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• BayesNet.java

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weka.datagenerators.classifiers.classification.BayesNet 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 .
 */

/*
 * BayesNet.java
 * Copyright (C) 2005-2012,2015 University of Waikato, Hamilton, New Zealand
 *
 */

package weka.datagenerators.classifiers.classification;

import weka.classifiers.bayes.net.BayesNetGenerator;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.RevisionUtils;
import weka.core.Utils;
import weka.datagenerators.ClassificationGenerator;

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

/**
 
 * Generates random instances based on a Bayes network.
 * 


 
 * 
 
 * Valid options are: 

 * 
 * 
 -h
 *  Prints this help.
 * 
 * 
 -o <file>
 *  The name of the output file, otherwise the generated data is
 *  printed to stdout.
 * 
 * 
 -r <name>
 *  The name of the relation.
 * 
 * 
 -d
 *  Whether to print debug informations.
 * 
 * 
 -S
 *  The seed for random function (default 1)
 * 
 * 
 -n <num>
 *  The number of examples to generate (default 100)
 * 
 * 
 -A <num>
 *  The number of arcs to use. (default 20)
 * 
 * 
 -N <num>
 *  The number of attributes to generate. (default 10)
 * 
 * 
 -C <num>
 *  The cardinality of the attributes and the class. (default 2)
 * 
 
 * 
 * @author FracPete (fracpete at waikato dot ac dot nz)
 * @version $Revision: 11753 $
 * @see BayesNetGenerator
 */

public class BayesNet extends ClassificationGenerator {

  /** for serialization */
  static final long serialVersionUID = -796118162379901512L;

  /** the bayesian net generator, that produces the actual data */
  protected BayesNetGenerator m_Generator;

  /**
   * initializes the generator
   */
  public BayesNet() {
    super();

    setNumAttributes(defaultNumAttributes());
    setNumArcs(defaultNumArcs());
    setCardinality(defaultCardinality());
  }

  /**
   * Returns a string describing this data generator.
   * 
   * @return a description of the data generator suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String globalInfo() {
    return "Generates random instances based on a Bayes network.";
  }

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

    result.add(new Option("\tThe number of arcs to use. (default "
      + defaultNumArcs() + ")", "A", 1, "-A "));

    result.add(new Option("\tThe number of attributes to generate. (default "
      + defaultNumAttributes() + ")", "N", 1, "-N "));

    result.add(new Option(
      "\tThe cardinality of the attributes and the class. (default "
        + defaultCardinality() + ")", "C", 1, "-C "));

    return result.elements();
  }

  /**
   * Parses a list of options for this object.
   * 

   * 
   
   * Valid options are: 

   * 
   * 
 -h
   *  Prints this help.
   * 
   * 
 -o <file>
   *  The name of the output file, otherwise the generated data is
   *  printed to stdout.
   * 
   * 
 -r <name>
   *  The name of the relation.
   * 
   * 
 -d
   *  Whether to print debug informations.
   * 
   * 
 -S
   *  The seed for random function (default 1)
   * 
   * 
 -n <num>
   *  The number of examples to generate (default 100)
   * 
   * 
 -A <num>
   *  The number of arcs to use. (default 20)
   * 
   * 
 -N <num>
   *  The number of attributes to generate. (default 10)
   * 
   * 
 -C <num>
   *  The cardinality of the attributes and the class. (default 2)
   * 
   
   * 
   * @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;
    Vector list;

    super.setOptions(options);

    list = new Vector();

    list.add("-N");
    tmpStr = Utils.getOption('N', options);
    if (tmpStr.length() != 0) {
      list.add(tmpStr);
    } else {
      list.add("" + defaultNumAttributes());
    }

    // handled via -n option
    list.add("-M");
    list.add("" + getNumExamples());

    list.add("-S");
    tmpStr = Utils.getOption('S', options);
    if (tmpStr.length() != 0) {
      list.add(tmpStr);
    } else {
      list.add("" + defaultSeed());
    }

    list.add("-A");
    tmpStr = Utils.getOption('A', options);
    if (tmpStr.length() != 0) {
      list.add(tmpStr);
    } else {
      list.add("" + defaultNumArcs());
    }

    list.add("-C");
    tmpStr = Utils.getOption('C', options);
    if (tmpStr.length() != 0) {
      list.add(tmpStr);
    } else {
      list.add("" + defaultCardinality());
    }

    setGeneratorOptions(list);
  }

  /**
   * Gets the current settings of the datagenerator.
   * 
   * @return an array of strings suitable for passing to setOptions
   */
  @Override
  public String[] getOptions() {
    Vector result = new Vector();

    String[] options = removeBlacklist(super.getOptions());
    Collections.addAll(result, options);

    // determine options from generator
    options = getGenerator().getOptions();

    result.add("-N");
    result.add("" + getNumAttributes());

