Allow json mapping usage

[NathanMolinier]

Description

In this PR, 2 new parser variables were integrated -ref-map and -pred-map. They both point to JSON sidecars that can be used to remap values present inside the corresponding reference and prediction images.

This is especially useful when values between the prediction and the ground truth are not the same and also to simply remove some structures from the comparison.

JSON example:

{
        "T12":32,
        "T12-L1":91,
        "L1":41,
        "L1-L2":92,
        "L2":42,
        "L2-L3":93,
        "L3":43,
        "L3-L4":94,
        "L4":44,
        "L4-L5":95,
        "L5":45,
        "L5-S":100
}

Note: It can also be used to compute validation on a single structure present in the image whereas multiple other structures may appear:

For example:

{
        "lesion":2
}

This way we could get rid of these lines:

MetricsReloaded/compute_metrics_reloaded.py

Lines 160 to 163 in 2bad1f2

	# NOTE: this is hacky fix to try to speed up metrics computation, tread very carefully
	if len(unique_labels) == 2:
	# compute metrics only for lesions
	unique_labels = unique_labels[1:]

Final table

[valosekj]

Can you please provide an example of these JSON sidecars?

[NathanMolinier]

I updated my original comment with some complimentary information @valosekj

[valosekj]

Thank you, Nathan! I understand it now. Thanks for implementing this feature!

[valosekj]

Note: CI and unit tests are currently failing due to #18

[valosekj]

To proceed with the merge, we need to remove 54ead73 and 2bad1f2 commits from this branch (context: these two commits were removed from main in #18). I'll try to do it today with Mathieu.

[valosekj]

Okay, @mguaypaq and I did an interactive rebase ( git rebase -i 76dbb556ac0a5bad1a7aecdb80f5effec8af739b) to remove the two commits mentioned in #16 (comment).
@NathanMolinier, unfortunately, it might be dangerous to run git pull now. Better would be to completely re-clone the repo.