From 2b91c259d632462f1e0cbb57c9df754e73d201c0 Mon Sep 17 00:00:00 2001
From: Nelson Brown <nelson.brown@gmail.com>
Date: Sat, 12 Jul 2014 15:22:48 -0700
Subject: [PATCH 01/13] Add fallback decorator for 3D images

We don't support images greater than 2D, so fall back on ndimage
---
 skimage/morphology/binary.py          | 13 ++++------
 skimage/morphology/grey.py            | 37 ++++++++++-----------------
 skimage/morphology/misc.py            | 28 ++++++++++++++++++++
 skimage/morphology/selem.py           |  7 -----
 skimage/morphology/tests/test_grey.py | 24 +++++++++++++++++
 5 files changed, 71 insertions(+), 38 deletions(-)

diff --git a/skimage/morphology/binary.py b/skimage/morphology/binary.py
index 4612a35d..69634912 100644
--- a/skimage/morphology/binary.py
+++ b/skimage/morphology/binary.py
@@ -2,8 +2,10 @@ import warnings
 import numpy as np
 from scipy import ndimage
 from .selem import _default_selem
+from .misc import default_fallback
 
 
+@default_fallback
 def binary_erosion(image, selem=None, out=None):
     """Return fast binary morphological erosion of an image.
 
@@ -32,10 +34,6 @@ def binary_erosion(image, selem=None, out=None):
 
     """
 
-    # Default structure element
-    if selem is None:
-        selem = _default_selem(image.ndim)
-
     selem = (selem != 0)
     selem_sum = np.sum(selem)
 
@@ -52,6 +50,7 @@ def binary_erosion(image, selem=None, out=None):
     return np.equal(conv, selem_sum, out=out)
 
 
+@default_fallback
 def binary_dilation(image, selem=None, out=None):
     """Return fast binary morphological dilation of an image.
 
@@ -81,10 +80,6 @@ def binary_dilation(image, selem=None, out=None):
 
     """
 
-    # Default structure element
-    if selem is None:
-        selem = _default_selem(image.ndim)
-
     selem = (selem != 0)
 
     if np.sum(selem) <= 255:
@@ -100,6 +95,7 @@ def binary_dilation(image, selem=None, out=None):
     return np.not_equal(conv, 0, out=out)
 
 
+@default_fallback
 def binary_opening(image, selem=None, out=None):
     """Return fast binary morphological opening of an image.
 
@@ -133,6 +129,7 @@ def binary_opening(image, selem=None, out=None):
     return out
 
 
+@default_fallback
 def binary_closing(image, selem=None, out=None):
     """Return fast binary morphological closing of an image.
 
diff --git a/skimage/morphology/grey.py b/skimage/morphology/grey.py
index 565ec9a6..0d0290c4 100644
--- a/skimage/morphology/grey.py
+++ b/skimage/morphology/grey.py
@@ -2,7 +2,7 @@ import warnings
 from skimage import img_as_ubyte
 from scipy import ndimage
 from .selem import _default_selem
-
+from .misc import default_fallback
 
 from . import cmorph
 
@@ -11,6 +11,7 @@ __all__ = ['erosion', 'dilation', 'opening', 'closing', 'white_tophat',
            'black_tophat']
 
 
+@default_fallback
 def erosion(image, selem=None, out=None, shift_x=False, shift_y=False):
     """Return greyscale morphological erosion of an image.
 
@@ -56,9 +57,9 @@ def erosion(image, selem=None, out=None, shift_x=False, shift_y=False):
 
     """
 
-    # Default structure element
-    if selem is None:
-        selem = _default_selem(image.ndim)
+    # If image has more than 2 dimensions, use scipy.ndimage
+    if image.ndim > 2:
+        return ndimage.morphology.grey_erosion(image, footprint=selem, out=out)
 
     if image is out:
         raise NotImplementedError("In-place erosion not supported!")
@@ -68,6 +69,7 @@ def erosion(image, selem=None, out=None, shift_x=False, shift_y=False):
                          shift_x=shift_x, shift_y=shift_y)
 
 
+@default_fallback
 def dilation(image, selem=None, out=None, shift_x=False, shift_y=False):
     """Return greyscale morphological dilation of an image.
 
@@ -114,18 +116,20 @@ def dilation(image, selem=None, out=None, shift_x=False, shift_y=False):
 
     """
 
-    # Default structure element
-    if selem is None:
-        selem = _default_selem(image.ndim)
+    # If image has more than 2 dimensions, use scipy.ndimage
+    if image.ndim > 2:
+        return ndimage.morphology.grey_dilation(image, footprint=selem,out=out)
 
     if image is out:
         raise NotImplementedError("In-place dilation not supported!")
+
     image = img_as_ubyte(image)
     selem = img_as_ubyte(selem)
     return cmorph._dilate(image, selem, out=out,
                           shift_x=shift_x, shift_y=shift_y)
 
 
+@default_fallback
 def opening(image, selem=None, out=None):
     """Return greyscale morphological opening of an image.
 
@@ -169,10 +173,6 @@ def opening(image, selem=None, out=None):
 
     """
 
-    # Default structure element
-    if selem is None:
-        selem = _default_selem(image.ndim)
-
     h, w = selem.shape
     shift_x = True if (w % 2) == 0 else False
     shift_y = True if (h % 2) == 0 else False
@@ -182,6 +182,7 @@ def opening(image, selem=None, out=None):
     return out
 
 
+@default_fallback
 def closing(image, selem=None, out=None):
     """Return greyscale morphological closing of an image.
 
@@ -225,10 +226,6 @@ def closing(image, selem=None, out=None):
 
     """
 
-    # Default structure element
-    if selem is None:
-        selem = _default_selem(image.ndim)
-
     h, w = selem.shape
     shift_x = True if (w % 2) == 0 else False
     shift_y = True if (h % 2) == 0 else False
@@ -238,6 +235,7 @@ def closing(image, selem=None, out=None):
     return out
 
 
+@default_fallback
 def white_tophat(image, selem=None, out=None):
     """Return white top hat of an image.
 
