Merge branch 'master' into development

.github/workflows/cpython_tests.yml

@@ -11,7 +11,7 @@ jobs:
       fail-fast: true
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        pyversion: ["3.8", "3.9", "3.10", "3.11"]
+        pyversion: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         include:
           - name: Linux py310 full
             os: ubuntu-latest

.github/workflows/pypy_tests.yml

@@ -10,8 +10,8 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        os: ["ubuntu-latest", "macos-latest"]
-        pyversion: ["pypy-3.8", "pypy-3.9"]
+        os: ["ubuntu-latest", "macos-12"]
+        pyversion: ["pypy-3.8", "pypy-3.9", "pypy-3.10"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up pypy

CHANGELOG.md

@@ -7,6 +7,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 <!--next-version-placeholder-->
 
+## v2.34.1 (2024-04-22)
+
+### Fix
+
+* Fix bug of #1068 that `getattr` cannot get attribute with index directly ([#1069](https://github.com/imageio/imageio/issues/1069)) ([`05f0b37`](https://github.com/imageio/imageio/commit/05f0b372a7010debb39d2e8a65aed40bf2840f90))
+
+### Other
+
+* Update pyav.py ([#1070](https://github.com/imageio/imageio/issues/1070)) ([`0bc584e`](https://github.com/imageio/imageio/commit/0bc584ea79eb008be141b4b03bcf088194e219ba))
+* Trivial typo fixes ([#1072](https://github.com/imageio/imageio/issues/1072)) ([`9d1bced`](https://github.com/imageio/imageio/commit/9d1bced7703fc198f60b1d891cf85a10686822a7))
+
 ## v2.34.0 (2024-02-12)
 
 ### Feature

docs/development/index.rst

@@ -304,7 +304,7 @@ class to API calls using the plugin kwarg. For example::
 
 **Installation**
 
-To develop a new plugin, you can start off with a simple def install::
+To develop a new plugin, you can start off with a simple dev install::
     
     # 1. Fork the ImageIO repository
 
@@ -449,7 +449,7 @@ the file, define functions that have their name begin with ``test_`` (example:
 ``def test_png_reading():``) and fill them with code that uses your plugin.
 
 Our main requirement for tests of new plugins is that they cover the full
-plugin. Ideally, they also test readiing and writing of all supported formats,
+plugin. Ideally, they also test reading and writing of all supported formats,
 but this is not strictly necessary. Check the commands above for how to run
 tests and check test coverage of your plugin.
 

docs/formats/index.rst

@@ -6,7 +6,7 @@ Supported Formats
     you can search this page using ``Ctrl+F`` and then type the name of
     the extension or format.
 
-ImageIO reads and writes images by deligating your request to one of many
+ImageIO reads and writes images by delegating your request to one of many
 backends. Example backends are pillow, ffmpeg, tifffile among others. Each
 backend supports its own set of formats, which is how ImageIO manages to support
 so many of them.

docs/user_guide/freezing.rst

@@ -12,7 +12,7 @@ because plugins are lazy-loaded upon first use for better platform support and
 reduced loading times. This lazy-loading is an interesting case as (1) these
 plugins are exactly the kind of thing that PyInstaller_ tries desperately to
 avoid collecting to minimize package size and (2) these plugins are - by
-themself - super lightweight and won't bloat the package. 
+themselves - super lightweight and won't bloat the package.
 
 To add plugins to the application your first option is to add all of imageio to
 your package, which will also include the plugins. This can be done by using a

imageio/__init__.py

@@ -16,7 +16,7 @@
 
 # flake8: noqa
 
-__version__ = "2.34.0"
+__version__ = "2.34.1"
 
 import warnings
 

imageio/plugins/_dicom.py

@@ -703,7 +703,16 @@ def _append(self, dcm):
         self._entries.append(dcm)
 
     def _sort(self):
-        self._entries.sort(key=lambda k: k.InstanceNumber)
+        self._entries.sort(
+            key=lambda k: (
+                k.InstanceNumber,
+                (
+                    k.ImagePositionPatient[2]
+                    if hasattr(k, "ImagePositionPatient")
+                    else None
+                ),
+            )
+        )
 
     def _finish(self):
         """

imageio/plugins/pillow_legacy.py

@@ -137,10 +137,8 @@
     The number of iterations. Default 0 (meaning loop indefinitely).
 duration : {float, list}
     (Only available in GIF-PIL)
-    The duration (in seconds) of each frame. Either specify one value
+    The duration (in milliseconds) of each frame. Either specify one value
     that is used for all frames, or one value for each frame.
-    Note that in the GIF format the duration/delay is expressed in
-    hundredths of a second, which limits the precision of the duration.
 fps : float
     (Only available in GIF-PIL)
     The number of frames per second. If duration is not given, the

imageio/plugins/pyav.py

@@ -808,7 +808,7 @@ def init_video_stream(
         Parameters
         ----------
         codec : str
-            The codec to use, e.g. ``"x264"`` or ``"vp9"``.
+            The codec to use, e.g. ``"libx264"`` or ``"vp9"``.
         fps : float
             The desired framerate of the video stream (frames per second).
         pixel_format : str

tests/conftest.py

@@ -70,7 +70,7 @@ def working_directory(path):
 
 
 @pytest.fixture(scope="session")
-def test_images(request):
+def test_images(request, pytestconfig):
     """A collection of test images.
 
