OME-XML metadata support

[joshmoore]

NB: currently built on top of #42

Make use of metadata parsed via https://github.com/ome/ome-zarr-metadata for enriching the images in napari.

TODO:

• https://forum.image.sc/t/constructing-zarr-for-napari-ome-zarr/65398/4

[codecov-commenter]

Codecov Report

Base: 92.43% // Head: 91.62% // Decreases project coverage by -0.80% ⚠️

Coverage data is based on head (2ec3548) compared to base (d9ff37a).
Patch coverage: 71.42% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #47      +/-   ##
==========================================
- Coverage   92.43%   91.62%   -0.81%     
==========================================
  Files           3        3              
  Lines         185      191       +6     
==========================================
+ Hits          171      175       +4     
- Misses         14       16       +2     

Impacted Files	Coverage Δ
napari_ome_zarr/_reader.py	87.50% <71.42%> (-1.28%)	⬇️

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[joshmoore]

👍 Converted example&series=2.fake loads and has properly named layers:

viewer.open("/opt/ome-zarr-py/bf2raw/fake-series-2.zarr/")
/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0.  To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).!
Out[4]: 
[<Image layer 'series' at 0x1b43d4f70>,
 <Image layer 'series 2' at 0x1b44abee0>]

👎 For a converted plate&plates=1&plateRows=1.fake the naming does not get applied and only one image is loaded:

viewer.open("/opt/ome-zarr-py/bf2raw/plate-rows-2.zarr/")
/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0.  To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).!
Out[5]: [<Image layer 'unnamed' at 0x1b5336b50>]

viewer.open("/opt/ome-zarr-py/bf2raw/plate-no-bf2raw.zarr/")
Out[6]: [<Image layer 'unnamed [1]' at 0x1b4384dc0>]

Additionally: only loading from the internal console works. Loading from the command line with napari ...zarr hangs ⚠️

[joshmoore]

Ah, the lack of plate loading is apparently the ome-types validation issue:

Traceback (most recent call last):
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/ome_zarr/bioformats2raw.py", line 33, in __init__
    data = self.handle(node)
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/ome_zarr/bioformats2raw.py", line 98, in handle
    return self.parse_xml(metadata)
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/ome_zarr/bioformats2raw.py", line 92, in parse_xml
    return ome_types.from_xml(t.name)
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/ome_types/_convenience.py", line 106, in from_xml
    return OME(**d)
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/ome_types/model/ome.py", line 137, in __init__
    super().__init__(**data)
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/ome_types/_base_type.py", line 80, in __init__
    super().__init__(**data)
  File "pydantic/main.py", line 331, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 2 validation errors for OME
images -> 0 -> pixels -> planes -> 0 -> hash_sha1
  ensure this value has at most 20 characters (type=value_error.any_str.max_length; limit_value=20)
images -> 1 -> pixels -> planes -> 0 -> hash_sha1
  ensure this value has at most 20 characters (type=value_error.any_str.max_length; limit_value=20)

[will-moore]

is range(3) hard-coded for a 3-channel image?

[joshmoore]

Good question. I assume that's what that was about, yes.

[imagesc-bot]

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/saving-volumetric-data-with-voxel-size-colormap-annotations/85537/24

[imagesc-bot]

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/constructing-zarr-for-napari-ome-zarr/65398/4