Replace Image2DCollection with ImageCollection

- Replace 2D image collection with generical image collection that can
  be the base class for multiple multi-scale image types.
- Move axis order specification from LevelProperties to fixed collection
  property.

python-spec/src/somacore/__init__.py

@@ -26,7 +26,7 @@
 from .data import SparseNDArray
 from .data import SparseRead
 from .experiment import Experiment
-from .images import Image2DCollection
+from .images import ImageCollection
 from .measurement import Measurement
 from .options import BatchSize
 from .options import IOfN
@@ -60,7 +60,7 @@
     "Experiment",
     "Measurement",
     "Scene",
-    "Image2DCollection",
+    "ImageCollection",
     "BatchSize",
     "IOfN",
     "ResultOrder",

python-spec/src/somacore/ephemeral/__init__.py

@@ -7,14 +7,14 @@
 
 from .collections import Collection
 from .collections import Experiment
-from .collections import Image2DCollection
+from .collections import ImageCollection
 from .collections import Measurement
 from .collections import Scene
 
 __all__ = (
     "Collection",
     "Experiment",
     "Measurement",
-    "Image2DCollection",
+    "ImageCollection",
     "Scene",
 )

python-spec/src/somacore/ephemeral/collections.py

@@ -7,7 +7,6 @@
     Optional,
     Sequence,
     TypeVar,
-    Union,
 )
 
 import pyarrow as pa
@@ -135,7 +134,7 @@ class Collection(  # type: ignore[misc]  # __eq__ false positive
 """The loosest possible constraint of the abstract Measurement type."""
 
 _BasicAbstractScene = scene.Scene[
-    data.DataFrame, images.Image2DCollection, base.SOMAObject
+    data.DataFrame, images.ImageCollection, base.SOMAObject
 ]
 """The loosest possible constraint of the abstract Scene type."""
 
@@ -166,11 +165,11 @@ def transformations(self) -> MutableMapping[str, coordinates.CoordinateTransform
         raise NotImplementedError()
 
 
-class Image2DCollection(  # type: ignore[misc]   # __eq__ false positive
+class ImageCollection(  # type: ignore[misc]   # __eq__ false positive
     BaseCollection[base.SOMAObject],
-    images.Image2DCollection[data.DenseNDArray, base.SOMAObject],
+    images.ImageCollection[data.DenseNDArray, base.SOMAObject],
 ):
-    """An in-memory Collection with Image2D semantics."""
+    """An in-memory Collection with Image semantics."""
 
     __slots__ = ()
 
@@ -181,15 +180,18 @@ def add_new_level(
         uri: Optional[str] = None,
         type: pa.DataType,
         shape: Sequence[int],
-        axis_order: Union[str, Sequence[str]],
     ) -> data.DenseNDArray:
         raise NotImplementedError()
 
+    @property
+    def axis_order(self) -> str:
+        raise NotImplementedError()
+
     @property
     def level_count(self) -> int:
         raise NotImplementedError()
 
-    def level_properties(self, level: int) -> images.Image2DCollection.LevelProperties:
+    def level_properties(self, level: int) -> images.ImageCollection.LevelProperties:
         raise NotImplementedError()
 
     def read_level(

python-spec/src/somacore/images.py

@@ -1,7 +1,7 @@
 """Implementation of the SOMA image collection for spatial data"""
 
 import abc
-from typing import Generic, Optional, Sequence, Tuple, TypeVar, Union
+from typing import Generic, Optional, Sequence, Tuple, TypeVar
 
 import pyarrow as pa
 from typing_extensions import Final, Protocol
@@ -20,7 +20,7 @@
 _RO_AUTO = options.ResultOrder.AUTO
 
 
-class Image2DCollection(
+class ImageCollection(
     collection.BaseCollection[_RootSO],
     Generic[_DenseND, _RootSO],
 ):
@@ -34,30 +34,21 @@ class Image2DCollection(
     #
     #     # This type-ignore comment will always be needed due to limitations
     #     # of type annotations; it is (currently) expected.
-    #     class Image2DCollection(  # type: ignore[type-var]
+    #     class ImageCollection(  # type: ignore[type-var]
     #         ImplBaseCollection[ImplSOMAObject],
-    #         somacore.Image2DCollection[ImplDenseNDArray, ImpSOMAObject],
+    #         somacore.ImageCollection[ImplDenseNDArray, ImpSOMAObject],
     #     ):
     #         ...
 
     __slots__ = ()
-    soma_type: Final = "SOMAImage2DCollection"  # type: ignore[misc]
+    soma_type: Final = "SOMAImageCollection"  # type: ignore[misc]
 
     class LevelProperties(Protocol):
-        """Class requirements for level properties of 2D images."""
-
-        @property
-        def axis_order(self) -> Tuple[str, ...]:
-            """Axis order for the underlying data.
-
-            Must contain 'X' and 'Y' for single-channel images and 'X', 'Y', and 'C'
-            for multi-channel images. Here `X' denotes the axis along the width of
-            the image and `Y' denotes the axis along the height of an image.
-            """
+        """Class requirements for level properties of images."""
 
         @property
         def name(self) -> str:
-            """The key for the level inside the Image2DCollection."""
+            """The key for the image."""
 
         @property
         def shape(self) -> Tuple[int, ...]:
@@ -71,17 +62,24 @@ def add_new_level(
         uri: Optional[str] = None,
         type: pa.DataType,
         shape: Sequence[int],
-        axis_order: Union[str, Sequence[str]],
     ) -> data.DenseNDArray:
+        """TODO: Add dcoumentation."""
+        raise NotImplementedError()
+
+    @property
+    def axis_order(self) -> str:
+        """The order of the axes in the stored images."""
         raise NotImplementedError()
 
     @property
     @abc.abstractmethod
     def level_count(self) -> int:
+        """The number of image levels stored in the ImageCollection."""
         raise NotImplementedError()
 
     @abc.abstractmethod
     def level_properties(self, level: int) -> LevelProperties:
+        """The properties of an image at the specified level."""
         raise NotImplementedError()
 
     @abc.abstractmethod

python-spec/src/somacore/scene.py

@@ -16,7 +16,7 @@
     "_SpatialDF", bound=data.DataFrame
 )  # TODO: Update to GeometryDataFrame or PointCloud
 """A particular implementation of GeometryDataFrame and PointCloud."""
-_ImageColl = TypeVar("_ImageColl", bound=images.Image2DCollection)
+_ImageColl = TypeVar("_ImageColl", bound=images.ImageCollection)
 """A particular implementation of a collection of spatial arrays."""
 _RootSO = TypeVar("_RootSO", bound=base.SOMAObject)
 """The root SomaObject type of the implementation."""

python-spec/testing/test_collection.py

@@ -42,5 +42,5 @@ def test_method_resolution_order(self):
         self.assertEqual("SOMAExperiment", exp.soma_type)
         scene = ephemeral.Scene()
         self.assertEqual("SOMAScene", scene.soma_type)
-        img = ephemeral.Image2DCollection()
-        self.assertEqual("SOMAImage2DCollection", img.soma_type)
+        img = ephemeral.ImageCollection()
+        self.assertEqual("SOMAImageCollection", img.soma_type)