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Merge pull request #105 from stefanv/label_cleanup

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ENH: Allow choice between 4 and 8 neighbor mode.  Improve documentation.
This commit is contained in:
tonysyu
2012-02-03 21:12:47 -08:00
parent cfc1dfa16b e18fb678ec
commit 118cd49c18
2 changed files with 129 additions and 34 deletions
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skimage/morphology/ccomp.pyx
+105 -34
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@@ -16,66 +16,91 @@ See also:
Paper LBNL-56864, 2005,
Lawrence Berkeley National Laboratory
(University of California),
http://repositories.cdlib.org/lbnl/LBNL-56864.
http://repositories.cdlib.org/lbnl/LBNL-56864
"""
# Tree operations implemented by an array as described in Wu et al.
# The term "forest" is used to indicate an array that stores one or more trees
DTYPE = np.int
ctypedef np.int_t DTYPE_t
cdef DTYPE_t find_root(np.int_t *work, np.int_t n):
cdef DTYPE_t find_root(np.int_t *forest, np.int_t n):
"""Find the root of node n.
"""
cdef np.int_t root = n
while (work[root] < root):
root = work[root]
while (forest[root] < root):
root = forest[root]
return root
cdef set_root(np.int_t *work, np.int_t n, np.int_t root):
cdef set_root(np.int_t *forest, np.int_t n, np.int_t root):
"""
Set all nodes on a path to point to new_root.
"""
cdef np.int_t j
while (work[n] < n):
j = work[n]
work[n] = root
while (forest[n] < n):
j = forest[n]
forest[n] = root
n = j
work[n] = root
forest[n] = root
cdef join_trees(np.int_t *work, np.int_t n, np.int_t m):
cdef join_trees(np.int_t *forest, np.int_t n, np.int_t m):
"""Join two trees containing nodes n and m.
"""
cdef np.int_t root = find_root(work, n)
cdef np.int_t root = find_root(forest, n)
cdef np.int_t root_m
if (n != m):
root_m = find_root(work, m)
root_m = find_root(forest, m)
if (root > root_m):
root = root_m
set_root(work, n, root)
set_root(work, m, root)
set_root(forest, n, root)
set_root(forest, m, root)
cdef link_bg(np.int_t *forest, np.int_t n, np.int_t *background_node):
"""
Link a node to the background node.
"""
if background_node[0] == -999:
background_node[0] = n
join_trees(forest, n, background_node[0])
# Connected components search as described in Fiorio et al.
def label(np.ndarray[DTYPE_t, ndim=2] input):
def label(np.ndarray[DTYPE_t, ndim=2] input,
np.int_t neighbors=8, np.int_t background=-1):
"""Label connected regions of an integer array.
Connectivity is defined as two (8-connected) neighboring entries
having equal value.
Two pixels are connected when they are neighbors and have the same value.
They can be neighbors either in a 4- or 8-connected sense::
4-connectivity 8-connectivity
[ ] [ ] [ ] [ ]
| \ | /
[ ]--[ ]--[ ] [ ]--[ ]--[ ]
| / | \
[ ] [ ] [ ] [ ]
Parameters
----------
input : ndarray of dtype int
Image to label.
neighbors : {4, 8}, int
Whether to use 4- or 8-connectivity.
background : int
Consider all pixels with this value as background pixels, and label
them as -1.
Returns
-------
@@ -83,56 +108,102 @@ def label(np.ndarray[DTYPE_t, ndim=2] input):
Labeled array, where all connected regions are assigned the
same integer value.