@@ -280,10 +278,6 @@ def white_tophat(image, selem=None, out=None):
 
     """
 
-    # Default structure element
-    if selem is None:
-        selem = _default_selem(image.ndim)
-
     if image is out:
         raise NotImplementedError("Cannot perform white top hat in place.")
 
@@ -292,6 +286,7 @@ def white_tophat(image, selem=None, out=None):
     return out
 
 
+@default_fallback
 def black_tophat(image, selem=None, out=None):
     """Return black top hat of an image.
 
@@ -335,10 +330,6 @@ def black_tophat(image, selem=None, out=None):
 
     """
 
-    # Default structure element
-    if selem is None:
-        selem = _default_selem(image.ndim)
-
     if image is out:
         raise NotImplementedError("Cannot perform white top hat in place.")
 
diff --git a/skimage/morphology/misc.py b/skimage/morphology/misc.py
index dc8290d2..f61d4e56 100644
--- a/skimage/morphology/misc.py
+++ b/skimage/morphology/misc.py
@@ -1,5 +1,33 @@
 import numpy as np
 import scipy.ndimage as nd
+from .selem import _default_selem
+
+skimage2ndimage = {x: 'grey_' + x
+                   for x in ('erosion','dilation','opening','closing')}
+skimage2ndimage.update({x: x
+                        for x in ('binary_erosion','binary_dilation',
+                                  'binary_opening','binary_closing',
+                                  'black_tophat','white_tophat')})
+
+
+def default_fallback(func):
+    def func_out(image, selem=None, out=None, **kwargs):
+        # Default structure element
+        if selem is None:
+            selem = _default_selem(image.ndim)
+
+        # If image has more than 2 dimensions, use scipy.ndimage
+        if image.ndim > 2:
+            function = getattr(nd, skimage2ndimage[func.__name__])
+            try:
+                return function(image, footprint=selem, output=out, **kwargs)
+            except TypeError:
+                # nd.binary_* take structure instead of footprint
+                return function(image, structure=selem, output=out, **kwargs)
+        else:
+            return func(image, selem=selem, out=out, **kwargs)
+
+    return func_out
 
 
 def remove_small_objects(ar, min_size=64, connectivity=1, in_place=False):
diff --git a/skimage/morphology/selem.py b/skimage/morphology/selem.py
index 1822c8b3..5e0606c0 100644
--- a/skimage/morphology/selem.py
+++ b/skimage/morphology/selem.py
@@ -311,10 +311,3 @@ def _default_selem(ndim):
 
     """
     return ndimage.morphology.generate_binary_structure(ndim, 1)
-
-
-
-
-
-
-
diff --git a/skimage/morphology/tests/test_grey.py b/skimage/morphology/tests/test_grey.py
index 359a2832..840b9c42 100644
--- a/skimage/morphology/tests/test_grey.py
+++ b/skimage/morphology/tests/test_grey.py
@@ -142,6 +142,30 @@ def test_default_selem():
         im_test = function(image)
         yield testing.assert_array_equal, im_expected, im_test
 
+def test_3d_fallback_default_selem():
+    # 3x3x3 cube inside a 7x7x7 image:
+    image = np.zeros((7, 7, 7), np.bool)
+    image[2:-2, 2:-2, 2:-2] = 1
+
+    opened = morphology.opening(image)
+
+    # expect a "hyper-cross" centered in the 5x5x5:
+    image_expected = np.zeros((7, 7, 7), dtype=bool)
+    image_expected[2:5, 2:5, 2:5] = ndimage.generate_binary_structure(3, 1)
+    testing.assert_array_equal(opened, image_expected)
+
+def test_3d_fallback_default_selem():
+    # 3x3x3 cube inside a 7x7x7 image:
+    image = np.zeros((7, 7, 7), np.bool)
+    image[2:-2, 2:-2, 2:-2] = 1
+
+    cube = np.ones((3, 3, 3),dtype=np.uint8)
+
+    for function in [grey.closing, grey.opening]:
+        new_image = function(image, cube)
+        yield testing.assert_array_equal, new_image, image
+
+
 class TestDTypes():
 
     def setUp(self):

From ea3e65f25a4b847c66a4e645fb52831391284726 Mon Sep 17 00:00:00 2001
From: Nelson Brown <nelson.brown@gmail.com>
Date: Sat, 12 Jul 2014 16:54:35 -0700
Subject: [PATCH 02/13] Add 3d-fallback tests for binary functions

---
 skimage/morphology/tests/test_binary.py | 24 ++++++++++++++++++++++++
 skimage/morphology/tests/test_grey.py   |  7 ++++---
 2 files changed, 28 insertions(+), 3 deletions(-)

diff --git a/skimage/morphology/tests/test_binary.py b/skimage/morphology/tests/test_binary.py
index 6ac5e8d8..c0c4c682 100644
--- a/skimage/morphology/tests/test_binary.py
+++ b/skimage/morphology/tests/test_binary.py
@@ -4,6 +4,7 @@ from numpy import testing
 from skimage import data, color
 from skimage.util import img_as_bool
 from skimage.morphology import binary, grey, selem
+from scipy import ndimage
 
 
 lena = color.rgb2gray(data.lena())
@@ -86,5 +87,28 @@ def test_default_selem():
         im_test = function(image)
         yield testing.assert_array_equal, im_expected, im_test
 
