Merge pull request #129 from thewtex/omero

omero

Author: thewtex

ngff_zarr/__init__.py

@@ -32,6 +32,9 @@
     Transform,
     Dataset,
     Metadata,
+    Omero,
+    OmeroChannel,
+    OmeroWindow,
 )
 
 __all__ = [
@@ -67,4 +70,7 @@
     "Transform",
     "Dataset",
     "Metadata",
+    "Omero",
+    "OmeroChannel",
+    "OmeroWindow",
 ]

ngff_zarr/from_ngff_zarr.py

@@ -16,7 +16,15 @@
 
 from .ngff_image import NgffImage
 from .to_multiscales import Multiscales
-from .v04.zarr_metadata import Axis, Dataset, Scale, Translation
+from .v04.zarr_metadata import (
+    Axis,
+    Dataset,
+    Scale,
+    Translation,
+    Omero,
+    OmeroChannel,
+    OmeroWindow,
+)
 from .validate import validate as validate_ngff
 
 zarr_version = packaging.version.parse(zarr.__version__)
@@ -145,9 +153,29 @@ def from_ngff_zarr(
             Axis(name="y", type="space"),
             Axis(name="x", type="space"),
         ]
+
     coordinateTransformations = None
     if "coordinateTransformations" in metadata:
         coordinateTransformations = metadata["coordinateTransformations"]
+
+    omero = None
+    if "omero" in root.attrs:
+        omero_data = root.attrs["omero"]
+        omero = Omero(
+            channels=[
+                OmeroChannel(
+                    color=channel["color"],
+                    window=OmeroWindow(
+                        min=channel["window"]["min"],
+                        max=channel["window"]["max"],
+                        start=channel["window"]["start"],
+                        end=channel["window"]["end"],
+                    ),
+                )
+                for channel in omero_data["channels"]
+            ]
+        )
+
     if version == "0.5":
         from .v05.zarr_metadata import Metadata
 
@@ -156,6 +184,7 @@ def from_ngff_zarr(
             datasets=datasets,
             name=name,
             coordinateTransformations=coordinateTransformations,
+            omero=omero,
         )
     else:
         from .v04.zarr_metadata import Metadata
@@ -166,6 +195,7 @@ def from_ngff_zarr(
             name=name,
             version=metadata["version"],
             coordinateTransformations=coordinateTransformations,
+            omero=omero,
         )
 
     return Multiscales(images, metadata)

ngff_zarr/to_ngff_zarr.py

@@ -47,6 +47,9 @@ def _pop_metadata_optionals(metadata_dict):
     if metadata_dict["coordinateTransformations"] is None:
         metadata_dict.pop("coordinateTransformations")
 
+    if metadata_dict["omero"] is None:
+        metadata_dict.pop("omero")
+
     return metadata_dict
 
 
@@ -231,6 +234,9 @@ def to_ngff_zarr(
             **format_kwargs,
         )
 
+    if "omero" in metadata_dict:
+        root.attrs["omero"] = metadata_dict.pop("omero")
+
     if version != "0.4":
         # RFC 2, Zarr 3
         root.attrs["ome"] = {"version": version, "multiscales": [metadata_dict]}

ngff_zarr/v04/zarr_metadata.py

@@ -2,6 +2,7 @@
 from typing import List, Optional, Union
 
 from typing_extensions import Literal
+import re
 
 SupportedDims = Union[
     Literal["c"], Literal["x"], Literal["y"], Literal["z"], Literal["t"]
@@ -165,10 +166,34 @@ class Dataset:
     coordinateTransformations: List[Transform]
 
 
+@dataclass
+class OmeroWindow:
+    min: float
+    max: float
+    start: float
+    end: float
+
+
+@dataclass
+class OmeroChannel:
+    color: str
+    window: OmeroWindow
+
+    def validate_color(self):
+        if not re.fullmatch(r"[0-9A-Fa-f]{6}", self.color):
+            raise ValueError(f"Invalid color '{self.color}'. Must be 6 hex digits.")
+
+
+@dataclass
+class Omero:
+    channels: List[OmeroChannel]
+
+
 @dataclass
 class Metadata:
     axes: List[Axis]
     datasets: List[Dataset]
     coordinateTransformations: Optional[List[Transform]]
+    omero: Optional[Omero] = None
     name: str = "image"
     version: str = "0.4"

ngff_zarr/v05/zarr_metadata.py

@@ -1,12 +1,13 @@
 from typing import List, Optional
 from dataclasses import dataclass
 
-from ..v04.zarr_metadata import Axis, Transform, Dataset
+from ..v04.zarr_metadata import Axis, Transform, Dataset, Omero
 
