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add py wrappers

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This commit is contained in:
Olivier Debeir
2012-10-05 10:56:05 +02:00
parent 806bbbcb65
commit db3803fd72
7 changed files with 215 additions and 14 deletions
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skimage/rank/__init__.py
+3
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@@ -0,0 +1,3 @@
from .rank import *
from .percentile_rank import *
from .bilateral_rank import *
skimage/rank/bilateral_rank.py
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"""
:author: Olivier Debeir, 2012
:license: modified BSD
"""
__docformat__ = 'restructuredtext en'
import warnings
from skimage import img_as_ubyte
__all__ = ['bilateral_mean']
def bilateral_mean(image, selem, out=None, shift_x=False, shift_y=False, s0=10, s1=10):
pass
skimage/rank/percentile_rank.py
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"""
:author: Olivier Debeir, 2012
:license: modified BSD
"""
__docformat__ = 'restructuredtext en'
import warnings
from skimage import img_as_ubyte
__all__ = ['percentile_mean']
def percentile_mean(image, selem, out=None, shift_x=False, shift_y=False, p0=.0, p1=1.):
"""Return greyscale local mean of an image.
Mean is computed on the given structuring element. Only pixel values contained inside the
percentile interval [p0,p1] are taken into account.
Parameters
----------
image : ndarray
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
The array to store the result of the morphology. If None is
passed, a new array will be allocated.
shift_x, shift_y : bool
shift structuring element about center point. This only affects
eccentric structuring elements (i.e. selem with even numbered sides).
Shift is bounded to the structuring element sizes.
Returns
-------
local mean : uint8 array or uint16 array depending on input image
The result of the local mean.
Examples
--------
to be updated
>>> # Erosion shrinks bright regions
>>> from skimage.morphology import square
>>> bright_square = np.array([[0, 0, 0, 0, 0],
... [0, 1, 1, 1, 0],
... [0, 1, 1, 1, 0],
... [0, 1, 1, 1, 0],
... [0, 0, 0, 0, 0]], dtype=np.uint8)
>>> erosion(bright_square, square(3))
array([[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 1, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0]], dtype=uint8)
"""
pass
skimage/rank/rank.py
+112
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@@ -0,0 +1,112 @@
"""
:author: Olivier Debeir, 2012
:license: modified BSD
"""
__docformat__ = 'restructuredtext en'
import warnings
from skimage import img_as_ubyte
__all__ = ['mean','percentile_mean','bilateral_mean']
def percentile_mean(image, selem, out=None, shift_x=False, shift_y=False, p0=.0, p1=1.):
"""Return greyscale local mean of an image.
Mean is computed on the given structuring element. Only pixel values contained inside the
percentile interval [p0,p1] are taken into account.
Parameters
----------
image : ndarray
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
The array to store the result of the morphology. If None is
passed, a new array will be allocated.
shift_x, shift_y : bool
shift structuring element about center point. This only affects
eccentric structuring elements (i.e. selem with even numbered sides).
Shift is bounded to the structuring element sizes.
Returns
-------
local mean : uint8 array or uint16 array depending on input image
The result of the local mean.
Examples
--------
to be updated
>>> # Erosion shrinks bright regions
>>> from skimage.morphology import square
>>> bright_square = np.array([[0, 0, 0, 0, 0],
... [0, 1, 1, 1, 0],
... [0, 1, 1, 1, 0],
... [0, 1, 1, 1, 0],
... [0, 0, 0, 0, 0]], dtype=np.uint8)
>>> erosion(bright_square, square(3))
array([[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 1, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0]], dtype=uint8)
"""
pass
def bilateral_mean(image, selem, out=None, shift_x=False, shift_y=False, s0=10, s1=10):
pass
def mean(image, selem, out=None, shift_x=False, shift_y=False):
"""Return greyscale local mean of an image.
Mean is computed on the given structuring element.
Parameters
----------
image : ndarray
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
The array to store the result of the morphology. If None is
passed, a new array will be allocated.
shift_x, shift_y : bool
shift structuring element about center point. This only affects
eccentric structuring elements (i.e. selem with even numbered sides).
Shift is bounded to the structuring element sizes.
