JLCoverTree.h

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#ifndef JLCOVERTREE_H
#define JLCOVERTREE_H

#include <shogun/lib/config.h>

#include <shogun/lib/JLCoverTreePoint.h>
#include <shogun/mathematics/Math.h>

#include<math.h>
#include<stdio.h>
#ifndef NDEBUG
#define NDEBUG
#endif  // NDEBUG
#include<assert.h>

/* First written by John Langford jl@hunch.net
   Templatization by Dinoj Surendran dinojs@gmail.com
   Adaptation to Shogun by Fernando José Iglesias García
*/

// the files below may not need to be included

/* Whatever structure/class/type is used for P, it must have the following functions defined:

   float distance(P v1, P v2, float upper_bound);
   : this returns the distance between two P objects
   : the distance does not have to be calculated fully if it's more than upper_bound

   v_array<P> parse_points(char *filename);
   : this fills up a v_array of P objects from the input file

   void print(point &P);
   : this prints out the contents of a P object.
*/

using namespace shogun;

template<class P>
struct node {

  P p;

  float max_dist;

  float parent_dist;

  node<P>* children;

  unsigned short int num_children;

  short int scale;

};

//template<class P>
//node<P> insert(P newpoint, node<P> *top_node); // not yet implemented
//
//template<class P>
//void remove(P byepoint, node<P> *top_node); // not yet implemented
//query

template<class P>
struct ds_node {

  v_array<float> dist;

  P p;

};

static float base = 1.3;


static float il2 = 1. / log(base);

inline float dist_of_scale (int s)
{
  return CMath::pow(base, s);
}

inline int get_scale(float d)
{
  return (int) CMath::ceil(il2 * log(d));
}

template<class P>
node<P> new_node(const P &p)
{
  node<P> new_node;
  new_node.p = p;
  return new_node;
}

template<class P>
node<P> new_leaf(const P &p)
{
  node<P> new_leaf = {p,0.,0.,NULL,0,100};
  return new_leaf;
}

template<class P>
float max_set(v_array<ds_node<P> > &v)
{
  float max = 0.;
  for (int i = 0; i < v.index; i++)
    if ( max < v[i].dist.last())
      max = v[i].dist.last();
  return max;
}

void print_space(int s)
{
  for (int i = 0; i < s; i++)
    SG_SPRINT(" ")
}

template<class P>
void print(int depth, node<P> &top_node)
{
  print_space(depth);
  print(top_node.p);
  if ( top_node.num_children > 0 )
  {
    print_space(depth);
    SG_SPRINT("scale = %i\n",top_node.scale)
    print_space(depth);
    SG_SPRINT("max_dist = %f\n",top_node.max_dist)
    print_space(depth);
    SG_SPRINT("num children = %i\n",top_node.num_children)
    for (int i = 0; i < top_node.num_children;i++)
      print(depth+1, top_node.children[i]);
  }
}

template<class P>
void split(v_array<ds_node<P> >& point_set, v_array<ds_node<P> >& far_set, int max_scale)
{
  unsigned int new_index = 0;
  float fmax = dist_of_scale(max_scale);
  for (int i = 0; i < point_set.index; i++)
  {
    if (point_set[i].dist.last() <= fmax)
    {
      point_set[new_index++] = point_set[i];
    }
    else
      push(far_set,point_set[i]);
  }
  point_set.index=new_index;
}

template<class P>
void dist_split(v_array<ds_node<P> >& point_set,
        v_array<ds_node<P> >& new_point_set,
        P new_point,
        int max_scale)
{
  unsigned int new_index = 0;
  float fmax = dist_of_scale(max_scale);
  for(int i = 0; i < point_set.index; i++)
    {
      float new_d;
      new_d = distance(new_point, point_set[i].p, fmax);
      if (new_d <= fmax )
      {
    push(point_set[i].dist, new_d);
    push(new_point_set,point_set[i]);
      }
      else
    point_set[new_index++] = point_set[i];
    }
  point_set.index = new_index;
}




