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coverage: 66.737% (-0.3%) from 66.994%
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Increased smoothness of default bspline centerline fitting algorithm  (#2214)

* sct_straighten_spinalcord.py: Simplified variable assignment

* centerline/core: Now throwing exception if algo_fitting does not exist

* centerline/core: Replaced sct.log with logging

* sct_straighten_spinalcord: Now accepting flag -param degree

For poly degree fitting of centerline

* centerline/core: Set default degree to 10 (versus 3)

* centerline/core: Got rid of ParamCenterline class

Was an overkill

* centerline/core: Assigned default degree value based on algo

* test_centerline: Now testing for centerline derivatives

Isolated tests for nurbs because it does not pass most centerline tests

* centerline/curve_fitting: Now computes smoothness parameter automatically

Provides more robustness to outliers

* test_centerline: Added TODO

* sct_download_data: Removed useless import

* create_test_data: Now converting array to uint16 to allow large values

Also added debug mode to save img files

* centerline/core: Replaced deg by smooth input param for bspline

Also initialized parameters directly in function definition

* centerline/curve_fitting: Replaced deg by smooth for bspline

* test_centerline: Enabled to add params, added tests with different smoothing

* test_centerline: Removed TODO

* straightening: Moved sct_straighten_spinalcord core function to new Python module

* sct_straighten_spinalcord: Moved core function to new "straightening" Python module

* straightening: PEP8 cleanup

* straightening: Cleanup, moved imports to the top

* straightening: Removed the (very) long try/except.

If an exception occur, it would be caught anyway

* straightening: cleanup, used logging

* sct_straighten_spinalcord: Cleanup

* straighten: Divides by 2 xy_size as should be expected by user

* sct_straighten_spinalcord: Clarified doc

* test_straightening: Added new UT

* test_sct_straighten_spinalcord: ... (continued)

9757 of 14620 relevant lines covered (66.74%)

0.67 hits per line

Source Files on job 10729.1 (SCT_MINICONDA=2 MPLBACKEND=Agg)