From fbbe38765d4afa7de1126540c31150a3ba94f862 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Thu, 8 Dec 2011 22:58:14 -0500
Subject: [PATCH 01/13] Add thresholding module with Otsu's method to calculate
 threshold.

---
 skimage/thresholding/__init__.py              |   1 +
 .../thresholding/tests/test_thresholding.py   |  53 +++++++++
 skimage/thresholding/thresholding.py          | 105 ++++++++++++++++++
 3 files changed, 159 insertions(+)
 create mode 100644 skimage/thresholding/__init__.py
 create mode 100644 skimage/thresholding/tests/test_thresholding.py
 create mode 100644 skimage/thresholding/thresholding.py

diff --git a/skimage/thresholding/__init__.py b/skimage/thresholding/__init__.py
new file mode 100644
index 00000000..d588eda0
--- /dev/null
+++ b/skimage/thresholding/__init__.py
@@ -0,0 +1 @@
+from .thresholding import otsu_threshold, binarize
diff --git a/skimage/thresholding/tests/test_thresholding.py b/skimage/thresholding/tests/test_thresholding.py
new file mode 100644
index 00000000..713defe4
--- /dev/null
+++ b/skimage/thresholding/tests/test_thresholding.py
@@ -0,0 +1,53 @@
+import numpy as np
+
+import skimage
+from skimage import data
+from skimage.thresholding import otsu_threshold, binarize
+
+
+class TestSimpleImage():
+    def setup(self):
+        self.image = np.array([[0, 0, 1, 3, 5],
+                               [0, 1, 4, 3, 4],
+                               [1, 2, 5, 4, 1],
+                               [2, 4, 5, 2, 1],
+                               [4, 5, 1, 0, 0]], dtype=int)
+
+    def test_otsu(self):
+        assert otsu_threshold(self.image) == 2
+
+    @np.testing.raises(NotImplementedError)
+    def test_otsu_raises_error(self):
+        image = self.image - 2
+        otsu_threshold(image)
+
+    def test_otsu_float_image(self):
+        image = np.float64(self.image)
+        assert 2 <= otsu_threshold(image) < 3
+
+    def test_binarize(self):
+        expected = np.array([[0, 0, 0, 1, 1],
+                             [0, 0, 1, 1, 1],
+                             [0, 0, 1, 1, 0],
+                             [0, 1, 1, 0, 0],
+                             [1, 1, 0, 0, 0]])
+        assert np.all(binarize(self.image) == expected)
+
+
+def test_otsu_camera_image():
+    assert otsu_threshold(data.camera()) == 87
+
+def test_otsu_coins_image():
+    assert otsu_threshold(data.coins()) == 107
+
+def test_otsu_coins_image_as_float():
+    coins = skimage.img_as_float(data.coins())
+    assert 0.41 < otsu_threshold(coins) < 0.42
+
+def test_otsu_lena_image():
+    assert otsu_threshold(data.lena()) == 141
+
+
+if __name__ == '__main__':
+    np.testing.run_module_suite()
+
diff --git a/skimage/thresholding/thresholding.py b/skimage/thresholding/thresholding.py
new file mode 100644
index 00000000..b5699f7e
--- /dev/null
+++ b/skimage/thresholding/thresholding.py
@@ -0,0 +1,105 @@
+import numpy as np
+
+
+__all__ = ['otsu_threshold', 'binarize']
+
+
+def otsu_threshold(image, bins=256):
+    """Return threshold value based on Otsu's method.
+
+    Parameters
+    ----------
+    image : array
+        Input image.
+    bins : int
+        Number of bins used to calculate histogram. This value is ignored for
+        integer arrays.
+
+    Returns
+    -------
+    threshold : numeric
+        Threshold value. int or float depending on input image.
+
+    References
+    ----------
+    .. [1] Wikipedia, http://en.wikipedia.org/wiki/Otsu's_Method
+
+    """
+    hist, bin_centers = histogram(image, bins)
+    hist = hist.astype(float)
+
+    # class probabilities for all possible thresholds
+    weight1 = np.cumsum(hist)
+    weight2 = np.cumsum(hist[::-1])[::-1]
+    # class means for all possible thresholds
+    mean1 = np.cumsum(hist * bin_centers) / weight1
+    mean2 = (np.cumsum((hist * bin_centers)[::-1]) / weight2[::-1])[::-1]
+
+    # Clip ends to align class 1 and class 2 variables:
+    # The last value of `weight1`/`mean1` should pair with zero values in
+    # `weight2`/`mean2`, which do not exist.
+    variance12 = weight1[:-1] * weight2[1:] * (mean1[:-1] - mean2[1:])**2
+
+    idx = np.argmax(variance12)
+    threshold = bin_centers[:-1][idx]
+    return threshold
+
+
+_threshold_funcs = {'otsu': otsu_threshold}
+def binarize(image, method='otsu'):
+    """Return binary image using an automatic thresholding method.
+
+    Parameters
+    ----------
+    image : array
+        Input array.
+    method : {'otsu'}
+        Method used to calculate threshold value. Currently, only Otsu's method
+        is implemented.
+
+    Returns
+    -------
+    out : array
+        Thresholded image.
+    """
+    get_threshold = _threshold_funcs[method]
+    threshold = get_threshold(image)
+    return image > threshold
+
+
+def histogram(image, bins):
+    """Return histogram of image.
+
+    Unlike `numpy.histogram`, this function returns the centers of bins and
+    does not rebin integer arrays.
+
+    Parameters
+    ----------
+    image : array
+        Input image.
+    bins : int
+        Number of bins used to calculate histogram. This value is ignored for
+        integer arrays.
+
+    Returns
+    -------
+    hist : array
+        The values of the histogram.
+    bin_centers : array
+        The values at the center of the bins.
+    """
+    if np.issubdtype(image.dtype, np.integer):
+        if np.min(image) < 0:
+            msg = "Images with negative values not allowed"
+            raise NotImplementedError(msg)
+        hist = np.bincount(image.flat)
+        bin_centers = np.arange(len(hist))
+
+        # clip histogram to return only non-zero bins
+        idx = np.nonzero(hist)[0][0]
+        return hist[idx:], bin_centers[idx:]
+    else:
+        hist, bin_edges = np.histogram(image, bins=bins)
+        bin_centers = (bin_edges[:-1] + bin_edges[1:]) / 2.
+        return hist, bin_centers
+

