chore: add more testing

.github/workflows/ci.yml

@@ -50,6 +50,7 @@ jobs:
           python -m pip install -U pip
           # if running a cron job, we add the --pre flag to test against pre-releases
           python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+          python -m pip install git+https://github.com/zarr-developers/zarr-python.git
 
       - name: 🧪 Run Tests
         run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing

src/ngio/ngff_meta/meta_handler.py

@@ -53,9 +53,9 @@ def find_ngff_image_meta_handler_version(zarr_path: str) -> str:
 
 
 def get_ngff_image_meta_handler(
-    zarr_path: str, meta_mode: Literal["image", "label"]
+    zarr_path: str, meta_mode: Literal["image", "label"], cache: bool = False
 ) -> NgffImageMetaHandler:
     """Load the NGFF image metadata handler."""
     version = find_ngff_image_meta_handler_version(zarr_path)
     handler = _available_load_ngff_image_meta_handlers[version]
-    return handler(zarr_path, meta_mode=meta_mode)
+    return handler(zarr_path, meta_mode=meta_mode, cache=cache)

src/ngio/ngff_meta/v04/specs.py

@@ -22,11 +22,11 @@ class Window04(BaseModel):
 class Channel04(BaseWithExtraFields):
     """Model for `Omero.channels`."""
 
-    active: bool | None = None
-    coefficient: int | None = None
+    # active: bool | None = None
+    # coefficient: int | None = None
     color: str
-    family: str | None = None
-    inverted: bool | None = None
+    # family: str | None = None
+    # inverted: bool | None = None
     label: str | None = None
     window: Window04 | None = None
 

src/ngio/ngff_meta/v04/zarr_utils.py

@@ -2,8 +2,7 @@
 
 from typing import Literal
 
-from zarr import open_group
-
+from ngio.io import read_group_attrs, update_group_attrs
 from ngio.ngff_meta.fractal_image_meta import (
     Axis,
     Dataset,
@@ -16,8 +15,11 @@
     TranslationCoordinateTransformation,
 )
 from ngio.ngff_meta.v04.specs import (
+    Axis04,
     Dataset04,
+    Multiscale04,
     NgffImageMeta04,
+    Omero04,
     ScaleCoordinateTransformation04,
     Transformation04,
     TranslationCoordinateTransformation04,
@@ -26,8 +28,8 @@
 
 def check_ngff_image_meta_v04(zarr_path: str) -> bool:
     """Check if a Zarr Group contains the OME-NGFF v0.4."""
-    group = open_group(store=zarr_path, mode="r", zarr_format=2)
-    multiscales = group.attrs.get("multiscales", None)
+    group = read_group_attrs(store=zarr_path, zarr_format=2)
+    multiscales = group.get("multiscales", None)
     if multiscales is None:
         return False
 
@@ -46,8 +48,8 @@ def check_ngff_image_meta_v04(zarr_path: str) -> bool:
 
 def load_vanilla_ngff_image_meta_v04(zarr_path: str) -> NgffImageMeta04:
     """Load the OME-NGFF 0.4 image meta model."""
-    group = open_group(store=zarr_path, mode="r", zarr_format=2)
-    return NgffImageMeta04(**group.attrs)
+    attrs = read_group_attrs(store=zarr_path, zarr_format=2)
+    return NgffImageMeta04(**attrs)
 
 
 def _transform_dataset(
@@ -143,17 +145,50 @@ def vanilla_ngff_image_meta_v04_to_fractal(
     )
 
 
+def fractal_ngff_image_meta_to_vanilla_v04(
+    meta: FractalImageLabelMeta,
+) -> NgffImageMeta04:
+    """Convert the FractalImageMeta to NgffImageMeta."""
+    axes04 = [Axis04(**axis.model_dump()) for axis in meta.multiscale.axes]
+    dataset04 = []
+    for dataset in meta.multiscale.datasets:
+        transformations = [t.model_dump() for t in dataset.coordinateTransformations]
+        dataset04.append(
+            Dataset04(path=dataset.path, coordinateTransformations=transformations)
+        )
+    multiscale04 = Multiscale04(
+        name=meta.name,
+        axes=axes04,
+        datasets=dataset04,
+        version="0.4",
+    )
+    omero04 = None if meta.omero is None else Omero04(**meta.omero.model_dump())
+    return NgffImageMeta04(
+        multiscales=[multiscale04],
+        omero=omero04,
+    )
+
+
 def load_ngff_image_meta_v04(zarr_path: str) -> FractalImageLabelMeta:
     """Load the OME-NGFF 0.4 image meta model."""
-    check_ngff_image_meta_v04(zarr_path=zarr_path)
+    if not check_ngff_image_meta_v04(zarr_path=zarr_path):
+        raise ValueError(
+            "The Zarr store does not contain the correct OME-Zarr version."
+        )
     meta04 = load_vanilla_ngff_image_meta_v04(zarr_path=zarr_path)
     return vanilla_ngff_image_meta_v04_to_fractal(meta04=meta04)
 
