add omero metadata to writer

.pre-commit-config.yaml

@@ -58,8 +58,10 @@ repos:
  # default black line length is 88
  "--max-line-length=88",
  # Conflicts with black: E203 whitespace before ':'
+ # Conflicts with PEP8 and black:
+ # W503 line break before binary operator
  # Does not recognize deprecated directive in docstrings
- "--ignore=E203,RST303",
+ "--ignore=E203,RST303, W503",
  "--rst-roles=class,func,ref,mod,meth,const",
  ]
 

ome_zarr/data.py

@@ -136,38 +136,48 @@ def create_zarr(
  chunks[zct] = 1
 
  storage_options = dict(chunks=tuple(chunks))
- write_multiscale(pyramid, grp, axes=axes, storage_options=storage_options)
 
  if size_c == 1:
  image_data = {
- "channels": [{"window": {"start": 0, "end": 255}, "color": "FF0000"}],
+ "channels": [
+ {
+ "window": {"start": 0, "end": 255, "min": 0, "max": 255},
+ "color": "FF0000",
+ }
+ ],
  "rdefs": {"model": "greyscale"},
  }
  else:
  image_data = {
  "channels": [
  {
  "color": "FF0000",
- "window": {"start": 0, "end": 255},
+ "window": {"start": 0, "end": 255, "min": 0, "max": 255},
  "label": "Red",
  "active": True,
  },
  {
  "color": "00FF00",
- "window": {"start": 0, "end": 255},
+ "window": {"start": 0, "end": 255, "min": 0, "max": 255},
  "label": "Green",
  "active": True,
  },
  {
  "color": "0000FF",
- "window": {"start": 0, "end": 255},
+ "window": {"start": 0, "end": 255, "min": 0, "max": 255},
  "label": "Blue",
  "active": True,
  },
  ],
  "rdefs": {"model": "color"},
  }
- grp.attrs["omero"] = image_data
+ write_multiscale(
+ pyramid,
+ grp,
+ axes=axes,
+ storage_options=storage_options,
+ metadata={"omero": image_data},
+ )
 
  if labels:
  labels_grp = grp.create_group("labels")

ome_zarr/reader.py

@@ -382,7 +382,7 @@ def __init__(self, node: Node) -> None:
  elif contrast_limits is not None:
  contrast_limits[idx] = [start, end]
 
- node.metadata["name"] = names
+ node.metadata["channel_names"] = names
  node.metadata["visible"] = visibles
  node.metadata["contrast_limits"] = contrast_limits
  node.metadata["colormap"] = colormaps

ome_zarr/writer.py

@@ -321,6 +321,29 @@ def write_multiscales_metadata(
  axes = _get_valid_axes(axes=axes, fmt=fmt)
  if axes is not None:
  ndim = len(axes)
+ if (
+ isinstance(metadata, dict)
+ and metadata.get("metadata")
+ and isinstance(metadata["metadata"], dict)
+ and "omero" in metadata["metadata"]
+ ):
+ omero_metadata = metadata["metadata"].get("omero")
+ if omero_metadata is None:
+ raise KeyError("If `'omero'` is present, value cannot be `None`.")
+ for c in omero_metadata["channels"]:
+ if "color" in c:
+ if not isinstance(c["color"], str) or len(c["color"]) != 6:
+ raise TypeError("`'color'` must be a hex code string.")
+ if "window" in c:
+ if not isinstance(c["window"], dict):
+ raise TypeError("`'window'` must be a dict.")
+ for p in ["min", "max", "start", "end"]:
+ if p not in c["window"]:
+ raise KeyError(f"`'{p}'` not found in `'window'`.")
+ if not isinstance(c["window"][p], (int, float)):
+ raise TypeError(f"`'{p}'` must be an int or float.")
+
+ group.attrs["omero"] = omero_metadata
 
  # note: we construct the multiscale metadata via dict(), rather than {}
  # to avoid duplication of protected keys like 'version' in **metadata

tests/test_reader.py

@@ -34,6 +34,14 @@ def test_label(self):
  reader = Reader(parse_url(filename))
  assert len(list(reader())) == 3
 
+ def test_omero(self):
+ reader = Reader(parse_url(str(self.path)))()
+ image_node = list(reader)[0]
+ omero = image_node.zarr.root_attrs.get("omero")
+ assert "channels" in omero
+ assert isinstance(omero["channels"], list)
+ assert len(omero["channels"]) == 1
+
 
 class TestInvalid:
  @pytest.fixture(autouse=True)

tests/test_writer.py

@@ -1,6 +1,7 @@
 import filecmp
 import pathlib
 from tempfile import TemporaryDirectory
+from typing import Any, Dict, Optional
 
 import dask.array as da
 import numpy as np
@@ -557,6 +558,80 @@ def test_invalid_transformations(self, coordinateTransformations):
  with pytest.raises(ValueError):
  write_multiscales_metadata(self.root, datasets, axes=axes)
 
+ @pytest.mark.parametrize(
+ "metadata",
+ [
+ {
+ "channels": [
+ {
+ "color": "FF0000",
+ "window": {"start": 0, "end": 255, "min": 0, "max": 255},
+ }
+ ]
+ },
+ {"channels": [{"color": "FF0000"}]},
+ {"channels": [{"color": "FF000"}]}, # test wrong metadata
+ {"channels": [{"window": []}]}, # test wrong metadata
+ {
+ "channels": [ # test wrong metadata
+ {"color": "FF0000", "window": {"start": 0, "end": 255, "min": 0}},
+ ]
+ },
+ None,
+ ],
+ )
+ def test_omero_metadata(self, metadata: Optional[Dict[str, Any]]):
+ datasets = []
+ for level, transf in enumerate(TRANSFORMATIONS):
+ datasets.append({"path": str(level), "coordinateTransformations": transf})
+ if metadata is None:
+ with pytest.raises(
+ KeyError, match="If `'omero'` is present, value cannot be `None`."
+ ):
+ write_multiscales_metadata(
+ self.root, datasets, axes="tczyx", metadata={"omero": metadata}
+ )
+ else:
+ window_metadata = (
+ metadata["channels"][0].get("window")
+ if "window" in metadata["channels"][0]
+ else None
+ )
+ color_metadata = (
+ metadata["channels"][0].get("color")
+ if "color" in metadata["channels"][0]
+ else None
+ )
+ if window_metadata is not None and len(window_metadata) < 4:
+ if isinstance(window_metadata, dict):
+ with pytest.raises(KeyError, match=".*`'window'`.*"):
+ write_multiscales_metadata(
+ self.root,
+ datasets,
+ axes="tczyx",
+ metadata={"omero": metadata},
+ )
+ elif isinstance(window_metadata, list):
+ with pytest.raises(TypeError, match=".*`'window'`.*"):
+ write_multiscales_metadata(
+ self.root,
+ datasets,
+ axes="tczyx",
+ metadata={"omero": metadata},
+ )
+ elif color_metadata is not None and len(color_metadata) != 6:
+ with pytest.raises(TypeError, match=".*`'color'`.*"):
+ write_multiscales_metadata(
+ self.root,
+ datasets,
+ axes="tczyx",
+ metadata={"omero": metadata},
+ )
+ else:
+ write_multiscales_metadata(
+ self.root, datasets, axes="tczyx", metadata={"omero": metadata}
+ )
+
 
 class TestPlateMetadata:
  @pytest.fixture(autouse=True)