Masking in FitData

[jvelazquez-reyes]

Purpose

Carry out the data masking process internally. Issue: #312

Approach

The masking process is carried out by the FitData function, instead of on the model functions.

Voxelwise=1 case:
https://github.com/qMRLab/qMRLab/blob/master/src/Common/FitData.m#L96-L112

Voxelwise=0 case:
https://github.com/qMRLab/qMRLab/blob/master/src/Common/FitData.m#L253-L284

Open Questions and Pre-Merge TODOs

• Use github checklists. When solved, check the box and explain the answer.

• Review that changed source files/lines are related to the pull request/issue
  If any files/commits were accidentally included, cherry-pick them into another branch.

• Review that changed source files/lines were not accidentally deleted
  Fix appropriately if so.

• Test new features or bug fix
  If not implemented/resolved adequately, solve it or inform the developer by requesting changes in your review.
  Preferably, set breakpoints in the locations that the code was changed and follow allong line by line to see if the code behaves as intended.

Manual GUI tests (general)

• Does the qMRLab GUI open?
• Can you change models?
• Can you load a data folder for a model?
• Can you view data?
• Can you zoom in the image?
• Can you pan out of the image?
• Can you view the histogram of the data?
• Can you change the color map?
• Can you fit dataset (Fit data)?
• Can you save/load the results?
• Can you open the options panel?
• Can you change option parameters?
• Can you save/load option paramters?
• Can you select a voxel?
• Can you fit the data of that voxel ("View data fit")?
• Can you simulate and fit a voxel ("Single Voxel Curve")?
• Can you run a Sensitivity Analysis?
• Can you simulate a Multi Voxel Distribution?

Specifications

• Version:
• Platform:
• Subsystem:

[codecov]

Codecov Report

Merging #475 (3960998) into master (8b8fb39) will decrease coverage by 5.31%.
The diff coverage is n/a.

❗ Current head 3960998 differs from pull request most recent head d803d21. Consider uploading reports for the commit d803d21 to get more accurate results

@@            Coverage Diff             @@
##           master     #475      +/-   ##
==========================================
- Coverage   47.40%   42.08%   -5.32%     
==========================================
  Files         260      260              
  Lines        8647     8637      -10     
==========================================
- Hits         4099     3635     -464     
- Misses       4548     5002     +454     

Flag	Coverage Δ
matlab	42.08% <ø> (-4.54%)	⬇️
octave	?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/Models/Magnetization_transfer/mt_ratio.m	100.00% <ø> (ø)
src/Models/T1_relaxometry/mp2rage.m	72.72% <ø> (+4.67%)	⬆️
src/Common/sim/computeR1.m	0.00% <0.00%> (-100.00%)	⬇️
..._Functions/MTVfun/mtv_correct_receive_profile_v2.m	0.00% <0.00%> (-100.00%)	⬇️
...rc/Models_Functions/bSSFPfun/functions/bSSFP_fit.m	0.00% <0.00%> (-96.43%)	⬇️
src/Models_Functions/Filter/polyfit_3D.m	0.00% <0.00%> (-94.92%)	⬇️
src/Models_Functions/MTVfun/ordfilt3D.m	0.00% <0.00%> (-92.86%)	⬇️
.../Models_Functions/SIRFSEfun/functions/SIRFSE_fit.m	0.00% <0.00%> (-89.29%)	⬇️
src/Models/T1_relaxometry/mtv.m	11.76% <0.00%> (-88.24%)	⬇️
src/Models_Functions/MTVfun/mtv_fit3dsplinemodel.m	0.00% <0.00%> (-80.00%)	⬇️
... and 33 more

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[mathieuboudreau]

What did these names have to do with masking? I think changing the names might break existing pipeline because it's a change to the API

[jvelazquez-reyes]

Nothing :) I wanted to follow the naming convention we adopted for exporting B1 corrected maps. I just recalled this is already implemented in this branch.

For clarity, let me revert that FitResult.T1cor -> FitResult.T1, as these changes will eventually be implemented.