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Parse multiplexing datasets #210

Merged
merged 31 commits into from
Nov 21, 2022
Merged

Parse multiplexing datasets #210

merged 31 commits into from
Nov 21, 2022

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tcompa
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@tcompa tcompa commented Nov 16, 2022

Ref #34

tcompa added 24 commits November 16, 2022 16:35
@tcompa
BROKEN init create_zarr_structure_multiplex.py
3610001
@tcompa
Keep working on multiplex parsing
5fd0e58
@tcompa
Sandbox multiplex / run example
9742baf
@tcompa
Sandbox multiplex / run example
88554aa
@tcompa
Update create_zarr_structure_multiplex.py prototype
1ad0bab
@tcompa
Update create_zarr_structure_multiplex.py prototype
ccf8a62
@tcompa
BROKEN make yokogawa parsing acquisition-aware
8ee63a5
@tcompa
Provisionally allow yokogawa-to-zarr to work for both multiplex or st…
a4e8434 
…andard datasets
@tcompa
.gitignore
7e35a47
@tcompa
Remove debug statements
4c9ef58
@tcompa
Remove debug statements + style
ce32270
@tcompa
Move define_omero_channels to specific module
d46eada
@tcompa
Fix handling of zattrs
c5fbba4
@tcompa
Validate OME-Zarr JSON schema
84020f2
@tcompa
Multiple updates to multiplexing (notably: lib_read_fractal_metadata)
5d9c043
@tcompa
Update test to load manifest schema from fractal-common repo
b8b9bba
@tcompa
Rename well->image in manifest and tests
4483259
@tcompa
Rename well->image in create_zarr_structure
7df3277
@tcompa
Fix discover_acquisition_from_ome_zarr function
50875a4
@tcompa
Fix import
3f5aff0
@tcompa
Preliminary update to replicate_zarr_structure, to update plate/well/…
974713c 
…image metadata lists
@tcompa
Also store plate in metadata, im create_zarr_structure_multiplex, for…
8849e5c 
… consistence with other tasks
@tcompa
Rename well->image in one more test
6d81db7
@tcompa
Update 0.4.0 changelog
d361181
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tcompa commented Nov 18, 2022 •
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Missing for this PR:

  • Add a warning for when the logic of acquisition discovery (look in the zattrs of the parent folder) breaks.
  • Add a test for that discovery function.
  • Add a test with a full multiplex workflow (just parsing, for the time being, and by creating a fake multiplexing dataset starting from the tiny dataset on Zenodo).
  • Fill in some minimalistic docstrings here and there.
  • Include new task in manifest.

Then I would merge, and address the multiplex workflows somewhere else.

@tcompa tcompa merged commit e49bfd8 into main Nov 21, 2022
@tcompa tcompa deleted the multiplexing_parsing branch November 21, 2022 11:37
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