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Merge pull request #187 from tonysyu/morph-cleanup

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ENH: Grey morphology cleanup.
This commit is contained in:
Stefan van der Walt
2012-05-03 15:15:38 -07:00
parent 71c8edae88 dc6c3d0222
commit 03aa64da39
2 changed files with 145 additions and 61 deletions
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skimage/morphology/grey.py
+78 -34
View File
@@ -5,11 +5,20 @@
__docformat__ = 'restructuredtext en'
import warnings
import numpy as np
eps = np.finfo(float).eps
import skimage
def greyscale_erode(image, selem, out=None, shift_x=False, shift_y=False):
__all__ = ['erosion', 'dilation', 'opening', 'closing', 'white_tophat',
'black_tophat', 'greyscale_erode', 'greyscale_dilate',
'greyscale_open', 'greyscale_close', 'greyscale_white_top_hat',
'greyscale_black_top_hat']
def erosion(image, selem, out=None, shift_x=False, shift_y=False):
"""Return greyscale morphological erosion of an image.
Morphological erosion sets a pixel at (i,j) to the minimum over all pixels
@@ -19,7 +28,7 @@ def greyscale_erode(image, selem, out=None, shift_x=False, shift_y=False):
Parameters
----------
image : ndarray
The image as a uint8 ndarray.
Image array.
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
@@ -34,7 +43,7 @@ def greyscale_erode(image, selem, out=None, shift_x=False, shift_y=False):
Returns
-------
eroded : ndarray
eroded : uint8 array
The result of the morphological erosion.
Examples
@@ -46,7 +55,7 @@ def greyscale_erode(image, selem, out=None, shift_x=False, shift_y=False):
... [0, 1, 1, 1, 0],
... [0, 1, 1, 1, 0],
... [0, 0, 0, 0, 0]], dtype=np.uint8)
>>> greyscale_erode(bright_square, square(3))
>>> erosion(bright_square, square(3))
array([[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 1, 0, 0],
@@ -56,6 +65,8 @@ def greyscale_erode(image, selem, out=None, shift_x=False, shift_y=False):
"""
if image is out:
raise NotImplementedError("In-place erosion not supported!")
image = skimage.img_as_ubyte(image)
try:
import skimage.morphology.cmorph as cmorph
out = cmorph.erode(image, selem, out=out,
@@ -64,7 +75,8 @@ def greyscale_erode(image, selem, out=None, shift_x=False, shift_y=False):
except ImportError:
raise ImportError("cmorph extension not available.")
def greyscale_dilate(image, selem, out=None, shift_x=False, shift_y=False):
def dilation(image, selem, out=None, shift_x=False, shift_y=False):
"""Return greyscale morphological dilation of an image.
Morphological dilation sets a pixel at (i,j) to the maximum over all pixels
@@ -75,7 +87,7 @@ def greyscale_dilate(image, selem, out=None, shift_x=False, shift_y=False):
----------
image : ndarray
The image as a uint8 ndarray.
Image array.
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
@@ -90,7 +102,7 @@ def greyscale_dilate(image, selem, out=None, shift_x=False, shift_y=False):
Returns
-------
dilated : ndarray
dilated : uint8 array
The result of the morphological dilation.
Examples
@@ -102,7 +114,7 @@ def greyscale_dilate(image, selem, out=None, shift_x=False, shift_y=False):
... [0, 0, 1, 0, 0],
... [0, 0, 0, 0, 0],
... [0, 0, 0, 0, 0]], dtype=np.uint8)
>>> greyscale_dilate(bright_pixel, square(3))
>>> dilation(bright_pixel, square(3))
array([[0, 0, 0, 0, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
@@ -112,6 +124,8 @@ def greyscale_dilate(image, selem, out=None, shift_x=False, shift_y=False):
"""
if image is out:
raise NotImplementedError("In-place dilation not supported!")
image = skimage.img_as_ubyte(image)
try:
from . import cmorph
out = cmorph.dilate(image, selem, out=out,
@@ -120,7 +134,8 @@ def greyscale_dilate(image, selem, out=None, shift_x=False, shift_y=False):
except ImportError:
raise ImportError("cmorph extension not available.")
def greyscale_open(image, selem, out=None):
def opening(image, selem, out=None):
"""Return greyscale morphological opening of an image.
