Add pcv.filters.eccentricity #1430

HaleySchuhl · 2024-01-18T19:31:52Z

Describe your changes
Add a new filtering function to the main plantcv workspace that filters objects in a binary mask based on it's eccentricity e.g. keep more circular things while long/oblong objects get filled in.

Type of update
Is this a:

New feature

Associated issues

functionality originally added during Interactive object count #754 but splitting apart into more manageable PRs, and updating interactive-object-count from main so we can also merge all those commits eventually.

Additional context
Highly helpful for stomata and pollen grain image cleanup

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

codecov · 2024-01-18T19:34:42Z

Codecov Report

Attention: Patch coverage is 47.05882% with 9 lines in your changes are missing coverage. Please review.

Project coverage is 99.85%. Comparing base (ec2e2df) to head (3a0628d).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1430      +/-   ##
==========================================
- Coverage   99.98%   99.85%   -0.13%     
==========================================
  Files         159      161       +2     
  Lines        7048     7066      +18     
==========================================
+ Hits         7047     7056       +9     
- Misses          1       10       +9

Flag	Coverage Δ
unittests	`99.85% <47.05%> (-0.13%)`	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files	Coverage Δ
plantcv/plantcv/__init__.py	`100.00% <ø> (ø)`
plantcv/plantcv/filter/__init__.py	`100.00% <100.00%> (ø)`
plantcv/plantcv/filter/eccentricity.py	`40.00% <40.00%> (ø)`

... and 1 file with indirect coverage changes

whitespace corrections

one more whitespace

trailing whitespace

whitespace

try to hit coverage

different test data?

add new function

HaleySchuhl · 2024-01-22T16:12:54Z

Just added materials for the reviewer to the shared google drive, in a folder called detect_discs_1430

annacasto

Added a test notebook called pr1430_detect-discs to the shared google drive in the detect_dics folder

update import in test file

…plantcv into add_detect_discs

Re-definition found for builtin function, so cannot name subpackage "filter", try to be more specific

filter to filters

I believe deepsource thinks it is a circular import because the test module was named eccentricity.py vs test_eccentricity.py

codecov-commenter · 2024-02-27T18:33:00Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.98%. Comparing base (ec2e2df) to head (a5ede9b).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1430   +/-   ##
=======================================
  Coverage   99.98%   99.98%           
=======================================
  Files         159      161    +2     
  Lines        7048     7066   +18     
=======================================
+ Hits         7047     7065   +18     
  Misses          1        1

Flag	Coverage Δ
unittests	`99.98% <100.00%> (+<0.01%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files	Coverage Δ
plantcv/plantcv/__init__.py	`100.00% <ø> (ø)`
plantcv/plantcv/filters/__init__.py	`100.00% <100.00%> (ø)`
plantcv/plantcv/filters/eccentricity.py	`100.00% <100.00%> (ø)`

... and 1 file with indirect coverage changes

…plantcv into add_detect_discs

HaleySchuhl

Looks good to me now! Apologies for not pushing my re-naming commits sooner to save you a minute or two but thanks for the help @nfahlgren for getting this function all fixed up.

Only minor thing I noticed, but didn't want to rerun test for this, is updating.md I think was meant to call the output variable filtered_mask instead of filterec_mask.

HaleySchuhl added 3 commits January 18, 2024 12:06

Create detect_discs.py

c8deb86

add documentation page and images

503aceb

Create test_detect_discs.py

cbdf40c

HaleySchuhl added new feature New feature ideas and solutions work in progress Mark work in progress labels Jan 18, 2024

HaleySchuhl self-assigned this Jan 18, 2024

HaleySchuhl added 12 commits January 18, 2024 13:36

Update updating.md

c2a03b0

Update mkdocs.yml

1ce5d10

Update test_detect_discs.py

3a67030

whitespace corrections

Update test_detect_discs.py

e956fab

one more whitespace

Update detect_discs.py

e64b2d7

trailing whitespace

Create test_detect_discs.py

c3871ec

Update test_detect_discs.py

7c25cb7

whitespace

Delete test_detect_discs.py

23397d3

Update test_detect_discs.py

338e529

Update test_detect_discs.py

f384af1

try to hit coverage

Update test_detect_discs.py

7e81144

different test data?

decrease threshold for eccentricity

fea707a

HaleySchuhl added ready to review and removed work in progress Mark work in progress labels Jan 22, 2024

Update __init__.py

77b4654

add new function

HaleySchuhl requested a review from annacasto January 22, 2024 19:31

Merge branch 'main' into add_detect_discs

c38cfdb

annacasto approved these changes Jan 30, 2024

View reviewed changes

nfahlgren and others added 4 commits January 30, 2024 13:59

Merge branch 'main' into add_detect_discs

6732538

Update test_detect_discs.py

712f253

update import in test file

Merge branch 'add_detect_discs' of https://github.com/danforthcenter/…

5d6f3c5

…plantcv into add_detect_discs

trying to resolve deepsource complaint

77766ae

HaleySchuhl and others added 16 commits February 27, 2024 11:13

refactor filter subpackage to filter_mask

b9591e3

Re-definition found for builtin function, so cannot name subpackage "filter", try to be more specific

refactor to "filters"

7054019

more refactoring

c564efb

Update __init__.py

352a771

filter to filters

Add two line returns between functions

01df82c

Remove unused import

304dd3b

Remove unused imports

52f5347

Remove trailing whitespace

166eb73

Add space between inputs

09dfcf0

Add missing line return at end of file

02dad0b

Rename module filter to filters to avoid masking builtin

d835a0e

Rename filter to filters

90cb5d3

Rename test module and test file

c37d7e0

I believe deepsource thinks it is a circular import because the test module was named eccentricity.py vs test_eccentricity.py

Finish renaming submodule

8d634e4

Define datadir

baba1f3

Fix assertion direction and lower threshold for coverage

6c58ab4

nfahlgren added ready to review and removed work in progress Mark work in progress labels Feb 27, 2024

HaleySchuhl added 2 commits February 28, 2024 07:45

update test data variable name

fde5e19

Merge branch 'add_detect_discs' of https://github.com/danforthcenter/…

038d5d4

…plantcv into add_detect_discs

HaleySchuhl changed the title ~~Add pcv.filter.eccentricity~~ Add pcv.filters.eccentricity Feb 28, 2024

Update mkdocs.yml doc name filters_eccentricity

a5ede9b

HaleySchuhl commented Feb 28, 2024

View reviewed changes

nfahlgren added 3 commits February 28, 2024 11:23

Merge branch 'main' into add_detect_discs

0267710

Add two line returns between functions

27f2882

Fix typo

24a76ce

nfahlgren merged commit 8a69fe0 into main Feb 28, 2024

nfahlgren deleted the add_detect_discs branch February 28, 2024 17:49

nfahlgren added this to the PlantCV v4.3 milestone Apr 20, 2024

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Add pcv.filters.eccentricity #1430

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HaleySchuhl commented Jan 18, 2024 •

edited by nfahlgren

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HaleySchuhl commented Jan 22, 2024

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HaleySchuhl commented Jan 18, 2024 •

edited by nfahlgren

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