kdtree2.cpp

kd tree java implementation 2

//
// (c) Matthew B. Kennel, Institute for Nonlinear Science, UCSD (2004)
//
// Licensed under the Academic Free License version 1.1 found in file LICENSE
// with additional provisions in that same file.


#include "kdtree2.hpp"

#include <algorithm> 
#include <iostream>

// utility

inline float squared(const float x) {
  return(x*x);
}

inline void swap(int& a, int&b) {
  int tmp;
  tmp = a;
  a = b;
  b = tmp; 
}

inline void swap(float& a, float&b) {
  float tmp;
  tmp = a;
  a = b;
  b = tmp; 
}


//
//       KDTREE2_RESULT implementation
// 

inline bool operator<(const kdtree2_result& e1, const kdtree2_result& e2) {
  return (e1.dis < e2.dis);
}

//
//       KDTREE2_RESULT_VECTOR implementation
// 
float kdtree2_result_vector::max_value() {
  return( (*begin()).dis ); // very first element
}

void kdtree2_result_vector::push_element_and_heapify(kdtree2_result& e) {
  push_back(e); // what a vector does.
  push_heap( begin(), end() ); // and now heapify it, with the new elt.
}
float kdtree2_result_vector::replace_maxpri_elt_return_new_maxpri(kdtree2_result& e) {
  // remove the maximum priority element on the queue and replace it
  // with 'e', and return its priority.
  //
  // here, it means replacing the first element [0] with e, and re heapifying.
  
  pop_heap( begin(), end() );
  pop_back();
  push_back(e); // insert new
  push_heap(begin(), end() );  // and heapify. 
  return( (*this)[0].dis );
}

//
//        KDTREE2 implementation
//

// constructor
kdtree2::kdtree2(kdtree2_array& data_in,bool rearrange_in,int dim_in)
  : the_data(data_in),
    N  ( data_in.shape()[0] ),
    dim( data_in.shape()[1] ),
    sort_results(false),
    rearrange(rearrange_in), 
    root(NULL),
    data(NULL),
    ind(N)
{
  //
  // initialize the constant references using this unusual C++
  // feature.
  //
  if (dim_in > 0) 
    dim = dim_in;
  
  build_tree();

  if (rearrange) {
    // if we have a rearranged tree.
    // allocate the memory for it. 
    printf("rearranging\n"); 
    rearranged_data.resize( extents[N][dim] );
    
    // permute the data for it.
    for (int i=0; i<N; i++) {
      for (int j=0; j<dim; j++) {
	rearranged_data[i][j] = the_data[ind[i]][j];
	// wouldn't F90 be nice here? 
      }
    }
    data = &rearranged_data;
  } else {
    data = &the_data;
  }
}


// destructor
kdtree2::~kdtree2() {
  delete root;
}

// building routines
void kdtree2::build_tree() {
  for (int i=0; i<N; i++) ind[i] = i; 
  root = build_tree_for_range(0,N-1,NULL); 
}

kdtree2_node* kdtree2::build_tree_for_range(int l, int u, kdtree2_node* parent) {
  // recursive function to build 
  kdtree2_node* node = new kdtree2_node(dim);
  // the newly created node. 

  if (u<l) {
    return(NULL); // no data in this node. 
  }
      

  if ((u-l) <= bucketsize) {
    // create a terminal node. 

    // always compute true bounding box for terminal node. 
    for (int i=0;i<dim;i++) {
      spread_in_coordinate(i,l,u,node->box[i]);
    }
    
    node->cut_dim = 0; 
    node->cut_val = 0.0;
    node->l = l;
    node->u = u;
    node->left = node->right = NULL;
    

  } else {
    //
    // Compute an APPROXIMATE bounding box for this node.
    // if parent == NULL, then this is the root node, and 
    // we compute for all dimensions.
    // Otherwise, we copy the bounding box from the parent for
    // all coordinates except for the parent's cut dimension.  
    // That, we recompute ourself.
    //
    int c = -1;
    float maxspread = 0.0;
    int m; 

    for (int i=0;i<dim;i++) {
      if ((parent == NULL) || (parent->cut_dim == i)) {
	spread_in_coordinate(i,l,u,node->box[i]);
      } else {
	node->box[i] = parent->box[i];
      }
      float spread = node->box[i].upper - node->box[i].lower; 
      if (spread>maxspread) {
	maxspread = spread;
	c=i; 
      }
    }

    // 
    // now, c is the identity of which coordinate has the greatest spread
    //

    if (false) {
      m = (l+u)/2;
      select_on_coordinate(c,m,l,u);  
    } else {
      float sum; 
      float average;

      if (true) {
	sum = 0.0;
	for (int k=l; k <= u; k++) {
	  sum += the_data[ind[k]][c];
	}
	average = sum / static_cast<float> (u-l+1);
      } else {
	// average of top and bottom nodes.
	average = (node->box[c].upper + node->box[c].lower)*0.5; 
      }
	
      m = select_on_coordinate_value(c,average,l,u);
    }


    // move the indices around to cut on dim 'c'.
    node->cut_dim=c;
    node->l = l;
    node->u = u;

    node->left = build_tree_for_range(l,m,node);
    node->right = build_tree_for_range(m+1,u,node);

