From 6a8889d0b0bb89714755e6f7f0821cd533076af4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Sch=C3=B6nberger?= <jsch@demuc.de>
Date: Thu, 3 Oct 2013 08:39:15 +0200
Subject: [PATCH 1/7] Fix numpy 1.8 bug

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

diff --git a/skimage/morphology/binary.py b/skimage/morphology/binary.py
index e2e0f20b..eaea6773 100644
--- a/skimage/morphology/binary.py
+++ b/skimage/morphology/binary.py
@@ -29,7 +29,7 @@ def binary_erosion(image, selem, out=None):
 
     """
 
-    conv = ndimage.convolve(image > 0, selem, output=out,
+    conv = ndimage.convolve((image > 0).view(np.uint8), selem, output=out,
                             mode='constant', cval=1)
     if conv is not None:
         out = conv
@@ -64,7 +64,7 @@ def binary_dilation(image, selem, out=None):
 
     """
 
-    conv = ndimage.convolve(image > 0, selem, output=out,
+    conv = ndimage.convolve((image > 0).view(np.uint8), selem, output=out,
                             mode='constant', cval=0)
     if conv is not None:
         out = conv

From 895b025a3a875b49ab183c5f43dd7f5364d8faed Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Sch=C3=B6nberger?= <jsch@demuc.de>
Date: Thu, 3 Oct 2013 08:39:19 +0200
Subject: [PATCH 2/7] Split grey and binary erosion tests in two files

---
 skimage/morphology/tests/test_binary.py | 49 +++++++++++++++++++++++++
 skimage/morphology/tests/test_grey.py   | 37 +------------------
 2 files changed, 50 insertions(+), 36 deletions(-)
 create mode 100644 skimage/morphology/tests/test_binary.py

diff --git a/skimage/morphology/tests/test_binary.py b/skimage/morphology/tests/test_binary.py
new file mode 100644
index 00000000..2f47c917
--- /dev/null
+++ b/skimage/morphology/tests/test_binary.py
@@ -0,0 +1,49 @@
+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_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()
diff --git a/skimage/morphology/tests/test_grey.py b/skimage/morphology/tests/test_grey.py
index 244ec566..e2a3928d 100644
--- a/skimage/morphology/tests/test_grey.py
+++ b/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()

From 95a5a98c937a1f8d9cdb5e09de90620704e6cc0b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Sch=C3=B6nberger?= <jsch@demuc.de>
Date: Mon, 7 Oct 2013 22:56:56 +0200
Subject: [PATCH 3/7] Fix overflow error

---
 skimage/morphology/binary.py            | 45 +++++++++++++++++++------
 skimage/morphology/tests/test_binary.py | 21 ++++++++++++
 2 files changed, 56 insertions(+), 10 deletions(-)

diff --git a/skimage/morphology/binary.py b/skimage/morphology/binary.py
index eaea6773..70fcd6b4 100644
--- a/skimage/morphology/binary.py
+++ b/skimage/morphology/binary.py
@@ -1,7 +1,38 @@
 import numpy as np
+import warnings
 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
+    elif selem_sum < 2 ** 16:
+        out_dtype = np.uint16
+    else:
+        out_dtype = np.uint32
+
+    if out is None:
+        out = np.zeros_like(image, dtype=out_dtype)
+    else:
+        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 +60,8 @@ def binary_erosion(image, selem, out=None):
 
     """
 
-    conv = ndimage.convolve((image > 0).view(np.uint8), 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.equal(out, selem_sum, out=out).astype(np.bool, copy=False)
 
 
 def binary_dilation(image, selem, out=None):
@@ -64,11 +92,8 @@ def binary_dilation(image, selem, out=None):
 
     """
 
-    conv = ndimage.convolve((image > 0).view(np.uint8), 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.not_equal(out, 0, out=out).astype(np.bool, copy=False)
 
 
 def binary_opening(image, selem, out=None):
diff --git a/skimage/morphology/tests/test_binary.py b/skimage/morphology/tests/test_binary.py
index 2f47c917..5f831669 100644
--- a/skimage/morphology/tests/test_binary.py
+++ b/skimage/morphology/tests/test_binary.py
@@ -17,6 +17,27 @@ def test_non_square_image():
     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)

