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{{py:
implementation_specific_values = [
# Values are the following ones:
#
# name_suffix, DistanceMetric, INPUT_DTYPE_t, INPUT_DTYPE
#
# We use DistanceMetric for float64 for backward naming compatibility.
#
('64', 'DistanceMetric', 'DTYPE_t', 'DTYPE'),
('32', 'DistanceMetric32', 'cnp.float32_t', 'np.float32')
]
}}
import numpy as np
cimport numpy as cnp
from cython cimport final
from ...utils._typedefs cimport DTYPE_t, ITYPE_t
from ...metrics._dist_metrics cimport DistanceMetric
from scipy.sparse import issparse, csr_matrix
from ...utils._typedefs import DTYPE, SPARSE_INDEX_TYPE
cnp.import_array()
{{for name_suffix, DistanceMetric, INPUT_DTYPE_t, INPUT_DTYPE in implementation_specific_values}}
cdef class DatasetsPair{{name_suffix}}:
"""Abstract class which wraps a pair of datasets (X, Y).
This class allows computing distances between a single pair of rows of
of X and Y at a time given the pair of their indices (i, j). This class is
specialized for each metric thanks to the :func:`get_for` factory classmethod.
The handling of parallelization over chunks to compute the distances
and aggregation for several rows at a time is done in dedicated
subclasses of :class:`BaseDistancesReductionDispatcher` that in-turn rely on
subclasses of :class:`DatasetsPair` for each pair of rows in the data. The
goal is to make it possible to decouple the generic parallelization and
aggregation logic from metric-specific computation as much as possible.
X and Y can be stored as C-contiguous np.ndarrays or CSR matrices
in subclasses.
This class avoids the overhead of dispatching distance computations
to :class:`sklearn.metrics.DistanceMetric` based on the physical
representation of the vectors (sparse vs. dense). It makes use of
cython.final to remove the overhead of dispatching method calls.
Parameters
----------
distance_metric: {{DistanceMetric}}
The distance metric responsible for computing distances
between two vectors of (X, Y).
"""
@classmethod
def get_for(
cls,
X,
Y,
str metric="euclidean",
dict metric_kwargs=None,
) -> DatasetsPair{{name_suffix}}:
"""Return the DatasetsPair implementation for the given arguments.
Parameters
----------
X : {ndarray, sparse matrix} of shape (n_samples_X, n_features)
Input data.
If provided as a ndarray, it must be C-contiguous.
If provided as a sparse matrix, it must be in CSR format.
Y : {ndarray, sparse matrix} of shape (n_samples_Y, n_features)
Input data.
If provided as a ndarray, it must be C-contiguous.
If provided as a sparse matrix, it must be in CSR format.
metric : str, default='euclidean'
The distance metric to compute between rows of X and Y.
The default metric is a fast implementation of the Euclidean
metric. For a list of available metrics, see the documentation
of :class:`~sklearn.metrics.DistanceMetric`.
metric_kwargs : dict, default=None
Keyword arguments to pass to specified metric function.
Returns
-------
datasets_pair: DatasetsPair{{name_suffix}}
The suited DatasetsPair{{name_suffix}} implementation.
"""
# Y_norm_squared might be propagated down to DatasetsPairs
# via metrics_kwargs when the Euclidean specialisations
# can't be used. To prevent Y_norm_squared to be passed
# down to DistanceMetrics (whose constructors would raise
# a RuntimeError), we pop it here.
if metric_kwargs is not None:
metric_kwargs.pop("Y_norm_squared", None)
cdef:
{{DistanceMetric}} distance_metric = {{DistanceMetric}}.get_metric(
metric,
**(metric_kwargs or {})
)
# Metric-specific checks that do not replace nor duplicate `check_array`.
distance_metric._validate_data(X)
distance_metric._validate_data(Y)
X_is_sparse = issparse(X)
Y_is_sparse = issparse(Y)
if not X_is_sparse and not Y_is_sparse:
return DenseDenseDatasetsPair{{name_suffix}}(X, Y, distance_metric)
if X_is_sparse and Y_is_sparse:
return SparseSparseDatasetsPair{{name_suffix}}(X, Y, distance_metric)
if X_is_sparse and not Y_is_sparse:
return SparseDenseDatasetsPair{{name_suffix}}(X, Y, distance_metric)
return DenseSparseDatasetsPair{{name_suffix}}(X, Y, distance_metric)
@classmethod
def unpack_csr_matrix(cls, X: csr_matrix):
"""Ensure that the CSR matrix is indexed with SPARSE_INDEX_TYPE."""
X_data = np.asarray(X.data, dtype={{INPUT_DTYPE}})
X_indices = np.asarray(X.indices, dtype=SPARSE_INDEX_TYPE)
X_indptr = np.asarray(X.indptr, dtype=SPARSE_INDEX_TYPE)
return X_data, X_indices, X_indptr
def __init__(self, {{DistanceMetric}} distance_metric, ITYPE_t n_features):
self.distance_metric = distance_metric
self.n_features = n_features
cdef ITYPE_t n_samples_X(self) nogil:
"""Number of samples in X."""
