Switch to ome-zarr-models

Author: imagejan

.github/workflows/ci.yml

@@ -37,7 +37,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.9, "3.10", 3.11, 3.12]
+        python-version: [3.11, 3.12, 3.13]
         os: [ubuntu-latest, macos-latest, macos-13, windows-latest]
 
     steps:

bioio/writers/ome_zarr_writer_2.py

@@ -1,5 +1,5 @@
 import logging
-from dataclasses import asdict, dataclass
+from dataclasses import dataclass
 from math import prod
 from typing import Any, List, Tuple, Union
 
@@ -8,7 +8,12 @@
 import numpy as np
 import skimage.transform
 import zarr
-from ngff_zarr.zarr_metadata import Axis, Dataset, Metadata, Scale, Translation
+from ome_zarr_models.v04.axes import Axis
+from ome_zarr_models.v04.coordinate_transformations import (
+    VectorScale,
+    VectorTranslation,
+)
+from ome_zarr_models.v04.multiscales import Dataset, Multiscale
 from zarr.storage import DirectoryStore, FSStore, default_compressor
 
 from bioio import BioImage
@@ -646,19 +651,23 @@ def generate_metadata(
                 # TODO handle optional translations e.g. xy stage position,
                 # start time etc
                 translation.append(0.0)
-            coordinateTransformations = [Scale(scale), Translation(translation)]
+            coordinateTransformations = (
+                VectorScale(type="scale", scale=scale),
+                VectorTranslation(type="translation", translation=translation),
+            )
             dataset = Dataset(
                 path=path, coordinateTransformations=coordinateTransformations
             )
             datasets.append(dataset)
-        metadata = Metadata(
+        metadata = Multiscale(
+            version=OME_NGFF_VERSION,
             axes=axes,
             datasets=datasets,
             name="/",
             coordinateTransformations=None,
         )
 
-        metadata_dict = asdict(metadata)
+        metadata_dict = metadata.model_dump()
         metadata_dict = _pop_metadata_optionals(metadata_dict)
 
         # get the total shape as dict:

pyproject.toml

@@ -22,20 +22,20 @@ authors = [
 classifiers = [
   "Development Status :: 4 - Beta",
   "Natural Language :: English",
-  "Programming Language :: Python :: 3.9",
-  "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
 ]
 dynamic = ["version"]
 dependencies = [
   "bioio-base>=0.9.1",
   "dask[array]>=2021.4.1",
   "fsspec>=2022.8.0",
   "imageio[ffmpeg]>=2.11.0,<2.28.0",
-  "ngff-zarr>=0.8.2",
   "numpy>=1.21.0,<2.0.0",
   "ome-types[lxml]>=0.4.0",
   "ome-zarr>=0.6.1",
+  "ome-zarr-models>=0.1.1",
   # This version was revoked from PyPi, but in case of using a stale version
   # or a private package index, this will prevent usage
   "scikit-image!=0.23.0",