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The Waikato Environment for Knowledge Analysis (WEKA), a machine learning workbench. This version represents the developer version, the "bleeding edge" of development, you could say. New functionality gets added to this version.

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/*
 *   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 .
 */

/*
 *    AbstractTimeSeries.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.filters.Filter;
import weka.filters.UnsupervisedFilter;

/**
 * An abstract instance filter that assumes instances form time-series data and
 * performs some merging of attribute values in the current instance with
 * attribute attribute values of some previous (or future) instance. For
 * instances where the desired value is unknown either the instance may be
 * dropped, or missing values used.
 * 

 * 
 * Valid filter-specific options are:
 * 

 * 
 * -R index1,index2-index4,...

 * Specify list of columns to calculate new values for. First and last are valid
 * indexes. (default none)
 * 

 * 
 * -V 

 * Invert matching sense (i.e. calculate for all non-specified columns)
 * 

 * 
 * -I num 

 * The number of instances forward to merge values between. A negative number
 * indicates taking values from a past instance. (default -1)
 * 

 * 
 * -M 

 * For instances at the beginning or end of the dataset where the translated
 * values are not known, remove those instances (default is to use missing
 * values).
 * 

 * 
 * @author Len Trigg ([email protected])
 * @version $Revision: 14508 $
 */
public abstract class AbstractTimeSeries extends Filter implements
  UnsupervisedFilter, OptionHandler, WeightedAttributesHandler, WeightedInstancesHandler {

  /** for serialization */
  private static final long serialVersionUID = -3795656792078022357L;

  /** Stores which columns to copy */
  protected Range m_SelectedCols = new Range();

  /**
   * True if missing values should be used rather than removing instances where
   * the translated value is not known (due to border effects).
   */
  protected boolean m_FillWithMissing = true;

  /**
   * The number of instances forward to translate values between. A negative
   * number indicates taking values from a past instance.
   */
  protected int m_InstanceRange = -1;

  /** Stores the historical instances to copy values between */
  protected Queue m_History;

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

   * 
   * -R index1,index2-index4,...

   * Specify list of columns to copy. First and last are valid indexes. (default
   * none)
   * 

   * 
   * -V

   * Invert matching sense (i.e. calculate for all non-specified columns)
   * 

   * 
   * -I num 

   * The number of instances forward to translate values between. A negative
   * number indicates taking values from a past instance. (default -1)
   * 

   * 
   * -M 

   * For instances at the beginning or end of the dataset where the translated
   * values are not known, remove those instances (default is to use missing
   * values).
   * 

   * 
   * @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);
    } else {
      setAttributeIndices("");
    }

    setInvertSelection(Utils.getFlag('V', options));

    setFillWithMissing(!Utils.getFlag('M', options));

    String instanceRange = Utils.getOption('I', options);
    if (instanceRange.length() != 0) {
      setInstanceRange(Integer.parseInt(instanceRange));
    } else {
      setInstanceRange(-1);
    }

    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());
    }
    if (getInvertSelection()) {
      options.add("-V");
    }
    options.add("-I");
    options.add("" + getInstanceRange());
    if (!getFillWithMissing()) {
      options.add("-M");
    }

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

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

    super.setInputFormat(instanceInfo);
    resetHistory();
    m_SelectedCols.setUpper(instanceInfo.numAttributes() - 1);
    return false;
  }

  /**
   * 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 Exception if the input instance was not of the correct format or if
   *           there was a problem with the filtering.
   */
  @Override
  public boolean input(Instance instance) throws Exception {

    if (getInputFormat() == null) {
      throw new NullPointerException("No input instance format defined");
    }
    if (m_NewBatch) {
      resetQueue();
      m_NewBatch = false;
      resetHistory();
    }

    Instance newInstance = historyInput(instance);
    if (newInstance != null) {
      push(newInstance);
      return true;
    } else {
      return false;
    }
  }

  /**
   * Signifies 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 (getFillWithMissing() && (m_InstanceRange > 0)) {
      while (!m_History.empty()) {
        push(mergeInstances(null, (Instance) m_History.pop()));
      }
    }
    flushInput();
    m_NewBatch = true;
    m_FirstBatchDone = true;
    return (numPendingOutput() != 0);
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String fillWithMissingTipText() {
    return "For instances at the beginning or end of the dataset where the translated "
      + "values are not known, use missing values (default is to remove those "
      + "instances)";
  }

  /**
   * Gets whether missing values should be used rather than removing instances
   * where the translated value is not known (due to border effects).
   * 
   * @return true if so
   */
  public boolean getFillWithMissing() {

    return m_FillWithMissing;
  }

  /**
   * Sets whether missing values should be used rather than removing instances
   * where the translated value is not known (due to border effects).
   * 
   * @param newFillWithMissing true if so
   */
  public void setFillWithMissing(boolean newFillWithMissing) {

    m_FillWithMissing = newFillWithMissing;
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String instanceRangeTipText() {
    return "The number of instances forward/backward to merge values between. "
      + "A negative number indicates taking values from a past instance.";
  }

  /**
   * Gets the number of instances forward to translate values between. A
   * negative number indicates taking values from a past instance.
   * 
   * @return Value of InstanceRange.
   */
  public int getInstanceRange() {

    return m_InstanceRange;
  }

  /**
   * Sets the number of instances forward to translate values between. A
   * negative number indicates taking values from a past instance.
   * 
   * @param newInstanceRange Value to assign to InstanceRange.
   */
  public void setInstanceRange(int newInstanceRange) {

    m_InstanceRange = newInstanceRange;
  }

  /**
   * 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 "Invert matching sense. ie calculate for all non-specified columns.";
  }

  /**
   * 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_SelectedCols.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.
   * 
   * @param invert the new invert setting
   */
  public void setInvertSelection(boolean invert) {

    m_SelectedCols.setInvert(invert);
  }

  /**
   * 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\".";
  }

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

    return m_SelectedCols.getRanges();
  }

  /**
   * 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
   */
  public void setAttributeIndices(String rangeList) {

    m_SelectedCols.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.
   */
  public void setAttributeIndicesArray(int[] attributes) {

    setAttributeIndices(Range.indicesToRangeList(attributes));
  }

  /** Clears any instances from the history queue. */
  protected void resetHistory() {

    if (m_History == null) {
      m_History = new Queue();
    } else {
      m_History.removeAllElements();
    }
  }

  /**
   * Adds an instance to the history buffer. If enough instances are in the
   * buffer, a new instance may be output, with selected attribute values copied
   * from one to another.
   * 
   * @param instance the input instance
   * @return a new instance with translated values, or null if no output
   *         instance is produced
   */
  protected Instance historyInput(Instance instance) {

    m_History.push(instance);
    if (m_History.size() <= Math.abs(m_InstanceRange)) {
      if (getFillWithMissing() && (m_InstanceRange < 0)) {
        return mergeInstances(null, instance);
      } else {
        return null;
      }
    }
    if (m_InstanceRange < 0) {
      return mergeInstances((Instance) m_History.pop(), instance);
    } else {
      return mergeInstances(instance, (Instance) m_History.pop());
    }
  }

  /**
   * Creates a new instance the same as one instance (the "destination") but
   * with some attribute values copied from another instance (the "source")
   * 
   * @param source the source instance
   * @param dest the destination instance
   * @return the new merged instance
   */
  protected abstract Instance mergeInstances(Instance source, Instance dest);

}




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