When used in batch mode, subsequent batches are "
      + "NOT resampled.";
  }

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

    result.addElement(new Option(
      "\tSpecify the random number seed (default 1)", "S", 1, "-S "));

    result.addElement(new Option(
      "\tThe size of the output dataset, as a percentage of\n"
        + "\tthe input dataset (default 100)", "Z", 1, "-Z "));

    result
    .addElement(new Option("\tDisables replacement of instances\n"
      + "\t(default: with replacement)", "no-replacement", 0,
      "-no-replacement"));

    result.addElement(new Option(
      "\tInverts the selection - only available with '-no-replacement'.", "V",
      0, "-V"));

    return result.elements();
  }

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

   * 
   *  Valid options are:
   * 

   * 
   * 
   * -S <num>
   *  Specify the random number seed (default 1)
   * 
   * 
   * 
   * -Z <num>
   *  The size of the output dataset, as a percentage of
   *  the input dataset (default 100)
   * 
   * 
   * 
   * -no-replacement
   *  Disables replacement of instances
   *  (default: with replacement)
   * 
   * 
   * 
   * -V
   *  Inverts the selection - only available with '-no-replacement'.
   * 
   * 
   * 
   * 
   * @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 tmpStr = Utils.getOption('S', options);
    if (tmpStr.length() != 0) {
      setRandomSeed(Integer.parseInt(tmpStr));
    } else {
      setRandomSeed(1);
    }

    tmpStr = Utils.getOption('Z', options);
    if (tmpStr.length() != 0) {
      setSampleSizePercent(Double.parseDouble(tmpStr));
    } else {
      setSampleSizePercent(100);
    }

    setNoReplacement(Utils.getFlag("no-replacement", options));

    if (getNoReplacement()) {
      setInvertSelection(Utils.getFlag('V', options));
    }

    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 result = new Vector();

    result.add("-S");
    result.add("" + getRandomSeed());

    result.add("-Z");
    result.add("" + getSampleSizePercent());

    if (getNoReplacement()) {
      result.add("-no-replacement");
      if (getInvertSelection()) {
        result.add("-V");
      }
    }

    return result.toArray(new String[result.size()]);
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String randomSeedTipText() {
    return "The seed used for random sampling.";
  }

  /**
   * Gets the random number seed.
   * 
   * @return the random number seed.
   */
  public int getRandomSeed() {
    return m_RandomSeed;
  }

  /**
   * Sets the random number seed.
   * 
   * @param newSeed the new random number seed.
   */
  public void setRandomSeed(int newSeed) {
    m_RandomSeed = newSeed;
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String sampleSizePercentTipText() {
    return "Size of the subsample as a percentage of the original dataset.";
  }

  /**
   * Gets the subsample size as a percentage of the original set.
   * 
   * @return the subsample size
   */
  public double getSampleSizePercent() {
    return m_SampleSizePercent;
  }

  /**
   * Sets the size of the subsample, as a percentage of the original set.
   * 
   * @param newSampleSizePercent the subsample set size, between 0 and 100.
   */
  public void setSampleSizePercent(double newSampleSizePercent) {
    m_SampleSizePercent = newSampleSizePercent;
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String noReplacementTipText() {
    return "Disables the replacement of instances.";
  }

  /**
   * Gets whether instances are drawn with or without replacement.
   * 
   * @return true if the replacement is disabled
   */
  public boolean getNoReplacement() {
    return m_NoReplacement;
  }

  /**
   * Sets whether instances are drawn with or with out replacement.
   * 
   * @param value if true then the replacement of instances is disabled
   */
  public void setNoReplacement(boolean value) {
    m_NoReplacement = value;
  }

  /**
   * 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 "Inverts the selection (only if instances are drawn WITHOUT replacement).";
  }

  /**
   * Gets whether selection is inverted (only if instances are drawn WIHTOUT
   * replacement).
   * 
   * @return true if the replacement is disabled
   * @see #m_NoReplacement
   */
  public boolean getInvertSelection() {
    return m_InvertSelection;
  }

  /**
   * Sets whether the selection is inverted (only if instances are drawn WIHTOUT
   * replacement).
   * 
   * @param value if true then selection is inverted
   */
  public void setInvertSelection(boolean value) {
    m_InvertSelection = value;
  }

  /**
   * 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 the input format can't be set successfully
   */
  @Override
  public boolean setInputFormat(Instances instanceInfo) throws Exception {

    super.setInputFormat(instanceInfo);
    setOutputFormat(instanceInfo);
    return true;
  }

  /**
   * Input an instance for filtering. Filter requires all training 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 structure 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;
    }
    if (isFirstBatchDone()) {
      push(instance);
      return true;
    } else {
      bufferInput(instance);
      return false;
    }
  }

  /**
   * Signify that this batch of input to the filter is finished. If the filter
   * requires all instances prior to filtering, output() may now be called to
   * retrieve the filtered instances.
   * 
   * @return true if there are instances pending output
   * @throws IllegalStateException if no input structure has been defined
   */
  @Override
  public boolean batchFinished() {

    if (getInputFormat() == null) {
      throw new IllegalStateException("No input instance format defined");
    }

    if (!isFirstBatchDone()) {
      // Do the subsample, and clear the input instances.
      createSubsample();
    }
    flushInput();

    m_NewBatch = true;
    m_FirstBatchDone = true;
    return (numPendingOutput() != 0);
  }

  /**
   * Creates a subsample of the current set of input instances. The output
   * instances are pushed onto the output queue for collection.
   */
  protected void createSubsample() {

    Instances data = getInputFormat();
    int numEligible = data.numInstances();
    int sampleSize = (int) (numEligible * m_SampleSizePercent / 100);
    Random random = new Random(m_RandomSeed);

    if (getNoReplacement()) {

      // Set up array of indices
      int[] selected = new int[numEligible];
      for (int j = 0; j < numEligible; j++) {
        selected[j] = j;
      }
      for (int i = 0; i < sampleSize; i++) {

        // Sampling without replacement
        int chosenLocation = random.nextInt(numEligible);
        int chosen = selected[chosenLocation];
        numEligible--;
        selected[chosenLocation] = selected[numEligible];
        selected[numEligible] = chosen;
      }

      // Do we need to invert the selection?
      if (getInvertSelection()) {

        // Take the first numEligible instances
        // because they have not been selected
        for (int j = 0; j < numEligible; j++) {
          push(data.instance(selected[j]), false); // No need to copy instance
        }
      } else {

        // Take the elements that have been selected
        for (int j = numEligible; j < data.numInstances(); j++) {
          push(data.instance(selected[j]), false); // No need to copy instance
        }
      }
    } else {

      // Sampling with replacement
      for (int i = 0; i < sampleSize; i++) {
        push(data.instance(random.nextInt(numEligible)), false); // No need to copy instance
      }
    }
  }

  /**
   * Returns the revision string.
   * 
   * @return the revision
   */
  @Override
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 12037 $");
  }

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