[ENH] Add BIDS URI option for IntendedFor mapping

Author: Dan Levitas

handler/convert.js

@@ -473,7 +473,12 @@ def modify_uploaded_dataset_list(uploaded_img_list):
     config_file = ""
     exclude_data = False
 
-    config_file_list = natsorted([x for x in os.listdir(DATA_DIR) if x.endswith('ezBIDS_template.json')])
+    config_file_list = []
+    for root, dirs, files in os.walk(DATA_DIR):
+        for file in files:
+            if file.endswith('ezBIDS_template.json'):
+                config_file_list.append(os.path.join(root, file))
+
     if len(config_file_list):
         # Ideally only one config file uploaded, but if multiple configurations found, select last one (most recent?)
         config = True
@@ -1392,7 +1397,7 @@ def determine_sub_ses_IDs(dataset_list, bids_compliant):
         List of dictionaries containing pertinent and unique information about
         the data, primarily coming from the metadata in the json files.
 
-    subjects_information : list
+    subs_information : list
         List of dictionaries containing subject identification info, such as
         PatientID, PatientName, PatientBirthDate, and corresponding session
         information.
@@ -1402,7 +1407,7 @@ def determine_sub_ses_IDs(dataset_list, bids_compliant):
     """
     date_counter = 1
     subject_idx_counter = 0
-    subjects_information = []
+    subs_information = []
     participants_info = {}
     # Determine unique subjects from uploaded dataset
     for sub in np.unique([x["subject"] for x in dataset_list]):
@@ -1550,9 +1555,9 @@ def determine_sub_ses_IDs(dataset_list, bids_compliant):
             "validationErrors": []
         }
 
-        subjects_information.append(subject_ids_info)
+        subs_information.append(subject_ids_info)
 
-    return dataset_list, subjects_information, participants_info
+    return dataset_list, subs_information, participants_info
 
 
 def determine_unique_series(dataset_list, bids_compliant):
@@ -1638,15 +1643,15 @@ def determine_unique_series(dataset_list, bids_compliant):
     return dataset_list, dataset_list_unique_series
 
 
-def template_configuration(dataset_list_unique_series, subjects_information, config_file):
+def template_configuration(dataset_list_unique_series, subs_information, config_file):
     """
     Parameters
     ----------
     dataset_list_unique_series : list of dictionaries
         A modified version of dataset_list, where this list contains only the
         dictionaries of acquisitions with a unique series group ID.
 
-    subjects_information : list
+    subs_information : list
         List of dictionaries containing subject identification info, such as
         PatientID, PatientName, PatientBirthDate, and corresponding session
         information.
@@ -1669,13 +1674,16 @@ def template_configuration(dataset_list_unique_series, subjects_information, con
         A modified version of dataset_list, where this list contains only the
         dictionaries of acquisitions with a unique series group ID.
 
-    subjects_information : list
+    subs_information : list
         List of dictionaries containing subject identification info, such as
         PatientID, PatientName, PatientBirthDate, and corresponding session
         information.
 
     events : dictionary
         Information pertaining to the events timing files for func/bold data.
+
+    bids_uri : boolean
+        Specifies whether or not user wants BIDS URI format for IntendedFor metadata mapping
     """
 
     config_data = open(config_file)
@@ -1687,6 +1695,7 @@ def template_configuration(dataset_list_unique_series, subjects_information, con
     subjects_sessions_info = config_data["subjects"]
     config_dataset_list_unique_series = config_data["series"]
     config_dataset_list_objects = config_data["objects"]
+    bids_uri = config_data["BIDSURI"]
 
     # Try to determine subject (and session) mapping from what's in the configuration
     match_start_index = None
@@ -1712,7 +1721,7 @@ def template_configuration(dataset_list_unique_series, subjects_information, con
         "AcquisitionDateTime"
     ]
 
-    for sub_info in subjects_information:
+    for sub_info in subs_information:
         sub = sub_info["subject"]
         for key in ref_patient_info.keys():
             if ref_subject_id in ref_patient_info[key]:
@@ -1819,7 +1828,7 @@ def template_configuration(dataset_list_unique_series, subjects_information, con
     events["sampleValues"] = {}
 
     return (readme, dataset_description_dic, participants_column_info,
-            dataset_list_unique_series, subjects_information, events)
+            dataset_list_unique_series, subs_information, events, bids_uri)
 
 
 def create_lookup_info():
@@ -3106,15 +3115,15 @@ def check_dwi_b0maps(dataset_list_unique_series):
 dataset_list = organize_dataset(dataset_list)
 
