shimming-toolbox / shimming-toolbox / 9701470147

90%

Build Type

push

github

Committed by web-flow

Commit Message

Signal recovery optimizer (#429)

* add signal recovery function

* try to address: 'weighting-signal-loss' is only relavant to

* optimize both Gz and B0 in eroded mask, plot B0, Gz, Signal loss maps in symmetrical colorbar

* Fix the bug for plotting when shimming slice by slice --slice sequential

* Fix the bug for plotting when shimming slice by slice --slice sequential

* Fix the bug for slice-sequential and ensure slice-volume also works. Specificaly, Gz must be calculated at each shimming slices deck (e.g., the target slice and slices before; Do not calculate Gz after concatenating slice-by-slice B0 map to form volumetric B0 maps

* Add a timer in B0_shim to report the time it takes for shim_sequencer to run

* address Alex's code review on Jan 14

* Address Alex's code review on Jan14

* Add comment: epi-time is in seconds

* eroded mask test

* Change mask when plotting to avoid edges

* Resolve flag

* change fontsize

* optimized signal loss opti for speed

* Better optimizing

* Update shimmingtoolbox/optimizer/lsq_optimizer.py

Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>

* Update shimmingtoolbox/cli/b0shim.py

Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>

* Update shimmingtoolbox/optimizer/lsq_optimizer.py

Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>

* Update shimmingtoolbox/optimizer/lsq_optimizer.py

Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>

* comments

* temp

* Fix signal recovery metrics when using different resolutions between anat and fm

* temp commit

* split weights between Gx, Gy and Gz

* fix interleaved mode

* faster temp modifications

* remove unnecessary code

* test for fixing qp test

* temp corection to tests

* Allow more iterati... (continued)

Run Details

292 of 345 new or added lines in 9 files covered. (84.64%)

10 existing lines in 3 files now uncovered.

4889 of 5326 relevant lines covered (91.79%)

3.67 hits per line