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

    try {
      result.add("-A");
      result.add(Utils.getOption('A', options));
    } catch (Exception e) {
      e.printStackTrace();
    }

    try {
      result.add("-C");
      result.add(Utils.getOption('C', options));
    } catch (Exception e) {
      e.printStackTrace();
    }

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

  /**
   * sets the given options of the BayesNetGenerator
   * 
   * @param generator the generator to set the options for
   * @param options the options to set
   */
  protected void setGeneratorOptions(BayesNetGenerator generator,
    Vector options) {

    try {
      generator.setOptions(options.toArray(new String[options.size()]));
    } catch (Exception e) {
      e.printStackTrace();
    }
  }

  /**
   * returns the actual datagenerator
   * 
   * @return the actual datagenerator
   */
  protected BayesNetGenerator getGenerator() {
    if (m_Generator == null) {
      m_Generator = new BayesNetGenerator();
    }

    return m_Generator;
  }

  /**
   * sets the given options of the BayesNetGenerator
   * 
   * @param options the options to set
   */
  protected void setGeneratorOptions(Vector options) {
    setGeneratorOptions(getGenerator(), options);
  }

  /**
   * sets a specific option/value of the generator (option must be w/o then '-')
   * 
   * @param generator the generator to set the option for
   * @param option the option to set
   * @param value the new value for the option
   */
  protected void setGeneratorOption(BayesNetGenerator generator, String option,
    String value) {

    String[] options;
    Vector list;
    int i;

    try {
      // get options and remove specific option
      options = generator.getOptions();
      Utils.getOption(option, options);

      // add option and set the new options
      list = new Vector();
      for (i = 0; i < options.length; i++) {
        if (options[i].length() != 0) {
          list.add(options[i]);
        }
      }
      list.add("-" + option);
      list.add(value);
      setGeneratorOptions(generator, list);
    } catch (Exception e) {
      e.printStackTrace();
    }
  }

  /**
   * sets a specific option/value of the generator (option must be w/o then '-')
   * 
   * @param option the option to set
   * @param value the new value for the option
   */
  protected void setGeneratorOption(String option, String value) {
    setGeneratorOption(getGenerator(), option, value);
  }

  /**
   * returns the default number of attributes
   * 
   * @return the default number of attributes
   */
  protected int defaultNumAttributes() {
    return 10;
  }

  /**
   * Sets the number of attributes the dataset should have.
   * 
   * @param numAttributes the new number of attributes
   */
  public void setNumAttributes(int numAttributes) {
    setGeneratorOption("N", "" + numAttributes);
  }

  /**
   * Gets the number of attributes that should be produced.
   * 
   * @return the number of attributes that should be produced
   */
  public int getNumAttributes() {
    int result;

    result = -1;
    try {
      result = Integer.parseInt(Utils.getOption('N', getGenerator()
        .getOptions()));
    } catch (Exception e) {
      e.printStackTrace();
      result = -1;
    }

    return result;
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String numAttributesTipText() {
    return "The number of attributes the generated data will contain (including class attribute), ie the number of nodes in the bayesian net.";
  }

  /**
   * returns the default cardinality
   * 
   * @return the default cardinality
   */
  protected int defaultCardinality() {
    return 2;
  }

  /**
   * Sets the cardinality of the attributes (incl class attribute)
   * 
   * @param value the cardinality
   */
  public void setCardinality(int value) {
    setGeneratorOption("C", "" + value);
  }

  /**
   * Gets the cardinality of the attributes (incl class attribute)
   * 
   * @return the cardinality of the attributes
   */
  public int getCardinality() {
    int result;

    result = -1;
    try {
      result = Integer.parseInt(Utils.getOption('C', getGenerator()
        .getOptions()));
    } catch (Exception e) {
      e.printStackTrace();
      result = -1;
    }

    return result;
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String cardinalityTipText() {
    return "The cardinality of the attributes, incl the class attribute.";
  }

  /**
   * returns the default number of arcs
   * 
   * @return the default number of arcs
   */
  protected int defaultNumArcs() {
    return 20;
  }

  /**
   * Sets the number of arcs for the bayesian net
   * 
   * @param value the number of arcs
   */
  public void setNumArcs(int value) {
    int nodes;
    int minArcs;
    int maxArcs;

    nodes = getNumAttributes();
    minArcs = nodes - 1;
    maxArcs = nodes * (nodes - 1) / 2;

    if (value > maxArcs) {
      throw new IllegalArgumentException(
        "Number of arcs should be at most nodes * (nodes - 1) / 2 = " + maxArcs
          + " instead of " + value + " (nodes = numAttributes)!");
    } else if (value < minArcs) {
      throw new IllegalArgumentException(
        "Number of arcs should be at least (nodes - 1) = " + minArcs
          + " instead of " + value + " (nodes = numAttributes)!");
    } else {
      setGeneratorOption("A", "" + value);
    }
  }

