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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 .
 */

/*
 *    Distribution.java
 *    Copyright (C) 1999-2012 University of Waikato, Hamilton, New Zealand
 *
 */

package weka.classifiers.trees.j48;

import java.io.Serializable;
import java.util.Enumeration;

import weka.core.Instance;
import weka.core.Instances;
import weka.core.RevisionHandler;
import weka.core.RevisionUtils;
import weka.core.Utils;

/**
 * Class for handling a distribution of class values.
 * 
 * @author Eibe Frank ([email protected])
 * @version $Revision: 10531 $
 */
public class Distribution implements Cloneable, Serializable, RevisionHandler {

  /** for serialization */
  private static final long serialVersionUID = 8526859638230806576L;

  /** Weight of instances per class per bag. */
  protected final double m_perClassPerBag[][];

  /** Weight of instances per bag. */
  protected final double m_perBag[];

  /** Weight of instances per class. */
  protected final double m_perClass[];

  /** Total weight of instances. */
  protected double totaL;

  /**
   * Creates and initializes a new distribution.
   */
  public Distribution(int numBags, int numClasses) {

    int i;

    m_perClassPerBag = new double[numBags][0];
    m_perBag = new double[numBags];
    m_perClass = new double[numClasses];
    for (i = 0; i < numBags; i++) {
      m_perClassPerBag[i] = new double[numClasses];
    }
    totaL = 0;
  }

  /**
   * Creates and initializes a new distribution using the given array. WARNING:
   * it just copies a reference to this array.
   */
  public Distribution(double[][] table) {

    int i, j;

    m_perClassPerBag = table;
    m_perBag = new double[table.length];
    m_perClass = new double[table[0].length];
    for (i = 0; i < table.length; i++) {
      for (j = 0; j < table[i].length; j++) {
        m_perBag[i] += table[i][j];
        m_perClass[j] += table[i][j];
        totaL += table[i][j];
      }
    }
  }

  /**
   * Creates a distribution with only one bag according to instances in source.
   * 
   * @exception Exception if something goes wrong
   */
  public Distribution(Instances source) throws Exception {

    m_perClassPerBag = new double[1][0];
    m_perBag = new double[1];
    totaL = 0;
    m_perClass = new double[source.numClasses()];
    m_perClassPerBag[0] = new double[source.numClasses()];
    Enumeration enu = source.enumerateInstances();
    while (enu.hasMoreElements()) {
      add(0, enu.nextElement());
    }
  }

  /**
   * Creates a distribution according to given instances and split model.
   * 
   * @exception Exception if something goes wrong
   */

  public Distribution(Instances source, ClassifierSplitModel modelToUse) throws Exception {

    int index;
    Instance instance;
    double[] weights;

    m_perClassPerBag = new double[modelToUse.numSubsets()][0];
    m_perBag = new double[modelToUse.numSubsets()];
    totaL = 0;
    m_perClass = new double[source.numClasses()];
    for (int i = 0; i < modelToUse.numSubsets(); i++) {
      m_perClassPerBag[i] = new double[source.numClasses()];
    }
    Enumeration enu = source.enumerateInstances();
    while (enu.hasMoreElements()) {
      instance = enu.nextElement();
      index = modelToUse.whichSubset(instance);
      if (index != -1) {
        add(index, instance);
      } else {
        weights = modelToUse.weights(instance);
        addWeights(instance, weights);
      }
    }
  }

  /**
   * Creates distribution with only one bag by merging all bags of given
   * distribution.
   */
  public Distribution(Distribution toMerge) {

    totaL = toMerge.totaL;
    m_perClass = new double[toMerge.numClasses()];
    System
      .arraycopy(toMerge.m_perClass, 0, m_perClass, 0, toMerge.numClasses());
    m_perClassPerBag = new double[1][0];
    m_perClassPerBag[0] = new double[toMerge.numClasses()];
    System.arraycopy(toMerge.m_perClass, 0, m_perClassPerBag[0], 0,
      toMerge.numClasses());
    m_perBag = new double[1];
    m_perBag[0] = totaL;
  }

