User:Skilgannon/KDTree

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<code><syntaxhighlight>/*
/*
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** KDTree.java by Julian Kent
 
** KDTree.java by Julian Kent
 
**
 
**
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**
 
**
 
** Licence summary:
 
** Licence summary:
  ** Under this licence you are free to:
+
** Under this licence you are free to:
  **    Share — copy and redistribute the material in any medium or format
+
**    Share — copy and redistribute the material in any medium or format
  **    Adapt — remix, transform, and build upon the material
+
**    Adapt — remix, transform, and build upon the material
  **    The licensor cannot revoke these freedoms as long as you follow the license terms.
+
**    The licensor cannot revoke these freedoms as long as you follow the license terms.
  **  
+
**  
  ** Under the following terms:
+
** Under the following terms:
  **    Attribution  — You must give appropriate credit, provide a link to the license, and indicate  
+
**    Attribution  — You must give appropriate credit, provide a link to the license, and indicate  
  **                    if changes were made. You may do so in any reasonable manner, but not in any  
+
**                    if changes were made. You may do so in any reasonable manner, but not in any  
  **                    way that suggests the licensor endorses you or your use.
+
**                    way that suggests the licensor endorses you or your use.
  **    NonCommercial — You may not use the material for commercial purposes.
+
**    NonCommercial — You may not use the material for commercial purposes.
  **    ShareAlike    — If you remix, transform, or build upon the material, you must distribute your  
+
**    ShareAlike    — If you remix, transform, or build upon the material, you must distribute your  
  **                    contributions under the same license as the original.
+
**                    contributions under the same license as the original.
  **    No additional restrictions  
+
**    No additional restrictions  
  **                  — You may not apply legal terms or technological measures that legally restrict
+
**                  — You may not apply legal terms or technological measures that legally restrict
  **                    others from doing anything the license permits.
+
**                    others from doing anything the license permits.
  **
+
**
 
** See full licencing details here: http://creativecommons.org/licenses/by-nc-sa/3.0/
 
** See full licencing details here: http://creativecommons.org/licenses/by-nc-sa/3.0/
 
**
 
**

Revision as of 12:24, 28 November 2013

/*
** KDTree.java by Julian Kent
**
** Licenced under the  Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License
**
** Licence summary:
** Under this licence you are free to:
**     Share — copy and redistribute the material in any medium or format
**     Adapt — remix, transform, and build upon the material
**     The licensor cannot revoke these freedoms as long as you follow the license terms.
** 
** Under the following terms:
**     Attribution   — You must give appropriate credit, provide a link to the license, and indicate 
**                     if changes were made. You may do so in any reasonable manner, but not in any 
**                     way that suggests the licensor endorses you or your use.
**     NonCommercial — You may not use the material for commercial purposes.
**     ShareAlike    — If you remix, transform, or build upon the material, you must distribute your 
**                     contributions under the same license as the original.
**     No additional restrictions 
**                   — You may not apply legal terms or technological measures that legally restrict
**                     others from doing anything the license permits.
**
** See full licencing details here: http://creativecommons.org/licenses/by-nc-sa/3.0/
**
** For additional licencing rights please contact jkflying@gmail.com
**
*/
 
 
package jk.mega;
 
import java.util.ArrayList;
import java.util.Arrays;
 
public abstract class KDTree<T>{
 
//use a big bucketSize so that we have less node bounds (for more cache hits) and better splits
   private static final int  _bucketSize = 50;
 
   private final int _dimensions;
   private int _nodes;   
   private final Node root;
   private final ArrayList<Node> nodeList = new ArrayList<Node>();
 
   //prevent GC from having to collect _bucketSize*dimensions*8 bytes each time a leaf splits
   private double[] mem_recycle;
 
   //the starting values for bounding boxes, for easy access
   private final double[] bounds_template;
 
   //one big self-expanding array to keep all the node bounding boxes so that they stay in cache
   // node bounds available at:
   //low:  2 * _dimensions * node.index + 2 * dim
   //high: 2 * _dimensions * node.index + 2 * dim + 1
   private final ContiguousDoubleArrayList nodeMinMaxBounds;
 
   private KDTree(int dimensions){
      _dimensions = dimensions;
 
   //initialise this big so that it ends up in 'old' memory
      nodeMinMaxBounds = new ContiguousDoubleArrayList(512 * 1024 / 8 + 2*_dimensions);
      mem_recycle = new double[_bucketSize*dimensions];
 
      bounds_template = new double[2*_dimensions];
      Arrays.fill(bounds_template,Double.NEGATIVE_INFINITY);
      for(int i = 0, max = 2*_dimensions; i < max; i+=2)
         bounds_template[i] = Double.POSITIVE_INFINITY;
 