    if (node->right == NULL) {
      for (int i=0; i<dim; i++) 
	node->box[i] = node->left->box[i]; 
       node->cut_val = node->left->box[c].upper;
       node->cut_val_left = node->cut_val_right = node->cut_val;
    } else if (node->left == NULL) {
      for (int i=0; i<dim; i++) 
	node->box[i] = node->right->box[i]; 
      node->cut_val =  node->right->box[c].upper;
      node->cut_val_left = node->cut_val_right = node->cut_val;
    } else {
      node->cut_val_right = node->right->box[c].lower;
      node->cut_val_left  = node->left->box[c].upper;
      node->cut_val = (node->cut_val_left + node->cut_val_right) / 2.0; 
      //
      // now recompute true bounding box as union of subtree boxes.
      // This is now faster having built the tree, being logarithmic in
      // N, not linear as would be from naive method.
      //
      for (int i=0; i<dim; i++) {
	node->box[i].upper = max(node->left->box[i].upper,
				 node->right->box[i].upper);
	
	node->box[i].lower = min(node->left->box[i].lower,
				 node->right->box[i].lower);
      }
    }
  }
  return(node);
}



void kdtree2:: spread_in_coordinate(int c, int l, int u, interval& interv)
{
  // return the minimum and maximum of the indexed data between l and u in
  // smin_out and smax_out.
  float smin, smax;
  float lmin, lmax;
  int i; 

  smin = the_data[ind[l]][c];
  smax = smin;
  

  // process two at a time.
  for (i=l+2; i<= u; i+=2) {
    lmin = the_data[ind[i-1]] [c];
    lmax = the_data[ind[i]  ] [c];

    if (lmin > lmax) {
      swap(lmin,lmax); 
      //      float t = lmin;
      //      lmin = lmax;
      //      lmax = t;
    }

    if (smin > lmin) smin = lmin;
    if (smax <lmax) smax = lmax;
  }
  // is there one more element? 
  if (i == u+1) {
    float last = the_data[ind[u]] [c];
    if (smin>last) smin = last;
    if (smax<last) smax = last;
  }
  interv.lower = smin;
  interv.upper = smax;
  //  printf("Spread in coordinate %d=[%f,%f]\n",c,smin,smax);
}


void kdtree2::select_on_coordinate(int c, int k, int l, int u) {
  //
  //  Move indices in ind[l..u] so that the elements in [l .. k] 
  //  are less than the [k+1..u] elmeents, viewed across dimension 'c'. 
  // 
  while (l < u) {
    int t = ind[l];
    int m = l;

    for (int i=l+1; i<=u; i++) {
      if ( the_data[ ind[i] ] [c] < the_data[t][c]) {
	m++;
	swap(ind[i],ind[m]); 
      }
    } // for i 
    swap(ind[l],ind[m]);

    if (m <= k) l = m+1;
    if (m >= k) u = m-1;
  } // while loop
}

int kdtree2::select_on_coordinate_value(int c, float alpha, int l, int u) {
  //
  //  Move indices in ind[l..u] so that the elements in [l .. return]
  //  are <= alpha, and hence are less than the [return+1..u]
  //  elmeents, viewed across dimension 'c'.
  // 
  int lb = l, ub = u;

  while (lb < ub) {
    if (the_data[ind[lb]][c] <= alpha) {
      lb++; // good where it is.
    } else {
      swap(ind[lb],ind[ub]); 
      ub--;
    }
  }

  // here ub=lb
  if (the_data[ind[lb]][c] <= alpha)
    return(lb);
  else
    return(lb-1);
  
}


// void kdtree2::dump_data() {
//   int upper1, upper2;
  
//   upper1 = N;
//   upper2 = dim;

//   printf("Rearrange=%d\n",rearrange);
//   printf("N=%d, dim=%d\n", upper1, upper2);
//   for (int i=0; i<upper1; i++) {
//     printf("the_data[%d][*]=",i); 
//     for (int j=0; j<upper2; j++)
//       printf("%f,",the_data[i][j]); 
//     printf("\n"); 
//   }
//   for (int i=0; i<upper1; i++)
//     printf("Indexes[%d]=%d\n",i,ind[i]); 
//   for (int i=0; i<upper1; i++) {
//     printf("data[%d][*]=",i); 
//     for (int j=0; j<upper2; j++)
//       printf("%f,",(*data)[i][j]); 
//     printf("\n"); 
//   }
// }



//
// search record substructure
//
// one of these is created for each search.
// this holds useful information  to be used
// during the search



static const float infinity = 1.0e38;

class searchrecord {

private:
  friend class kdtree2;
  friend class kdtree2_node;

  vector<float>& qv; 
  int dim;
  bool rearrange;
  unsigned int nn; // , nfound;
  float ballsize;
  int centeridx, correltime;

  kdtree2_result_vector& result;  // results
  const kdtree2_array* data; 
  const vector<int>& ind; 
  // constructor

public:
  searchrecord(vector<float>& qv_in, kdtree2& tree_in,
	       kdtree2_result_vector& result_in) :  
    qv(qv_in),
    result(result_in),
    data(tree_in.data),
    ind(tree_in.ind) 
  {
    dim = tree_in.dim;
    rearrange = tree_in.rearrange;
    ballsize = infinity; 
    nn = 0; 
  };

};


void kdtree2::n_nearest_brute_force(vector<float>& qv, int nn, kdtree2_result_vector& result) {

  result.clear();

  for (int i=0; i<N; i++) {
    float dis = 0.0;
    kdtree2_result e;