neuropoly / spinalcordtoolbox / 10704
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Major modifications to simplify usage and fix various issues with shape analysis (#2200)

* test_process_seg: Re-activated shape analysis with angled seg

* msct_shape: First step of major refactoring for computing shape

shape is now computing slicewise, by stretching the image using the angle between the centerline and the normal to the 2D patch plane. Partly fixes #1395

* process_seg: Moved msct_shape --> process_seg

Making msct_shape.py obsolete

* process_seg: new implementation of shape analysis now working

A few fixes needed

* process_seg: Added angle_RL and angle_AP as output

* process_seg: Renamed dict field AP_diameter --> diameter_AP

for consistency with angle_AP. Same with RL.

* process_seg: Cleanup

* process_seg: Upsample image to increase precision in shape analysis

* process_seg: Added progress bar

* unit_testing/create_test_data: New file to create testing data

* test_centerline: Refactored to use create_test_data.py

* test_centerline.py: Cleanup

* test_centerline: Cleanup

* test_process_seg: Refactoring with parametrized dummy seg (WIP)

* process_seg.py: Added angle_correction

* process_seg.py: Fixed index bug

* create_test_data.py: Added size_arr flag and updated test_process_seg

Tests now pass

* create_test_data.py: Added proper file name for saving in debug

* centerline/core.py: Cleanup

* centerline/core.py: Fixed indexation bug

* test_centerline.py: Now testing for case with minmax=True

* process_seg.py: Few fixes and test added regarding angle correction

* test_process_seg.py: Compressed code

* create_test_data.py: Added comments

* create_test_data.py: Now possible to specify pixdim

* create_test_data.py: Added IS angle for test data generation

* test_process_seg.py: Merged with/without angle test functions

* test_process_seg.py: Cleanup

* create_test_data.py: Now using resampling to fit desired pixdim

Because creating nii object af... (continued)

9796 of 14631 relevant lines covered (66.95%)

1.34 hits per line

Jobs
ID Job ID Ran Files Coverage
1 10704.1 (SCT_MINICONDA=2 MPLBACKEND=Agg) 85
66.95
 Travis Job 10704.1
2 10704.2 (SCT_MINICONDA=2 MPLBACKEND=Agg) 85
66.96
 Travis Job 10704.2
Source Files on build 10704