From f3e5a30125c3f1269407be19bc0d9a1430bac1b0 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Thu, 8 Dec 2011 23:24:48 -0500
Subject: [PATCH 02/13] Rename otsu_threshold to threshold_otsu

---
 skimage/thresholding/__init__.py                |  2 +-
 skimage/thresholding/tests/test_thresholding.py | 16 ++++++++--------
 skimage/thresholding/thresholding.py            |  6 +++---
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/skimage/thresholding/__init__.py b/skimage/thresholding/__init__.py
index d588eda0..d5d6eddf 100644
--- a/skimage/thresholding/__init__.py
+++ b/skimage/thresholding/__init__.py
@@ -1 +1 @@
-from .thresholding import otsu_threshold, binarize
+from .thresholding import threshold_otsu, binarize
diff --git a/skimage/thresholding/tests/test_thresholding.py b/skimage/thresholding/tests/test_thresholding.py
index 713defe4..485ffbca 100644
--- a/skimage/thresholding/tests/test_thresholding.py
+++ b/skimage/thresholding/tests/test_thresholding.py
@@ -2,7 +2,7 @@ import numpy as np
 
 import skimage
 from skimage import data
-from skimage.thresholding import otsu_threshold, binarize
+from skimage.thresholding import threshold_otsu, binarize
 
 
 class TestSimpleImage():
@@ -14,16 +14,16 @@ class TestSimpleImage():
                                [4, 5, 1, 0, 0]], dtype=int)
 
     def test_otsu(self):
-        assert otsu_threshold(self.image) == 2
+        assert threshold_otsu(self.image) == 2
 
