8000 Implement MultiplePrimaryRootPipeline by andrewjoc · Pull Request #117 · talmolab/sleap-roots · GitHub
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Implement MultiplePrimaryRootPipeline #117

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Merged
merged 29 commits into from
Jun 23, 2025
Merged

Implement MultiplePrimaryRootPipeline #117

merged 29 commits into from
Jun 23, 2025

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andrewjoc
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@andrewjoc andrewjoc commented Apr 21, 2025 •
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  • Implements the MultiplePrimaryRootPipeline which calculates traits of multiple primary roots on a single image
  • Tests the output of the pipeline with a manual calculation and fixtures, on both cylinder scans and plate images
  • Adds new test dataset for plate images rice_graviscan
  • Adds tutorial notebook for the MultiplePrimaryRootPipeline with examples for cylinder scans and plates
  • Adds MultiplePrimaryRootPipeline to mermaid diagrams notebook
  • Adds csv fixtures to tests/data/multiple_arabidopsis_11do and tests/data/rice_graviscan

Fixes #114, #119

andrewjoc added 14 commits April 16, 2025 15:13
@andrewjoc andrewjoc changed the title upload first implementation of multiple primary root pipeline Add MultiplePrimaryRootPipeline Apr 21, 2025
@andrewjoc andrewjoc changed the title Add MultiplePrimaryRootPipeline Implement MultiplePrimaryRootPipeline Apr 21, 2025
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codecov bot commented Apr 21, 2025 •
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Codecov Report

Attention: Patch coverage is 71.19565% with 53 lines in your changes missing coverage. Please review.

Project coverage is 83.98%. Comparing base (fc943be) to head (380e90f).
Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
sleap_roots/trait_pipelines.py 69.54% 53 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #117      +/-   ##
==========================================
- Coverage   85.33%   83.98%   -1.35%     
==========================================
  Files          13       13              
  Lines        1452     1636     +184     
==========================================
+ Hits         1239     1374     +135     
- Misses        213      262      +49

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@andrewjoc andrewjoc marked this pull request as ready for review April 28, 2025 02:07
Base automatically changed from andrew/implement-PrimaryRootPipeline to main May 5, 2025 01:05
eberrigan
eberrigan requested changes Jun 12, 2025
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test it with plate
add plate fixture -- inspecting the json output of compute_multiple_primary_roots_traits to make sure per plant values are correct

@andrewjoc andrewjoc requested a review from eberrigan June 16, 2025 01:17
eberrigan
eberrigan approved these changes Jun 17, 2025
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looks good! just knitpick comment

@andrewjoc andrewjoc merged commit 5bf4c9e into main Jun 23, 2025
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@andrewjoc andrewjoc deleted the andrew/implement-MultiplePrimaryRootPipeline branch June 23, 2025 01:02
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@eberrigan eberrigan eberrigan approved these changes

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Add multiple primary root pipeline
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