  /**
   * Creates distribution with two bags by merging all bags apart of the
   * indicated one.
   */
  public Distribution(Distribution toMerge, int index) {

    int i;

    totaL = toMerge.totaL;
    m_perClass = new double[toMerge.numClasses()];
    System
      .arraycopy(toMerge.m_perClass, 0, m_perClass, 0, toMerge.numClasses());
    m_perClassPerBag = new double[2][0];
    m_perClassPerBag[0] = new double[toMerge.numClasses()];
    System.arraycopy(toMerge.m_perClassPerBag[index], 0, m_perClassPerBag[0],
      0, toMerge.numClasses());
    m_perClassPerBag[1] = new double[toMerge.numClasses()];
    for (i = 0; i < toMerge.numClasses(); i++) {
      m_perClassPerBag[1][i] = toMerge.m_perClass[i] - m_perClassPerBag[0][i];
    }
    m_perBag = new double[2];
    m_perBag[0] = toMerge.m_perBag[index];
    m_perBag[1] = totaL - m_perBag[0];
  }

  /**
   * Returns number of non-empty bags of distribution.
   */
  public final int actualNumBags() {

    int returnValue = 0;
    int i;

    for (i = 0; i < m_perBag.length; i++) {
      if (Utils.gr(m_perBag[i], 0)) {
        returnValue++;
      }
    }

    return returnValue;
  }

  /**
   * Returns number of classes actually occuring in distribution.
   */
  public final int actualNumClasses() {

    int returnValue = 0;
    int i;

    for (i = 0; i < m_perClass.length; i++) {
      if (Utils.gr(m_perClass[i], 0)) {
        returnValue++;
      }
    }

    return returnValue;
  }

  /**
   * Returns number of classes actually occuring in given bag.
   */
  public final int actualNumClasses(int bagIndex) {

    int returnValue = 0;
    int i;

    for (i = 0; i < m_perClass.length; i++) {
      if (Utils.gr(m_perClassPerBag[bagIndex][i], 0)) {
        returnValue++;
      }
    }

    return returnValue;
  }

  /**
   * Adds given instance to given bag.
   * 
   * @exception Exception if something goes wrong
   */
  public final void add(int bagIndex, Instance instance) throws Exception {

    int classIndex;
    double weight;

    classIndex = (int) instance.classValue();
    weight = instance.weight();
    m_perClassPerBag[bagIndex][classIndex] = m_perClassPerBag[bagIndex][classIndex]
      + weight;
    m_perBag[bagIndex] = m_perBag[bagIndex] + weight;
    m_perClass[classIndex] = m_perClass[classIndex] + weight;
    totaL = totaL + weight;
  }

  /**
   * Subtracts given instance from given bag.
   * 
   * @exception Exception if something goes wrong
   */
  public final void sub(int bagIndex, Instance instance) throws Exception {

    int classIndex;
    double weight;

    classIndex = (int) instance.classValue();
    weight = instance.weight();
    m_perClassPerBag[bagIndex][classIndex] = m_perClassPerBag[bagIndex][classIndex]
      - weight;
    m_perBag[bagIndex] = m_perBag[bagIndex] - weight;
    m_perClass[classIndex] = m_perClass[classIndex] - weight;
    totaL = totaL - weight;
  }

  /**
   * Adds counts to given bag.
   */
  public final void add(int bagIndex, double[] counts) {

    double sum = Utils.sum(counts);

    for (int i = 0; i < counts.length; i++) {
      m_perClassPerBag[bagIndex][i] += counts[i];
    }
    m_perBag[bagIndex] = m_perBag[bagIndex] + sum;
    for (int i = 0; i < counts.length; i++) {
      m_perClass[i] = m_perClass[i] + counts[i];
    }
    totaL = totaL + sum;
  }

