Merge pull request #10 from bioio-devs/feature/allow-setting-resoluti…

…on-level

Feature/allow setting resolution level

bioio_base/image_container.py

@@ -44,6 +44,20 @@ def current_scene_index(self) -> int:
     def set_scene(self, scene_id: Union[str, int]) -> None:
         pass
 
+    @property
+    @abstractmethod
+    def resolution_levels(self) -> Tuple[int, ...]:
+        pass
+
+    @property
+    @abstractmethod
+    def current_resolution_level(self) -> int:
+        pass
+
+    @abstractmethod
+    def set_resolution_level(self, resolution_level: int) -> None:
+        pass
+
     @property
     @abstractmethod
     def xarray_dask_data(self) -> xr.DataArray:

bioio_base/reader.py

@@ -47,6 +47,7 @@ class Reader(ImageContainer, ABC):
     _metadata: Optional[Any] = None
     _scenes: Optional[Tuple[str, ...]] = None
     _current_scene_index: int = 0
+    _current_resolution_level: int = 0
     # Do not default because they aren't used by all readers
     _fs: AbstractFileSystem
     _path: str
@@ -194,6 +195,28 @@ def current_scene_index(self) -> int:
         """
         return self._current_scene_index
 
+    @property
+    def resolution_levels(self) -> Tuple[int, ...]:
+        """
+        Returns
+        -------
+        resolution_levels: Tuple[str, ...]
+            Return the available resolution levels for the current scene.
+            By default these are ordered from highest resolution to lowest
+            resolution.
+        """
+        return (self._current_resolution_level,)
+
+    @property
+    def current_resolution_level(self) -> int:
+        """
+        Returns
+        -------
+        resolution_level: int
+            The current resolution level.
+        """
+        return self._current_resolution_level
+
     def _reset_self(self) -> None:
         # Reset the data stored in the Reader object
         self._xarray_dask_data = None
@@ -261,6 +284,33 @@ def set_scene(self, scene_id: Union[str, int]) -> None:
                 f"or integer (for scene index). Provided: {scene_id} ({type(scene_id)}."
             )
 
+    def set_resolution_level(self, resolution_level: int) -> None:
+        """
+        Set the resolution level.
+
+        Parameters
+        ----------
+        resolution_level: int
+            The resolution level to access the image at.
+
+        Raises
+        ------
+        IndexError
+            The provided resolution level is not found in the
+            available resolution level list.
+        """
+        # Validate resolution level
+        if resolution_level not in self.resolution_levels:
+            raise IndexError(
+                f"Resolution level: '{resolution_level}' "
+                "is not present in available image resolution levels: "
+                f"{self.resolution_levels}. Readers are not required by `bioio-base` "
+                "to support resolution levels and therefore may not have any "
+                "available besides the default of 0."
+            )
+
+        self._current_resolution_level = resolution_level
+
     @abstractmethod
     def _read_delayed(self) -> xr.DataArray:
         """

bioio_base/test_utilities.py

@@ -67,6 +67,9 @@ def run_image_container_checks(
         Optional[float], Optional[float], Optional[float]
     ],
     expected_metadata_type: Union[type, Tuple[Union[type, Tuple[Any, ...]], ...]],
+    set_resolution_level: int = 0,
+    expected_current_resolution_level: int = 0,
+    expected_resolution_levels: Tuple[int, ...] = (0,),
 ) -> ImageContainer:
     """
     A general suite of tests to run against readers.
@@ -82,6 +85,13 @@ def run_image_container_checks(
     assert image_container.scenes == expected_scenes
     assert image_container.current_scene == expected_current_scene
 
+    # Set resolution level
+    image_container.set_resolution_level(set_resolution_level)
+
+    # Check resolution level info
+    assert image_container.resolution_levels == expected_resolution_levels
+    assert image_container.current_resolution_level == expected_current_resolution_level
+
     # Check basics
     assert image_container.shape == expected_shape
     assert image_container.dtype == expected_dtype
@@ -158,6 +168,9 @@ def run_image_file_checks(
         Optional[float], Optional[float], Optional[float]
     ],
     expected_metadata_type: Union[type, Tuple[Union[type, Tuple[Any, ...]], ...]],
+    set_resolution_level: int = 0,
+    expected_current_resolution_level: int = 0,
+    expected_resolution_levels: Tuple[int, ...] = (0,),
 ) -> ImageContainer:
     # Init container
     image_container = ImageContainer(image, fs_kwargs=dict(anon=True))
@@ -169,8 +182,11 @@ def run_image_file_checks(
     run_image_container_checks(
         image_container=image_container,
         set_scene=set_scene,
+        set_resolution_level=set_resolution_level,
         expected_scenes=expected_scenes,
         expected_current_scene=expected_current_scene,
+        expected_resolution_levels=expected_resolution_levels,
+        expected_current_resolution_level=expected_current_resolution_level,
         expected_shape=expected_shape,
         expected_dtype=expected_dtype,
         expected_dims_order=expected_dims_order,