Use zarr v3 and updated ome-zarr-py

.github/workflows/omero_plugin.yml

@@ -27,8 +27,9 @@ jobs:
       - name: Checkout omero-test-infra
         uses: actions/checkout@master
         with:
-          repository: ome/omero-test-infra
+          repository: jburel/omero-test-infra
           path: .omero
-          ref: ${{ secrets.OMERO_TEST_INFRA_REF }}
+          ref: python3.12
+          # ref: ${{ secrets.OMERO_TEST_INFRA_REF }}
       - name: Build and run OMERO tests
         run: .omero/docker $STAGE

.isort.cfg

@@ -1,2 +1,2 @@
 [settings]
-known_third_party = dask,numpy,ome_zarr,omero,omero_rois,omero_version,omero_zarr,pytest,setuptools,skimage,zarr
+known_third_party = dask,numcodecs,numpy,ome_zarr,omero,omero_rois,omero_version,omero_zarr,pytest,setuptools,skimage,zarr

README.rst

@@ -86,6 +86,9 @@ To export Images or Plates via the OMERO API::
     # Plate will be saved in current directory as 2.ome.zarr
     $ omero zarr export Plate:2
 
+    # Specify the OME-Zarr format, e.g. 0.4. Default is 0.5
+    $ omero zarr --format 0.4 export Image:1
+
     # Use the Image or Plate 'name' to save e.g. my_image.ome.zarr
     $ omero zarr --name_by name export Image:1
 
@@ -96,7 +99,7 @@ To export Images or Plates via the OMERO API::
     $ omero zarr export Image:1 --tile_width 256 --tile_height 256
 
 
-NB: If the connection to OMERO is lost and the Image is partially exported,
+NB: If the connection to OMERO is lost and the Image or Plate is partially exported,
 re-running the command will attempt to complete the export.
 
 To export images via bioformats2raw we use the ```--bf``` flag::

setup.py

@@ -51,7 +51,10 @@ def get_long_description() -> str:
     author="The Open Microscopy Team",
     author_email="",
     python_requires=">=3",
-    install_requires=["omero-py>=5.6.0", "ome-zarr>=0.5.0,<0.12.0"],
+    install_requires=[
+        "omero-py>=5.6.0",
+        "ome-zarr>=0.12.0",
+    ],
     long_description=long_description,
     keywords=["OMERO.CLI", "plugin"],
     url="https://github.com/ome/omero-cli-zarr/",

src/omero_zarr/__init__.py

@@ -16,12 +16,8 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-from ome_zarr.format import CurrentFormat
-
 from ._version import version as __version__
 
-ngff_version = CurrentFormat().version
-
 __all__ = [
     "__version__",
 ]

src/omero_zarr/cli.py

@@ -26,8 +26,8 @@
 from omero.cli import CLI, BaseControl, Parser, ProxyStringType
 from omero.gateway import BlitzGateway, BlitzObjectWrapper
 from omero.model import ImageI, PlateI
-from zarr.hierarchy import open_group
-from zarr.storage import FSStore
+from zarr.api.synchronous import open_group
+from zarr.storage import LocalStore
 
 from .masks import (
     MASK_DTYPE_SIZE,
@@ -323,6 +323,12 @@ def _configure(self, parser: Parser) -> None:
             subcommand.add_argument(
                 "--output", type=str, default="", help="The output directory"
             )
+            subcommand.add_argument(
+                "--format",
+                type=str,
+                choices=["0.4", "0.5"],
+                help="OME-Zarr version. Default is '0.5'",
+            )
         for subcommand in (polygons, masks):
             subcommand.add_argument(
                 "--overlaps",
@@ -399,6 +405,12 @@ def export(self, args: argparse.Namespace) -> None:
         if isinstance(args.object, ImageI):
             image = self._lookup(self.gateway, "Image", args.object.id)
             if args.bf or args.bfpath:
+                if args.format and args.format != "0.4":
+                    self.ctx.die(
+                        110,
+                        "bioformats2raw does not support OME-Zarr format %s"
+                        % args.format,
+                    )
                 self._bf_export(image, args)
             else:
                 image_to_zarr(image, args)
@@ -484,7 +496,7 @@ def _bf_export(self, image: BlitzObjectWrapper, args: argparse.Namespace) -> Non
             self.ctx.out(f"Image exported to {image_target.resolve()}")
 
