From 1ac289c5887bca11b4278d855dca70f8fbaa26cc Mon Sep 17 00:00:00 2001
From: James Bergstra <james.bergstra@gmail.com>
Date: Fri, 17 Aug 2012 17:57:43 -0400
Subject: [PATCH 01/16] FIX: corrected docstring for transform.warp

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

diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index c055247e..422737a7 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -721,7 +721,7 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
     mode : string
         How to handle values outside the image borders.  See
         `scipy.ndimage.map_coordinates` for detail.
-    cval : string
+    cval : float
         Used in conjunction with mode 'constant', the value outside
         the image boundaries.
 

From 0749f8d9f008fcc32ab533bcc0c87c7cda521d7d Mon Sep 17 00:00:00 2001
From: James Bergstra <james.bergstra@gmail.com>
Date: Fri, 17 Aug 2012 17:59:28 -0400
Subject: [PATCH 02/16] FIX: transform.warp supports cval outside 0-1 range

---
 skimage/transform/_geometric.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index 422737a7..2aecfe48 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -785,4 +785,9 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
 
     # The spline filters sometimes return results outside [0, 1],
     # so clip to ensure valid data
-    return np.clip(mapped.squeeze(), 0, 1)
+    clipped = np.clip(mapped, 0, 1)
+    if mode == 'constant' and not (0 <= cval <= 1):
+        clipped[mapped == cval] = cval
+
+    # Remove singleton dim introduced by atleast_3d
+    return clipped.squeeze()

From e710fac03e1b8a4fb4bebba3e6dc732546da2722 Mon Sep 17 00:00:00 2001
From: James Bergstra <james.bergstra@gmail.com>
Date: Mon, 20 Aug 2012 19:11:58 -0400
Subject: [PATCH 03/16] Added test case for warp() when cval out of clipping
 range

---
 skimage/transform/_geometric.py       |  1 +
 skimage/transform/tests/test_warps.py | 10 +++++++++-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index 2aecfe48..5baaeba1 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -786,6 +786,7 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
     # The spline filters sometimes return results outside [0, 1],
     # so clip to ensure valid data
     clipped = np.clip(mapped, 0, 1)
+
     if mode == 'constant' and not (0 <= cval <= 1):
         clipped[mapped == cval] = cval
 
diff --git a/skimage/transform/tests/test_warps.py b/skimage/transform/tests/test_warps.py
index f35b7f57..3ef5a2ee 100644
--- a/skimage/transform/tests/test_warps.py
+++ b/skimage/transform/tests/test_warps.py
@@ -2,7 +2,8 @@ from numpy.testing import assert_array_almost_equal, run_module_suite
 import numpy as np
 
 from skimage.transform import (warp, homography, fast_homography,
-                               SimilarityTransform, ProjectiveTransform)
+                               SimilarityTransform, ProjectiveTransform,
+                               AffineTransform)
 from skimage import transform as tf, data, img_as_float
 from skimage.color import rgb2gray
 
@@ -74,5 +75,12 @@ def test_swirl():
     assert np.mean(np.abs(image - unswirled)) < 0.01
 
 
+def test_const_cval_out_of_range():
+    img = np.random.randn(100, 100)
+    warped = warp(img, AffineTransform(translation=(10, 10)), cval=-10)
+    assert np.any(warped < 0)
+
+
+
 if __name__ == "__main__":
     run_module_suite()

From c22a176e8d8c368e108cef65144e062abbd87121 Mon Sep 17 00:00:00 2001
From: James Bergstra <james.bergstra@gmail.com>
Date: Mon, 20 Aug 2012 19:13:04 -0400
Subject: [PATCH 04/16] ENH: moved code generating coords out of warp() to
 _warp_coords

---
 skimage/transform/_geometric.py | 63 ++++++++++++++++++++++-----------
 1 file changed, 42 insertions(+), 21 deletions(-)

diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index 5baaeba1..9d394372 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -27,6 +27,45 @@ def _stackcopy(a, b):
         a[:] = b
 
