From 69f5e9d5fe9d6f07d44f7d1e63c5bac7e7f2939b Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Thu, 10 Apr 2014 12:11:45 +1000
Subject: [PATCH 01/16] Update viewer example to use plugin outputs

---
 doc/source/user_guide/viewer.txt | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/doc/source/user_guide/viewer.txt b/doc/source/user_guide/viewer.txt
index da7f0c50..4cdde7db 100644
--- a/doc/source/user_guide/viewer.txt
+++ b/doc/source/user_guide/viewer.txt
@@ -32,7 +32,14 @@ let's see an example of how a pre-defined plugin is added to the viewer:
 
    viewer = ImageViewer(image)
    viewer += LineProfile(viewer)
-   viewer.show()
+   overlay, data = viewer.show()[0]
+
+The viewer's ``show`` method will return an overlay (of the same shape as the
+input image) and data (possibly ``None``) for each attached plugin. In this
+case, there is only one plugin, so we can directly name both. You can see the
+plugin class's ``output`` method to see what will be returned. Here,
+``overlay`` contains a drawing of the line (including its width), and ``data``
+contains the measured line profile.
 
 At the moment, there are not many plugins pre-defined, but there is a really
 simple interface for creating your own plugin. First, let us create a plugin to
@@ -74,8 +81,10 @@ All that's left is to create an image viewer and add the plugin to that viewer.
 
    viewer = ImageViewer(image)
    viewer += denoise_plugin
-   viewer.show()
+   denoised = viewer.show()[0][0]
 
+When we close the viewer, ``denoised`` will contain the filtered image for the
+last used setting of ``weight``.
 
 .. image:: data/denoise_viewer_window.png
 .. image:: data/denoise_plugin_window.png

From 9ef9045875d09d1ed324ceb398f9133ea0ddb2aa Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Thu, 10 Apr 2014 12:16:14 +1000
Subject: [PATCH 02/16] Update lineprofile examples to use returned output

---
 viewer_examples/plugins/lineprofile.py     | 2 +-
 viewer_examples/plugins/lineprofile_rgb.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/viewer_examples/plugins/lineprofile.py b/viewer_examples/plugins/lineprofile.py
index 2f1b2cdc..dd80e277 100644
--- a/viewer_examples/plugins/lineprofile.py
+++ b/viewer_examples/plugins/lineprofile.py
@@ -6,4 +6,4 @@ from skimage.viewer.plugins.lineprofile import LineProfile
 image = data.camera()
 viewer = ImageViewer(image)
 viewer += LineProfile()
-viewer.show()
+line, profile = viewer.show()[0]
diff --git a/viewer_examples/plugins/lineprofile_rgb.py b/viewer_examples/plugins/lineprofile_rgb.py
index 86b71d5d..b08f5a00 100644
--- a/viewer_examples/plugins/lineprofile_rgb.py
+++ b/viewer_examples/plugins/lineprofile_rgb.py
@@ -6,4 +6,4 @@ from skimage.viewer.plugins.lineprofile import LineProfile
 image = data.chelsea()
 viewer = ImageViewer(image)
 viewer += LineProfile()
-viewer.show()
+line, profiles = viewer.show()[0]

From 17541e2cdc43d8ea26e870b72281c8ef3719423c Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Thu, 10 Apr 2014 12:19:23 +1000
Subject: [PATCH 03/16] Update plugin class doc example to use output

---
 skimage/viewer/plugins/base.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/skimage/viewer/plugins/base.py b/skimage/viewer/plugins/base.py
index dd3aebb0..baded1cb 100644
--- a/skimage/viewer/plugins/base.py
+++ b/skimage/viewer/plugins/base.py
@@ -63,9 +63,9 @@ class Plugin(QtGui.QDialog):
     >>> plugin += Slider('threshold', 0, 255)       # doctest: +SKIP
     >>>
     >>> image = data.coins()
-    >>> viewer = ImageViewer(image) # doctest: +SKIP
-    >>> viewer += plugin            # doctest: +SKIP
-    >>> viewer.show()               # doctest: +SKIP
+    >>> viewer = ImageViewer(image)       # doctest: +SKIP
+    >>> viewer += plugin                  # doctest: +SKIP
+    >>> thresholded = viewer.show()[0][0] # doctest: +SKIP
 
     The plugin will automatically delegate parameters to `image_filter` based
     on its parameter type, i.e., `ptype` (widgets for required arguments must

From f2699bd731760b9d938680a7c4ed5fc5874ce228 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Mon, 21 Apr 2014 00:11:55 +0200
Subject: [PATCH 04/16] Update Canny examples

---
 viewer_examples/plugins/canny.py        | 2 +-
 viewer_examples/plugins/canny_simple.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/viewer_examples/plugins/canny.py b/viewer_examples/plugins/canny.py
index eaa33330..686034b2 100644
--- a/viewer_examples/plugins/canny.py
+++ b/viewer_examples/plugins/canny.py
@@ -6,4 +6,4 @@ from skimage.viewer.plugins.canny import CannyPlugin
 image = data.camera()
 viewer = ImageViewer(image)
 viewer += CannyPlugin()
-viewer.show()
+canny_edges = viewer.show()[0][0]
diff --git a/viewer_examples/plugins/canny_simple.py b/viewer_examples/plugins/canny_simple.py
index c26ca08d..641ca138 100644
--- a/viewer_examples/plugins/canny_simple.py
+++ b/viewer_examples/plugins/canny_simple.py
@@ -21,4 +21,4 @@ plugin += SaveButtons(name='Save overlay to:')
 # Finally, attach the plugin to an image viewer.
 viewer = ImageViewer(image)
 viewer += plugin
-viewer.show()
+canny_edges = viewer.show()[0][0]

From 00b4fa45e70b16454864c57f5b3b5b32dab3fa91 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Fri, 2 May 2014 16:01:35 +0200
Subject: [PATCH 05/16] Always interpret provided shapes as int. Add a note on
 using output_shape for color images.