From ecf10a7a48ed0205a61da10a91153345266dcd1d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Sch=C3=B6nberger?= <jsch@demuc.de>
Date: Mon, 7 Oct 2013 23:33:12 +0200
Subject: [PATCH 4/7] Reduce number of specializations

---
 skimage/morphology/binary.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/skimage/morphology/binary.py b/skimage/morphology/binary.py
index 70fcd6b4..7262c573 100644
--- a/skimage/morphology/binary.py
+++ b/skimage/morphology/binary.py
@@ -10,10 +10,8 @@ def _convolve(image, selem, out, cval):
     selem_sum = np.sum(selem)
     if selem_sum < 2 ** 8:
         out_dtype = np.uint8
-    elif selem_sum < 2 ** 16:
-        out_dtype = np.uint16
     else:
-        out_dtype = np.uint32
+        out_dtype = np.intp
 
     if out is None:
         out = np.zeros_like(image, dtype=out_dtype)

From 2a84e4538927a689fec6d6aa26c1af482fb2f933 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Sch=C3=B6nberger?= <jsch@demuc.de>
Date: Mon, 7 Oct 2013 23:35:54 +0200
Subject: [PATCH 5/7] Remove unused import

---
 skimage/morphology/binary.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/skimage/morphology/binary.py b/skimage/morphology/binary.py
index 7262c573..4a7b1578 100644
--- a/skimage/morphology/binary.py
+++ b/skimage/morphology/binary.py
@@ -1,5 +1,4 @@
 import numpy as np
-import warnings
 from scipy import ndimage
 
 

From b187144a5fe24d0370a77d36c656eeabfd885690 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Sch=C3=B6nberger?= <jsch@demuc.de>
Date: Thu, 10 Oct 2013 09:04:17 +0200
Subject: [PATCH 6/7] Add support older numpy versions

---
 skimage/morphology/binary.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/skimage/morphology/binary.py b/skimage/morphology/binary.py
index 4a7b1578..d248d8db 100644
--- a/skimage/morphology/binary.py
+++ b/skimage/morphology/binary.py
@@ -58,7 +58,8 @@ def binary_erosion(image, selem, out=None):
     """
 
     out, selem_sum = _convolve(image, selem, out, 1)
-    return np.equal(out, selem_sum, out=out).astype(np.bool, copy=False)
+    return np.array(np.equal(out, selem_sum, out=out), dtype=np.bool,
+                    copy=False)
 
 
 def binary_dilation(image, selem, out=None):
@@ -90,7 +91,7 @@ def binary_dilation(image, selem, out=None):
     """
 
     out, _ = _convolve(image, selem, out, 0)
-    return np.not_equal(out, 0, out=out).astype(np.bool, copy=False)
+    return np.array(np.not_equal(out, 0, out=out), dtype=np.bool, copy=False)
 
 
 def binary_opening(image, selem, out=None):

From f8d34e8bf91f1fed3970b770abdfec94efc949df Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Sch=C3=B6nberger?= <jsch@demuc.de>
Date: Thu, 10 Oct 2013 09:10:42 +0200
Subject: [PATCH 7/7] Deprecate out parameter

---
 TODO.txt                     | 1 +
 skimage/morphology/binary.py | 4 ++++
 2 files changed, 5 insertions(+)

diff --git a/TODO.txt b/TODO.txt
index db7ffe48..29d1ebac 100644
--- a/TODO.txt
+++ b/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
 -----------
diff --git a/skimage/morphology/binary.py b/skimage/morphology/binary.py
index d248d8db..11a14d49 100644
--- a/skimage/morphology/binary.py
+++ b/skimage/morphology/binary.py
@@ -1,3 +1,4 @@
+import warnings
 import numpy as np
 from scipy import ndimage
 
@@ -15,6 +16,9 @@ def _convolve(image, selem, out, cval):
     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 '