/*
   max_scale is the maximum scale of the node we might create here.
   point_set contains points which are 2*max_scale or less away.
*/

template <class P>
node<P> batch_insert(const P& p,
          int max_scale,
          int top_scale,
          v_array<ds_node<P> >& point_set,
          v_array<ds_node<P> >& consumed_set,
          v_array<v_array<ds_node<P> > >& stack)
{
  if (point_set.index == 0)
    return new_leaf(p);
  else {
    float max_dist = max_set(point_set); //O(|point_set|)
    int next_scale = CMath::min(max_scale - 1, get_scale(max_dist));
    if (next_scale == -2147483647-1) // We have points with distance 0.
      {
    v_array<node<P> > children;
    push(children,new_leaf(p));
    while (point_set.index > 0)
      {
        push(children,new_leaf(point_set.last().p));
        push(consumed_set,point_set.last());
        point_set.decr();
      }
    node<P> n = new_node(p);
    n.scale = 100; // A magic number meant to be larger than all scales.
    n.max_dist = 0;
    alloc(children,children.index);
    n.num_children = children.index;
    n.children = children.elements;
    return n;
      }
    else
      {
    v_array<ds_node<P> > far = pop(stack);
    split(point_set,far,max_scale); //O(|point_set|)

    node<P> child = batch_insert(p, next_scale, top_scale, point_set, consumed_set, stack);

    if (point_set.index == 0)
      {
        push(stack,point_set);
        point_set=far;
        return child;
      }
    else {
      node<P> n = new_node(p);
      v_array<node<P> > children;
      push(children, child);
      v_array<ds_node<P> > new_point_set = pop(stack);
      v_array<ds_node<P> > new_consumed_set = pop(stack);
      while (point_set.index != 0) { //O(|point_set| * num_children)
        P new_point = point_set.last().p;
        float new_dist = point_set.last().dist.last();
        push(consumed_set, point_set.last());
        point_set.decr();

        dist_split(point_set, new_point_set, new_point, max_scale); //O(|point_saet|)
        dist_split(far,new_point_set,new_point,max_scale); //O(|far|)

        node<P> new_child =
          batch_insert(new_point, next_scale, top_scale, new_point_set, new_consumed_set, stack);
        new_child.parent_dist = new_dist;

        push(children, new_child);

        float fmax = dist_of_scale(max_scale);
        for(int i = 0; i< new_point_set.index; i++) //O(|new_point_set|)
          {
        new_point_set[i].dist.decr();
        if (new_point_set[i].dist.last() <= fmax)
          push(point_set, new_point_set[i]);
        else
          push(far, new_point_set[i]);
          }
        for(int i = 0; i< new_consumed_set.index; i++) //O(|new_point_set|)
          {
        new_consumed_set[i].dist.decr();
        push(consumed_set, new_consumed_set[i]);
          }
        new_point_set.index = 0;
        new_consumed_set.index = 0;
      }
      push(stack,new_point_set);
      push(stack,new_consumed_set);
      push(stack,point_set);
      point_set=far;
      n.scale = top_scale - max_scale;
      n.max_dist = max_set(consumed_set);
      alloc(children,children.index);
      n.num_children = children.index;
      n.children = children.elements;
      return n;
    }
      }
  }
}

template<class P>
node<P> batch_create(v_array<P> points)
{
  assert(points.index > 0);
  v_array<ds_node<P> > point_set;
  v_array<v_array<ds_node<P> > > stack;

  for (int i = 1; i < points.index; i++) {
    ds_node<P> temp;
    push(temp.dist, distance(points[0], points[i], FLT_MAX));
    temp.p = points[i];
    push(point_set,temp);
  }

  v_array<ds_node<P> > consumed_set;

  float max_dist = max_set(point_set);

  node<P> top = batch_insert (points[0],
               get_scale(max_dist),
               get_scale(max_dist),
                point_set,
                consumed_set,
                stack);
  for (int i = 0; i<consumed_set.index;i++)
    free(consumed_set[i].dist.elements);
  free(consumed_set.elements);
  for (int i = 0; i<stack.index;i++)
    free(stack[i].elements);
  free(stack.elements);
  free(point_set.elements);
  return top;
}

void add_height(int d, v_array<int> &heights)
{
  if (heights.index <= d)
    for(;heights.index <= d;)
      push(heights,0);
  heights[d] = heights[d] + 1;
}

