/usr/include/shogun/lib/JLCoverTree.h is in libshogun-dev 3.2.0-7.3build4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#define JLCOVERTREE_H
#include <shogun/lib/JLCoverTreePoint.h>
#include <shogun/mathematics/Math.h>
#include<math.h>
#include<stdio.h>
#define 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 std;
using namespace shogun;
/**
* Cover tree node TODO better doc
*/
template<class P>
struct node {
/** Point */
P p;
/** The maximum distance to any grandchild */
float max_dist;
/** The distance to the parent */
float parent_dist;
/** Pointer to the list of children of this node */
node<P>* children;
/** The number of children nodes of this node */
unsigned short int num_children;
/** Essentially, an upper bound on the distance to any child */
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
/**
* Cover tree node with an associated set of distances TODO better doc
*/
template<class P>
struct ds_node {
/** Vector of distances TODO better doc*/
v_array<float> dist;
/** Point TODO better doc */
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);
}
}
/**
* List of cover tree nodes associated to a distance TODO better doc
*/
template <class P>
struct d_node {
/** Distance TODO better doc*/
float dist;
/** List of nodes TODO better doc*/
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
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