---
 skimage/transform/_geometric.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index 883aa88d..3c14f709 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -1003,7 +1003,8 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
         Keyword arguments passed to `inverse_map`.
     output_shape : tuple (rows, cols), optional
         Shape of the output image generated. By default the shape of the input
-        image is preserved.
+        image is preserved.  Note that, even for multi-band images, only rows
+        and columns need to be specified.
     order : int, optional
         The order of interpolation. The order has to be in the range 0-5:
         * 0: Nearest-neighbor
@@ -1073,6 +1074,7 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
     image = np.atleast_3d(img_as_float(image))
     ishape = np.array(image.shape)
     bands = ishape[2]
+    output_shape = np.array(output_shape, dtype=int)
 
     out = None
 
@@ -1102,8 +1104,8 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
             dims = []
             for dim in range(image.shape[2]):
                 dims.append(_warp_fast(image[..., dim], matrix,
-                            output_shape=output_shape,
-                            order=order, mode=mode, cval=cval))
+                                       output_shape=output_shape,
+                                       order=order, mode=mode, cval=cval))
             out = np.dstack(dims)
             if orig_ndim == 2:
                 out = out[..., 0]

From 4c7cd9bd654c1a088c72391048ced98f5c97bdc7 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Fri, 2 May 2014 16:23:41 +0200
Subject: [PATCH 06/16] Add unit test to catch non-integer output shape bug

---
 skimage/transform/_geometric.py       | 11 ++++++-----
 skimage/transform/tests/test_warps.py |  5 +++++
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index 3c14f709..53074c00 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -1074,7 +1074,12 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
     image = np.atleast_3d(img_as_float(image))
     ishape = np.array(image.shape)
     bands = ishape[2]
-    output_shape = np.array(output_shape, dtype=int)
+
+    if output_shape is None:
+        output_shape = ishape
+    else:
+        output_shape = np.array(output_shape, dtype=int)
+
 
     out = None
 
@@ -1111,10 +1116,6 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
                 out = out[..., 0]
 
     if out is None:  # use ndimage.map_coordinates
-
-        if output_shape is None:
-            output_shape = ishape
-
         rows, cols = output_shape[:2]
 
         # inverse_map is a transformation matrix as numpy array
diff --git a/skimage/transform/tests/test_warps.py b/skimage/transform/tests/test_warps.py
index e49ab098..f85125d0 100644
--- a/skimage/transform/tests/test_warps.py
+++ b/skimage/transform/tests/test_warps.py
@@ -248,5 +248,10 @@ def test_inverse():
     assert_array_equal(warp(image, inverse_tform), warp(image, tform.inverse))
 
 
+def test_slow_warp_nonint_oshape():
+    image = np.random.random((5, 5))
+    warp(image, lambda xy: xy, output_shape=(13.1, 19.5))
+
+
 if __name__ == "__main__":
     run_module_suite()

From e9c793eb177661b34d39f0acaa834d7349b3d88c Mon Sep 17 00:00:00 2001
From: "Josh Warner (Mac)" <warner.joshua@mayo.edu>
Date: Tue, 6 May 2014 13:09:03 -0500
Subject: [PATCH 07/16] FEAT: Shared function for safe int casting

---
 skimage/_shared/safe_int_cast.py            | 61 +++++++++++++++++++++
 skimage/_shared/tests/test_safe_int_cast.py | 36 ++++++++++++
 2 files changed, 97 insertions(+)
 create mode 100644 skimage/_shared/safe_int_cast.py
 create mode 100644 skimage/_shared/tests/test_safe_int_cast.py