template <class P>
int height_dist(const node<P> top_node,v_array<int> &heights)
{
  if (top_node.num_children == 0)
    {
      add_height(0,heights);
      return 0;
    }
  else
    {
      int max_v=0;
      for (int i = 0; i<top_node.num_children ;i++)
    {
      int d = height_dist(top_node.children[i], heights);
      if (d > max_v)
        max_v = d;
    }
      add_height(1 + max_v, heights);
      return (1 + max_v);
    }
}

template <class P>
void depth_dist(int top_scale, const node<P> top_node,v_array<int> &depths)
{
  if (top_node.num_children > 0)
      for (int i = 0; i<top_node.num_children ;i++)
    {
      add_height(top_node.scale, depths);
      depth_dist(top_scale, top_node.children[i], depths);
    }
}

template <class P>
void breadth_dist(const node<P> top_node,v_array<int> &breadths)
{
  if (top_node.num_children == 0)
    add_height(0,breadths);
  else
    {
      for (int i = 0; i<top_node.num_children ;i++)
    breadth_dist(top_node.children[i], breadths);
      add_height(top_node.num_children, breadths);
    }
}

template <class P>
struct d_node {

  float dist;

  const node<P> *n;
};

template <class P>
inline float compare(const d_node<P> *p1, const d_node<P>* p2)
{
  return p1 -> dist - p2 -> dist;
}

template <class P>
void halfsort (v_array<d_node<P> > cover_set)
{

  if (cover_set.index <= 1)
    return;
  register d_node<P> *base_ptr =  cover_set.elements;

  d_node<P> *hi = &base_ptr[cover_set.index - 1];
  d_node<P> *right_ptr = hi;
  d_node<P> *left_ptr;

  while (right_ptr > base_ptr)
    {
      d_node<P> *mid = base_ptr + ((hi - base_ptr) >> 1);

      if (compare ( mid,  base_ptr) < 0.)
    CMath::swap(*mid, *base_ptr);
      if (compare ( hi,  mid) < 0.)
    CMath::swap(*mid, *hi);
      else
    goto jump_over;
      if (compare ( mid,  base_ptr) < 0.)
    CMath::swap(*mid, *base_ptr);
    jump_over:;

      left_ptr  = base_ptr + 1;
      right_ptr = hi - 1;

      do
    {
      while (compare (left_ptr, mid) < 0.)
        left_ptr ++;

      while (compare (mid, right_ptr) < 0.)
        right_ptr --;

      if (left_ptr < right_ptr)
        {
          CMath::swap(*left_ptr, *right_ptr);
          if (mid == left_ptr)
        mid = right_ptr;
          else if (mid == right_ptr)
        mid = left_ptr;
          left_ptr ++;
          right_ptr --;
        }
      else if (left_ptr == right_ptr)
        {
          left_ptr ++;
          right_ptr --;
          break;
        }
    }
      while (left_ptr <= right_ptr);

      hi = right_ptr;
    }
}


template <class P>
v_array<v_array<d_node<P> > > get_cover_sets(v_array<v_array<v_array<d_node<P> > > > &spare_cover_sets)
{
  v_array<v_array<d_node<P> > > ret = pop(spare_cover_sets);
  while (ret.index < 101)
    {
      v_array<d_node<P> > temp;
      push(ret, temp);
    }
  return ret;
}

inline bool shell(float parent_query_dist, float child_parent_dist, float upper_bound)
{
  return parent_query_dist - child_parent_dist <= upper_bound;
  //    && child_parent_dist - parent_query_dist <= upper_bound;
}

int internal_k =1;
void update_k(float *k_upper_bound, float upper_bound)
{
  float *end = k_upper_bound + internal_k-1;
  float *begin = k_upper_bound;
  for (;end != begin; begin++)
    {
      if (upper_bound < *(begin+1))
    *begin = *(begin+1);
      else {
    *begin = upper_bound;
    break;
      }
    }
  if (end == begin)
    *begin = upper_bound;
}
float *alloc_k()
{
  return (float *)malloc(sizeof(float) * internal_k);
}
void set_k(float* begin, float max)
{
  for(float *end = begin+internal_k;end != begin; begin++)
    *begin = max;
}

