Deprecate skimage.io

.github/workflows/docs.yaml

@@ -11,7 +11,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Install Python dependencies
-        run: pip install ipython numpydoc pytest scikit-image sphinx sphinx-copybutton sphinx-rtd-theme
+        run: pip install ipython numpydoc pytest imageio sphinx sphinx-copybutton sphinx-rtd-theme
 
       - name: Install pims
         run: python -m pip install -v .

.github/workflows/tests.yaml

@@ -32,7 +32,7 @@ jobs:
         set -vxeuo pipefail
         python -m pip install -v .
         if [[ ${{ matrix.optional-deps }} = extras ]]; then
-          python -mpip install av jinja2 jpype1 matplotlib moviepy scikit-image tifffile
+          python -mpip install av jinja2 jpype1 matplotlib moviepy imageio tifffile
         fi
         python -m pip install coverage pytest
         python -m pip list

doc/source/install.rst

@@ -10,6 +10,7 @@ PIMS is easy to install on Windows, OSX, or Linux. Its dependencies are:
 
 For basic image reading one of the following is required:
 
+* `imageio <https://imageio.github.io/>`_
 * `scikit-image <http://scikit-image.org/>`_
 * `matplotlib <http://matplotlib.org/>`_
 

environment.yml

@@ -7,7 +7,6 @@ dependencies:
 - slicerator
 - pillow
 - matplotlib
-- scikit-image
 - jinja2
 - av
 - tifffile

pims/image_reader.py

@@ -4,16 +4,15 @@
 from pims.frame import Frame
 
 try:
-    from skimage.io import imread
-except ImportError:
     try:
         from imageio import v2 as iio
     except ImportError:
         import imageio as iio
 
     def imread(*args, **kwargs):  # Strip metadata for consistency.
         return np.asarray(iio.imread(*args, **kwargs))
-
+except ImportError:
+    from skimage.io import imread
 
 class ImageReader(FramesSequence):
     """Reads a single image into a length-1 reader.

pims/image_sequence.py

@@ -27,7 +27,7 @@ class ImageSequence(FramesSequence):
         which will ignore extraneous files or a list of files to open
         in the order they should be loaded. When a path to a zipfile is
         specified, all files in the zipfile will be loaded.
-    plugin : string
+    plugin : string, optional, deprecated
         Passed on to skimage.io.imread if scikit-image is available.
         If scikit-image is not available, this will be ignored and a warning
         will be issued. Not available in combination with zipfiles.
@@ -51,15 +51,15 @@ class ImageSequence(FramesSequence):
     >>> frame_count = len(video) # Number of frames in video
     >>> frame_shape = video.frame_shape # Pixel dimensions of video
     """
-    def __init__(self, path_spec, plugin=None):
-        if not imread.__module__.startswith("skimage"):
-            if plugin is not None:
-                warn("A plugin was specified but ignored. Plugins can only "
-                     "be specified if scikit-image is available. Instead, "
-                     "ImageSequence will use imageio")
-            self.kwargs = dict()
-        else:
-            self.kwargs = dict(plugin=plugin)
+    def __init__(self, path_spec, **kwargs):
+        self.kwargs = kwargs
+        if 'plugin' in self.kwargs:
+            warn_msg = "The 'plugin' parameter is deprecated and will be removed in a future release."
+            if imread.__module__.startswith("skimage"):
+                warn(warn_msg, DeprecationWarning)
+            else:
+                warn(warn_msg + " 'plugin' will be ignored because imageio is used for image reading.", DeprecationWarning)
+                self.kwargs.pop('plugin')
 
         self._is_zipfile = False
         self._zipfile = None
@@ -333,7 +333,7 @@ class ImageSequenceND(FramesSequenceND, ImageSequence):
         specified, all files in the zipfile will be loaded. The filenames
         should contain the indices of T, Z and C, preceded by a axis
         identifier such as: 'file_t001c05z32'.
-    plugin : string, optional
+    plugin : string, optional, deprecated
         Passed on to skimage.io.imread if scikit-image is available.
         If scikit-image is not available, this will be ignored and a warning
         will be issued. Not available in combination with zipfiles.

pims/tests/test_imseq.py

@@ -28,9 +28,8 @@ def setUp(self):
         self.filename = os.path.join(self.filepath, '*.png')
         self.frame0 = frames[0]
         self.frame1 = frames[1]
-        self.kwargs = dict(plugin='pil')
         self.klass = pims.ImageSequence
-        self.v = self.klass(self.filename, **self.kwargs)
+        self.v = self.klass(self.filename)
         self.expected_shape = shape
         self.expected_len = 5
         self.tempdir = tempfile.mkdtemp()
@@ -52,6 +51,10 @@ def tearDown(self):
         os.remove(self.tempfile)
         os.rmdir(self.tempdir)
 
+    def test_plugin_deprecation(self):
+        with self.assertWarns(DeprecationWarning):
+            pims.ImageSequence(self.filename, plugin='PIL')
+
 
 class TestImageSequenceWithMPL(_image_series, unittest.TestCase):
     def setUp(self):
@@ -65,9 +68,8 @@ def setUp(self):
         self.filename = os.path.join(self.filepath, '*.png')
         self.frame0 = frames[0]
         self.frame1 = frames[1]
-        self.kwargs = dict(plugin='matplotlib')
         self.klass = pims.ImageSequence
-        self.v = self.klass(self.filename, **self.kwargs)
+        self.v = self.klass(self.filename)
         self.expected_shape = shape
         self.expected_len = 5
 
@@ -89,9 +91,8 @@ def setUp(self):
                          for fn in self.filenames]
         self.frame0 = frames[0]
         self.frame1 = frames[1]
-        self.kwargs = dict(plugin='matplotlib')
         self.klass = pims.ImageSequence
-        self.v = self.klass(self.filename, **self.kwargs)
+        self.v = self.klass(self.filename)
         self.expected_shape = shape
         self.expected_len = len(self.filenames)
 
@@ -112,9 +113,8 @@ def setUp(self):
         self.filename = os.path.join(self.filepath, 'T76*.png')
         self.frame0 = frames[0]
         self.frame1 = frames[2]
-        self.kwargs = dict(plugin='matplotlib')
         self.klass = pims.ImageSequence
-        self.v = self.klass(self.filename, **self.kwargs)
+        self.v = self.klass(self.filename)
         self.expected_shape = shape
         self.expected_len = len(self.filenames)