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• LinearNNSearch.java

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weka.core.neighboursearch.LinearNNSearch 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 .
 */

/*
 *    LinearNNSearch.java
 *    Copyright (C) 1999-2012 University of Waikato
 */

package weka.core.neighboursearch;

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

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

/**
 
 * Class implementing the brute force search algorithm for nearest neighbour search.
 * 

 
 * 
 
 * Valid options are: 

 * 
 * 
 -S
 *  Skip identical instances (distances equal to zero).
 * 
 * 
 
 *
 * @author Ashraf M. Kibriya (amk14[at-the-rate]cs[dot]waikato[dot]ac[dot]nz)
 * @version $Revision: 10141 $
 */
public class LinearNNSearch
  extends NearestNeighbourSearch {

  /** for serialization. */
  private static final long serialVersionUID = 1915484723703917241L;

  /** Array holding the distances of the nearest neighbours. It is filled up
   *  both by nearestNeighbour() and kNearestNeighbours(). 
   */
  protected double[] m_Distances;
    
  /** Whether to skip instances from the neighbours that are identical to the query instance. */
  protected boolean m_SkipIdentical = false;

  /**
   * Constructor. Needs setInstances(Instances) 
   * to be called before the class is usable.
   */
  public LinearNNSearch() {
    super();
  }
  
  /**
   * Constructor that uses the supplied set of 
   * instances.
   * 
   * @param insts	the instances to use
   */
  public LinearNNSearch(Instances insts) {
    super(insts);
    m_DistanceFunction.setInstances(insts);
  }
  
  /**
   * Returns a string describing this nearest neighbour search algorithm.
   * 
   * @return 		a description of the algorithm for displaying in the 
   * 			explorer/experimenter gui
   */
  public String globalInfo() {
    return 
        "Class implementing the brute force search algorithm for nearest "
      + "neighbour search.";  
  }
  
  /**
   * Returns an enumeration describing the available options.
   *
   * @return 		an enumeration of all the available options.
   */
  public Enumeration listOptions() {
    Vector result = new Vector();
    
    result.add(new Option(
	"\tSkip identical instances (distances equal to zero).\n",
	"S", 1,"-S"));
    
    result.addAll(Collections.list(super.listOptions()));
    
    return result.elements();
  }
  
  /**
   * Parses a given list of options. 

   *
   
   * Valid options are: 

   * 
   * 
 -S
   *  Skip identical instances (distances equal to zero).
   * 
   * 
   
   *
   * @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 {
    super.setOptions(options);

    setSkipIdentical(Utils.getFlag('S', options));
    
    Utils.checkForRemainingOptions(options);
  }

  /**
   * Gets the current settings.
   *
   * @return 		an array of strings suitable for passing to setOptions()
   */
  public String[] getOptions() {
    Vector	result = new Vector();
    
    Collections.addAll(result, super.getOptions());
    
    if (getSkipIdentical())
      result.add("-S");

    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 skipIdenticalTipText() {
    return "Whether to skip identical instances (with distance 0 to the target)";
  }
  
  /**
   * Sets the property to skip identical instances (with distance zero from 
   * the target) from the set of neighbours returned.
   * 
   * @param skip 	if true, identical intances are skipped
   */
  public void setSkipIdentical(boolean skip) {
    m_SkipIdentical = skip;
  }
  
  /**
   * Gets whether if identical instances are skipped from the neighbourhood.
   * 
   * @return 		true if identical instances are skipped
   */
  public boolean getSkipIdentical() {
    return m_SkipIdentical;
  }

  
  /** 
   * Returns the nearest instance in the current neighbourhood to the supplied
   * instance.
   *  
   * @param target 	The instance to find the nearest neighbour for.
   * @return		the nearest instance
   * @throws Exception 	if the nearest neighbour could not be found.
   */
  public Instance nearestNeighbour(Instance target) throws Exception {
    return (kNearestNeighbours(target, 1)).instance(0);
  }
  
  /**
   * Returns k nearest instances in the current neighbourhood to the supplied
   * instance.
   *  
   * @param target 	The instance to find the k nearest neighbours for.
   * @param kNN		The number of nearest neighbours to find.
   * @return		the k nearest neighbors
   * @throws Exception  if the neighbours could not be found.
   */
  public Instances kNearestNeighbours(Instance target, int kNN) throws Exception {
  
    //debug
    boolean print=false;

    if(m_Stats!=null)
      m_Stats.searchStart();
 
    MyHeap heap = new MyHeap(kNN);
    double distance; int firstkNN=0;
    for(int i=0; i0) {
      h = heap.getKthNearest();
      indices[indices.length-i] = h.index;
      m_Distances[indices.length-i] = h.distance;
      i++;
    }
    while(heap.size()>0) {
      h = heap.get();
      indices[indices.length-i] = h.index;
      m_Distances[indices.length-i] = h.distance;
      i++;
    }
    
    m_DistanceFunction.postProcessDistances(m_Distances);
    
    for(int k=0; k