Merge pull request #756 from ahojnnes/morph

Fix binary erosion and dilation for NumPy 1.8

TODO.txt

@@ -6,6 +6,7 @@ Version 0.10
 * Remove {`ratio`, `sigma`} deprecation warnings of `skimage.segmentation.slic`
 * Change default mode of random_walker segmentation to 'cg_mg' > 'cg' > 'bf',
   depending on which optional dependencies are available.
+* Remove deprecated `out` parameter of `skimage.morphology.binary_*`
 
 Version 0.9
 -----------

skimage/morphology/binary.py

@@ -1,7 +1,39 @@
+import warnings
 import numpy as np
 from scipy import ndimage
 
 
+def _convolve(image, selem, out, cval):
+
+    # determine the smallest integer dtype which does not overflow
+    selem = selem != 0
+    selem_sum = np.sum(selem)
+    if selem_sum < 2 ** 8:
+        out_dtype = np.uint8
+    else:
+        out_dtype = np.intp
+
+    if out is None:
+        out = np.zeros_like(image, dtype=out_dtype)
+    else:
+        warnings.warn('Parameter `out` is deprecated and it does not equal '
+                      'the output image if the sum of the structuring element '
+                      'overflows the dtype of `out`.')
+        iinfo = np.iinfo(out.dtype)
+        if iinfo.max - iinfo.min < selem_sum:
+            raise ValueError('Sum of structuring (=%d) element results in '
+                             'overflow for dtype of `out`. You must raise the '
+                             'bit-depth.')
+
+    conv = ndimage.convolve(image > 0, selem, output=out,
+                            mode='constant', cval=cval)
+
+    if conv is not None:
+        out = conv
+
+    return out, selem_sum
+
+
 def binary_erosion(image, selem, out=None):
     """Return fast binary morphological erosion of an image.
 
@@ -29,11 +61,9 @@ def binary_erosion(image, selem, out=None):
 
     """
 
-    conv = ndimage.convolve(image > 0, selem, output=out,
-                            mode='constant', cval=1)
-    if conv is not None:
-        out = conv
-    return np.equal(out, np.sum(selem), out=out)
+    out, selem_sum = _convolve(image, selem, out, 1)
+    return np.array(np.equal(out, selem_sum, out=out), dtype=np.bool,
+                    copy=False)
 
 
 def binary_dilation(image, selem, out=None):
@@ -64,11 +94,8 @@ def binary_dilation(image, selem, out=None):
 
     """
 
-    conv = ndimage.convolve(image > 0, selem, output=out,
-                            mode='constant', cval=0)
-    if conv is not None:
-        out = conv
-    return np.not_equal(out, 0, out=out)
+    out, _ = _convolve(image, selem, out, 0)
+    return np.array(np.not_equal(out, 0, out=out), dtype=np.bool, copy=False)
 
 
 def binary_opening(image, selem, out=None):

skimage/morphology/tests/test_binary.py

@@ -0,0 +1,70 @@
+import numpy as np
+from numpy import testing
+
+from skimage import data, color
+from skimage.util import img_as_bool
+from skimage.morphology import binary, grey, selem
+
+
+lena = color.rgb2gray(data.lena())
+bw_lena = lena > 100
+
+
+def test_non_square_image():
+    strel = selem.square(3)
+    binary_res = binary.binary_erosion(bw_lena[:100, :200], strel)
+    grey_res = img_as_bool(grey.erosion(bw_lena[:100, :200], strel))
+    testing.assert_array_equal(binary_res, grey_res)
+
+
+def test_selem_overflow():
+    strel = np.ones((17, 17), dtype=np.uint8)
+    img = np.zeros((20, 20))
+    img[2:19, 2:19] = 1
+    binary_res = binary.binary_erosion(img, strel)
+    grey_res = img_as_bool(grey.erosion(img, strel))
+    testing.assert_array_equal(binary_res, grey_res)
+
+
+def test_selem_overflow_exception():
+    strel = np.ones((17, 17), dtype=np.uint8)
+    img = np.zeros((20, 20))
+    img[2:19, 2:19] = 1
+    out = np.zeros((20, 20), dtype=np.uint8)
+    testing.assert_raises(ValueError, binary.binary_erosion, img, strel, out)
+    out = np.zeros((20, 20), dtype=np.uint16)
+    binary_res = binary.binary_erosion(img, strel, out=out)
+    grey_res = img_as_bool(grey.erosion(img, strel))
+    testing.assert_array_equal(binary_res, grey_res)
+
+
+def test_binary_erosion():
+    strel = selem.square(3)
+    binary_res = binary.binary_erosion(bw_lena, strel)
+    grey_res = img_as_bool(grey.erosion(bw_lena, strel))
+    testing.assert_array_equal(binary_res, grey_res)
+
+
+def test_binary_dilation():
+    strel = selem.square(3)
+    binary_res = binary.binary_dilation(bw_lena, strel)
+    grey_res = img_as_bool(grey.dilation(bw_lena, strel))
+    testing.assert_array_equal(binary_res, grey_res)
+
+
+def test_binary_closing():
+    strel = selem.square(3)
+    binary_res = binary.binary_closing(bw_lena, strel)
+    grey_res = img_as_bool(grey.closing(bw_lena, strel))
+    testing.assert_array_equal(binary_res, grey_res)
+
+
+def test_binary_opening():
+    strel = selem.square(3)
+    binary_res = binary.binary_opening(bw_lena, strel)
+    grey_res = img_as_bool(grey.opening(bw_lena, strel))
+    testing.assert_array_equal(binary_res, grey_res)
+
+
+if __name__ == '__main__':
+    testing.run_module_suite()

skimage/morphology/tests/test_grey.py

@@ -6,7 +6,7 @@ from numpy import testing
 import skimage
 from skimage import data_dir
 from skimage.util import img_as_bool
-from skimage.morphology import binary, grey, selem
+from skimage.morphology import grey, selem
 
 
 lena = np.load(os.path.join(data_dir, 'lena_GRAY_U8.npy'))
@@ -155,40 +155,5 @@ class TestDTypes():
         self._test_image(image)
 
 
-def test_non_square_image():
-    strel = selem.square(3)
-    binary_res = binary.binary_erosion(bw_lena[:100, :200], strel)
-    grey_res = img_as_bool(grey.erosion(bw_lena[:100, :200], strel))
-    testing.assert_array_equal(binary_res, grey_res)
-
-
-def test_binary_erosion():
-    strel = selem.square(3)
-    binary_res = binary.binary_erosion(bw_lena, strel)
-    grey_res = img_as_bool(grey.erosion(bw_lena, strel))
-    testing.assert_array_equal(binary_res, grey_res)
-
-
-def test_binary_dilation():
-    strel = selem.square(3)
-    binary_res = binary.binary_dilation(bw_lena, strel)
-    grey_res = img_as_bool(grey.dilation(bw_lena, strel))
-    testing.assert_array_equal(binary_res, grey_res)
-
-
-def test_binary_closing():
-    strel = selem.square(3)
-    binary_res = binary.binary_closing(bw_lena, strel)
-    grey_res = img_as_bool(grey.closing(bw_lena, strel))
-    testing.assert_array_equal(binary_res, grey_res)
-
-
-def test_binary_opening():
-    strel = selem.square(3)
-    binary_res = binary.binary_opening(bw_lena, strel)
-    grey_res = img_as_bool(grey.opening(bw_lena, strel))
-    testing.assert_array_equal(binary_res, grey_res)
-
-
 if __name__ == '__main__':
     testing.run_module_suite()