     Note: The images are cached persistently (across test runs) in
@@ -81,6 +81,7 @@ def test_images(request):
     # downloaded once in the beginning
 
     checkout_dir = request.config.cache.get("imageio_test_binaries", None)
+    use_internet = "not needs_internet" not in pytestconfig.getoption("-m")
 
     if checkout_dir is not None and not Path(checkout_dir).exists():
         # cache value set, but cache is gone :( ... recreate
@@ -90,6 +91,8 @@ def test_images(request):
         # download test images and other binaries
         checkout_dir = Path(__file__).parents[1] / ".test_images"
 
+        if not checkout_dir.exists() and not use_internet:
+            pytest.skip("Internet use disabled and `.test_images` not found.")
         try:
             checkout_dir.mkdir()
         except FileExistsError:
@@ -103,14 +106,15 @@ def test_images(request):
 
     checkout_dir = Path(checkout_dir)
 
-    with working_directory(checkout_dir):
-        result = os.system("git pull")
+    if use_internet:
+        with working_directory(checkout_dir):
+            result = os.system("git pull")
 
-    if result != 0:
-        request.config.cache.set("imageio_test_binaries", None)
-        raise RuntimeError(
-            "Cache directory is corrupt. Delete `.test_images` at project root."
-        )
+        if result != 0:
+            request.config.cache.set("imageio_test_binaries", None)
+            raise RuntimeError(
+                "Cache directory is corrupt. Delete `.test_images` at project root."
+            )
 
     return checkout_dir
 
@@ -175,12 +179,6 @@ def tmp_userdir(tmp_path):
         del os.environ[user_dir_env]
 
 
-def pytest_collection_modifyitems(items):
-    for item in items:
-        if "test_images" in getattr(item, "fixturenames", ()):
-            item.add_marker("needs_internet")
-
-
 def deprecated_test(fn):
     @wraps(fn)
     def wrapper(*args, **kwargs):

tests/test_dicom.py

@@ -191,3 +191,15 @@ def test_v3_reading(test_images):
     actual = iio3.imread(test_images / "dicom_file01.dcm")
 
     assert np.allclose(actual, expected)
+
+
+def test_contiguous_dicom_series(test_images, tmp_path):
+    # this is a regression test for
+    # https://github.com/imageio/imageio/issues/1067
+    fname = test_images / "dicom_issue_1067.zip"
+    with ZipFile(fname) as zip_ref:
+        zip_ref.extractall(tmp_path)
+
+    dname = tmp_path / "modified_dicom_sample1"
+    ims = iio.volread(dname, "DICOM")
+    assert ims.shape == (25, 512, 512)

tests/test_ffmpeg.py

@@ -30,6 +30,11 @@
     "imageio_ffmpeg", reason="imageio-ffmpeg is not installed"
 )
 
+try:
+    imageio_ffmpeg.get_ffmpeg_version()
+except RuntimeError:
+    pytest.skip("No compatible FFMPEG binary could be found.", allow_module_level=True)
+
 
 def get_ffmpeg_pids():
     pids = set()

tests/test_ffmpeg_info.py

@@ -6,8 +6,14 @@
 import imageio
 import sys
 
+imageio_ffmpeg = pytest.importorskip(
+    "imageio_ffmpeg", reason="imageio-ffmpeg is not installed"
+)
 
-pytest.importorskip("imageio_ffmpeg", reason="imageio-ffmpeg is not installed")
+try:
+    imageio_ffmpeg.get_ffmpeg_version()
+except RuntimeError:
+    pytest.skip("No compatible FFMPEG binary could be found.", allow_module_level=True)
 
 
 def dedent(text, dedent=8):

tests/test_freeimage.py

@@ -72,8 +72,11 @@ def setup_library(tmp_path_factory, vendored_lib):
         add = core.appdata_dir("imageio")
         os.makedirs(add, exist_ok=True)
         shutil.copytree(vendored_lib, os.path.join(add, "freeimage"))
+
+    try:
         fi.load_freeimage()
-        assert fi.has_lib(), "imageio-binaries' version of libfreeimage was not found"
+    except OSError:
+        pytest.skip("Could not find a compatible FreeImage version for this OS.")
 
     yield
 

tests/test_pyav.py

@@ -424,8 +424,8 @@ def test_bayer_write():
 
 def test_sequential_reading(test_images):
     expected_imgs = [
-        iio.imread(test_images / "cockatoo.mp4", index=1),
-        iio.imread(test_images / "cockatoo.mp4", index=5),
+        iio.imread(test_images / "cockatoo.mp4", plugin="pyav", index=1),
+        iio.imread(test_images / "cockatoo.mp4", plugin="pyav", index=5),
     ]
 
     with iio.imopen(test_images / "cockatoo.mp4", "r", plugin="pyav") as img_file: