MT/ihMT scripts: cleanup and adding B1+ correction

[karanphil]

Quick description

Hi,

I added B1+ field inhomogeneity correction to scil_mti_maps_MT.py and scil_mti_maps_ihMT.py. Doing so, I also cleaned up those scripts and the functions they call in scilpy.reconst.mti. I also added a script (scil_mti_adjust_B1_header.py) to correct the bug in the B1 map header, with the scaling issue. There is now a new correction method for B1+, called "model_based" and it requires .mat files obtained with Matlab at the moment. I will send these to the reviewers.

I tested the scripts and they produce the same results as before (without B1 correction). @Manonedde, you should still test them to make sure everything works fine.

Feel free to comment on the choices I made ;)

This PR doesn't have to be merged quickly.
...

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 @karanphil, Thank you for updating !

• In the file scilpy/reconst/mti.py:

Line 318:80: E501 line too long (82 > 79 characters)
Line 319:80: E501 line too long (81 > 79 characters)

Comment last updated at 2024-02-21 16:05:10 UTC

[arnaudbore]

Build passed ! Good Job 🍻 !

[codecov]

Codecov Report

Attention: 53 lines in your changes are missing coverage. Please review.

Comparison is base (41956e7) 1.95% compared to head (1008f29) 68.17%.
Report is 25 commits behind head on master.

❗ Current head 1008f29 differs from pull request most recent head 8cb2a5b. Consider uploading reports for the commit 8cb2a5b to get more accurate results

Additional details and impacted files

@@             Coverage Diff             @@
##           master     #870       +/-   ##
===========================================
+ Coverage    1.95%   68.17%   +66.22%     
===========================================
  Files         384      387        +3     
  Lines       13876    20865     +6989     
  Branches     1754     3213     +1459     
===========================================
+ Hits          271    14225    +13954     
+ Misses      13561     5358     -8203     
- Partials       44     1282     +1238     

Components	Coverage Δ
Scripts	70.85% <82.74%> (+68.93%)	⬆️
Library	63.56% <71.12%> (+61.58%)	⬆️

[arnaudbore]

Build passed ! Good Job 🍻 !

[arnaudbore]

Build passed ! Good Job 🍻 !

[Manonedde]

Some details for Warning messages, otherwise it's good for me!

INFO:root:Scilpy version: 1.7.dev0
WARNING:root:Repetition time found in mton.json does not seem to be given in seconds. MTsat results might be affected.
INFO:root:Loaded mton_Warped.nii.gz of shape (180, 240, 240) and data_type float64.
INFO:root:Loaded mtoff_Warped.nii.gz of shape (180, 240, 240) and data_type float64.
INFO:root:Loaded mt_t1.nii.gz of shape (180, 240, 240) and data_type int16.

[arnaudbore]

Build passed ! Good Job 🍻 !

[arnaudbore]

Build passed ! Good Job 🍻 !