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MAINT: avoid doing np.sum in the hot loop

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(you gotta be kidding me, x2 speed-up)
This commit is contained in:
Evgeni Burovski
2016-01-27 11:07:08 +00:00
parent 01e1f04b28
commit b7889b2c4f
1 changed files with 16 additions and 6 deletions
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skimage/morphology/_skel.pyx
+16 -6
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@@ -241,6 +241,18 @@ def is_surfacepoint(neighbors, points_LUT):
return True
@cython.boundscheck(False)
@cython.wraparound(False)
cdef inline bint is_endpoint(neighb_type neighbors):
"""An endpoint has exactly one neighbor in the 26-neighborhood.
"""
# The center pixel is counted, thus r.h.s. is 2
cdef int s = 0, j
for j in range(27):
s += neighbors[j]
return s == 2
@cython.boundscheck(False)
@cython.wraparound(False)
cdef bint is_Euler_invariant(neighb_type neighbors):
@@ -612,14 +624,12 @@ cdef list _loop_through(img_type img,
get_neighborhood(img, p, r, c, neighborhood)
# check if (p, r, c) is an endpoint. An endpoint has exactly
# one neighbor in the 26-neighborhood.
# The center pixel is counted, thus r.h.s. is 2
if np.sum(neighborhood) == 2:
# check if (p, r, c) is an endpoint: endpoints are not deletable.
if is_endpoint(neighborhood):
continue
# check if point is Euler invariant (condition 1 in [Lee94])
# if it is not, it's not deletable
# check if point is Euler invariant (condition 1 in [Lee94]):
# if it is not, it's not deletable.
if not is_Euler_invariant(neighborhood):
continue