Tractogram scripts part 5

[EmmaRenauld]

Quick description

Next step in tractogram scripts verification. All the next scripts were already pretty much ok! Yeah! Pretty much only formatting changes, and more verifications!

Stopped after 6 scripts. A part 6 will follow :)

• scil_tractogram_math
• scil_tractogram_pairwise_comparison
• scil_tractogram_project_maps_to_streamlines
• scil_tractogram_project_streamlines_to_map
• scil_tractogram_qbx
• scil_tractogram_register

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

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

[EmmaRenauld]

scil_tractogram_project_streamlines_to_map: all tests failed at line assert_headers_compatible. Indeed, in the test data, the tractogram did not fit with the chosen maps. Changed the data.

[codecov]

Codecov Report

Attention: Patch coverage is 89.47368% with 2 lines in your changes are missing coverage. Please review.

Project coverage is 67.98%. Comparing base (11f218b) to head (56e5a4a).

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #983      +/-   ##
==========================================
+ Coverage   67.97%   67.98%   +0.01%     
==========================================
  Files         419      419              
  Lines       21615    21610       -5     
  Branches     3251     3248       -3     
==========================================
- Hits        14693    14692       -1     
+ Misses       5633     5632       -1     
+ Partials     1289     1286       -3     

Components	Coverage Δ
Scripts	68.97% <88.88%> (+0.01%)	⬆️
Library	66.49% <100.00%> (ø)

[CHrlS98]

Do we really need this comment? the methods are already pretty explicit in what they do...

[EmmaRenauld]

So far, all scripts I checked have been separated into: verifications, loading, processing, saving. Easier to proof-read for me.

[frheault]

@EmmaRenauld I just realized that scil_connectivity_pairwise_agreement.py use the word agreement, not comparison. Should it be a small PR or should we wait for a big connectivity refactor?

[EmmaRenauld]

I just realized that scil_connectivity_pairwise_agreement.py use the word agreement, not comparison. Should it be a small PR or should we wait for a big connectivity refactor?

Indeed, I see that we have
-scil_tractogram_pairwise_comparison
-scil_bundle_pairwise_comparison
-scil_connectivity_pairwaise_agreement.

Is there a fundamental difference between these 3 scripts in the reason why we would want to use them, of the type of study?

If not, I can change it if you want, in any PR.

[frheault]

They all return json with scores of similarity (dice, correlation, etc). And I just did a PR for the same concept with volume (for masks and atlas): scil_volume_pairwise_comparison.py