ENH: Add transform analysis utils

[jhlegarreta]

Add transform analysis utils.

Transfer contents from the NiFreeze projects so that hey can be reused across projects requiring transform analysis:
https://github.com/nipreps/nifreeze/blob/d27ba7552bbd9095c3c13b46443d87a4b5504c4c/src/nifreeze/analysis/motion.py https://github.com/nipreps/nifreeze/blob/d27ba7552bbd9095c3c13b46443d87a4b5504c4c/src/nifreeze/data/utils.py

Add a fixture to be able to reuse a random number generator across tests.

Fixes #239.

[jhlegarreta]

I did not dare to create a data module the utils.py module at the root folder, as I do not know well the philosophy in this project, but let me know if it does belong to a data module.

I think the plotting should go to nireports.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
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@@            Coverage Diff             @@
##           master     #286      +/-   ##
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+ Coverage   96.74%   96.80%   +0.06%     
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  Files          16       17       +1     
  Lines        1994     2034      +40     
  Branches      267      267              
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+ Hits         1929     1969      +40     
  Misses         41       41              
  Partials       24       24              

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[jhlegarreta]

Pinging @oesteban.

[jhlegarreta]

Then should we remove these files from NiFreeze?
https://github.com/nipreps/nifreeze/blob/6723229312850a73cbe9e4f31144ade3502535da/src/nifreeze/data/utils.py
https://github.com/nipreps/nifreeze/blob/6723229312850a73cbe9e4f31144ade3502535da/test/test_data_utils.py
and use nitransforms.resampling.apply in
https://github.com/nipreps/nifreeze/blob/6723229312850a73cbe9e4f31144ade3502535da/src/nifreeze/registration/utils.py#L74
and
https://github.com/nipreps/nifreeze/blob/6723229312850a73cbe9e4f31144ade3502535da/src/nifreeze/registration/utils.py#L113

[oesteban]

Then should we remove these files from NiFreeze?
https://github.com/nipreps/nifreeze/blob/6723229312850a73cbe9e4f31144ade3502535da/src/nifreeze/data/utils.py
https://github.com/nipreps/nifreeze/blob/6723229312850a73cbe9e4f31144ade3502535da/test/test_data_utils.py

Yes

and use nitransforms.resampling.apply in
https://github.com/nipreps/nifreeze/blob/6723229312850a73cbe9e4f31144ade3502535da/src/nifreeze/registration/utils.py#L74
and
https://github.com/nipreps/nifreeze/blob/6723229312850a73cbe9e4f31144ade3502535da/src/nifreeze/registration/utils.py#L113

No, if you look at it closer, you'll see this is using apply_affine from nibabel.affines, which is not the same (that applies affines to points, our apply in nitransforms and the apply_affines (notice the 's' at the end) in nifreeze apply affines to images (internally to points, but that's not relevant here).

[oesteban]

Thanks for the update. I just realized of a little inconsistency. Other than that, I think this is almost ready.

[jhlegarreta]

Had a closer look at the apply_affines function: it calls nt.resampling.apply so ultimately its a wrapper around it to write transformed images to a NIfTI file. So, maybe it is useful if we rename/relocate it? Else, are there other nitransforms utils that do that job?

[oesteban]

Else, are there other nitransforms utils that do that job?

Yes, nitransforms.resampling.apply does the job. We created the apply_transforms wrapper in nifreeze because the multiple-volume resampling was not very well supported in nitransforms, but that changed.