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from libc.stdlib cimport free, malloc
from libc.float cimport DBL_MAX
from cython cimport final
from cython.parallel cimport parallel, prange
from ...utils._heap cimport heap_push
from ...utils._sorting cimport simultaneous_sort
from ...utils._typedefs cimport intp_t, float64_t
import numpy as np
import warnings
from numbers import Integral
from scipy.sparse import issparse
from ...utils import check_array, check_scalar, _in_unstable_openblas_configuration
from ...utils.fixes import threadpool_limits
{{for name_suffix in ['64', '32']}}
from ._base cimport (
BaseDistancesReduction{{name_suffix}},
_sqeuclidean_row_norms{{name_suffix}},
)
from ._datasets_pair cimport DatasetsPair{{name_suffix}}
from ._middle_term_computer cimport MiddleTermComputer{{name_suffix}}
cdef class ArgKmin{{name_suffix}}(BaseDistancesReduction{{name_suffix}}):
"""float{{name_suffix}} implementation of the ArgKmin."""
@classmethod
def compute(
cls,
X,
Y,
intp_t k,
metric="euclidean",
chunk_size=None,
dict metric_kwargs=None,
str strategy=None,
bint return_distance=False,
):
"""Compute the argkmin reduction.
This classmethod is responsible for introspecting the arguments
values to dispatch to the most appropriate implementation of
:class:`ArgKmin{{name_suffix}}`.
This allows decoupling the API entirely from the implementation details
whilst maintaining RAII: all temporarily allocated datastructures necessary
for the concrete implementation are therefore freed when this classmethod
returns.
No instance should directly be created outside of this class method.
"""
if metric in ("euclidean", "sqeuclidean"):
# Specialized implementation of ArgKmin for the Euclidean distance
# for the dense-dense and sparse-sparse cases.
# This implementation computes the distances by chunk using
# a decomposition of the Squared Euclidean distance.
# This specialisation has an improved arithmetic intensity for both
# the dense and sparse settings, allowing in most case speed-ups of
# several orders of magnitude compared to the generic ArgKmin
# implementation.
# For more information see MiddleTermComputer.
use_squared_distances = metric == "sqeuclidean"
pda = EuclideanArgKmin{{name_suffix}}(
X=X, Y=Y, k=k,
use_squared_distances=use_squared_distances,
chunk_size=chunk_size,
strategy=strategy,
metric_kwargs=metric_kwargs,
)
else:
# Fall back on a generic implementation that handles most scipy
# metrics by computing the distances between 2 vectors at a time.
pda = ArgKmin{{name_suffix}}(
datasets_pair=DatasetsPair{{name_suffix}}.get_for(X, Y, metric, metric_kwargs),
k=k,
chunk_size=chunk_size,
strategy=strategy,
)
# Limit the number of threads in second level of nested parallelism for BLAS
# to avoid threads over-subscription (in GEMM for instance).
with threadpool_limits(limits=1, user_api="blas"):
if pda.execute_in_parallel_on_Y:
pda._parallel_on_Y()
else:
pda._parallel_on_X()
return pda._finalize_results(return_distance)
def __init__(
self,
DatasetsPair{{name_suffix}} datasets_pair,
chunk_size=None,
strategy=None,
intp_t k=1,
):
super().__init__(
datasets_pair=datasets_pair,
chunk_size=chunk_size,
strategy=strategy,
)
self.k = check_scalar(k, "k", Integral, min_val=1)
# Allocating pointers to datastructures but not the datastructures themselves.
# There are as many pointers as effective threads.
#
# For the sake of explicitness:
# - when parallelizing on X, the pointers of those heaps are referencing
# (with proper offsets) addresses of the two main heaps (see below)
# - when parallelizing on Y, the pointers of those heaps are referencing
# small heaps which are thread-wise-allocated and whose content will be
# merged with the main heaps'.
self.heaps_r_distances_chunks = <float64_t **> malloc(
sizeof(float64_t *) * self.chunks_n_threads
)
self.heaps_indices_chunks = <intp_t **> malloc(
sizeof(intp_t *) * self.chunks_n_threads
)
