source: branches/MetisMQI/src/main/java/weka/classifiers/mi/SimpleMI.java

/*
 *    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 2 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, write to the Free Software
 *    Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 */

/*
 * SimpleMI.java
 * Copyright (C) 2005 University of Waikato, Hamilton, New Zealand
 */

package weka.classifiers.mi;

import weka.classifiers.SingleClassifierEnhancer;
import weka.core.Attribute;
import weka.core.Capabilities;
import weka.core.Instance;
import weka.core.DenseInstance;
import weka.core.Instances;
import weka.core.MultiInstanceCapabilitiesHandler;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionUtils;
import weka.core.SelectedTag;
import weka.core.Tag;
import weka.core.Utils;
import weka.core.Capabilities.Capability;

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

/**
 <!-- globalinfo-start -->
 * Reduces MI data into mono-instance data.
 * <p/>
 <!-- globalinfo-end -->
 *
 <!-- options-start -->
 * Valid options are: <p/>
 * 
 * <pre> -M [1|2|3]
 *  The method used in transformation:
 *  1.arithmatic average; 2.geometric centor;
 *  3.using minimax combined features of a bag (default: 1)
 * 
 *  Method 3:
 *  Define s to be the vector of the coordinate-wise maxima
 *  and minima of X, ie., 
 *  s(X)=(minx1, ..., minxm, maxx1, ...,maxxm), transform
 *  the exemplars into mono-instance which contains attributes
 *  s(X)</pre>
 * 
 * <pre> -D
 *  If set, classifier is run in debug mode and
 *  may output additional info to the console</pre>
 * 
 * <pre> -W
 *  Full name of base classifier.
 *  (default: weka.classifiers.rules.ZeroR)</pre>
 * 
 * <pre> 
 * Options specific to classifier weka.classifiers.rules.ZeroR:
 * </pre>
 * 
 * <pre> -D
 *  If set, classifier is run in debug mode and
 *  may output additional info to the console</pre>
 * 
 <!-- options-end -->
 *
 * @author Eibe Frank (eibe@cs.waikato.ac.nz)
 * @author Xin Xu (xx5@cs.waikato.ac.nz)
 * @author Lin Dong (ld21@cs.waikato.ac.nz)
 * @version $Revision: 5987 $ 
 */
public class SimpleMI 
  extends SingleClassifierEnhancer
  implements OptionHandler, MultiInstanceCapabilitiesHandler {  

  /** for serialization */
  static final long serialVersionUID = 9137795893666592662L;
  
  /** arithmetic average */
  public static final int TRANSFORMMETHOD_ARITHMETIC = 1;
  /** geometric average */
  public static final int TRANSFORMMETHOD_GEOMETRIC = 2;
  /** using minimax combined features of a bag */
  public static final int TRANSFORMMETHOD_MINIMAX = 3;
  /** the transformation methods */
  public static final Tag[] TAGS_TRANSFORMMETHOD = {
    new Tag(TRANSFORMMETHOD_ARITHMETIC, "arithmetic average"),
    new Tag(TRANSFORMMETHOD_GEOMETRIC, "geometric average"),
    new Tag(TRANSFORMMETHOD_MINIMAX, "using minimax combined features of a bag")
  };

  /** the method used in transformation */
  protected int m_TransformMethod = TRANSFORMMETHOD_ARITHMETIC;

  /**
   * Returns a string describing this filter
   *
   * @return a description of the filter suitable for
   * displaying in the explorer/experimenter gui
   */
  public String globalInfo() {
    return "Reduces MI data into mono-instance data.";
  }

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

    result.addElement(new Option(
          "\tThe method used in transformation:\n"
          + "\t1.arithmatic average; 2.geometric centor;\n"
          + "\t3.using minimax combined features of a bag (default: 1)\n\n"
          + "\tMethod 3:\n"
          + "\tDefine s to be the vector of the coordinate-wise maxima\n"
          + "\tand minima of X, ie., \n"
          + "\ts(X)=(minx1, ..., minxm, maxx1, ...,maxxm), transform\n"
          + "\tthe exemplars into mono-instance which contains attributes\n"
          + "\ts(X)",
          "M", 1, "-M [1|2|3]"));

    Enumeration enu = super.listOptions();
    while (enu.hasMoreElements()) {
      result.addElement(enu.nextElement());
    }

    return result.elements();
  }


  /**
   * Parses a given list of options. <p/>
   *
   <!-- options-start -->
   * Valid options are: <p/>
   * 
   * <pre> -M [1|2|3]
   *  The method used in transformation:
   *  1.arithmatic average; 2.geometric centor;
   *  3.using minimax combined features of a bag (default: 1)
   * 
   *  Method 3:
   *  Define s to be the vector of the coordinate-wise maxima
   *  and minima of X, ie., 
   *  s(X)=(minx1, ..., minxm, maxx1, ...,maxxm), transform
   *  the exemplars into mono-instance which contains attributes
   *  s(X)</pre>
   * 
   * <pre> -D
   *  If set, classifier is run in debug mode and
   *  may output additional info to the console</pre>
   * 
   * <pre> -W
   *  Full name of base classifier.
   *  (default: weka.classifiers.rules.ZeroR)</pre>
   * 
   * <pre> 
   * Options specific to classifier weka.classifiers.rules.ZeroR:
   * </pre>
   * 
   * <pre> -D
   *  If set, classifier is run in debug mode and
   *  may output additional info to the console</pre>
   * 
   <!-- options-end -->
   *
   * @param options the list of options as an array of strings
   * @throws Exception if an option is not supported
   */
  public void setOptions(String[] options) throws Exception {   

    setDebug(Utils.getFlag('D', options));

