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Made the scan code cleaner and faster (but longer)

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Matěj Týč
2014-11-19 23:02:34 +01:00
parent 06c46ec51e
commit fe4a9b5847
1 changed files with 139 additions and 39 deletions
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skimage/measure/_ccomp.pyx
+139 -39
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@@ -502,7 +502,6 @@ cdef void scan1D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
for x in range(1, shapeinfo.x):
rindex += 1
# Handle the first row
# First row => rindex == j
if data_p[rindex] == bgval:
# Nothing to do if we are background
continue
@@ -519,6 +518,7 @@ cdef void scan2D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
cdef INTS_t *DEX = shapeinfo.DEX
scan1D(data_p, forest_p, shapeinfo, bg, connectivity, 0, z)
for y in range(1, shapeinfo.y):
# BEGINNING of x = 0
rindex = shapeinfo.ravel_index(0, y, 0, shapeinfo)
# Handle the first column
if data_p[rindex] != bgval:
@@ -528,9 +528,9 @@ cdef void scan2D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
# END of x = 0
# Handle the rest of columns
for x in range(1, shapeinfo.x):
for x in range(1, shapeinfo.x - 1):
# We have just moved to another column (of the same row)
# so we increment the raveled index. It will be reset when we get
# to another row, so we don't have to worry about altering it here.
@@ -544,14 +544,27 @@ cdef void scan2D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
if x + 1 < shapeinfo.x:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
# Finally, the last column
# BEGINNING of x = max
rindex += 1
if data_p[rindex] != bgval:
# Nothing to do if we are background
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
# END of x = max
cdef void scan3D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
bginfo *bg, DTYPE_t connectivity):
"""
Perform forward scan on a 2D array.
"""
cdef DTYPE_t x, y, z, rindex, bgval = bg.background_val
cdef INTS_t *DEX = shapeinfo.DEX
@@ -559,6 +572,8 @@ cdef void scan3D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
scan2D(data_p, forest_p, shapeinfo, bg, connectivity, 0)
for z in range(1, shapeinfo.z):
# Handle first row in 3D manner
# BEGINNING of y = 0
# BEGINNING of x = 0
rindex = shapeinfo.ravel_index(0, 0, z, shapeinfo)
if data_p[rindex] != bgval:
# Nothing to do if we are background
@@ -571,28 +586,45 @@ cdef void scan3D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
# END of x = 0
for x in range(1, shapeinfo.x):
for x in range(1, shapeinfo.x - 1):
rindex += 1
# Handle the first row
if data_p[rindex] != bgval:
if data_p[rindex] == bgval:
# Nothing to do if we are background
continue
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
if x + 1 < shapeinfo.x:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
if x + 1 < shapeinfo.x:
join_trees_wrapper(data_p, forest_p, rindex,
DEX[D_en])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
for y in range(1, shapeinfo.y):
# BEGINNING of x = max
rindex += 1
# Handle the last element of the first row
if data_p[rindex] != bgval:
# Nothing to do if we are background
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
# END of x = max
# END of y = 0
for y in range(1, shapeinfo.y - 1):
# BEGINNING of y = ...
# BEGINNING of x = 0
rindex = shapeinfo.ravel_index(0, y, z, shapeinfo)
# Handle the first column in 3D manner
if data_p[rindex] != bgval:
@@ -605,17 +637,14 @@ cdef void scan3D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
if y + 1 < shapeinfo.y:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eh])
if y + 1 < shapeinfo.y:
join_trees_wrapper(data_p, forest_p, rindex,
DEX[D_en])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
# END of x = 0
# Handle the rest of columns
for x in range(1, shapeinfo.x):
for x in range(1, shapeinfo.x - 1):
rindex += 1
if data_p[rindex] == bgval:
# Nothing to do if we are background
@@ -629,17 +658,88 @@ cdef void scan3D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
if x + 1 < shapeinfo.x:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
if y + 1 < shapeinfo.y:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ef])
if x + 1 < shapeinfo.x:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eh])
if y + 1 < shapeinfo.y:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
if x + 1 < shapeinfo.x:
join_trees_wrapper(data_p, forest_p,
rindex, DEX[D_en])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eh])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
# BEGINNING of x = max
rindex += 1
if data_p[rindex] != bgval:
# Nothing to do if we are background
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ef])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
# END of x = max
# END of y = ...
# BEGINNING of y = max
# BEGINNING of x = 0
rindex = shapeinfo.ravel_index(0, shapeinfo.y, z, shapeinfo)
# Handle the first column in 3D manner
if data_p[rindex] != bgval:
# Nothing to do if we are background
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eh])
# END of x = 0
# Handle the rest of columns
for x in range(1, shapeinfo.x - 1):
rindex += 1
if data_p[rindex] == bgval:
# Nothing to do if we are background
continue
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ef])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eh])
# BEGINNING of x = max
rindex += 1
if data_p[rindex] != bgval:
# Nothing to do if we are background
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ef])
# END of x = max
# END of y = max