     @np.testing.raises(NotImplementedError)
     def test_otsu_raises_error(self):
         image = self.image - 2
-        otsu_threshold(image)
+        threshold_otsu(image)
 
     def test_otsu_float_image(self):
         image = np.float64(self.image)
-        assert 2 <= otsu_threshold(image) < 3
+        assert 2 <= threshold_otsu(image) < 3
 
     def test_binarize(self):
         expected = np.array([[0, 0, 0, 1, 1],
@@ -35,17 +35,17 @@ class TestSimpleImage():
 
 
 def test_otsu_camera_image():
-    assert otsu_threshold(data.camera()) == 87
+    assert threshold_otsu(data.camera()) == 87
 
 def test_otsu_coins_image():
-    assert otsu_threshold(data.coins()) == 107
+    assert threshold_otsu(data.coins()) == 107
 
 def test_otsu_coins_image_as_float():
     coins = skimage.img_as_float(data.coins())
-    assert 0.41 < otsu_threshold(coins) < 0.42
+    assert 0.41 < threshold_otsu(coins) < 0.42
 
 def test_otsu_lena_image():
-    assert otsu_threshold(data.lena()) == 141
+    assert threshold_otsu(data.lena()) == 141
 
 
 if __name__ == '__main__':
diff --git a/skimage/thresholding/thresholding.py b/skimage/thresholding/thresholding.py
index b5699f7e..62af6d8d 100644
--- a/skimage/thresholding/thresholding.py
+++ b/skimage/thresholding/thresholding.py
@@ -1,10 +1,10 @@
 import numpy as np
 
 
-__all__ = ['otsu_threshold', 'binarize']
+__all__ = ['threshold_otsu', 'binarize']
 
 
-def otsu_threshold(image, bins=256):
+def threshold_otsu(image, bins=256):
     """Return threshold value based on Otsu's method.
 
     Parameters
@@ -45,7 +45,7 @@ def otsu_threshold(image, bins=256):
     return threshold
 
 
-_threshold_funcs = {'otsu': otsu_threshold}
+_threshold_funcs = {'otsu': threshold_otsu}
 def binarize(image, method='otsu'):
     """Return binary image using an automatic thresholding method.
 

From 9a89fab612cadc46b73a09391d22d401c0e93ac3 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Thu, 8 Dec 2011 23:34:08 -0500
Subject: [PATCH 03/13] Add handling for images with negative integers

---
 skimage/thresholding/tests/test_thresholding.py | 5 ++---
 skimage/thresholding/thresholding.py            | 8 ++++----
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/skimage/thresholding/tests/test_thresholding.py b/skimage/thresholding/tests/test_thresholding.py
index 485ffbca..6fc3f020 100644
--- a/skimage/thresholding/tests/test_thresholding.py
+++ b/skimage/thresholding/tests/test_thresholding.py
@@ -16,10 +16,9 @@ class TestSimpleImage():
     def test_otsu(self):
         assert threshold_otsu(self.image) == 2
 
-    @np.testing.raises(NotImplementedError)
-    def test_otsu_raises_error(self):
+    def test_otsu_negative_int(self):
         image = self.image - 2
-        threshold_otsu(image)
+        assert threshold_otsu(image) == 0
 
     def test_otsu_float_image(self):
         image = np.float64(self.image)
diff --git a/skimage/thresholding/thresholding.py b/skimage/thresholding/thresholding.py
index 62af6d8d..e346efba 100644
--- a/skimage/thresholding/thresholding.py
+++ b/skimage/thresholding/thresholding.py
@@ -89,11 +89,11 @@ def histogram(image, bins):
         The values at the center of the bins.
     """
     if np.issubdtype(image.dtype, np.integer):
+        offset = 0
         if np.min(image) < 0:
-            msg = "Images with negative values not allowed"
-            raise NotImplementedError(msg)
-        hist = np.bincount(image.flat)
-        bin_centers = np.arange(len(hist))
+            offset = np.min(image)
+        hist = np.bincount(image.ravel() - offset)
+        bin_centers = np.arange(len(hist)) + offset
 
