From 9adbca13e774849751405c4fc804af08b2470eed Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Fri, 14 Oct 2011 11:00:10 -0400
Subject: [PATCH 01/13] Add parameter to flip structuring element about its
 origin

This parameter only affects structuring elements (selem) with even-numbered sides, since an odd-numbered selem is centered about its origin. Note the selem isn't actually flipped, but shifted (i.e. I assume a selem that is symmetric in *shape*)
---
 scikits/image/morphology/cmorph.pyx | 15 +++++++++++++--
 scikits/image/morphology/grey.py    | 17 +++++++++++++----
 2 files changed, 26 insertions(+), 6 deletions(-)

diff --git a/scikits/image/morphology/cmorph.pyx b/scikits/image/morphology/cmorph.pyx
index 5572102c..8ca24752 100644
--- a/scikits/image/morphology/cmorph.pyx
+++ b/scikits/image/morphology/cmorph.pyx
@@ -8,6 +8,7 @@ import numpy as np
 
 cimport numpy as np
 cimport cython
+from cpython cimport bool
 
 STREL_DTYPE = np.uint8
 ctypedef np.uint8_t STREL_DTYPE_t
@@ -21,9 +22,14 @@ cdef inline int int_min(int a, int b): return a if a <= b else b
 @cython.boundscheck(False)
 def dilate(np.ndarray[IMAGE_DTYPE_t, ndim=2] image not None,
            np.ndarray[IMAGE_DTYPE_t, ndim=2] selem not None,
-           np.ndarray[IMAGE_DTYPE_t, ndim=2] out):
+           np.ndarray[IMAGE_DTYPE_t, ndim=2] out,
+           bool flip):
     cdef int hw = selem.shape[0] // 2
     cdef int hh = selem.shape[1] // 2
+    if flip:
+        hw -= 1
+        hh -= 1
+
     cdef int width = image.shape[0], height = image.shape[1]
     if out is None:
         out = np.zeros([width, height], dtype=IMAGE_DTYPE)
@@ -64,9 +70,14 @@ def dilate(np.ndarray[IMAGE_DTYPE_t, ndim=2] image not None,
 @cython.boundscheck(False)
 def erode(np.ndarray[IMAGE_DTYPE_t, ndim=2] image not None,
           np.ndarray[IMAGE_DTYPE_t, ndim=2] selem not None,
-          np.ndarray[IMAGE_DTYPE_t, ndim=2] out):
+          np.ndarray[IMAGE_DTYPE_t, ndim=2] out,
+          bool flip):
     cdef int hw = selem.shape[0] // 2
     cdef int hh = selem.shape[1] // 2
+    if flip:
+        hw -= 1
+        hh -= 1
+
     cdef int width = image.shape[0], height = image.shape[1]
     if out is None:
         out = np.zeros([width, height], dtype=IMAGE_DTYPE)
diff --git a/scikits/image/morphology/grey.py b/scikits/image/morphology/grey.py
index 2eb94024..5592850f 100644
--- a/scikits/image/morphology/grey.py
+++ b/scikits/image/morphology/grey.py
@@ -9,7 +9,7 @@ import numpy as np
 
 eps = np.finfo(float).eps
 
-def greyscale_erode(image, selem, out=None):
+def greyscale_erode(image, selem, out=None, flip=False):
     """
     Performs a greyscale morphological erosion on an image given a flat
     structuring element. The eroded pixel at (i,j) is the minimum over all
@@ -27,6 +27,10 @@ def greyscale_erode(image, selem, out=None):
        The array to store the result of the morphology. If None is
        passed, a new array will be allocated.
 
+    flip : bool
+        Flip structuring element about center point. This only affects
+        eccentric structuring elements (i.e. selem with even numbered sides).
+
     Returns
     -------
     eroded : ndarray
@@ -36,12 +40,12 @@ def greyscale_erode(image, selem, out=None):
         raise NotImplementedError("In-place erosion not supported!")
     try:
         import scikits.image.morphology.cmorph as cmorph
-        out = cmorph.erode(image, selem, out=out)
+        out = cmorph.erode(image, selem, out=out, flip=flip)
         return out;
     except ImportError:
         raise ImportError("cmorph extension not available.")
 
-def greyscale_dilate(image, selem, out=None):
+def greyscale_dilate(image, selem, out=None, flip=False):
     """
     Performs a greyscale morphological dilation on an image given a flat
     structuring element. The dilated pixel at (i,j) is the maximum over all
@@ -60,6 +64,10 @@ def greyscale_dilate(image, selem, out=None):
        The array to store the result of the morphology. If None, is
        passed, a new array will be allocated.
 
+    flip : bool
+        Flip structuring element about center point. This only affects
+        eccentric structuring elements (i.e. selem with even numbered sides).
+
     Returns
     -------
     dilated : ndarray
@@ -69,7 +77,7 @@ def greyscale_dilate(image, selem, out=None):
         raise NotImplementedError("In-place dilation not supported!")
     try:
         from . import cmorph
-        out = cmorph.dilate(image, selem, out=out)
+        out = cmorph.dilate(image, selem, out=out, flip=flip)
         return out;
     except ImportError:
         raise ImportError("cmorph extension not available.")
@@ -79,6 +87,7 @@ def greyscale_open(image, selem, out=None):
     Performs a greyscale morphological opening on an image given a flat
     structuring element defined as a erosion followed by a dilation.
 