    String methodString = Utils.getOption('M', options);
    if (methodString.length() != 0) {
      setTransformMethod(
          new SelectedTag(
            Integer.parseInt(methodString), TAGS_TRANSFORMMETHOD));
    } else {
      setTransformMethod(
          new SelectedTag(
            TRANSFORMMETHOD_ARITHMETIC, TAGS_TRANSFORMMETHOD));
    }   

    super.setOptions(options);
  }

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

    result.add("-M");
    result.add("" + m_TransformMethod);

    options = super.getOptions();
    for (i = 0; i < options.length; i++)
      result.add(options[i]);

    return (String[]) 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 transformMethodTipText() {
    return "The method used in transformation.";
  }

  /**
   * Set the method used in transformation. 
   *
   * @param newMethod the index of method to use.
   */
  public void setTransformMethod(SelectedTag newMethod) {
    if (newMethod.getTags() == TAGS_TRANSFORMMETHOD)
      m_TransformMethod = newMethod.getSelectedTag().getID();
  }

  /**
   * Get the method used in transformation.
   *
   * @return the index of method used.
   */
  public SelectedTag getTransformMethod() {
    return new SelectedTag(m_TransformMethod, TAGS_TRANSFORMMETHOD);
  }

  /** 
   * Implements MITransform (3 type of transformation) 1.arithmatic average;
   * 2.geometric centor; 3.merge minima and maxima attribute value together
   *
   * @param train the multi-instance dataset (with relational attribute)  
   * @return the transformed dataset with each bag contain mono-instance
   * (without relational attribute) so that any classifier not for MI dataset
   * can be applied on it.
   * @throws Exception if the transformation fails
   */
  public Instances transform(Instances train) throws Exception{

    Attribute classAttribute = (Attribute) train.classAttribute().copy();
    Attribute bagLabel = (Attribute) train.attribute(0);
    double labelValue;

    Instances newData = train.attribute(1).relation().stringFreeStructure();

    //insert a bag label attribute at the begining
    newData.insertAttributeAt(bagLabel, 0);

    //insert a class attribute at the end
    newData.insertAttributeAt(classAttribute, newData.numAttributes());
    newData.setClassIndex(newData.numAttributes()-1);

    Instances mini_data = newData.stringFreeStructure();
    Instances max_data = newData.stringFreeStructure();

    Instance newInst = new DenseInstance(newData.numAttributes()); 
    Instance mini_Inst = new DenseInstance(mini_data.numAttributes());
    Instance max_Inst = new DenseInstance(max_data.numAttributes());
    newInst.setDataset(newData);
    mini_Inst.setDataset(mini_data);
    max_Inst.setDataset(max_data);

    double N= train.numInstances( );//number of bags   
    for(int i=0; i<N; i++){     
      int attIdx =1;
      Instance bag = train.instance(i); //retrieve the bag instance
      labelValue= bag.value(0);
      if (m_TransformMethod != TRANSFORMMETHOD_MINIMAX)     
        newInst.setValue(0, labelValue);
      else {
        mini_Inst.setValue(0, labelValue);
        max_Inst.setValue(0, labelValue);
      }

      Instances data = bag.relationalValue(1); // retrieve relational value for each bag 
      for(int j=0; j<data.numAttributes( ); j++){       
        double value;
        if(m_TransformMethod == TRANSFORMMETHOD_ARITHMETIC){
          value = data.meanOrMode(j); 
          newInst.setValue(attIdx++, value);
        }
        else if (m_TransformMethod == TRANSFORMMETHOD_GEOMETRIC){
          double[] minimax = minimax(data, j);
          value = (minimax[0]+minimax[1])/2.0;
          newInst.setValue(attIdx++, value);
        }
        else {  //m_TransformMethod == TRANSFORMMETHOD_MINIMAX
          double[] minimax = minimax(data, j);
          mini_Inst.setValue(attIdx, minimax[0]);//minima value
          max_Inst.setValue(attIdx, minimax[1]);//maxima value
          attIdx++;
        }
      }

      if (m_TransformMethod == TRANSFORMMETHOD_MINIMAX) {
        if (!bag.classIsMissing())
          max_Inst.setClassValue(bag.classValue()); //set class value
        mini_data.add(mini_Inst); 
        max_data.add(max_Inst);
      }
      else{
        if (!bag.classIsMissing())
          newInst.setClassValue(bag.classValue()); //set class value
        newData.add(newInst);           
      }  
    }

    if (m_TransformMethod == TRANSFORMMETHOD_MINIMAX) {
      mini_data.setClassIndex(-1);
      mini_data.deleteAttributeAt(mini_data.numAttributes()-1); //delete class attribute for the minima data
      max_data.deleteAttributeAt(0); // delete the bag label attribute for the maxima data

      newData = Instances.mergeInstances(mini_data, max_data); //merge minima and maxima data
      newData.setClassIndex(newData.numAttributes()-1);

