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Channels refactor #239

Merged
merged 52 commits into from
Dec 2, 2022
Merged

Channels refactor #239

merged 52 commits into from
Dec 2, 2022

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tcompa
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@tcompa tcompa commented Dec 1, 2022 •
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@tcompa tcompa linked an issue Dec 1, 2022 that may be closed by this pull request
Refactor: How do we refer to channels? #211
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tcompa added 19 commits December 1, 2022 13:32
@tcompa
Basic handling of missing label
81a966a
@tcompa
Fix test
bfbe513
@tcompa
Rename some channel-related variables (plus small refactors)
66261f8
@tcompa
Update some tests
7076d76
@tcompa
Rename group_FOV to group_image in parsing task
fb9e7ef
@tcompa
Add get_omero_channel_list function and always include wavelength_id …
f262e29 
…in define_omero_channels
@tcompa
Do not use metadata channel list, in yokogawa_to_ome_zarr
e7b1e9f
@tcompa
Move all channel-related functions to lib_channels
6af193d
@tcompa
Adapt cellpose_segmentation
9fcad3c
@tcompa
Add get_channel_from_image_zarr helper function, rename _get.. functi…
7c62e01 
…on into get.., update napari_workflows_wrapper task
@tcompa
Add docstrings
6abd17d
@tcompa
Fix wrong function name
3f61ab6
@tcompa
Remove channel_list from metadata
91d4c7f
@tcompa
Update channel addressing in illumination_correction task
57924a1
@tcompa
Introduce new channel logic into multiplexing parsing task
978090f
@tcompa
Add check_unique_labels function and improve usage of define_omero_ch…
24730ab 
…annels
@tcompa
Keep updating tests for new channel scheme
f2abef7
@tcompa
Check per-image channel-label unicity
3cff675
@tcompa
xfail a test
ea9333d
@tcompa tcompa mentioned this pull request Dec 1, 2022
Closed
This was referenced Dec 1, 2022
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tcompa added 13 commits December 2, 2022 11:36
@tcompa
Update lib_channels (mostly docstrings and variable names)
b333785
@tcompa
Update wording of a comment
367c3d9
@tcompa
Add validate_allowed_channel_input function, and use it in all create…
19b6275 
…-zarr tasks
@tcompa
Remove default labeling_level from cellpose_segmentation task (close #…
b5efadc 
…242)
@tcompa
Rename variables in cellpose task, and add also channel_name arg
5866776
@tcompa
Add ChannelNotFoundError and capture it in cellpose_segmentation task
fa77add
@tcompa
Cleanup cellpose task (docstrings and some variable names)
adfc5f2
@tcompa
Fix docstring
637c5fc
@tcompa
Fix docstring
9942bf2
@tcompa
Rename channel_name to wavelength_id in napari-workflows wrapper, and…
79780b8 
… improve docstring
@tcompa
can -> must in docstring
3b9e5e7
@tcompa
Support both wavelength_id and label specifications for channels, in …
d01b06c 
…napari-workflows wrapper
@tcompa
Add custom exception docstrings
56da93a
@tcompa tcompa merged commit 806d435 into main Dec 2, 2022
@tcompa tcompa deleted the 211-refactor-how-do-we-refer-to-channels branch December 2, 2022 14:48
@tcompa tcompa mentioned this pull request Dec 12, 2022
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Successfully merging this pull request may close these issues.

Enforce unique channel names Refactor: How do we refer to channels?
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@tcompa