 
+def _build_coords(orows, ocols, bands, coord_transform_fn,
+        dtype='float64'):
+    """
+    Return coords object suitable for scipy.ndimage.map_coordinates
+
+    Parameters
+    ----------
+    orows: number of output rows
+    ocols: number of output columns
+    bands: number of color bands (aka channels)
+    coord_transform_fn: something like GeometricTransform.inverse_map
+    interp_dtype: precision of interpolation e.g. 'float32' or 'float64'
+
+    """
+
+    coords = np.empty(np.r_[3, (orows, ocols, bands)], dtype=dtype)
+
+    # Reshape grid coordinates into a (P, 2) array of (x, y) pairs
+    tf_coords = np.indices((ocols, orows), dtype=dtype).reshape(2, -1).T
+
+    # Map each (x, y) pair to the source image according to
+    # the user-provided mapping
+    tf_coords = coord_transform_fn(tf_coords)
+
+    # Reshape back to a (2, M, N) coordinate grid
+    tf_coords = tf_coords.T.reshape((-1, ocols, orows)).swapaxes(1, 2)
+
+    # Place the y-coordinate mapping
+    _stackcopy(coords[1, ...], tf_coords[0, ...])
+
+    # Place the x-coordinate mapping
+    _stackcopy(coords[0, ...], tf_coords[1, ...])
+
+    # colour-coordinate mapping
+    coords[2, ...] = range(bands)
+
+    return coords
+
+
 class GeometricTransform(object):
     """Perform geometric transformations on a set of coordinates.
 
@@ -753,30 +792,12 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
     if output_shape is None:
         output_shape = ishape
 
-    coords = np.empty(np.r_[3, output_shape], dtype=float)
-
-    ## Construct transformed coordinates
-
     rows, cols = output_shape[:2]
 
-    # Reshape grid coordinates into a (P, 2) array of (x, y) pairs
-    tf_coords = np.indices((cols, rows), dtype=float).reshape(2, -1).T
+    def coord_transform_fn(*args):
+        return inverse_map(*args, **map_args)
 
-    # Map each (x, y) pair to the source image according to
-    # the user-provided mapping
-    tf_coords = inverse_map(tf_coords, **map_args)
-
-    # Reshape back to a (2, M, N) coordinate grid
-    tf_coords = tf_coords.T.reshape((-1, cols, rows)).swapaxes(1, 2)
-
-    # Place the y-coordinate mapping
-    _stackcopy(coords[1, ...], tf_coords[0, ...])
-
-    # Place the x-coordinate mapping
-    _stackcopy(coords[0, ...], tf_coords[1, ...])
-
-    # colour-coordinate mapping
-    coords[2, ...] = range(bands)
+    coords = _build_coords(rows, cols, bands, coord_transform_fn)
 
     # Prefilter not necessary for order 1 interpolation
     prefilter = order > 1

From ce200f570f2e7e4b67c24d42a0d0e6f3cdd95243 Mon Sep 17 00:00:00 2001
From: James Bergstra <james.bergstra@gmail.com>
Date: Mon, 20 Aug 2012 19:15:36 -0400
Subject: [PATCH 05/16] ENH: test_warp test case to make sure _warp_coords
 works for grey and rgb images

---
 skimage/transform/tests/test_warps.py | 29 +++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/skimage/transform/tests/test_warps.py b/skimage/transform/tests/test_warps.py
index 3ef5a2ee..2c2ecf53 100644
--- a/skimage/transform/tests/test_warps.py
+++ b/skimage/transform/tests/test_warps.py
@@ -1,6 +1,9 @@
+import sys
 from numpy.testing import assert_array_almost_equal, run_module_suite
 import numpy as np
 
+import scipy.misc # -- greyscale lena that works without PIL png support
+
 from skimage.transform import (warp, homography, fast_homography,
                                SimilarityTransform, ProjectiveTransform,
                                AffineTransform)
@@ -66,6 +69,10 @@ def test_fast_homography():
 
 
 def test_swirl():
+    if not data.checkerboard().shape:
+        print >> sys.stderr, ('Failed to read image data.checkerboard()'
+                ' -- Skipping test_fast_homography')
+        return
     image = img_as_float(data.checkerboard())
 
     swirl_params = {'radius': 80, 'rotation': 0, 'order': 2, 'mode': 'reflect'}
@@ -81,6 +88,28 @@ def test_const_cval_out_of_range():
     assert np.any(warped < 0)
 
