Open joshmoore opened 2 years ago
Base: 92.43% // Head: 91.62% // Decreases project coverage by -0.80%
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:+1: 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>]
:-1: 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 :warning:
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)
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
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.