Hyperplane update

[frheault]

Quick description

Attempt at having our improved RADTRACT Hyperplane subdivision !

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10246281/
...

Type of change

Check the relevant options.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

Provide data, screenshots, command line to test (if relevant)

...

Checklist

• My code follows the style guidelines of this project (run autopep8)
• I added relevant citations to scripts, modules and functions docstrings and descriptions
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I moved all functions from the script file (except the argparser and main) to scilpy modules
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes

[pep8speaks]

Hello @frheault, Thank you for updating !

• In the file scilpy/tractanalysis/bundle_operations.py:

Line 93:80: E501 line too long (80 > 79 characters)

• In the file scilpy/tractanalysis/distance_to_centroid.py:

Line 57:1: W293 blank line contains whitespace
Line 81:80: E501 line too long (81 > 79 characters)
Line 184:80: E501 line too long (80 > 79 characters)
Line 200:80: E501 line too long (80 > 79 characters)
Line 265:35: E203 whitespace before ','
Line 292:1: W293 blank line contains whitespace
Line 300:1: W293 blank line contains whitespace
Line 339:37: E127 continuation line over-indented for visual indent
Line 340:37: E127 continuation line over-indented for visual indent
Line 342:21: E127 continuation line over-indented for visual indent
Line 352:22: E128 continuation line under-indented for visual indent
Line 354:80: E501 line too long (83 > 79 characters)
Line 371:22: E128 continuation line under-indented for visual indent
Line 383:22: E128 continuation line under-indented for visual indent
Line 395:22: E128 continuation line under-indented for visual indent
Line 398:22: E128 continuation line under-indented for visual indent
Line 416:41: E128 continuation line under-indented for visual indent
Line 418:21: E128 continuation line under-indented for visual indent
Line 419:1: W293 blank line contains whitespace
Line 421:5: E303 too many blank lines (2)
Line 428:5: E303 too many blank lines (2)

• In the file scripts/scil_bundle_label_map.py:

Line 205:80: E501 line too long (80 > 79 characters)
Line 246:80: E501 line too long (92 > 79 characters)
Line 266:80: E501 line too long (81 > 79 characters)
Line 300:80: E501 line too long (84 > 79 characters)
Line 314:80: E501 line too long (81 > 79 characters)

Comment last updated at 2024-12-12 18:45:11 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 76.41791% with 79 lines in your changes missing coverage. Please review.

Project coverage is 56.73%. Comparing base (eb2e9ba) to head (23d65e5).

❗ There is a different number of reports uploaded between BASE (eb2e9ba) and HEAD (23d65e5). Click for more details.

HEAD has 1 upload less than BASE

Flag	BASE (eb2e9ba)	HEAD (23d65e5)
unittests	2	1

Additional details and impacted files

@@             Coverage Diff             @@
##           master    #1034       +/-   ##
===========================================
- Coverage   69.96%   56.73%   -13.24%     
===========================================
  Files         448      646      +198     
  Lines       24291    30209     +5918     
  Branches     3334     3413       +79     
===========================================
+ Hits        16996    17139      +143     
- Misses       5874    11633     +5759     
- Partials     1421     1437       +16     

Components	Coverage Δ
Scripts	53.71% <57.27%> (-17.02%)	⬇️
Library	61.30% <85.77%> (-7.64%)	⬇️

[CHrlS98]

Complicated code I don't fully understand, but apart from a few missing or incomplete docstring I didn't come across anything shocking. Also looks like there are a lot of remaining PEP8 issues.

[CHrlS98]

I trust you with the bitwise operations, but just want to make sure you didn't remove the ^ bool(swap) part by accident?

[frheault]

It's ok since the if at line 98 is swapping labels, this is checking orientation again based on that swap (so we don't want to cancel the previous swap)

[frheault]

@AntoineTheb Last time you tried that branch, everything was fine with the input/output?

[arnaudbore]

few comments but LGTM:

flake8 scilpy/tractograms/streamline_and_mask_operations.py 
scilpy/tractograms/streamline_and_mask_operations.py:634:5: F841 local variable 'orig_segment_len' is assigned to but never used

[arnaudbore]

@frheault still missing docstring here

[arnaudbore]

add
from scilpy.version import version_string