SimpleITK and PIL tests are testing with tifffile

[lagru]

Description:

If plugin=None (default) and a path ending in .tif are passed to skimage.io.imread the plugin order is ignored because of these lines

scikit-image/skimage/io/_io.py

Lines 54 to 56 in f4c1b34

	if plugin is None and hasattr(fname, 'lower'):
	if fname.lower().endswith(('.tiff', '.tif')):
	plugin = 'tifffile'

This looks like unintended behavior at a first glance. Because at least one test in test_pil.py is "secretly" using tifffile's imread. The autofixture calling and setting the plugin order via use_plugin("pil") has no effect here.

Forcing the correct plugin with plugin="pil" in this line will make the test fail because of the wrong dtype >u2 (big) were apparently <u2 (little) is expected? I'm not sure if this is the original intention of the test...

Test output

def test_imread_uint16_big_endian():
        expected = np.load(fetch('data/chessboard_GRAY_U8.npy'))
        img = imread(fetch('data/chessboard_GRAY_U16B.tif'), plugin="pil")
>       assert img.dtype == np.uint16
E       AssertionError: assert dtype('>u2') == <class 'numpy.uint16'>
E        +  where dtype('>u2') = array([[255, 255, 255, ...,   0,   0,   0],\n       [255, 255, 255, ...,   0,   0,   0],\n       [255, 255, 255, ...,   0,   0,   0],\n       ...,\n       [  0,   0,   0, ..., 255, 255, 255],\n       [  0,   0,   0, ..., 255, 255, 255],\n       [  0,   0,   0, ..., 255, 255, 255]], dtype='>u2').dtype
E        +  and   <class 'numpy.uint16'> = np.uint16

skimage/io/tests/test_pil.py:171: AssertionError

Putting a raise in tifffile's imread shows that the following tests use the wrong plugin:

FAILED test_pil.py::test_imread_separate_channels[False] - RuntimeError
FAILED test_pil.py::test_imread_separate_channels[True] - RuntimeError
FAILED test_pil.py::test_imread_multipage_rgb_tif - RuntimeError
FAILED test_pil.py::test_imread_uint16 - RuntimeError
FAILED test_pil.py::test_imread_uint16_big_endian - RuntimeError
FAILED test_simpleitk.py::test_imread_uint16 - RuntimeError
FAILED test_simpleitk.py::test_imread_uint16_big_endian - RuntimeError