 # Determine subject (and session) information
-dataset_list, subjects_information, participants_info = determine_sub_ses_IDs(dataset_list, bids_compliant)
+dataset_list, subs_information, participants_info = determine_sub_ses_IDs(dataset_list, bids_compliant)
 
 # Make a new list containing the dictionaries of only unique dataset acquisitions
 dataset_list, dataset_list_unique_series = determine_unique_series(dataset_list, bids_compliant)
 
 # If ezBIDS configuration file detected in upload, use that for datatype, suffix, and entity identifications
 if config is True:
-    readme, dataset_description_dic, participants_column_info, dataset_list_unique_series, subjects_information, events = \
-        template_configuration(dataset_list_unique_series, subjects_information, config_file)
+    readme, dataset_description_dic, participants_column_info, dataset_list_unique_series, subs_information, events, \
+        bids_uri = template_configuration(dataset_list_unique_series, subs_information, config_file)
 
 else:
     # README
@@ -3160,6 +3169,9 @@ def check_dwi_b0maps(dataset_list_unique_series):
         }
     }
 
+    # BIDS URI
+    bids_uri = False
+
 # Generate lookup information directory to help with datatype and suffix identification (and to some degree, entities)
 lookup_dic = create_lookup_info()
 
@@ -3212,12 +3224,13 @@ def check_dwi_b0maps(dataset_list_unique_series):
 EZBIDS = {
     "readme": readme,
     "datasetDescription": dataset_description_dic,
-    "subjects": subjects_information,
+    "subjects": subs_information,
     "participantsColumn": participants_column_info,
     "participantsInfo": participants_info,
     "series": ui_series_info_list,
     "objects": objects_list,
-    "events": events
+    "events": events,
+    "BIDSURI": bids_uri
 }
 
 # Write dictionary to ezBIDS_core.json

handler/ezBIDS_core/ezBIDS_core.py

@@ -204,6 +204,7 @@ export default defineComponent({
 
                     //things that convert.ts uses
                     objects: this.ezbids.objects, //most important thing that convert.ts needs
+                    BIDSURI: this.ezbids.BIDSURI,
                     events: this.ezbids.events,
                     entityMappings, //helps with convert
                     datasetDescription: this.ezbids.datasetDescription,

ui/src/Finalize.vue

@@ -48,6 +48,9 @@
                         The information you specify here will be applied to all subjects that uses matching
                         SeriesDescription. You can also override this information later for each subject.
                     </p>
+                    <el-checkbox v-model="this.ezbids.BIDSURI" @change="BIDSURI(this.ezbids, $event)">
+                        <small>Use BIDS URI format for IntendedFor metadata mapping (if applicable)</small>
+                    </el-checkbox>
                     <div style="background-color: white; padding: 10px; color: #666">
                         <i class="el-icon-back" /> &lt; Please select a series to view/edit
                     </div>
@@ -308,7 +311,7 @@ import ModalityForm from './components/modalityForm.vue';
 
 import { prettyBytes } from './filters';
 
-import { Series, IObject } from './store';
+import { Series, IObject, IEzbids } from './store';
 
 import { validateEntities, validate_B0FieldIdentifier_B0FieldSource, metadataAlerts } from './libUnsafe';
 import anatYaml from '../src/assets/schema/rules/sidecars/anat.yaml';
@@ -378,6 +381,16 @@ export default defineComponent({
             this.showInfo[entity] = !this.showInfo[entity];
         },
 
+        BIDSURI($root: IEzbids, b: boolean) {
+            if (b === true) {
+                $root.BIDSURI = true;
+                localStorage.setItem('checkboxState', 'true');
+            } else {
+                $root.BIDSURI = false;
+                localStorage.setItem('checkboxState', 'false');
+            }
+        },
+
         validate(s: Series | null) {
             if (!s) return;
 
@@ -389,7 +402,7 @@ export default defineComponent({
                 validate_B0FieldIdentifier_B0FieldSource(s);
             }
 
-            /* Alert users to metadata issues, such as missing required fields or 
+            /* Alert users to metadata issues, such as missing required fields or
             improperly-formmated metadata field values.
             */
             let bidsDatatypeMetadata = {};

ui/src/SeriesPage.vue

@@ -314,6 +314,7 @@ const state = {
         subjects: [] as Subject[],
         series: [] as Series[],
         objects: [] as IObject[],
+        BIDSURI: false,
 
         _organized: [] as OrganizedSubject[], //above things are organized into subs/ses/run/object hierarchy for quick access
 
@@ -509,6 +510,7 @@ const store = createStore({
                 subjects: [],
                 series: [],
                 objects: [],
+                BIDSURI: false,
 
                 _organized: [], //above things are organized into subs/ses/run/object hierarchy for quick access