+
     Parameters
     ----------
     image : ndarray

From b6e470dbd15f388819626d5943524d427e9f7ce4 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 15 Oct 2011 02:57:32 -0400
Subject: [PATCH 02/13] Remove unnecessary if-block.

This looks like it was a copy-paste error.
---
 scikits/image/morphology/grey.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/scikits/image/morphology/grey.py b/scikits/image/morphology/grey.py
index 5592850f..ac41c4f1 100644
--- a/scikits/image/morphology/grey.py
+++ b/scikits/image/morphology/grey.py
@@ -189,8 +189,5 @@ def greyscale_black_top_hat(image, selem, out=None):
         raise NotImplementedError("Cannot perform white top hat in place.")
     dilated = greyscale_dilate(image, selem)
     out = greyscale_erode(dilated, selem, out=out)
-
     out = out - image
-    if image is out:
-        raise NotImplementedError("Cannot perform black top hat in place.")
     return out

From 4f4f219788843bea2bd6d9ee2f811a1a87abf57c Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 15 Oct 2011 03:01:27 -0400
Subject: [PATCH 03/13] Reuse open/close operations for white/black tophat

---
 scikits/image/morphology/grey.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/scikits/image/morphology/grey.py b/scikits/image/morphology/grey.py
index ac41c4f1..0b8c49b8 100644
--- a/scikits/image/morphology/grey.py
+++ b/scikits/image/morphology/grey.py
@@ -159,8 +159,7 @@ def greyscale_white_top_hat(image, selem, out=None):
     if image is out:
         raise NotImplementedError("Cannot perform white top hat in place.")
 
-    eroded = greyscale_erode(image, selem)
-    out = greyscale_dilate(eroded, selem, out=out)
+    out = greyscale_open(image, selem, out=out)
     out = image - out
     return out
 
@@ -187,7 +186,6 @@ def greyscale_black_top_hat(image, selem, out=None):
     """
     if image is out:
         raise NotImplementedError("Cannot perform white top hat in place.")
-    dilated = greyscale_dilate(image, selem)
-    out = greyscale_erode(dilated, selem, out=out)
+    out = greyscale_close(image, selem, out=out)
     out = out - image
     return out

From fb92bfcf715c81f7343eef81518f4379bfdc88aa Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 15 Oct 2011 03:32:59 -0400
Subject: [PATCH 04/13] Add tests for correct behavior of square structuring
 elements

---
 .../image/morphology/tests/test_morphology.py | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/scikits/image/morphology/tests/test_morphology.py b/scikits/image/morphology/tests/test_morphology.py
index ff22c458..7cea1e07 100644
--- a/scikits/image/morphology/tests/test_morphology.py
+++ b/scikits/image/morphology/tests/test_morphology.py
@@ -61,3 +61,48 @@ class TestMorphology():
     def test_close_disk(self):
         self.morph_worker(lena, "disk-close-matlab-output.npz",
                           greyscale_close, disk)
+
+
+BLACK_PIXEL = 255 * np.ones((4, 4), dtype=np.uint8)
+BLACK_PIXEL[1, 1] = 0
+WHITE_PIXEL = 255 - BLACK_PIXEL
+SELEM = square(2)
+
+def test_dilate_erode_symmetry():
+    c = greyscale_erode(BLACK_PIXEL, SELEM)
+    d = greyscale_dilate(WHITE_PIXEL, SELEM)
+    assert np.all(c == (255 - d))
+
+
+def test_open_dark_pixel():
+    assert np.all(greyscale_open(BLACK_PIXEL, SELEM) == BLACK_PIXEL)
+
+def test_close_white_pixel():
+    assert np.all(greyscale_close(WHITE_PIXEL, SELEM) == WHITE_PIXEL)
+
+
+def test_open_white_pixel():
+    assert np.all(greyscale_open(WHITE_PIXEL, SELEM) == 0)
+
+def test_close_dark_pixel():
+    assert np.all(greyscale_close(BLACK_PIXEL, SELEM) == 255)
+
+
+def test_white_tophat_white_pixel():
+    tophat = greyscale_white_top_hat(WHITE_PIXEL, SELEM)
+    assert np.all(tophat == WHITE_PIXEL)
+
+def test_black_tophat_black_pixel():
+    tophat = greyscale_black_top_hat(BLACK_PIXEL, SELEM)
+    assert np.all(tophat == (255 - BLACK_PIXEL))
+
+
+def test_white_tophat_black_pixel():
+    tophat = greyscale_white_top_hat(BLACK_PIXEL, SELEM)
+    assert np.all(tophat == 0)
+
+def test_black_tophat_white_pixel():
+    tophat = greyscale_black_top_hat(WHITE_PIXEL, SELEM)
+    assert np.all(tophat == 0)
+
+

From ac2714d3c8e690e1de4e89cee1b8bac3191acfc8 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 15 Oct 2011 03:34:30 -0400
Subject: [PATCH 05/13] Fix morphological open/close for square structuring
 elements with even sides.

