Specify NGFF 0.6-dev in output data (#849)

* specify NGFF 0.6-dev in output data

* add RasterFormatV02

* fix ome-zarr patch after adding RasterFormatV02

Author: LucaMarconato

src/spatialdata/__init__.py

@@ -77,5 +77,6 @@
 from spatialdata._core.query.spatial_query import bounding_box_query, polygon_query
 from spatialdata._core.spatialdata import SpatialData
 from spatialdata._io._utils import get_dask_backing_files, save_transformations
+from spatialdata._io.format import SpatialDataFormat
 from spatialdata._io.io_zarr import read_zarr
 from spatialdata._utils import get_pyramid_levels, unpad_raster

src/spatialdata/_io/format.py

@@ -1,10 +1,12 @@
 from __future__ import annotations
 
+from collections.abc import Iterator
 from typing import Any
 
+import ome_zarr.format
 import zarr
 from anndata import AnnData
-from ome_zarr.format import CurrentFormat
+from ome_zarr.format import CurrentFormat, Format, FormatV01, FormatV02, FormatV03, FormatV04
 from pandas.api.types import CategoricalDtype
 from shapely import GeometryType
 
@@ -120,6 +122,22 @@ def validate_coordinate_transformations(
     def spatialdata_format_version(self) -> str:
         return "0.1"
 
+    @property
+    def version(self) -> str:
+        return "0.4"
+
+
+class RasterFormatV02(RasterFormatV01):
+    @property
+    def spatialdata_format_version(self) -> str:
+        return "0.2"
+
+    @property
+    def version(self) -> str:
+        # 0.1 -> 0.2 changed the version string for the NGFF format, from 0.4 to 0.6-dev-spatialdata as discussed here
+        # https://github.com/scverse/spatialdata/pull/849
+        return "0.4-dev-spatialdata"
+
 
 class ShapesFormatV01(SpatialDataFormat):
     """Formatter for shapes."""
@@ -211,7 +229,7 @@ def validate_table(
             raise ValueError("`table.obs[instance_key]` must not contain null values, but it does.")
 
 
-CurrentRasterFormat = RasterFormatV01
+CurrentRasterFormat = RasterFormatV02
 CurrentShapesFormat = ShapesFormatV02
 CurrentPointsFormat = PointsFormatV01
 CurrentTablesFormat = TablesFormatV01
@@ -229,12 +247,29 @@ def validate_table(
 }
 RasterFormats = {
     "0.1": RasterFormatV01(),
+    "0.2": RasterFormatV02(),
 }
 SpatialDataContainerFormats = {
     "0.1": SpatialDataContainerFormatV01(),
 }
 
 
+def format_implementations() -> Iterator[Format]:
+    """Return an instance of each format implementation, newest to oldest."""
+    yield RasterFormatV02()
+    # yield RasterFormatV01()  # same format string as FormatV04
+    yield FormatV04()
+    yield FormatV03()
+    yield FormatV02()
+    yield FormatV01()
+
+
+# monkeypatch the ome_zarr.format module to include the SpatialDataFormat (we want to use the APIs from ome_zarr to
+# read, but signal that the format we are using is a dev version of NGFF, since it builds on some open PR that are
+# not released yet)
+ome_zarr.format.format_implementations = format_implementations
+
+
 def _parse_formats(formats: SpatialDataFormat | list[SpatialDataFormat] | None) -> dict[str, SpatialDataFormat]:
     parsed = {
         "raster": CurrentRasterFormat(),

tests/io/test_format.py

@@ -1,9 +1,19 @@
+import json
+import tempfile
+from pathlib import Path
 from typing import Any
 
 import pytest
 from shapely import GeometryType
 
-from spatialdata._io.format import CurrentPointsFormat, CurrentShapesFormat, ShapesFormatV01
+from spatialdata._io.format import (
+    CurrentPointsFormat,
+    CurrentShapesFormat,
+    RasterFormatV01,
+    RasterFormatV02,
+    ShapesFormatV01,
+    SpatialDataFormat,
+)
 from spatialdata.models import PointsModel, ShapesModel
 
 Points_f = CurrentPointsFormat()
@@ -71,3 +81,17 @@ def test_format_shapes_v2(
         metadata: dict[str, Any] = {attrs_key: {"version": Shapes_f.spatialdata_format_version}}
         metadata[attrs_key].pop("version")
         assert metadata[attrs_key] == Shapes_f.attrs_to_dict({})
+
+    @pytest.mark.parametrize("format", [RasterFormatV01, RasterFormatV02])
+    def test_format_raster_v1_v2(self, images, format: type[SpatialDataFormat]) -> None:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            images.write(Path(tmpdir) / "images.zarr", format=format())
+            zattrs_file = Path(tmpdir) / "images.zarr/images/image2d/.zattrs"
+            with open(zattrs_file) as infile:
+                zattrs = json.load(infile)
+                ngff_version = zattrs["multiscales"][0]["version"]
+                if format == RasterFormatV01:
+                    assert ngff_version == "0.4"
+                else:
+                    assert format == RasterFormatV02
+                    assert ngff_version == "0.4-dev-spatialdata"