Skip QC if label file is empty

[valosekj]

Check if the label file is empty (i.e., no lesion was drawn in MS patient); if so, skip QC.

Resolves: #60

[NathanMolinier]

By doing that we accept the creation of empty masks for all the tasks. The user needs to be aware of that maybe.

[valosekj]

By doing that we accept the creation of empty masks for all the tasks. The user needs to be aware of that maybe.

Good point! Do you think it would be better to allow the empty mask only for the FILES_LESION key?

[jcohenadad]

also, don’t we want to check MS lesion mask even if it is empty? otherwise we will miss false negatives.

[valosekj]

also, don’t we want to check MS lesion mask even if it is empty? otherwise we will miss false negatives.

This is an excellent point! I initially thought that sct_qc does not allow to create QC if the mask is empty. But I was mistaken! The empty mask is not allowed for the sct_qc -p sct_label_utils flag. But, with the sct_qc -p sct_deepseg_lesion flag, empty QC can be created; investigation here.

[valosekj]

The QC is now skipped only for functions which do not support empty labels (sct_label_utils, sct_label_vertebrae, sct_detect_pmj, commit). In other words, an empty label mask is supported for sct_deepseg_sc, sct_deepseg_gm, and sct_deepseg_lesion.

[NathanMolinier]

Another point is, do we want to keep empty masks for every tasks ?

[valosekj]

Another point is, do we want to keep empty masks for every tasks ?

Good point! I would say that it is the responsibility of the user to correct/create a label when using the manual_correction.py script. If the user decides to keep the label empty, for example, in case of no MS lesion or no SC compression, it is absolutely fine. But it is true that, for instance, for disc labeling, the empty mask does not make much sense. However, I would not complicate this PR since this PR is about preventing the QC from failing.

[NathanMolinier]

I understand but this falling is also currently the only warning/error that we have regarding empty masks

[valosekj]

I understand but this falling is also currently the only warning/error that we have regarding empty masks

I added the following warning:

manual-correction/manual_correction.py

Line 595 in 8adb172

logging.warning(f"File {fname_label} is empty. Skipping QC.\n")

[NathanMolinier]

The solution seems to be good to me, I think can merge this PR 🎉