 
+def test_warp_identity():
+    lena = scipy.misc.lena().astype('float32') / 255
+    assert len(lena.shape) == 2
+    assert np.allclose(lena,
+            warp(lena, AffineTransform(rotation=0)))
+    assert not np.allclose(lena,
+            warp(lena, AffineTransform(rotation=0.1)))
+
+    rgb_lena = np.transpose(
+            np.asarray([lena, np.zeros_like(lena), lena]),
+            (1, 2, 0))
+    warped_rgb_lena = warp(rgb_lena, AffineTransform(rotation=0.1))
+
+    assert np.allclose(rgb_lena,
+            warp(rgb_lena, AffineTransform(rotation=0)))
+    assert not np.allclose(rgb_lena, warped_rgb_lena)
+    # assert no cross-talk between bands
+    assert np.all(0 == warped_rgb_lena[:, :, 1])
+
+
+
+
 
 if __name__ == "__main__":
     run_module_suite()

From e3585ad17a98ec374a4baa453585bcecea3acbee Mon Sep 17 00:00:00 2001
From: James Bergstra <james.bergstra@gmail.com>
Date: Mon, 20 Aug 2012 23:35:21 -0400
Subject: [PATCH 06/16] ENH: renamed and docd _build_coords -> warp_coords

---
 skimage/transform/_geometric.py | 107 ++++++++++++++++++++------------
 1 file changed, 67 insertions(+), 40 deletions(-)

diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index 9d394372..5dae2c7f 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -27,45 +27,6 @@ def _stackcopy(a, b):
         a[:] = b
 
 
-def _build_coords(orows, ocols, bands, coord_transform_fn,
-        dtype='float64'):
-    """
-    Return coords object suitable for scipy.ndimage.map_coordinates
-
-    Parameters
-    ----------
-    orows: number of output rows
-    ocols: number of output columns
-    bands: number of color bands (aka channels)
-    coord_transform_fn: something like GeometricTransform.inverse_map
-    interp_dtype: precision of interpolation e.g. 'float32' or 'float64'
-
-    """
-
-    coords = np.empty(np.r_[3, (orows, ocols, bands)], dtype=dtype)
-
-    # Reshape grid coordinates into a (P, 2) array of (x, y) pairs
-    tf_coords = np.indices((ocols, orows), dtype=dtype).reshape(2, -1).T
-
-    # Map each (x, y) pair to the source image according to
-    # the user-provided mapping
-    tf_coords = coord_transform_fn(tf_coords)
-
-    # Reshape back to a (2, M, N) coordinate grid
-    tf_coords = tf_coords.T.reshape((-1, ocols, orows)).swapaxes(1, 2)
-
-    # Place the y-coordinate mapping
-    _stackcopy(coords[1, ...], tf_coords[0, ...])
-
-    # Place the x-coordinate mapping
-    _stackcopy(coords[0, ...], tf_coords[1, ...])
-
-    # colour-coordinate mapping
-    coords[2, ...] = range(bands)
-
-    return coords
-
-
 class GeometricTransform(object):
     """Perform geometric transformations on a set of coordinates.
 
@@ -737,6 +698,72 @@ def matrix_transform(coords, matrix):
     return ProjectiveTransform(matrix)(coords)
 