+def test_3d_fallback_default_selem():
+    # 3x3x3 cube inside a 7x7x7 image:
+    image = np.zeros((7, 7, 7), np.bool)
+    image[2:-2, 2:-2, 2:-2] = 1
+
+    opened = binary.binary_opening(image)
+
+    # expect a "hyper-cross" centered in the 5x5x5:
+    image_expected = np.zeros((7, 7, 7), dtype=bool)
+    image_expected[2:5, 2:5, 2:5] = ndimage.generate_binary_structure(3, 1)
+    testing.assert_array_equal(opened, image_expected)
+
+def test_3d_fallback_cube_selem():
+    # 3x3x3 cube inside a 7x7x7 image:
+    image = np.zeros((7, 7, 7), np.bool)
+    image[2:-2, 2:-2, 2:-2] = 1
+
+    cube = np.ones((3, 3, 3), dtype=np.uint8)
+
+    for function in [binary.binary_closing, binary.binary_opening]:
+        new_image = function(image, cube)
+        yield testing.assert_array_equal, new_image, image
+
 if __name__ == '__main__':
     testing.run_module_suite()
diff --git a/skimage/morphology/tests/test_grey.py b/skimage/morphology/tests/test_grey.py
index 840b9c42..191613c4 100644
--- a/skimage/morphology/tests/test_grey.py
+++ b/skimage/morphology/tests/test_grey.py
@@ -2,6 +2,7 @@ import os.path
 
 import numpy as np
 from numpy import testing
+from scipy import ndimage
 
 import skimage
 from skimage import data_dir
@@ -147,19 +148,19 @@ def test_3d_fallback_default_selem():
     image = np.zeros((7, 7, 7), np.bool)
     image[2:-2, 2:-2, 2:-2] = 1
 
-    opened = morphology.opening(image)
+    opened = grey.opening(image)
 
     # expect a "hyper-cross" centered in the 5x5x5:
     image_expected = np.zeros((7, 7, 7), dtype=bool)
     image_expected[2:5, 2:5, 2:5] = ndimage.generate_binary_structure(3, 1)
     testing.assert_array_equal(opened, image_expected)
 
-def test_3d_fallback_default_selem():
+def test_3d_fallback_cube_selem():
     # 3x3x3 cube inside a 7x7x7 image:
     image = np.zeros((7, 7, 7), np.bool)
     image[2:-2, 2:-2, 2:-2] = 1
 
-    cube = np.ones((3, 3, 3),dtype=np.uint8)
+    cube = np.ones((3, 3, 3), dtype=np.uint8)
 
     for function in [grey.closing, grey.opening]:
         new_image = function(image, cube)

From f1a8132fbfadc8621f81423e238dc50f42027ff6 Mon Sep 17 00:00:00 2001
From: Nelson Brown <Nelson.Brown@gmail.com>
Date: Sun, 13 Jul 2014 11:28:27 -0700
Subject: [PATCH 03/13] Add doctrings and comments in response to reviewers

---
 skimage/morphology/binary.py | 17 +++++++++++++++-
 skimage/morphology/grey.py   | 35 ++++++++++++++++++++++-----------
 skimage/morphology/misc.py   | 38 +++++++++++++++++++++++++++++++++++-
 3 files changed, 77 insertions(+), 13 deletions(-)

diff --git a/skimage/morphology/binary.py b/skimage/morphology/binary.py
index 69634912..5324b0f5 100644
--- a/skimage/morphology/binary.py
+++ b/skimage/morphology/binary.py
@@ -1,10 +1,13 @@
 import warnings
 import numpy as np
 from scipy import ndimage
-from .selem import _default_selem
 from .misc import default_fallback
 
 
+# Our functions only work in 2D, so for 3D or higher input we should fall back
+# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
+# element of the appropriate dimension for each of these functions.
+# The `default_callback` provides all these.
 @default_fallback
 def binary_erosion(image, selem=None, out=None):
     """Return fast binary morphological erosion of an image.
@@ -50,6 +53,10 @@ def binary_erosion(image, selem=None, out=None):
     return np.equal(conv, selem_sum, out=out)
 
 
+# Our functions only work in 2D, so for 3D or higher input we should fall back
+# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
+# element of the appropriate dimension for each of these functions.
+# The `default_callback` provides all these.
 @default_fallback
 def binary_dilation(image, selem=None, out=None):
     """Return fast binary morphological dilation of an image.
@@ -95,6 +102,10 @@ def binary_dilation(image, selem=None, out=None):
     return np.not_equal(conv, 0, out=out)
 
 
+# Our functions only work in 2D, so for 3D or higher input we should fall back
+# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
+# element of the appropriate dimension for each of these functions.
+# The `default_callback` provides all these.
 @default_fallback
 def binary_opening(image, selem=None, out=None):
     """Return fast binary morphological opening of an image.
@@ -129,6 +140,10 @@ def binary_opening(image, selem=None, out=None):
     return out
 
 
+# Our functions only work in 2D, so for 3D or higher input we should fall back
+# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
+# element of the appropriate dimension for each of these functions.
+# The `default_callback` provides all these.
 @default_fallback
 def binary_closing(image, selem=None, out=None):
     """Return fast binary morphological closing of an image.
diff --git a/skimage/morphology/grey.py b/skimage/morphology/grey.py
index 0d0290c4..e09872cb 100644
--- a/skimage/morphology/grey.py
+++ b/skimage/morphology/grey.py
@@ -1,7 +1,5 @@
 import warnings
 from skimage import img_as_ubyte
-from scipy import ndimage
-from .selem import _default_selem
 from .misc import default_fallback
 
 from . import cmorph
@@ -10,7 +8,10 @@ from . import cmorph
 __all__ = ['erosion', 'dilation', 'opening', 'closing', 'white_tophat',
            'black_tophat']
 
-
+# Our functions only work in 2D, so for 3D or higher input we should fall back
+# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
+# element of the appropriate dimension for each of these functions.
+# The `default_callback` provides all these.
 @default_fallback
 def erosion(image, selem=None, out=None, shift_x=False, shift_y=False):
     """Return greyscale morphological erosion of an image.
@@ -57,10 +58,6 @@ def erosion(image, selem=None, out=None, shift_x=False, shift_y=False):
 
     """
 
