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from libc.math cimport sqrt, exp
from ..utils._typedefs cimport float64_t, float32_t, int32_t, intp_t
cdef class DistanceMetric:
pass
######################################################################
# Inline distance functions
#
# We use these for the default (euclidean) case so that they can be
# inlined. This leads to faster computation for the most common case
cdef inline float64_t euclidean_dist64(
const float64_t* x1,
const float64_t* x2,
intp_t size,
) except -1 nogil:
cdef float64_t tmp, d=0
cdef intp_t j
for j in range(size):
tmp = <float64_t> (x1[j] - x2[j])
d += tmp * tmp
return sqrt(d)
cdef inline float64_t euclidean_rdist64(
const float64_t* x1,
const float64_t* x2,
intp_t size,
) except -1 nogil:
cdef float64_t tmp, d=0
cdef intp_t j
for j in range(size):
tmp = <float64_t>(x1[j] - x2[j])
d += tmp * tmp
return d
cdef inline float64_t euclidean_dist_to_rdist64(const float64_t dist) except -1 nogil:
return dist * dist
cdef inline float64_t euclidean_rdist_to_dist64(const float64_t dist) except -1 nogil:
return sqrt(dist)
######################################################################
# DistanceMetric64 base class
cdef class DistanceMetric64(DistanceMetric):
# The following attributes are required for a few of the subclasses.
# we must define them here so that cython's limited polymorphism will work.
# Because we don't expect to instantiate a lot of these objects, the
# extra memory overhead of this setup should not be an issue.
cdef float64_t p
cdef const float64_t[::1] vec
cdef const float64_t[:, ::1] mat
cdef intp_t size
cdef object func
cdef object kwargs
cdef float64_t dist(
self,
const float64_t* x1,
const float64_t* x2,
intp_t size,
) except -1 nogil
cdef float64_t rdist(
self,
const float64_t* x1,
const float64_t* x2,
intp_t size,
) except -1 nogil
cdef float64_t dist_csr(
self,
const float64_t* x1_data,
const int32_t* x1_indices,
const float64_t* x2_data,
const int32_t* x2_indices,
const int32_t x1_start,
const int32_t x1_end,
const int32_t x2_start,
const int32_t x2_end,
const intp_t size,
) except -1 nogil
cdef float64_t rdist_csr(
self,
const float64_t* x1_data,
const int32_t* x1_indices,
const float64_t* x2_data,
const int32_t* x2_indices,
const int32_t x1_start,
const int32_t x1_end,
const int32_t x2_start,
const int32_t x2_end,
const intp_t size,
) except -1 nogil
cdef int pdist(
self,
const float64_t[:, ::1] X,
float64_t[:, ::1] D,
) except -1
cdef int cdist(
self,
const float64_t[:, ::1] X,
const float64_t[:, ::1] Y,
float64_t[:, ::1] D,
) except -1
cdef int pdist_csr(
self,
const float64_t* x1_data,
const int32_t[::1] x1_indices,
const int32_t[::1] x1_indptr,
const intp_t size,
float64_t[:, ::1] D,
) except -1 nogil
cdef int cdist_csr(
self,
const float64_t* x1_data,
const int32_t[::1] x1_indices,
const int32_t[::1] x1_indptr,
const float64_t* x2_data,
const int32_t[::1] x2_indices,
const int32_t[::1] x2_indptr,
const intp_t size,
float64_t[:, ::1] D,
) except -1 nogil
cdef float64_t _rdist_to_dist(self, float64_t rdist) except -1 nogil
cdef float64_t _dist_to_rdist(self, float64_t dist) except -1 nogil
######################################################################
# Inline distance functions
#
# We use these for the default (euclidean) case so that they can be
# inlined. This leads to faster computation for the most common case
cdef inline float64_t euclidean_dist32(
const float32_t* x1,
const float32_t* x2,
intp_t size,
) except -1 nogil:
cdef float64_t tmp, d=0
cdef intp_t j
for j in range(size):
tmp = <float64_t> (x1[j] - x2[j])
d += tmp * tmp
return sqrt(d)
cdef inline float64_t euclidean_rdist32(
const float32_t* x1,
const float32_t* x2,
intp_t size,
) except -1 nogil:
cdef float64_t tmp, d=0
cdef intp_t j
for j in range(size):
tmp = <float64_t>(x1[j] - x2[j])
d += tmp * tmp
return d
cdef inline float64_t euclidean_dist_to_rdist32(const float32_t dist) except -1 nogil:
return dist * dist
cdef inline float64_t euclidean_rdist_to_dist32(const float32_t dist) except -1 nogil:
return sqrt(dist)
######################################################################
# DistanceMetric32 base class
cdef class DistanceMetric32(DistanceMetric):
# The following attributes are required for a few of the subclasses.
# we must define them here so that cython's limited polymorphism will work.
# Because we don't expect to instantiate a lot of these objects, the
# extra memory overhead of this setup should not be an issue.
cdef float64_t p
cdef const float64_t[::1] vec
cdef const float64_t[:, ::1] mat
cdef intp_t size
cdef object func
cdef object kwargs
cdef float32_t dist(
self,
const float32_t* x1,
const float32_t* x2,
intp_t size,
) except -1 nogil
cdef float32_t rdist(
self,
const float32_t* x1,
const float32_t* x2,
intp_t size,
) except -1 nogil
cdef float32_t dist_csr(
self,
const float32_t* x1_data,
const int32_t* x1_indices,
const float32_t* x2_data,
const int32_t* x2_indices,
const int32_t x1_start,
const int32_t x1_end,
const int32_t x2_start,
const int32_t x2_end,
const intp_t size,
) except -1 nogil
cdef float32_t rdist_csr(
self,
const float32_t* x1_data,
const int32_t* x1_indices,
const float32_t* x2_data,
const int32_t* x2_indices,
const int32_t x1_start,
const int32_t x1_end,
const int32_t x2_start,
const int32_t x2_end,
const intp_t size,
) except -1 nogil
cdef int pdist(
self,
const float32_t[:, ::1] X,
float32_t[:, ::1] D,
) except -1
cdef int cdist(
self,
const float32_t[:, ::1] X,
const float32_t[:, ::1] Y,
float32_t[:, ::1] D,
) except -1
cdef int pdist_csr(
self,
const float32_t* x1_data,
const int32_t[::1] x1_indices,
const int32_t[::1] x1_indptr,
const intp_t size,
float32_t[:, ::1] D,
) except -1 nogil
cdef int cdist_csr(
self,
const float32_t* x1_data,
const int32_t[::1] x1_indices,
const int32_t[::1] x1_indptr,
const float32_t* x2_data,
const int32_t[::1] x2_indices,
const int32_t[::1] x2_indptr,
const intp_t size,
float32_t[:, ::1] D,
) except -1 nogil
cdef float32_t _rdist_to_dist(self, float32_t rdist) except -1 nogil
cdef float32_t _dist_to_rdist(self, float32_t dist) except -1 nogil
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