shimming-toolbox / shimming-toolbox / 16973016300

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Real-time B0 weighted shimming (#617)

* Add two basic soft masks functions

* Fix names of functions and add test function

* Add basic_sct_soft_mask function

* Adapted get_coil_mat_and_unshimmed for accepting softmasks

* Added a test for the creation of a basic softmask

* Add a gaussian softmask conversion function and its tests

* Add a linear softmask conversion function and its tests

* fix: Adjust softmask functions for anisotropic voxels

* Add tests for the softmasks functions

* Add tests for the pseudo-inverse optimizer with a softmask

* Add function to combine cylindric and gaussian masks from sct_create_mask and its test

* Test cli for gaussian_sct_softmask()

* Fix delays in gaussian_filter_softmask and in basic_softmask

* Fix cli integration of gaussian_sct_softmak

* Add cli function create_mask

* Unconclusive tests on softmask-adapted basic optimizer

* Add get_weighted_coil_mat_and_unshimmed() for softmask basic optimisation

* Adapt calculate_metric_within_mask to be compatible with weighted metrics

* Optimise calculate_metric_within_mask with faster operators

* Adapt sequencer for pseudo-inverse softmask optimisation

* Add function to calculate shimming stats improvement

* test for cli execution

* Fix softmask integration with optimizer and sequencer

* Add mean, mse and snr to the stats showed

* Add sequence to config

* Fix sequence added to config in last commit

* Fixes to perform fantom shimming

* Remove snr calculations

* Personalize figure colors for the poster

* Create and adapt function to generate figures for the poster

* Fix wighted pseudo-inverse optimizer

* Remove commits related to poster creation. See ag/poster_project_III (PR #601) for more details

* Adapt least squares optimizer for softmask b0 shimming. Softmask signal recovery still needs to be implemented

* Small fix in plot_full_mask

* revert back in commits and do minimal changes to add sfot mse residuals

* revert back in commits to adapt ... (continued)

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