Merge pull request #1498 from cgohlke/patch-2

Fix skimage.io.imread returns incorrect dimensions

skimage/io/_io.py

@@ -53,8 +53,16 @@ def imread(fname, as_grey=False, plugin=None, flatten=None,
     with file_or_url_context(fname) as fname:
         img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
 
-    if as_grey and getattr(img, 'ndim', 0) >= 3:
-        img = rgb2grey(img)
+    if not hasattr(img, 'ndim'):
+        return img
+
+    if img.ndim > 2:
+        if img.shape[-1] not in (3, 4) and img.shape[-3] in (3, 4):
+            img = np.swapaxes(img, -1, -3)
+            img = np.swapaxes(img, -2, -3)
+
+        if as_grey:
+            img = rgb2grey(img)
 
     return img
 

skimage/io/tests/test_imread.py

@@ -1,3 +1,4 @@
+import os
 import os.path
 import numpy as np
 from numpy.testing import *
@@ -60,6 +61,20 @@ def test_bilevel():
     assert_array_equal(img.astype(bool), expected)
 
 
+@skipif(not imread_available)
+def test_imread_separate_channels():
+    # Test that imread returns RGBA values contiguously even when they are
+    # stored in separate planes.
+    x = np.random.rand(3, 16, 8)
+    f = NamedTemporaryFile(suffix='.tif')
+    fname = f.name
+    f.close()
+    imsave(fname, x, plugin='tifffile')
+    img = imread(fname, plugin='tifffile')
+    os.remove(fname)
+    assert img.shape == (16, 8, 3), img.shape
+
+
 class TestSave:
     def roundtrip(self, x, scaling=1):
         f = NamedTemporaryFile(suffix='.png')