         # clip histogram to return only non-zero bins
         idx = np.nonzero(hist)[0][0]

From 10c1f471a0184151e64adb2378713757e324e949 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Thu, 8 Dec 2011 23:38:51 -0500
Subject: [PATCH 04/13] Change docstring threshold_otsu output

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

diff --git a/skimage/thresholding/thresholding.py b/skimage/thresholding/thresholding.py
index e346efba..131d33e7 100644
--- a/skimage/thresholding/thresholding.py
+++ b/skimage/thresholding/thresholding.py
@@ -17,8 +17,8 @@ def threshold_otsu(image, bins=256):
 
     Returns
     -------
-    threshold : numeric
-        Threshold value. int or float depending on input image.
+    threshold : float
+        Threshold value.
 
     References
     ----------

From 5a171a2bfb413d6c70a02f83a905d05c5e231797 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Thu, 8 Dec 2011 23:52:10 -0500
Subject: [PATCH 05/13] Remove binarize function

---
 skimage/thresholding/__init__.py              |  3 ++-
 .../thresholding/tests/test_thresholding.py   | 10 +-------
 skimage/thresholding/thresholding.py          | 24 +------------------
 3 files changed, 4 insertions(+), 33 deletions(-)

diff --git a/skimage/thresholding/__init__.py b/skimage/thresholding/__init__.py
index d5d6eddf..9b6e229c 100644
--- a/skimage/thresholding/__init__.py
+++ b/skimage/thresholding/__init__.py
@@ -1 +1,2 @@
-from .thresholding import threshold_otsu, binarize
+from .thresholding import threshold_otsu
+
diff --git a/skimage/thresholding/tests/test_thresholding.py b/skimage/thresholding/tests/test_thresholding.py
index 6fc3f020..2ec64da6 100644
--- a/skimage/thresholding/tests/test_thresholding.py
+++ b/skimage/thresholding/tests/test_thresholding.py
@@ -2,7 +2,7 @@ import numpy as np
 
 import skimage
 from skimage import data
-from skimage.thresholding import threshold_otsu, binarize
+from skimage.thresholding import threshold_otsu
 
 
 class TestSimpleImage():
@@ -24,14 +24,6 @@ class TestSimpleImage():
         image = np.float64(self.image)
         assert 2 <= threshold_otsu(image) < 3
 
-    def test_binarize(self):
-        expected = np.array([[0, 0, 0, 1, 1],
-                             [0, 0, 1, 1, 1],
-                             [0, 0, 1, 1, 0],
-                             [0, 1, 1, 0, 0],
-                             [1, 1, 0, 0, 0]])
-        assert np.all(binarize(self.image) == expected)
-
 
 def test_otsu_camera_image():
     assert threshold_otsu(data.camera()) == 87
diff --git a/skimage/thresholding/thresholding.py b/skimage/thresholding/thresholding.py
index 131d33e7..b274010f 100644
--- a/skimage/thresholding/thresholding.py
+++ b/skimage/thresholding/thresholding.py
@@ -1,7 +1,7 @@
 import numpy as np
 
 
-__all__ = ['threshold_otsu', 'binarize']
+__all__ = ['threshold_otsu']
 
 
 def threshold_otsu(image, bins=256):
@@ -45,28 +45,6 @@ def threshold_otsu(image, bins=256):
     return threshold
 
 
-_threshold_funcs = {'otsu': threshold_otsu}
-def binarize(image, method='otsu'):
-    """Return binary image using an automatic thresholding method.
-
-    Parameters
-    ----------
-    image : array
-        Input array.
-    method : {'otsu'}
-        Method used to calculate threshold value. Currently, only Otsu's method
-        is implemented.
-
-    Returns
-    -------
-    out : array
-        Thresholded image.
-    """
-    get_threshold = _threshold_funcs[method]
-    threshold = get_threshold(image)
-    return image > threshold
-
-
 def histogram(image, bins):
     """Return histogram of image.
 