The morphological opening on an image is defined as an erosion followed by
@@ -131,7 +146,7 @@ def greyscale_open(image, selem, out=None):
Parameters
----------
image : ndarray
The image as a uint8 ndarray.
Image array.
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
@@ -142,7 +157,7 @@ def greyscale_open(image, selem, out=None):
Returns
-------
opening : ndarray
opening : uint8 array
The result of the morphological opening.
Examples
@@ -154,7 +169,7 @@ def greyscale_open(image, selem, out=None):
... [1, 1, 1, 1, 1],
... [1, 1, 0, 1, 1],
... [1, 0, 0, 0, 1]], dtype=np.uint8)
>>> greyscale_open(bad_connection, square(3))
>>> opening(bad_connection, square(3))
array([[0, 0, 0, 0, 0],
[1, 1, 0, 1, 1],
[1, 1, 0, 1, 1],
@@ -166,12 +181,12 @@ def greyscale_open(image, selem, out=None):
shift_x = True if (w % 2) == 0 else False
shift_y = True if (h % 2) == 0 else False
eroded = greyscale_erode(image, selem)
out = greyscale_dilate(eroded, selem, out=out,
shift_x=shift_x, shift_y=shift_y)
eroded = erosion(image, selem)
out = dilation(eroded, selem, out=out, shift_x=shift_x, shift_y=shift_y)
return out
def greyscale_close(image, selem, out=None):
def closing(image, selem, out=None):
"""Return greyscale morphological closing of an image.
The morphological closing on an image is defined as a dilation followed by
@@ -182,7 +197,7 @@ def greyscale_close(image, selem, out=None):
Parameters
----------
image : ndarray
The image as a uint8 ndarray.
Image array.
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
@@ -193,8 +208,8 @@ def greyscale_close(image, selem, out=None):
Returns
-------
opening : ndarray
The result of the morphological opening.
closing : uint8 array
The result of the morphological closing.
Examples
--------
@@ -205,7 +220,7 @@ def greyscale_close(image, selem, out=None):
... [1, 1, 0, 1, 1],
... [0, 0, 0, 0, 0],
... [0, 0, 0, 0, 0]], dtype=np.uint8)
>>> greyscale_close(broken_line, square(3))
>>> closing(broken_line, square(3))
array([[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[1, 1, 1, 1, 1],
@@ -217,12 +232,12 @@ def greyscale_close(image, selem, out=None):
shift_x = True if (w % 2) == 0 else False
shift_y = True if (h % 2) == 0 else False
dilated = greyscale_dilate(image, selem)
out = greyscale_erode(dilated, selem, out=out,
shift_x=shift_x, shift_y=shift_y)
dilated = dilation(image, selem)
out = erosion(dilated, selem, out=out, shift_x=shift_x, shift_y=shift_y)
return out
def greyscale_white_top_hat(image, selem, out=None):
def white_tophat(image, selem, out=None):
"""Return white top hat of an image.
The white top hat of an image is defined as the image minus its
@@ -232,7 +247,7 @@ def greyscale_white_top_hat(image, selem, out=None):
Parameters
----------
image : ndarray
The image as a uint8 ndarray.
Image array.
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
@@ -243,7 +258,7 @@ def greyscale_white_top_hat(image, selem, out=None):
Returns
-------
opening : ndarray
opening : uint8 array
The result of the morphological white top hat.
Examples
@@ -255,7 +270,7 @@ def greyscale_white_top_hat(image, selem, out=None):
... [3, 5, 9, 5, 3],
... [3, 4, 5, 4, 3],
... [2, 3, 3, 3, 2]], dtype=np.uint8)
>>> greyscale_white_top_hat(bright_on_grey, square(3))
>>> white_tophat(bright_on_grey, square(3))
array([[0, 0, 0, 0, 0],
[0, 0, 1, 0, 0],
[0, 1, 5, 1, 0],
@@ -265,12 +280,14 @@ def greyscale_white_top_hat(image, selem, out=None):
"""
if image is out:
raise NotImplementedError("Cannot perform white top hat in place.")
image = skimage.img_as_ubyte(image)
out = greyscale_open(image, selem, out=out)
out = opening(image, selem, out=out)
out = image - out
return out
def greyscale_black_top_hat(image, selem, out=None):
def black_tophat(image, selem, out=None):
"""Return black top hat of an image.