-    # If image has more than 2 dimensions, use scipy.ndimage
-    if image.ndim > 2:
-        return ndimage.morphology.grey_erosion(image, footprint=selem, out=out)
-
     if image is out:
         raise NotImplementedError("In-place erosion not supported!")
     image = img_as_ubyte(image)
@@ -69,6 +66,10 @@ def erosion(image, selem=None, out=None, shift_x=False, shift_y=False):
                          shift_x=shift_x, shift_y=shift_y)
 
 
+# Our functions only work in 2D, so for 3D or higher input we should fall back
+# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
+# element of the appropriate dimension for each of these functions.
+# The `default_callback` provides all these.
 @default_fallback
 def dilation(image, selem=None, out=None, shift_x=False, shift_y=False):
     """Return greyscale morphological dilation of an image.
@@ -116,10 +117,6 @@ def dilation(image, selem=None, out=None, shift_x=False, shift_y=False):
 
     """
 
-    # If image has more than 2 dimensions, use scipy.ndimage
-    if image.ndim > 2:
-        return ndimage.morphology.grey_dilation(image, footprint=selem,out=out)
-
     if image is out:
         raise NotImplementedError("In-place dilation not supported!")
 
@@ -129,6 +126,10 @@ def dilation(image, selem=None, out=None, shift_x=False, shift_y=False):
                           shift_x=shift_x, shift_y=shift_y)
 
 
+# Our functions only work in 2D, so for 3D or higher input we should fall back
+# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
+# element of the appropriate dimension for each of these functions.
+# The `default_callback` provides all these.
 @default_fallback
 def opening(image, selem=None, out=None):
     """Return greyscale morphological opening of an image.
@@ -182,6 +183,10 @@ def opening(image, selem=None, out=None):
     return out
 
 
+# Our functions only work in 2D, so for 3D or higher input we should fall back
+# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
+# element of the appropriate dimension for each of these functions.
+# The `default_callback` provides all these.
 @default_fallback
 def closing(image, selem=None, out=None):
     """Return greyscale morphological closing of an image.
@@ -235,6 +240,10 @@ def closing(image, selem=None, out=None):
     return out
 
 
+# Our functions only work in 2D, so for 3D or higher input we should fall back
+# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
+# element of the appropriate dimension for each of these functions.
+# The `default_callback` provides all these.
 @default_fallback
 def white_tophat(image, selem=None, out=None):
     """Return white top hat of an image.
@@ -286,6 +295,10 @@ def white_tophat(image, selem=None, out=None):
     return out
 
 
+# Our functions only work in 2D, so for 3D or higher input we should fall back
+# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
+# element of the appropriate dimension for each of these functions.
+# The `default_callback` provides all these.
 @default_fallback
 def black_tophat(image, selem=None, out=None):
     """Return black top hat of an image.
diff --git a/skimage/morphology/misc.py b/skimage/morphology/misc.py
index f61d4e56..db922fd7 100644
--- a/skimage/morphology/misc.py
+++ b/skimage/morphology/misc.py
@@ -2,6 +2,8 @@ import numpy as np
 import scipy.ndimage as nd
 from .selem import _default_selem
 
+# Our function names don't exactly correspond to ndimages.
+# These dictionaries translate from our names to scipy's.
 skimage2ndimage = {x: 'grey_' + x
                    for x in ('erosion','dilation','opening','closing')}
 skimage2ndimage.update({x: x
@@ -9,9 +11,43 @@ skimage2ndimage.update({x: x
                                   'binary_opening','binary_closing',
                                   'black_tophat','white_tophat')})
 
-
 def default_fallback(func):
+    """Decorator to fall back on ndimage for images with more than 2 dimensions
+
+    Parameters
+    ----------
+    func : function
+        A morphology function such as erosion, dilation, opening, closing,
+        white_tophat, or black_tophat.
+
+    Returns
+    -------
+    func_out : function
+        If the image dimentionality is greater than 2D, the ndimage
+        function is returned, otherwise skimage function is used.
+    """
+    
     def func_out(image, selem=None, out=None, **kwargs):
+        """Select a function appropriate for the image dimensionality
+    
+        Parameters
+        ----------
+        image : ndarray
+            Image array.
+        selem : ndarray, optional
+            The neighborhood expressed as a 2-D array of 1's and 0's.
+            If None, use cross-shaped structuring element (connectivity=1).
+        out : ndarray of bool, optional
+            The array to store the result of the morphology. If None is
+            passed, a new array will be allocated.
+    
+        Returns
+        -------
+        func_out : function
+            If the image dimentionality is greater than 2D, the ndimage
+            function is returned, otherwise skimage function is used.
+        """
+        
         # Default structure element
         if selem is None:
             selem = _default_selem(image.ndim)

From d9909c4db927091fe9b6e6d30c27ecb6bb23a162 Mon Sep 17 00:00:00 2001
From: Nelson Brown <Nelson.Brown@gmail.com>
Date: Sun, 13 Jul 2014 12:36:05 -0700
Subject: [PATCH 04/13] Add tests for ndimage fallback for 3D white_tophat &
 black_tophat

---
 skimage/morphology/tests/test_grey.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/skimage/morphology/tests/test_grey.py b/skimage/morphology/tests/test_grey.py
index 191613c4..f9a7305d 100644
--- a/skimage/morphology/tests/test_grey.py
+++ b/skimage/morphology/tests/test_grey.py
@@ -166,6 +166,25 @@ def test_3d_fallback_cube_selem():
         new_image = function(image, cube)
         yield testing.assert_array_equal, new_image, image
 
+def test_3d_fallback_white_tophat():
+    image = np.zeros((7, 7, 7), dtype=bool)
+    image[2, 2:4, 2:4] = 1
+    image[3, 2:5, 2:5] = 1
+    image[4, 3:5, 3:5] = 1
+    new_image = grey.white_tophat(image)
+    footprint = ndimage.generate_binary_structure(3,1)
+    image_expected = ndimage.white_tophat(image,footprint=footprint)
+    testing.assert_array_equal(new_image, image_expected)
+    
+def test_3d_fallback_black_tophat():
+    image = np.ones((7, 7, 7), dtype=bool)
+    image[2, 2:4, 2:4] = 0
+    image[3, 2:5, 2:5] = 0
+    image[4, 3:5, 3:5] = 0
+    new_image = grey.black_tophat(image)
+    footprint = ndimage.generate_binary_structure(3,1)
+    image_expected = ndimage.black_tophat(image,footprint=footprint)
+    testing.assert_array_equal(new_image, image_expected)
 
 class TestDTypes():
 

