neuropoly / spinalcordtoolbox / 10584 / 2
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coverage: 67.492% (-0.08%) from 67.574%
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Various improvements on the QC report and resampling module (#2157)

* nipy_resample.py: Refactored to make it a pure nipy-based function

Also did some cleaning.
Unfinished

* test_resample: New unit test for resample

* slice: Started to refactor (minor changes)

* nipy_resample: Generalized to 4d and fixed compatibility

* resample: Renamed resample_nipy -> resample and move to spinalcord

* sct_deepseg_sc,deepseg_lesion,deepseg_sc: Updated with new resample

* spinalcordtoolbox/resample: Added comments (also in testing)

* reports/slice: Resampling is now done within the QC report

Not in parent function such as sct_propseg.
Unfinished

* sct_propseg: Cleaning

* reports/slice: Cleaning

* reports/slice: Removed legacy msct_image

* sct_deepseg_sc: Implemented new QC changes

* reports/slice: Fixed issue with n>2 dim of self._image

* reports/slice: Now resampling QC image to 0.6mm in-plane

* sct_register_multimodal: Implemented QC (unfinished)

* sct_register_multimodal: Removed requirement for both dseg and iseg

* reports/slice: Changed interpolation nn-->linear

Cleaner for images and segmentation.

* reports/slice: Now binarizing segmentation after resampling

* sct_register_multimodal: Now requiring dest seg for QC

* sct_register_multimodal: Fixed wrong path for QC

* reports/qc: Introduced green and red for segmentation overlay

To distinguish results from co-registration vs. segmentation

* sct_register_multimodal.py: Cleanup

* sct_deepseg_gm: Updated resampling method

* centerline/core: Added TODO

* sct_register_multimodal: Rolled back with QC showing images (not seg)

* reports/qc: Implemented contrast stretching equalization method

Less aggressive

* reports/qc: Added stretch_contrast_method as input param to QcImage

* reports/qc: Now retrive name of dataset, assuming BIDS convention

* reports/qc: Added microseconds in QC folder name

* reports/qc: Now display... (continued)

9862 of 14612 relevant lines covered (67.49%)

0.67 hits per line

Source Files on job 10584.2 (SCT_MINICONDA=2 MPLBACKEND=Agg)