sct_deepseg_sc, sct_deepseg_lesion: Allow to input image with one axial slice

[charleygros]

Goal: Allow to input image with only one axial slice.

Issue: isct_spine_detect requires nz>1.

Solution: If nz==1, then ask the user to use -centerline cnn instead of -centerline svm (default).

To test:

cd sct_example_data/t2s
sct_crop_image -i t2s.nii.gz -dim 2 -start 2 -end 2 -o t2s_Z010.nii.gz
sct_deepseg_sc -i t2s_Z010.nii.gz -c t2s

Raises an error message:

Your image contains only one axial slice, please re-run the function using -centerline cnn.

Then,

sct_deepseg_sc -i t2s_Z010.nii.gz -c t2s -centerline cnn

Same for sct_deepseg_lesion.

Note that I have remove some duplicated code: The centerline detection is now done by a function in sct_deepseg_sc named find_centerline, which is called by sct_deepseg_lesion.

[jcohenadad]

why not checking beforehand if the image is 2D, and if it is, duplicate the slice to create a 3D volume, then run the centerline detection, then crop back to 2D on the output centerline.
This will prevent from having an error with the default parameters if 2D image is input.

[charleygros]

Excellent idea, thank you.
It is ready to be reviewed (commit #5d2f492).

[jcohenadad]

successfully tested on 3D and 2D data using default params 👍
I've run into a few bugs (#2015, #2016) which don't seem to be related to this PR, so we can merge this PR and address those issues in other PRs.