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Update morphology tips outputs #1644

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@HaleySchuhl HaleySchuhl commented Dec 19, 2024

Describe your changes
The saved skeleton tips coordinates to Outputs was easily overwritten by other morphology functions that utilize the pcv.morphology.find_tips function. This branch contains changes to find_tips so that there is a helper function now that is used internally. Also adds pcv.morphology.segment_ends which saves both ends, the tip coordinates and the coordinates of the segment touching the branch point.

Type of update
Is this a:

  • Bug fix
  • New feature or feature enhancement
  • Work in progress

Associated issues

Additional context
Using the internal segment end coordinates for leaf ID order

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  • PR functionality reviewed in a Jupyter Notebook
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  • New documentation pages added to plantcv/mkdocs.yml
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Debug Options

  • use segment_img as required input and plot coordinates on top
    image

  • use mask as required input and plot segments + coordinates
    image

@HaleySchuhl HaleySchuhl added new feature New feature ideas and solutions bugfix Bug fixes work in progress Mark work in progress update Updates an existing feature/method labels Dec 19, 2024
@HaleySchuhl HaleySchuhl self-assigned this Dec 19, 2024
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deepsource-io bot commented Dec 19, 2024

Here's the code health analysis summary for commits c6105a7..fa7f689. View details on DeepSource ↗.

Analysis Summary

AnalyzerStatusSummaryLink
DeepSource Python LogoPython❌ Failure
❗ 1 occurence introduced
🎯 1 occurence resolved
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DeepSource Test coverage LogoTest coverage✅ SuccessView Check ↗

Code Coverage Report

MetricAggregatePython
Branch Coverage100%100%
Composite Coverage100%100%
Line Coverage100%100%
New Branch Coverage100%100%
New Composite Coverage100%100%
New Line Coverage100%, ✅ Above Threshold100%, ✅ Above Threshold

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@HaleySchuhl HaleySchuhl added ready to review and removed work in progress Mark work in progress labels Jan 3, 2025
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Jan 3 updates: the deepsource complaint about the complexity of segment_insertion_angle will be resolved in another PR branch (called "update_segment_insertion_angle").

While thinking about how to get biologically-ordered observations out from a morphology workflow given this new function, there is a reason to return a re-ordered list of objects. These can then get used downstream to get consistently labeled leaf segment observations.

@HaleySchuhl HaleySchuhl added work in progress Mark work in progress and removed ready to review labels Jan 3, 2025
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Skeleton tips easily overwritten within the plantcv.morphology sub-package
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