Reduce complexity and add helpers to `morphology.segment_insertion_angle` #1671

HaleySchuhl · 2025-02-06T15:51:16Z

Describe your changes
Add helper functions to pcv.morphology.segment_insertion_angle

Type of update

code cleanup
Work in progress

Associated issues

Additional context
Add helper functions to reduce the cyclomatic complexity that is currently a deepsource issue in #1647 and #1644

For the reviewer
See this page for instructions on how to review the pull request.

PR functionality reviewed in a Jupyter Notebook
All tests pass
Test coverage remains 100%
Documentation tested
New documentation pages added to plantcv/mkdocs.yml
Changes to function input/output signatures added to updating.md
Code reviewed
PR approved

avoid saving to outputs in the helper function but produce the same relevant outputs, update instances of find_tips getting used throughout morphology

img input not just for plotting debug

add optimal assignment input

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

rearrage ome imports and change where things are getting called from

helper function to combine stems and then removed the list initialization of insertion segments

…ertion_angle

deepsource-io · 2025-02-06T15:52:27Z

Here's the code health analysis summary for commits e160b2a..0076a1c. View details on DeepSource ↗.

Analysis Summary

Analyzer	Status	Summary	Link
Python	❌ Failure	❗ 2 occurences introduced 🎯 1 occurence resolved	View Check ↗
Test coverage	❌ Failure	❗ 1 occurence introduced 🚨 1 failing metric	View Check ↗

Code Coverage Report

Metric	Aggregate	Python
Branch Coverage	100%	100%
Composite Coverage	100%	100%
Line Coverage	100%	100%
New Branch Coverage	100%	100%
New Composite Coverage	99.5%	99.5%
New Line Coverage	99.5%, ❌ Below Threshold	99.5%, ❌ Below Threshold

💡 If you’re a repository administrator, you can configure the quality gates from the settings.

HaleySchuhl added 30 commits December 17, 2024 14:34

Create segment_ends.py

ac60d30

range rather than enumerate

a5ef615

helper for _find_tips

269137a

avoid saving to outputs in the helper function but produce the same relevant outputs, update instances of find_tips getting used throughout morphology

update more instances of find_tips to use helper

cf17f11

remove label from helper function

034ebac

Update __init__.py

d0f49b2

add label logic into the front facing function

0ea3128

update segment sort stop editing tip info

66f25fb

add segment_ends to morphology init

7558e8c

add segment_img as required input, add outputs

acffd97

img input not just for plotting debug

Create test_segment_ends.py

43cfbdb

update segment_id allow optimal_assignment of IDs

81d0574

Update test_segment_id.py

4c48eac

add optimal assignment input

convert to color for debug image

eddfab5

segment_ends check tip or branch_pt

49bdc78

test_segment_ends_no_mask

5753678

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

Re-defined variable from outer scope

be3cdb7

remove unused var

86db239

white space fixes

9e84adc

line length fixes

dcea2a9

remove trailing whitespace

333e353

more whitespaces fixes

ee3e4be

move _iterative_prune and _find_tips to _helpers

0b63217

rearrage ome imports and change where things are getting called from

whitespace fixes

554b499

move segment_end sorting logic into _helpers

f802504

add logic for returning the optimal segment assignment

d8fd5c0

updating.md add segment_ends

0b296b1

Create segment_ends.md

6fde9cd

whitespace deepsource fixes

a8c74a5

HaleySchuhl added 15 commits January 2, 2025 16:49

Update segment_insertion_angle.py

77dbe05

add debug images for segment ends

85c2c9f

return sorted objs instead of ordered labels

869c232

Update mkdocs.yml

2e4149d

update docs to reflect new sorting approach

fa7f689

start replacing code in insertion_angle

9e3a158

removed vars and add stem helper

b2847a7

helper function to combine stems and then removed the list initialization of insertion segments

updating output collection logic

0db7af2

debugging test errors

e1602ea

write _segment_ends helper

5ef9a23

Merge branch 'update_morphology_tips_outputs' into update_segment_ins…

05a813c

…ertion_angle

comment out the overflow unit test

f3db50b

add comments and remove unused code

ea992c3

rename inner_segments and cleanup comments

74f9c54

Merge branch 'main' into update_segment_insertion_angle

14cb5eb

HaleySchuhl added work in progress Mark work in progress update Updates an existing feature/method cleanup Code quality updates labels Feb 6, 2025

HaleySchuhl self-assigned this Feb 6, 2025

HaleySchuhl added 2 commits February 6, 2025 09:58

replace range(len(objs) with enumerate

94c0e56

resolved deepsource issues

0076a1c

HaleySchuhl marked this pull request as draft February 6, 2025 16:33

HaleySchuhl closed this Feb 7, 2025

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Reduce complexity and add helpers to `morphology.segment_insertion_angle` #1671

Reduce complexity and add helpers to `morphology.segment_insertion_angle` #1671

HaleySchuhl commented Feb 6, 2025

deepsource-io bot commented Feb 6, 2025 •

edited

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Analysis Summary

Code Coverage Report

Reduce complexity and add helpers to morphology.segment_insertion_angle #1671

Reduce complexity and add helpers to morphology.segment_insertion_angle #1671

Conversation

HaleySchuhl commented Feb 6, 2025

deepsource-io bot commented Feb 6, 2025 • edited Loading

Analysis Summary

Code Coverage Report

Reduce complexity and add helpers to `morphology.segment_insertion_angle` #1671

Reduce complexity and add helpers to `morphology.segment_insertion_angle` #1671

deepsource-io bot commented Feb 6, 2025 •

edited

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