# This is a abstract method.
# This _must_ always be overwritten in subclasses.
# TODO: add "with gil: raise" here when supporting Cython 3.0
return -999
cdef ITYPE_t n_samples_Y(self) nogil:
"""Number of samples in Y."""
# This is a abstract method.
# This _must_ always be overwritten in subclasses.
# TODO: add "with gil: raise" here when supporting Cython 3.0
return -999
cdef DTYPE_t surrogate_dist(self, ITYPE_t i, ITYPE_t j) nogil:
return self.dist(i, j)
cdef DTYPE_t dist(self, ITYPE_t i, ITYPE_t j) nogil:
# This is a abstract method.
# This _must_ always be overwritten in subclasses.
# TODO: add "with gil: raise" here when supporting Cython 3.0
return -1
@final
cdef class DenseDenseDatasetsPair{{name_suffix}}(DatasetsPair{{name_suffix}}):
"""Compute distances between row vectors of two arrays.
Parameters
----------
X: ndarray of shape (n_samples_X, n_features)
Rows represent vectors. Must be C-contiguous.
Y: ndarray of shape (n_samples_Y, n_features)
Rows represent vectors. Must be C-contiguous.
distance_metric: DistanceMetric
The distance metric responsible for computing distances
between two row vectors of (X, Y).
"""
def __init__(
self,
const {{INPUT_DTYPE_t}}[:, ::1] X,
const {{INPUT_DTYPE_t}}[:, ::1] Y,
{{DistanceMetric}} distance_metric,
):
super().__init__(distance_metric, n_features=X.shape[1])
# Arrays have already been checked
self.X = X
self.Y = Y
@final
cdef ITYPE_t n_samples_X(self) nogil:
return self.X.shape[0]
@final
cdef ITYPE_t n_samples_Y(self) nogil:
return self.Y.shape[0]
@final
cdef DTYPE_t surrogate_dist(self, ITYPE_t i, ITYPE_t j) nogil:
return self.distance_metric.rdist(&self.X[i, 0], &self.Y[j, 0], self.n_features)
@final
cdef DTYPE_t dist(self, ITYPE_t i, ITYPE_t j) nogil:
return self.distance_metric.dist(&self.X[i, 0], &self.Y[j, 0], self.n_features)
@final
cdef class SparseSparseDatasetsPair{{name_suffix}}(DatasetsPair{{name_suffix}}):
"""Compute distances between vectors of two CSR matrices.
Parameters
----------
X: sparse matrix of shape (n_samples_X, n_features)
Rows represent vectors. Must be in CSR format.
Y: sparse matrix of shape (n_samples_Y, n_features)
Rows represent vectors. Must be in CSR format.
distance_metric: DistanceMetric
The distance metric responsible for computing distances
between two vectors of (X, Y).
"""
def __init__(self, X, Y, {{DistanceMetric}} distance_metric):
super().__init__(distance_metric, n_features=X.shape[1])
self.X_data, self.X_indices, self.X_indptr = self.unpack_csr_matrix(X)
self.Y_data, self.Y_indices, self.Y_indptr = self.unpack_csr_matrix(Y)
@final
cdef ITYPE_t n_samples_X(self) nogil:
return self.X_indptr.shape[0] - 1
@final
cdef ITYPE_t n_samples_Y(self) nogil:
return self.Y_indptr.shape[0] - 1
@final
cdef DTYPE_t surrogate_dist(self, ITYPE_t i, ITYPE_t j) nogil:
return self.distance_metric.rdist_csr(
x1_data=&self.X_data[0],
x1_indices=self.X_indices,
x2_data=&self.Y_data[0],
x2_indices=self.Y_indices,
x1_start=self.X_indptr[i],
x1_end=self.X_indptr[i + 1],
x2_start=self.Y_indptr[j],
x2_end=self.Y_indptr[j + 1],
size=self.n_features,
)
@final
cdef DTYPE_t dist(self, ITYPE_t i, ITYPE_t j) nogil:
return self.distance_metric.dist_csr(
x1_data=&self.X_data[0],
x1_indices=self.X_indices,
x2_data=&self.Y_data[0],
x2_indices=self.Y_indices,
x1_start=self.X_indptr[i],
x1_end=self.X_indptr[i + 1],
x2_start=self.Y_indptr[j],
x2_end=self.Y_indptr[j + 1],
size=self.n_features,
)
@final
cdef class SparseDenseDatasetsPair{{name_suffix}}(DatasetsPair{{name_suffix}}):
"""Compute distances between vectors of a CSR matrix and a dense array.