Examples
--------
>>> x = np.eye(3).astype(int)
>>> print x
[[1 0 0]
[0 1 0]
[0 0 1]]
>>> print m.label(x, neighbors=4)
[[0 1 1]
[2 3 1]
[2 2 4]]
>>> print m.label(x, neighbors=8)
[[0 1 1]
[1 0 1]
[1 1 0]]
>>> x = np.array([[1, 0, 0],
... [1, 1, 5],
... [0, 0, 0]])
>>> print m.label(x, background=0)
[[ 0 -1 -1]
[ 0 0 1]
[-1 -1 -1]]
"""
cdef np.int_t rows = input.shape[0]
cdef np.int_t cols = input.shape[1]
cdef np.ndarray[DTYPE_t, ndim=2] data = input.copy()
cdef np.ndarray[DTYPE_t, ndim=2] work
cdef np.ndarray[DTYPE_t, ndim=2] forest
work = np.arange(data.size, dtype=DTYPE).reshape((rows, cols))
forest = np.arange(data.size, dtype=DTYPE).reshape((rows, cols))
cdef np.int_t *work_p = <np.int_t*>work.data
cdef np.int_t *forest_p = <np.int_t*>forest.data
cdef np.int_t *data_p = <np.int_t*>data.data
cdef np.int_t i, j
cdef np.int_t background_node = -999
if neighbors != 4 and neighbors != 8:
raise ValueError('Neighbors must be either 4 or 8.')
# Initialize the first row
for j in range(1, cols):
if data[0, j] == background:
link_bg(forest_p, j, &background_node)
if data[0, j] == data[0, j-1]:
join_trees(work_p, j, j-1)
join_trees(forest_p, j, j-1)
for i in range(1, rows):
# Handle the first column
if data[i, 0] == data[i-1, 0]:
join_trees(work_p, i*cols, (i-1)*cols)
if data[i, 0] == background:
link_bg(forest_p, i * cols, &background_node)
if data[i, 0] == data[i-1, 1]:
join_trees(work_p, i*cols, (i-1)*cols + 1)
if data[i, 0] == data[i-1, 0]:
join_trees(forest_p, i*cols, (i-1)*cols)
if neighbors == 8:
if data[i, 0] == data[i-1, 1]:
join_trees(forest_p, i*cols, (i-1)*cols + 1)
for j in range(1, cols):
if data[i, j] == data[i-1, j-1]:
join_trees(work_p, i*cols + j, (i-1)*cols + j - 1)
if data[i, j] == background:
link_bg(forest_p, i * cols + j, &background_node)
if neighbors == 8:
if data[i, j] == data[i-1, j-1]:
join_trees(forest_p, i*cols + j, (i-1)*cols + j - 1)
if data[i, j] == data[i-1, j]:
join_trees(work_p, i*cols + j, (i-1)*cols + j)
join_trees(forest_p, i*cols + j, (i-1)*cols + j)
if j < cols - 1:
if data[i, j] == data[i - 1, j + 1]:
join_trees(work_p, i*cols + j, (i-1)*cols + j + 1)
if neighbors == 8:
if j < cols - 1:
if data[i, j] == data[i - 1, j + 1]:
join_trees(forest_p, i*cols + j, (i-1)*cols + j + 1)
if data[i, j] == data[i, j-1]:
join_trees(work_p, i*cols + j, i*cols + j - 1)
join_trees(forest_p, i*cols + j, i*cols + j - 1)
# Label output
cdef np.int_t ctr = 0
for i in range(rows):
for j in range(cols):
if (i*cols + j) == work[i, j]:
if (i*cols + j) == background_node:
data[i, j] = -1
elif (i*cols + j) == forest[i, j]:
data[i, j] = ctr
ctr = ctr + 1
else:
data[i, j] = data_p[work[i, j]]
data[i, j] = data_p[forest[i, j]]
return data
skimage/morphology/tests/test_ccomp.py
+24
View File
@@ -37,5 +37,29 @@ class TestConnectedComponents:
assert_array_equal(label(x),
x)
def test_4_vs_8(self):
x = np.array([[0, 1],
[1, 0]], dtype=int)
assert_array_equal(label(x, 4),
[[0, 1],
[2, 3]])
assert_array_equal(label(x, 8),
[[0, 1],
[1, 0]])
def test_background(self):
x = np.array([[1, 0, 0],
[1, 1, 5],
[0, 0, 0]])
assert_array_equal(label(x), [[0, 1, 1],
[0, 0, 2],
[3, 3, 3]])
assert_array_equal(label(x, background=0),
[[0, -1, -1],
[0, 0, 1],
[-1, -1, -1]])
if __name__ == "__main__":
run_module_suite()