[WIP] Bundle fixel analysis script

[karanphil]

Quick description

Here is a script that computes a fixel_density_maps by associating each segment of streamlines in each voxel to one of the fixels. In other words, you give peaks and a list of bundles (.trk) as input, and it computes the fraction of each bundle per peak, for every voxel. It uses either the streamline count or some streamline weight in data_per_streamline, to compute the density of bundles. From the fixel_density_maps, we also get the fixel_density_masks (masked version of the map using thresholds), the voxel_density_maps, the voxel_density_masks, the nb_bundles_per_fixel and the nb_bundles_per_voxel. Please read the documentation of the script for more info.

@mdesco, @frheault this is the script we talked about! I would recommend using the default values to start with. So simply give the peaks and --in_bundles.

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Type of change

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• 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)

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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

Attention: Patch coverage is 76.08696% with 33 lines in your changes missing coverage. Please review.

Project coverage is 68.36%. Comparing base (99ad51e) to head (24da64a).
Report is 15 commits behind head on master.

Additional details and impacted files

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+ Coverage   68.24%   68.36%   +0.11%     
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  Files         419      422       +3     
  Lines       21405    21579     +174     
  Branches     3214     3232      +18     
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+ Hits        14608    14752     +144     
- Misses       5532     5561      +29     
- Partials     1265     1266       +1     

Components	Coverage Δ
Scripts	69.41% <97.43%> (+0.17%)	⬆️
Library	66.84% <48.33%> (+0.02%)	⬆️