 
+def warp_coords(orows, ocols, bands, coord_transform_fn,
+        dtype='float64'):
+    """
+    Return `coords` ndarray suitable for `scipy.ndimage.map_coordinates`, which will yield an
+    image of shape (orows, ocols, bands) by drawing from source points according to the
+    `coord_transform_fn`.
+
+    Parameters
+    ----------
+    orows: number of output rows
+    ocols: number of output columns
+    bands: number of color bands (aka channels)
+    coord_transform_fn: something like GeometricTransform.inverse_map
+    dtype: dtype for return value (should probably be 'float32' or 'float64')
+
+    Notes
+    -----
+    This is a lower-level routine that produces the source coordinates used by `warp()`.
+
+    It is provided separately from `warp` to give additional flexibility to users who would
+    like, for example, to re-use a particular coordinate mapping, to use specific dtypes at
+    various points along the the image-warping process, or to implement different
+    post-processing logic than `warp` performs after the call to `ndimage.map_coordinates`.
+
+
+    Examples
+    --------
+    Produce a coordinate map that Shifts an image to the right:
+
+    >>> from skimage import data
+    >>> from scipy.ndimage import map_coordinates
+    >>>
+    >>> def shift_right(xy):
+    ...     xy[:, 0] -= 10
+    ...     return xy
+    >>>
+    >>> coords = warp_coords(30, 30, 3, shift_right)
+    >>> image = data.camera()
+    >>> warped_image = map_coordinates(coords, image)
+
+    """
+
+    coords = np.empty(np.r_[3, (orows, ocols, bands)], dtype=dtype)
+
+    # Reshape grid coordinates into a (P, 2) array of (x, y) pairs
+    tf_coords = np.indices((ocols, orows), dtype=dtype).reshape(2, -1).T
+
+    # Map each (x, y) pair to the source image according to
+    # the user-provided mapping
+    tf_coords = coord_transform_fn(tf_coords)
+
+    # Reshape back to a (2, M, N) coordinate grid
+    tf_coords = tf_coords.T.reshape((-1, ocols, orows)).swapaxes(1, 2)
+
+    # Place the y-coordinate mapping
+    _stackcopy(coords[1, ...], tf_coords[0, ...])
+
+    # Place the x-coordinate mapping
+    _stackcopy(coords[0, ...], tf_coords[1, ...])
+
+    # colour-coordinate mapping
+    coords[2, ...] = range(bands)
+
+    return coords
+
+
 def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
          mode='constant', cval=0., reverse_map=None):
     """Warp an image according to a given coordinate transformation.
@@ -797,7 +824,7 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
     def coord_transform_fn(*args):
         return inverse_map(*args, **map_args)
 
-    coords = _build_coords(rows, cols, bands, coord_transform_fn)
+    coords = warp_coords(rows, cols, bands, coord_transform_fn)
 
     # Prefilter not necessary for order 1 interpolation
     prefilter = order > 1

From 96c022535495f6315a28c53e42f973ce1f6da7ef Mon Sep 17 00:00:00 2001
From: James Bergstra <james.bergstra@gmail.com>
Date: Mon, 20 Aug 2012 23:37:03 -0400
Subject: [PATCH 07/16] ENH: test warp with data.lena instead of
 scipy.misc.lena

---
 skimage/transform/tests/test_warps.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/skimage/transform/tests/test_warps.py b/skimage/transform/tests/test_warps.py
index 2c2ecf53..610c42a8 100644
--- a/skimage/transform/tests/test_warps.py
+++ b/skimage/transform/tests/test_warps.py
@@ -2,8 +2,6 @@ import sys
 from numpy.testing import assert_array_almost_equal, run_module_suite
 import numpy as np
 
-import scipy.misc # -- greyscale lena that works without PIL png support
-
 from skimage.transform import (warp, homography, fast_homography,
                                SimilarityTransform, ProjectiveTransform,
                                AffineTransform)
@@ -71,7 +69,7 @@ def test_fast_homography():
 def test_swirl():
     if not data.checkerboard().shape:
         print >> sys.stderr, ('Failed to read image data.checkerboard()'
-                ' -- Skipping test_fast_homography')
+                ' -- Skipping test_swirl')
         return
     image = img_as_float(data.checkerboard())
 
@@ -89,7 +87,12 @@ def test_const_cval_out_of_range():
 
 
 def test_warp_identity():
-    lena = scipy.misc.lena().astype('float32') / 255
+    lena = data.lena()
+    if not lena.shape:
+        print >> sys.stderr, ('Failed to read image data.lena()'
+                ' -- Skipping test_warp_identity')
+        return
+    lena = img_as_float(rgb2gray(lena))
     assert len(lena.shape) == 2
     assert np.allclose(lena,
             warp(lena, AffineTransform(rotation=0)))
@@ -108,8 +111,5 @@ def test_warp_identity():
     assert np.all(0 == warped_rgb_lena[:, :, 1])
 
 
-
-
-
 if __name__ == "__main__":
     run_module_suite()

From 5cce39a44ace53223ac547fa50a90d6b9aaf0646 Mon Sep 17 00:00:00 2001
From: James Bergstra <james.bergstra@gmail.com>
Date: Mon, 20 Aug 2012 23:44:31 -0400
Subject: [PATCH 08/16] ENH: remove call in tests to deprecated homography fn