This also fixes rectangular selems with even sides, but not rectangular selems with one odd and one even side.
---
 scikits/image/morphology/grey.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/scikits/image/morphology/grey.py b/scikits/image/morphology/grey.py
index 0b8c49b8..463e55b2 100644
--- a/scikits/image/morphology/grey.py
+++ b/scikits/image/morphology/grey.py
@@ -105,8 +105,13 @@ def greyscale_open(image, selem, out=None):
     opening : ndarray
        The result of the morphological opening.
     """
+    h, w = selem.shape
+    if (h % 2) == 0 and (w % 2) == 0:
+        flip = True
+    else:
+        flip = False
     eroded = greyscale_erode(image, selem)
-    out = greyscale_dilate(eroded, selem, out=out)
+    out = greyscale_dilate(eroded, selem, out=out, flip=flip)
     return out
 
 def greyscale_close(image, selem, out=None):
@@ -131,8 +136,13 @@ def greyscale_close(image, selem, out=None):
     opening : ndarray
        The result of the morphological opening.
     """
+    h, w = selem.shape
+    if (h % 2) == 0 and (w % 2) == 0:
+        flip = True
+    else:
+        flip = False
     dilated = greyscale_dilate(image, selem)
-    out = greyscale_erode(dilated, selem, out=out)
+    out = greyscale_erode(dilated, selem, out=out, flip=flip)
     return out
 
 def greyscale_white_top_hat(image, selem, out=None):

From 9ce5ee7d71fbfcc7e0cec9d91fbd91e6edcfb999 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 15 Oct 2011 03:59:41 -0400
Subject: [PATCH 06/13] Move test functions to test class

---
 .../image/morphology/tests/test_morphology.py | 81 ++++++++++---------
 1 file changed, 41 insertions(+), 40 deletions(-)

diff --git a/scikits/image/morphology/tests/test_morphology.py b/scikits/image/morphology/tests/test_morphology.py
index 7cea1e07..93606848 100644
--- a/scikits/image/morphology/tests/test_morphology.py
+++ b/scikits/image/morphology/tests/test_morphology.py
@@ -63,46 +63,47 @@ class TestMorphology():
                           greyscale_close, disk)
 
 
-BLACK_PIXEL = 255 * np.ones((4, 4), dtype=np.uint8)
-BLACK_PIXEL[1, 1] = 0
-WHITE_PIXEL = 255 - BLACK_PIXEL
-SELEM = square(2)
+class TestEccentricStructuringElements():
 
-def test_dilate_erode_symmetry():
-    c = greyscale_erode(BLACK_PIXEL, SELEM)
-    d = greyscale_dilate(WHITE_PIXEL, SELEM)
-    assert np.all(c == (255 - d))
-
-
-def test_open_dark_pixel():
-    assert np.all(greyscale_open(BLACK_PIXEL, SELEM) == BLACK_PIXEL)
-
-def test_close_white_pixel():
-    assert np.all(greyscale_close(WHITE_PIXEL, SELEM) == WHITE_PIXEL)
-
-
-def test_open_white_pixel():
-    assert np.all(greyscale_open(WHITE_PIXEL, SELEM) == 0)
-
-def test_close_dark_pixel():
-    assert np.all(greyscale_close(BLACK_PIXEL, SELEM) == 255)
-
-
-def test_white_tophat_white_pixel():
-    tophat = greyscale_white_top_hat(WHITE_PIXEL, SELEM)
-    assert np.all(tophat == WHITE_PIXEL)
-
-def test_black_tophat_black_pixel():
-    tophat = greyscale_black_top_hat(BLACK_PIXEL, SELEM)
-    assert np.all(tophat == (255 - BLACK_PIXEL))
-
-
-def test_white_tophat_black_pixel():
-    tophat = greyscale_white_top_hat(BLACK_PIXEL, SELEM)
-    assert np.all(tophat == 0)
-
-def test_black_tophat_white_pixel():
-    tophat = greyscale_black_top_hat(WHITE_PIXEL, SELEM)
-    assert np.all(tophat == 0)
+    def setUp(self):
+        self.black_pixel = 255 * np.ones((4, 4), dtype=np.uint8)
+        self.black_pixel[1, 1] = 0
+        self.white_pixel = 255 - self.black_pixel
+        self.selem = square(2)
+
+    def test_dilate_erode_symmetry(self):
+        c = greyscale_erode(self.black_pixel, self.selem)
+        d = greyscale_dilate(self.white_pixel, self.selem)
+        assert np.all(c == (255 - d))
+
+    def test_open_dark_pixel(self):
+        grey_open = greyscale_open(self.black_pixel, self.selem)
+        assert np.all(grey_open == self.black_pixel)
+
+    def test_close_white_pixel(self):
+        grey_close = greyscale_close(self.white_pixel, self.selem)
+        assert np.all(grey_close == self.white_pixel)
+
+    def test_open_white_pixel(self):
+        assert np.all(greyscale_open(self.white_pixel, self.selem) == 0)
+
+    def test_close_dark_pixel(self):
+        assert np.all(greyscale_close(self.black_pixel, self.selem) == 255)
+
+    def test_white_tophat_white_pixel(self):
+        tophat = greyscale_white_top_hat(self.white_pixel, self.selem)
+        assert np.all(tophat == self.white_pixel)
+
+    def test_black_tophat_black_pixel(self):
+        tophat = greyscale_black_top_hat(self.black_pixel, self.selem)
+        assert np.all(tophat == (255 - self.black_pixel))
+
+    def test_white_tophat_black_pixel(self):
+        tophat = greyscale_white_top_hat(self.black_pixel, self.selem)
+        assert np.all(tophat == 0)
+
+    def test_black_tophat_white_pixel(self):
+        tophat = greyscale_black_top_hat(self.white_pixel, self.selem)
+        assert np.all(tophat == 0)
 
 

From 6366da861a3fb5f16bdb15244cb850163cec8055 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 15 Oct 2011 04:19:04 -0400
Subject: [PATCH 07/13] Add tests for rectangular structuring elements