   //and.... start!
      root = new Node();
   }
   public int nodes(){
      return _nodes;
   }
   public int size(){
      return root.entries;
   }
   public int addPoint(double[] location, T payload){
 
      Node addNode = root;
   //Do a Depth First Search to find the Node where 'location' should be stored
      while(addNode.pointLocations == null){
         addNode.expandBounds(location);
         if(location[addNode.splitDim] < addNode.splitVal)
            addNode = nodeList.get(addNode.lessIndex);
         else
            addNode = nodeList.get(addNode.moreIndex);
      }
      addNode.expandBounds(location);
 
      int nodeSize = addNode.add(location,payload);
 
      if(nodeSize % _bucketSize == 0)
      //try splitting again once every time the node passes a _bucketSize multiple
      //in case it is full of points of the same location and won't split
         addNode.split();
 
      return root.entries;
   }
 
 
   public ArrayList<SearchResult<T>> nearestNeighbours(double[] searchLocation, int K){
      IntStack stack = new IntStack();
      PrioQueue<T> results = new PrioQueue<T>(K,true);
 
      stack.push(root.index);
 
      int added = 0;
 
      while(stack.size() > 0 ){
         int nodeIndex = stack.pop();
         if(added < K || results.peekPrio() > pointRectDist(nodeIndex,searchLocation)){
            Node node = nodeList.get(nodeIndex);
            if(node.pointLocations == null)
               node.search(searchLocation,stack);
            else
               added += node.search(searchLocation,results);
         }
      }
 
      ArrayList<SearchResult<T>> returnResults = new ArrayList<SearchResult<T>>(K);
      double[] priorities = results.priorities;
      Object[] elements = results.elements;
      for(int i = 0; i < K; i++){//forward (closest first)
         SearchResult s = new SearchResult(priorities[i],(T)elements[i]);
         returnResults.add(s);
      }
      return returnResults;
   }
 
   public ArrayList<T> ballSearch(double[] searchLocation, double radius){
      IntStack stack = new IntStack();
      ArrayList<T> results = new ArrayList<T>();
 
      stack.push(root.index);
 
      while(stack.size() > 0 ){
         int nodeIndex = stack.pop();
         if(radius > pointRectDist(nodeIndex, searchLocation)){
            Node node = nodeList.get(nodeIndex);
            if(node.pointLocations == null)
               stack.push(node.moreIndex).push(node.lessIndex);
            else
               node.searchBall(searchLocation, radius, results);
         }
      }
      return results;
   }
   public ArrayList<T> rectSearch(double[] mins, double[] maxs){
      IntStack stack = new IntStack();
      ArrayList<T> results = new ArrayList<T>();
 
      stack.push(root.index);
 
      while(stack.size() > 0 ){
         int nodeIndex = stack.pop();
         if(overlaps(mins,maxs,nodeIndex)){
            Node node = nodeList.get(nodeIndex);
            if(node.pointLocations == null)
               stack.push(node.moreIndex).push(node.lessIndex);
            else
               node.searchRect(mins, maxs, results);
         }
      }
      return results;
 
   }
 
 
   abstract double pointRectDist(int offset, final double[] location);
   abstract double pointDist(double[] arr, double[] location, int index);
 
   boolean contains(double[] arr, double[] mins, double[] maxs, int index){
 
      int offset = (index+1)*mins.length;
 
      for(int i = mins.length; i-- > 0 ;){
         double d = arr[--offset];
         if(mins[i] > d | d > maxs[i])
            return false;
      }
      return true;
   }
 
   boolean overlaps(double[] mins, double[] maxs, int offset){
      offset *= (2*maxs.length);
      final double[] array = nodeMinMaxBounds.array;
      for(int i = 0; i < maxs.length; i++,offset += 2){
         double bmin = array[offset], bmax = array[offset+1];
         if(mins[i] > bmax | maxs[i] < bmin)
            return false;
      }
 
      return true;
   }
 
 
   public static class Euclidean<T> extends KDTree<T>{
      public Euclidean(int dims){
         super(dims);
      }
      double pointRectDist(int offset, final double[] location){
         offset *= (2*super._dimensions);
         double distance=0;
         final double[] array = super.nodeMinMaxBounds.array;
         for(int i = 0; i < location.length; i++,offset += 2){
 
            double diff = 0;
            double bv = array[offset];
            double lv = location[i];
            if(bv > lv)
               diff = bv-lv;
            else{
               bv=array[offset+1];
               if(lv>bv)
                  diff = lv-bv;
            }
            distance += sqr(diff);
         }
         return distance;
      }
      double pointDist(double[] arr, double[] location, int index){
         double distance = 0;
         int offset = (index+1)*super._dimensions;
 
         for(int i = super._dimensions; i-- > 0 ;){
            distance += sqr(arr[--offset] - location[i]);
         }
         return distance;
      }
 