diff --git a/skimage/_shared/safe_int_cast.py b/skimage/_shared/safe_int_cast.py
new file mode 100644
index 00000000..0733cf61
--- /dev/null
+++ b/skimage/_shared/safe_int_cast.py
@@ -0,0 +1,61 @@
+import numpy as np
+
+__all__ == ['_safe_int']
+
+
+def _safe_int_cast(val, atol=1e-7):
+    """
+    Attempt to safely cast values to integer format.
+
+    Parameters
+    ----------
+    val : scalar or iterable of scalars
+        Number or container of numbers which are intended to be interpreted as
+        integers, e.g., for indexing purposes, but which may not carry integer
+        type.
+    atol : float
+        Absolute tolerance away from nearest integer to consider values in
+        ``val`` functionally integers.
+
+    Returns
+    -------
+    val_int : NumPy scalar or ndarray of dtype `np.int32`
+        Returns the input value(s) coerced to dtype `np.int32` assuming all
+        were within ``atol`` of the nearest integer.
+
+    Notes
+    -----
+    This operation calculates ``val`` modulo 1, which returns the mantissa of
+    all values. Then all mantissas greater than 0.5 are subtracted from one.
+    Finally, the absolute tolerance from zero is calculated. If it is less
+    than ``atol`` for all value(s) in ``val``, they are rounded and returned
+    in an integer array. Or, if ``val`` was a scalar, a NumPy scalar type is
+    returned.
+
+    If any value(s) are outside the specified tolerance, an informative error
+    is raised.
+
+    Examples
+    --------
+    >>> _safe_int_cast(7.0)
+    7
+    >>> _safe_int_cast([9, 4, 2.9999999999])
+    array([9, 4, 3], dtype=int32)
+
+    """
+    mod = np.asarray(val) % 1                # Modulo 1
+
+    # Check for and subtract any mod values > 0.5 from 1
+    if mod.ndim == 0:                        # Scalar input, cannot be indexed
+        if mod > 0.5:
+            mod = 1 - mod
+    else:                                    # Iterable input, now ndarray
+        mod[mod > 0.5] = 1 - mod[mod > 0.5]  # Test on each side of nearest int
+
+    try:
+        np.testing.assert_allclose(mod, 0, atol=atol)
+    except AssertionError:
+        raise ValueError("Integer argument required but received "
+                         "{0}, check inputs.".format(val))
+
+    return np.round(val).astype(np.int32)
diff --git a/skimage/_shared/tests/test_safe_int_cast.py b/skimage/_shared/tests/test_safe_int_cast.py
new file mode 100644
index 00000000..27f88323
--- /dev/null
+++ b/skimage/_shared/tests/test_safe_int_cast.py
@@ -0,0 +1,36 @@
+import numpy as np
+from skimage._shared.safe_int_cast import _safe_int_cast
+
+
+def test_int_cast_not_possible():
+    np.testing.assert_raises(ValueError, _safe_int_cast, 7.1)
+    np.testing.assert_raises(ValueError, _safe_int_cast, [7.1, 0.9])
+    np.testing.assert_raises(ValueError, _safe_int_cast, np.r_[7.1, 0.9])
+    np.testing.assert_raises(ValueError, _safe_int_cast, (7.1, 0.9))
+    np.testing.assert_raises(ValueError, _safe_int_cast, ((3,   4,   1),
+                                                          (2, 7.6, 289)))
+
+    np.testing.assert_raises(ValueError, _safe_int_cast, 7.1, 0.09)
+    np.testing.assert_raises(ValueError, _safe_int_cast, [7.1, 0.9], 0.09)
+    np.testing.assert_raises(ValueError, _safe_int_cast, np.r_[7.1, 0.9], 0.09)
+    np.testing.assert_raises(ValueError, _safe_int_cast, (7.1, 0.9), 0.09)
+    np.testing.assert_raises(ValueError, _safe_int_cast, ((3,   4,   1),
+                                                          (2, 7.6, 289)), 0.25)
+
+
+def test_int_cast_possible():
+    np.testing.assert_equal(_safe_int_cast(7.1, atol=0.11), 7)
+    np.testing.assert_equal(_safe_int_cast(-7.1, atol=0.11), -7)
+    np.testing.assert_equal(_safe_int_cast(41.9, atol=0.11), 42)
+    np.testing.assert_array_equal(_safe_int_cast([2, 42, 5789234.0, 87, 4]),
+                                  np.r_[2, 42, 5789234, 87, 4])
+    np.testing.assert_array_equal(_safe_int_cast(np.r_[[[3, 4,  1.000000001],
+                                                        [7, 2, -8.999999999],
+                                                        [6, 9, -4234918347.]]]),
+                                  np.r_[[[3, 4,           1],
+                                         [7, 2,          -9],
+                                         [6, 9, -4234918347]]])
+
+
+if __name__ == '__main__':
+    np.testing.run_module_suite()

From 07d3e6ede458093efa9b738c544f5e6e534718dc Mon Sep 17 00:00:00 2001
From: "Josh Warner (Mac)" <warner.joshua@mayo.edu>
Date: Wed, 7 May 2014 19:09:18 -0500
Subject: [PATCH 08/16] Convert name to _safe_as_int, output np.int64, expand
 Examples

---
 .../{safe_int_cast.py => safe_as_int.py}      | 25 ++++++++-----
 skimage/_shared/tests/test_safe_as_int.py     | 36 +++++++++++++++++++
 skimage/_shared/tests/test_safe_int_cast.py   | 36 -------------------
 3 files changed, 53 insertions(+), 44 deletions(-)
 rename skimage/_shared/{safe_int_cast.py => safe_as_int.py} (75%)
 create mode 100644 skimage/_shared/tests/test_safe_as_int.py
 delete mode 100644 skimage/_shared/tests/test_safe_int_cast.py

diff --git a/skimage/_shared/safe_int_cast.py b/skimage/_shared/safe_as_int.py
similarity index 75%
rename from skimage/_shared/safe_int_cast.py
rename to skimage/_shared/safe_as_int.py
index 0733cf61..0d665f9f 100644
--- a/skimage/_shared/safe_int_cast.py
+++ b/skimage/_shared/safe_as_int.py
@@ -1,9 +1,9 @@
 import numpy as np
 
-__all__ == ['_safe_int']
+__all__ = ['_safe_as_int']
 
 
-def _safe_int_cast(val, atol=1e-7):
+def _safe_as_int(val, atol=1e-7):
     """
     Attempt to safely cast values to integer format.
 
@@ -19,8 +19,8 @@ def _safe_int_cast(val, atol=1e-7):
 
     Returns
     -------
-    val_int : NumPy scalar or ndarray of dtype `np.int32`
-        Returns the input value(s) coerced to dtype `np.int32` assuming all
+    val_int : NumPy scalar or ndarray of dtype `np.int64`
+        Returns the input value(s) coerced to dtype `np.int64` assuming all
         were within ``atol`` of the nearest integer.
 