These tests fail.
---
 .../image/morphology/tests/test_morphology.py | 51 +++++++++++--------
 1 file changed, 30 insertions(+), 21 deletions(-)

diff --git a/scikits/image/morphology/tests/test_morphology.py b/scikits/image/morphology/tests/test_morphology.py
index 93606848..330518c2 100644
--- a/scikits/image/morphology/tests/test_morphology.py
+++ b/scikits/image/morphology/tests/test_morphology.py
@@ -69,41 +69,50 @@ class TestEccentricStructuringElements():
         self.black_pixel = 255 * np.ones((4, 4), dtype=np.uint8)
         self.black_pixel[1, 1] = 0
         self.white_pixel = 255 - self.black_pixel
-        self.selem = square(2)
+        self.selems = [square(2), rectangle(2, 2),
+                       rectangle(2, 1), rectangle(1, 2)]
 
     def test_dilate_erode_symmetry(self):
-        c = greyscale_erode(self.black_pixel, self.selem)
-        d = greyscale_dilate(self.white_pixel, self.selem)
-        assert np.all(c == (255 - d))
+        for s in self.selems:
+            c = greyscale_erode(self.black_pixel, s)
+            d = greyscale_dilate(self.white_pixel, s)
+            assert np.all(c == (255 - d))
 
-    def test_open_dark_pixel(self):
-        grey_open = greyscale_open(self.black_pixel, self.selem)
-        assert np.all(grey_open == self.black_pixel)
+    def test_open_black_pixel(self):
+        for s in self.selems:
+            grey_open = greyscale_open(self.black_pixel, s)
+            assert np.all(grey_open == self.black_pixel)
 
     def test_close_white_pixel(self):
-        grey_close = greyscale_close(self.white_pixel, self.selem)
-        assert np.all(grey_close == self.white_pixel)
+        for s in self.selems:
+            grey_close = greyscale_close(self.white_pixel, s)
+            assert np.all(grey_close == self.white_pixel)
 
     def test_open_white_pixel(self):
-        assert np.all(greyscale_open(self.white_pixel, self.selem) == 0)
+        for s in self.selems:
+            assert np.all(greyscale_open(self.white_pixel, s) == 0)
 
-    def test_close_dark_pixel(self):
-        assert np.all(greyscale_close(self.black_pixel, self.selem) == 255)
+    def test_close_black_pixel(self):
+        for s in self.selems:
+            assert np.all(greyscale_close(self.black_pixel, s) == 255)
 
     def test_white_tophat_white_pixel(self):
-        tophat = greyscale_white_top_hat(self.white_pixel, self.selem)
-        assert np.all(tophat == self.white_pixel)
+        for s in self.selems:
+            tophat = greyscale_white_top_hat(self.white_pixel, s)
+            assert np.all(tophat == self.white_pixel)
 
     def test_black_tophat_black_pixel(self):
-        tophat = greyscale_black_top_hat(self.black_pixel, self.selem)
-        assert np.all(tophat == (255 - self.black_pixel))
+        for s in self.selems:
+            tophat = greyscale_black_top_hat(self.black_pixel, s)
+            assert np.all(tophat == (255 - self.black_pixel))
 
     def test_white_tophat_black_pixel(self):
-        tophat = greyscale_white_top_hat(self.black_pixel, self.selem)
-        assert np.all(tophat == 0)
+        for s in self.selems:
+            tophat = greyscale_white_top_hat(self.black_pixel, s)
+            assert np.all(tophat == 0)
 
     def test_black_tophat_white_pixel(self):
-        tophat = greyscale_black_top_hat(self.white_pixel, self.selem)
-        assert np.all(tophat == 0)
-
+        for s in self.selems:
+            tophat = greyscale_black_top_hat(self.white_pixel, s)
+            assert np.all(tophat == 0)
 

From b0376721ebfede6904a351b69ae6a7c745a8ba67 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 15 Oct 2011 04:23:37 -0400
Subject: [PATCH 08/13] Replace flip parameter in erode/dilate with shift_x and
 shift_y

This change allows morphological open/close and white/black tophat to correctly use rectangular structuring element that has one even-numbered dimension. Note: dilate and erode functions flip the definitions of x/y and width/height, but it does so consistently so it doesn't really matter.
---
 scikits/image/morphology/cmorph.pyx | 14 ++++++-----
 scikits/image/morphology/grey.py    | 38 +++++++++++++++--------------
 2 files changed, 28 insertions(+), 24 deletions(-)

diff --git a/scikits/image/morphology/cmorph.pyx b/scikits/image/morphology/cmorph.pyx
index 8ca24752..6870b500 100644
--- a/scikits/image/morphology/cmorph.pyx
+++ b/scikits/image/morphology/cmorph.pyx
@@ -23,12 +23,13 @@ cdef inline int int_min(int a, int b): return a if a <= b else b
 def dilate(np.ndarray[IMAGE_DTYPE_t, ndim=2] image not None,
            np.ndarray[IMAGE_DTYPE_t, ndim=2] selem not None,
            np.ndarray[IMAGE_DTYPE_t, ndim=2] out,
-           bool flip):
+           bool shift_x, bool shift_y):
     cdef int hw = selem.shape[0] // 2
     cdef int hh = selem.shape[1] // 2
-    if flip:
-        hw -= 1
+    if shift_x:
         hh -= 1
+    if shift_y:
+        hw -= 1
 
