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Update morphology tips outputs #1644

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Update morphology tips outputs #1644

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HaleySchuhl
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@HaleySchuhl HaleySchuhl commented Dec 19, 2024 •
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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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  • Documentation tested
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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 •
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Here's the code health analysis summary for commits c6105a7..fa7f689. View details on DeepSource ↗.

Analysis Summary

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

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Branch Coverage100%100%
Composite Coverage100%100%
Line Coverage100%100%
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New Composite Coverage100%100%
New Line Coverage100%, ✅ Above Threshold100%, ✅ Above Threshold
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@HaleySchuhl
add segment_ends to morphology init
7558e8c
@HaleySchuhl
add segment_img as required input, add outputs
acffd97 
img input not just for plotting debug
@HaleySchuhl
Create test_segment_ends.py
43cfbdb
@HaleySchuhl
update segment_id allow optimal_assignment of IDs
81d0574
@HaleySchuhl
Update test_segment_id.py
4c48eac 
add optimal assignment input
@HaleySchuhl
convert to color for debug image
eddfab5
@HaleySchuhl
segment_ends check tip or branch_pt
49bdc78
@HaleySchuhl
test_segment_ends_no_mask
5753678
@HaleySchuhl
segment_sort no need to store label
fc6074d 
since no outputs in sorting, skip the label storage. wasn't used downstream but also don't need to store anymore since _find_tips also doesn't store to outputs
@HaleySchuhl
Re-defined variable from outer scope
be3cdb7
@HaleySchuhl
remove unused var
86db239
@HaleySchuhl
white space fixes
9e84adc
@HaleySchuhl
line length fixes
dcea2a9
@HaleySchuhl
remove trailing whitespace
333e353
@HaleySchuhl
more whitespaces fixes
ee3e4be
@HaleySchuhl
move _iterative_prune and _find_tips to _helpers
0b63217 
rearrage ome imports and change where things are getting called from
@HaleySchuhl HaleySchuhl added ready to review and removed work in progress Mark work in progress labels Jan 3, 2025
@HaleySchuhl
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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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Labels
bugfix Bug fixes new feature New feature ideas and solutions update Updates an existing feature/method work in progress Mark work in progress
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PlantCV4
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Successfully merging this pull request may close these issues.

Skeleton tips easily overwritten within the plantcv.morphology sub-package
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@HaleySchuhl