float internal_epsilon =0.;
void update_epsilon(float *upper_bound, float new_dist) {}
float *alloc_epsilon()
{
  return (float *)malloc(sizeof(float));
}
void set_epsilon(float* begin, float max)
{
  *begin = internal_epsilon;
}

void update_unequal(float *upper_bound, float new_dist)
{
  if (new_dist != 0.)
    *upper_bound = new_dist;
}
float* (*alloc_unequal)() = alloc_epsilon;
void set_unequal(float* begin, float max)
{
  *begin = max;
}

void (*update)(float *foo, float bar) = update_k;
void (*setter)(float *foo, float bar) = set_k;
float* (*alloc_upper)() = alloc_k;

template <class P>
inline void copy_zero_set(node<P>* query_chi, float* new_upper_bound,
                v_array<d_node<P> > &zero_set, v_array<d_node<P> > &new_zero_set)
{
  new_zero_set.index = 0;
  d_node<P> *end = zero_set.elements + zero_set.index;
  for (d_node<P> *ele = zero_set.elements; ele != end ; ele++)
    {
      float upper_dist = *new_upper_bound + query_chi->max_dist;
      if (shell(ele->dist, query_chi->parent_dist, upper_dist))
    {
      float d = distance(query_chi->p, ele->n->p, upper_dist);

      if (d <= upper_dist)
        {
          if (d < *new_upper_bound)
        update(new_upper_bound, d);
          d_node<P> temp = {d, ele->n};
          push(new_zero_set,temp);
        }
    }
    }
}

template <class P>
inline void copy_cover_sets(node<P>* query_chi, float* new_upper_bound,
                  v_array<v_array<d_node<P> > > &cover_sets,
                  v_array<v_array<d_node<P> > > &new_cover_sets,
                  int current_scale, int max_scale)
{
  for (; current_scale <= max_scale; current_scale++)
    {
      d_node<P>* ele = cover_sets[current_scale].elements;
      d_node<P>* end = cover_sets[current_scale].elements + cover_sets[current_scale].index;
      for (; ele != end; ele++)
    {
      float upper_dist = *new_upper_bound + query_chi->max_dist + ele->n->max_dist;
      if (shell(ele->dist, query_chi->parent_dist, upper_dist))
        {
          float d = distance(query_chi->p, ele->n->p, upper_dist);

          if (d <= upper_dist)
        {
          if (d < *new_upper_bound)
            update(new_upper_bound,d);
          d_node<P> temp = {d, ele->n};
          push(new_cover_sets[current_scale],temp);
        }
        }
    }
    }
}

template <class P>
void print_query(const node<P> *top_node)
{
  SG_SPRINT ("query = \n")
  print(top_node->p);
  if ( top_node->num_children > 0 ) {
    SG_SPRINT("scale = %i\n",top_node->scale)
    SG_SPRINT("max_dist = %f\n",top_node->max_dist)
    SG_SPRINT("num children = %i\n",top_node->num_children)
  }
}

template <class P>
void print_cover_sets(v_array<v_array<d_node<P> > > &cover_sets,
              v_array<d_node<P> > &zero_set,
              int current_scale, int max_scale)
{
  SG_SPRINT("cover set = \n")
  for (; current_scale <= max_scale; current_scale++)
    {
      d_node<P> *ele = cover_sets[current_scale].elements;
      d_node<P> *end = cover_sets[current_scale].elements + cover_sets[current_scale].index;
      SG_SPRINT ("%i\n", current_scale)
      for (; ele != end; ele++)
    {
      node<P> *n = (node<P> *)ele->n;
      print(n->p);
    }
    }
  d_node<P> *end = zero_set.elements + zero_set.index;
  SG_SPRINT ("infinity\n")
  for (d_node<P> *ele = zero_set.elements; ele != end ; ele++)
    {
      node<P> *n = (node<P> *)ele->n;
      print(n->p);
    }
}


/*
  An optimization to consider:
  Make all distance evaluations occur in descend.

  Instead of passing a cover_set, pass a stack of cover sets.  The
  last element holds d_nodes with your distance.  The next lower
  element holds a d_node with the distance to your query parent,
  next = query grand parent, etc..

