Clean up tests and add to bento.info.

Remove "no plugin" test because we will always have a plugin.

Fix handling of bools in ubyte check

Fix integration of tifffile.c

Clean up new tests.

Fix _tifffile import and add to bento.info

Add tifffile.py and fix pil_plugin import

Add tifffile tests to test_pil and remove PIL import checks

bento.info

@@ -157,6 +157,9 @@ Library:
     Extension: skimage.graph._ncut_cy
         Sources:
             skimage/graph/_ncut_cy.pyx
+    Extension: skimage.io._plugins._tifffile
+        Sources:
+            skimage/io/_plugins/tifffile.c
 
 Executable: skivi
     Module: skimage.scripts.skivi

skimage/io/_plugins/pil_plugin.py

@@ -14,7 +14,7 @@ except ImportError:
 from skimage.util import img_as_ubyte, img_as_uint, img_as_int
 
 from six import string_types
-from tifffile import imread as tif_imread, imsave as tif_imsave
+from .tifffile import imread as tif_imread, imsave as tif_imsave
 
 
 def imread(fname, dtype=None):
@@ -29,13 +29,9 @@ def imread(fname, dtype=None):
 
 
     """
-    if hasattr(fname, 'name'):
-        name = fname.name.lower()
-    else:
-        name = fname.lower()
-
-    if name.endswith(('.tiff', '.tif')) and dtype is None:
-        return tif_imread(fname)
+    if hasattr(fname, 'lower') and dtype is None:
+        if fname.lower().endswith(('.tiff', '.tif')):
+            return tif_imread(fname)
 
     im = Image.open(fname)
     try:
@@ -185,12 +181,15 @@ def imsave(fname, arr, format_str=None):
     if arr.dtype.kind == 'b':
         arr = arr.astype(np.uint8)
 
-    if hasattr(fname, 'name'):
-        name = fname.name.lower()
-    else:
-        name = fname.lower()
+    use_tif = False
+    if hasattr(fname, 'lower'):
+        if fname.lower().endswith(('.tiff', '.tif')):
+            use_tif = True
+    if not format_str is None:
+        if format_str.lower() in ['tiff', 'tif']:
+            use_tif = True
 
-    if name.endswith(('.tiff', '.tif')):
+    if use_tif:
         tif_imsave(fname, arr)
 
     else:

skimage/io/tests/test_io.py

@@ -29,17 +29,5 @@ def test_imread_url():
     assert image.shape == (512, 512)
 
 
-@raises(RuntimeError)
-def test_imread_no_plugin():
-    # tweak data path so that file URI works on both unix and windows.
-    image_path = os.path.join(data_dir, 'lena.png')
-    plugins = plugin_store['imread']
-    plugin_store['imread'] = []
-    try:
-        io.imread(image_path)
-    finally:
-        plugin_store['imread'] = plugins
-
-
 if __name__ == "__main__":
     run_module_suite()

skimage/io/tests/test_pil.py

@@ -8,19 +8,13 @@ from tempfile import NamedTemporaryFile
 from skimage import data_dir
 from skimage.io import (imread, imsave, use_plugin, reset_plugins,
                         Image as ioImage)
-from skimage.io.test.utils import ubyte_check, full_range_check
+from skimage.io.tests.utils import ubyte_check, full_range_check
 
 from six import BytesIO
 
-
-try:
-    from PIL import Image
-    from skimage.io._plugins.pil_plugin import pil_to_ndarray, ndarray_to_pil, _palette_is_grayscale
-    use_plugin('pil')
-except ImportError:
-    PIL_available = False
-else:
-    PIL_available = True
+from PIL import Image
+from skimage.io._plugins.pil_plugin import pil_to_ndarray, ndarray_to_pil, _palette_is_grayscale
+use_plugin('pil')
 
 np.random.seed(0)
 
@@ -40,8 +34,6 @@ def setup_module(self):
         pass
 
 
-
-@skipif(not PIL_available)
 def test_imread_flatten():
     # a color image is flattened
     img = imread(os.path.join(data_dir, 'color.png'), flatten=True)
@@ -52,7 +44,6 @@ def test_imread_flatten():
     assert np.sctype2char(img.dtype) in np.typecodes['AllInteger']
 