     cdef int width = image.shape[0], height = image.shape[1]
     if out is None:
@@ -71,12 +72,13 @@ def dilate(np.ndarray[IMAGE_DTYPE_t, ndim=2] image not None,
 def erode(np.ndarray[IMAGE_DTYPE_t, ndim=2] image not None,
           np.ndarray[IMAGE_DTYPE_t, ndim=2] selem not None,
           np.ndarray[IMAGE_DTYPE_t, ndim=2] out,
-          bool flip):
+          bool shift_x, bool shift_y):
     cdef int hw = selem.shape[0] // 2
     cdef int hh = selem.shape[1] // 2
-    if flip:
-        hw -= 1
+    if shift_x:
         hh -= 1
+    if shift_y:
+        hw -= 1
 
     cdef int width = image.shape[0], height = image.shape[1]
     if out is None:
diff --git a/scikits/image/morphology/grey.py b/scikits/image/morphology/grey.py
index 463e55b2..dec12100 100644
--- a/scikits/image/morphology/grey.py
+++ b/scikits/image/morphology/grey.py
@@ -9,7 +9,7 @@ import numpy as np
 
 eps = np.finfo(float).eps
 
-def greyscale_erode(image, selem, out=None, flip=False):
+def greyscale_erode(image, selem, out=None, shift_x=False, shift_y=False):
     """
     Performs a greyscale morphological erosion on an image given a flat
     structuring element. The eroded pixel at (i,j) is the minimum over all
@@ -27,8 +27,8 @@ def greyscale_erode(image, selem, out=None, flip=False):
        The array to store the result of the morphology. If None is
        passed, a new array will be allocated.
 
-    flip : bool
-        Flip structuring element about center point. This only affects
+    shift_x, shift_y : bool
+        shift structuring element about center point. This only affects
         eccentric structuring elements (i.e. selem with even numbered sides).
 
     Returns
@@ -40,12 +40,13 @@ def greyscale_erode(image, selem, out=None, flip=False):
         raise NotImplementedError("In-place erosion not supported!")
     try:
         import scikits.image.morphology.cmorph as cmorph
-        out = cmorph.erode(image, selem, out=out, flip=flip)
+        out = cmorph.erode(image, selem, out=out,
+                           shift_x=shift_x, shift_y=shift_y)
         return out;
     except ImportError:
         raise ImportError("cmorph extension not available.")
 
-def greyscale_dilate(image, selem, out=None, flip=False):
+def greyscale_dilate(image, selem, out=None, shift_x=False, shift_y=False):
     """
     Performs a greyscale morphological dilation on an image given a flat
     structuring element. The dilated pixel at (i,j) is the maximum over all
@@ -64,8 +65,8 @@ def greyscale_dilate(image, selem, out=None, flip=False):
        The array to store the result of the morphology. If None, is
        passed, a new array will be allocated.
 
-    flip : bool
-        Flip structuring element about center point. This only affects
+    shift_x, shift_y : bool
+        shift structuring element about center point. This only affects
         eccentric structuring elements (i.e. selem with even numbered sides).
 
     Returns
@@ -77,7 +78,8 @@ def greyscale_dilate(image, selem, out=None, flip=False):
         raise NotImplementedError("In-place dilation not supported!")
     try:
         from . import cmorph
-        out = cmorph.dilate(image, selem, out=out, flip=flip)
+        out = cmorph.dilate(image, selem, out=out,
+                            shift_x=shift_x, shift_y=shift_y)
         return out;
     except ImportError:
         raise ImportError("cmorph extension not available.")
@@ -106,12 +108,12 @@ def greyscale_open(image, selem, out=None):
        The result of the morphological opening.
     """
     h, w = selem.shape
-    if (h % 2) == 0 and (w % 2) == 0:
-        flip = True
-    else:
-        flip = False
+    shift_x = True if (w % 2) == 0 else False
+    shift_y = True if (h % 2) == 0 else False
+
     eroded = greyscale_erode(image, selem)
-    out = greyscale_dilate(eroded, selem, out=out, flip=flip)
+    out = greyscale_dilate(eroded, selem, out=out,
+                           shift_x=shift_x, shift_y=shift_y)
     return out
 
 def greyscale_close(image, selem, out=None):
@@ -137,12 +139,12 @@ def greyscale_close(image, selem, out=None):
        The result of the morphological opening.
     """
     h, w = selem.shape
-    if (h % 2) == 0 and (w % 2) == 0:
-        flip = True
-    else:
-        flip = False
+    shift_x = True if (w % 2) == 0 else False
+    shift_y = True if (h % 2) == 0 else False
+
     dilated = greyscale_dilate(image, selem)
-    out = greyscale_erode(dilated, selem, out=out, flip=flip)
+    out = greyscale_erode(dilated, selem, out=out,
+                          shift_x=shift_x, shift_y=shift_y)
     return out
 
 def greyscale_white_top_hat(image, selem, out=None):

From 65b6b6bed7aabd0c392d021dfac0ca811914ea60 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 15 Oct 2011 04:27:35 -0400
Subject: [PATCH 09/13] Minor fix to docstring

---
 scikits/image/morphology/selem.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scikits/image/morphology/selem.py b/scikits/image/morphology/selem.py
index cf786d6d..4a5ee0bd 100644
--- a/scikits/image/morphology/selem.py
+++ b/scikits/image/morphology/selem.py
@@ -69,7 +69,7 @@ def diamond(radius, dtype=np.uint8):
     Parameters
     ----------
     radius : string
-       The radius of the disk-shaped structuring element.
+       The radius of the diamond-shaped structuring element.
 
     dtype : data-type
        The data type of the structuring element.