# Main heaps which will be returned as results by `ArgKmin{{name_suffix}}.compute`.
self.argkmin_indices = np.full((self.n_samples_X, self.k), 0, dtype=np.intp)
self.argkmin_distances = np.full((self.n_samples_X, self.k), DBL_MAX, dtype=np.float64)
def __dealloc__(self):
if self.heaps_indices_chunks is not NULL:
free(self.heaps_indices_chunks)
if self.heaps_r_distances_chunks is not NULL:
free(self.heaps_r_distances_chunks)
cdef void _compute_and_reduce_distances_on_chunks(
self,
intp_t X_start,
intp_t X_end,
intp_t Y_start,
intp_t Y_end,
intp_t thread_num,
) noexcept nogil:
cdef:
intp_t i, j
intp_t n_samples_X = X_end - X_start
intp_t n_samples_Y = Y_end - Y_start
float64_t *heaps_r_distances = self.heaps_r_distances_chunks[thread_num]
intp_t *heaps_indices = self.heaps_indices_chunks[thread_num]
# Pushing the distances and their associated indices on a heap
# which by construction will keep track of the argkmin.
for i in range(n_samples_X):
for j in range(n_samples_Y):
heap_push(
values=heaps_r_distances + i * self.k,
indices=heaps_indices + i * self.k,
size=self.k,
val=self.datasets_pair.surrogate_dist(X_start + i, Y_start + j),
val_idx=Y_start + j,
)
cdef void _parallel_on_X_init_chunk(
self,
intp_t thread_num,
intp_t X_start,
intp_t X_end,
) noexcept nogil:
# As this strategy is embarrassingly parallel, we can set each
# thread's heaps pointer to the proper position on the main heaps.
self.heaps_r_distances_chunks[thread_num] = &self.argkmin_distances[X_start, 0]
self.heaps_indices_chunks[thread_num] = &self.argkmin_indices[X_start, 0]
cdef void _parallel_on_X_prange_iter_finalize(
self,
intp_t thread_num,
intp_t X_start,
intp_t X_end,
) noexcept nogil:
cdef:
intp_t idx
# Sorting the main heaps portion associated to `X[X_start:X_end]`
# in ascending order w.r.t the distances.
for idx in range(X_end - X_start):
simultaneous_sort(
self.heaps_r_distances_chunks[thread_num] + idx * self.k,
self.heaps_indices_chunks[thread_num] + idx * self.k,
self.k
)
cdef void _parallel_on_Y_init(
self,
) noexcept nogil:
cdef:
# Maximum number of scalar elements (the last chunks can be smaller)
intp_t heaps_size = self.X_n_samples_chunk * self.k
intp_t thread_num
# The allocation is done in parallel for data locality purposes: this way
# the heaps used in each threads are allocated in pages which are closer
# to the CPU core used by the thread.
# See comments about First Touch Placement Policy:
# https://www.openmp.org/wp-content/uploads/openmp-webinar-vanderPas-20210318.pdf #noqa
for thread_num in prange(self.chunks_n_threads, schedule='static', nogil=True,
num_threads=self.chunks_n_threads):
# As chunks of X are shared across threads, so must their
# heaps. To solve this, each thread has its own heaps
# which are then synchronised back in the main ones.
self.heaps_r_distances_chunks[thread_num] = <float64_t *> malloc(
heaps_size * sizeof(float64_t)
)
self.heaps_indices_chunks[thread_num] = <intp_t *> malloc(
heaps_size * sizeof(intp_t)
)
cdef void _parallel_on_Y_parallel_init(
self,
intp_t thread_num,
intp_t X_start,
intp_t X_end,
) noexcept nogil:
# Initialising heaps (memset can't be used here)
for idx in range(self.X_n_samples_chunk * self.k):
self.heaps_r_distances_chunks[thread_num][idx] = DBL_MAX
self.heaps_indices_chunks[thread_num][idx] = -1
@final
cdef void _parallel_on_Y_synchronize(
self,
intp_t X_start,
intp_t X_end,
) noexcept nogil:
cdef:
intp_t idx, jdx, thread_num
with nogil, parallel(num_threads=self.effective_n_threads):
