protocol

Author: Peyman-N

bids2openminds/converter.py

@@ -21,7 +21,7 @@ def convert(input_path, output_path=None, multiple_files=False, include_empty_pr
 
     subjects_id = bids_layout.get_subjects()
 
-    tasks = bids_layout.get_task()
+    protocols, protocols_dict = main.create_protocol(bids_layout, collection)
 
     # imprting the dataset description file containing some of the
     dataset_description_path = utility.table_filter(layout_df, "description")
@@ -35,7 +35,7 @@ def convert(input_path, output_path=None, multiple_files=False, include_empty_pr
         layout_df, input_path, collection)
 
     dataset_version = main.create_dataset_version(
-        bids_layout, dataset_description, layout_df, subjects_list, file_repository, collection)
+        bids_layout, dataset_description, layout_df, subjects_list, file_repository, protocols, collection)
 
     dataset = main.create_dataset(
         dataset_description, dataset_version, collection)

bids2openminds/main.py

@@ -72,6 +72,21 @@ def create_persons(dataset_description, collection):
     return openminds_list
 
 
+def create_protocol(layout, collection):
+    protocols_dict = {}
+    protocols = []
+    tasks = layout.get_tasks()
+
+    for task in tasks:
+
+        protocol = omcore.Protocol(name=task)
+        protocols.append(protocol)
+        protocols_dict[task] = protocol
+        collection.add(protocol)
+
+    return protocols, protocols_dict
+
+
 def create_techniques(layout_df):
     suffixs = layout_df["suffix"].unique().tolist()
     techniques = []
@@ -126,7 +141,7 @@ def create_openminds_age(data_subject):
         return None
 
 
-def create_dataset_version(bids_layout, dataset_description, layout_df, studied_specimens, file_repository, collection):
+def create_dataset_version(bids_layout, dataset_description, layout_df, studied_specimens, file_repository, protocols, collection):
 
     # Fetch the dataset type from dataset description file
 
@@ -179,6 +194,7 @@ def create_dataset_version(bids_layout, dataset_description, layout_df, studied_
         techniques=techniques,
         how_to_cite=how_to_cite,
         repository=file_repository,
+        protocols=protocols
         # other_contributions=other_contribution  # needs to be a Contribution object
         # version_identifier
     )