From 6872e9cdf3ab5030cc3ccbbac6d614c0656252ac Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Fri, 9 Dec 2011 00:13:49 -0500
Subject: [PATCH 06/13] Add thresholding example

---
 doc/examples/plot_otsu.py | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 doc/examples/plot_otsu.py

diff --git a/doc/examples/plot_otsu.py b/doc/examples/plot_otsu.py
new file mode 100644
index 00000000..03534bc9
--- /dev/null
+++ b/doc/examples/plot_otsu.py
@@ -0,0 +1,23 @@
+"""
+============
+Thresholding
+============
+
+Thresholding is used to create a binary image. This example uses Otsu's method to calculate the threshold value.
+
+"""
+
+import matplotlib.pyplot as plt
+
+from skimage.data import camera
+from skimage.thresholding import threshold_otsu
+
+
+image = camera()
+thresh = threshold_otsu(camera())
+binary = image > thresh
+
+plt.imshow(binary)
+plt.axis('off')
+plt.show()
+

From 6a6e273d0679e35237db877056b4e85e8ca41e56 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Fri, 9 Dec 2011 10:16:23 -0500
Subject: [PATCH 07/13] Remove thresholding example from user guide in favor of
 docstring example.

---
 doc/examples/plot_otsu.py            | 23 -----------------------
 skimage/thresholding/thresholding.py |  6 ++++++
 2 files changed, 6 insertions(+), 23 deletions(-)
 delete mode 100644 doc/examples/plot_otsu.py

diff --git a/doc/examples/plot_otsu.py b/doc/examples/plot_otsu.py
deleted file mode 100644
index 03534bc9..00000000
--- a/doc/examples/plot_otsu.py
+++ /dev/null
@@ -1,23 +0,0 @@
-"""
-============
-Thresholding
-============
-
-Thresholding is used to create a binary image. This example uses Otsu's method to calculate the threshold value.
-
-"""
-
-import matplotlib.pyplot as plt
-
-from skimage.data import camera
-from skimage.thresholding import threshold_otsu
-
-
-image = camera()
-thresh = threshold_otsu(camera())
-binary = image > thresh
-
-plt.imshow(binary)
-plt.axis('off')
-plt.show()
-
diff --git a/skimage/thresholding/thresholding.py b/skimage/thresholding/thresholding.py
index b274010f..861d2647 100644
--- a/skimage/thresholding/thresholding.py
+++ b/skimage/thresholding/thresholding.py
@@ -24,6 +24,12 @@ def threshold_otsu(image, bins=256):
     ----------
     .. [1] Wikipedia, http://en.wikipedia.org/wiki/Otsu's_Method
 
+    Examples
+    --------
+    >>> from skimage.data import camera
+    >>> image = camera()
+    >>> thresh = threshold_otsu(camera())
+    >>> binary = image > thresh
     """
     hist, bin_centers = histogram(image, bins)
     hist = hist.astype(float)

From e7d37997d92b911dd2662112474e8574246e513a Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 10 Dec 2011 19:33:29 -0500
Subject: [PATCH 08/13] Fix minor typo in docstring example

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

diff --git a/skimage/thresholding/thresholding.py b/skimage/thresholding/thresholding.py
index 861d2647..980dfeba 100644
--- a/skimage/thresholding/thresholding.py
+++ b/skimage/thresholding/thresholding.py
@@ -28,7 +28,7 @@ def threshold_otsu(image, bins=256):
     --------
     >>> from skimage.data import camera
     >>> image = camera()
-    >>> thresh = threshold_otsu(camera())
+    >>> thresh = threshold_otsu(image)
     >>> binary = image > thresh
     """
     hist, bin_centers = histogram(image, bins)

From d9186c90a1bcc9adf90de8567cb473e4382bc838 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sun, 11 Dec 2011 17:04:46 -0500
Subject: [PATCH 09/13] Remove thresholding subpackage and integrate into
 filter subpackage.