     Notes
@@ -37,13 +37,22 @@ def _safe_int_cast(val, atol=1e-7):
 
     Examples
     --------
-    >>> _safe_int_cast(7.0)
+    >>> _safe_as_int(7.0)
     7
-    >>> _safe_int_cast([9, 4, 2.9999999999])
+
+    >>> _safe_as_int([9, 4, 2.9999999999])
     array([9, 4, 3], dtype=int32)
 
+    >>> _safe_as_int(53.01)
+    Traceback (most recent call last):
+        ...
+    ValueError: Integer argument required but received 53.1, check inputs.
+
+    >>> _safe_as_int(53.01, atol=0.01)
+    53
+
     """
-    mod = np.asarray(val) % 1                # Modulo 1
+    mod = np.asarray(val) % 1                # Extract mantissa
 
     # Check for and subtract any mod values > 0.5 from 1
     if mod.ndim == 0:                        # Scalar input, cannot be indexed
@@ -58,4 +67,4 @@ def _safe_int_cast(val, atol=1e-7):
         raise ValueError("Integer argument required but received "
                          "{0}, check inputs.".format(val))
 
-    return np.round(val).astype(np.int32)
+    return np.round(val).astype(np.int64)
diff --git a/skimage/_shared/tests/test_safe_as_int.py b/skimage/_shared/tests/test_safe_as_int.py
new file mode 100644
index 00000000..1a3674e0
--- /dev/null
+++ b/skimage/_shared/tests/test_safe_as_int.py
@@ -0,0 +1,36 @@
+import numpy as np
+from skimage._shared.safe_int_cast import _safe_as_int
+
+
+def test_int_cast_not_possible():
+    np.testing.assert_raises(ValueError, _safe_as_int, 7.1)
+    np.testing.assert_raises(ValueError, _safe_as_int, [7.1, 0.9])
+    np.testing.assert_raises(ValueError, _safe_as_int, np.r_[7.1, 0.9])
+    np.testing.assert_raises(ValueError, _safe_as_int, (7.1, 0.9))
+    np.testing.assert_raises(ValueError, _safe_as_int, ((3,   4,   1),
+                                                          (2, 7.6, 289)))
+
+    np.testing.assert_raises(ValueError, _safe_as_int, 7.1, 0.09)
+    np.testing.assert_raises(ValueError, _safe_as_int, [7.1, 0.9], 0.09)
+    np.testing.assert_raises(ValueError, _safe_as_int, np.r_[7.1, 0.9], 0.09)
+    np.testing.assert_raises(ValueError, _safe_as_int, (7.1, 0.9), 0.09)
+    np.testing.assert_raises(ValueError, _safe_as_int, ((3,   4,   1),
+                                                          (2, 7.6, 289)), 0.25)
+
+
+def test_int_cast_possible():
+    np.testing.assert_equal(_safe_as_int(7.1, atol=0.11), 7)
+    np.testing.assert_equal(_safe_as_int(-7.1, atol=0.11), -7)
+    np.testing.assert_equal(_safe_as_int(41.9, atol=0.11), 42)
+    np.testing.assert_array_equal(_safe_as_int([2, 42, 5789234.0, 87, 4]),
+                                  np.r_[2, 42, 5789234, 87, 4])
+    np.testing.assert_array_equal(_safe_as_int(np.r_[[[3, 4,  1.000000001],
+                                                        [7, 2, -8.999999999],
+                                                        [6, 9, -4234918347.]]]),
+                                  np.r_[[[3, 4,           1],
+                                         [7, 2,          -9],
+                                         [6, 9, -4234918347]]])
+
+
+if __name__ == '__main__':
+    np.testing.run_module_suite()
diff --git a/skimage/_shared/tests/test_safe_int_cast.py b/skimage/_shared/tests/test_safe_int_cast.py
deleted file mode 100644
index 27f88323..00000000
--- a/skimage/_shared/tests/test_safe_int_cast.py
+++ /dev/null
@@ -1,36 +0,0 @@
-import numpy as np
-from skimage._shared.safe_int_cast import _safe_int_cast
-
-
-def test_int_cast_not_possible():
-    np.testing.assert_raises(ValueError, _safe_int_cast, 7.1)
-    np.testing.assert_raises(ValueError, _safe_int_cast, [7.1, 0.9])
-    np.testing.assert_raises(ValueError, _safe_int_cast, np.r_[7.1, 0.9])
-    np.testing.assert_raises(ValueError, _safe_int_cast, (7.1, 0.9))
-    np.testing.assert_raises(ValueError, _safe_int_cast, ((3,   4,   1),
-                                                          (2, 7.6, 289)))
-
-    np.testing.assert_raises(ValueError, _safe_int_cast, 7.1, 0.09)
-    np.testing.assert_raises(ValueError, _safe_int_cast, [7.1, 0.9], 0.09)
-    np.testing.assert_raises(ValueError, _safe_int_cast, np.r_[7.1, 0.9], 0.09)
-    np.testing.assert_raises(ValueError, _safe_int_cast, (7.1, 0.9), 0.09)
-    np.testing.assert_raises(ValueError, _safe_int_cast, ((3,   4,   1),
-                                                          (2, 7.6, 289)), 0.25)
-
-
-def test_int_cast_possible():
-    np.testing.assert_equal(_safe_int_cast(7.1, atol=0.11), 7)
-    np.testing.assert_equal(_safe_int_cast(-7.1, atol=0.11), -7)
-    np.testing.assert_equal(_safe_int_cast(41.9, atol=0.11), 42)
-    np.testing.assert_array_equal(_safe_int_cast([2, 42, 5789234.0, 87, 4]),
-                                  np.r_[2, 42, 5789234, 87, 4])
-    np.testing.assert_array_equal(_safe_int_cast(np.r_[[[3, 4,  1.000000001],
-                                                        [7, 2, -8.999999999],
-                                                        [6, 9, -4234918347.]]]),
-                                  np.r_[[[3, 4,           1],
-                                         [7, 2,          -9],
-                                         [6, 9, -4234918347]]])
-
-
-if __name__ == '__main__':
-    np.testing.run_module_suite()

