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

HaleySchuhl · 2025-01-09T18:04:38Z

Describe your changes
Rather than pruning by size, we can prune leaves by height which is helpful for tillering grasses.

Type of update
Is this a:

New feature
Work in progress

Associated issues
Reference associated issue numbers. Does this pull request close any issues?

Additional context
Merged changes in #1644 into this branch too, so that all new tools could be used from this location. Merge only AFTER #1644 has been merged.

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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

rearrage ome imports and change where things are getting called from

deepsource-io · 2025-01-09T18:06:29Z

Here's the code health analysis summary for commits c6105a7..09ee6b8. View details on DeepSource ↗.

Analysis Summary

Analyzer	Status	Summary	Link
Python	❌ Failure	❗ 12 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	99.6% (down 0.4% from `main`)	99.6% (down 0.4% from `main`)
Line Coverage	99.6% (down 0.4% from `main`)	99.6% (down 0.4% from `main`)
New Branch Coverage	100%	100%
New Composite Coverage	88.4%	88.4%
New Line Coverage	88.4%, ❌ Below Threshold	88.4%, ❌ Below Threshold

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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 18 commits December 23, 2024 09:36

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

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

Merge branch 'update_morphology_tips_outputs' into add_prune_by_height

a7f93c7

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 3 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

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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

deepsource-io bot commented Jan 9, 2025 •

edited

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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

deepsource-io bot commented Jan 9, 2025 • edited Loading

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deepsource-io bot commented Jan 9, 2025 •

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