# Synchronising the thread heaps with the main heaps.
# This is done in parallel sample-wise (no need for locks).
#
# This might break each thread's data locality as each heap which
# was allocated in a thread is being now being used in several threads.
#
# Still, this parallel pattern has shown to be efficient in practice.
for idx in prange(X_end - X_start, schedule="static"):
for thread_num in range(self.chunks_n_threads):
for jdx in range(self.k):
heap_push(
values=&self.argkmin_distances[X_start + idx, 0],
indices=&self.argkmin_indices[X_start + idx, 0],
size=self.k,
val=self.heaps_r_distances_chunks[thread_num][idx * self.k + jdx],
val_idx=self.heaps_indices_chunks[thread_num][idx * self.k + jdx],
)
cdef void _parallel_on_Y_finalize(
self,
) noexcept nogil:
cdef:
intp_t idx, thread_num
with nogil, parallel(num_threads=self.chunks_n_threads):
# Deallocating temporary datastructures
for thread_num in prange(self.chunks_n_threads, schedule='static'):
free(self.heaps_r_distances_chunks[thread_num])
free(self.heaps_indices_chunks[thread_num])
# Sorting the main in ascending order w.r.t the distances.
# This is done in parallel sample-wise (no need for locks).
for idx in prange(self.n_samples_X, schedule='static'):
simultaneous_sort(
&self.argkmin_distances[idx, 0],
&self.argkmin_indices[idx, 0],
self.k,
)
return
cdef void compute_exact_distances(self) noexcept nogil:
cdef:
intp_t i, j
float64_t[:, ::1] distances = self.argkmin_distances
for i in prange(self.n_samples_X, schedule='static', nogil=True,
num_threads=self.effective_n_threads):
for j in range(self.k):
distances[i, j] = self.datasets_pair.distance_metric._rdist_to_dist(
# Guard against potential -0., causing nan production.
max(distances[i, j], 0.)
)
def _finalize_results(self, bint return_distance=False):
if return_distance:
# We need to recompute distances because we relied on
# surrogate distances for the reduction.
self.compute_exact_distances()
# Values are returned identically to the way `KNeighborsMixin.kneighbors`
# returns values. This is counter-intuitive but this allows not using
# complex adaptations where `ArgKmin.compute` is called.
return np.asarray(self.argkmin_distances), np.asarray(self.argkmin_indices)
return np.asarray(self.argkmin_indices)
cdef class EuclideanArgKmin{{name_suffix}}(ArgKmin{{name_suffix}}):
"""EuclideanDistance-specialisation of ArgKmin{{name_suffix}}."""
@classmethod
def is_usable_for(cls, X, Y, metric) -> bool:
return (ArgKmin{{name_suffix}}.is_usable_for(X, Y, metric) and
not _in_unstable_openblas_configuration())
def __init__(
self,
X,
Y,
intp_t k,
bint use_squared_distances=False,
chunk_size=None,
strategy=None,
metric_kwargs=None,
):
if (
isinstance(metric_kwargs, dict) and
(metric_kwargs.keys() - {"X_norm_squared", "Y_norm_squared"})
):
warnings.warn(
f"Some metric_kwargs have been passed ({metric_kwargs}) but aren't "
f"usable for this case (EuclideanArgKmin64) and will be ignored.",
UserWarning,
stacklevel=3,
)
super().__init__(
# The datasets pair here is used for exact distances computations
datasets_pair=DatasetsPair{{name_suffix}}.get_for(X, Y, metric="euclidean"),
chunk_size=chunk_size,
strategy=strategy,
k=k,
)
cdef:
intp_t dist_middle_terms_chunks_size = self.Y_n_samples_chunk * self.X_n_samples_chunk
self.middle_term_computer = MiddleTermComputer{{name_suffix}}.get_for(
X,
Y,
self.effective_n_threads,
self.chunks_n_threads,
dist_middle_terms_chunks_size,
n_features=X.shape[1],
chunk_size=self.chunk_size,
)
if metric_kwargs is not None and "Y_norm_squared" in metric_kwargs:
self.Y_norm_squared = check_array(
metric_kwargs.pop("Y_norm_squared"),
ensure_2d=False,
input_name="Y_norm_squared",
dtype=np.float64,
)
else:
self.Y_norm_squared = _sqeuclidean_row_norms{{name_suffix}}(
Y,
self.effective_n_threads,
)
if metric_kwargs is not None and "X_norm_squared" in metric_kwargs:
self.X_norm_squared = check_array(
metric_kwargs.pop("X_norm_squared"),
ensure_2d=False,
input_name="X_norm_squared",
dtype=np.float64,
)
else:
