neuropoly / qMRLab / 1416 / 2
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coverage: 41.847% (+0.1%) from 41.744%
1416.2

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Qsm add model (#266)

* Add Berkin Bilgic's QSM processing scripts

* [REF] Create function for padding volumes

* [REF&TEST] Refactor pad_volume_for_sharp to get a single volume as arg, write tests for it

* [BUG] Fix coverage json file directory

* [REF] Move Laplacian phase unwrapping into it's own function; add references

* [BUG] Add missing term in function to calculate volume matrix size

* [REF&DOC] Refractored lines for clarity, added documentation for algorithm:

* Fix image plot proportions

* [REF] Refactor SHARP processing script segment into functions

* [BUG] Add mask_sharp to output

* [REF] Refactor split bergman QSM routine from scripts into functions

* Refractor qsm split bregman with preconditioner and magnitude weighting

* [Bug] Fix arg input formatting. Scripts now duplicate originals

* [REF] Refactor differenciation operator into its own function, add flag for both scripts case

* [REF] Refactor lambda_L1 calculation into it's own function. Remove figure numbers

* [BUG] Add FOV as param to new function. Delete old calc_fdr file

* [REF] Rename function to calc_fdr

* [REF] Refactor Lambda L2 calculation into its own function

* [REF] Refactor final plots into seperate function; refactor magnitude image gradient mask calculation into its own function

* [BUG] Fix minor typo in index

* [REF] Cleanup scripts (grouped together configuration vars, cleared vars when no longer needed to free memory, etc)

* [REF] Improve memory management to function

* [REF] Improved memory management

* [REF] Refactor lambda L1 and L2 optimization ranges outside of functions so they may be configurable in the script

* [REF] Refactor cubic spline differentiation to find Kappa (largest curvature) into its own function

* [REF] Renamed functions to follow qMRLab coding standards. Added Bilgic references to all files

* [BUG] Missing Kappa var - give it as a return value of function

* [REF] Ren... (continued)

2782 of 6648 relevant lines covered (41.85%)

843.61 hits per line

Source Files on job 1416.2