From 873520456531a7c4bedbf0b0b5a06de223bfe785 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 15 Oct 2011 11:57:01 -0400
Subject: [PATCH 10/13] Improve docstrings in grey morphology module

---
 scikits/image/morphology/grey.py | 50 ++++++++++++++++++++------------
 1 file changed, 32 insertions(+), 18 deletions(-)

diff --git a/scikits/image/morphology/grey.py b/scikits/image/morphology/grey.py
index dec12100..ca452eec 100644
--- a/scikits/image/morphology/grey.py
+++ b/scikits/image/morphology/grey.py
@@ -10,10 +10,11 @@ import numpy as np
 eps = np.finfo(float).eps
 
 def greyscale_erode(image, selem, out=None, shift_x=False, shift_y=False):
-    """
-    Performs a greyscale morphological erosion on an image given a flat
-    structuring element. The eroded pixel at (i,j) is the minimum over all
-    pixels in the neighborhood centered at (i,j).
+    """Return greyscale morphological erosion of an image.
+
+    Morphological erosion sets a pixel at (i,j) to the minimum over all pixels
+    in the neighborhood centered at (i,j). Erosion shrinks bright regions and
+    enlarges dark regions.
 
     Parameters
     ----------
@@ -47,10 +48,11 @@ def greyscale_erode(image, selem, out=None, shift_x=False, shift_y=False):
         raise ImportError("cmorph extension not available.")
 
 def greyscale_dilate(image, selem, out=None, shift_x=False, shift_y=False):
-    """
-    Performs a greyscale morphological dilation on an image given a flat
-    structuring element. The dilated pixel at (i,j) is the maximum over all
-    pixels in the neighborhood centered at (i,j).
+    """Return greyscale morphological dilation of an image.
+
+    Morphological dilation sets a pixel at (i,j) to the maximum over all pixels
+    in the neighborhood centered at (i,j). Dilation enlarges bright regions
+    and shrinks dark regions.
 
     Parameters
     ----------
@@ -85,10 +87,12 @@ def greyscale_dilate(image, selem, out=None, shift_x=False, shift_y=False):
         raise ImportError("cmorph extension not available.")
 
 def greyscale_open(image, selem, out=None):
-    """
-    Performs a greyscale morphological opening on an image given a flat
-    structuring element defined as a erosion followed by a dilation.
+    """Return greyscale morphological opening of an image.
 
+    The morphological opening on an image is defined as an erosion followed by
+    a dilation. Opening can remove small bright spots (i.e. "salt") and connect
+    small dark cracks. This tends to "open" up (dark) gaps between (bright)
+    features.
 
     Parameters
     ----------
@@ -117,9 +121,12 @@ def greyscale_open(image, selem, out=None):
     return out
 
 def greyscale_close(image, selem, out=None):
-    """
-    Performs a greyscale morphological closing on an image given a flat
-    structuring element defined as a dilation followed by an erosion.
+    """Return greyscale morphological closing of an image.
+
+    The morphological closing on an image is defined as a dilation followed by
+    an erosion. Closing can remove small dark spots (i.e. "pepper") and connect
+    small bright cracks. This tends to "close" up (dark) gaps between (bright)
+    features.
 
     Parameters
     ----------
@@ -148,8 +155,11 @@ def greyscale_close(image, selem, out=None):
     return out
 
 def greyscale_white_top_hat(image, selem, out=None):
-    """
-    Applies a white top hat on an image given a flat structuring element.
+    """Return white top hat of an image.
+
+    The white top hat of an image is defined as the image minus its
+    morphological opening. This operation returns the bright spots of the image
+    that are smaller than the structuring element.
 
     Parameters
     ----------
@@ -176,8 +186,12 @@ def greyscale_white_top_hat(image, selem, out=None):
     return out
 
 def greyscale_black_top_hat(image, selem, out=None):
-    """
-    Applies a black top hat on an image given a flat structuring element.
+    """Return black top hat of an image.
+
+    The black top hat of an image is defined as its morphological closing minus
+    the original image. This operation returns the dark spots of the image that
+    are smaller than the structuring element. Note that dark spots in the
+    original image are bright spots after the black top hat.
 
     Parameters
     ----------

From c7c0798d1c89600688a6585fcef22b1533bec414 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 15 Oct 2011 12:37:25 -0400
Subject: [PATCH 11/13] Add examples to grey morphology docstrings

---
 scikits/image/morphology/grey.py | 105 ++++++++++++++++++++++++++++++-
 1 file changed, 104 insertions(+), 1 deletion(-)

