Support metadata for .zarr converted from .nd2 using bioformats2raw conversion
#272
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talonchandler
changed the title
.zarr converted from .nd2 using bioformats2raw conversion.zarr converted from .nd2 using bioformats2raw conversion
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I'm noticing some OMERO-related issues. Might also be related to #270. |
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I'm trying to understand the changes to the metadata models, but the file in OP has been removed. @talonchandler can you point me to an example? |
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Pardon me! Here's a test. Thank you @ziw-liu. |
ziw-liu
reviewed
Mar 11, 2025
| @@ -166,7 +166,7 @@ class TimeAxisMeta(NamedAxisMeta): | |||
| "zettasecond", | |||
| ] | |||
| | None | |||
| ) | |||
| ) = None | |||
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Is there an example where not having this change causes a validation error?
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Does Pydantic error when an optional field is not present (instead of having the value null in JSON)?
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Yes. Without this change:
iohub info /hpc/projects/virtual_staining/datasets/shiau-lab/Examples_Tests_Talon/2025-02-15-93a-4dpf-test/250215_93a_4dpf_em2_sib_2048_002.zarr/0
gives
WARNING:iohub.ngff.nodes:Zarr group at does not have valid metadata for <class 'iohub.ngff.nodes.Position'>
Traceback (most recent call last):
File "/home/talon.chandler/.conda/envs/iohub-dev/bin/iohub", line 8, in <module>
sys.exit(cli())
File "/home/talon.chandler/.conda/envs/iohub-dev/lib/python3.10/site-packages/click/core.py", line 1161, in __call__
return self.main(*args, **kwargs)
File "/home/talon.chandler/.conda/envs/iohub-dev/lib/python3.10/site-packages/click/core.py", line 1082, in main
rv = self.invoke(ctx)
File "/home/talon.chandler/.conda/envs/iohub-dev/lib/python3.10/site-packages/click/core.py", line 1697, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/talon.chandler/.conda/envs/iohub-dev/lib/python3.10/site-packages/click/core.py", line 1443, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/talon.chandler/.conda/envs/iohub-dev/lib/python3.10/site-packages/click/core.py", line 788, in invoke
return __callback(*args, **kwargs)
File "/home/talon.chandler/iohub/iohub/cli/cli.py", line 50, in info
print_info(file, verbose=verbose)
File "/home/talon.chandler/iohub/iohub/reader.py", line 213, in print_info
ch_msg = f"Channel names:\t\t {reader.channel_names}"
File "/home/talon.chandler/iohub/iohub/ngff/nodes.py", line 142, in channel_names
return self._channel_names
AttributeError: 'Position' object has no attribute '_channel_names'. Did you mean: 'channel_names'?
After the change. The same call prints
Reading file: /hpc/projects/virtual_staining/datasets/shiau-lab/Examples_Tests_Talon/2025-02-15-93a-4dpf-test/250215_93a_4dpf_em2_sib_2048_002.zarr/0
Zarr hierarchy:
/
├── 0 (10, 3, 66, 2048, 2048) >u2
├── 1 (10, 3, 66, 1024, 1024) >u2
├── 2 (10, 3, 66, 512, 512) >u2
└── 3 (10, 3, 66, 256, 256) >u2
=== Summary ===
Format: omezarr v0.4
Axes: t (time); c (channel); z (space); y (space); x (space);
Channel names: ['DIA', 'GFP', 'RFP']
(Z, Y, X) scale (um): (1.0, 0.157177107973598, 0.157177107973598)
Chunk size: (1, 1, 1, 1024, 1024)
No. bytes decompressed: 16609443840 [15.5 GiB]
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So removing these causes the node to not parse the metadata, but I wonder if that is a logic bug like #270 instead of a schema modeling bug.
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This PR contains minor spec-mismatch bug fixes to enable
iohub infoto work with.zarrfiles converted from.nd2usingbioformats2rawconversion tool.For example:
prints
Note:
bioformats2rawseems to create single positions stacked one layer deeper than our typical single positions, so I calliohub infoon.zarr/0.Note: @ziw-liu @mattersoflight I'm tagging you here to keep you in the loop. I'll plan to request your review after we've completed a phase reconstruction during the week of March 3.