  /**
   * Adds all instances with unknown values for given attribute, weighted
   * according to frequency of instances in each bag.
   * 
   * @exception Exception if something goes wrong
   */
  public final void addInstWithUnknown(Instances source, int attIndex)
    throws Exception {

    double[] probs;
    double weight, newWeight;
    int classIndex;
    Instance instance;
    int j;

    probs = new double[m_perBag.length];
    for (j = 0; j < m_perBag.length; j++) {
      if (Utils.eq(totaL, 0)) {
        probs[j] = 1.0 / probs.length;
      } else {
        probs[j] = m_perBag[j] / totaL;
      }
    }
    Enumeration enu = source.enumerateInstances();
    while (enu.hasMoreElements()) {
      instance = enu.nextElement();
      if (instance.isMissing(attIndex)) {
        classIndex = (int) instance.classValue();
        weight = instance.weight();
        m_perClass[classIndex] = m_perClass[classIndex] + weight;
        totaL = totaL + weight;
        for (j = 0; j < m_perBag.length; j++) {
          newWeight = probs[j] * weight;
          m_perClassPerBag[j][classIndex] = m_perClassPerBag[j][classIndex]
            + newWeight;
          m_perBag[j] = m_perBag[j] + newWeight;
        }
      }
    }
  }

  /**
   * Adds all instances in given range to given bag.
   * 
   * @exception Exception if something goes wrong
   */
  public final void addRange(int bagIndex, Instances source, int startIndex,
    int lastPlusOne) throws Exception {

    double sumOfWeights = 0;
    int classIndex;
    Instance instance;
    int i;

    for (i = startIndex; i < lastPlusOne; i++) {
      instance = source.instance(i);
      classIndex = (int) instance.classValue();
      sumOfWeights = sumOfWeights + instance.weight();
      m_perClassPerBag[bagIndex][classIndex] += instance.weight();
      m_perClass[classIndex] += instance.weight();
    }
    m_perBag[bagIndex] += sumOfWeights;
    totaL += sumOfWeights;
  }

  /**
   * Adds given instance to all bags weighting it according to given weights.
   * 
   * @exception Exception if something goes wrong
   */
  public final void addWeights(Instance instance, double[] weights)
    throws Exception {

    int classIndex;
    int i;

    classIndex = (int) instance.classValue();
    for (i = 0; i < m_perBag.length; i++) {
      double weight = instance.weight() * weights[i];
      m_perClassPerBag[i][classIndex] = m_perClassPerBag[i][classIndex]
        + weight;
      m_perBag[i] = m_perBag[i] + weight;
      m_perClass[classIndex] = m_perClass[classIndex] + weight;
      totaL = totaL + weight;
    }
  }

  /**
   * Checks if at least two bags contain a minimum number of instances.
   */
  public final boolean check(double minNoObj) {

    int counter = 0;
    int i;

    for (i = 0; i < m_perBag.length; i++) {
      if (Utils.grOrEq(m_perBag[i], minNoObj)) {
        counter++;
      }
    }
    if (counter > 1) {
      return true;
    } else {
      return false;
    }
  }

  /**
   * Clones distribution (Deep copy of distribution).
   */
  @Override
  public final Object clone() {

    int i, j;

    Distribution newDistribution = new Distribution(m_perBag.length,
      m_perClass.length);
    for (i = 0; i < m_perBag.length; i++) {
      newDistribution.m_perBag[i] = m_perBag[i];
      for (j = 0; j < m_perClass.length; j++) {
        newDistribution.m_perClassPerBag[i][j] = m_perClassPerBag[i][j];
      }
    }
    for (j = 0; j < m_perClass.length; j++) {
      newDistribution.m_perClass[j] = m_perClass[j];
    }
    newDistribution.totaL = totaL;

    return newDistribution;
  }

  /**
   * Deletes given instance from given bag.
   * 
   * @exception Exception if something goes wrong
   */
  public final void del(int bagIndex, Instance instance) throws Exception {

    int classIndex;
    double weight;

    classIndex = (int) instance.classValue();
    weight = instance.weight();
    m_perClassPerBag[bagIndex][classIndex] = m_perClassPerBag[bagIndex][classIndex]
      - weight;
    m_perBag[bagIndex] = m_perBag[bagIndex] - weight;
    m_perClass[classIndex] = m_perClass[classIndex] - weight;
    totaL = totaL - weight;
  }