From 4aa162fc783629075baaf1a4bc615c95551ee3fa Mon Sep 17 00:00:00 2001
From: "Josh Warner (Mac)" <warner.joshua@mayo.edu>
Date: Wed, 7 May 2014 22:10:27 -0500
Subject: [PATCH 09/16] FIX: Remove unnecessary .transpose introduced in PR
 #984

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

diff --git a/skimage/segmentation/random_walker_segmentation.py b/skimage/segmentation/random_walker_segmentation.py
index d722569b..731518e3 100644
--- a/skimage/segmentation/random_walker_segmentation.py
+++ b/skimage/segmentation/random_walker_segmentation.py
@@ -389,7 +389,7 @@ def random_walker(data, labels, beta=130, mode='bf', tol=1.e-3, copy=True,
         dims = data[..., 0].shape  # To reshape final labeled result
         data = img_as_float(data)
         if data.ndim == 3:  # 2D multispectral, needs singleton in 3rd axis
-            data = data[:, :, np.newaxis, :].transpose((0, 1, 3, 2))
+            data = data[:, :, np.newaxis, :]
 
     # Spacing kwarg checks
     if spacing is None:

From b8334e85c800c7bdf3068c96ffd932c6ac2a2819 Mon Sep 17 00:00:00 2001
From: "Josh Warner (Mac)" <warner.joshua@mayo.edu>
Date: Wed, 7 May 2014 23:16:42 -0500
Subject: [PATCH 10/16] failUnless -> assertTrue

---
 skimage/morphology/tests/test_watershed.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/skimage/morphology/tests/test_watershed.py b/skimage/morphology/tests/test_watershed.py
index 5dc0f07c..788d999e 100644
--- a/skimage/morphology/tests/test_watershed.py
+++ b/skimage/morphology/tests/test_watershed.py
@@ -154,7 +154,7 @@ class TestWatershed(unittest.TestCase):
                       [-1, -1,  1,  1,  1, -1, -1],
                       [-1, -1, -1, -1, -1, -1, -1],
                       [-1, -1, -1, -1, -1, -1, -1]], out)
-        self.failUnless(error < eps)
+        self.assertTrue(error < eps)
 
     def test_watershed03(self):
         "watershed 3"
@@ -189,7 +189,7 @@ class TestWatershed(unittest.TestCase):
                       [-1, -1, -1, -1, -1, -1, -1],
                       [-1, -1, -1, -1, -1, -1, -1],
                       [-1, -1, -1, -1, -1, -1, -1]], out)
-        self.failUnless(error < eps)
+        self.assertTrue(error < eps)
 
     def test_watershed04(self):
         "watershed 4"
@@ -224,7 +224,7 @@ class TestWatershed(unittest.TestCase):
                       [-1, -1, -1, -1, -1, -1, -1],
                       [-1, -1, -1, -1, -1, -1, -1],
                       [-1, -1, -1, -1, -1, -1, -1]], out)
-        self.failUnless(error < eps)
+        self.assertTrue(error < eps)
 
     def test_watershed05(self):
         "watershed 5"
@@ -259,7 +259,7 @@ class TestWatershed(unittest.TestCase):
                       [-1, -1, -1, -1, -1, -1, -1],
                       [-1, -1, -1, -1, -1, -1, -1],
                       [-1, -1, -1, -1, -1, -1, -1]], out)
-        self.failUnless(error < eps)
+        self.assertTrue(error < eps)
 
     def test_watershed06(self):
         "watershed 6"
@@ -291,7 +291,7 @@ class TestWatershed(unittest.TestCase):
                       [-1, -1, -1, -1, -1, -1, -1],
                       [-1, -1, -1, -1, -1, -1, -1],
                       [-1, -1, -1, -1, -1, -1, -1]], out)
-        self.failUnless(error < eps)
+        self.assertTrue(error < eps)
 
     def test_watershed07(self):
         "A regression test of a competitive case that failed"

From 548423bb940a38c599ac3b82bf8a1207b5112646 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Thu, 8 May 2014 16:24:50 +1000
Subject: [PATCH 11/16] Update variable name for RGB line profile

---
 viewer_examples/plugins/lineprofile_rgb.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/viewer_examples/plugins/lineprofile_rgb.py b/viewer_examples/plugins/lineprofile_rgb.py
index b08f5a00..577933a1 100644
--- a/viewer_examples/plugins/lineprofile_rgb.py
+++ b/viewer_examples/plugins/lineprofile_rgb.py
@@ -6,4 +6,4 @@ from skimage.viewer.plugins.lineprofile import LineProfile
 image = data.chelsea()
 viewer = ImageViewer(image)
 viewer += LineProfile()
-line, profiles = viewer.show()[0]
+line, rgb_profiles = viewer.show()[0]

From 3d2af717444ee80563f7eb00b4b957a6b43aee74 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Thu, 8 May 2014 17:21:35 +1000
Subject: [PATCH 12/16] Update description of viewer output in docs

---
 doc/source/user_guide/viewer.txt | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/doc/source/user_guide/viewer.txt b/doc/source/user_guide/viewer.txt
index 4cdde7db..73c4dc00 100644
--- a/doc/source/user_guide/viewer.txt
+++ b/doc/source/user_guide/viewer.txt
@@ -34,12 +34,16 @@ let's see an example of how a pre-defined plugin is added to the viewer:
    viewer += LineProfile(viewer)
    overlay, data = viewer.show()[0]
 
