1#!python
2#cython: boundscheck=False
3#cython: wraparound=False
4#cython: cdivision=True
5
6import cython
7cimport cython
8
9import numpy as np
10cimport numpy as np
11
12from libc.math cimport fabs, sqrt, exp, cos, pow
13
14ctypedef np.double_t DTYPE_t
15ctypedef np.intp_t ITYPE_t
16
17cdef enum:
18    DTYPECODE = np.NPY_FLOAT64
19    ITYPECODE = np.NPY_INTP
20
21# Fused type for certain operations
22ctypedef fused DITYPE_t:
23    ITYPE_t
24    DTYPE_t
25
26ITYPE = np.intp
27
28DTYPE = np.double
29
30######################################################################
31# Inline distance functions
32#
33#  We use these for the default (euclidean) case so that they can be
34#  inlined.  This leads to faster computation for the most common case
35cdef inline DTYPE_t euclidean_dist(DTYPE_t* x1, DTYPE_t* x2,
36                                   ITYPE_t size) nogil except -1:
37    cdef DTYPE_t tmp, d=0
38    cdef np.intp_t j
39    for j in range(size):
40        tmp = x1[j] - x2[j]
41        d += tmp * tmp
42    return sqrt(d)
43
44
45cdef inline DTYPE_t euclidean_rdist(DTYPE_t* x1, DTYPE_t* x2,
46                                    ITYPE_t size) nogil except -1:
47    cdef DTYPE_t tmp, d=0
48    cdef np.intp_t j
49    for j in range(size):
50        tmp = x1[j] - x2[j]
51        d += tmp * tmp
52    return d
53
54
55cdef inline DTYPE_t euclidean_dist_to_rdist(DTYPE_t dist) nogil except -1:
56    return dist * dist
57
58
59cdef inline DTYPE_t euclidean_rdist_to_dist(DTYPE_t dist) except -1:
60    return sqrt(dist)
61
62
63######################################################################
64# DistanceMetric base class
65cdef class DistanceMetric:
66    # The following attributes are required for a few of the subclasses.
67    # we must define them here so that cython's limited polymorphism will work.
68    # Because we don't expect to instantiate a lot of these objects, the
69    # extra memory overhead of this setup should not be an issue.
70    cdef DTYPE_t p
71    #cdef DTYPE_t[::1] vec
72    #cdef DTYPE_t[:, ::1] mat
73    cdef np.ndarray vec
74    cdef np.ndarray mat
75    cdef DTYPE_t* vec_ptr
76    cdef DTYPE_t* mat_ptr
77    cdef ITYPE_t size
78    cdef object func
79    cdef object kwargs
80
81    cdef DTYPE_t dist(self, DTYPE_t* x1, DTYPE_t* x2,
82                      ITYPE_t size) nogil except -1
83
84    cdef DTYPE_t rdist(self, DTYPE_t* x1, DTYPE_t* x2,
85                       ITYPE_t size) nogil except -1
86
87    cdef int pdist(self, DTYPE_t[:, ::1] X, DTYPE_t[:, ::1] D) except -1
88
89    cdef int cdist(self, DTYPE_t[:, ::1] X, DTYPE_t[:, ::1] Y,
90                   DTYPE_t[:, ::1] D) except -1
91
92    cdef DTYPE_t _rdist_to_dist(self, DTYPE_t rdist) except -1
93
94    cdef DTYPE_t _dist_to_rdist(self, DTYPE_t dist) nogil except -1
95