Include JSON metadata created by SCT

manual_correction.py

@@ -245,9 +245,12 @@ def get_parser():
     )
     parser.add_argument(
         '-json-metadata', metavar="<file>", required=False,
-        help="R|A custom JSON file containing metadata to be added to the JSON sidecar of all corrected labels. "
+        help="R|A custom JSON file containing metadata to be added to the output JSON sidecar of all corrected labels. "
              "This flag is useful, for example, when a label was obtained automatically and you want to include this "
-             "information into the JSON sidecar. "
+             "information into the JSON sidecar. \n"
+             "NOTE: the script automatically checks whether the JSON file already exists (for example when "
+             "automatically created by SCT 6.4+). If so, the script will reuse its metadata. In such cases, you do not "
+             "need to use this flag.\n"
              "Below is an example JSON file:\n"
              + dedent(
              """
@@ -514,11 +517,11 @@ def correct_centerline(fname, fname_label, viewer='sct_get_centerline'):
         viewer_not_found(viewer)
 
 
-def load_custom_json(fname):
+def load_json(fname):
     """
-    Load custom JSON file.
-    :param fname: path to the custom JSON file.
-    :return: dictionary with the metadata to be added to the JSON sidecar.
+    Load existing JSON file. The content of the JSON file will be added to the JSON file produced by this script.
+    :param fname: path to the existing JSON file.
+    :return: dictionary with the metadata to be added to the output JSON sidecar.
     """
     if not os.path.isfile(fname):
         sys.exit("ERROR: The file {} does not exist.".format(fname))
@@ -794,7 +797,7 @@ def main():
             sys.exit("ERROR: No segmentation file found in {}.".format(args.path_label))
 
     # If a custom JSON file containing metadata was provided, load it, and verify that it is a valid JSON file
-    json_metadata = load_custom_json(args.json_metadata) if args.json_metadata else None
+    json_metadata = load_json(args.json_metadata) if args.json_metadata else None
 
     # Get name of expert rater (skip if -qc-only is true)
     if not args.qc_only:
@@ -906,6 +909,15 @@ def main():
                             if copy:
                                 shutil.copyfile(fname_label, fname_out)
                                 print(f'Copying: {fname_label} to {fname_out}')
+                                # If the label has a JSON sidecar, read its content
+                                # Context: SCT v6.4+ produces JSON sidecars for some outputs that track the provenance
+                                # of the function, models, etc.
+                                # Details: https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/4466
+                                # We want to include this information in the final JSON sidecar
+                                fname_label_json = fname_label.replace('.nii.gz', '.json')
+                                if os.path.isfile(fname_label_json):
+                                    # Read the JSON file to include the metadata in the final JSON sidecar
+                                    json_metadata = load_json(fname_label_json)
                             # Create empty mask in derivatives folder
                             elif create_empty_mask:
                                 utils.create_empty_mask(fname, fname_out)