diff --git a/scikits/image/morphology/grey.py b/scikits/image/morphology/grey.py
index ca452eec..12b74d14 100644
--- a/scikits/image/morphology/grey.py
+++ b/scikits/image/morphology/grey.py
@@ -36,6 +36,23 @@ def greyscale_erode(image, selem, out=None, shift_x=False, shift_y=False):
     -------
     eroded : ndarray
        The result of the morphological erosion.
+
+    Examples
+    --------
+    >>> # Erosion shrinks bright regions
+    >>> from scikits.image.morphology import square
+    >>> bright_square = np.array([[0, 0, 0, 0, 0],
+    ...                           [0, 1, 1, 1, 0],
+    ...                           [0, 1, 1, 1, 0],
+    ...                           [0, 1, 1, 1, 0],
+    ...                           [0, 0, 0, 0, 0]], dtype=np.uint8)
+    >>> greyscale_erode(bright_square, square(3))
+    array([[0, 0, 0, 0, 0],
+           [0, 0, 0, 0, 0],
+           [0, 0, 1, 0, 0],
+           [0, 0, 0, 0, 0],
+           [0, 0, 0, 0, 0]], dtype='uint8')
+
     """
     if image is out:
         raise NotImplementedError("In-place erosion not supported!")
@@ -75,6 +92,23 @@ def greyscale_dilate(image, selem, out=None, shift_x=False, shift_y=False):
     -------
     dilated : ndarray
        The result of the morphological dilation.
+
+    Examples
+    --------
+    >>> # Dilation enlarges bright regions
+    >>> from scikits.image.morphology import square
+    >>> bright_pixel = np.array([[0, 0, 0, 0, 0],
+    ...                          [0, 0, 0, 0, 0],
+    ...                          [0, 0, 1, 0, 0],
+    ...                          [0, 0, 0, 0, 0],
+    ...                          [0, 0, 0, 0, 0]], dtype=np.uint8)
+    >>> greyscale_dilate(bright_pixel, square(3))
+    array([[0, 0, 0, 0, 0],
+           [0, 1, 1, 1, 0],
+           [0, 1, 1, 1, 0],
+           [0, 1, 1, 1, 0],
+           [0, 0, 0, 0, 0]], dtype='uint8')
+
     """
     if image is out:
         raise NotImplementedError("In-place dilation not supported!")
@@ -110,6 +144,23 @@ def greyscale_open(image, selem, out=None):
     -------
     opening : ndarray
        The result of the morphological opening.
+
+    Examples
+    --------
+    >>> # Open up gap between two bright regions (but also shrink regions)
+    >>> from scikits.image.morphology import square
+    >>> bad_connection = np.array([[1, 0, 0, 0, 1],
+    ...                            [1, 1, 0, 1, 1],
+    ...                            [1, 1, 1, 1, 1],
+    ...                            [1, 1, 0, 1, 1],
+    ...                            [1, 0, 0, 0, 1]], dtype=np.uint8)
+    >>> greyscale_open(bad_connection, square(3))
+    array([[0, 0, 0, 0, 0],
+           [1, 1, 0, 1, 1],
+           [1, 1, 0, 1, 1],
+           [1, 1, 0, 1, 1],
+           [0, 0, 0, 0, 0]], dtype='uint8')
+
     """
     h, w = selem.shape
     shift_x = True if (w % 2) == 0 else False
@@ -144,6 +195,23 @@ def greyscale_close(image, selem, out=None):
     -------
     opening : ndarray
        The result of the morphological opening.
+
+    Examples
+    --------
+    >>> # Close a gap between two bright lines
+    >>> from scikits.image.morphology import square
+    >>> broken_line = np.array([[0, 0, 0, 0, 0],
+    ...                         [0, 0, 0, 0, 0],
+    ...                         [1, 1, 0, 1, 1],
+    ...                         [0, 0, 0, 0, 0],
+    ...                         [0, 0, 0, 0, 0]], dtype=np.uint8)
+    >>> greyscale_close(broken_line, square(3))
+    array([[0, 0, 0, 0, 0],
+           [0, 0, 0, 0, 0],
+           [1, 1, 1, 1, 1],
+           [0, 0, 0, 0, 0],
+           [0, 0, 0, 0, 0]], dtype='uint8')
+
     """
     h, w = selem.shape
     shift_x = True if (w % 2) == 0 else False
@@ -177,7 +245,24 @@ def greyscale_white_top_hat(image, selem, out=None):
     -------
     opening : ndarray
        The result of the morphological white top hat.
-    """
+
+    Examples
+    --------
+    >>> # Subtract grey background from bright peak
+    >>> from scikits.image.morphology import square
+    >>> bright_on_grey = np.array([[2, 3, 3, 3, 2],
+    ...                            [3, 4, 5, 4, 3],
+    ...                            [3, 5, 9, 5, 3],
+    ...                            [3, 4, 5, 4, 3],
+    ...                            [2, 3, 3, 3, 2]], dtype=np.uint8)
+    >>> greyscale_white_top_hat(bright_on_grey, square(3))
+    array([[0, 0, 0, 0, 0],
+           [0, 0, 1, 0, 0],
+           [0, 1, 5, 1, 0],
+           [0, 0, 1, 0, 0],
+           [0, 0, 0, 0, 0]], dtype='uint8')
+
+   """
     if image is out:
         raise NotImplementedError("Cannot perform white top hat in place.")
 
