fix imread bug and allow AICSImage class to close its reader

README.md

@@ -31,10 +31,17 @@ from aicsimageio import AICSImage, imread
 im = imread("/path/to/your/file_or_buffer.ome.tiff")
 
 # For AICSImage object that
-im = AICSImage("/path/to/your/file_or_buffer.ome.tiff")
+with AICSImage("/path/to/your/file_or_buffer.ome.tiff") as im:
+    # use im object
 
 # To specify a known dimension order
-im = AICSImage("/path/to/your/file_or_buffer.ome.tiff", known_dims="SYX")
+with AICSImage("/path/to/your/file_or_buffer.ome.tiff", known_dims="SYX") as im:
+    # use im object
+
+# if you instantiate an AICSImage:
+im = AICSImage("/path/to/your/file_or_buffer.ome.tiff")
+# you should close it when done:
+im.close()
 
 # Image data is stored in `data` attribute
 im.data  # returns the image data numpy array

aicsimageio/aics_image.py

@@ -33,18 +33,29 @@ class AICSImage:
 
     zstack_t10 = data[0, 10, 0, :, :, :]  # access the S=0, T=10, C=0 "ZYX" cube
 
-
     File Examples
     -------------
+
+    with AICSImage("filename.ome.tif") as img:
+        # do work with img
+        data = img.data
+        metadata = img.metadata
+        # img will be closed automatically at end of scope
+
     OmeTif
         img = AICSImage("filename.ome.tif")
+        img.close()
     CZI (Zeiss)
         img = AICSImage("filename.czi") or AICSImage("filename.czi", max_workers=8)
+        img.close()
     Tiff
         img = AICSImage("filename.tif")
+        img.close()
     Png/Gif/...
         img = AICSImage("filename.png")
+        img.close()
         img = AICSImage("filename.gif")
+        img.close()
 
     Bytestream Examples
     -------------------
@@ -291,9 +302,20 @@ def get_channel_names(self, scene: int = 0):
             names = [str(i) for i in range(self.size_c)]
         return names
 
+    def close(self):
+        self.reader.close()
+
     def __repr__(self) -> str:
         return f"<AICSImage [{type(self.reader).__name__}]>"
 
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        self.close()
+
 
-def imread(data: types.ImageLike, **kwargs):
-    return AICSImage(data, **kwargs).data
+def imread(data: types.ImageLike, **kwargs) -> np.ndarray:
+    with AICSImage(data, **kwargs) as image:
+        imagedata = image.data
+    return imagedata

aicsimageio/tests/test_aics_image.py

@@ -197,3 +197,22 @@ def test_imread(resources_dir, filename, expected_shape):
 def test_channel_names(resources_dir, filename, expected_channel_names):
     img = AICSImage(resources_dir / filename)
     assert img.get_channel_names() == expected_channel_names
+
+
+@pytest.mark.parametrize(
+    "filename",
+    [
+        PNG_FILE,
+        TIF_FILE,
+        CZI_FILE,
+        OME_FILE,
+    ],
+)
+def test_aicsimage_close(resources_dir, filename):
+    img = AICSImage(resources_dir / filename)
+    assert img.reader._bytes.closed is False
+    img.close()
+
+    with AICSImage(resources_dir / filename) as img:
+        img.metadata
+    assert img.reader._bytes.closed is True