---
 skimage/transform/tests/test_warps.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/skimage/transform/tests/test_warps.py b/skimage/transform/tests/test_warps.py
index 610c42a8..72604b03 100644
--- a/skimage/transform/tests/test_warps.py
+++ b/skimage/transform/tests/test_warps.py
@@ -2,9 +2,10 @@ import sys
 from numpy.testing import assert_array_almost_equal, run_module_suite
 import numpy as np
 
-from skimage.transform import (warp, homography, fast_homography,
-                               SimilarityTransform, ProjectiveTransform,
-                               AffineTransform)
+from skimage.transform import (warp, fast_homography,
+                               AffineTransform,
+                               ProjectiveTransform,
+                               SimilarityTransform)
 from skimage import transform as tf, data, img_as_float
 from skimage.color import rgb2gray
 
@@ -31,7 +32,10 @@ def test_homography():
     M = np.array([[np.cos(theta),-np.sin(theta),0],
                   [np.sin(theta), np.cos(theta),4],
                   [0,             0,            1]])
-    x90 = homography(x, M, order=1)
+
+    x90 = warp(x,
+            inverse_map=ProjectiveTransform(M).inverse,
+            order=1)
     assert_array_almost_equal(x90, np.rot90(x))
 
 

From c5dc55cd52e605b7a27be1dd6786cce6f85758ba Mon Sep 17 00:00:00 2001
From: James Bergstra <james.bergstra@gmail.com>
Date: Tue, 21 Aug 2012 16:09:47 -0400
Subject: [PATCH 09/16] ENH: better docstring and test for warp_coords

---
 skimage/transform/__init__.py         |  2 +-
 skimage/transform/_geometric.py       | 29 ++++++++++++++++++---------
 skimage/transform/tests/test_warps.py | 18 ++++++++++++++++-
 3 files changed, 37 insertions(+), 12 deletions(-)

diff --git a/skimage/transform/__init__.py b/skimage/transform/__init__.py
index 4721e7d1..b0eee512 100644
--- a/skimage/transform/__init__.py
+++ b/skimage/transform/__init__.py
@@ -3,7 +3,7 @@ from .radon_transform import *
 from .finite_radon_transform import *
 from ._project import homography as fast_homography
 from .integral import *
-from ._geometric import (warp, estimate_transform,
+from ._geometric import (warp, warp_coords, estimate_transform,
                          SimilarityTransform, AffineTransform,
                          ProjectiveTransform, PolynomialTransform)
 from ._warps import swirl, homography
diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index 5dae2c7f..0e590487 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -699,19 +699,28 @@ def matrix_transform(coords, matrix):
 
 
 def warp_coords(orows, ocols, bands, coord_transform_fn,
-        dtype='float64'):
-    """
-    Return `coords` ndarray suitable for `scipy.ndimage.map_coordinates`, which will yield an
-    image of shape (orows, ocols, bands) by drawing from source points according to the
-    `coord_transform_fn`.
+                dtype=np.float64):
+    """Build the source coordinates for the output pixels of an image warp.
 
     Parameters
     ----------
-    orows: number of output rows
-    ocols: number of output columns
-    bands: number of color bands (aka channels)
-    coord_transform_fn: something like GeometricTransform.inverse_map
-    dtype: dtype for return value (should probably be 'float32' or 'float64')
+    orows : int
+        number of output rows
+    ocols : int
+        number of output columns
+    bands : int
+        number of color bands (aka channels)
+    coord_transform_fn : callable like GeometricTransform.inverse_map
+        Return input coordinates for given output coordinates
+    dtype : np.dtype or string
+        dtype for return value (sane choices: float32 or float64)
+
+    Returns
+    -------
+    coords : (orows * ocols, ) array 
+            Coordinates for `scipy.ndimage.map_coordinates`, that will yield
+            an image of shape (orows, ocols, bands) by drawing from source
+            points according to the `coord_transform_fn`.
 
