Merge pull request #1787 from ahojnnes/rpropsfix

Various fixes and improvements

CONTRIBUTORS.txt

@@ -215,3 +215,6 @@
 
 - Jim Fienup, Alexander Iacchetta
   In-depth review of sub-pixel shift registration
+
+- Damian Eads
+  Structuring elements in morphology module.

skimage/filters/_gabor.py

@@ -56,7 +56,7 @@ def gabor_kernel(frequency, theta=0, bandwidth=1, sigma_x=None, sigma_y=None,
 
     Examples
     --------
-    >>> from skimage.filter import gabor_kernel
+    >>> from skimage.filters import gabor_kernel
     >>> from skimage import io
     >>> from matplotlib import pyplot as plt  # doctest: +SKIP
 
@@ -148,7 +148,7 @@ def gabor(image, frequency, theta=0, bandwidth=1, sigma_x=None,
 
     Examples
     --------
-    >>> from skimage.filter import gabor
+    >>> from skimage.filters import gabor
     >>> from skimage import data, io
     >>> from matplotlib import pyplot as plt  # doctest: +SKIP
 

skimage/measure/_label.py

@@ -1,7 +1,7 @@
 from ._ccomp import label as _label
 
 def label(input, neighbors=None, background=None, return_num=False,
-        connectivity=None):
+          connectivity=None):
     return _label(input, neighbors, background, return_num, connectivity)
 
 label.__doc__ = _label.__doc__

skimage/measure/_regionprops.py

@@ -157,7 +157,7 @@ class _RegionProperties(object):
     @property
     def euler_number(self):
         euler_array = self.filled_image != self.image
-        _, num = label(euler_array, neighbors=8, return_num=True)
+        _, num = label(euler_array, neighbors=8, return_num=True, background=-1)
         return -num + 1
 
     @property
@@ -473,7 +473,7 @@ def regionprops(label_image, intensity_image=None, cache=True):
     Examples
     --------
     >>> from skimage import data, util
-    >>> from skimage.morphology import label
+    >>> from skimage.measure import label
     >>> img = util.img_as_ubyte(data.coins()) > 110
     >>> label_img = label(img, connectivity=img.ndim)
     >>> props = regionprops(label_img)

skimage/measure/tests/test_regionprops.py

@@ -128,14 +128,12 @@ def test_equiv_diameter():
 
 
 def test_euler_number():
-    with expected_warnings(['`background`|CObject type']):
-        en = regionprops(SAMPLE)[0].euler_number
+    en = regionprops(SAMPLE)[0].euler_number
     assert en == 0
 
     SAMPLE_mod = SAMPLE.copy()
     SAMPLE_mod[7, -3] = 0
-    with expected_warnings(['`background`|CObject type']):
-        en = regionprops(SAMPLE_mod)[0].euler_number
+    en = regionprops(SAMPLE_mod)[0].euler_number
     assert en == -1
 
 
@@ -374,9 +372,8 @@ def test_equals():
     r2 = regions[0]
     r3 = regions[1]
 
-    with expected_warnings(['`background`|CObject type']):
-        assert_equal(r1 == r2, True, "Same regionprops are not equal")
-        assert_equal(r1 != r3, True, "Different regionprops are equal")
+    assert_equal(r1 == r2, True, "Same regionprops are not equal")
+    assert_equal(r1 != r3, True, "Different regionprops are equal")
 
 
 if __name__ == "__main__":

skimage/morphology/convex_hull.py

@@ -1,11 +1,16 @@
 __all__ = ['convex_hull_image', 'convex_hull_object']
 
 import numpy as np
-from ..measure import grid_points_in_poly
+from ..measure._pnpoly import grid_points_in_poly
 from ._convex_hull import possible_hull
 from ..measure._label import label
 from ..util import unique_rows
 
+try:
+    from scipy.spatial import Delaunay
+except ImportError:
+    Delaunay = None
+
 
 def convex_hull_image(image):
     """Compute the convex hull image of a binary image.
@@ -15,12 +20,12 @@ def convex_hull_image(image):
 
     Parameters
     ----------
-    image : ndarray
+    image : (M, N) array
         Binary input image. This array is cast to bool before processing.
 
     Returns
     -------
-    hull : ndarray of bool
+    hull : (M, N) array of bool
         Binary image with pixels in convex hull set to True.
 
     References
@@ -29,12 +34,13 @@ def convex_hull_image(image):
 
     """
 
-    image = image.astype(bool)
+    if Delaunay is None:
+        raise ImportError("Could not import scipy.spatial.Delaunay, "
+                          "only available in scipy >= 0.9.")
 
     # Here we do an optimisation by choosing only pixels that are
     # the starting or ending pixel of a row or column.  This vastly
-    # limits the number of coordinates to examine for the virtual
-    # hull.
+    # limits the number of coordinates to examine for the virtual hull.
     coords = possible_hull(image.astype(np.uint8))
     N = len(coords)
 
@@ -48,12 +54,6 @@ def convex_hull_image(image):
     # scipy.spatial.Delaunay, so we remove them.
     coords = unique_rows(coords_corners)
 
-    try:
-        from scipy.spatial import Delaunay
-    except ImportError:
-        raise ImportError('Could not import scipy.spatial, only available in '
-                          'scipy >= 0.9.')
-
     # Subtract offset
     offset = coords.mean(axis=0)
     coords -= offset

skimage/morphology/selem.py

@@ -1,12 +1,8 @@
-"""
-:author: Damian Eads, 2009
-:license: modified BSD
-"""
-
 import numpy as np
 from scipy import ndimage as ndi
 from .. import draw
 
+
 def square(width, dtype=np.uint8):
     """Generates a flat, square-shaped structuring element.
 
@@ -37,7 +33,7 @@ def rectangle(width, height, dtype=np.uint8):
     """Generates a flat, rectangular-shaped structuring element.
 
     Every pixel in the rectangle generated for a given width and given height
-    belongs to the neighboorhood.
+    belongs to the neighborhood.
 
     Parameters
     ----------
@@ -65,7 +61,7 @@ def diamond(radius, dtype=np.uint8):
     """Generates a flat, diamond-shaped structuring element.
 
     A pixel is part of the neighborhood (i.e. labeled 1) if
-    the city block/manhattan distance between it and the center of
+    the city block/Manhattan distance between it and the center of
     the neighborhood is no greater than radius.
 
     Parameters
@@ -193,7 +189,7 @@ def octahedron(radius, dtype=np.uint8):
 
     This is the 3D equivalent of a diamond.
     A pixel is part of the neighborhood (i.e. labeled 1) if
-    the city block/manhattan distance between it and the center of
+    the city block/Manhattan distance between it and the center of
     the neighborhood is no greater than radius.
 
     Parameters

skimage/morphology/tests/test_convex_hull.py

@@ -139,5 +139,6 @@ def test_object():
 
     assert_raises(ValueError, convex_hull_object, image, 7)
 
+
 if __name__ == "__main__":
     np.testing.run_module_suite()