  Compute distances in the presence of the tighter upper bound.
 */

template <class P>
inline
void descend(const node<P>* query, float* upper_bound,
              int current_scale,
              int &max_scale, v_array<v_array<d_node<P> > > &cover_sets,
              v_array<d_node<P> > &zero_set)
{
  d_node<P> *end = cover_sets[current_scale].elements + cover_sets[current_scale].index;
  for (d_node<P> *parent = cover_sets[current_scale].elements; parent != end; parent++)
    {
      const node<P> *par = parent->n;
      float upper_dist = *upper_bound + query->max_dist + query->max_dist;
      if (parent->dist <= upper_dist + par->max_dist)
    {
      node<P> *chi = par->children;
      if (parent->dist <= upper_dist + chi->max_dist)
            {
        if (chi->num_children > 0)
          {
        if (max_scale < chi->scale)
          max_scale = chi->scale;
        d_node<P> temp = {parent->dist, chi};
        push(cover_sets[chi->scale], temp);
          }
        else if (parent->dist <= upper_dist)
          {
        d_node<P> temp = {parent->dist, chi};
        push(zero_set, temp);
          }
        }
      node<P> *child_end = par->children + par->num_children;
      for (chi++; chi != child_end; chi++)
        {
          float upper_chi = *upper_bound + chi->max_dist + query->max_dist + query->max_dist;
          if (shell(parent->dist, chi->parent_dist, upper_chi))
        {
          float d = distance(query->p, chi->p, upper_chi);
          if (d <= upper_chi)
            {
              if (d < *upper_bound)
            update(upper_bound, d);
              if (chi->num_children > 0)
            {
              if (max_scale < chi->scale)
                max_scale = chi->scale;
              d_node<P> temp = {d, chi};
              push(cover_sets[chi->scale],temp);
            }
              else
            if (d <= upper_chi - chi->max_dist)
              {
                d_node<P> temp = {d, chi};
                push(zero_set, temp);
              }
            }
        }
        }
    }
    }
}

template <class P>
void brute_nearest(const node<P>* query,v_array<d_node<P> > zero_set,
           float* upper_bound,
           v_array<v_array<P> > &results,
           v_array<v_array<d_node<P> > > &spare_zero_sets)
{
  if (query->num_children > 0)
    {
      v_array<d_node<P> > new_zero_set = pop(spare_zero_sets);
      node<P> * query_chi = query->children;
      brute_nearest(query_chi, zero_set, upper_bound, results, spare_zero_sets);
      float* new_upper_bound = alloc_upper();

      node<P> *child_end = query->children + query->num_children;
      for (query_chi++;query_chi != child_end; query_chi++)
    {
      setter(new_upper_bound,*upper_bound + query_chi->parent_dist);
      copy_zero_set(query_chi, new_upper_bound, zero_set, new_zero_set);
      brute_nearest(query_chi, new_zero_set, new_upper_bound, results, spare_zero_sets);
    }
      free (new_upper_bound);
      new_zero_set.index = 0;
      push(spare_zero_sets, new_zero_set);
    }
  else
    {
      v_array<P> temp;
      push(temp, query->p);
      d_node<P> *end = zero_set.elements + zero_set.index;
      for (d_node<P> *ele = zero_set.elements; ele != end ; ele++)
    if (ele->dist <= *upper_bound)
      push(temp, ele->n->p);
      push(results,temp);
    }
}

template <class P>
void internal_batch_nearest_neighbor(const node<P> *query,
                     v_array<v_array<d_node<P> > > &cover_sets,
                     v_array<d_node<P> > &zero_set,
                     int current_scale,
                     int max_scale,
                     float* upper_bound,
                     v_array<v_array<P> > &results,
                     v_array<v_array<v_array<d_node<P> > > > &spare_cover_sets,
                     v_array<v_array<d_node<P> > > &spare_zero_sets)
{
  if (current_scale > max_scale) // All remaining points are in the zero set.
    brute_nearest(query, zero_set, upper_bound, results, spare_zero_sets);
  else
    if (query->scale <= current_scale && query->scale != 100)
      // Our query has too much scale.  Reduce.
      {
    node<P> *query_chi = query->children;
    v_array<d_node<P> > new_zero_set = pop(spare_zero_sets);
    v_array<v_array<d_node<P> > > new_cover_sets = get_cover_sets(spare_cover_sets);
    float* new_upper_bound = alloc_upper();

