shimming-toolbox / shimming-toolbox / 592
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Add ability to create fieldmaps (#169)

* Initial set up for CLI and test

* Add st_prepare_fieldmap as an entry_point

* Added comments and started to implement

* Added read_nii and echo_time_diff

* Now checking the input phase is a phase diff

For the "single-echo" case, which corresponds to phase diff input

* Added TODOs, added call to prelude, added unwrapper case

* Fixed wrong input for mag

* Deal with 4d phase data

* Divide by echo_time, output fieldmap, add support for 2d fieldmaps

* start implementing dual echo

* Seperate single and dual echo test

* Update dual echo method

* Add magnitude and remove unecessary debug lines

* Move unwrapper to seperate API

* Add unwrap_phase

* Add tests for unwrap_phase and update unwrap_phase to correct found errors

* Cleanup

* Transfer to an API

* Rename dli test to follow convention

* Add tests for prepare_fieldmap API and fix errors found with tests

* Add new tests for error handling

* Add comments

* Updated help

* Added TODO

* Minor comments

* Added integrity test for prepare fieldmap

* More intuitive if, and add NotImplementedError test

* Add and fix comments

* Add not implemented error

* Switch phasediff variable to phase_img

* Refactor unwrap_phase

* Fix merge with master, make mag optional in unwrap phase and prepare fieldmap and fix comments

Co-authored-by: Julien Cohen-Adad <jcohen@polymtl.ca>

809 of 900 relevant lines covered (89.89%)

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Jobs
ID Job ID Ran Files Coverage
1 592.1 0
89.89
 Travis Job 592.1
Source Files on build 592
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