# Do not recompute norms if datasets are identical.
self.X_norm_squared = (
self.Y_norm_squared if X is Y else
_sqeuclidean_row_norms{{name_suffix}}(
X,
self.effective_n_threads,
)
)
self.use_squared_distances = use_squared_distances
@final
cdef void compute_exact_distances(self) noexcept nogil:
if not self.use_squared_distances:
ArgKmin{{name_suffix}}.compute_exact_distances(self)
@final
cdef void _parallel_on_X_parallel_init(
self,
intp_t thread_num,
) noexcept nogil:
ArgKmin{{name_suffix}}._parallel_on_X_parallel_init(self, thread_num)
self.middle_term_computer._parallel_on_X_parallel_init(thread_num)
@final
cdef void _parallel_on_X_init_chunk(
self,
intp_t thread_num,
intp_t X_start,
intp_t X_end,
) noexcept nogil:
ArgKmin{{name_suffix}}._parallel_on_X_init_chunk(self, thread_num, X_start, X_end)
self.middle_term_computer._parallel_on_X_init_chunk(thread_num, X_start, X_end)
@final
cdef void _parallel_on_X_pre_compute_and_reduce_distances_on_chunks(
self,
intp_t X_start,
intp_t X_end,
intp_t Y_start,
intp_t Y_end,
intp_t thread_num,
) noexcept nogil:
ArgKmin{{name_suffix}}._parallel_on_X_pre_compute_and_reduce_distances_on_chunks(
self,
X_start, X_end,
Y_start, Y_end,
thread_num,
)
self.middle_term_computer._parallel_on_X_pre_compute_and_reduce_distances_on_chunks(
X_start, X_end, Y_start, Y_end, thread_num,
)
@final
cdef void _parallel_on_Y_init(
self,
) noexcept nogil:
ArgKmin{{name_suffix}}._parallel_on_Y_init(self)
self.middle_term_computer._parallel_on_Y_init()
@final
cdef void _parallel_on_Y_parallel_init(
self,
intp_t thread_num,
intp_t X_start,
intp_t X_end,
) noexcept nogil:
ArgKmin{{name_suffix}}._parallel_on_Y_parallel_init(self, thread_num, X_start, X_end)
self.middle_term_computer._parallel_on_Y_parallel_init(thread_num, X_start, X_end)
@final
cdef void _parallel_on_Y_pre_compute_and_reduce_distances_on_chunks(
self,
intp_t X_start,
intp_t X_end,
intp_t Y_start,
intp_t Y_end,
intp_t thread_num,
) noexcept nogil:
ArgKmin{{name_suffix}}._parallel_on_Y_pre_compute_and_reduce_distances_on_chunks(
self,
X_start, X_end,
Y_start, Y_end,
thread_num,
)
self.middle_term_computer._parallel_on_Y_pre_compute_and_reduce_distances_on_chunks(
X_start, X_end, Y_start, Y_end, thread_num
)
@final
cdef void _compute_and_reduce_distances_on_chunks(
self,
intp_t X_start,
intp_t X_end,
intp_t Y_start,
intp_t Y_end,
intp_t thread_num,
) noexcept nogil:
cdef:
intp_t i, j
float64_t sqeuclidean_dist_i_j
intp_t n_X = X_end - X_start
intp_t n_Y = Y_end - Y_start
float64_t * dist_middle_terms = self.middle_term_computer._compute_dist_middle_terms(
X_start, X_end, Y_start, Y_end, thread_num
)
float64_t * heaps_r_distances = self.heaps_r_distances_chunks[thread_num]
intp_t * heaps_indices = self.heaps_indices_chunks[thread_num]
# Pushing the distance and their associated indices on heaps
# which keep tracks of the argkmin.
for i in range(n_X):
for j in range(n_Y):
sqeuclidean_dist_i_j = (
self.X_norm_squared[i + X_start] +
dist_middle_terms[i * n_Y + j] +
self.Y_norm_squared[j + Y_start]
)
# Catastrophic cancellation might cause -0. to be present,
# e.g. when computing d(x_i, y_i) when X is Y.
sqeuclidean_dist_i_j = max(0., sqeuclidean_dist_i_j)
heap_push(
values=heaps_r_distances + i * self.k,
indices=heaps_indices + i * self.k,
size=self.k,
val=sqeuclidean_dist_i_j,
val_idx=j + Y_start,
)
{{endfor}}
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