Module tractogram operations

[EmmaRenauld]

Continuing the refactoring work, as discussed in group.

Explanation:

Based on our analysis of the scripts, we will create a new section scilpy.tractograms, which should contain:

• streamline_operations.py --> operations on the points of the streamlines. Ex: resampling, smoothing, etc.
• tractogram_operations.py (CURRENT PULL REQUEST!) --> operations on the streamlines as parts of the tractogram. Ex: upsampling the number of streamlines, splitting into two sub-stractograms, registration, concatenation, union of tractograms, etc.
• segment/filtering --> segmentation of the tractogram based on user-defined criteria (ex, based on anatomy) or recobundles.
• I am also adding: lazy_tractogram_operations, which are a little different as they include loading in the methods, which we usually keep in the mains.

This PR:

Creation of tractogram_operations.py and lazy_tractogram_operations.

Fonctions that were copy-pasted with no change:

• most of what was in utils.streamlines.
• io.streamlines.lazy_streamlines_count
• split methods from tracking.tools
• utils.transformation (flip_sft)

New methods created to clean mains in scripts:

• shuffle_streamlines()
• lazy_concatenate()

Other change:

• Renamed scil_streamlines_math.py to scil_tractograms_math.py to reflect our new category understanding.

@frheault , @AntoineTheb , @AlexVCaron

[EmmaRenauld]

On our toDo list for this PR:
there was to verify if there is still a reason for scil_remove_similar_streamlines compared to scil_resample_tractogram. I did not touch it for now. @frheault

[arnaudbore]

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[arnaudbore]

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[arnaudbore]

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[frheault]

I tested a few scripts and it still works (I think, I need to do it again with better data).

Do you think its possible to leave the old script that would print a warning (deprecated script) and then just call the new one (or may just point the user to the new one).

I am afraid changing scil_streamlines_math.py to scil_tractogram_math.py will generate a ton of email like 'WHERE IS THAT SCRIPT' for the next year.
A explicit warning for the next release at least could help the transition.

PS: Yes, just delete the scil_remove_similar_streamlines.py, and delete functions that are unique to that script (or not reusable) It is an over- engineered script that no one use. I will keep a copy in a personal graveyard.

[arnaudbore]

Build Failed 💥
https://jenkins.scil.usherbrooke.ca/job/scilpy/job/PR-658/4/

[arnaudbore]

Build passed ! Good Job 🍻 !

[arnaudbore]

Build passed ! Good Job 🍻 !

[arnaudbore]

Build passed ! Good Job 🍻 !

[frheault]

I think it would be important to leave a warning in scil_streamlines_math.py until the next release, but make it so it still works for a few months as a transition.

The easiest way would be that scil_tractogram_math.py has a main() with the argparser build, but then the whole content of the main is moved to another function that accepts args and parser as arguments.

Then scil_streamlines_math could display the warning, but then call the sub-function from the other script with its own parser and args.

This way, without duplication of code, the user can still use it and get a warning without all the flows and scripts crashing. This will be removed a few months later, so a complete deprecation cycle).

[arnaudbore]

Build passed ! Good Job 🍻 !