  /**
   * Deletes all instances in given range from given bag.
   * 
   * @exception Exception if something goes wrong
   */
  public final void delRange(int bagIndex, Instances source, int startIndex,
    int lastPlusOne) throws Exception {

    double sumOfWeights = 0;
    int classIndex;
    Instance instance;
    int i;

    for (i = startIndex; i < lastPlusOne; i++) {
      instance = source.instance(i);
      classIndex = (int) instance.classValue();
      sumOfWeights = sumOfWeights + instance.weight();
      m_perClassPerBag[bagIndex][classIndex] -= instance.weight();
      m_perClass[classIndex] -= instance.weight();
    }
    m_perBag[bagIndex] -= sumOfWeights;
    totaL -= sumOfWeights;
  }

  /**
   * Prints distribution.
   */

  public final String dumpDistribution() {

    StringBuffer text;
    int i, j;

    text = new StringBuffer();
    for (i = 0; i < m_perBag.length; i++) {
      text.append("Bag num " + i + "\n");
      for (j = 0; j < m_perClass.length; j++) {
        text.append("Class num " + j + " " + m_perClassPerBag[i][j] + "\n");
      }
    }
    return text.toString();
  }

  /**
   * Sets all counts to zero.
   */
  public final void initialize() {

    for (int i = 0; i < m_perClass.length; i++) {
      m_perClass[i] = 0;
    }
    for (int i = 0; i < m_perBag.length; i++) {
      m_perBag[i] = 0;
    }
    for (int i = 0; i < m_perBag.length; i++) {
      for (int j = 0; j < m_perClass.length; j++) {
        m_perClassPerBag[i][j] = 0;
      }
    }
    totaL = 0;
  }

  /**
   * Returns matrix with distribution of class values.
   */
  public final double[][] matrix() {

    return m_perClassPerBag;
  }

  /**
   * Returns index of bag containing maximum number of instances.
   */
  public final int maxBag() {

    double max;
    int maxIndex;
    int i;

    max = 0;
    maxIndex = -1;
    for (i = 0; i < m_perBag.length; i++) {
      if (Utils.grOrEq(m_perBag[i], max)) {
        max = m_perBag[i];
        maxIndex = i;
      }
    }
    return maxIndex;
  }

  /**
   * Returns class with highest frequency over all bags.
   */
  public final int maxClass() {

    double maxCount = 0;
    int maxIndex = 0;
    int i;

    for (i = 0; i < m_perClass.length; i++) {
      if (Utils.gr(m_perClass[i], maxCount)) {
        maxCount = m_perClass[i];
        maxIndex = i;
      }
    }

    return maxIndex;
  }

  /**
   * Returns class with highest frequency for given bag.
   */
  public final int maxClass(int index) {

    double maxCount = 0;
    int maxIndex = 0;
    int i;

    if (Utils.gr(m_perBag[index], 0)) {
      for (i = 0; i < m_perClass.length; i++) {
        if (Utils.gr(m_perClassPerBag[index][i], maxCount)) {
          maxCount = m_perClassPerBag[index][i];
          maxIndex = i;
        }
      }
      return maxIndex;
    } else {
      return maxClass();
    }
  }