    }   

    return newData;
  }

  /**
   * Get the minimal and maximal value of a certain attribute in a certain data
   *
   * @param data the data
   * @param attIndex the index of the attribute
   * @return the double array containing in entry 0 for min and 1 for max.
   */
  public static double[] minimax(Instances data, int attIndex){
    double[] rt = {Double.POSITIVE_INFINITY, Double.NEGATIVE_INFINITY};
    for(int i=0; i<data.numInstances(); i++){
      double val = data.instance(i).value(attIndex);
      if(val > rt[1])
        rt[1] = val;
      if(val < rt[0])
        rt[0] = val;
    }

    for(int j=0; j<2; j++)
      if(Double.isInfinite(rt[j]))
        rt[j] = Double.NaN;

    return rt;
  }

  /**
   * Returns default capabilities of the classifier.
   *
   * @return      the capabilities of this classifier
   */
  public Capabilities getCapabilities() {
    Capabilities result = super.getCapabilities();

    // attributes
    result.enable(Capability.NOMINAL_ATTRIBUTES);
    result.enable(Capability.RELATIONAL_ATTRIBUTES);
    result.enable(Capability.MISSING_VALUES);

    // class
    result.disableAllClasses();
    result.disableAllClassDependencies();
    if (super.getCapabilities().handles(Capability.NOMINAL_CLASS))
      result.enable(Capability.NOMINAL_CLASS);
    if (super.getCapabilities().handles(Capability.BINARY_CLASS))
      result.enable(Capability.BINARY_CLASS);
    result.enable(Capability.MISSING_CLASS_VALUES);
    
    // other
    result.enable(Capability.ONLY_MULTIINSTANCE);
    
    return result;
  }

  /**
   * Returns the capabilities of this multi-instance classifier for the
   * relational data.
   *
   * @return            the capabilities of this object
   * @see               Capabilities
   */
  public Capabilities getMultiInstanceCapabilities() {
    Capabilities result = super.getCapabilities();
    
    // attributes
    result.enable(Capability.NOMINAL_ATTRIBUTES);
    result.enable(Capability.NUMERIC_ATTRIBUTES);
    result.enable(Capability.DATE_ATTRIBUTES);
    result.enable(Capability.MISSING_VALUES);

    // class
    result.disableAllClasses();
    result.enable(Capability.NO_CLASS);
    
    return result;
  }

  /**
   * Builds the classifier
   *
   * @param train the training data to be used for generating the
   * boosted classifier.
   * @throws Exception if the classifier could not be built successfully
   */
  public void buildClassifier(Instances train) throws Exception {

    // can classifier handle the data?
    getCapabilities().testWithFail(train);

    // remove instances with missing class
    train = new Instances(train);
    train.deleteWithMissingClass();
    
    if (m_Classifier == null) {
      throw new Exception("A base classifier has not been specified!");
    }

    if (getDebug())
      System.out.println("Start training ...");
    Instances data = transform(train); 

    data.deleteAttributeAt(0); // delete the bagID attribute
    m_Classifier.buildClassifier(data);

    if (getDebug())
      System.out.println("Finish building model");
  }             

  /**
   * Computes the distribution for a given exemplar
   *
   * @param newBag the exemplar for which distribution is computed
   * @return the distribution
   * @throws Exception if the distribution can't be computed successfully
   */
  public double[] distributionForInstance(Instance newBag)
    throws Exception {

    double [] distribution = new double[2];
    Instances test = new Instances (newBag.dataset(), 0);       
    test.add(newBag);   

    test = transform(test);
    test.deleteAttributeAt(0);
    Instance newInst=test.firstInstance();

    distribution = m_Classifier.distributionForInstance(newInst);

    return distribution;           
  }

  /**
   * Gets a string describing the classifier.
   *
   * @return a string describing the classifer built.
   */
  public String toString() {    
    return "SimpleMI with base classifier: \n"+m_Classifier.toString();
  }
  
  /**
   * Returns the revision string.
   * 
   * @return            the revision
   */
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 5987 $");
  }

  /**
   * Main method for testing this class.
   *
   * @param argv should contain the command line arguments to the
   * scheme (see Evaluation)
   */
  public static void main(String[] argv) {
    runClassifier(new SimpleMI(), argv);
  }
}