Cleaning reconst scripts part2

[EmmaRenauld]

Quick description

Part 2 in my meticulous verification of reconst scripts. Read the 9 next scripts in our excel list!

Almost all already correct! Changes a few small code style along the way. The only real changes:

• In fodf_max_in_ventricles:
  • Removed the "useful for 2D data" in the help. We don't manage the 2D. We manage 3D data with one dimension set to 1, but we don't add the 3rd dimension ourselves.
    • Changed the method it calls so that we don't send args. Will be easier to create a script.
• scil_freewater_priors: only calls noddi_priors, but had a coverage of 0%. Added a test.

That's it! ...

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
• [x] Verifications

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

...

Checklist

• [x] My code follows the style guidelines of this project (run autopep8)
• [x] I added relevant citations to scripts, modules and functions docstrings and descriptions
• [x] I have performed a self-review of my code
• [x] I have commented my code, particularly in hard-to-understand areas
• [ ] I have made corresponding changes to the documentation
• [x] My changes generate no new warnings
• [x] 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
• [x] New and existing unit tests pass locally with my changes

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 73.39450% with 29 lines in your changes are missing coverage. Please review.

Project coverage is 69.46%. Comparing base (d319ad2) to head (c32176a).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #924 +/- ## ========================================== + Coverage 69.38% 69.46% +0.07% ========================================== Files 389 389 Lines 20997 20989 -8 Branches 3231 3225 -6 ========================================== + Hits 14568 14579 +11 + Misses 5114 5102 -12 + Partials 1315 1308 -7 ``` | [Components](https://app.codecov.io/gh/scilus/scilpy/pull/924/components?src=pr&el=components&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | Coverage Δ | | |---|---|---| | [Scripts](https://app.codecov.io/gh/scilus/scilpy/pull/924/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `71.99% <86.15%> (+0.18%)` | :arrow_up: | | [Library](https://app.codecov.io/gh/scilus/scilpy/pull/924/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `65.19% <54.54%> (-0.07%)` | :arrow_down: |

[pep8speaks]

Hello @EmmaRenauld, Thank you for updating !

There are currently no PEP 8 issues detected in this Pull Request. Cheers! :beers:

Comment last updated at 2024-02-29 21:31:15 UTC

[EmmaRenauld]

Finally I added a bit more changes!

• Combined common sections in fodf_memst, fodf_msmt.
• Added small changes in bingham_metrics, which I just found was not in our excel sheet.
• Encapsulated things in frf_set_diffusivities.

Overall, I thus have mainly small changes, and 4 new functions (created without changing any line of code!). I was not always sure where to put them though.