     Notes
     -----
diff --git a/skimage/transform/tests/test_warps.py b/skimage/transform/tests/test_warps.py
index 72604b03..28350ff6 100644
--- a/skimage/transform/tests/test_warps.py
+++ b/skimage/transform/tests/test_warps.py
@@ -2,7 +2,7 @@ import sys
 from numpy.testing import assert_array_almost_equal, run_module_suite
 import numpy as np
 
-from skimage.transform import (warp, fast_homography,
+from skimage.transform import (warp, warp_coords, fast_homography,
                                AffineTransform,
                                ProjectiveTransform,
                                SimilarityTransform)
@@ -115,5 +115,21 @@ def test_warp_identity():
     assert np.all(0 == warped_rgb_lena[:, :, 1])
 
 
+def test_warp_coords_example():
+    from skimage import data
+    from scipy.ndimage import map_coordinates
+    def shift_right(xy):
+        print 'xyshape', xy.shape
+        xy[:, 0] -= 10
+        return xy
+
+    image = data.lena().astype(np.float32)
+    print 'testing'
+    print image.dtype, image.shape
+    coords = warp_coords(512, 512, 3, shift_right)
+    print 'warp_coords', coords.dtype, coords.shape
+    warped_image = map_coordinates(coords, image)
+
+
 if __name__ == "__main__":
     run_module_suite()

From e859520872736a0564a896fd96aab8515fc1debe Mon Sep 17 00:00:00 2001
From: James Bergstra <james.bergstra@gmail.com>
Date: Tue, 21 Aug 2012 16:52:04 -0400
Subject: [PATCH 10/16] FIX: doctest of warp_coords

---
 skimage/transform/_geometric.py       | 9 +++++----
 skimage/transform/tests/test_warps.py | 9 +++------
 2 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index 0e590487..2fd2a694 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -717,7 +717,7 @@ def warp_coords(orows, ocols, bands, coord_transform_fn,
 
     Returns
     -------
-    coords : (orows * ocols, ) array 
+    coords : (3, orows, ocols, bands) array 
             Coordinates for `scipy.ndimage.map_coordinates`, that will yield
             an image of shape (orows, ocols, bands) by drawing from source
             points according to the `coord_transform_fn`.
@@ -744,12 +744,12 @@ def warp_coords(orows, ocols, bands, coord_transform_fn,
     ...     return xy
     >>>
     >>> coords = warp_coords(30, 30, 3, shift_right)
-    >>> image = data.camera()
-    >>> warped_image = map_coordinates(coords, image)
+    >>> image = data.lena().astype(np.float32)
+    >>> warped_image = map_coordinates(image, coords)
 
     """
 
-    coords = np.empty(np.r_[3, (orows, ocols, bands)], dtype=dtype)
+    coords = np.empty((3, orows, ocols, bands), dtype=dtype)
 
     # Reshape grid coordinates into a (P, 2) array of (x, y) pairs
     tf_coords = np.indices((ocols, orows), dtype=dtype).reshape(2, -1).T
@@ -833,6 +833,7 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
     def coord_transform_fn(*args):
         return inverse_map(*args, **map_args)
 
+
     coords = warp_coords(rows, cols, bands, coord_transform_fn)
 
     # Prefilter not necessary for order 1 interpolation
diff --git a/skimage/transform/tests/test_warps.py b/skimage/transform/tests/test_warps.py
index 28350ff6..3cde47ac 100644
--- a/skimage/transform/tests/test_warps.py
+++ b/skimage/transform/tests/test_warps.py
@@ -119,16 +119,13 @@ def test_warp_coords_example():
     from skimage import data
     from scipy.ndimage import map_coordinates
     def shift_right(xy):
-        print 'xyshape', xy.shape
         xy[:, 0] -= 10
         return xy
 
     image = data.lena().astype(np.float32)
-    print 'testing'
-    print image.dtype, image.shape
-    coords = warp_coords(512, 512, 3, shift_right)
-    print 'warp_coords', coords.dtype, coords.shape
-    warped_image = map_coordinates(coords, image)
+    assert 3 == image.shape[2]
+    coords = warp_coords(30, 30, 3, shift_right)
+    warped_image = map_coordinates(image[:, :, 0], coords[:2])
 
 
 if __name__ == "__main__":

From 47c0a506bcdaf2cec28a63bd3aceac970f312124 Mon Sep 17 00:00:00 2001
From: James Bergstra <james.bergstra@gmail.com>
Date: Tue, 21 Aug 2012 16:53:04 -0400
Subject: [PATCH 11/16] ENH: warp_coords docstring

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

diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index 2fd2a694..d29baac0 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -717,7 +717,7 @@ def warp_coords(orows, ocols, bands, coord_transform_fn,
 
     Returns
     -------
-    coords : (3, orows, ocols, bands) array 
+    coords : (3, orows, ocols, bands) array of dtype `dtype`
             Coordinates for `scipy.ndimage.map_coordinates`, that will yield
             an image of shape (orows, ocols, bands) by drawing from source
             points according to the `coord_transform_fn`.

