feature/time_interval

bioio_base/image_container.py

@@ -9,7 +9,7 @@
 import xarray as xr
 
 from .dimensions import Dimensions
-from .types import ImageLike, PhysicalPixelSizes
+from .types import ImageLike, PhysicalPixelSizes, TimeInterval
 
 ###############################################################################
 
@@ -119,3 +119,8 @@ def channel_names(self) -> Optional[List[str]]:
     @abstractmethod
     def physical_pixel_sizes(self) -> PhysicalPixelSizes:
         pass
+
+    @property
+    @abstractmethod
+    def time_interval(self) -> TimeInterval:
+        pass

bioio_base/reader.py

@@ -15,7 +15,7 @@
 from .dimensions import DEFAULT_DIMENSION_ORDER, DimensionNames, Dimensions
 from .image_container import ImageContainer
 from .io import pathlike_to_fs
-from .types import PhysicalPixelSizes
+from .types import PhysicalPixelSizes, TimeInterval
 
 ###############################################################################
 
@@ -863,6 +863,22 @@ def physical_pixel_sizes(self) -> PhysicalPixelSizes:
         """
         return PhysicalPixelSizes(None, None, None)
 
+    @property
+    def time_interval(self) -> TimeInterval:
+        """
+        Returns
+        -------
+        sizes: Time Interval
+            Using available metadata, the floats representing time interval sizes for
+            dimension T.
+
+        Notes
+        -----
+        We currently do not handle unit attachment to these values. Please see the file
+        metadata for unit information.
+        """
+        return TimeInterval(None)
+
     def get_mosaic_tile_position(
         self, mosaic_tile_index: int, **kwargs: int
     ) -> Tuple[int, int]:

bioio_base/test_utilities.py

@@ -66,6 +66,7 @@ def run_image_container_checks(
     expected_physical_pixel_sizes: Tuple[
         Optional[float], Optional[float], Optional[float]
     ],
+    expected_time_interval: Tuple[Optional[float]],
     expected_metadata_type: Union[type, Tuple[Union[type, Tuple[Any, ...]], ...]],
     set_resolution_level: int = 0,
     expected_current_resolution_level: int = 0,
@@ -99,6 +100,7 @@ def run_image_container_checks(
     assert image_container.dims.shape == expected_shape
     assert image_container.channel_names == expected_channel_names
     assert image_container.physical_pixel_sizes == expected_physical_pixel_sizes
+    assert image_container.time_interval == expected_time_interval
     assert isinstance(image_container.metadata, expected_metadata_type)
 
     # Read different chunks
@@ -167,6 +169,7 @@ def run_image_file_checks(
     expected_physical_pixel_sizes: Tuple[
         Optional[float], Optional[float], Optional[float]
     ],
+    expected_time_interval: Tuple[Optional[float]],
     expected_metadata_type: Union[type, Tuple[Union[type, Tuple[Any, ...]], ...]],
     set_resolution_level: int = 0,
     expected_current_resolution_level: int = 0,
@@ -192,6 +195,7 @@ def run_image_file_checks(
         expected_dims_order=expected_dims_order,
         expected_channel_names=expected_channel_names,
         expected_physical_pixel_sizes=expected_physical_pixel_sizes,
+        expected_time_interval=expected_time_interval,
         expected_metadata_type=expected_metadata_type,
     )
 

bioio_base/types.py

@@ -24,3 +24,7 @@ class PhysicalPixelSizes(NamedTuple):
     Z: Optional[float]
     Y: Optional[float]
     X: Optional[float]
+
+
+class TimeInterval(NamedTuple):
+    T: Optional[float]