/
_util.pyx
210 lines (172 loc) · 5.89 KB
/
_util.pyx
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
import numpy as np
cimport numpy as np
cimport cython
cimport libc.math as cmath
from libc.math cimport atan, pow
from libc.stdlib cimport malloc, free
from cython.parallel cimport prange
ctypedef fused fused_float:
np.float32_t
np.float64_t
ctypedef fused fused_float_2:
np.float32_t
np.float64_t
ctypedef fused fused_float_3:
np.float32_t
np.float64_t
ctypedef fused fused_int:
np.int32_t
np.int64_t
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
def find_boundaries(np.ndarray[np.long_t, ndim=1] ordered) :
"""Given an ascending-ordered integer array starting at zero, return an array that gives the first
element for each number. For example, calling with [0,0,0,1,2,2,3] should return [0,3,4,6]."""
cdef np.ndarray[np.long_t, ndim=1] boundaries = np.zeros(ordered[len(ordered)-1]+1,dtype=int) - 1
cdef int n, size = len(ordered), current=ordered[0]-1
ordered[0] = 0
with nogil :
for n in range(size) :
if current<ordered[n] :
current = ordered[n]
boundaries[current] = n
return boundaries
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
def _grid_gen_from_slice(sl, int nx, int ny, int nz, np.ndarray[fused_float, ndim=2] pos):
cdef float x,y,z
cdef int i,n, start, stop, step
start = sl.start
stop = sl.stop
step = sl.step
if step is None:
step = 1
with nogil:
n = start
i=0
while n<stop :
x=n%nx
y=(n//nx)%ny
z=(n//(nx*ny))%nz
pos[i,0]=(<fused_float>(x)+0.5)/nx
pos[i,1]=(<fused_float>(y)+0.5)/ny
pos[i,2]=(<fused_float>(z)+0.5)/nz
i+=1
n+=step
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
def _grid_gen_from_indices(np.ndarray[fused_int, ndim=1] ind, int nx, int ny, int nz, np.ndarray[fused_float, ndim=2] pos):
cdef float x,y,z
cdef int i,n_i,N=len(ind)
with nogil:
for i in range(N):
n_i = ind[i]
x=n_i%nx
y=(n_i//nx)%ny
z=(n_i//(nx*ny))%nz
pos[i,0]=(<fused_float>(x)+0.5)/nx
pos[i,1]=(<fused_float>(y)+0.5)/ny
pos[i,2]=(<fused_float>(z)+0.5)/nz
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
def grid_gen(indices_or_slice, nx, ny, nz, pos=None):
"""Generate the x,y,z grid coordinates in the interval (0,1) for the
specified indices (relative to the start of a GrafIC file) or slice of the
file. nx,ny,nz are the number of particles in each dimension (presumably
the same for all sane cases, but the file format allows for different
values). If *pos* is not None, copy the results into the array; otherwise
create a new array for the results and return it."""
from . import util
if pos is None:
pos = np.empty((util.indexing_length(indices_or_slice), 3),dtype=float)
if isinstance(indices_or_slice, slice):
_grid_gen_from_slice(indices_or_slice,nx,ny,nz,pos)
else:
_grid_gen_from_indices(np.asarray(indices_or_slice),nx,ny,nz,pos)
return pos
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
def sum(np.ndarray[fused_float, ndim=1] ar):
"""OpenMP summation algorithm equivalent to numpy.sum(ar)"""
cdef fused_float v
cdef long i
cdef long N=len(ar)
for i in prange(N,nogil=True,schedule='static'):
v+=ar[i]
return v
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
def sum_if_gt(np.ndarray[fused_float, ndim=1] ar,
np.ndarray[fused_float_2, ndim=1] cmp_ar,
double cmp_ar_val):
"""OpenMP summation algorithm equivalent to numpy.sum(ar*(cmp_ar>cmp_ar_val))"""
cdef fused_float v
cdef long i
cdef long N=len(ar)
assert len(cmp_ar)==len(ar)
for i in prange(N,nogil=True,schedule='static'):
if cmp_ar[i]>cmp_ar_val:
v+=(ar[i])
return v
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
def sum_if_lt(np.ndarray[fused_float, ndim=1] ar,
np.ndarray[fused_float_2, ndim=1] cmp_ar,
double cmp_ar_val):
"""OpenMP summation algorithm equivalent to numpy.sum(ar*(cmp_ar<cmp_ar_val))"""
cdef fused_float v
cdef long i
cdef long N=len(ar)
assert len(cmp_ar)==len(ar)
for i in prange(N,nogil=True,schedule='static'):
v+=(ar[i])*(cmp_ar[i]<cmp_ar_val)
return v
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
def _sphere_selection(np.ndarray[fused_float, ndim=2] pos_ar,
np.ndarray[fused_float, ndim=1] cen,
double r_max, double wrap):
"""OpenMP sphere selection algorithm.
Returns an array of booleans, True where the distance from
pos_ar to cen is less than r_max."""
cdef long i
cdef long N=len(pos_ar)
cdef fused_float cx,cy,cz,x,y,z,r2
cdef fused_float r_max_2
cdef np.ndarray[np.uint8_t, ndim=1] output = np.empty(len(pos_ar),dtype=np.uint8)
cdef double wrap_by_two = wrap/2
r_max_2 = r_max*r_max
assert pos_ar.shape[1]==3
assert len(cen)==3
cx = cen[0]
cy = cen[1]
cz = cen[2]
for i in prange(N,nogil=True,schedule='static'):
x=pos_ar[i,0]-cx
y=pos_ar[i,1]-cy
z=pos_ar[i,2]-cz
if wrap>0:
if x>wrap_by_two:
x=x-wrap
if y>wrap_by_two:
y=y-wrap
if z>wrap_by_two:
z=z-wrap
if x<-wrap_by_two:
x=x+wrap
if y<-wrap_by_two:
y=y+wrap
if z<-wrap_by_two:
z=z+wrap
output[i]=(x*x+y*y+z*z)<r_max_2
return output
__all__ = ['grid_gen','find_boundaries', 'sum', 'sum_if_gt', 'sum_if_lt',
'_sphere_selection']