Add CurrentFormat = FormatV05 and tweak writing to give valid v0.5 image

ome · Dec 10, 2024 · 080de7f · 080de7f
1 parent 499531f
commit 080de7f
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Showing 3 changed files with 35 additions and 12 deletions.
diff --git a/ome_zarr/format.py b/ome_zarr/format.py
@@ -24,6 +24,7 @@ def format_implementations() -> Iterator["Format"]:
     """
     Return an instance of each format implementation, newest to oldest.
     """
+    yield FormatV05()
     yield FormatV04()
     yield FormatV03()
     yield FormatV02()
@@ -329,4 +330,14 @@ def validate_coordinate_transformations(
                         )
 
 
-CurrentFormat = FormatV04
+class FormatV05(FormatV04):
+    """
+    Changelog: added FormatV05 (December 2024)
+    """
+
+    @property
+    def version(self) -> str:
+        return "0.5"
+
+
+CurrentFormat = FormatV05
diff --git a/ome_zarr/io.py b/ome_zarr/io.py
@@ -80,7 +80,10 @@ def __init_metadata(self) -> None:
         if self.__mode == "w":
             # For now, let's support writing of zarr v2
             # TODO: handle writing of zarr v2 OR zarr v3
-            zarr_format = 2
+            if self.__fmt.version in ("0.1", "0.2", "0.3", "0.4"):
+                zarr_format = 2
+            else:
+                zarr_format = 3
         try:
             group = zarr.open_group(
                 store=self.__store, path="/", mode=self.__mode, zarr_format=zarr_format

diff --git a/ome_zarr/writer.py b/ome_zarr/writer.py
@@ -273,15 +273,20 @@ def write_multiscale(
 
         else:
             # v2 arguments
-            options["shape"] = data.shape
-            options["chunks"] = chunks_opt
-            options["dimension_separator"] = "/"
-
-            # default to zstd compression
-            options["compressor"] = options.get(
-                "compressor", Blosc(cname="zstd", clevel=5, shuffle=Blosc.SHUFFLE)
-            )
+            if fmt.version in ("0.1", "0.2", "0.3", "0.4"):
+                options["chunks"] = chunks_opt
+                options["dimension_separator"] = "/"
+                # default to zstd compression
+                options["compressor"] = options.get(
+                    "compressor", Blosc(cname="zstd", clevel=5, shuffle=Blosc.SHUFFLE)
+                )
+            else:
+                if axes is not None:
+                    options["dimension_names"] = [
+                        axis["name"] for axis in axes if isinstance(axis, dict)
+                    ]
 
+            options["shape"] = data.shape
             # otherwise we get 'null'
             options["fill_value"] = 0
 
@@ -380,7 +385,6 @@ def write_multiscales_metadata(
     # (for {} this would silently over-write it, with dict() it explicitly fails)
     multiscales = [
         dict(
-            version=fmt.version,
             datasets=_validate_datasets(datasets, ndim, fmt),
             name=name if name else group.name,
             **metadata,
@@ -389,7 +393,12 @@ def write_multiscales_metadata(
     if axes is not None:
         multiscales[0]["axes"] = axes
 
-    group.attrs["multiscales"] = multiscales
+    if fmt.version in ("0.1", "0.2", "0.3", "0.4"):
+        multiscales[0]["version"] = fmt.version
+        group.attrs["multiscales"] = multiscales
+    else:
+        # Zarr v3 metadata under 'ome' with top-level version
+        group.attrs["ome"] = {"version": fmt.version, "multiscales": multiscales}
 
 
 def write_plate_metadata(