neuropoly / spinalcordtoolbox / 10234
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Major refactoring to bring few improvements (#1931)

* sct_process_segmentation refactor

- removed smoothing_param feature in compute_csa: nobody should use it
- removed pickle support
- disabled output CSA and angle nifti volume (people don’t use it)
- major refactoring: output is csv only and changed vert_level output
management
- started to deal with different scenario for z/vert output (WIP)
- implemented perlevel option
- now list slices in descending mode (from head to toes)
  because more intuitive
- clarified doc on CSA computation (#1841)
- added flag -o and specified -ofolder as deprecated (unfinished)
- introduced process_seg in spinalcordtoolbox package
- refactored process_seg.extract_centerline()
- added integrity test for process_seg.extract_metric
- added test for process_seg.compute_csa
- removed unused functions
- minor cleanup, changed output folder with output file in compute_shape
- removed computation of patch_borders (not used)
- introduced new spinalcordtoolbox.metrics module to deal with i/o and
  metrics extraction
- removed ‘centerline’ property from compute_properties_along_centerline
- added input params to compute_shape(), added integrity test
- created function msct_shape.assign_AP_and_RL_diameter()
- removed fname_disc from compute_shape() because it is now externalized
- created wrapper compute_shape_from_file()
- process_seg: now outputs metrics dict
- added new module to deal with writing data struct
- Started to work with module dedicated to save csv

* process_seg: Fixed wrong import

* test_process_seg: Increased test image resolution

For better precision

* process_seg/compute_shape: Removed metric aggregation

* process_seg: Introduced dict of class Metric()

* sct_straighten_spinalcord: Fixed wrong pixel scalar correction

* test_process_seg: Adapted header of dummy seg to be realistic size

* test_process_seg: Added parameters to fixture function

To specify ang... (continued)

10144 of 15344 relevant lines covered (66.11%)

1.32 hits per line

Jobs
ID Job ID Ran Files Coverage
1 10234.1 (SCT_MINICONDA=2 MPLBACKEND=Agg) 0
66.11
 Travis Job 10234.1
2 10234.2 (SCT_MINICONDA=2 MPLBACKEND=Agg) 0
66.12
 Travis Job 10234.2
Source Files on build 10234
Detailed source file information is not available for this build.