    node<P> *child_end = query->children + query->num_children;
    for (query_chi++; query_chi != child_end; query_chi++)
      {
        setter(new_upper_bound,*upper_bound + query_chi->parent_dist);
        copy_zero_set(query_chi, new_upper_bound, zero_set, new_zero_set);
        copy_cover_sets(query_chi, new_upper_bound, cover_sets, new_cover_sets,
                  current_scale, max_scale);
        internal_batch_nearest_neighbor(query_chi, new_cover_sets, new_zero_set,
                        current_scale, max_scale, new_upper_bound,
                        results, spare_cover_sets, spare_zero_sets);
      }
    free (new_upper_bound);
    new_zero_set.index = 0;
    push(spare_zero_sets, new_zero_set);
    push(spare_cover_sets, new_cover_sets);
    internal_batch_nearest_neighbor(query->children, cover_sets, zero_set,
                    current_scale, max_scale, upper_bound, results,
                    spare_cover_sets, spare_zero_sets);
      }
    else // reduce cover set scale
      {
    halfsort(cover_sets[current_scale]);
    descend(query, upper_bound, current_scale, max_scale,cover_sets, zero_set);
    cover_sets[current_scale++].index = 0;
    internal_batch_nearest_neighbor(query, cover_sets, zero_set,
                    current_scale, max_scale, upper_bound, results,
                    spare_cover_sets, spare_zero_sets);
      }
}

template <class P>
void batch_nearest_neighbor(const node<P> &top_node, const node<P> &query,
                v_array<v_array<P> > &results)
{
  v_array<v_array<v_array<d_node<P> > > > spare_cover_sets;
  v_array<v_array<d_node<P> > > spare_zero_sets;

  v_array<v_array<d_node<P> > > cover_sets = get_cover_sets(spare_cover_sets);
  v_array<d_node<P> > zero_set = pop(spare_zero_sets);

  float* upper_bound = alloc_upper();
  setter(upper_bound,FLT_MAX);

  float top_dist = distance(query.p, top_node.p, FLT_MAX);
  update(upper_bound, top_dist);

  d_node<P> temp = {top_dist, &top_node};
  push(cover_sets[0], temp);

  internal_batch_nearest_neighbor(&query,cover_sets,zero_set,0,0,upper_bound,results,
                  spare_cover_sets,spare_zero_sets);

  free(upper_bound);
  push(spare_cover_sets, cover_sets);

  for (int i = 0; i < spare_cover_sets.index; i++)
    {
      v_array<v_array<d_node<P> > > cover_sets2 = spare_cover_sets[i];
      for (int j = 0; j < cover_sets2.index; j++)
    free (cover_sets2[j].elements);
      free(cover_sets2.elements);
    }
  free(spare_cover_sets.elements);

  push(spare_zero_sets, zero_set);

  for (int i = 0; i < spare_zero_sets.index; i++)
    free(spare_zero_sets[i].elements);
  free(spare_zero_sets.elements);
}

template <class P>
void k_nearest_neighbor(const node<P> &top_node, const node<P> &query,
            v_array<v_array<P> > &results, int k)
{
  internal_k = k;
  update = update_k;
  setter = set_k;
  alloc_upper = alloc_k;

  batch_nearest_neighbor(top_node, query,results);
}

template <class P>
void epsilon_nearest_neighbor(const node<P> &top_node, const node<P> &query,
                  v_array<v_array<P> > &results, float epsilon)
{
  internal_epsilon = epsilon;
  update = update_epsilon;
  setter = set_epsilon;
  alloc_upper = alloc_epsilon;

  batch_nearest_neighbor(top_node, query,results);
}

template <class P>
void unequal_nearest_neighbor(const node<P> &top_node, const node<P> &query,
                  v_array<v_array<P> > &results)
{
  update = update_unequal;
  setter = set_unequal;
  alloc_upper = alloc_unequal;

  batch_nearest_neighbor(top_node, query, results);
}

#endif