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ENH start cythonizing quickshift, get rid of hstack.

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This commit is contained in:
Andreas Mueller
2012-08-03 11:37:10 +01:00
parent eb5c2fe5d4
commit 8c735b6470
2 changed files with 25 additions and 18 deletions
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skimage/segmentation/quickshift.py → skimage/segmentation/quickshift.pyx
+14 -11
View File
@@ -1,8 +1,10 @@
import numpy as np
cimport numpy as np
from itertools import product
def quickshift(image, sigma=5, tau=10):
def quickshift(np.ndarray[dtype=np.float_t, ndim=3, mode="c"] image, sigma=5, tau=10):
"""Computes quickshift clustering in RGB-(x,y) space.
Parameters
@@ -31,37 +33,38 @@ def quickshift(image, sigma=5, tau=10):
# window size for neighboring pixels to consider
if sigma < 1:
raise ValueError("Sigma should be >= 1")
w = int(2 * sigma)
cdef int w = int(2 * sigma)
cdef int width = image.shape[0]
cdef int height = image.shape[1]
width, height = image.shape[:2]
densities = np.zeros((width, height))
cdef np.ndarray[dtype=np.float_t, ndim=2] densities = np.zeros((width, height))
# compute densities
for x, y in product(xrange(width), xrange(height)):
current_pixel = np.hstack([image[x, y, :], x, y])
current_pixel = image[x, y, :]
for xx, yy in product(xrange(-w / 2, w / 2 + 1), repeat=2):
x_, y_ = x + xx, y + yy
if 0 <= x_ < width and 0 <= y_ < height:
other_pixel = np.hstack([image[x_, y_, :], x_, y_])
dist = np.sum((current_pixel - other_pixel) ** 2)
dist = np.sum((current_pixel - image[x_, y_, :])**2) + (x - x_)**2 + (y - y_)**2
densities[x, y] += np.exp(-dist / sigma)
# this will break ties that otherwise would give us headache
densities += np.random.normal(scale=0.00001, size=densities.shape)
densities += np.random.normal(scale=0.00001, size=(width, height))
# default parent to self:
parent = np.arange(width * height).reshape(width, height)
dist_parent = np.zeros((width, height))
# find nearest node with higher density
for x, y in product(xrange(width), xrange(height)):
current_density = densities[x, y]
current_pixel = np.hstack([image[x, y, :], x, y])
current_pixel = image[x, y, :]
closest = np.inf
for xx, yy in product(xrange(-w / 2, w / 2 + 1), repeat=2):
x_, y_ = x + xx, y + yy
if 0 <= x_ < width and 0 <= y_ < height:
if densities[x_, y_] > current_density:
other_pixel = np.hstack([image[x_, y_, :], x_, y_])
dist = np.sum((current_pixel - other_pixel) ** 2)
dist = np.sum((current_pixel - image[x_, y_, :])**2) + (x - x_)**2 + (y - y_)**2
if dist < closest:
closest = dist
parent[x, y] = x_ * width + y_
skimage/segmentation/setup.py
+11 -7
View File
@@ -5,23 +5,27 @@ from skimage._build import cython
base_path = os.path.abspath(os.path.dirname(__file__))
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('segmentation', parent_package, top_path)
cython(['felzenszwalb.pyx'], working_path=base_path)
config.add_extension('felzenszwalb', sources=['felzenszwalb.c'],
#cython(['felzenszwalb.pyx'], working_path=base_path)
#config.add_extension('felzenszwalb', sources=['felzenszwalb.c'],
#include_dirs=[get_numpy_include_dirs()])
cython(['quickshift.pyx'], working_path=base_path)
config.add_extension('quickshift', sources=['quickshift.c'],
include_dirs=[get_numpy_include_dirs()])
return config
if __name__ == '__main__':
from numpy.distutils.core import setup
setup(maintainer = 'scikits-image Developers',
maintainer_email = 'scikits-image@googlegroups.com',
description = 'Segmentation Algorithms',
url = 'https://github.com/scikits-image/scikits-image',
license = 'SciPy License (BSD Style)',
setup(maintainer='scikits-image Developers',
maintainer_email='scikits-image@googlegroups.com',
description='Segmentation Algorithms',
url='https://github.com/scikits-image/scikits-image',
license='SciPy License (BSD Style)',
**(configuration(top_path='').todict())
)