The black top hat of an image is defined as its morphological closing minus
@@ -281,7 +298,7 @@ def greyscale_black_top_hat(image, selem, out=None):
Parameters
----------
image : ndarray
The image as a uint8 ndarray.
Image array.
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
@@ -292,7 +309,7 @@ def greyscale_black_top_hat(image, selem, out=None):
Returns
-------
opening : ndarray
opening : uint8 array
The result of the black top filter.
Examples
@@ -304,7 +321,7 @@ def greyscale_black_top_hat(image, selem, out=None):
... [6, 4, 0, 4, 6],
... [6, 5, 4, 5, 6],
... [7, 6, 6, 6, 7]], dtype=np.uint8)
>>> greyscale_black_top_hat(dark_on_grey, square(3))
>>> black_tophat(dark_on_grey, square(3))
array([[0, 0, 0, 0, 0],
[0, 0, 1, 0, 0],
[0, 1, 5, 1, 0],
@@ -314,7 +331,34 @@ def greyscale_black_top_hat(image, selem, out=None):
"""
if image is out:
raise NotImplementedError("Cannot perform white top hat in place.")
out = greyscale_close(image, selem, out=out)
image = skimage.img_as_ubyte(image)
out = closing(image, selem, out=out)
out = out - image
return out
def greyscale_erode(*args, **kwargs):
warnings.warn("`greyscale_erode` renamed `erosion`.")
return erosion(*args, **kwargs)
def greyscale_dilate(*args, **kwargs):
warnings.warn("`greyscale_dilate` renamed `dilation`.")
return dilation(*args, **kwargs)
def greyscale_open(*args, **kwargs):
warnings.warn("`greyscale_open` renamed `opening`.")
return opening(*args, **kwargs)
def greyscale_close(*args, **kwargs):
warnings.warn("`greyscale_close` renamed `closing`.")
return closing(*args, **kwargs)
def greyscale_white_top_hat(*args, **kwargs):
warnings.warn("`greyscale_white_top_hat` renamed `white_tophat`.")
return white_tophat(*args, **kwargs)
def greyscale_black_top_hat(*args, **kwargs):
warnings.warn("`greyscale_black_top_hat` renamed `black_tophat`.")
return black_tophat(*args, **kwargs)
skimage/morphology/tests/test_morphology.py → skimage/morphology/tests/test_grey.py
+67 -27
View File
@@ -1,12 +1,13 @@
import os.path
import numpy as np
from numpy.testing import *
from numpy import testing
import skimage
from skimage import data_dir
from skimage.io import imread
from skimage import data_dir
from skimage.morphology import *
from skimage.morphology import grey
from skimage.morphology import selem
lena = np.load(os.path.join(data_dir, 'lena_GRAY_U8.npy'))
@@ -19,48 +20,48 @@ class TestMorphology():
expected_result = matlab_results[arrname]
mask = strel_func(k)
actual_result = morph_func(lena, mask)
assert_equal(expected_result, actual_result)
testing.assert_equal(expected_result, actual_result)
k = k + 1
def test_erode_diamond(self):
self.morph_worker(lena, "diamond-erode-matlab-output.npz",
greyscale_erode, diamond)
grey.erosion, selem.diamond)
def test_dilate_diamond(self):
self.morph_worker(lena, "diamond-dilate-matlab-output.npz",
greyscale_dilate, diamond)
grey.dilation, selem.diamond)
def test_open_diamond(self):
self.morph_worker(lena, "diamond-open-matlab-output.npz",
greyscale_open, diamond)
grey.opening, selem.diamond)
def test_close_diamond(self):
self.morph_worker(lena, "diamond-close-matlab-output.npz",
greyscale_close, diamond)
grey.closing, selem.diamond)
def test_tophat_diamond(self):
self.morph_worker(lena, "diamond-tophat-matlab-output.npz",
greyscale_white_top_hat, diamond)
grey.white_tophat, selem.diamond)
def test_bothat_diamond(self):
self.morph_worker(lena, "diamond-bothat-matlab-output.npz",
greyscale_black_top_hat, diamond)
grey.black_tophat, selem.diamond)
def test_erode_disk(self):
self.morph_worker(lena, "disk-erode-matlab-output.npz",
