mirror of
https://github.com/wassname/scikit-image.git
synced 2026-07-17 11:32:45 +08:00
Redone the background handling = considerable speedup
This commit is contained in:
Matěj Týč
+76
-62
@@ -272,17 +272,6 @@ cdef inline void join_trees(DTYPE_t *forest, DTYPE_t n, DTYPE_t m):
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set_root(forest, m, root)
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cdef inline void link_bg(DTYPE_t *forest, DTYPE_t n, DTYPE_t *background_node):
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"""
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Link a node to the background node.
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"""
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if background_node[0] == -999:
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background_node[0] = n
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join_trees(forest, n, background_node[0])
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# Connected components search as described in Fiorio et al.
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def label(input, DTYPE_t neighbors=8, background=None, return_num=False):
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"""Label connected regions of an integer array.
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@@ -371,6 +360,7 @@ def label(input, DTYPE_t neighbors=8, background=None, return_num=False):
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if neighbors != 4 and neighbors != 8:
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raise ValueError('Neighbors must be either 4 or 8.')
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scanBG(data_p, forest_p, & shapeinfo, & bg)
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if shapeinfo.ndim == 1:
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scan1D(data_p, forest_p, & shapeinfo, & bg, neighbors, 0, 0)
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elif shapeinfo.ndim == 2:
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@@ -416,6 +406,30 @@ cdef DTYPE_t resolve_labels(DTYPE_t *data_p, DTYPE_t *forest_p,
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return counter
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cdef void scanBG(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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bginfo *bg):
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"""
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Settle all background pixels now and don't bother with them later.
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Since this only requires one linar sweep through the array, it is fast
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and it makes sense to do it separately.
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The result of this function is update of forest_p and bg parameter.
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"""
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cdef DTYPE_t i, bgval = bg.background_val, firstbg
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# We find the provisional label of the background, which is the index of
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# the first background pixel
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for i in range(shapeinfo.numels):
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if data_p[i] == bgval:
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firstbg = i
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bg.background_node = firstbg
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break
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# And then we apply this provisional label to the whole background
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for i in range(firstbg, shapeinfo.numels):
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if data_p[i] == bgval:
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forest_p[i] = firstbg
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# Here, we work with flat arrays regardless whether the data is 1, 2 or 3D.
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# The lookup to the neighbor in a 2D array is achieved by precalculating an
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# offset and adding it to the index.
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@@ -435,19 +449,17 @@ cdef void scan1D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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Perform forward scan on a 1D object, usually the first row of an image
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"""
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# Initialize the first row
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cdef DTYPE_t x, rindex
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cdef DTYPE_t x, rindex, bgval = bg.background_val
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cdef INTS_t *DEX = shapeinfo.DEX
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rindex = shapeinfo.ravel_index(0, y, z, shapeinfo)
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if data_p[rindex] == bg.background_val:
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link_bg(forest_p, rindex, & bg.background_node)
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for x in range(1, shapeinfo.x):
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rindex += 1
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# Handle the first row
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# First row => rindex == j
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if data_p[rindex] == bg.background_val:
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link_bg(forest_p, rindex, & bg.background_node)
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if data_p[rindex] == bgval:
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# Nothing to do if we are background
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continue
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
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@@ -457,19 +469,19 @@ cdef void scan2D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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"""
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Perform forward scan on a 2D array.
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"""
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cdef DTYPE_t x, y, rindex
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cdef DTYPE_t x, y, rindex, bgval = bg.background_val
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cdef INTS_t *DEX = shapeinfo.DEX
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scan1D(data_p, forest_p, shapeinfo, bg, neighbors, 0, z)
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for y in range(1, shapeinfo.y):
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rindex = shapeinfo.ravel_index(0, y, 0, shapeinfo)
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# Handle the first column
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if data_p[rindex] == bg.background_val:
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link_bg(forest_p, rindex, & bg.background_node)
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if data_p[rindex] != bgval:
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# Nothing to do if we are background
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
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# Handle the rest of columns
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for x in range(1, shapeinfo.x):
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@@ -477,8 +489,9 @@ cdef void scan2D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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# so we increment the raveled index. It will be reset when we get
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# to another row, so we don't have to worry about altering it here.
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rindex += 1
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if data_p[rindex] == bg.background_val:
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link_bg(forest_p, rindex, & bg.background_node)
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if data_p[rindex] == bgval:
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# Nothing to do if we are background
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continue
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
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@@ -497,75 +510,76 @@ cdef void scan3D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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"""
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Perform forward scan on a 2D array.
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"""
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cdef DTYPE_t x, y, z, rindex
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cdef DTYPE_t x, y, z, rindex, bgval = bg.background_val
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cdef INTS_t *DEX = shapeinfo.DEX
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# Handle first plane
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scan2D(data_p, forest_p, shapeinfo, bg, neighbors, 0)
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for z in range(1, shapeinfo.z):
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# Handle first row in 3D manner
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rindex = shapeinfo.ravel_index(0, 0, z, shapeinfo)
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if data_p[rindex] == bg.background_val:
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link_bg(forest_p, rindex, & bg.background_node)
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if data_p[rindex] != bgval:
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# Nothing to do if we are background
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# Now we have pixels below
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
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# Now we have pixels below
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
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for x in range(1, shapeinfo.x):
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rindex += 1
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# Handle the first row
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if data_p[rindex] == bg.background_val:
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link_bg(forest_p, rindex, & bg.background_node)
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if data_p[rindex] != bgval:
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# Nothing to do if we are background
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
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if neighbors == 8:
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if x + 1 < shapeinfo.x:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
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if neighbors == 8:
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if x + 1 < shapeinfo.x:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
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if x + 1 < shapeinfo.x:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
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if x + 1 < shapeinfo.x:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
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for y in range(1, shapeinfo.y):
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rindex = shapeinfo.ravel_index(0, y, z, shapeinfo)
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# Handle the first column in 3D manner
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if data_p[rindex] == bg.background_val:
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link_bg(forest_p, rindex, & bg.background_node)
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if data_p[rindex] != bgval:
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# Nothing to do if we are background
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eh])
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eh])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
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if y + 1 < shapeinfo.y:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
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if y + 1 < shapeinfo.y:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
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# Handle the rest of columns
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for x in range(1, shapeinfo.x):
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rindex += 1
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if data_p[rindex] == bg.background_val:
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link_bg(forest_p, rindex, & bg.background_node)
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if data_p[rindex] == bgval:
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# Nothing to do if we are background
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continue
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
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