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multi channel segmentation support #423

Merged
merged 12 commits into from
Jul 8, 2024
Merged

multi channel segmentation support #423

merged 12 commits into from
Jul 8, 2024

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saeliddp
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@saeliddp saeliddp commented Jun 28, 2024

Context

See #374 . In order to implement support for multi-channel segmentations, I found it easiest to do some light refactoring to use slots/signals and our task executor framework. This is definitely not a full refactor of training to align with curation, but it is a start.

Main Changes

  1. channel_extraction.py: add an optional arg to the function that gets an image path from a provided csv.
  2. training_model.py: add state related to segmentation channels, remove unused state and associated functions
  3. training_service.py: implement async directory data extraction using the task executor pattern
  4. image_selection_widget.py: add UI elements for selecting segmentation channels + handlers for what happens when channels are set/selected
  5. cyto_overrides_manager.py: add overrides for segmentation channels

Testing

Added unit tests for image_selection_widget.py and training_model.py. Fixed any failing unit tests. Edit: I have now manually verified that we can run through curation/training with channel overrides for segmentations.

Screenshots

Screenshot 2024-06-28 at 3 14 49 PM Screenshot 2024-06-28 at 3 15 33 PM

@saeliddp saeliddp requested review from yrkim98 and hughes036 June 28, 2024 22:16
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@hughes036 hughes036 left a comment

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If this implements the plugin side of the contract with cyto-dl, i think we can merge. if the contract changes, we can make a followup pr.

@saeliddp
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saeliddp commented Jul 2, 2024

@hughes036

If this implements the plugin side of the contract with cyto-dl, i think we can merge

It does, but if we merge without the corresponding changes in cyto-dl being released, training will fail

@saeliddp saeliddp changed the title [Draft] multi channel segmentation support multi channel segmentation support Jul 2, 2024
@saeliddp saeliddp merged commit e21b33a into main Jul 8, 2024
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@saeliddp saeliddp deleted the 374-multi-channel-seg branch July 8, 2024 16:40
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3 participants