   }
   public static class Manhattan<T> extends KDTree<T>{
      public Manhattan(int dims){
         super(dims);
      }
      double pointRectDist(int offset, final double[] location){
         offset *= (2*super._dimensions);
         double distance=0;
         final double[] array = super.nodeMinMaxBounds.array;
         for(int i = 0; i < location.length; i++,offset += 2){
 
            double diff = 0;
            double bv = array[offset];
            double lv = location[i];
            if(bv > lv)
               diff = bv-lv;
            else{
               bv=array[offset+1];
               if(lv>bv)
                  diff = lv-bv;
            }
            distance += (diff);
         }
         return distance;
      }
      double pointDist(double[] arr, double[] location, int index){
         double distance = 0;
         int offset = (index+1)*super._dimensions;
 
         for(int i = super._dimensions; i-- > 0 ;){
            distance += Math.abs(arr[--offset] - location[i]);
         }
         return distance;
      }
   }
 
     //NB! This Priority Queue keeps things with the LOWEST priority. 
//If you want highest priority items kept, negate your values
   private static class PrioQueue<S>{
 
      Object[] elements;
      double[] priorities;
      private double minPrio;
      private int size;
 
      PrioQueue(int size, boolean prefill){
         elements = new Object[size];
         priorities = new double[size];
         Arrays.fill(priorities,Double.POSITIVE_INFINITY);
         if(prefill){
            minPrio = Double.POSITIVE_INFINITY;
            this.size = size;
         }
      }
       //uses O(log(n)) comparisons and one big shift of size O(N)
       //and is MUCH simpler than a heap --> faster on small sets, faster JIT
 
      void addNoGrow(S value, double priority){
         int index = searchFor(priority);
         int nextIndex = index + 1;
         int length = size - index - 1;
         System.arraycopy(elements,index,elements,nextIndex,length);
         System.arraycopy(priorities,index,priorities,nextIndex,length);
         elements[index]=value;
         priorities[index]=priority;
 
         minPrio = priorities[size-1];
      }
 
      int searchFor(double priority){
         int i = size-1;
         int j = 0;   
         while(i>=j){
            int index = (i+j)>>>1;
            if( priorities[index] < priority)
               j = index+1;
            else 
               i = index-1;
         }
         return j;
      }
      double peekPrio(){
         return minPrio;
      }
   }
 
   public static class SearchResult<S>{
      public double distance;
      public S payload;
      SearchResult(double dist, S load){
         distance = dist;
         payload = load;
      }
   }
 
   private class Node {
 
   //for accessing bounding box data 
   // - if trees weren't so unbalanced might be better to use an implicit heap?
      int index;
 
   //keep track of size of subtree
      int entries;
 
   //leaf
      ContiguousDoubleArrayList pointLocations ;
      ArrayList<T> pointPayloads = new ArrayList<T>(_bucketSize);
 
   //stem
      //Node less, more;
      int lessIndex, moreIndex;
      int splitDim;
      double splitVal;
 
      Node(){
         this(new double[_bucketSize*_dimensions]);
      }
      Node(double[] pointMemory){
         pointLocations = new ContiguousDoubleArrayList(pointMemory);
         index = _nodes++;
         nodeList.add(this);
         nodeMinMaxBounds.add(bounds_template);
      }
 
 
      //returns number of points added to results
      void search(double[] searchLocation, IntStack stack){
         if(searchLocation[splitDim] < splitVal)
            stack.push(moreIndex).push(lessIndex);//less will be popped first
         else
            stack.push(lessIndex).push(moreIndex);//more will be popped first
      }
      int search(double[] searchLocation, PrioQueue<T> results){
         int updated = 0;
         for(int j = entries; j-- > 0;){
            double distance = pointDist(pointLocations.array,searchLocation,j);
            if(results.peekPrio() > distance){
               updated++;
               results.addNoGrow(pointPayloads.get(j),distance);
            }
         }
         return updated;
      }
 
      void searchBall(double[] searchLocation, double radius, ArrayList<T> results){
 
         for(int j = entries; j-- > 0;){
            double distance = pointDist(pointLocations.array,searchLocation,j);
            if(radius >= distance){
               results.add(pointPayloads.get(j));
            }
         }
      }
 
      void searchRect(double[] mins, double[] maxs, ArrayList<T> results){
 
         for(int j = entries; j-- > 0;)
            if(contains(pointLocations.array,mins,maxs,j))
               results.add(pointPayloads.get(j));
 