Parameters
----------
X: sparse matrix of shape (n_samples_X, n_features)
Rows represent vectors. Must be in CSR format.
Y: ndarray of shape (n_samples_Y, n_features)
Rows represent vectors. Must be C-contiguous.
distance_metric: DistanceMetric
The distance metric responsible for computing distances
between two vectors of (X, Y).
"""
def __init__(self, X, Y, {{DistanceMetric}} distance_metric):
super().__init__(distance_metric, n_features=X.shape[1])
self.X_data, self.X_indices, self.X_indptr = self.unpack_csr_matrix(X)
# We support the sparse-dense case by using the sparse-sparse interfaces
# of `DistanceMetric` (namely `DistanceMetric.{dist_csr,rdist_csr}`) to
# avoid introducing a new complex set of interfaces. In this case, we
# need to convert `Y` (the dense array) into a CSR matrix.
#
# Here we motive using another simpler CSR representation to use for `Y`.
#
# If we were to use the usual CSR representation for `Y`, storing all
# the columns indices in `indices` would have required allocating an
# array of n_samples × n_features elements with repeated contiguous
# integers from 0 to n_features - 1. This would have been very wasteful
# from a memory point of view. This alternative representation just uses
# the necessary amount of information needed and only necessitates
# shifting the address of `data` before calling the CSR × CSR routines.
#
# In this representation:
#
# - the `data` array is the original dense array, `Y`, whose first
# element's address is shifted before calling the CSR × CSR routine
#
# - the `indices` array is a single row of `n_features` elements:
#
# [0, 1, ..., n_features-1]
#
# - the `indptr` array is not materialised as the indices pointers'
# offset is constant (the offset equals `n_features`). Moreover, as
# `data` is shifted, constant `start` and `end` indices pointers
# respectively equalling 0 and n_features are used.
# Y array already has been checked here
self.n_Y = Y.shape[0]
self.Y_data = np.ravel(Y)
self.Y_indices = np.arange(self.n_features, dtype=SPARSE_INDEX_TYPE)
@final
cdef ITYPE_t n_samples_X(self) nogil:
return self.X_indptr.shape[0] - 1
@final
cdef ITYPE_t n_samples_Y(self) nogil:
return self.n_Y
@final
cdef DTYPE_t surrogate_dist(self, ITYPE_t i, ITYPE_t j) nogil:
return self.distance_metric.rdist_csr(
x1_data=&self.X_data[0],
x1_indices=self.X_indices,
# Increment the data pointer such that x2_start=0 is aligned with the
# j-th row
x2_data=&self.Y_data[0] + j * self.n_features,
x2_indices=self.Y_indices,
x1_start=self.X_indptr[i],
x1_end=self.X_indptr[i + 1],
x2_start=0,
x2_end=self.n_features,
size=self.n_features,
)
@final
cdef DTYPE_t dist(self, ITYPE_t i, ITYPE_t j) nogil:
return self.distance_metric.dist_csr(
x1_data=&self.X_data[0],
x1_indices=self.X_indices,
# Increment the data pointer such that x2_start=0 is aligned with the
# j-th row
x2_data=&self.Y_data[0] + j * self.n_features,
x2_indices=self.Y_indices,
x1_start=self.X_indptr[i],
x1_end=self.X_indptr[i + 1],
x2_start=0,
x2_end=self.n_features,
size=self.n_features,
)
@final
cdef class DenseSparseDatasetsPair{{name_suffix}}(DatasetsPair{{name_suffix}}):
"""Compute distances between vectors of a dense array and a CSR matrix.
Parameters
----------
X: ndarray of shape (n_samples_X, n_features)
Rows represent vectors. Must be C-contiguous.
Y: sparse matrix of shape (n_samples_Y, n_features)
Rows represent vectors. Must be in CSR format.
distance_metric: DistanceMetric
The distance metric responsible for computing distances
between two vectors of (X, Y).
"""
def __init__(self, X, Y, {{DistanceMetric}} distance_metric):
super().__init__(distance_metric, n_features=X.shape[1])
# Swapping arguments on the constructor
self.datasets_pair = SparseDenseDatasetsPair{{name_suffix}}(Y, X, distance_metric)
@final
cdef ITYPE_t n_samples_X(self) nogil:
# Swapping interface
return self.datasets_pair.n_samples_Y()
@final
cdef ITYPE_t n_samples_Y(self) nogil:
# Swapping interface
return self.datasets_pair.n_samples_X()
@final
cdef DTYPE_t surrogate_dist(self, ITYPE_t i, ITYPE_t j) nogil:
# Swapping arguments on the same interface
return self.datasets_pair.surrogate_dist(j, i)
@final
cdef DTYPE_t dist(self, ITYPE_t i, ITYPE_t j) nogil:
# Swapping arguments on the same interface
return self.datasets_pair.dist(j, i)
{{endfor}}
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