Returns
-------
local mean : uint8 array or uint16 array depending on input image
The result of the local mean.
Examples
--------
to be updated
>>> # Erosion shrinks bright regions
>>> from skimage.morphology import square
>>> bright_square = np.array([[0, 0, 0, 0, 0],
... [0, 1, 1, 1, 0],
... [0, 1, 1, 1, 0],
... [0, 1, 1, 1, 0],
... [0, 0, 0, 0, 0]], dtype=np.uint8)
>>> erosion(bright_square, square(3))
array([[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 1, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0]], dtype=uint8)
"""
pass
# if image is out:
# raise NotImplementedError("In-place erosion not supported!")
# image = img_as_ubyte(image)
# selem = img_as_ubyte(selem)
# return cmorph.erode(image, selem, out=out,
# shift_x=shift_x, shift_y=shift_y)
skimage/rank/setup.py
+10 -10
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@@ -6,11 +6,11 @@ from Cython.Distutils import build_ext
setup(
cmdclass = {'build_ext': build_ext},
ext_modules = [Extension("crank8", ["_crank8.pyx"], include_dirs=[np.get_include()]),
Extension("crank8_percentiles", ["_crank8_percentiles.pyx"], include_dirs=[np.get_include()]),
Extension("crank16", ["_crank16.pyx"], include_dirs=[np.get_include()]),
Extension("crank16_bilateral", ["_crank16_bilateral.pyx"], include_dirs=[np.get_include()]),
Extension("crank16_percentiles", ["_crank16_percentiles.pyx"], include_dirs=[np.get_include()])]
ext_modules = [Extension("_crank8", ["_crank8.pyx"], include_dirs=[np.get_include()]),
Extension("_crank8_percentiles", ["_crank8_percentiles.pyx"], include_dirs=[np.get_include()]),
Extension("_crank16", ["_crank16.pyx"], include_dirs=[np.get_include()]),
Extension("_crank16_bilateral", ["_crank16_bilateral.pyx"], include_dirs=[np.get_include()]),
Extension("_crank16_percentiles", ["_crank16_percentiles.pyx"], include_dirs=[np.get_include()])]
)
@@ -34,15 +34,15 @@ setup(
# cython(['_crank16_percentiles.pyx'], working_path=base_path)
# cython(['_crank16_bilateral.pyx'], working_path=base_path)
#
# config.add_extension('crank8', sources=['_crank8.c'],
# config.add_extension('_crank8', sources=['_crank8.c'],
# include_dirs=[get_numpy_include_dirs()])
# config.add_extension('crank8_percentiles', sources=['_crank8_percentiles.c'],
# config.add_extension('_crank8_percentiles', sources=['_crank8_percentiles.c'],
# include_dirs=[get_numpy_include_dirs()])
# config.add_extension('crank16', sources=['_crank16.c'],
# config.add_extension('_crank16', sources=['_crank16.c'],
# include_dirs=[get_numpy_include_dirs()])
# config.add_extension('crank16_percentiles', sources=['_crank16_percentiles.c'],
# config.add_extension('_crank16_percentiles', sources=['_crank16_percentiles.c'],
# include_dirs=[get_numpy_include_dirs()])
# config.add_extension('crank16_bilateral', sources=['_crank16_bilateral.c'],
# config.add_extension('_crank16_bilateral', sources=['_crank16_bilateral.c'],
# include_dirs=[get_numpy_include_dirs()])
#
# return config
skimage/rank/tests/demo_benchmark.py
+4 -4
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@@ -2,18 +2,18 @@ import numpy as np
import matplotlib.pyplot as plt
from skimage import data
from skimage.morphology import cmorph
from skimage.rank import crank8
from skimage.morphology import dilation
from skimage.rank import _crank8
from tools import log_timing
@log_timing
def cr_max(image,selem):
return crank8.maximum(image=image,selem = selem)
return _crank8.maximum(image=image,selem = selem)
@log_timing
def cm_dil(image,selem):
return cmorph.dilate(image=image,selem = selem)
return dilation(image=image,selem = selem)
def compare():
skimage/rank/tests/test_rank.py
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import numpy as np
import matplotlib.pyplot as plt
from skimage import data
import skimage.rank as rank
print dir(rank)