  /**
   * Returns number of bags.
   */
  public final int numBags() {

    return m_perBag.length;
  }

  /**
   * Returns number of classes.
   */
  public final int numClasses() {

    return m_perClass.length;
  }

  /**
   * Returns perClass(maxClass()).
   */
  public final double numCorrect() {

    return m_perClass[maxClass()];
  }

  /**
   * Returns perClassPerBag(index,maxClass(index)).
   */
  public final double numCorrect(int index) {

    return m_perClassPerBag[index][maxClass(index)];
  }

  /**
   * Returns total-numCorrect().
   */
  public final double numIncorrect() {

    return totaL - numCorrect();
  }

  /**
   * Returns perBag(index)-numCorrect(index).
   */
  public final double numIncorrect(int index) {

    return m_perBag[index] - numCorrect(index);
  }

  /**
   * Returns number of (possibly fractional) instances of given class in given
   * bag.
   */
  public final double perClassPerBag(int bagIndex, int classIndex) {

    return m_perClassPerBag[bagIndex][classIndex];
  }

  /**
   * Returns number of (possibly fractional) instances in given bag.
   */
  public final double perBag(int bagIndex) {

    return m_perBag[bagIndex];
  }

  /**
   * Returns number of (possibly fractional) instances of given class.
   */
  public final double perClass(int classIndex) {

    return m_perClass[classIndex];
  }

  /**
   * Returns relative frequency of class over all bags with Laplace correction.
   */
  public final double laplaceProb(int classIndex) {

    return (m_perClass[classIndex] + 1) / (totaL + m_perClass.length);
  }

  /**
   * Returns relative frequency of class for given bag.
   */
  public final double laplaceProb(int classIndex, int intIndex) {

    if (Utils.gr(m_perBag[intIndex], 0)) {
      return (m_perClassPerBag[intIndex][classIndex] + 1.0)
        / (m_perBag[intIndex] + m_perClass.length);
    } else {
      return laplaceProb(classIndex);
    }

  }

  /**
   * Returns relative frequency of class over all bags.
   */
  public final double prob(int classIndex) {

    if (!Utils.eq(totaL, 0)) {
      return m_perClass[classIndex] / totaL;
    } else {
      return 0;
    }
  }

  /**
   * Returns relative frequency of class for given bag.
   */
  public final double prob(int classIndex, int intIndex) {

    if (Utils.gr(m_perBag[intIndex], 0)) {
      return m_perClassPerBag[intIndex][classIndex] / m_perBag[intIndex];
    } else {
      return prob(classIndex);
    }
  }

  /**
   * Subtracts the given distribution from this one. The results has only one
   * bag.
   */
  public final Distribution subtract(Distribution toSubstract) {

    Distribution newDist = new Distribution(1, m_perClass.length);

    newDist.m_perBag[0] = totaL - toSubstract.totaL;
    newDist.totaL = newDist.m_perBag[0];
    for (int i = 0; i < m_perClass.length; i++) {
      newDist.m_perClassPerBag[0][i] = m_perClass[i]
        - toSubstract.m_perClass[i];
      newDist.m_perClass[i] = newDist.m_perClassPerBag[0][i];
    }
    return newDist;
  }

  /**
   * Returns total number of (possibly fractional) instances.
   */
  public final double total() {

    return totaL;
  }

  /**
   * Shifts given instance from one bag to another one.
   * 
   * @exception Exception if something goes wrong
   */
  public final void shift(int from, int to, Instance instance) throws Exception {

    int classIndex;
    double weight;

    classIndex = (int) instance.classValue();
    weight = instance.weight();
    m_perClassPerBag[from][classIndex] -= weight;
    m_perClassPerBag[to][classIndex] += weight;
    m_perBag[from] -= weight;
    m_perBag[to] += weight;
  }

  /**
   * Shifts all instances in given range from one bag to another one.
   * 
   * @exception Exception if something goes wrong
   */
  public final void shiftRange(int from, int to, Instances source,
    int startIndex, int lastPlusOne) throws Exception {

    int classIndex;
    double weight;
    Instance instance;
    int i;

    for (i = startIndex; i < lastPlusOne; i++) {
      instance = source.instance(i);
      classIndex = (int) instance.classValue();
      weight = instance.weight();
      m_perClassPerBag[from][classIndex] -= weight;
      m_perClassPerBag[to][classIndex] += weight;
      m_perBag[from] -= weight;
      m_perBag[to] += weight;
    }
  }

  /**
   * Returns the revision string.
   * 
   * @return the revision
   */
  @Override
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 10531 $");
  }
}