From 3e6a6e37b1b9a4c6ddb6e86ef316b407f9f1de47 Mon Sep 17 00:00:00 2001
From: James Bergstra <james.bergstra@gmail.com>
Date: Tue, 21 Aug 2012 16:55:08 -0400
Subject: [PATCH 12/16] ENH: stricter check on test_const_cval_out_of_range

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

diff --git a/skimage/transform/tests/test_warps.py b/skimage/transform/tests/test_warps.py
index 3cde47ac..226a0520 100644
--- a/skimage/transform/tests/test_warps.py
+++ b/skimage/transform/tests/test_warps.py
@@ -87,7 +87,7 @@ def test_swirl():
 def test_const_cval_out_of_range():
     img = np.random.randn(100, 100)
     warped = warp(img, AffineTransform(translation=(10, 10)), cval=-10)
-    assert np.any(warped < 0)
+    assert np.sum(warped < 0) == (2 * 100 * 10 - 10 * 10)
 
 
 def test_warp_identity():

From 8faf1489556649728be1a58fe2c38eef373e18ae Mon Sep 17 00:00:00 2001
From: James Bergstra <james.bergstra@gmail.com>
Date: Wed, 22 Aug 2012 09:08:14 -0400
Subject: [PATCH 13/16] FIX: wordwrap to 78

---
 skimage/transform/_geometric.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index d29baac0..ce2eb7b6 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -724,12 +724,14 @@ def warp_coords(orows, ocols, bands, coord_transform_fn,
 
     Notes
     -----
-    This is a lower-level routine that produces the source coordinates used by `warp()`.
+    This is a lower-level routine that produces the source coordinates used by
+    `warp()`.
 
-    It is provided separately from `warp` to give additional flexibility to users who would
-    like, for example, to re-use a particular coordinate mapping, to use specific dtypes at
-    various points along the the image-warping process, or to implement different
-    post-processing logic than `warp` performs after the call to `ndimage.map_coordinates`.
+    It is provided separately from `warp` to give additional flexibility to
+    users who would like, for example, to re-use a particular coordinate
+    mapping, to use specific dtypes at various points along the the
+    image-warping process, or to implement different post-processing logic
+    than `warp` performs after the call to `ndimage.map_coordinates`.
 
 
     Examples

From acc86a55084d23d7ef3c0b3b9bdf8f2b2ac38288 Mon Sep 17 00:00:00 2001
From: James Bergstra <james.bergstra@gmail.com>
Date: Wed, 22 Aug 2012 09:11:22 -0400
Subject: [PATCH 14/16] FIX: docstring mentions inverse instead of inverse_map

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

diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index ce2eb7b6..f83f65d1 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -710,7 +710,7 @@ def warp_coords(orows, ocols, bands, coord_transform_fn,
         number of output columns
     bands : int
         number of color bands (aka channels)
-    coord_transform_fn : callable like GeometricTransform.inverse_map
+    coord_transform_fn : callable like GeometricTransform.inverse
         Return input coordinates for given output coordinates
     dtype : np.dtype or string
         dtype for return value (sane choices: float32 or float64)

From 58bddb1cf2875b5c4a1ae74486ce43b8617706eb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Sch=C3=B6nberger?= <hannesschoenberger@gmail.com>
Date: Fri, 24 Aug 2012 00:05:53 +0200
Subject: [PATCH 15/16] Remove empty line

---
 skimage/transform/_geometric.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index f83f65d1..cec591a9 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -835,7 +835,6 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
     def coord_transform_fn(*args):
         return inverse_map(*args, **map_args)
 
-
     coords = warp_coords(rows, cols, bands, coord_transform_fn)
 
     # Prefilter not necessary for order 1 interpolation

From f750e633c8aad5b499a851b39855cdae7fb02634 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Sch=C3=B6nberger?= <hannesschoenberger@gmail.com>
Date: Fri, 24 Aug 2012 00:14:37 +0200
Subject: [PATCH 16/16] Fix test cases of warps

