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Switch from ngff-zarr to ome-zarr-models #80

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Switch from ngff-zarr to ome-zarr-models #80

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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
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19 changes: 14 additions & 5 deletions bioio/writers/ome_zarr_writer_2.py
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@@ -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

Expand All @@ -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
Expand Down Expand Up @@ -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:
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6 changes: 3 additions & 3 deletions pyproject.toml
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Expand Up @@ -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",
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