      }   
 
      void expandBounds(double[] location){
         entries++;
         int mio = index*2*_dimensions;
         for(int i = 0; i < _dimensions;i++){
            nodeMinMaxBounds.array[mio] = Math.min(nodeMinMaxBounds.array[mio++],location[i]);
            nodeMinMaxBounds.array[mio] = Math.max(nodeMinMaxBounds.array[mio++],location[i]);
         }
      }
 
      int add(double[] location, T load){
         pointLocations.add(location);
         pointPayloads.add(load);
         return entries;
      }
      void split(){
         int offset = index*2*_dimensions;
 
         double diff = 0;
         for(int i = 0; i < _dimensions; i++){
            double min = nodeMinMaxBounds.array[offset];
            double max = nodeMinMaxBounds.array[offset+1];
            if(max-min>diff){
               double mean = 0;
               for(int j = 0; j < entries; j++)
                  mean += pointLocations.array[i+_dimensions*j];
 
               mean = mean/entries;
               double varianceSum = 0;
 
               for(int j = 0; j < entries; j++)
                  varianceSum += sqr(mean-pointLocations.array[i+_dimensions*j]);
 
               if(varianceSum>diff*entries){
                  diff = varianceSum/entries;
                  splitVal = mean;
 
                  splitDim = i;
               }
            }
            offset += 2;
         }
 
         //kill all the nasties
         if(splitVal == Double.POSITIVE_INFINITY)
            splitVal = Double.MAX_VALUE;
         else if(splitVal == Double.NEGATIVE_INFINITY)
            splitVal = Double.MIN_VALUE;
         else if(splitVal == nodeMinMaxBounds.array[index*2*_dimensions + 2*splitDim + 1])
            splitVal = nodeMinMaxBounds.array[index*2*_dimensions + 2*splitDim];   
 
         Node less = new Node(mem_recycle);//recycle that memory!
         Node more = new Node();
         lessIndex = less.index;
         moreIndex = more.index;
 
         //reduce garbage by factor of _bucketSize by recycling this array
         double[] pointLocation = new double[_dimensions];
         for(int i = 0; i < entries; i++){
            System.arraycopy(pointLocations.array,i*_dimensions,pointLocation,0,_dimensions);
            T load = pointPayloads.get(i);
 
            if(pointLocation[splitDim] < splitVal){
               less.expandBounds(pointLocation);
               less.add(pointLocation,load);
            }
            else{
               more.expandBounds(pointLocation);   
               more.add(pointLocation,load);
            }
         }
         if(less.entries*more.entries == 0){
         //one of them was 0, so the split was worthless. throw it away.
            _nodes -= 2;//recall that bounds memory
            nodeList.remove(moreIndex);
            nodeList.remove(lessIndex);
         }
         else{
 
         //we won't be needing that now, so keep it for the next split to reduce garbage
            mem_recycle = pointLocations.array;
 
            pointLocations = null;
 
            pointPayloads.clear();
            pointPayloads = null;
         }
      }
 
   }
 
 
   private static class ContiguousDoubleArrayList{
      double[] array;
      int size;
      ContiguousDoubleArrayList(){this(300);}
      ContiguousDoubleArrayList(int size){this(new double[size]);}
      ContiguousDoubleArrayList(double[] data){array = data;}
 
      ContiguousDoubleArrayList add(double[] da){
         if(size + da.length > array.length)
            array = Arrays.copyOf(array,(array.length+da.length)*2);
 
         System.arraycopy(da,0,array,size,da.length);
         size += da.length;
         return this;
      }
   }
   private static class IntStack{
      int[] array;
      int size;
      IntStack(){this(64);}
      IntStack(int size){this(new int[size]);}
      IntStack(int[] data){array = data;}
 
      IntStack push(int i){
         if(size>= array.length)
            array = Arrays.copyOf(array,(array.length+1)*2);
 
         array[size++] = i;
         return this;
      }
      int pop(){
         return array[--size];
      }
      int size(){
         return size;
      }
   }
 
   static final double sqr(double d){
      return d*d;}
 
}
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