feature/dimension-properties

bioio_base/image_container.py

@@ -10,7 +10,13 @@
 
 from .dimensions import Dimensions
 from .standard_metadata import StandardMetadata
-from .types import ImageLike, PhysicalPixelSizes, Scale, TimeInterval
+from .types import (
+    DimensionProperties,
+    ImageLike,
+    PhysicalPixelSizes,
+    Scale,
+    TimeInterval,
+)
 
 ###############################################################################
 
@@ -126,6 +132,11 @@ def physical_pixel_sizes(self) -> PhysicalPixelSizes:
     def scale(self) -> Scale:
         pass
 
+    @property
+    @abstractmethod
+    def dimension_properties(self) -> DimensionProperties:
+        pass
+
     @property
     @abstractmethod
     def time_interval(self) -> TimeInterval:

bioio_base/reader.py

@@ -24,7 +24,13 @@
     timelapse_interval,
     total_time_duration,
 )
-from .types import PhysicalPixelSizes, Scale, TimeInterval
+from .types import (
+    DimensionProperties,
+    DimensionProperty,
+    PhysicalPixelSizes,
+    Scale,
+    TimeInterval,
+)
 
 ###############################################################################
 
@@ -915,6 +921,49 @@ def scale(self) -> Scale:
             X=self.physical_pixel_sizes.X,
         )
 
+    @property
+    def dimension_properties(self) -> DimensionProperties:
+        """
+        Returns
+        -------
+        dimension_properties: DimensionProperties
+            Per-dimension properties.
+
+            Each dimension stores:
+            * value: The numeric scaling value.
+            * type: A semantic label for the dimension (e.g. "temporal", "spatial").
+            * unit: The unit associated with the value.
+        """
+        s = self.scale
+
+        return DimensionProperties(
+            T=DimensionProperty(
+                value=s.T,
+                type="temporal" if s.T is not None else None,
+                unit=None,
+            ),
+            C=DimensionProperty(
+                value=s.C,
+                type="channel" if s.C is not None else None,
+                unit=None,
+            ),
+            Z=DimensionProperty(
+                value=s.Z,
+                type="spatial" if s.Z is not None else None,
+                unit=None,
+            ),
+            Y=DimensionProperty(
+                value=s.Y,
+                type="spatial" if s.Y is not None else None,
+                unit=None,
+            ),
+            X=DimensionProperty(
+                value=s.X,
+                type="spatial" if s.X is not None else None,
+                unit=None,
+            ),
+        )
+
     def get_mosaic_tile_position(
         self, mosaic_tile_index: int, **kwargs: int
     ) -> Tuple[int, int]:

bioio_base/standard_metadata.py

@@ -43,7 +43,7 @@ class StandardMetadata:
     imaged_by: Optional[str]
         The experimentalist who produced this data.
 
-    imaging_date: Optional[str]
+    imaging_datetime: Optional[datetime]
         Date this file was imaged.
 
     objective: Optional[str]

bioio_base/types.py

@@ -36,3 +36,34 @@ class Scale(NamedTuple):
     Z: Optional[float]
     Y: Optional[float]
     X: Optional[float]
+
+
+class DimensionProperty(NamedTuple):
+    """
+    Per-dimension descriptor for dimension metadata.
+
+    value:
+        The numeric value for this dimension (e.g. from Scale or PhysicalPixelSizes).
+    type:
+        Semantic meaning of the dimension (e.g. "spatial", "temporal", "channel").
+    unit:
+        Unit string associated with the value (e.g. "micrometer", "second", "index").
+    """
+
+    value: Optional[float]
+    type: Optional[str]
+    unit: Optional[str]
+
+
+class DimensionProperties(NamedTuple):
+    """
+    Container for dimension properties for all supported dims.
+
+    These align with the standard bioio dimension order (T, C, Z, Y, X).
+    """
+
+    T: DimensionProperty
+    C: DimensionProperty
+    Z: DimensionProperty
+    Y: DimensionProperty
+    X: DimensionProperty