Fix nested GeneratedBy key in JSON sidecar

[valosekj]

Description

This PR removes redundant nested GeneratedBy key in the output JSON sidecar.

main:

{
    "SpatialReference": "orig",
    "GeneratedBy": [
        {
            "GeneratedBy": [
                {
                    "Name": "spinalcordtoolbox: sct_deepseg -task seg_sc_contrast_agnostic -i sub-05_T2w.nii.gz -qc qc -qc-subject sub-05",
                    "Version": "git-master-64f55fdf022659db5d5c779f01c605d91ca7d052",
                    "CodeURL": "https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/64f55fdf022659db5d5c779f01c605d91ca7d052/spinalcordtoolbox/scripts/sct_deepseg.py",
                    "ModelURL": "https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/releases/download/v2.5/model_contrast-agnostic_20240930-1002.zip"
                }
            ]
        },
        {
            "Name": "Manual",
            "Author": "Jan Valosek",
            "Date": "2024-12-10 18:05:31"
        }
    ]
}

This branch:

{
    "SpatialReference": "orig",
    "GeneratedBy": [
        {
            "Name": "spinalcordtoolbox: sct_deepseg -task seg_sc_contrast_agnostic -i sub-05_T2w.nii.gz -qc qc -qc-subject sub-05",
            "Version": "git-master-64f55fdf022659db5d5c779f01c605d91ca7d052",
            "CodeURL": "https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/64f55fdf022659db5d5c779f01c605d91ca7d052/spinalcordtoolbox/scripts/sct_deepseg.py",
            "ModelURL": "https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/releases/download/v2.5/model_contrast-agnostic_20240930-1002.zip"    
        },
        {
            "Name": "Manual",
            "Author": "Jan Valosek",
            "Date": "2024-12-10 18:05:31"
        }
    ]
}

How to test this PR

cd ~/code/manual-correction
git fetch
git checkout jv/108-fix_nested_GeneratedBy_key_in_JSON_sidecar

sct_download_data -d sct_course_data -o sct_course_data_2024
cd sct_course_data_2024/multi_subject
chmod +x process_data.sh
sct_run_batch -script process_data.sh -config config.yml -jobs 3
# Note: you can add `exit` to line 115 to run only the contrast-agnostic model on T2w to save time

$SCT_DIR/python/envs/venv_sct/bin/python ~/code/manual-correction/manual_correction.py -config qc_fail.yml -path-img output/data_processed/ -path-label output/data_processed -path-out data/derivatives/labels

cat data/derivatives/labels/sub-05/anat/sub-05_T2w_seg.json

---

Resolves: #108

[NathanMolinier]

Don't miss this #108 (comment) or maybe this is already what you suggested

[NathanMolinier]

I tested it and I only get this output:

Is the aim of the PR #105 to automatically fetch the metadata without supplying the flag -json-metadata ?

[valosekj]

Thanks for testing the PR, @NathanMolinier!

It's weird; the script is supposed to automatically read (no need for the -json-metadata arg) the JSON created by SCT by these lines and include its content into the output JSON. The output should look like this:

{
    "SpatialReference": "orig",
    "GeneratedBy": [
        {
            "Name": "spinalcordtoolbox: sct_deepseg -task seg_sc_contrast_agnostic -i sub-05_T2w.nii.gz -qc qc -qc-subject sub-05",
            "Version": "git-master-64f55fdf022659db5d5c779f01c605d91ca7d052",
            "CodeURL": "https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/64f55fdf022659db5d5c779f01c605d91ca7d052/spinalcordtoolbox/scripts/sct_deepseg.py",
            "ModelURL": "https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/releases/download/v2.5/model_contrast-agnostic_20240930-1002.zip"    
        },
        {
            "Name": "Manual",
            "Author": "Jan Valosek",
            "Date": "2024-12-10 18:05:31"
        }
    ]
}

[NathanMolinier]

I removed the folders and redo the commands and it worked, maybe I did something wrong previously:

{
    "SpatialReference": "orig",
    "GeneratedBy": [
        {
            "Name": "spinalcordtoolbox: sct_deepseg -task seg_sc_contrast_agnostic -i sub-05_T2w.nii.gz -qc qc -qc-subject sub-05",
            "Version": "git-master-1671e1ff4a54f0228743feb621f68bc84a80024e",
            "CodeURL": "https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/1671e1ff4a54f0228743feb621f68bc84a80024e/spinalcordtoolbox/scripts/sct_deepseg.py",
            "ModelURL": "https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/releases/download/v2.5/model_contrast-agnostic_20240930-1002.zip"
        },
        {
            "Name": "Manual",
            "Author": "Nathan",
            "Date": "2025-01-08 09:03:47"
        }
    ]
} 

[NathanMolinier]

Not a lot of modification, seems to work great. Thank @valosekj for the PR !

[valosekj]

Thank you for your review, @NathanMolinier!