- OmeCache: detect changes in ome.xml

.github/workflows/pytest.yml

@@ -10,9 +10,9 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies

README.md

@@ -24,7 +24,7 @@ pip install ndbioimage
 ```
 import matplotlib.pyplot as plt
 from ndbioimage import Imread
-with Imread('image_file.tif', axes='ctxy', dtype=int) as im:
+with Imread('image_file.tif', axes='ctyx', dtype=int) as im:
     plt.imshow(im[2, 1])
 ```        
         
@@ -41,7 +41,7 @@ with Imread('image_file.tif') as im:
 
 ```
 from ndbioimage import Imread
-with Imread('image_file.tif', axes='cztxy') as im:
+with Imread('image_file.tif', axes='cztyx') as im:
     sliced_im = im[1, :, :, 100:200, 100:200]
 ```
 
@@ -53,7 +53,7 @@ sliced_im is an instance of Imread which will load any image data from file only
 ```
 from ndbioimage import Imread
 import numpy as np
-with Imread('image_file.tif', axes='cztxy') as im:
+with Imread('image_file.tif', axes='cztyx') as im:
     array = np.asarray(im[0, 0])
 ```
 

ndbioimage/__init__.py

@@ -159,9 +159,10 @@ class OmeCache(DequeDict):
         return super().__contains__(self.path_and_lstat(path))
 
     @staticmethod
-    def path_and_lstat(path: str | Path) -> tuple[Path, Optional[os.stat_result]]:
+    def path_and_lstat(path: str | Path) -> tuple[Path, Optional[os.stat_result], Optional[os.stat_result]]:
         path = Path(path)
-        return path, (path.lstat() if path.exists() else None)
+        return (path, (path.lstat() if path.exists() else None),
+                (path.with_suffix('.ome.xml').lstat() if path.with_suffix('.ome.xml').exists() else None))
 
 
 class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "ndbioimage"
-version = "2024.4.3"
+version = "2024.4.4"
 description = "Bio image reading, metadata and some affine registration."
 authors = ["W. Pomp <w.pomp@nki.nl>"]
 license = "GPLv3"