greyscale_erode, disk)
grey.erosion, selem.disk)
def test_dilate_disk(self):
self.morph_worker(lena, "disk-dilate-matlab-output.npz",
greyscale_dilate, disk)
grey.dilation, selem.disk)
def test_open_disk(self):
self.morph_worker(lena, "disk-open-matlab-output.npz",
greyscale_open, disk)
grey.opening, selem.disk)
def test_close_disk(self):
self.morph_worker(lena, "disk-close-matlab-output.npz",
greyscale_close, disk)
grey.closing, selem.disk)
class TestEccentricStructuringElements():
@@ -69,50 +70,89 @@ class TestEccentricStructuringElements():
self.black_pixel = 255 * np.ones((4, 4), dtype=np.uint8)
self.black_pixel[1, 1] = 0
self.white_pixel = 255 - self.black_pixel
self.selems = [square(2), rectangle(2, 2),
rectangle(2, 1), rectangle(1, 2)]
self.selems = [selem.square(2), selem.rectangle(2, 2),
selem.rectangle(2, 1), selem.rectangle(1, 2)]
def test_dilate_erode_symmetry(self):
for s in self.selems:
c = greyscale_erode(self.black_pixel, s)
d = greyscale_dilate(self.white_pixel, s)
c = grey.erosion(self.black_pixel, s)
d = grey.dilation(self.white_pixel, s)
assert np.all(c == (255 - d))
def test_open_black_pixel(self):
for s in self.selems:
grey_open = greyscale_open(self.black_pixel, s)
grey_open = grey.opening(self.black_pixel, s)
assert np.all(grey_open == self.black_pixel)
def test_close_white_pixel(self):
for s in self.selems:
grey_close = greyscale_close(self.white_pixel, s)
grey_close = grey.closing(self.white_pixel, s)
assert np.all(grey_close == self.white_pixel)
def test_open_white_pixel(self):
for s in self.selems:
assert np.all(greyscale_open(self.white_pixel, s) == 0)
assert np.all(grey.opening(self.white_pixel, s) == 0)
def test_close_black_pixel(self):
for s in self.selems:
assert np.all(greyscale_close(self.black_pixel, s) == 255)
assert np.all(grey.closing(self.black_pixel, s) == 255)
def test_white_tophat_white_pixel(self):
for s in self.selems:
tophat = greyscale_white_top_hat(self.white_pixel, s)
tophat = grey.white_tophat(self.white_pixel, s)
assert np.all(tophat == self.white_pixel)
def test_black_tophat_black_pixel(self):
for s in self.selems:
tophat = greyscale_black_top_hat(self.black_pixel, s)
tophat = grey.black_tophat(self.black_pixel, s)
assert np.all(tophat == (255 - self.black_pixel))
def test_white_tophat_black_pixel(self):
for s in self.selems:
tophat = greyscale_white_top_hat(self.black_pixel, s)
tophat = grey.white_tophat(self.black_pixel, s)
assert np.all(tophat == 0)
def test_black_tophat_white_pixel(self):
for s in self.selems:
tophat = greyscale_black_top_hat(self.white_pixel, s)
tophat = grey.black_tophat(self.white_pixel, s)
assert np.all(tophat == 0)
class TestDTypes():
def setUp(self):
k = 5
arrname = '%03i' % k
self.disk = selem.disk(k)
fname_opening = os.path.join(data_dir, "disk-open-matlab-output.npz")
self.expected_opening = np.load(fname_opening)[arrname]
fname_closing = os.path.join(data_dir, "disk-close-matlab-output.npz")
self.expected_closing = np.load(fname_closing)[arrname]
def _test_image(self, image):
result_opening = grey.opening(image, self.disk)
testing.assert_equal(result_opening, self.expected_opening)
result_closing = grey.closing(image, self.disk)
testing.assert_equal(result_closing, self.expected_closing)
def test_float(self):
image = skimage.img_as_float(lena)
self._test_image(image)
@testing.decorators.skipif(True)
def test_int(self):
image = skimage.img_as_int(lena)
self._test_image(image)
def test_uint(self):
image = skimage.img_as_uint(lena)
self._test_image(image)
if __name__ == '__main__':
testing.run_module_suite()