Changes to RFC4 (#264)

* Update orientation field name

* Check that orientation can only be set on spatial axes

* Use new orientation data structure

Author: dstansby

src/ome_zarr_models/_v06/axes.py

@@ -1,40 +1,38 @@
 from collections.abc import Sequence
-from typing import Literal
+from typing import Self
+
+from pydantic import BaseModel, JsonValue, model_validator
 
 from ome_zarr_models.common.axes import Axis as BaseAxis
 from ome_zarr_models.common.axes import AxisType
 
 __all__ = ["Axes", "Axis", "AxisType"]
 
 
-Orientation = Literal[
-    "left-to-right",
-    "right-to-left",
-    "anterior-to-posterior",
-    "posterior-to-anterior",
-    "inferior-to-superior",
-    "superior-to-inferior",
-    "dorsal-to-ventral",
-    "ventral-to-dorsal",
-    "dorsal-to-palmar",
-    "palmar-to-dorsal",
-    "dorsal-to-plantar",
-    "plantar-to-dorsal",
-    "rostral-to-caudal",
-    "caudal-to-rostral",
-    "cranial-to-caudal",
-    "caudal-to-cranial",
-    "proximal-to-distal",
-    "distal-to-proximal",
-]
+class Orientation(BaseModel):
+    """
+    Model for an orientation object.
+    """
+
+    type: JsonValue
+    value: JsonValue
 
 
 class Axis(BaseAxis):
     """
-    Model for an element of multiscale axes.
+    Model for an element of `Multiscale.axes`.
     """
 
-    anatomicalOrientation: Orientation | None = None
+    orientation: Orientation | None = None
+
+    @model_validator(mode="after")
+    def _check_orientation_only_on_spatial(self) -> Self:
+        if self.type != "space" and self.orientation is not None:
+            raise ValueError(
+                f"Orientation can only be set on a spatial axis "
+                f"(got Axis type='{self.type}')"
+            )
+        return self
 
 
 Axes = Sequence[Axis]

src/ome_zarr_models/_v06/multiscales.py

@@ -1,8 +1,8 @@
 from typing import Self
 
-from pydantic import model_validator
+from pydantic import JsonValue, model_validator
 
-from ome_zarr_models._v06.axes import Axes, Orientation
+from ome_zarr_models._v06.axes import Axes
 from ome_zarr_models.common.multiscales import Dataset, MultiscaleBase
 
 __all__ = ["Dataset", "Multiscale"]
@@ -20,10 +20,8 @@ def _ensure_valid_orientations(self: Self) -> Self:
         """
         Validate anatomical orientations.
         """
-        orientations: list[Orientation] = [
-            a.anatomicalOrientation
-            for a in self.axes
-            if a.anatomicalOrientation is not None
+        orientations: list[JsonValue] = [
+            a.orientation.value for a in self.axes if a.orientation is not None
         ]
         _check_only_one_value(
             orientations=orientations, values=["right-to-left", "left-to-right"]
@@ -55,7 +53,7 @@ def _ensure_valid_orientations(self: Self) -> Self:
 
 
 def _check_only_one_value(
-    *, orientations: list[Orientation], values: list[Orientation]
+    *, orientations: list[JsonValue], values: list[JsonValue]
 ) -> None:
     counter = 0
     for value in values:

tests/_v06/test_axes.py

@@ -0,0 +1,15 @@
+import pytest
+from pydantic import ValidationError
+
+from ome_zarr_models._v06.axes import Axis
+
+
+def test_orientation_only_spatial() -> None:
+    with pytest.raises(
+        ValidationError, match="Orientation can only be set on a spatial axis"
+    ):
+        Axis(
+            name="my_axis",
+            type="time",
+            orientation={"type": "anatomical", "value": "anterior-to-posterior"},
+        )

tests/_v06/test_image.py

@@ -43,28 +43,28 @@ def test_image(store: Store) -> None:
                         name="t",
                         type="time",
                         unit="millisecond",
-                        anatomicalOrientation="left-to-right",
-                    ),
-                    Axis(
-                        name="c", type="channel", unit=None, anatomicalOrientation=None
                     ),
+                    Axis(name="c", type="channel", unit=None, orientation=None),
                     Axis(
                         name="z",
                         type="space",
                         unit="micrometer",
-                        anatomicalOrientation=None,
+                        orientation=None,
                     ),
                     Axis(
                         name="y",
                         type="space",
                         unit="micrometer",
-                        anatomicalOrientation=None,
+                        orientation=None,
                     ),
                     Axis(
                         name="x",
                         type="space",
                         unit="micrometer",
-                        anatomicalOrientation=None,
+                        orientation={
+                            "type": "anatomical",
+                            "value": "left-to-right",
+                        },
                     ),
                 ],
                 datasets=(
@@ -280,13 +280,13 @@ def test_invalid_orientations() -> None:
                     name="z",
                     type="space",
                     unit="micrometer",
-                    anatomicalOrientation="left-to-right",
+                    orientation={"type": "anatomical", "value": "left-to-right"},
                 ),
                 Axis(
                     name="y",
                     type="space",
                     unit="micrometer",
-                    anatomicalOrientation="right-to-left",
+                    orientation={"type": "anatomical", "value": "right-to-left"},
                 ),
             ],
             datasets=(

tests/data/examples/v06/image_example.json

@@ -8,13 +8,17 @@
           {
             "name": "t",
             "type": "time",
-            "unit": "millisecond",
-            "anatomicalOrientation": "left-to-right"
+            "unit": "millisecond"
           },
           { "name": "c", "type": "channel" },
           { "name": "z", "type": "space", "unit": "micrometer" },
           { "name": "y", "type": "space", "unit": "micrometer" },
-          { "name": "x", "type": "space", "unit": "micrometer" }
+          {
+            "name": "x",
+            "type": "space",
+            "unit": "micrometer",
+            "orientation": { "type": "anatomical", "value": "left-to-right" }
+          }
         ],
         "datasets": [
           {