Add "prune by height" function to morphology subpackage #1647

HaleySchuhl · 2025-01-09T18:04:38Z

Describe your changes

Adds a new function prune_by_height

Type of update
Is this a:

New feature

Associated issues

Closes Prune by location (rather than by size) #1624

Additional context

Merged changes in Add segment_ends and Update morphology tips outputs #1644 into this branch too, so that all new tools could be used from this location. Merge only AFTER Add segment_ends and Update morphology tips outputs #1644 has been merged.
Rather than pruning by size, we can prune leaves by height which is helpful for tillering grasses.
segment_ends extracts both leaf tips and branch point coordinates, saves them to outputs, and returns re-ordered segments based on segments branch point y-coordinates.

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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

added comments, combine imports

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

deepsource-io · 2025-01-09T18:06:29Z

Here's the code health analysis summary for commits e160b2a..da9b1b8. View details on DeepSource ↗.

Analysis Summary

Analyzer	Status	Summary	Link
Python	❌ Failure	❗ 16 occurences introduced 🎯 1 occurence resolved	View Check ↗
Test coverage	❌ Failure	❗ 3 occurences introduced 🚨 1 failing metric	View Check ↗

Code Coverage Report

Metric	Aggregate	Python
Branch Coverage	100%	100%
Composite Coverage	99.9% (down 0.1% from `main`)	99.9% (down 0.1% from `main`)
Line Coverage	99.9% (down 0.1% from `main`)	99.9% (down 0.1% from `main`)
New Branch Coverage	100%	100%
New Composite Coverage	93.7%	93.7%
New Line Coverage	93.7%, ❌ Below Threshold	93.7%, ❌ Below Threshold

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add observation for missing branch point & start sorting on distance if no branch point found, plus debug image

HaleySchuhl added 30 commits November 5, 2024 13:26

code dump, adding prune_by_height

4cd2b8e

update line boundary logic & add prune_by_height_partial

c8d0b9b

prune by height partial logic update

ea4212e

Update prune.py

dddd76e

change line position default and add logic to auto find it

ad14cc5

update prune_by_height_partial imports

2616ace

added comments, combine imports

remove duplication of skeleton in pruning functions

bc92207

morphology init add prune by height partial

9a523de

add label param to prune_by_height

9e5e7b8

add observations for segment number

9ac44c2

index out the y-position for auto line_boundary setting

45bb939

remove extra print statement

64bcdd5

simplify segment_id debug

b034f69

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

HaleySchuhl added work in progress Mark work in progress merge in order Set of PRs that need to be merged sequentially labels Jan 9, 2025

HaleySchuhl added this to the PlantCV v4.7 milestone Jan 9, 2025

HaleySchuhl self-assigned this Jan 9, 2025

HaleySchuhl added 18 commits January 9, 2025 13:50

add variable definition outside of if statement

3cfd8b4

remove optimal assignment from testing

9213ab1

prune by height init

09ee6b8

update segment_ends sorting logic

2b8480a

add prune_by_height to updating.md

ed6fcf6

add prune_by_height to mkdocs

31037aa

add params.saved_color_scale = None to morphology tests

1de2a6c

add tests for prune by height

bdc0c88

Merge branch 'main' into add_prune_by_height

c59c272

minor tweaks to docs for clarity and accuracy

a3d0cff

Merge branch 'main' into update_morphology_tips_outputs

bd17ad8

Create prune_by_height.png

8604210

Create prune_by_height.md

cb519cd

whitespace

0b8d69d

update docstring in prune.py

753f205

Merge branch 'update_morphology_tips_outputs' into add_prune_by_height

279aeb6

Merge branch 'main' into add_prune_by_height

484d1ed

resolve deepsource issues in prune_by_height

ef26ecb

HaleySchuhl added new feature New feature ideas and solutions ready to review and removed work in progress Mark work in progress labels Feb 6, 2025

HaleySchuhl mentioned this pull request Feb 6, 2025

Reduce complexity and add helpers to morphology.segment_insertion_angle #1671

Closed

8 tasks

HaleySchuhl added 3 commits February 14, 2025 16:05

detect and REMOVE objs without branch_pt

2424c8a

segment ordering for orphaned leaf

8640dcf

add observation for missing branch point & start sorting on distance if no branch point found, plus debug image

return debug image

da9b1b8

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Add "prune by height" function to morphology subpackage #1647

Add "prune by height" function to morphology subpackage #1647

HaleySchuhl commented Jan 9, 2025 •

edited

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deepsource-io bot commented Jan 9, 2025 •

edited

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Code Coverage Report

Add "prune by height" function to morphology subpackage #1647

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Add "prune by height" function to morphology subpackage #1647

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HaleySchuhl commented Jan 9, 2025 • edited Loading

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HaleySchuhl commented Jan 9, 2025 •

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