From 042d85ad435ab61092c1a05cf2733c6f4333aa41 Mon Sep 17 00:00:00 2001
From: Nelson Brown <Nelson.Brown@gmail.com>
Date: Sun, 13 Jul 2014 16:31:58 -0700
Subject: [PATCH 05/13] Adjust hanging indentation whitespace in dict
 comprehension

---
 skimage/morphology/misc.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/skimage/morphology/misc.py b/skimage/morphology/misc.py
index db922fd7..26d40a72 100644
--- a/skimage/morphology/misc.py
+++ b/skimage/morphology/misc.py
@@ -5,11 +5,11 @@ from .selem import _default_selem
 # Our function names don't exactly correspond to ndimages.
 # These dictionaries translate from our names to scipy's.
 skimage2ndimage = {x: 'grey_' + x
-                   for x in ('erosion','dilation','opening','closing')}
+    for x in ('erosion','dilation','opening','closing')}
 skimage2ndimage.update({x: x
-                        for x in ('binary_erosion','binary_dilation',
-                                  'binary_opening','binary_closing',
-                                  'black_tophat','white_tophat')})
+    for x in ('binary_erosion','binary_dilation',
+        'binary_opening','binary_closing',
+        'black_tophat','white_tophat')})
 
 def default_fallback(func):
     """Decorator to fall back on ndimage for images with more than 2 dimensions

From b677c400df7c37293f62f285776b928e59af3bcf Mon Sep 17 00:00:00 2001
From: Nelson Brown <Nelson.Brown@gmail.com>
Date: Sun, 13 Jul 2014 16:55:06 -0700
Subject: [PATCH 06/13] Add whitespace following comma

---
 skimage/morphology/misc.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/skimage/morphology/misc.py b/skimage/morphology/misc.py
index 26d40a72..40ec6c25 100644
--- a/skimage/morphology/misc.py
+++ b/skimage/morphology/misc.py
@@ -3,13 +3,14 @@ import scipy.ndimage as nd
 from .selem import _default_selem
 
 # Our function names don't exactly correspond to ndimages.
-# These dictionaries translate from our names to scipy's.
-skimage2ndimage = {x: 'grey_' + x
-    for x in ('erosion','dilation','opening','closing')}
-skimage2ndimage.update({x: x
-    for x in ('binary_erosion','binary_dilation',
-        'binary_opening','binary_closing',
-        'black_tophat','white_tophat')})
+# This dictionary translates from our names to scipy's.
+funcs = ('erosion', 'dilation', 'opening', 'closing')
+skimage2ndimage = {x: 'grey_' + x for x in funcs}
+
+# These function names are the same in ndimage.
+funcs = ('binary_erosion', 'binary_dilation', 'binary_opening', 
+         'binary_closing', 'black_tophat', 'white_tophat')
+skimage2ndimage.update({x: x for x in funcs})
 
 def default_fallback(func):
     """Decorator to fall back on ndimage for images with more than 2 dimensions

From a1519a015ead5d164a2d2c87a61c7ee41fbf5502 Mon Sep 17 00:00:00 2001
From: Nelson Brown <Nelson.Brown@gmail.com>
Date: Sun, 13 Jul 2014 19:59:43 -0700
Subject: [PATCH 07/13] Change binary morphology functions to output numpy.bool
 dtype

---
 skimage/morphology/binary.py            |  4 +--
 skimage/morphology/tests/test_binary.py | 40 +++++++++++++++++++++++++
 2 files changed, 42 insertions(+), 2 deletions(-)

diff --git a/skimage/morphology/binary.py b/skimage/morphology/binary.py
index 5324b0f5..69d3eb08 100644
--- a/skimage/morphology/binary.py
+++ b/skimage/morphology/binary.py
@@ -49,7 +49,7 @@ def binary_erosion(image, selem=None, out=None):
     ndimage.convolve(binary, selem, mode='constant', cval=1, output=conv)
 
     if out is None:
-        out = conv
+        out = np.empty_like(conv, dtype=np.bool)
     return np.equal(conv, selem_sum, out=out)
 
 
@@ -98,7 +98,7 @@ def binary_dilation(image, selem=None, out=None):
     ndimage.convolve(binary, selem, mode='constant', cval=0, output=conv)
 
     if out is None:
-        out = conv
+        out = np.empty_like(conv, dtype=np.bool)
     return np.not_equal(conv, 0, out=out)
 
 
diff --git a/skimage/morphology/tests/test_binary.py b/skimage/morphology/tests/test_binary.py
index c0c4c682..e0db7416 100644
--- a/skimage/morphology/tests/test_binary.py
+++ b/skimage/morphology/tests/test_binary.py
@@ -110,5 +110,45 @@ def test_3d_fallback_cube_selem():
         new_image = function(image, cube)
         yield testing.assert_array_equal, new_image, image
 
