feat: download scenes

ome_zarr/classes/scene.py

@@ -449,8 +449,8 @@ def _ozmp_tf_to_tnd(
             tnd_sub_transforms = [
                 tnd.transforms.by_dimension.SubTransform(
                     transform=self._ozmp_tf_to_tnd(sub_tf.transformation),
-                    input_axes=sub_tf.input_axes,
-                    output_axes=sub_tf.output_axes,
+                    input_axes=sub_tf.inputAxes,
+                    output_axes=sub_tf.outputAxes,
                 )
                 for sub_tf in sub_transformations
             ]

ome_zarr/utils.py

@@ -24,7 +24,7 @@
 # Not needed with python 3.15+? https://github.com/python/cpython/issues/86809
 from RangeHTTPServer import RangeRequestHandler
 
-from . import USE_DASK_ARRAY_KWARGS
+from . import USE_DASK_ARRAY_KWARGS, OMEZarrScene
 from .format import format_from_version
 from .io import parse_url
 from .reader import Multiscales, Node, Reader
@@ -333,6 +333,14 @@ def download(input_path: str, output_dir: str = ".") -> None:
     location = parse_url(input_path)
     assert location, f"not a zarr: {location}"
 
+    if "scene" in location.root_attrs:
+        # ponytail: scene coordinate systems/axes vary by version; the
+        # ome_zarr_models-backed OMEZarrScene already handles this round-trip.
+        name = Path(location.path).name or "scene.zarr"
+        scene = OMEZarrScene.from_ome_zarr(location.store)
+        scene.to_ome_zarr(Path(output_dir) / name, overwrite=True)
+        return
+
     reader = Reader(location)
     nodes: list[Node] = list()
     paths: list[list[str]] = list()

pyproject.toml

@@ -27,7 +27,7 @@ dependencies = [
     "toolz",
     "rangehttpserver",
     "transformnd>=0.6.0,<0.8.0",
-    "ome-zarr-models>=1.8.0",
+    "ome-zarr-models>=1.8.1",
     "Deprecated",
 ]
 classifiers = [

tests/test_scene.py

@@ -9,6 +9,7 @@
 from pydantic import TypeAdapter
 
 from ome_zarr import OMEZarrImage, OMEZarrMultiscale, OMEZarrScene
+from ome_zarr.utils import download
 
 transform_adapter = TypeAdapter(AnyTransform)
 
@@ -29,13 +30,13 @@
         "type": "byDimension",
         "transformations": [
             {
-                "input_axes": [1],
-                "output_axes": [1],
+                "inputAxes": [1],
+                "outputAxes": [1],
                 "transformation": {"type": "translation", "translation": (0.0,)},
             },
             {
-                "input_axes": [0],
-                "output_axes": [0],
+                "inputAxes": [0],
+                "outputAxes": [0],
                 "transformation": {"type": "scale", "scale": (1.0,)},
             },
         ],
@@ -125,7 +126,12 @@ def test_create_scene_without_coordinate_systems(test_data_dir, transform):
         coordinate_transformations=[transform],
     )
 
-    scene.to_ome_zarr("test_scene.zarr", overwrite=True)
+    scene.to_ome_zarr(test_data_dir / "test_scene.zarr", overwrite=True)
+
+    # test "downloading" the scene elsewhere
+    download(
+        test_data_dir / "test_scene.zarr", test_data_dir / "test_scene_downloaded.zarr"
+    )
 
     # check that the graph is created correctly
     assert scene._graph is not None
@@ -250,6 +256,14 @@ def test_create_scene_with_coordinate_systems(test_data_dir, transform):
     assert len(scene._graph.graph.nodes) == 4
 
     scene.to_ome_zarr(str(test_data_dir / "test_scene_with_cs.zarr"), overwrite=True)
+
+    # test "downloading" the scene elsewhere
+    download(
+        test_data_dir / "test_scene_with_cs.zarr",
+        test_data_dir / "test_scene_with_cs_downloaded.zarr",
+    )
+
+    # read in saved scene and check everything's there
     scene_read = OMEZarrScene.from_ome_zarr(
         str(test_data_dir / "test_scene_with_cs.zarr")
     )