---
 skimage/filter/__init__.py                                  | 1 +
 skimage/{thresholding => filter}/tests/test_thresholding.py | 2 +-
 skimage/{thresholding => filter}/thresholding.py            | 0
 skimage/thresholding/__init__.py                            | 2 --
 4 files changed, 2 insertions(+), 3 deletions(-)
 rename skimage/{thresholding => filter}/tests/test_thresholding.py (95%)
 rename skimage/{thresholding => filter}/thresholding.py (100%)
 delete mode 100644 skimage/thresholding/__init__.py

diff --git a/skimage/filter/__init__.py b/skimage/filter/__init__.py
index d3baf934..1acc33f2 100644
--- a/skimage/filter/__init__.py
+++ b/skimage/filter/__init__.py
@@ -4,3 +4,4 @@ from canny import canny
 from edges import sobel, hsobel, vsobel, hprewitt, vprewitt, prewitt
 from tv_denoise import tv_denoise
 from rank_order import rank_order
+from thresholding import threshold_otsu
diff --git a/skimage/thresholding/tests/test_thresholding.py b/skimage/filter/tests/test_thresholding.py
similarity index 95%
rename from skimage/thresholding/tests/test_thresholding.py
rename to skimage/filter/tests/test_thresholding.py
index 2ec64da6..b0044a47 100644
--- a/skimage/thresholding/tests/test_thresholding.py
+++ b/skimage/filter/tests/test_thresholding.py
@@ -2,7 +2,7 @@ import numpy as np
 
 import skimage
 from skimage import data
-from skimage.thresholding import threshold_otsu
+from skimage.filter.thresholding import threshold_otsu
 
 
 class TestSimpleImage():
diff --git a/skimage/thresholding/thresholding.py b/skimage/filter/thresholding.py
similarity index 100%
rename from skimage/thresholding/thresholding.py
rename to skimage/filter/thresholding.py
diff --git a/skimage/thresholding/__init__.py b/skimage/thresholding/__init__.py
deleted file mode 100644
index 9b6e229c..00000000
--- a/skimage/thresholding/__init__.py
+++ /dev/null
@@ -1,2 +0,0 @@
-from .thresholding import threshold_otsu
-

From 756dfd5020eb03447233e7d2dc3b70c4d05b0535 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Mon, 12 Dec 2011 13:51:27 -0500
Subject: [PATCH 10/13] Rename `bins` parameter to `nbins`.

This change distinguishes it from the `bins` argument in numpy.histogram, which can accept both the number of bins or a sequence bin edges. Also, this name matches other function parameters in the scikit (e.g. `histograms` in io/_plugins/util.py).
---
 skimage/filter/thresholding.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/skimage/filter/thresholding.py b/skimage/filter/thresholding.py
index 980dfeba..800e18b8 100644
--- a/skimage/filter/thresholding.py
+++ b/skimage/filter/thresholding.py
@@ -4,14 +4,14 @@ import numpy as np
 __all__ = ['threshold_otsu']
 
 
-def threshold_otsu(image, bins=256):
+def threshold_otsu(image, nbins=256):
     """Return threshold value based on Otsu's method.
 
     Parameters
     ----------
     image : array
         Input image.
-    bins : int
+    nbins : int
         Number of bins used to calculate histogram. This value is ignored for
         integer arrays.
 
@@ -31,7 +31,7 @@ def threshold_otsu(image, bins=256):
     >>> thresh = threshold_otsu(image)
     >>> binary = image > thresh
     """
-    hist, bin_centers = histogram(image, bins)
+    hist, bin_centers = histogram(image, nbins)
     hist = hist.astype(float)
 
     # class probabilities for all possible thresholds
@@ -51,7 +51,7 @@ def threshold_otsu(image, bins=256):
     return threshold
 
 
-def histogram(image, bins):
+def histogram(image, nbins):
     """Return histogram of image.
 
     Unlike `numpy.histogram`, this function returns the centers of bins and
@@ -61,7 +61,7 @@ def histogram(image, bins):
     ----------
     image : array
         Input image.
-    bins : int
+    nbins : int
         Number of bins used to calculate histogram. This value is ignored for
         integer arrays.
 