         # Add OMERO metadata
-        store = FSStore(
+        store = LocalStore(
             str(image_target.resolve()),
             auto_mkdir=False,
             normalize_keys=False,

src/omero_zarr/masks.py

@@ -26,25 +26,17 @@
 from typing import Dict, List, Optional, Set, Tuple
 
 import numpy as np
-import omero.clients  # noqa
+import omero.clients
 from ome_zarr.conversions import int_to_rgba_255
-from ome_zarr.io import parse_url
-from ome_zarr.reader import Multiscales, Node
 from ome_zarr.scale import Scaler
 from ome_zarr.types import JSONDict
-from ome_zarr.writer import write_multiscale_labels
+from ome_zarr.writer import get_metadata, write_multiscale_labels
 from omero.model import MaskI, PolygonI
 from omero.rtypes import unwrap
 from skimage.draw import polygon as sk_polygon
-from zarr.hierarchy import open_group
+from zarr.api.synchronous import open_group
 
-from .util import (
-    get_zarr_name,
-    marshal_axes,
-    marshal_transformations,
-    open_store,
-    print_status,
-)
+from .util import get_zarr_name, marshal_axes, marshal_transformations, print_status
 
 LOGGER = logging.getLogger("omero_zarr.masks")
 
@@ -96,6 +88,7 @@ def plate_shapes_to_zarr(
         args.overlaps,
         args.output,
         args.name_by,
+        args.format,
     )
 
     count = 0
@@ -195,6 +188,7 @@ def image_shapes_to_zarr(
             args.overlaps,
             args.output,
             args.name_by,
+            args.format,
         )
 
         if args.style == "split":
@@ -231,6 +225,7 @@ def __init__(
         overlaps: str = "error",
         output: Optional[str] = None,
         name_by: str = "id",
+        ome_zarr_fmt: Optional[str] = None,
     ) -> None:
         self.dtype = dtype
         self.path = path
@@ -241,6 +236,7 @@ def __init__(
         self.overlaps = overlaps
         self.output = output
         self.name_by = name_by
+        self.format = ome_zarr_fmt
         if image:
             self.image = image
             self.size_t = image.getSizeT()
@@ -324,14 +320,13 @@ def save(self, masks: List[omero.model.Shape], name: str) -> None:
         image_path = source_image
         if self.output:
             image_path = os.path.join(self.output, source_image)
-        src = parse_url(image_path)
-        assert src, f"Source image does not exist at {image_path}"
-        input_pyramid = Node(src, [])
-        assert input_pyramid.load(Multiscales), "No multiscales metadata found"
-        input_pyramid_levels = len(input_pyramid.data)
+        img_group = open_group(image_path)
+        img_attrs = get_metadata(img_group)
+        assert "multiscales" in img_attrs, "No multiscales metadata found"
+        input_pyramid_levels = len(img_attrs["multiscales"][0]["datasets"])
 
-        store = open_store(image_path)
-        label_group = open_group(store)
+        # If image is zarr v2, labels will be too
+        write_group = open_group(image_path, mode="a")
 
         _mask_shape: List[int] = list(self.image_shape)
         mask_shape: Tuple[int, ...] = tuple(_mask_shape)
@@ -385,7 +380,7 @@ def save(self, masks: List[omero.model.Shape], name: str) -> None:
 
         write_multiscale_labels(
             label_pyramid,
-            label_group,
+            write_group,
             name,
             axes=axes,
             coordinate_transformations=transformations,