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