Merge branch 'master' of git://github.com/scikit-image/scikit-image

bento.info

@@ -64,9 +64,9 @@ Library:
     Extension: skimage.filter._ctmf
         Sources:
             skimage/filter/_ctmf.pyx
-    Extension: skimage.filter._denoise
+    Extension: skimage.filter._denoise_cy
         Sources:
-            skimage/filter/_denoise.pyx
+            skimage/filter/_denoise_cy.pyx
     Extension: skimage.morphology.ccomp
         Sources:
             skimage/morphology/ccomp.pyx
@@ -91,6 +91,9 @@ Library:
     Extension: skimage.morphology._greyreconstruct
         Sources:
             skimage/morphology/_greyreconstruct.pyx
+    Extension: skimage.feature.corner_cy
+        Sources:
+            skimage/feature/corner_cy.pyx
     Extension: skimage.feature._texture
         Sources:
             skimage/feature/_texture.pyx

setup.py

@@ -138,7 +138,7 @@ if __name__ == "__main__":
 
         configuration=configuration,
 
-        packages=setuptools.find_packages(),
+        packages=setuptools.find_packages(exclude=['doc']),
         include_package_data=True,
         zip_safe=False, # the package can run out of an .egg file
 

skimage/draw/__init__.py

@@ -1,2 +1,5 @@
-from ._draw import line, polygon, ellipse, circle, circle_perimeter, ellipse_perimeter, set_color
+from ._draw import line, polygon, ellipse, ellipse_perimeter, \
+                   circle, circle_perimeter, set_color
+
+
 bresenham = line

skimage/draw/_draw.pyx

@@ -28,6 +28,7 @@ def line(int y, int x, int y2, int x2):
         ``img[rr, cc] = 1``.
 
     """
+
     cdef np.ndarray[np.int32_t, ndim=1, mode="c"] rr, cc
 
     cdef int steep = 0
@@ -92,7 +93,9 @@ def polygon(y, x, shape=None):
         Pixel coordinates of polygon.
         May be used to directly index into an array, e.g.
         ``img[rr, cc] = 1``.
+
     """
+
     cdef int nr_verts = x.shape[0]
     cdef int minr = <int>max(0, y.min())
     cdef int maxr = <int>math.ceil(y.max())
@@ -142,7 +145,9 @@ def ellipse(double cy, double cx, double yradius, double xradius, shape=None):
         Pixel coordinates of ellipse.
         May be used to directly index into an array, e.g.
         ``img[rr, cc] = 1``.
+
     """
+
     cdef int minr = <int>max(0, cy - yradius)
     cdef int maxr = <int>math.ceil(cy + yradius)
     cdef int minc = <int>max(0, cx - xradius)
@@ -184,7 +189,9 @@ def circle(double cy, double cx, double radius, shape=None):
         Pixel coordinates of circle.
         May be used to directly index into an array, e.g.
         ``img[rr, cc] = 1``.
+
     """
+
     return ellipse(cy, cx, radius, radius, shape)
 
 
@@ -287,16 +294,16 @@ def ellipse_perimeter(int cy, int cx, int yradius, int xradius):
     ----------
     .. [1] J. Kennedy "A fast Bresenham type algorithm for
         drawing ellipses".
+
     """
-    # If both radii == 0, return the center
-    # to avoid infinite loop in 2nd set
+
+    # If both radii == 0, return the center to avoid infinite loop in 2nd set
     if xradius == 0 and yradius == 0:
         return np.array(cy), np.array(cx)
 
-    # a and b are xradius an yradius
-    # compute 2a^2 and 2b^2
-    cdef int twoasquared = 2 * xradius * xradius
-    cdef int twobsquared = 2 * yradius * yradius
+    # a and b are xradius an yradius compute 2a^2 and 2b^2
+    cdef int twoasquared = 2 * xradius**2
+    cdef int twobsquared = 2 * yradius**2
 
     # Pixels
     cdef list px = list()
@@ -353,8 +360,9 @@ def ellipse_perimeter(int cy, int cx, int yradius, int xradius):
 
 
 def set_color(img, coords, color):
-    """Set pixel color in the image at the given coordinates. Coordinates that
-    exceed the shape of the image will be ignored.
+    """Set pixel color in the image at the given coordinates.
+
+    Coordinates that exceed the shape of the image will be ignored.
 
     Parameters
     ----------
@@ -369,7 +377,9 @@ def set_color(img, coords, color):
     -------
     img : (M, N, D) ndarray
         The updated image.
+
     """
+
     rr, cc = coords
     rr_inside = np.logical_and(rr >= 0, rr < img.shape[0])
     cc_inside = np.logical_and(cc >= 0, cc < img.shape[1])

skimage/draw/setup.py

@@ -15,7 +15,7 @@ def configuration(parent_package='', top_path=None):
     cython(['_draw.pyx'], working_path=base_path)
 
     config.add_extension('_draw', sources=['_draw.c'],
-                         include_dirs=[get_numpy_include_dirs(), '../shared'])
+                         include_dirs=[get_numpy_include_dirs(), '../_shared'])
 
     return config
 

skimage/feature/_hog.py

@@ -142,8 +142,8 @@ def hog(image, orientations=9, pixels_per_cell=(8, 8),
                     centre = tuple([y * cy + cy // 2, x * cx + cx // 2])
                     dx = radius * cos(float(o) / orientations * np.pi)
                     dy = radius * sin(float(o) / orientations * np.pi)
-                    rr, cc = draw.bresenham(centre[0] - dy, centre[1] - dx,
-                                            centre[0] + dy, centre[1] + dx)
+                    rr, cc = draw.bresenham(centre[0] - dx, centre[1] - dy,
+                                            centre[0] + dx, centre[1] + dy)
                     hog_image[rr, cc] += orientation_histogram[y, x, o]
 
     """

skimage/feature/tests/test_corner.py

@@ -31,6 +31,7 @@ def test_square_image():
 def test_noisy_square_image():
     im = np.zeros((50, 50)).astype(float)
     im[:25, :25] = 1.
+    np.random.seed(seed=1234)
     im = im + np.random.uniform(size=im.shape) * .2
 
     # Moravec

skimage/filter/tests/test_denoise.py

@@ -4,6 +4,9 @@ from numpy.testing import run_module_suite, assert_raises, assert_equal
 from skimage import filter, data, color, img_as_float
 
 
+np.random.seed(1234)
+
+
 lena = img_as_float(data.lena()[:256, :256])
 lena_gray = color.rgb2gray(lena)
 

skimage/measure/tests/test_structural_similarity.py

@@ -4,6 +4,9 @@ from numpy.testing import assert_equal, assert_raises
 from skimage.measure import structural_similarity as ssim
 
 
+np.random.seed(1234)
+
+
 def test_ssim_patch_range():
     N = 51
     X = (np.random.random((N, N)) * 255).astype(np.uint8)

skimage/morphology/setup.py

@@ -29,7 +29,7 @@ def configuration(parent_package='', top_path=None):
     config.add_extension('_skeletonize_cy', sources=['_skeletonize_cy.c'],
                          include_dirs=[get_numpy_include_dirs()])
     config.add_extension('_pnpoly', sources=['_pnpoly.c'],
-                         include_dirs=[get_numpy_include_dirs(), '../shared'])
+                         include_dirs=[get_numpy_include_dirs(), '../_shared'])
     config.add_extension('_convex_hull', sources=['_convex_hull.c'],
                          include_dirs=[get_numpy_include_dirs()])
     config.add_extension('_greyreconstruct', sources=['_greyreconstruct.c'],