Fix nii insertion mri protocol group id bug

python/lib/dcm2bids_imaging_pipeline_lib/nifti_insertion_pipeline.py

@@ -117,8 +117,8 @@ def __init__(self, loris_getopt_obj, script_name):
         # ---------------------------------------------------------------------------------------------
         # Determine acquisition protocol (or register into mri_protocol_violated_scans and exits)
         # ---------------------------------------------------------------------------------------------
+        self.scan_type_id, self.mri_protocol_group_id = self._determine_acquisition_protocol()
         if not self.loris_scan_type:
-            self.scan_type_id, self.mri_protocol_group_id = self._determine_acquisition_protocol()
             if not self.scan_type_id:
                 self._move_to_trashbin()
                 self._register_protocol_violated_scan()
@@ -129,7 +129,6 @@ def __init__(self, loris_getopt_obj, script_name):
             else:
                 self.scan_type_name = self.imaging_obj.get_scan_type_name_from_id(self.scan_type_id)
         else:
-            self.scan_type_id = self.imaging_obj.get_scan_type_id_from_scan_type_name(self.loris_scan_type)
             if not self.scan_type_id:
                 self._move_to_trashbin()
                 self._register_protocol_violated_scan()
@@ -154,6 +153,8 @@ def __init__(self, loris_getopt_obj, script_name):
         # ---------------------------------------------------------------------------------------------
         # Run extra file checks to determine possible protocol violations
         # ---------------------------------------------------------------------------------------------
+        self.warning_violations_list = []
+        self.exclude_violations_list = []
         if not self.bypass_extra_checks:
             self.violations_summary = self.imaging_obj.run_extra_file_checks(
                 self.session_obj.session_info_dict['ProjectID'],
@@ -162,8 +163,8 @@ def __init__(self, loris_getopt_obj, script_name):
                 self.scan_type_id,
                 self.json_file_dict
             )
-        self.warning_violations_list = self.violations_summary['warning']
-        self.exclude_violations_list = self.violations_summary['exclude']
+            self.warning_violations_list = self.violations_summary['warning']
+            self.exclude_violations_list = self.violations_summary['exclude']
 
         # ---------------------------------------------------------------------------------------------
         # Register files in the proper tables
@@ -350,7 +351,9 @@ def _determine_acquisition_protocol(self):
             self.scanner_id
         )
 
-        protocol_info = self.imaging_obj.get_acquisition_protocol_info(protocols_list, nifti_name, scan_param)
+        protocol_info = self.imaging_obj.get_acquisition_protocol_info(
+            protocols_list, nifti_name, scan_param, self.loris_scan_type
+        )
         self.log_info(protocol_info['error_message'], is_error="N", is_verbose="Y")
 
         return protocol_info['scan_type_id'], protocol_info['mri_protocol_group_id']
@@ -396,7 +399,7 @@ def _move_to_assembly_and_insert_file_info(self):
         self.log_info(message, is_error='N', is_verbose='Y')
 
         # add an entry in the violations log table if there is a warning violation associated to the file
-        if self.violations_summary['warning']:
+        if self.warning_violations_list:
             message = f"Inserting warning violations related to {self.assembly_nifti_rel_path}." \
                       f"  List of violations found: {self.warning_violations_list}"
             self.log_info(message, is_error='N', is_verbose='Y')

python/lib/imaging.py

@@ -567,7 +567,7 @@ def map_bids_param_to_loris_param(self, file_parameters):
 
         return file_parameters
 
-    def get_acquisition_protocol_info(self, protocols_list, nifti_name, scan_param):
+    def get_acquisition_protocol_info(self, protocols_list, nifti_name, scan_param, scan_type=None):
         """
         Get acquisition protocol information (scan_type_id or message to be printed in the log).
         - If the protocols list provided as input is empty, the scan_type_id will be set to None and proper message
@@ -608,7 +608,7 @@ def get_acquisition_protocol_info(self, protocols_list, nifti_name, scan_param):
 
         # look for matching protocols
         mri_protocol_group_id = protocols_list[0]['MriProtocolGroupID']
-        matching_protocols_list = self.look_for_matching_protocols(protocols_list, scan_param)
+        matching_protocols_list = self.look_for_matching_protocols(protocols_list, scan_param, scan_type)
 
         # if more than one protocol matching, return False, otherwise, return the scan type ID
         if not matching_protocols_list:
@@ -648,7 +648,7 @@ def get_bids_categories_mapping_for_scan_type_id(self, scan_type_id):
 
         return self.mri_prot_db_obj.get_bids_info_for_scan_type_id(scan_type_id)
 
-    def look_for_matching_protocols(self, protocols_list, scan_param):
+    def look_for_matching_protocols(self, protocols_list, scan_param, scan_type=None):
         """
         Look for matching protocols in protocols_list given scan parameters stored in scan_param.
 
@@ -661,9 +661,13 @@ def look_for_matching_protocols(self, protocols_list, scan_param):
          :rtype: list
         """
 
+        scan_type_id = self.get_scan_type_id_from_scan_type_name(scan_type) if scan_type else None
+
         matching_protocols_list = []
         for protocol in protocols_list:
-            if protocol['series_description_regex']:
+            if scan_type_id and protocol['Scan_type'] == scan_type_id:
+                matching_protocols_list.append(protocol['Scan_type'])
+            elif protocol['series_description_regex']:
                 if re.search(
                         rf"{protocol['series_description_regex']}", scan_param['SeriesDescription'], re.IGNORECASE
                 ):