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Merge branch 'main' into refactor/cxxopts
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@lisitsyn
lisitsyn committed Apr 15, 2024
2 parents 1d63010 + 009d7a8 commit b166065
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Showing 7 changed files with 194 additions and 183 deletions.
20 changes: 13 additions & 7 deletions include/stichwort/parameter.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,8 @@ class Parameter
}
}

void throwIfInvalid() {
void throwIfInvalid()
{
if (!valid)
{
throw wrong_parameter_error(invalidity_reasons);
Expand Down Expand Up @@ -200,8 +201,7 @@ class CheckedParameter
return parameter.is<T>(v);
}

template <template <class> class F, class Q>
inline const CheckedParameter& satisfies(const F<Q>& cond) const
template <template <class> class F, class Q> inline const CheckedParameter& satisfies(const F<Q>& cond) const
{
if (!parameter.isCondition(cond))
parameter.invalidate(cond.failureMessage(parameter));
Expand Down Expand Up @@ -271,15 +271,21 @@ class ParametersSet
}
void merge(const ParametersSet& pg)
{
typedef ParametersMap::const_iterator MapIter;
for (MapIter iter = pg.pmap.begin(); iter != pg.pmap.end(); ++iter)
for (auto each : pg.pmap)
{
if (!pmap.count(iter->first))
if (!pmap.count(each.first))
{
pmap[iter->first] = iter->second;
pmap[each.first] = each.second;
}
}
}
void visit(std::function<void(const Parameter&)> visitor)
{
for (auto each : pmap)
{
visitor(each.second);
}
}
Parameter operator[](const std::string& name) const
{
ParametersMap::const_iterator it = pmap.find(name);
Expand Down
3 changes: 3 additions & 0 deletions include/tapkee/embed.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,9 @@ TapkeeOutput embed(RandomAccessIterator begin, RandomAccessIterator end, KernelC
{
parameters.check();
parameters.merge(tapkee_internal::defaults);
parameters.visit([] (const stichwort::Parameter& p) {
tapkee::LoggingSingleton::instance().message_debug(fmt::format("Parameter {} = [{}]", p.name(), p.repr()));
});

DimensionReductionMethod selected_method = parameters[method];

Expand Down
116 changes: 65 additions & 51 deletions include/tapkee/methods.hpp
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220 changes: 103 additions & 117 deletions include/tapkee/neighbors/covertree.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
#pragma once

/* Tapkee includes */
#include <tapkee/neighbors/covertree_point.hpp>
#include <tapkee/neighbors/covertree/structures.hpp>
#include <tapkee/neighbors/covertree_point.hpp>
/* End of Tapkee includes */

#include <assert.h>
Expand All @@ -27,107 +27,97 @@ namespace tapkee
namespace tapkee_internal
{

template <class P, class DistanceCallback>
class CoverTreeWrapper
template <class P, class DistanceCallback> class CoverTreeWrapper
{
public:
CoverTreeWrapper() :
base(COVERTREE_BASE),
il2(1. / log(base)),
internal_k(1)
{

}
public:
CoverTreeWrapper() : base(COVERTREE_BASE), il2(1. / log(base)), internal_k(1)
{
}

void split(v_array<ds_node<P>>& point_set, v_array<ds_node<P>>& far_set, int max_scale);
void split(v_array<ds_node<P>>& point_set, v_array<ds_node<P>>& far_set, int max_scale);

void dist_split(DistanceCallback& dcb, v_array<ds_node<P>>& point_set, v_array<ds_node<P>>& new_point_set, P new_point, int max_scale);
void dist_split(DistanceCallback& dcb, v_array<ds_node<P>>& point_set, v_array<ds_node<P>>& new_point_set,
P new_point, int max_scale);

node<P> batch_insert(DistanceCallback& dcb, 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);
node<P> batch_insert(DistanceCallback& dcb, 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);

node<P> batch_create(DistanceCallback& dcb, v_array<P> points);
node<P> batch_create(DistanceCallback& dcb, v_array<P> points);

void k_nearest_neighbor(DistanceCallback& dcb, const node<P>& top_node, const node<P>& query, v_array<v_array<P>>& results, int k);
void k_nearest_neighbor(DistanceCallback& dcb, const node<P>& top_node, const node<P>& query,
v_array<v_array<P>>& results, int k);

void batch_nearest_neighbor(DistanceCallback& dcb, const node<P>& top_node, const node<P>& query, v_array<v_array<P>>& results);
void batch_nearest_neighbor(DistanceCallback& dcb, const node<P>& top_node, const node<P>& query,
v_array<v_array<P>>& results);

void internal_batch_nearest_neighbor(
DistanceCallback& dcb, 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, std::vector<ScalarType>& 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
);
void internal_batch_nearest_neighbor(DistanceCallback& dcb, 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, std::vector<ScalarType>& 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);

void brute_nearest(
DistanceCallback& dcb, const node<P>* query, v_array<d_node<P>> zero_set, std::vector<ScalarType>& upper_bound,
v_array<v_array<P>>& results, v_array<v_array<d_node<P>>>& spare_zero_sets
);
void brute_nearest(DistanceCallback& dcb, const node<P>* query, v_array<d_node<P>> zero_set,
std::vector<ScalarType>& upper_bound, v_array<v_array<P>>& results,
v_array<v_array<d_node<P>>>& spare_zero_sets);