+def test_binary_output_2d():
+    image = np.zeros((9, 9), np.uint16)
+    image[2:-2, 2:-2] = 2**14
+    image[3:-3, 3:-3] = 2**15
+    image[4, 4] = 2**16-1
+    
+    bin_opened = binary.binary_opening(image)
+    bin_closed = binary.binary_closing(image)
+    
+    int_opened = np.empty_like(image, dtype=np.uint8)
+    int_closed = np.empty_like(image, dtype=np.uint8)
+    binary.binary_opening(image, out=int_opened)
+    binary.binary_closing(image, out=int_closed)
+    
+    testing.assert_equal(bin_opened.dtype, np.bool)
+    testing.assert_equal(bin_closed.dtype, np.bool)
+    
+    testing.assert_equal(int_opened.dtype, np.uint8)
+    testing.assert_equal(int_closed.dtype, np.uint8)
+ 
+def test_binary_output_3d():
+    image = np.zeros((9, 9, 9), np.uint16)
+    image[2:-2, 2:-2, 2:-2] = 2**14
+    image[3:-3, 3:-3, 3:-3] = 2**15
+    image[4, 4, 4] = 2**16-1
+
+    bin_opened = binary.binary_opening(image)
+    bin_closed = binary.binary_closing(image)
+    
+    int_opened = np.empty_like(image, dtype=np.uint8)
+    int_closed = np.empty_like(image, dtype=np.uint8)
+    binary.binary_opening(image, out=int_opened)
+    binary.binary_closing(image, out=int_closed)
+    
+    testing.assert_equal(bin_opened.dtype, np.bool)
+    testing.assert_equal(bin_closed.dtype, np.bool)
+    
+    testing.assert_equal(int_opened.dtype, np.uint8)
+    testing.assert_equal(int_closed.dtype, np.uint8)   
+
 if __name__ == '__main__':
     testing.run_module_suite()

From 001a63bd21c3afe652458b021bcefeddb760831d Mon Sep 17 00:00:00 2001
From: Nelson Brown <nelson.a.brown@nasa.gov>
Date: Tue, 15 Jul 2014 08:03:31 -0700
Subject: [PATCH 08/13] Remove repeated comments

---
 skimage/morphology/binary.py | 12 ------------
 skimage/morphology/grey.py   | 24 ------------------------
 2 files changed, 36 deletions(-)

diff --git a/skimage/morphology/binary.py b/skimage/morphology/binary.py
index 69d3eb08..216e3690 100644
--- a/skimage/morphology/binary.py
+++ b/skimage/morphology/binary.py
@@ -53,10 +53,6 @@ def binary_erosion(image, selem=None, out=None):
     return np.equal(conv, selem_sum, out=out)
 
 
-# Our functions only work in 2D, so for 3D or higher input we should fall back
-# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
-# element of the appropriate dimension for each of these functions.
-# The `default_callback` provides all these.
 @default_fallback
 def binary_dilation(image, selem=None, out=None):
     """Return fast binary morphological dilation of an image.
@@ -102,10 +98,6 @@ def binary_dilation(image, selem=None, out=None):
     return np.not_equal(conv, 0, out=out)
 
 
-# Our functions only work in 2D, so for 3D or higher input we should fall back
-# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
-# element of the appropriate dimension for each of these functions.
-# The `default_callback` provides all these.
 @default_fallback
 def binary_opening(image, selem=None, out=None):
     """Return fast binary morphological opening of an image.
@@ -140,10 +132,6 @@ def binary_opening(image, selem=None, out=None):
     return out
 
 
-# Our functions only work in 2D, so for 3D or higher input we should fall back
-# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
-# element of the appropriate dimension for each of these functions.
-# The `default_callback` provides all these.
 @default_fallback
 def binary_closing(image, selem=None, out=None):
     """Return fast binary morphological closing of an image.
diff --git a/skimage/morphology/grey.py b/skimage/morphology/grey.py
index e09872cb..19a4a346 100644
--- a/skimage/morphology/grey.py
+++ b/skimage/morphology/grey.py
@@ -8,10 +8,6 @@ from . import cmorph
 __all__ = ['erosion', 'dilation', 'opening', 'closing', 'white_tophat',
            'black_tophat']
 
-# Our functions only work in 2D, so for 3D or higher input we should fall back
-# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
-# element of the appropriate dimension for each of these functions.
-# The `default_callback` provides all these.
 @default_fallback
 def erosion(image, selem=None, out=None, shift_x=False, shift_y=False):
     """Return greyscale morphological erosion of an image.
@@ -66,10 +62,6 @@ def erosion(image, selem=None, out=None, shift_x=False, shift_y=False):
                          shift_x=shift_x, shift_y=shift_y)
 
 
-# Our functions only work in 2D, so for 3D or higher input we should fall back
-# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
-# element of the appropriate dimension for each of these functions.
-# The `default_callback` provides all these.
 @default_fallback
 def dilation(image, selem=None, out=None, shift_x=False, shift_y=False):
     """Return greyscale morphological dilation of an image.
@@ -126,10 +118,6 @@ def dilation(image, selem=None, out=None, shift_x=False, shift_y=False):
                           shift_x=shift_x, shift_y=shift_y)
 
 
-# Our functions only work in 2D, so for 3D or higher input we should fall back
-# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
-# element of the appropriate dimension for each of these functions.
-# The `default_callback` provides all these.
 @default_fallback
 def opening(image, selem=None, out=None):
     """Return greyscale morphological opening of an image.
@@ -183,10 +171,6 @@ def opening(image, selem=None, out=None):
     return out
 
 
-# Our functions only work in 2D, so for 3D or higher input we should fall back
-# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
-# element of the appropriate dimension for each of these functions.
-# The `default_callback` provides all these.
 @default_fallback
 def closing(image, selem=None, out=None):
     """Return greyscale morphological closing of an image.
@@ -240,10 +224,6 @@ def closing(image, selem=None, out=None):
     return out
 
 
-# Our functions only work in 2D, so for 3D or higher input we should fall back
-# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
-# element of the appropriate dimension for each of these functions.
-# The `default_callback` provides all these.
 @default_fallback
 def white_tophat(image, selem=None, out=None):
     """Return white top hat of an image.
@@ -295,10 +275,6 @@ def white_tophat(image, selem=None, out=None):
     return out
 
 
-# Our functions only work in 2D, so for 3D or higher input we should fall back
-# on `scipy.ndimage`. Additionally, we want to use a cross-shaped structuring
-# element of the appropriate dimension for each of these functions.
-# The `default_callback` provides all these.
 @default_fallback
 def black_tophat(image, selem=None, out=None):
     """Return black top hat of an image.

