Cleaning reconst scripts part1

[EmmaRenauld]

Quick description

Encapsulating some parts of the main() in a few scripts in the column "reconst"

• scil_aodf_metrics: was clean
• scil_btensor_metrics: was clean
• scil_dki_compute_metrics:
  - encapsulated the residuals
  - encapsulated the smooth_to_fwhm
  - changed the residuals computation: removed the norm. Discussed with Maxime.
  - added many del variable, like is done in dti_metrics
  - Added the residual computation in the script testing. It created a fail at line data_p = dkifit.predict(gtab, S0). With the way dipy does thing, we needed to send the keywords, data_p = dkifit.predict(gtab=gtab, S0=S0)
• scil_dti_metrics:
  • encapsulated the residuals
  • made it clearer that FA is computed for both FA and RGB options.

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
• Cleaning scripts.

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 @EmmaRenauld, Thank you for updating !

• In the file scripts/scil_dti_metrics.py:

Line 150:80: E501 line too long (80 > 79 characters)

Comment last updated at 2024-02-22 22:48:19 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 67.16418% with 44 lines in your changes are missing coverage. Please review.

Project coverage is 68.53%. Comparing base (9412961) to head (d0697aa).
Report is 100 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #908      +/-   ##
==========================================
+ Coverage   68.12%   68.53%   +0.41%     
==========================================
  Files         386      388       +2     
  Lines       20678    20924     +246     
  Branches     3160     3219      +59     
==========================================
+ Hits        14087    14341     +254     
+ Misses       5326     5293      -33     
- Partials     1265     1290      +25     

Components	Coverage Δ
Scripts	71.34% <69.76%> (+0.66%)	⬆️
Library	63.72% <62.50%> (-0.05%)	⬇️

[arnaudbore]

a quick fix and GTG !

[EmmaRenauld]

I created again a new function in operations.

I also added a mask in the test of dti_metrics to have more coverage of residuals things.

Please see new line # 183. There were a lot of questions there. Can we delete that?

[arnaudbore]

GTG