Fresh upstream release - includes slicing-error.patch freeimage-fix.patch

debian/changelog

@@ -1,3 +1,10 @@
+skimage (0.11.0-1) experimental; urgency=medium
+
+  * Fresh upstream release
+    - includes slicing-error.patch freeimage-fix.patch
+
+ -- Yaroslav Halchenko <debian@onerussian.com>  Thu, 05 Mar 2015 08:32:02 -0500
+
 skimage (0.10.1-2) unstable; urgency=medium
 
   * build with -fsigned-char to fix test failures on unsigned ports

debian/patches/freeimage-fix.patch

@@ -1,77 +0,0 @@
-Author: Stefan van der Walt <stefan@sun.ac.za>
-Description: freeimage: Correctly handle saving uint16 images and fix big endian
-
-Origin: 2b1dde20 051c54c577b3 84f3835106aaeb
-Applied-Upstream: 0.11
---- a/skimage/io/_plugins/freeimage_plugin.py
-+++ b/skimage/io/_plugins/freeimage_plugin.py
-@@ -493,7 +493,6 @@ def _array_from_bitmap(bitmap):
-     # swizzle the color components and flip the scanlines to go from
-     # FreeImage's BGR[A] and upside-down internal memory format to something
-     # more normal
--
-     def n(arr):
-         return arr[..., ::-1].T
-     if len(shape) == 3 and _FI.FreeImage_IsLittleEndian() and \
-@@ -637,17 +636,28 @@ def _array_to_bitmap(array):
-         raise RuntimeError('Could not allocate image for storage')
-     try:
-         def n(arr):  # normalise to freeimage's in-memory format
--            return arr.T[:, ::-1]
-+            return arr.T[..., ::-1]
-+
-         wrapped_array = _wrap_bitmap_bits_in_array(bitmap, w_shape, dtype)
-         # swizzle the color components and flip the scanlines to go to
-         # FreeImage's BGR[A] and upside-down internal memory format
--        if len(shape) == 3 and _FI.FreeImage_IsLittleEndian() and \
--               dtype.type == numpy.uint8:
--            wrapped_array[0] = n(array[:, :, 2])
--            wrapped_array[1] = n(array[:, :, 1])
--            wrapped_array[2] = n(array[:, :, 0])
-+        if len(shape) == 3 and _FI.FreeImage_IsLittleEndian():
-+            R = array[:, :, 0]
-+            G = array[:, :, 1]
-+            B = array[:, :, 2]
-+
-+            if dtype.type == numpy.uint8:
-+                wrapped_array[0] = n(B)
-+                wrapped_array[1] = n(G)
-+                wrapped_array[2] = n(R)
-+            elif dtype.type == numpy.uint16:
-+                wrapped_array[0] = n(R)
-+                wrapped_array[1] = n(G)
-+                wrapped_array[2] = n(B)
-+
-             if shape[2] == 4:
--                wrapped_array[3] = n(array[:, :, 3])
-+                A = array[:, :, 3]
-+                wrapped_array[3] = n(A)
-         else:
-             wrapped_array[:] = n(array)
-         if len(shape) == 2 and dtype.type == numpy.uint8:
-diff --git a/skimage/io/tests/test_freeimage.py b/skimage/io/tests/test_freeimage.py
-index 32e01bd..308f1ee 100644
---- a/skimage/io/tests/test_freeimage.py
-+++ b/skimage/io/tests/test_freeimage.py
-@@ -74,15 +74,15 @@ class TestSave:
-         f.close()
-         sio.imsave(fname, x)
-         y = sio.imread(fname)
--        assert_array_equal(x, y)
-+        assert_array_equal(y, x)
- 
-     @skipif(not FI_available)
-     def test_imsave_roundtrip(self):
-         for shape, dtype, format in [
-               [(10, 10), (np.uint8, np.uint16), ('tif', 'png')],
-               [(10, 10), (np.float32,), ('tif',)],
--              [(10, 10, 3), (np.uint8,), ('png',)],
--              [(10, 10, 4), (np.uint8,), ('png',)]
-+              [(10, 10, 3), (np.uint8, np.uint16), ('png',)],
-+              [(10, 10, 4), (np.uint8, np.uint16), ('png',)]
-             ]:
-             tests = [(d, f) for d in dtype for f in format]
-             for d, f in tests:
--- 
-1.9.1
-

debian/patches/series

@@ -1,5 +1,3 @@
 search-html.patch
 fix-doc-links.patch
 doc-privacy.patch
-slicing-error.patch
-freeimage-fix.patch

debian/patches/slicing-error.patch

@@ -1,19 +0,0 @@
-Description: Fix slicing error revealed by numpy 1.9.0.
- Numpy 1.9.0 no longer allows oversize data to be assigned to a
- boolean indexed 1-d array by discarding excess elements.
-Author: Charles Harris <charlesr.harris@gmail.com>
-Origin: 7a074d5dd165536cb05fd87ea94a29510edac1a7
-Date: Fri, 4 Jul 2014 20:04:32 -0600
-Bug: https://github.com/scikit-image/scikit-image/issues/1050
-
---- a/skimage/segmentation/_join.py
-+++ b/skimage/segmentation/_join.py
-@@ -124,7 +124,7 @@ def relabel_sequential(label_field, offs
-     if m == len(labels0):  # nothing to do, already 1...n labels
-         return label_field, labels, labels
-     forward_map = np.zeros(m + 1, int)
--    forward_map[labels0] = np.arange(offset, offset + len(labels0) + 1)
-+    forward_map[labels0] = np.arange(offset, offset + len(labels0))
-     if not (labels == 0).any():
-         labels = np.concatenate(([0], labels))
-     inverse_map = np.zeros(offset - 1 + len(labels), dtype=np.intp)