-The viewer's ``show`` method will return an overlay (of the same shape as the
-input image) and data (possibly ``None``) for each attached plugin. In this
-case, there is only one plugin, so we can directly name both. You can see the
-plugin class's ``output`` method to see what will be returned. Here,
-``overlay`` contains a drawing of the line (including its width), and ``data``
-contains the measured line profile.
+The viewer's ``show()`` method returns a list of tuples, one for each attached
+plugin. Each tuple contains two elements: an overlay of the same shape as the
+input image, and a data field (which may be ``None``). A plugin class documents
+its return value in its ``output`` method.
+
+In this example, only one plugin is attached, so the list returned by ``show``
+will have length 1. We extract that single tuple and bind its ``overlay`` and
+``data`` elements to individual variables. Here, ``overlay`` contains an image
+of the line drawn on the viewer, and ``data`` contains the 1-dimensional
+intensity profile along that line.
 
 At the moment, there are not many plugins pre-defined, but there is a really
 simple interface for creating your own plugin. First, let us create a plugin to
@@ -83,8 +87,8 @@ All that's left is to create an image viewer and add the plugin to that viewer.
    viewer += denoise_plugin
    denoised = viewer.show()[0][0]
 
-When we close the viewer, ``denoised`` will contain the filtered image for the
-last used setting of ``weight``.
+Here, we access only the overlay returned by the plugin, which contains the
+filtered image for the last used setting of ``weight``.
 
 .. image:: data/denoise_viewer_window.png
 .. image:: data/denoise_plugin_window.png

From 53de0db1649fda3b219bc03302a43d2b5eeda35f Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Thu, 8 May 2014 18:19:57 +1000
Subject: [PATCH 13/16] Very minor text change

---
 doc/source/user_guide/viewer.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/user_guide/viewer.txt b/doc/source/user_guide/viewer.txt
index 73c4dc00..3145effd 100644
--- a/doc/source/user_guide/viewer.txt
+++ b/doc/source/user_guide/viewer.txt
@@ -40,7 +40,7 @@ input image, and a data field (which may be ``None``). A plugin class documents
 its return value in its ``output`` method.
 
 In this example, only one plugin is attached, so the list returned by ``show``
-will have length 1. We extract that single tuple and bind its ``overlay`` and
+will have length 1. We extract the single tuple and bind its ``overlay`` and
 ``data`` elements to individual variables. Here, ``overlay`` contains an image
 of the line drawn on the viewer, and ``data`` contains the 1-dimensional
 intensity profile along that line.

From 0b6e48fe2a2d13d82d10e0e12bba89ccd279e428 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Thu, 8 May 2014 10:45:04 +0200
Subject: [PATCH 14/16] Clarify regionprops output

---
 skimage/measure/_regionprops.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/skimage/measure/_regionprops.py b/skimage/measure/_regionprops.py
index 88f7f843..7bcfcf81 100644
--- a/skimage/measure/_regionprops.py
+++ b/skimage/measure/_regionprops.py
@@ -344,9 +344,9 @@ def regionprops(label_image, intensity_image=None, cache=True):
 
     Returns
     -------
-    properties : list
-        List containing a properties for each region. The properties of each
-        region can be accessed as attributes and keys.
+    properties : list of RegionProperties
+        Each item describes one labeled region, and can be accessed using the
+        attributes listed below.
 
     Notes
     -----

From a9dcdc37131ee8e1a3b71e3fd77af3e3b5458e43 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Thu, 8 May 2014 19:28:29 +0200
Subject: [PATCH 15/16] Use safe_as_int to check provided output shape

---
 skimage/_shared/{safe_as_int.py => _safe_as_int.py} | 2 +-
 skimage/_shared/utils.py                            | 4 +++-
 skimage/transform/_geometric.py                     | 4 ++--
 skimage/transform/tests/test_warps.py               | 6 +++++-
 4 files changed, 11 insertions(+), 5 deletions(-)
 rename skimage/_shared/{safe_as_int.py => _safe_as_int.py} (98%)

diff --git a/skimage/_shared/safe_as_int.py b/skimage/_shared/_safe_as_int.py
similarity index 98%
rename from skimage/_shared/safe_as_int.py
rename to skimage/_shared/_safe_as_int.py
index 0d665f9f..200d6efb 100644
--- a/skimage/_shared/safe_as_int.py
+++ b/skimage/_shared/_safe_as_int.py
@@ -3,7 +3,7 @@ import numpy as np
 __all__ = ['_safe_as_int']
 
 
-def _safe_as_int(val, atol=1e-7):
+def safe_as_int(val, atol=1e-3):
     """
     Attempt to safely cast values to integer format.
 
diff --git a/skimage/_shared/utils.py b/skimage/_shared/utils.py
index 9148e7ff..f94edfc5 100644
--- a/skimage/_shared/utils.py
+++ b/skimage/_shared/utils.py
@@ -5,8 +5,10 @@ import sys
 import six
 
 from ._warnings import all_warnings
+from ._safe_as_int import safe_as_int
 
-__all__ = ['deprecated', 'get_bound_method_class', 'all_warnings']
+__all__ = ['deprecated', 'get_bound_method_class', 'all_warnings',
+           'safe_as_int']
 
 
 class skimage_deprecation(Warning):
diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index 53074c00..6eb0f70a 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -4,7 +4,7 @@ import warnings
 import numpy as np
 from scipy import ndimage, spatial
 
