neuropoly / spinalcordtoolbox / 10458 / 1
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coverage: 67.542% (+1.1%) from 66.444%
SCT_MINICONDA=2 MPLBACKEND=Agg

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Major refactoring of centerline routine (#2147)

* sct_get_centerline: Fixed inconsistent input params

* centerline/curve_fitting: New module that deals with curve fitting

Will eventually migrate nurbs and hanning there

* centerline/core: New module that deals with get_centerline

* sct_get_centerline,process_seg: Refactoring to use centerline

Unfinished!

* test_centerline: Added unit test for centerline

* optic: Refactoring to minimize i/o, clarified code

* Moved all nurbs-related functions inside centerline.nurbs

unfinished business...

* centerline.core: Added nurbs method and added unit test

* unit_testing: Now moving to tempdir for some unit test function

To avoid dumping a lot of stuff within SCT dir

* Optic: Refactoring to integrate API in centerline.get_centerline

Also minimized i/o, copy, etc.

* sct_get_centerline: Made compatible with changes in sct.centerline

* centerline/core: Fixed bug on centerline img creation

* sct_label_utils: Removed method extract_centerline

Fixes #1937

* centerline/core: Moved _call_viewer_centerline() there

* deepseg_sc/core: New module. Moved functions out of scripts/

* sct_deepseg_sc: Rename flag manual->file. More intuitive

Also, a file can be generated automatically.

* curve_fitting: Added sinc interpolation, updated unit test

* curve_fitting: Implemented bspline interpolation

* test_centerline: Generalized dummy centerline creation

* deepseg_lesion/core: New module. Moved functions out of scripts/

* centerline/core: Cosmetic modifications on the debug figures

Also updated test to be able to vary image size

* test_centerline: Parametrized im_centerline with various sizes

* test_centerline: Improved parametrization

* centerline/curve_fitting.py: Fixed computation of derivatives

* spinalcordtoolbox/centerline/core.py: Now output derivatives as arr

* spinalcordtoolbox/process_seg: Refactored to use centerline/

* sc... (continued)

9874 of 14619 relevant lines covered (67.54%)

0.68 hits per line

Source Files on job 10458.1 (SCT_MINICONDA=2 MPLBACKEND=Agg)