 
-@skipif(not PIL_available)
 def test_imread_palette():
     img = imread(os.path.join(data_dir, 'palette_gray.png'))
     assert img.ndim == 2
@@ -60,7 +51,6 @@ def test_imread_palette():
     assert img.ndim == 3
 
 
-@skipif(not PIL_available)
 def test_palette_is_gray():
     gray = Image.open(os.path.join(data_dir, 'palette_gray.png'))
     assert _palette_is_grayscale(gray)
@@ -68,7 +58,6 @@ def test_palette_is_gray():
     assert not _palette_is_grayscale(color)
 
 
-@skipif(not PIL_available)
 def test_bilevel():
     expected = np.zeros((10, 10))
     expected[::2] = 255
@@ -77,7 +66,6 @@ def test_bilevel():
     assert_array_equal(img, expected)
 
 
-@skipif(not PIL_available)
 def test_imread_uint16():
     expected = np.load(os.path.join(data_dir, 'chessboard_GRAY_U8.npy'))
     img = imread(os.path.join(data_dir, 'chessboard_GRAY_U16.tif'))
@@ -85,7 +73,6 @@ def test_imread_uint16():
     assert_array_almost_equal(img, expected)
 
 
-@skipif(not PIL_available)
 def test_repr_png():
     img_path = os.path.join(data_dir, 'camera.png')
     original_img = ioImage(imread(img_path))
@@ -98,14 +85,12 @@ def test_repr_png():
 
     assert np.all(original_img == round_trip)
 
-@skipif(not PIL_available)
+
 def test_imread_truncated_jpg():
     assert_raises((IOError, ValueError), imread,
                   os.path.join(data_dir, 'truncated.jpg'))
 
-# Big endian images not correctly loaded for PIL < 1.1.7
-# Renable test when PIL 1.1.7 is more common.
-@skipif(True)
+
 def test_imread_uint16_big_endian():
     expected = np.load(os.path.join(data_dir, 'chessboard_GRAY_U8.npy'))
     img = imread(os.path.join(data_dir, 'chessboard_GRAY_U16B.tif'))
@@ -141,11 +126,9 @@ class TestSave:
                     x = (x * 255).astype(dtype)
                     yield self.verify_roundtrip, dtype, x, roundtrip_function(x)
 
-    @skipif(not PIL_available)
     def test_imsave_roundtrip_file(self):
          self.verify_imsave_roundtrip(self.roundtrip_file)
 
-    @skipif(not PIL_available)
     def test_imsave_roundtrip_pil_image(self):
          self.verify_imsave_roundtrip(self.roundtrip_pil_image)
 
@@ -175,17 +158,35 @@ def test_imexport_imimport():
     assert out.shape == shape
 
 
-@skip(not PIL_available)
-def test_all_color(self):
+@skipif(not PIL_available)
+def test_all_color():
     ubyte_check('pil')
     ubyte_check('pil', 'bmp')
 
 
-@skip(not PIL_available)
-def test_all_mono(self):
+@skipif(not PIL_available)
+def test_all_mono():
     full_range_check('pil')
     full_range_check('pil', 'tiff')
 
 
+class TestSaveTIF:
+    def roundtrip(self, dtype, x):
+        f = NamedTemporaryFile(suffix='.tif')
+        fname = f.name
+        f.close()
+        sio.imsave(fname, x)
+        y = sio.imread(fname)
+        assert_array_equal(x, y)
+
+    def test_imsave_roundtrip(self):
+        for shape in [(10, 10), (10, 10, 3), (10, 10, 4)]:
+            for dtype in (np.uint8, np.uint16, np.float32, np.float64):
+                x = np.ones(shape, dtype=dtype) * np.random.rand(*shape)
+
+                if not np.issubdtype(dtype, float):
+                    x = (x * 255).astype(dtype)
+                yield self.roundtrip, dtype, x
+
 if __name__ == "__main__":
     run_module_suite()

skimage/io/tests/utils.py

@@ -29,7 +29,7 @@ def ubyte_check(plugin, fmt='png'):
 
     img2 = img > 128
     r2 = roundtrip(img2, plugin, fmt)
-    testing.assert_allclose(img2, img_as_bool(r2))
+    testing.assert_allclose(img2.astype(np.uint8), r2)
 
     img3 = img_as_float(img)
     r3 = roundtrip(img3, plugin, fmt)