@@ -209,9 +294,27 @@ def greyscale_black_top_hat(image, selem, out=None):
     -------
     opening : ndarray
        The result of the black top filter.
+
+    Examples
+    --------
+    >>> # Change dark peak to bright peak and subtract background
+    >>> from scikits.image.morphology import square
+    >>> dark_on_grey = np.array([[7, 6, 6, 6, 7],
+    ...                          [6, 5, 4, 5, 6],
+    ...                          [6, 4, 0, 4, 6],
+    ...                          [6, 5, 4, 5, 6],
+    ...                          [7, 6, 6, 6, 7]], dtype=np.uint8)
+    >>> greyscale_black_top_hat(dark_on_grey, square(3))
+    array([[0, 0, 0, 0, 0],
+           [0, 0, 1, 0, 0],
+           [0, 1, 5, 1, 0],
+           [0, 0, 1, 0, 0],
+           [0, 0, 0, 0, 0]], dtype='uint8')
+
     """
     if image is out:
         raise NotImplementedError("Cannot perform white top hat in place.")
     out = greyscale_close(image, selem, out=out)
     out = out - image
     return out
+

From 9e81cecbb6aa340c9d38d5293066fe42b2b98351 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 15 Oct 2011 12:40:06 -0400
Subject: [PATCH 12/13] Specify that input arrays to grey morphology filters
 must be uint8

---
 scikits/image/morphology/grey.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/scikits/image/morphology/grey.py b/scikits/image/morphology/grey.py
index 12b74d14..1b5552ff 100644
--- a/scikits/image/morphology/grey.py
+++ b/scikits/image/morphology/grey.py
@@ -19,7 +19,7 @@ def greyscale_erode(image, selem, out=None, shift_x=False, shift_y=False):
     Parameters
     ----------
     image : ndarray
-       The image as an ndarray.
+       The image as a uint8 ndarray.
 
     selem : ndarray
        The neighborhood expressed as a 2-D array of 1's and 0's.
@@ -75,7 +75,7 @@ def greyscale_dilate(image, selem, out=None, shift_x=False, shift_y=False):
     ----------
 
     image : ndarray
-       The image as an ndarray.
+       The image as a uint8 ndarray.
 
     selem : ndarray
        The neighborhood expressed as a 2-D array of 1's and 0's.
@@ -131,7 +131,7 @@ def greyscale_open(image, selem, out=None):
     Parameters
     ----------
     image : ndarray
-       The image as an ndarray.
+       The image as a uint8 ndarray.
 
     selem : ndarray
        The neighborhood expressed as a 2-D array of 1's and 0's.
@@ -182,7 +182,7 @@ def greyscale_close(image, selem, out=None):
     Parameters
     ----------
     image : ndarray
-       The image as an ndarray.
+       The image as a uint8 ndarray.
 
     selem : ndarray
        The neighborhood expressed as a 2-D array of 1's and 0's.
@@ -232,7 +232,7 @@ def greyscale_white_top_hat(image, selem, out=None):
     Parameters
     ----------
     image : ndarray
-       The image as an ndarray.
+       The image as a uint8 ndarray.
 
     selem : ndarray
        The neighborhood expressed as a 2-D array of 1's and 0's.
@@ -281,7 +281,7 @@ def greyscale_black_top_hat(image, selem, out=None):
     Parameters
     ----------
     image : ndarray
-       The image as an ndarray.
+       The image as a uint8 ndarray.
 
     selem : ndarray
        The neighborhood expressed as a 2-D array of 1's and 0's.

From 1cc0f36d1568d1be49f846f7ecd115ea1fbdfa74 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 15 Oct 2011 12:44:26 -0400
Subject: [PATCH 13/13] Reformat doctests so that tests pass

I believe the dtype print out was changed to a string in a recent version of numpy, so this change may actually break the doctest for older versions.
---
 scikits/image/morphology/watershed.py | 30 +++++++++++++--------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/scikits/image/morphology/watershed.py b/scikits/image/morphology/watershed.py
index 1065dbd3..5c74374a 100644
--- a/scikits/image/morphology/watershed.py
+++ b/scikits/image/morphology/watershed.py
@@ -249,32 +249,32 @@ def is_local_maximum(image, labels=None, footprint=None):
     >>> image[3, 3] = 1
     >>> image
     array([[ 0.,  0.,  0.,  0.],
-        [ 0.,  0.,  2.,  0.],
-        [ 0.,  0.,  0.,  0.],
-        [ 0.,  0.,  0.,  1.]])
+           [ 0.,  0.,  2.,  0.],
+           [ 0.,  0.,  0.,  0.],
+           [ 0.,  0.,  0.,  1.]])
     >>> is_local_maximum(image)
     array([[ True, False, False, False],
-        [ True, False,  True, False],
-        [ True, False, False, False],
-        [ True,  True, False,  True]], dtype=bool)
+           [ True, False,  True, False],
+           [ True, False, False, False],
+           [ True,  True, False,  True]], dtype='bool')
     >>> image = np.arange(16).reshape((4, 4))
     >>> labels = np.array([[1, 2], [3, 4]])
     >>> labels = np.repeat(np.repeat(labels, 2, axis=0), 2, axis=1)
     >>> labels
     array([[1, 1, 2, 2],
-        [1, 1, 2, 2],
-        [3, 3, 4, 4],
-        [3, 3, 4, 4]])
+           [1, 1, 2, 2],
+           [3, 3, 4, 4],
+           [3, 3, 4, 4]])
     >>> image
     array([[ 0,  1,  2,  3],
-        [ 4,  5,  6,  7],
-        [ 8,  9, 10, 11],
-        [12, 13, 14, 15]])
+           [ 4,  5,  6,  7],
+           [ 8,  9, 10, 11],
+           [12, 13, 14, 15]])
     >>> is_local_maximum(image, labels=labels)
     array([[False, False, False, False],
-        [False,  True, False,  True],
-        [False, False, False, False],
-        [False,  True, False,  True]], dtype=bool)
+           [False,  True, False,  True],
+           [False, False, False, False],
+           [False,  True, False,  True]], dtype='bool')
     """
     if labels is None:
         labels = np.ones(image.shape, dtype=np.uint8)