 
 def write_ngff_image_meta_v04(zarr_path: str, meta: FractalImageLabelMeta) -> None:
     """Write the OME-NGFF 0.4 image meta model."""
-    # TODO: Implement the conversion from FractalImageMeta to NgffImageMeta
-    pass
+    if not check_ngff_image_meta_v04(zarr_path=zarr_path):
+        raise ValueError(
+            "The Zarr store does not contain the correct OME-Zarr version."
+        )
+    meta04 = fractal_ngff_image_meta_to_vanilla_v04(meta=meta)
+    update_group_attrs(
+        store=zarr_path, attrs=meta04.model_dump(exclude_none=True), zarr_format=2
+    )
 
 
 class NgffImageMetaZarrHandlerV04:

tests/data/meta_v04/base_ome_zarr_image_meta.json

@@ -0,0 +1,70 @@
+{
+    "multiscales": [
+        {
+            "axes": [
+                {"name": "c", "type": "channel"},
+                {"name": "z", "type": "space", "unit": "micrometer"},
+                {"name": "y", "type": "space", "unit": "micrometer"},
+                {"name": "x", "type": "space", "unit": "micrometer"}
+            ],
+            "datasets": [
+                {
+                    "coordinateTransformations": [
+                        {"scale": [1.0, 1.0, 0.1625, 0.1625], "type": "scale"}
+                    ],
+                    "path": "0"
+                },
+                {
+                    "coordinateTransformations": [
+                        {"scale": [1.0, 1.0, 0.325, 0.325], "type": "scale"}
+                    ],
+                    "path": "1"
+                },
+                {
+                    "coordinateTransformations": [
+                        {"scale": [1.0, 1.0, 0.65, 0.65], "type": "scale"}
+                    ],
+                    "path": "2"
+                },
+                {
+                    "coordinateTransformations": [
+                        {"scale": [1.0, 1.0, 1.3, 1.3], "type": "scale"}
+                    ],
+                    "path": "3"
+                },
+                {
+                    "coordinateTransformations": [
+                        {"scale": [1.0, 1.0, 2.6, 2.6], "type": "scale"}
+                    ],
+                    "path": "4"
+                }
+            ],
+            "version": "0.4"
+        }
+    ],
+    "omero": {
+        "channels": [
+            {
+                "color": "00FFFF",
+                "label": "DAPI",
+                "wavelength_id": "A01_C01",
+                "window": {"end": 700, "max": 65535, "min": 0, "start": 0}
+            },
+            {
+                "color": "FF00FF",
+                "label": "nanog",
+                "wavelength_id": "A01_C02",
+                "window": {"end": 180, "max": 65535, "min": 0, "start": 0}
+            },
+            {
+                "color": "FFFF00",
+                "label": "Lamin B1",
+                "wavelength_id": "A02_C03",
+                "window": {"end": 1500, "max": 65535, "min": 0, "start": 0}
+            }
+        ],
+        "id": 1,
+        "name": "TBD",
+        "version": "0.4"
+    }
+}

tests/ngff_meta/conftest.py

@@ -0,0 +1,20 @@
+import json
+from pathlib import Path
+
+import zarr
+import zarr.store
+from pytest import fixture
+
+
+@fixture
+def ome_zarr_image_v04_path(tmpdir):
+    zarr_path = Path(tmpdir) / "test_ome_ngff_v04.zarr"
+
+    group = zarr.open_group(store=zarr_path, mode="w", zarr_format=2)
+
+    with open("tests/data/meta_v04/base_ome_zarr_image_meta.json") as f:
+        base_ome_zarr_meta = json.load(f)
+
+    base_ome_zarr_meta = base_ome_zarr_meta
+    group.attrs.update(base_ome_zarr_meta)
+    return zarr_path

tests/ngff_meta/test_v04.py

@@ -0,0 +1,37 @@
+import json
+
+
+class TestOMEZarrHandlerV04:
+    def test_basic_workflow(self, ome_zarr_image_v04_path):
+        from ngio.io import read_group_attrs
+        from ngio.ngff_meta import get_ngff_image_meta_handler
+
+        handler = get_ngff_image_meta_handler(
+            zarr_path=ome_zarr_image_v04_path, meta_mode="image"
+        )
+
+        meta = handler.load_meta()
+        handler.write_meta(meta)
+
+        with open("tests/data/meta_v04/base_ome_zarr_image_meta.json") as f:
+            base_ome_zarr_meta = json.load(f)
+
+        saved_meta = read_group_attrs(store=ome_zarr_image_v04_path, zarr_format=2)
+        assert saved_meta == base_ome_zarr_meta
+
+    def test_basic_workflow_with_cache(self, ome_zarr_image_v04_path):
+        from ngio.io import read_group_attrs
+        from ngio.ngff_meta import get_ngff_image_meta_handler
+
+        handler = get_ngff_image_meta_handler(
+            zarr_path=ome_zarr_image_v04_path, meta_mode="image", cache=True
+        )
+
+        meta = handler.load_meta()
+        handler.write_meta(meta)
+
+        with open("tests/data/meta_v04/base_ome_zarr_image_meta.json") as f:
+            base_ome_zarr_meta = json.load(f)
+
+        saved_meta = read_group_attrs(store=ome_zarr_image_v04_path, zarr_format=2)
+        assert saved_meta == base_ome_zarr_meta