Merge pull request #1604 from blink1073/pil-close

FIX: Do not let PIL manage the file handle.

skimage/_shared/testing.py

@@ -93,8 +93,8 @@ def roundtrip(img, plugin, suffix):
     if not '.' in suffix:
         suffix = '.' + suffix
     temp_file = NamedTemporaryFile(suffix=suffix, delete=False)
-    temp_file.close()
     fname = temp_file.name
+    temp_file.close()
     io.imsave(fname, img, plugin=plugin)
     new = io.imread(fname, plugin=plugin)
     try:
@@ -119,7 +119,7 @@ def color_check(plugin, fmt='png'):
     testing.assert_allclose(img2.astype(np.uint8), r2)
 
     img3 = img_as_float(img)
-    with expected_warnings(['precision loss|unclosed file']):
+    with expected_warnings(['precision loss']):
         r3 = roundtrip(img3, plugin, fmt)
     testing.assert_allclose(r3, img)
 
@@ -131,12 +131,12 @@ def color_check(plugin, fmt='png'):
             r4 = roundtrip(img4, plugin, fmt)
         testing.assert_allclose(r4, img4)
     else:
-        with expected_warnings(['sign loss|precision loss|unclosed file']):
+        with expected_warnings(['sign loss|precision loss']):
             r4 = roundtrip(img4, plugin, fmt)
             testing.assert_allclose(r4, img_as_ubyte(img4))
 
     img5 = img_as_uint(img)
-    with expected_warnings(['precision loss|unclosed file']):
+    with expected_warnings(['precision loss']):
         r5 = roundtrip(img5, plugin, fmt)
     testing.assert_allclose(r5, img)
 
@@ -156,14 +156,14 @@ def mono_check(plugin, fmt='png'):
     testing.assert_allclose(img2.astype(np.uint8), r2)
 
     img3 = img_as_float(img)
-    with expected_warnings(['precision|unclosed file|\A\Z']):
+    with expected_warnings(['precision|\A\Z']):
         r3 = roundtrip(img3, plugin, fmt)
     if r3.dtype.kind == 'f':
         testing.assert_allclose(img3, r3)
     else:
         testing.assert_allclose(r3, img_as_uint(img))
 
-    with expected_warnings(['precision loss|unclosed file']):
+    with expected_warnings(['precision loss']):
         img4 = img_as_int(img)
     if fmt.lower() in (('tif', 'tiff')):
         img4 -= 100
@@ -171,7 +171,7 @@ def mono_check(plugin, fmt='png'):
             r4 = roundtrip(img4, plugin, fmt)
         testing.assert_allclose(r4, img4)
     else:
-        with expected_warnings(['precision loss|sign loss|unclosed file']):
+        with expected_warnings(['precision loss|sign loss']):
             r4 = roundtrip(img4, plugin, fmt)
             testing.assert_allclose(r4, img_as_uint(img4))
 

skimage/io/_plugins/pil_plugin.py

@@ -5,7 +5,7 @@ from six import string_types
 from PIL import Image
 
 from ...util import img_as_ubyte, img_as_uint
-from ...external.tifffile import imread as tif_imread, imsave as tif_imsave
+from .tifffile_plugin import imread as tif_imread, imsave as tif_imsave
 
 
 def imread(fname, dtype=None, img_num=None, **kwargs):
@@ -13,8 +13,8 @@ def imread(fname, dtype=None, img_num=None, **kwargs):
 
     Parameters
     ----------
-    fname : str
-       File name.
+    fname : str or file
+       File name or file-like-object.
     dtype : numpy dtype object or string specifier
        Specifies data type of array elements.
     img_num : int, optional
@@ -43,18 +43,12 @@ def imread(fname, dtype=None, img_num=None, **kwargs):
         if fname.lower().endswith(('.tiff', '.tif')):
             return tif_imread(fname, **kwargs)
 
-    im = Image.open(fname)
-    try:
-        # this will raise an IOError if the file is not readable
-        im.getdata()[0]
-    except IOError as e:
-        site = "http://pillow.readthedocs.org/en/latest/installation.html#external-libraries"
-        pillow_error_message = str(e)
-        error_message = ('Could not load "%s" \n'
-            'Reason: "%s"\n'
-            'Please see documentation at: %s') % (fname, pillow_error_message, site)
-        raise ValueError(error_message)
+    if isinstance(fname, string_types):
+        with open(fname, 'rb') as f:
+            im = Image.open(f)
+            return pil_to_ndarray(im, dtype=dtype, img_num=img_num)
     else:
+        im = Image.open(fname)
         return pil_to_ndarray(im, dtype=dtype, img_num=img_num)
 
 
@@ -66,6 +60,17 @@ def pil_to_ndarray(im, dtype=None, img_num=None):
     Refer to ``imread``.
 
     """
+    try:
+        # this will raise an IOError if the file is not readable
+        im.getdata()[0]
+    except IOError as e:
+        site = "http://pillow.readthedocs.org/en/latest/installation.html#external-libraries"
+        pillow_error_message = str(e)
+        error_message = ('Could not load "%s" \n'
+            'Reason: "%s"\n'
+            'Please see documentation at: %s'
+             % (im.filename, pillow_error_message, site))
+        raise ValueError(error_message)
     frames = []
     grayscale = None
     i = 0

skimage/io/_plugins/tifffile_plugin.py

@@ -1 +1,28 @@
-from ...external.tifffile import imread, imsave
+from ...external.tifffile import TiffFile, imsave
+
+
+def imread(fname, dtype=None, **kwargs):
+    """Load a tiff image from file.
+
+    Parameters
+    ----------
+    fname : str or file
+       File name or file-like-object.
+    dtype : numpy dtype object or string specifier
+       Specifies data type of array elements (Not currently used).
+    kwargs : keyword pairs, optional
+        Addition keyword arguments to pass through (see `tifffile`'s `imread` function).
+
+    Notes
+    -----
+    Provided by Christophe Golhke's tifffile.py [1]_, and supports many
+    advanced image types including multi-page and floating point.
+
+    References
+    ----------
+    .. [1] http://www.lfd.uci.edu/~gohlke/code/tifffile.py
+
+    """
+    with open(fname, 'rb') as f:
+        tif = TiffFile(f)
+        return tif.asarray(**kwargs)

skimage/io/collection.py

@@ -199,8 +199,9 @@ class ImageCollection(object):
         index = []
         for fname in self._files:
             if fname.lower().endswith(('.tiff', '.tif')):
-                img = TiffFile(fname)
-                index += [(fname, i) for i in range(len(img.pages))]
+                with open(fname, 'rb') as f:
+                    img = TiffFile(f)
+                    index += [(fname, i) for i in range(len(img.pages))]
             else:
                 try:
                     im = Image.open(fname)

skimage/io/tests/test_pil.py

@@ -160,7 +160,7 @@ def test_imsave_filelike():
     s = BytesIO()
 
     # save to file-like object
-    with expected_warnings(['precision loss|unclosed file',
+    with expected_warnings(['precision loss',
                             'is a low contrast image']):
         imsave(s, image)
 
@@ -230,9 +230,9 @@ class TestSaveTIF:
     def roundtrip(self, dtype, x, compress):
         with temporary_file(suffix='.tif') as fname:
             if dtype == np.bool:
-                expected = ['low contrast|unclosed file']
+                expected = ['low contrast']
             else:
-                expected = ['unclosed file|\A\Z']
+                expected = ['\A\Z']
             with expected_warnings(expected):
                 if compress > 0:
                     imsave(fname, x, compress=compress)