First draft of classifier generation pipeline - #89
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bergsalex merged 11 commits intoOct 7, 2025
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bergsalex
requested review from
C-1337ka,
SkepticRaven,
gbeane,
jacobbeierle and
keithshep
September 30, 2025 11:29
…s-classifier-artifact-generation
…s-classifier-artifact-generation
C-1337ka
approved these changes
Oct 7, 2025
SkepticRaven
approved these changes
Oct 7, 2025
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Do we want configs outside the configs folder?
| "stitch_value": 5, | ||
| "filter_value": 5, | ||
| ], | ||
| // "Leg_splaying": [ // Currently can't be exported successfully |
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JABS v0.34 + should have this fixed. I was able to build that artifact for #75. This classifier should be okay to uncomment and include.
| script: | ||
| def project_path = "${params.classifier_project_folders}/${project_folder_name}" | ||
| """ | ||
| jabs-init "${project_path}" ${window_sizes} -p 16 |
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Does this write into the frozen project folder? This may cause conflicts in 2 situations:
- no write permission (maybe we want it this way, because it'll fail later when trying to publish results)
- 2 builds running at the same time will compete writing feature files to the same location
| "filter_value": 3*30, | ||
| 'grooming': [ | ||
| classifier_path: '/projects/kumar-lab/data/jabs/classifiers/v0.37.0/grooming/12199145d31213f79e23669d211cfa2fd33cedb9f11197b44f90a4b71297b6d2.pickle', | ||
| stitch_value: 300, |
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😢 I like the multiplication to see 10s and 3s more clearly.
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These look like patches for something not working. These should have been in a different PR to fix the main modules.
bergsalex
marked this pull request as ready for review
October 7, 2025 19:11
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This PR adds a new workflow that automates the generation of classifier artifacts for the main workflow.
This will allow us to easily regenerate classifiers existing for new versions of JABs, as well as add new classifiers by placing their project directory into the
/projects/kumar-lab/projectsdirectory and updating theclassifier_source.configfile.There are still some tasks left to-do before this PR is ready to merge:
jabs-initstep to allow the classifiers to be generated in paralleljabs-initstep/projects/kumar-lab/data/and/projects/kumar-lab/projectsdirectories for use with this workflowReview of the current state would be appreciated given acknowledgement of the above.