[CSimon-A]

DO NOT MERGE UNTIL PR #1373 AND #1376 ARE MERGED!!

Quick description

Fixes #1374 and #1375.

Builds on #1376, which builds on #1373: until they are merged, this PR also shows their commits. Please review only the last two commits.

Type of change

• bundleseg.py: in _register_model_to_neighb, 'scaling' skipped the similarity step, so slm.xopt[6] did not exist and it raised IndexError. The SLR steps now build on each other (translation → rigid → similarity → scaling), like the translation and rigid steps already did. 'similarity', the only type used by VotingScheme, runs exactly the same steps as before.
• test_bundleseg.py: test_register_model_to_neighb now runs for the four SLR types.
• voting_scheme.py: removed single_recognize_parallel, which was never called and could not work (it called single_recognize with separate arguments instead of a single tuple).

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

Validation

• test_register_model_to_neighb passes for the four SLR types ('scaling' raised IndexError before).
• Compared with Refactor BundleSeg: steps take arguments and return values #1376 on the same 56 cases used there: identical indices and scores, except the two 'scaling' cases (error before, results now).
• single_recognize_parallel is not used anywhere else in scilpy.
• pytest src/scilpy/segment and test_tractogram_segment_with_bundleseg.py pass.

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

[codecov]

Codecov Report

❌ Patch coverage is 92.30769% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 72.91%. Comparing base (c787973) to head (d4d9ba9).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1377      +/-   ##
==========================================
+ Coverage   72.57%   72.91%   +0.33%     
==========================================
  Files         301      301              
  Lines       26279    26272       -7     
  Branches     3702     3700       -2     
==========================================
+ Hits        19073    19157      +84     
+ Misses       5655     5558      -97     
- Partials     1551     1557       +6     

Flag	Coverage Δ
smoketests	69.73% <13.46%> (-0.01%)	⬇️
unittests	14.74% <90.38%> (+0.51%)	⬆️

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

Components	Coverage Δ
Scripts	75.28% <ø> (ø)
Library	70.07% <92.30%> (+0.74%)	⬆️

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