void descend(
DistanceCallback& dcb, const node<P>* query, std::vector<ScalarType>& upper_bound, int current_scale,
int& max_scale, v_array<v_array<d_node<P>>>& cover_sets, v_array<d_node<P>>& zero_set
);
void descend(DistanceCallback& dcb, const node<P>* query, std::vector<ScalarType>& upper_bound, int current_scale,
int& max_scale, v_array<v_array<d_node<P>>>& cover_sets, v_array<d_node<P>>& zero_set);

void copy_cover_sets(
DistanceCallback& dcb, const node<P>* query_chi, std::vector<ScalarType>& 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
);
void copy_cover_sets(DistanceCallback& dcb, const node<P>* query_chi, std::vector<ScalarType>& 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);

void copy_zero_set(
DistanceCallback& dcb, const node<P>* query_chi, std::vector<ScalarType>& new_upper_bound,
v_array<d_node<P>>& zero_set, v_array<d_node<P>>& new_zero_set
);
void copy_zero_set(DistanceCallback& dcb, const node<P>* query_chi, std::vector<ScalarType>& new_upper_bound,
v_array<d_node<P>>& zero_set, v_array<d_node<P>>& new_zero_set);

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>>> get_cover_sets(v_array<v_array<v_array<d_node<P>>>>& spare_cover_sets);

inline ScalarType dist_of_scale(int s)
{
return pow(base, s);
}
inline ScalarType dist_of_scale(int s)
{
return pow(base, s);
}

inline int get_scale(ScalarType d)
{
return (int)ceil(il2 * log(d));
}
inline int get_scale(ScalarType d)
{
return (int)ceil(il2 * log(d));
}

void update(std::vector<ScalarType>& k_upper_bound, ScalarType upper_bound)
void update(std::vector<ScalarType>& k_upper_bound, ScalarType upper_bound)
{
auto end = k_upper_bound.begin() + internal_k - 1;
auto begin = k_upper_bound.begin();
for (; end != begin; begin++)
{
auto end = k_upper_bound.begin() + internal_k - 1;
auto begin = k_upper_bound.begin();
for (; end != begin; begin++)
if (upper_bound < *(begin + 1))
*begin = *(begin + 1);
else
{
if (upper_bound < *(begin + 1))
*begin = *(begin + 1);
else
{
*begin = upper_bound;
break;
}
}
if (end == begin)
*begin = upper_bound;
break;
}
}
if (end == begin)
*begin = upper_bound;
}

void setter(std::vector<ScalarType>& vector, ScalarType max)
{
auto begin = vector.begin();
for (auto end = begin + internal_k; end != begin; begin++)
*begin = max;
}
void setter(std::vector<ScalarType>& vector, ScalarType max)
{
auto begin = vector.begin();
for (auto end = begin + internal_k; end != begin; begin++)
*begin = max;
}

std::vector<ScalarType> alloc_upper()
{
return std::vector<ScalarType>(internal_k);
}
std::vector<ScalarType> alloc_upper()
{
return std::vector<ScalarType>(internal_k);
}

private:
ScalarType base;
ScalarType il2;
int internal_k;
private:
ScalarType base;
ScalarType il2;
int internal_k;
};

template <class P> ScalarType max_set(v_array<ds_node<P>>& v)
Expand Down Expand Up @@ -157,9 +147,8 @@ void CoverTreeWrapper<P, D>::split(v_array<ds_node<P>>& point_set, v_array<ds_no
}

template <class P, class DistanceCallback>
void CoverTreeWrapper<P, DistanceCallback>::dist_split(
DistanceCallback& dcb, v_array<ds_node<P>>& point_set, v_array<ds_node<P>>& new_point_set, P new_point, int max_scale
)
void CoverTreeWrapper<P, DistanceCallback>::dist_split(DistanceCallback& dcb, v_array<ds_node<P>>& point_set,
v_array<ds_node<P>>& new_point_set, P new_point, int max_scale)
{
IndexType new_index = 0;
ScalarType fmax = dist_of_scale(max_scale);
Expand All @@ -183,10 +172,10 @@ void CoverTreeWrapper<P, DistanceCallback>::dist_split(
point_set contains points which are 2*max_scale or less away.
*/
template <class P, class DistanceCallback>
node<P> CoverTreeWrapper<P, DistanceCallback>::batch_insert(
DistanceCallback& dcb, 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
)
node<P> CoverTreeWrapper<P, DistanceCallback>::batch_insert(DistanceCallback& dcb, 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 (size(point_set) == 0)
return new_leaf(p);
Expand Down Expand Up @@ -412,7 +401,8 @@ template <class P> void halfsort(v_array<d_node<P>> cover_set)
}

template <class P, class D>
v_array<v_array<d_node<P>>> CoverTreeWrapper<P, D>::get_cover_sets(v_array<v_array<v_array<d_node<P>>>>& spare_cover_sets)
v_array<v_array<d_node<P>>> CoverTreeWrapper<P, D>::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 (size(ret) < 101)
Expand All @@ -430,10 +420,10 @@ inline bool shell(ScalarType parent_query_dist, ScalarType child_parent_dist, Sc
}

