Merge pull request #1744 from blink1073/always-use-tiff

Move tiff-file handling to top level

skimage/io/_io.py

@@ -26,7 +26,10 @@ def imread(fname, as_grey=False, plugin=None, flatten=None,
         If True, convert color images to grey-scale (32-bit floats).
         Images that are already in grey-scale format are not converted.
     plugin : str
-        Name of plugin to use (Python Imaging Library by default).
+        Name of plugin to use.  By default, the different plugins are
+        tried (starting with the Python Imaging Library) until a suitable
+        candidate is found.  If not given and fname is a tiff file, the
+        tifffile plugin will be used.
 
     Other Parameters
     ----------------
@@ -50,6 +53,10 @@ def imread(fname, as_grey=False, plugin=None, flatten=None,
     if flatten is not None:
         as_grey = flatten
 
+    if plugin is None and hasattr(fname, 'lower'):
+        if fname.lower().endswith(('.tiff', '.tif')):
+            plugin = 'tifffile'
+
     with file_or_url_context(fname) as fname:
         img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
 
@@ -109,7 +116,8 @@ def imsave(fname, arr, plugin=None, **plugin_args):
     plugin : str
         Name of plugin to use.  By default, the different plugins are
         tried (starting with the Python Imaging Library) until a suitable
-        candidate is found.
+        candidate is found.  If not given and fname is a tiff file, the
+        tifffile plugin will be used.
 
     Other parameters
     ----------------
@@ -117,6 +125,9 @@ def imsave(fname, arr, plugin=None, **plugin_args):
         Passed to the given plugin.
 
     """
+    if plugin is None and hasattr(fname, 'lower'):
+        if fname.lower().endswith(('.tiff', '.tif')):
+            plugin = 'tifffile'
     if is_low_contrast(arr):
         warnings.warn('%s is a low contrast image' % fname)
     return call_plugin('imsave', fname, arr, plugin=plugin, **plugin_args)

skimage/io/_plugins/pil_plugin.py

@@ -5,7 +5,6 @@ from six import string_types
 from PIL import Image
 
 from ...util import img_as_ubyte, img_as_uint
-from .tifffile_plugin import imread as tif_imread, imsave as tif_imsave
 
 
 def imread(fname, dtype=None, img_num=None, **kwargs):
@@ -21,28 +20,17 @@ def imread(fname, dtype=None, img_num=None, **kwargs):
        Specifies which image to read in a file with multiple images
        (zero-indexed).
     kwargs : keyword pairs, optional
-        Addition keyword arguments to pass through (only applicable to Tiff
-        files for now,  see `tifffile`'s `imread` function).
+        Addition keyword arguments to pass through.
 
     Notes
     -----
-    Tiff files are handled by Christophe Golhke's tifffile.py [1]_, and support
-    many advanced image types including multi-page and floating point.
-
-    All other files are read using the Python Imaging Libary.
-    See PIL docs [2]_ for a list of supported formats.
+    Files are read using the Python Imaging Libary.
+    See PIL docs [1]_ for a list of supported formats.
 
     References
     ----------
-    .. [1] http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html
-    .. [2] http://pillow.readthedocs.org/en/latest/handbook/image-file-formats.html
-
+    .. [1] http://pillow.readthedocs.org/en/latest/handbook/image-file-formats.html
     """
-    if hasattr(fname, 'lower') and dtype is None:
-        kwargs.setdefault('key', img_num)
-        if fname.lower().endswith(('.tiff', '.tif')):
-            return tif_imread(fname, **kwargs)
-
     if isinstance(fname, string_types):
         with open(fname, 'rb') as f:
             im = Image.open(f)
@@ -234,12 +222,8 @@ def imsave(fname, arr, format_str=None, **kwargs):
 
     Notes
     -----
-    Tiff files are handled by Christophe Golhke's tifffile.py [1]_,
-    and support many advanced image types including multi-page and
-    floating point.
-
-    All other image formats use the Python Imaging Libary.
-    See PIL docs [2]_ for a list of other supported formats.
+    Use the Python Imaging Libary.
+    See PIL docs [1]_ for a list of other supported formats.
     All images besides single channel PNGs are converted using `img_as_uint8`.
     Single Channel PNGs have the following behavior:
     - Integer values in [0, 255] and Boolean types -> img_as_uint8
@@ -247,8 +231,7 @@ def imsave(fname, arr, format_str=None, **kwargs):
 
     References
     ----------
-    .. [1] http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html
-    .. [2] http://pillow.readthedocs.org/en/latest/handbook/image-file-formats.html
+    .. [1] http://pillow.readthedocs.org/en/latest/handbook/image-file-formats.html
     """
     # default to PNG if file-like object
     if not isinstance(fname, string_types) and format_str is None:
@@ -263,18 +246,6 @@ def imsave(fname, arr, format_str=None, **kwargs):
     if arr.dtype.kind == 'b':
         arr = arr.astype(np.uint8)
 
-    use_tif = False
-    if hasattr(fname, 'lower'):
-        if fname.lower().endswith(('.tiff', '.tif')):
-            use_tif = True
-    if format_str is not None:
-        if format_str.lower() in ['tiff', 'tif']:
-            use_tif = True
-
-    if use_tif:
-        tif_imsave(fname, arr, **kwargs)
-        return
-
     if arr.ndim not in (2, 3):
         raise ValueError("Invalid shape for image array: %s" % arr.shape)
 

skimage/io/_plugins/tifffile_plugin.py

@@ -24,6 +24,8 @@ def imread(fname, dtype=None, **kwargs):
     .. [1] http://www.lfd.uci.edu/~gohlke/code/tifffile.py
 
     """
+    if 'img_num' in kwargs:
+        kwargs['key'] = kwargs.pop('img_num')
     with open(fname, 'rb') as f:
         tif = TiffFile(f)
         return tif.asarray(**kwargs)

skimage/io/tests/test_pil.py

@@ -196,7 +196,6 @@ def test_all_color():
 
 def test_all_mono():
     mono_check('pil')
-    mono_check('pil', 'tiff')
 
 
 def test_multi_page_gif():
@@ -234,35 +233,5 @@ def test_cmyk():
         sim = ssim(refi, newi, dynamic_range=refi.max() - refi.min())
         assert sim > 0.99
 
-
-class TestSaveTIF:
-    def roundtrip(self, dtype, x, compress):
-        with temporary_file(suffix='.tif') as fname:
-            if dtype == np.bool:
-                expected = ['low contrast']
-            else:
-                expected = ['\A\Z']
-            with expected_warnings(expected):
-                if compress > 0:
-                    imsave(fname, x, compress=compress)
-                else:
-                    imsave(fname, x)
-            y = 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.int16, np.float32,
-                          np.float64, np.bool):
-                for compress in [0, 2]:
-                    x = np.random.rand(*shape)
-
-                    if not np.issubdtype(dtype, float) and \
-                                                        not dtype == np.bool:
-                        x = (x * np.iinfo(dtype).max).astype(dtype)
-                    else:
-                        x = x.astype(dtype)
-                    yield self.roundtrip, dtype, x, compress
-
 if __name__ == "__main__":
     run_module_suite()