From 8c2b9b1784efbe43fe01da6ebea81643673a853b Mon Sep 17 00:00:00 2001
From: Nelson Brown <nelson.a.brown@nasa.gov>
Date: Tue, 15 Jul 2014 08:07:30 -0700
Subject: [PATCH 09/13] Updated docstrings

---
 skimage/morphology/misc.py | 24 +++---------------------
 1 file changed, 3 insertions(+), 21 deletions(-)

diff --git a/skimage/morphology/misc.py b/skimage/morphology/misc.py
index 40ec6c25..181fe5a4 100644
--- a/skimage/morphology/misc.py
+++ b/skimage/morphology/misc.py
@@ -14,7 +14,9 @@ skimage2ndimage.update({x: x for x in funcs})
 
 def default_fallback(func):
     """Decorator to fall back on ndimage for images with more than 2 dimensions
-
+    Decorator also provides a default structuring element, `selem`, with the
+    appropriate dimensionality if none is specified.
+    
     Parameters
     ----------
     func : function
@@ -29,26 +31,6 @@ def default_fallback(func):
     """
     
     def func_out(image, selem=None, out=None, **kwargs):
-        """Select a function appropriate for the image dimensionality
-    
-        Parameters
-        ----------
-        image : ndarray
-            Image array.
-        selem : ndarray, optional
-            The neighborhood expressed as a 2-D array of 1's and 0's.
-            If None, use cross-shaped structuring element (connectivity=1).
-        out : ndarray of bool, optional
-            The array to store the result of the morphology. If None is
-            passed, a new array will be allocated.
-    
-        Returns
-        -------
-        func_out : function
-            If the image dimentionality is greater than 2D, the ndimage
-            function is returned, otherwise skimage function is used.
-        """
-        
         # Default structure element
         if selem is None:
             selem = _default_selem(image.ndim)

From 7976520e7af7102e76fd9139617b7c953535a623 Mon Sep 17 00:00:00 2001
From: Nelson Brown <nelson.a.brown@nasa.gov>
Date: Tue, 15 Jul 2014 08:25:17 -0700
Subject: [PATCH 10/13] Add test that the 2D results correspond to scipy's
 Remove trailing whitespace

---
 skimage/morphology/misc.py              |  7 ++---
 skimage/morphology/tests/test_binary.py | 34 ++++++++++++++++++-------
 skimage/morphology/tests/test_grey.py   | 18 ++++++++++++-
 3 files changed, 46 insertions(+), 13 deletions(-)

diff --git a/skimage/morphology/misc.py b/skimage/morphology/misc.py
index 181fe5a4..94aadf7a 100644
--- a/skimage/morphology/misc.py
+++ b/skimage/morphology/misc.py
@@ -8,15 +8,16 @@ funcs = ('erosion', 'dilation', 'opening', 'closing')
 skimage2ndimage = {x: 'grey_' + x for x in funcs}
 
 # These function names are the same in ndimage.
-funcs = ('binary_erosion', 'binary_dilation', 'binary_opening', 
+funcs = ('binary_erosion', 'binary_dilation', 'binary_opening',
          'binary_closing', 'black_tophat', 'white_tophat')
 skimage2ndimage.update({x: x for x in funcs})
 
 def default_fallback(func):
     """Decorator to fall back on ndimage for images with more than 2 dimensions
+
     Decorator also provides a default structuring element, `selem`, with the
     appropriate dimensionality if none is specified.
-    
+
     Parameters
     ----------
     func : function
@@ -29,7 +30,7 @@ def default_fallback(func):
         If the image dimentionality is greater than 2D, the ndimage
         function is returned, otherwise skimage function is used.
     """
-    
+
     def func_out(image, selem=None, out=None, **kwargs):
         # Default structure element
         if selem is None:
diff --git a/skimage/morphology/tests/test_binary.py b/skimage/morphology/tests/test_binary.py
index e0db7416..a8284103 100644
--- a/skimage/morphology/tests/test_binary.py
+++ b/skimage/morphology/tests/test_binary.py
@@ -110,26 +110,42 @@ def test_3d_fallback_cube_selem():
         new_image = function(image, cube)
         yield testing.assert_array_equal, new_image, image
 
+def test_2d_ndimage_equivalence():
+    image = np.zeros((9, 9), np.uint16)
+    image[2:-2, 2:-2] = 2**14
+    image[3:-3, 3:-3] = 2**15
+    image[4, 4] = 2**16-1
+
+    bin_opened = binary.binary_opening(image)
+    bin_closed = binary.binary_closing(image)
+
+    selem = ndimage.generate_binary_structure(2, 1)
+    ndimage_opened = ndimage.binary_opening(image, structure=selem)
+    ndimage_closed = ndimage.binary_closing(image, structure=selem)
+
+    testing.assert_array_equal(bin_opened, ndimage_opened)
+    testing.assert_array_equal(bin_closed, ndimage_closed)
+
 def test_binary_output_2d():
     image = np.zeros((9, 9), np.uint16)
     image[2:-2, 2:-2] = 2**14
     image[3:-3, 3:-3] = 2**15
     image[4, 4] = 2**16-1
-    
+
     bin_opened = binary.binary_opening(image)
     bin_closed = binary.binary_closing(image)
-    
+
     int_opened = np.empty_like(image, dtype=np.uint8)
     int_closed = np.empty_like(image, dtype=np.uint8)
     binary.binary_opening(image, out=int_opened)
     binary.binary_closing(image, out=int_closed)
-    
+
     testing.assert_equal(bin_opened.dtype, np.bool)
     testing.assert_equal(bin_closed.dtype, np.bool)
-    
+
     testing.assert_equal(int_opened.dtype, np.uint8)
     testing.assert_equal(int_closed.dtype, np.uint8)
- 
+
 def test_binary_output_3d():
     image = np.zeros((9, 9, 9), np.uint16)
     image[2:-2, 2:-2, 2:-2] = 2**14
@@ -138,17 +154,17 @@ def test_binary_output_3d():
 
