Bug Fix for sidecar flag on ecat2bids (#358)

Fixes template json and sidecar issues posted by users

Specifically fixes issues #352 and #354 posted on the github
Rolling into version 1.4.4

Author: bendhouseart

pypet2bids/pypet2bids/dcm2niix4pet.py

@@ -82,16 +82,24 @@
     default_metadata_json = helper_functions.check_pet2bids_config(
         "DEFAULT_METADATA_JSON"
     )
-    if default_metadata_json and Path(default_metadata_json).exists():
+    if default_metadata_json and Path(str(default_metadata_json)).exists():
         # do nothing
         pass
-    else:
+    elif default_metadata_json and not Path(str(default_metadata_json)).exists():
+        # Copy template to the specified path
         try:
+            # Ensure the parent directory exists before copying
+            Path(default_metadata_json).parent.mkdir(parents=True, exist_ok=True)
             shutil.copy(
                 Path(metadata_folder) / "template_json.json", default_metadata_json
             )
         except FileNotFoundError:
+            # Fallback to module folder template
+            Path(default_metadata_json).parent.mkdir(parents=True, exist_ok=True)
             shutil.copy(module_folder / "template_json.json", default_metadata_json)
+    else:
+        # No DEFAULT_METADATA_JSON set in config, do nothing
+        pass
 else:
     # if it doesn't exist use the default one included in this library
     helper_functions.modify_config_file(

pypet2bids/pypet2bids/ecat.py

@@ -523,11 +523,11 @@ def show_sidecar(self, output_path=None):
                     )
                 else:
                     collection_of_fields[field] = self.sidecar_template.get(field)
-
-        if helper_functions.collect_bids_part("ses", self.output_path) != "":
-            collection_of_fields["ses"] = helper_functions.collect_bids_part(
-                "ses", self.output_path
-            )
+        if self.output_path:
+            if helper_functions.collect_bids_part("ses", self.output_path) != "":
+                collection_of_fields["ses"] = helper_functions.collect_bids_part(
+                    "ses", self.output_path
+                )
 
         if self.ezbids:
             hash_string = helper_functions.hash_fields(**collection_of_fields)

pypet2bids/pypet2bids/ecat_cli.py

@@ -282,7 +282,7 @@ def main():
         os.environ["PET2BIDS_TELEMETRY_ENABLED"] = "False"
 
     collect_pixel_data = False
-    if cli_args.convert or cli_args.update:
+    if cli_args.convert or cli_args.update or cli_args.sidecar:
         collect_pixel_data = True
     if cli_args.scannerparams is not None:
         # if no args are supplied to --scannerparams/-s