-from skimage._shared.utils import get_bound_method_class
+from skimage._shared.utils import get_bound_method_class, safe_as_int
 from skimage.util import img_as_float
 from ._warps_cy import _warp_fast
 
@@ -1078,7 +1078,7 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
     if output_shape is None:
         output_shape = ishape
     else:
-        output_shape = np.array(output_shape, dtype=int)
+        output_shape = safe_as_int(output_shape)
 
 
     out = None
diff --git a/skimage/transform/tests/test_warps.py b/skimage/transform/tests/test_warps.py
index f85125d0..07054ab7 100644
--- a/skimage/transform/tests/test_warps.py
+++ b/skimage/transform/tests/test_warps.py
@@ -250,7 +250,11 @@ def test_inverse():
 
 def test_slow_warp_nonint_oshape():
     image = np.random.random((5, 5))
-    warp(image, lambda xy: xy, output_shape=(13.1, 19.5))
+
+    assert_raises(ValueError, warp, image, lambda xy: xy,
+                  output_shape=(13.1, 19.5))
+
+    warp(image, lambda xy: xy, output_shape=(13.0001, 19.9999))
 
 
 if __name__ == "__main__":

From e9c0cde8d46b0b0ff30aea175af70ea1e4cd1caf Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Thu, 8 May 2014 20:11:17 +0200
Subject: [PATCH 16/16] Move safe_as_int into utils

---
 skimage/_shared/_safe_as_int.py           | 70 -----------------------
 skimage/_shared/tests/test_safe_as_int.py | 32 +++++------
 skimage/_shared/utils.py                  | 69 +++++++++++++++++++++-
 3 files changed, 84 insertions(+), 87 deletions(-)
 delete mode 100644 skimage/_shared/_safe_as_int.py

diff --git a/skimage/_shared/_safe_as_int.py b/skimage/_shared/_safe_as_int.py
deleted file mode 100644
index 200d6efb..00000000
--- a/skimage/_shared/_safe_as_int.py
+++ /dev/null
@@ -1,70 +0,0 @@
-import numpy as np
-
-__all__ = ['_safe_as_int']
-
-
-def safe_as_int(val, atol=1e-3):
-    """
-    Attempt to safely cast values to integer format.
-
-    Parameters
-    ----------
-    val : scalar or iterable of scalars
-        Number or container of numbers which are intended to be interpreted as
-        integers, e.g., for indexing purposes, but which may not carry integer
-        type.
-    atol : float
-        Absolute tolerance away from nearest integer to consider values in
-        ``val`` functionally integers.
-
-    Returns
-    -------
-    val_int : NumPy scalar or ndarray of dtype `np.int64`
-        Returns the input value(s) coerced to dtype `np.int64` assuming all
-        were within ``atol`` of the nearest integer.
-
-    Notes
-    -----
-    This operation calculates ``val`` modulo 1, which returns the mantissa of
-    all values. Then all mantissas greater than 0.5 are subtracted from one.
-    Finally, the absolute tolerance from zero is calculated. If it is less
-    than ``atol`` for all value(s) in ``val``, they are rounded and returned
-    in an integer array. Or, if ``val`` was a scalar, a NumPy scalar type is
-    returned.
-
-    If any value(s) are outside the specified tolerance, an informative error
-    is raised.
-
-    Examples
-    --------
-    >>> _safe_as_int(7.0)
-    7
-
-    >>> _safe_as_int([9, 4, 2.9999999999])
-    array([9, 4, 3], dtype=int32)
-
-    >>> _safe_as_int(53.01)
-    Traceback (most recent call last):
-        ...
-    ValueError: Integer argument required but received 53.1, check inputs.
-
-    >>> _safe_as_int(53.01, atol=0.01)
-    53
-
-    """
-    mod = np.asarray(val) % 1                # Extract mantissa
-
-    # Check for and subtract any mod values > 0.5 from 1
-    if mod.ndim == 0:                        # Scalar input, cannot be indexed
-        if mod > 0.5:
-            mod = 1 - mod
-    else:                                    # Iterable input, now ndarray
-        mod[mod > 0.5] = 1 - mod[mod > 0.5]  # Test on each side of nearest int
-
-    try:
-        np.testing.assert_allclose(mod, 0, atol=atol)
-    except AssertionError:
-        raise ValueError("Integer argument required but received "
-                         "{0}, check inputs.".format(val))
-
-    return np.round(val).astype(np.int64)
diff --git a/skimage/_shared/tests/test_safe_as_int.py b/skimage/_shared/tests/test_safe_as_int.py
index 1a3674e0..009fa9a4 100644
--- a/skimage/_shared/tests/test_safe_as_int.py
+++ b/skimage/_shared/tests/test_safe_as_int.py
@@ -1,30 +1,30 @@
 import numpy as np
-from skimage._shared.safe_int_cast import _safe_as_int
+from skimage._shared.utils import safe_as_int
 
 
 def test_int_cast_not_possible():
-    np.testing.assert_raises(ValueError, _safe_as_int, 7.1)
-    np.testing.assert_raises(ValueError, _safe_as_int, [7.1, 0.9])
-    np.testing.assert_raises(ValueError, _safe_as_int, np.r_[7.1, 0.9])
-    np.testing.assert_raises(ValueError, _safe_as_int, (7.1, 0.9))
-    np.testing.assert_raises(ValueError, _safe_as_int, ((3,   4,   1),
+    np.testing.assert_raises(ValueError, safe_as_int, 7.1)
+    np.testing.assert_raises(ValueError, safe_as_int, [7.1, 0.9])
+    np.testing.assert_raises(ValueError, safe_as_int, np.r_[7.1, 0.9])
+    np.testing.assert_raises(ValueError, safe_as_int, (7.1, 0.9))
+    np.testing.assert_raises(ValueError, safe_as_int, ((3,   4,   1),
                                                           (2, 7.6, 289)))
 