@@ -83,7 +83,7 @@ def histogram(image, bins):
         idx = np.nonzero(hist)[0][0]
         return hist[idx:], bin_centers[idx:]
     else:
-        hist, bin_edges = np.histogram(image, bins=bins)
+        hist, bin_edges = np.histogram(image, bins=nbins)
         bin_centers = (bin_edges[:-1] + bin_edges[1:]) / 2.
         return hist, bin_centers
 

From 8ed834a3ab6651e35ecca487f69d0dc85ee18435 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 17 Dec 2011 22:02:10 -0500
Subject: [PATCH 11/13] Add example for threshoding

This example was removed in a previous commit.
---
 doc/examples/plot_otsu.py | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 doc/examples/plot_otsu.py

diff --git a/doc/examples/plot_otsu.py b/doc/examples/plot_otsu.py
new file mode 100644
index 00000000..3557bc2c
--- /dev/null
+++ b/doc/examples/plot_otsu.py
@@ -0,0 +1,23 @@
+"""
+============
+Thresholding
+============
+
+Thresholding is used to create a binary image. This example uses Otsu's method to calculate the threshold value.
+
+"""
+
+import matplotlib.pyplot as plt
+
+from skimage.data import camera
+from skimage.filter import threshold_otsu
+
+
+image = camera()
+thresh = threshold_otsu(image)
+binary = image > thresh
+
+plt.imshow(binary)
+plt.axis('off')
+plt.show()
+

From 1e12ca0044d640e62f06f786d668be2b8b846ff9 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sun, 18 Dec 2011 09:31:10 -0500
Subject: [PATCH 12/13] Improve thresholding example

---
 doc/examples/plot_otsu.py | 25 +++++++++++++++++++++++--
 1 file changed, 23 insertions(+), 2 deletions(-)

diff --git a/doc/examples/plot_otsu.py b/doc/examples/plot_otsu.py
index 3557bc2c..62bd6836 100644
--- a/doc/examples/plot_otsu.py
+++ b/doc/examples/plot_otsu.py
@@ -3,7 +3,14 @@
 Thresholding
 ============
 
-Thresholding is used to create a binary image. This example uses Otsu's method to calculate the threshold value.
+Thresholding is used to create a binary image. This example uses Otsu's method
+to calculate the threshold value.
+
+Otsu's method calculates an "optimal" threshold by maximizing the variance
+between the two classes of pixels, which are separated by the threshold.
+Equivalently, the optimal threshold minimizes the intra-class variance.
+
+.. [1] http://en.wikipedia.org/wiki/Otsu's_method
 
 """
 
@@ -17,7 +24,21 @@ image = camera()
 thresh = threshold_otsu(image)
 binary = image > thresh
 
-plt.imshow(binary)
+plt.figure(figsize=(10, 3.5))
+plt.subplot(1, 3, 1)
+plt.imshow(image)
+plt.title('original')
 plt.axis('off')
+
+plt.subplot(1, 3, 2)
+plt.hist(image)
+plt.title('histogram')
+plt.axvline(thresh, color='r')
+
+plt.subplot(1, 3, 3)
+plt.imshow(binary)
+plt.title('thresholded')
+plt.axis('off')
+
 plt.show()
 

From 8941798daf23df1fe3ad6dd6cd652619ae3724d8 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sun, 18 Dec 2011 10:10:00 -0500
Subject: [PATCH 13/13] DOC: emphasize annotation in histogram.

---
 doc/examples/plot_otsu.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/doc/examples/plot_otsu.py b/doc/examples/plot_otsu.py
index 62bd6836..060f54c6 100644
--- a/doc/examples/plot_otsu.py
+++ b/doc/examples/plot_otsu.py
@@ -6,9 +6,10 @@ Thresholding
 Thresholding is used to create a binary image. This example uses Otsu's method
 to calculate the threshold value.
 
-Otsu's method calculates an "optimal" threshold by maximizing the variance
-between the two classes of pixels, which are separated by the threshold.
-Equivalently, the optimal threshold minimizes the intra-class variance.
+Otsu's method calculates an "optimal" threshold (marked by a red line in the
+histogram below) by maximizing the variance between two classes of pixels,
+which are separated by the threshold. Equivalently, this threshold minimizes
+the intra-class variance.
 
 .. [1] http://en.wikipedia.org/wiki/Otsu's_method