     bin_opened = binary.binary_opening(image)
     bin_closed = binary.binary_closing(image)
-    
+
     int_opened = np.empty_like(image, dtype=np.uint8)
     int_closed = np.empty_like(image, dtype=np.uint8)
     binary.binary_opening(image, out=int_opened)
     binary.binary_closing(image, out=int_closed)
-    
+
     testing.assert_equal(bin_opened.dtype, np.bool)
     testing.assert_equal(bin_closed.dtype, np.bool)
-    
+
     testing.assert_equal(int_opened.dtype, np.uint8)
-    testing.assert_equal(int_closed.dtype, np.uint8)   
+    testing.assert_equal(int_closed.dtype, np.uint8)
 
 if __name__ == '__main__':
     testing.run_module_suite()
diff --git a/skimage/morphology/tests/test_grey.py b/skimage/morphology/tests/test_grey.py
index f9a7305d..9f8e95b3 100644
--- a/skimage/morphology/tests/test_grey.py
+++ b/skimage/morphology/tests/test_grey.py
@@ -175,7 +175,7 @@ def test_3d_fallback_white_tophat():
     footprint = ndimage.generate_binary_structure(3,1)
     image_expected = ndimage.white_tophat(image,footprint=footprint)
     testing.assert_array_equal(new_image, image_expected)
-    
+
 def test_3d_fallback_black_tophat():
     image = np.ones((7, 7, 7), dtype=bool)
     image[2, 2:4, 2:4] = 0
@@ -186,6 +186,22 @@ def test_3d_fallback_black_tophat():
     image_expected = ndimage.black_tophat(image,footprint=footprint)
     testing.assert_array_equal(new_image, image_expected)
 
+def test_2d_ndimage_equivalence():
+    image = np.zeros((9, 9), np.uint16)
+    image[2:-2, 2:-2] = 2**14
+    image[3:-3, 3:-3] = 2**15
+    image[4, 4] = 2**16-1
+
+    opened = grey.opening(image)
+    closed = grey.closing(image)
+
+    selem = ndimage.generate_binary_structure(2, 1)
+    ndimage_opened = ndimage.grey_opening(image, structure=selem)
+    ndimage_closed = ndimage.grey_closing(image, structure=selem)
+
+    testing.assert_array_equal(opened, ndimage_opened)
+    testing.assert_array_equal(closed, ndimage_closed)
+
 class TestDTypes():
 
     def setUp(self):

From 4449c7788402e46edbf839ce1718c45291c2ecb4 Mon Sep 17 00:00:00 2001
From: Nelson Brown <nelson.a.brown@nasa.gov>
Date: Tue, 15 Jul 2014 08:39:34 -0700
Subject: [PATCH 11/13] Fix calls to ndimage to use footprint argument

---
 skimage/morphology/tests/test_grey.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/skimage/morphology/tests/test_grey.py b/skimage/morphology/tests/test_grey.py
index 9f8e95b3..ecc0e89e 100644
--- a/skimage/morphology/tests/test_grey.py
+++ b/skimage/morphology/tests/test_grey.py
@@ -196,8 +196,8 @@ def test_2d_ndimage_equivalence():
     closed = grey.closing(image)
 
     selem = ndimage.generate_binary_structure(2, 1)
-    ndimage_opened = ndimage.grey_opening(image, structure=selem)
-    ndimage_closed = ndimage.grey_closing(image, structure=selem)
+    ndimage_opened = ndimage.grey_opening(image, footprint=selem)
+    ndimage_closed = ndimage.grey_closing(image, footprint=selem)
 
     testing.assert_array_equal(opened, ndimage_opened)
     testing.assert_array_equal(closed, ndimage_closed)

From eb4725826d4cbedcd8b375746f0ed8a6da6f9ead Mon Sep 17 00:00:00 2001
From: Nelson Brown <Nelson.Brown@gmail.com>
Date: Wed, 16 Jul 2014 19:57:25 -0700
Subject: [PATCH 12/13] Change test of ndimage equivalence to use uint8 test
 image

---
 skimage/morphology/tests/test_grey.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skimage/morphology/tests/test_grey.py b/skimage/morphology/tests/test_grey.py
index ecc0e89e..b7703ec2 100644
--- a/skimage/morphology/tests/test_grey.py
+++ b/skimage/morphology/tests/test_grey.py
@@ -187,7 +187,7 @@ def test_3d_fallback_black_tophat():
     testing.assert_array_equal(new_image, image_expected)
 
 def test_2d_ndimage_equivalence():
-    image = np.zeros((9, 9), np.uint16)
+    image = np.zeros((9, 9), np.uint8)
     image[2:-2, 2:-2] = 2**14
     image[3:-3, 3:-3] = 2**15
     image[4, 4] = 2**16-1

From 6e8ae37f0726c3e8a71534cd6b61e48cae90d5fd Mon Sep 17 00:00:00 2001
From: Nelson Brown <Nelson.Brown@gmail.com>
Date: Wed, 16 Jul 2014 20:03:37 -0700
Subject: [PATCH 13/13] Change ndimage test image to fit uint8 range

---
 skimage/morphology/tests/test_grey.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/skimage/morphology/tests/test_grey.py b/skimage/morphology/tests/test_grey.py
index b7703ec2..83d10b45 100644
--- a/skimage/morphology/tests/test_grey.py
+++ b/skimage/morphology/tests/test_grey.py
@@ -188,9 +188,9 @@ def test_3d_fallback_black_tophat():
 
 def test_2d_ndimage_equivalence():
     image = np.zeros((9, 9), np.uint8)
-    image[2:-2, 2:-2] = 2**14
-    image[3:-3, 3:-3] = 2**15
-    image[4, 4] = 2**16-1
+    image[2:-2, 2:-2] = 128
+    image[3:-3, 3:-3] = 196
+    image[4, 4] = 255
 
     opened = grey.opening(image)
     closed = grey.closing(image)