Create new script compute_simple_matrix

[EmmaRenauld]

Quick description

Moved a script that I was using in dwi_ml.

To create a (streamline count) connectivity matrix directly from tractogram, without going through the whole connectivity flow process with hdf5.

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

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 !

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

Comment last updated at 2024-11-28 17:26:41 UTC

[frheault]

I like it ! Very useful to finally have something simpler than the other one.

[codecov]

Codecov Report

Attention: Patch coverage is 81.25000% with 24 lines in your changes missing coverage. Please review.

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Additional details and impacted files

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Components	Coverage Δ
Scripts	70.26% <87.05%> (?)
Library	68.25% <69.76%> (?)

[arnaudbore]

A couple of comments but LGTM

[frheault]

I am 99% sure this can be done for all streamlines with map_coordinates with streamlines resamples to 2 points. I think this could be a new function 'map_endpoints'.

(sft with streamlines resamples to 2 points)
data = map_coordinates(labels, sft.streamlines._data.T, order=0)
This will give an array where all the even position are starts and all the odds are ends.

(I believe it would be a lot faster)

[EmmaRenauld]

Wow, I agree, but I'm not very familiar with this. Can we merge and then I let you do it? (--insert praying emoji--)

[frheault]

That's fair, but add an issue to me (and @arnaudbore that can be on my hackathon list)