template <class P, class DistanceCallback>
void CoverTreeWrapper<P, DistanceCallback>::copy_zero_set(
DistanceCallback& dcb, const node<P>* query_chi, std::vector<ScalarType>& new_upper_bound,
v_array<d_node<P>>& zero_set, v_array<d_node<P>>& new_zero_set
)
void CoverTreeWrapper<P, DistanceCallback>::copy_zero_set(DistanceCallback& dcb, const node<P>* query_chi,
std::vector<ScalarType>& new_upper_bound,
v_array<d_node<P>>& zero_set,
v_array<d_node<P>>& new_zero_set)
{
resize(new_zero_set, 0);
auto end = begin(zero_set) + size(zero_set);
Expand All @@ -456,11 +446,11 @@ void CoverTreeWrapper<P, DistanceCallback>::copy_zero_set(
}

template <class P, class DistanceCallback>
void CoverTreeWrapper<P, DistanceCallback>::copy_cover_sets(
DistanceCallback& dcb, const node<P>* query_chi, std::vector<ScalarType>& 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
)
void CoverTreeWrapper<P, DistanceCallback>::copy_cover_sets(DistanceCallback& dcb, const node<P>* query_chi,
std::vector<ScalarType>& 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++)
{
Expand Down Expand Up @@ -497,10 +487,10 @@ void CoverTreeWrapper<P, DistanceCallback>::copy_cover_sets(
Compute distances in the presence of the tighter upper bound.
*/
template <class P, class DistanceCallback>
void CoverTreeWrapper<P, DistanceCallback>::descend(
DistanceCallback& dcb, const node<P>* query, std::vector<ScalarType>& upper_bound, int current_scale,
int& max_scale, v_array<v_array<d_node<P>>>& cover_sets, v_array<d_node<P>>& zero_set
)
void CoverTreeWrapper<P, DistanceCallback>::descend(DistanceCallback& dcb, const node<P>* query,
std::vector<ScalarType>& upper_bound, int current_scale,
int& max_scale, v_array<v_array<d_node<P>>>& cover_sets,
v_array<d_node<P>>& zero_set)
{
auto end = begin(cover_sets[current_scale]) + size(cover_sets[current_scale]);
for (auto parent = begin(cover_sets[current_scale]); parent != end; parent++)
Expand Down Expand Up @@ -556,10 +546,11 @@ void CoverTreeWrapper<P, DistanceCallback>::descend(
}

template <class P, class DistanceCallback>
void CoverTreeWrapper<P, DistanceCallback>::brute_nearest(
DistanceCallback& dcb, const node<P>* query, v_array<d_node<P>> zero_set, std::vector<ScalarType>& upper_bound,
v_array<v_array<P>>& results, v_array<v_array<d_node<P>>>& spare_zero_sets
)
void CoverTreeWrapper<P, DistanceCallback>::brute_nearest(DistanceCallback& dcb, const node<P>* query,
v_array<d_node<P>> zero_set,
std::vector<ScalarType>& upper_bound,
v_array<v_array<P>>& results,
v_array<v_array<d_node<P>>>& spare_zero_sets)
{
if (query->num_children > 0)
{
Expand Down Expand Up @@ -592,13 +583,9 @@ void CoverTreeWrapper<P, DistanceCallback>::brute_nearest(

template <class P, class DistanceCallback>
void CoverTreeWrapper<P, DistanceCallback>::internal_batch_nearest_neighbor(
DistanceCallback& dcb, 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, std::vector<ScalarType>& 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
)
DistanceCallback& dcb, 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, std::vector<ScalarType>& 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(dcb, query, zero_set, upper_bound, results, spare_zero_sets);
Expand Down Expand Up @@ -636,9 +623,8 @@ void CoverTreeWrapper<P, DistanceCallback>::internal_batch_nearest_neighbor(
}

template <class P, class DistanceCallback>
void CoverTreeWrapper<P, DistanceCallback>::batch_nearest_neighbor(
DistanceCallback& dcb, const node<P>& top_node, const node<P>& query, v_array<v_array<P>>& results
)
void CoverTreeWrapper<P, DistanceCallback>::batch_nearest_neighbor(DistanceCallback& dcb, 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;
Expand Down Expand Up @@ -669,9 +655,9 @@ void CoverTreeWrapper<P, DistanceCallback>::batch_nearest_neighbor(
}

template <class P, class DistanceCallback>
void CoverTreeWrapper<P, DistanceCallback>::k_nearest_neighbor(
DistanceCallback& dcb, const node<P>& top_node, const node<P>& query, v_array<v_array<P>>& results, int k
)
void CoverTreeWrapper<P, DistanceCallback>::k_nearest_neighbor(DistanceCallback& dcb, const node<P>& top_node,
const node<P>& query, v_array<v_array<P>>& results,
int k)
{
internal_k = k;
batch_nearest_neighbor(dcb, top_node, query, results);
Expand Down
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