Display vertebral level when using -perslice 1 option

[jcohenadad]

When running sct_process_segmentation (or sct_extract_metric) with option perslice 1, each row corresponds to a slice. However, when doing so, the column "VertLevel" is empty:

Filename	Slice (I->S)	VertLevel	MEAN(area)
/Users/julien/temp/20201217_inspired/results6/data_processed/HC02/bl/cord/processing_sct/t2_tra_seg.nii.gz	0		70.41316501066880
/Users/julien/temp/20201217_inspired/results6/data_processed/HC02/bl/cord/processing_sct/t2_tra_seg.nii.gz	1		76.68867922117070
/Users/julien/temp/20201217_inspired/results6/data_processed/HC02/bl/cord/processing_sct/t2_tra_seg.nii.gz	2		76.84621033344560
/Users/julien/temp/20201217_inspired/results6/data_processed/HC02/bl/cord/processing_sct/t2_tra_seg.nii.gz	3		81.27146085321930
/Users/julien/temp/20201217_inspired/results6/data_processed/HC02/bl/cord/processing_sct/t2_tra_seg.nii.gz	4		82.83952355053640

It shouldn't be empty, because we know the information about vertebral level, if user input vertebral labeling file, as was done here, with the flag -vertfile.

So as a feature, we should fill this column "VertLevel" when the vertebral level for each slice is known.

[joshuacwnewton]

I very much agree with this suggestion. The blank space stood out to me too while writing #3094.

We already have the capability to get the level values, e.g. when we do -perslice 1 -vert:

spinalcordtoolbox/spinalcordtoolbox/aggregate_slicewise.py

Line 260 in 997c82e

vertgroups = [tuple([get_vertebral_level_from_slice(im_vert_level, i[0])]) for i in slicegroups]

But, for -perslice 1 -z we don't bother getting the level values for some reason.

spinalcordtoolbox/spinalcordtoolbox/aggregate_slicewise.py

Line 269 in 997c82e

vertgroups = None

So, I think a small tweak to this line in aggregate_per_slice_or_level() is all we need.