 
 @dataclass
 class Metadata:
     axes: List[Axis]
     datasets: List[Dataset]
     coordinateTransformations: Optional[List[Transform]]
+    omero: Optional[Omero] = None
     name: str = "image"

test/test_omero.py

@@ -0,0 +1,116 @@
+import pytest
+import numpy as np
+from zarr.storage import MemoryStore
+from ngff_zarr import (
+    Omero,
+    OmeroChannel,
+    OmeroWindow,
+    from_ngff_zarr,
+    to_ngff_image,
+    to_multiscales,
+    to_ngff_zarr,
+)
+
+from ._data import test_data_dir
+
+
+def test_read_omero(input_images):  # noqa: ARG001
+    dataset_name = "13457537"
+    store_path = test_data_dir / "input" / f"{dataset_name}.zarr"
+    multiscales = from_ngff_zarr(store_path, validate=True)
+
+    omero = multiscales.metadata.omero
+    assert omero is not None
+    assert len(omero.channels) == 6
+
+    # Channel 0
+    assert omero.channels[0].color == "FFFFFF"
+    assert omero.channels[0].window.min == 0.0
+    assert omero.channels[0].window.max == 65535.0
+    assert omero.channels[0].window.start == 0.0
+    assert omero.channels[0].window.end == 1200.0
+
+    # Channel 1
+    assert omero.channels[1].color == "FFFFFF"
+    assert omero.channels[1].window.min == 0.0
+    assert omero.channels[1].window.max == 65535.0
+    assert omero.channels[1].window.start == 0.0
+    assert omero.channels[1].window.end == 1200.0
+
+    # Channel 2
+    assert omero.channels[2].color == "FFFFFF"
+    assert omero.channels[2].window.min == 0.0
+    assert omero.channels[2].window.max == 65535.0
+    assert omero.channels[2].window.start == 0.0
+    assert omero.channels[2].window.end == 1200.0
+
+    # Channel 3
+    assert omero.channels[3].color == "FFFFFF"
+    assert omero.channels[3].window.min == 0.0
+    assert omero.channels[3].window.max == 65535.0
+    assert omero.channels[3].window.start == 0.0
+    assert omero.channels[3].window.end == 1200.0
+
+    # Channel 4
+    assert omero.channels[4].color == "0000FF"
+    assert omero.channels[4].window.min == 0.0
+    assert omero.channels[4].window.max == 65535.0
+    assert omero.channels[4].window.start == 0.0
+    assert omero.channels[4].window.end == 5000.0
+
+    # Channel 5
+    assert omero.channels[5].color == "FF0000"
+    assert omero.channels[5].window.min == 0.0
+    assert omero.channels[5].window.max == 65535.0
+    assert omero.channels[5].window.start == 0.0
+    assert omero.channels[5].window.end == 100.0
+
+
+def test_write_omero():
+    data = np.random.randint(0, 256, 262144).reshape((2, 32, 64, 64)).astype(np.uint8)
+    image = to_ngff_image(data, dims=["c", "z", "y", "x"])
+    multiscales = to_multiscales(image, scale_factors=[2, 4], chunks=32)
+
+    omero = Omero(
+        channels=[
+            OmeroChannel(
+                color="008000",
+                window=OmeroWindow(min=0.0, max=255.0, start=10.0, end=150.0),
+            ),
+            OmeroChannel(
+                color="0000FF",
+                window=OmeroWindow(min=0.0, max=255.0, start=30.0, end=200.0),
+            ),
+        ]
+    )
+    multiscales.metadata.omero = omero
+
+    store = MemoryStore()
+    version = "0.4"
+    to_ngff_zarr(store, multiscales, version=version)
+
+    multiscales_read = from_ngff_zarr(store, validate=True, version=version)
+    read_omero = multiscales_read.metadata.omero
+
+    assert read_omero is not None
+    assert len(read_omero.channels) == 2
+    assert read_omero.channels[0].color == "008000"
+    assert read_omero.channels[0].window.start == 10.0
+    assert read_omero.channels[0].window.end == 150.0
+    assert read_omero.channels[1].color == "0000FF"
+    assert read_omero.channels[1].window.start == 30.0
+    assert read_omero.channels[1].window.end == 200.0
+
+
+def test_validate_color():
+    valid_channel = OmeroChannel(
+        color="1A2B3C", window=OmeroWindow(min=0.0, max=255.0, start=0.0, end=100.0)
+    )
+    # This should not raise an error
+    valid_channel.validate_color()
+
+    invalid_channel = OmeroChannel(
+        color="ZZZZZZ", window=OmeroWindow(min=0.0, max=255.0, start=0.0, end=100.0)
+    )
+    with pytest.raises(ValueError, match=r"Invalid color 'ZZZZZZ'"):
+        invalid_channel.validate_color()