-    np.testing.assert_raises(ValueError, _safe_as_int, 7.1, 0.09)
-    np.testing.assert_raises(ValueError, _safe_as_int, [7.1, 0.9], 0.09)
-    np.testing.assert_raises(ValueError, _safe_as_int, np.r_[7.1, 0.9], 0.09)
-    np.testing.assert_raises(ValueError, _safe_as_int, (7.1, 0.9), 0.09)
-    np.testing.assert_raises(ValueError, _safe_as_int, ((3,   4,   1),
+    np.testing.assert_raises(ValueError, safe_as_int, 7.1, 0.09)
+    np.testing.assert_raises(ValueError, safe_as_int, [7.1, 0.9], 0.09)
+    np.testing.assert_raises(ValueError, safe_as_int, np.r_[7.1, 0.9], 0.09)
+    np.testing.assert_raises(ValueError, safe_as_int, (7.1, 0.9), 0.09)
+    np.testing.assert_raises(ValueError, safe_as_int, ((3,   4,   1),
                                                           (2, 7.6, 289)), 0.25)
 
 
 def test_int_cast_possible():
-    np.testing.assert_equal(_safe_as_int(7.1, atol=0.11), 7)
-    np.testing.assert_equal(_safe_as_int(-7.1, atol=0.11), -7)
-    np.testing.assert_equal(_safe_as_int(41.9, atol=0.11), 42)
-    np.testing.assert_array_equal(_safe_as_int([2, 42, 5789234.0, 87, 4]),
+    np.testing.assert_equal(safe_as_int(7.1, atol=0.11), 7)
+    np.testing.assert_equal(safe_as_int(-7.1, atol=0.11), -7)
+    np.testing.assert_equal(safe_as_int(41.9, atol=0.11), 42)
+    np.testing.assert_array_equal(safe_as_int([2, 42, 5789234.0, 87, 4]),
                                   np.r_[2, 42, 5789234, 87, 4])
-    np.testing.assert_array_equal(_safe_as_int(np.r_[[[3, 4,  1.000000001],
+    np.testing.assert_array_equal(safe_as_int(np.r_[[[3, 4,  1.000000001],
                                                         [7, 2, -8.999999999],
                                                         [6, 9, -4234918347.]]]),
                                   np.r_[[[3, 4,           1],
diff --git a/skimage/_shared/utils.py b/skimage/_shared/utils.py
index f94edfc5..612a2b63 100644
--- a/skimage/_shared/utils.py
+++ b/skimage/_shared/utils.py
@@ -1,11 +1,11 @@
 import warnings
 import functools
 import sys
+import numpy as np
 
 import six
 
 from ._warnings import all_warnings
-from ._safe_as_int import safe_as_int
 
 __all__ = ['deprecated', 'get_bound_method_class', 'all_warnings',
            'safe_as_int']
@@ -74,3 +74,70 @@ def get_bound_method_class(m):
 
     """
     return m.im_class if sys.version < '3' else m.__self__.__class__
+
+
+def safe_as_int(val, atol=1e-3):
+    """
+    Attempt to safely cast values to integer format.
+
+    Parameters
+    ----------
+    val : scalar or iterable of scalars
+        Number or container of numbers which are intended to be interpreted as
+        integers, e.g., for indexing purposes, but which may not carry integer
+        type.
+    atol : float
+        Absolute tolerance away from nearest integer to consider values in
+        ``val`` functionally integers.
+
+    Returns
+    -------
+    val_int : NumPy scalar or ndarray of dtype `np.int64`
+        Returns the input value(s) coerced to dtype `np.int64` assuming all
+        were within ``atol`` of the nearest integer.
+
+    Notes
+    -----
+    This operation calculates ``val`` modulo 1, which returns the mantissa of
+    all values. Then all mantissas greater than 0.5 are subtracted from one.
+    Finally, the absolute tolerance from zero is calculated. If it is less
+    than ``atol`` for all value(s) in ``val``, they are rounded and returned
+    in an integer array. Or, if ``val`` was a scalar, a NumPy scalar type is
+    returned.
+
+    If any value(s) are outside the specified tolerance, an informative error
+    is raised.
+
+    Examples
+    --------
+    >>> _safe_as_int(7.0)
+    7
+
+    >>> _safe_as_int([9, 4, 2.9999999999])
+    array([9, 4, 3], dtype=int32)
+
+    >>> _safe_as_int(53.01)
+    Traceback (most recent call last):
+        ...
+    ValueError: Integer argument required but received 53.1, check inputs.
+
+    >>> _safe_as_int(53.01, atol=0.01)
+    53
+
+    """
+    mod = np.asarray(val) % 1                # Extract mantissa
+
+    # Check for and subtract any mod values > 0.5 from 1
+    if mod.ndim == 0:                        # Scalar input, cannot be indexed
+        if mod > 0.5:
+            mod = 1 - mod
+    else:                                    # Iterable input, now ndarray
+        mod[mod > 0.5] = 1 - mod[mod > 0.5]  # Test on each side of nearest int
+
+    try:
+        np.testing.assert_allclose(mod, 0, atol=atol)
+    except AssertionError:
+        raise ValueError("Integer argument required but received "
+                         "{0}, check inputs.".format(val))
+
+    return np.round(val).astype(np.int64)