---
 skimage/transform/tests/test_warps.py | 50 ++++++++-------------------
 1 file changed, 15 insertions(+), 35 deletions(-)

diff --git a/skimage/transform/tests/test_warps.py b/skimage/transform/tests/test_warps.py
index 226a0520..ac241722 100644
--- a/skimage/transform/tests/test_warps.py
+++ b/skimage/transform/tests/test_warps.py
@@ -1,6 +1,6 @@
-import sys
 from numpy.testing import assert_array_almost_equal, run_module_suite
 import numpy as np
+from scipy.ndimage import map_coordinates
 
 from skimage.transform import (warp, warp_coords, fast_homography,
                                AffineTransform,
@@ -28,10 +28,10 @@ def test_homography():
     x = np.zeros((5, 5), dtype=np.uint8)
     x[1, 1] = 255
     x = img_as_float(x)
-    theta = -np.pi/2
-    M = np.array([[np.cos(theta),-np.sin(theta),0],
-                  [np.sin(theta), np.cos(theta),4],
-                  [0,             0,            1]])
+    theta = -np.pi / 2
+    M = np.array([[np.cos(theta), - np.sin(theta), 0],
+                  [np.sin(theta),   np.cos(theta), 4],
+                  [0,               0,             1]])
 
     x90 = warp(x,
             inverse_map=ProjectiveTransform(M).inverse,
@@ -40,7 +40,7 @@ def test_homography():
 
 
 def test_fast_homography():
-    img = rgb2gray(data.lena())
+    img = rgb2gray(data.lena()).astype(np.uint8)
     img = img[:, :100]
 
     theta = np.deg2rad(30)
@@ -71,10 +71,6 @@ def test_fast_homography():
 
 
 def test_swirl():
-    if not data.checkerboard().shape:
-        print >> sys.stderr, ('Failed to read image data.checkerboard()'
-                ' -- Skipping test_swirl')
-        return
     image = img_as_float(data.checkerboard())
 
     swirl_params = {'radius': 80, 'rotation': 0, 'order': 2, 'mode': 'reflect'}
@@ -91,41 +87,25 @@ def test_const_cval_out_of_range():
 
 
 def test_warp_identity():
-    lena = data.lena()
-    if not lena.shape:
-        print >> sys.stderr, ('Failed to read image data.lena()'
-                ' -- Skipping test_warp_identity')
-        return
-    lena = img_as_float(rgb2gray(lena))
+    lena = img_as_float(rgb2gray(data.lena()))
     assert len(lena.shape) == 2
-    assert np.allclose(lena,
-            warp(lena, AffineTransform(rotation=0)))
-    assert not np.allclose(lena,
-            warp(lena, AffineTransform(rotation=0.1)))
-
-    rgb_lena = np.transpose(
-            np.asarray([lena, np.zeros_like(lena), lena]),
-            (1, 2, 0))
+    assert np.allclose(lena, warp(lena, AffineTransform(rotation=0)))
+    assert not np.allclose(lena, warp(lena, AffineTransform(rotation=0.1)))
+    rgb_lena = np.transpose(np.asarray([lena, np.zeros_like(lena), lena]),
+                            (1, 2, 0))
     warped_rgb_lena = warp(rgb_lena, AffineTransform(rotation=0.1))
-
-    assert np.allclose(rgb_lena,
-            warp(rgb_lena, AffineTransform(rotation=0)))
+    assert np.allclose(rgb_lena, warp(rgb_lena, AffineTransform(rotation=0)))
     assert not np.allclose(rgb_lena, warped_rgb_lena)
     # assert no cross-talk between bands
     assert np.all(0 == warped_rgb_lena[:, :, 1])
 
 
 def test_warp_coords_example():
-    from skimage import data
-    from scipy.ndimage import map_coordinates
-    def shift_right(xy):
-        xy[:, 0] -= 10
-        return xy
-
     image = data.lena().astype(np.float32)
     assert 3 == image.shape[2]
-    coords = warp_coords(30, 30, 3, shift_right)
-    warped_image = map_coordinates(image[:, :, 0], coords[:2])
+    tform = SimilarityTransform(translation=(0, -10))
+    coords = warp_coords(30, 30, 3, tform)
+    warped_image1 = map_coordinates(image[:, :, 0], coords[:2])
 
 
 if __name__ == "__main__":