  /**
   * Gets the number of arcs for the bayesian net
   * 
   * @return the number of arcs
   */
  public int getNumArcs() {
    int result;

    result = -1;
    try {
      result = Integer.parseInt(Utils.getOption('A', getGenerator()
        .getOptions()));
    } catch (Exception e) {
      e.printStackTrace();
      result = -1;
    }

    return result;
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String numArcsTipText() {
    return "The number of arcs in the bayesian net, at most: n * (n - 1) / 2 and at least: (n - 1); with n = numAttributes";
  }

  /**
   * Sets the number of examples, given by option.
   * 
   * @param numExamples the new number of examples
   */
  @Override
  public void setNumExamples(int numExamples) {
    super.setNumExamples(numExamples);
    setGeneratorOption("M", "" + numExamples);
  }

  /**
   * Gets the number of examples, given by option.
   * 
   * @return the number of examples, given by option
   */
  @Override
  public int getNumExamples() {
    int result;

    result = -1;
    try {
      result = Integer.parseInt(Utils.getOption('M', getGenerator()
        .getOptions()));
    } catch (Exception e) {
      e.printStackTrace();
      result = -1;
    }

    return result;
  }

  /**
   * Gets the random number seed.
   *
   * @return the random number seed.
   */
  @Override
  public int getSeed() {
    int result;

    result = -1;
    try {
      result = Integer.parseInt(Utils.getOption('S', getGenerator()
        .getOptions()));
    } catch (Exception e) {
      e.printStackTrace();
      result = -1;
    }

    return result;
  }

  /**
   * Sets the random number seed.
   *
   * @param newSeed the new random number seed.
   */
  @Override
  public void setSeed(int newSeed) {
    super.setSeed(newSeed);
    setGeneratorOption("S", "" + newSeed);
  }

  /**
   * Return if single mode is set for the given data generator mode depends on
   * option setting and or generator type.
   * 
   * @return single mode flag
   * @throws Exception if mode is not set yet
   */
  @Override
  public boolean getSingleModeFlag() throws Exception {
    return false;
  }

  /**
   * Initializes the format for the dataset produced. Must be called before the
   * generateExample or generateExamples methods are used. Re-initializes the
   * random number generator with the given seed.
   * 
   * @return the format for the dataset
   * @throws Exception if the generating of the format failed
   * @see #getSeed()
   */
  @Override
  public Instances defineDataFormat() throws Exception {
    BayesNetGenerator bng;

    bng = new BayesNetGenerator();
    bng.setOptions(getGenerator().getOptions());
    setGeneratorOption(bng, "M", "1");
    bng.generateRandomNetwork();
    bng.generateInstances();
    bng.m_Instances.renameAttribute(0, "class");
    bng.m_Instances.setRelationName(getRelationNameToUse());

    return bng.m_Instances;
  }

  /**
   * Generates one example of the dataset.
   * 
   * @return the generated example
   * @throws Exception if the format of the dataset is not yet defined
   * @throws Exception if the generator only works with generateExamples which
   *           means in non single mode
   */
  @Override
  public Instance generateExample() throws Exception {
    throw new Exception("Cannot generate examples one-by-one!");
  }

  /**
   * Generates all examples of the dataset. Re-initializes the random number
   * generator with the given seed, before generating instances.
   * 
   * @return the generated dataset
   * @throws Exception if the format of the dataset is not yet defined
   * @throws Exception if the generator only works with generateExample, which
   *           means in single mode
   * @see #getSeed()
   */
  @Override
  public Instances generateExamples() throws Exception {
    getGenerator().setOptions(getGenerator().getOptions());
    getGenerator().generateRandomNetwork();
    getGenerator().generateInstances();
    getGenerator().m_Instances.renameAttribute(0, "class");
    getGenerator().m_Instances.setRelationName(getRelationNameToUse());

    return getGenerator().m_Instances;
  }

  /**
   * Generates a comment string that documentates the data generator. By default
   * this string is added at the beginning of the produced output as ARFF file
   * type, next after the options.
   * 
   * @return string contains info about the generated rules
   */
  @Override
  public String generateStart() {
    return "";
  }

  /**
   * Generates a comment string that documentats the data generator. By default
   * this string is added at the end of theproduces output as ARFF file type.
   * 
   * @return string contains info about the generated rules
   * @throws Exception if the generating of the documentaion fails
   */
  @Override
  public String generateFinished() throws Exception {
    return "";
  }

  /**
   * Returns the revision string.
   * 
   * @return the revision
   */
  @Override
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 11753 $");
  }

  /**
   * Main method for executing this class.
   * 
   * @param args should contain arguments for the data producer:
   */
  public static void main(String[] args) {
    runDataGenerator(new BayesNet(), args);
  }
}