From 3c8bf02fa5a9749f5de1bc4bbd6b2e2abb7d1a25 Mon Sep 17 00:00:00 2001
From: Christoph Gohlke <cgohlke@uci.edu>
Date: Thu, 7 May 2015 15:03:25 -0700
Subject: [PATCH 1/4] Fix skimage.io.imread returns incorrect dimensions

Fixes #1496
---
 skimage/io/_io.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index 2f957ac2..f8305aaf 100644
--- a/skimage/io/_io.py
+++ b/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, -1, -2)
+
+        if as_grey:
+            img = rgb2grey(img)
 
     return img
 

From 47cfcb4b8b2cf4cd483427b5d1aaddee1fe74119 Mon Sep 17 00:00:00 2001
From: Christoph Gohlke <cgohlke@uci.edu>
Date: Thu, 7 May 2015 15:07:59 -0700
Subject: [PATCH 2/4] TST skimage.io.imread returns incorrect dimensions

---
 skimage/io/tests/test_imread.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/skimage/io/tests/test_imread.py b/skimage/io/tests/test_imread.py
index 759e8c67..4f172ebb 100644
--- a/skimage/io/tests/test_imread.py
+++ b/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.zeros((3, 16, 8), np.uint8)
+    f = NamedTemporaryFile(suffix='.tif')
+    fname = f.name
+    f.close()
+    imsave(fname, x, plugin='tifffile')
+    img = imread(fname)
+    os.remove(fname)
+    assert img.shape == (16, 8, 3), img.shape
+
+
 class TestSave:
     def roundtrip(self, x, scaling=1):
         f = NamedTemporaryFile(suffix='.png')

From 3d3351b9faaee80b9c848171e6933cecde069343 Mon Sep 17 00:00:00 2001
From: Christoph Gohlke <cgohlke@uci.edu>
Date: Thu, 7 May 2015 17:34:05 -0700
Subject: [PATCH 3/4] Fix failing test

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

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index f8305aaf..8dbc3600 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -59,7 +59,7 @@ def imread(fname, as_grey=False, plugin=None, flatten=None,
     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, -1, -2)
+            img = np.swapaxes(img, -2, -3)
 
         if as_grey:
             img = rgb2grey(img)

From 549def734eaf6de2c0bd9929b83bdf9a9469d55c Mon Sep 17 00:00:00 2001
From: Christoph Gohlke <cgohlke@uci.edu>
Date: Thu, 7 May 2015 17:35:48 -0700
Subject: [PATCH 4/4] Fix failing test

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

diff --git a/skimage/io/tests/test_imread.py b/skimage/io/tests/test_imread.py
index 4f172ebb..c8d380a5 100644
--- a/skimage/io/tests/test_imread.py
+++ b/skimage/io/tests/test_imread.py
@@ -65,12 +65,12 @@ def test_bilevel():
 def test_imread_separate_channels():
     # Test that imread returns RGBA values contiguously even when they are
     # stored in separate planes.
-    x = np.zeros((3, 16, 8), np.uint8)
+    x = np.random.rand(3, 16, 8)
     f = NamedTemporaryFile(suffix='.tif')
     fname = f.name
     f.close()
     imsave(fname, x, plugin='tifffile')
-    img = imread(fname)
+    img = imread(fname, plugin='tifffile')
     os.remove(fname)
     assert img.shape == (16, 8, 3), img.shape