[FIX] fix IntendedFor issue on DS, organize objs by AcqTim, tighten entity labels

Author: Dan Levitas

handler/ezBIDS_core/ezBIDS_core.py

@@ -946,12 +946,6 @@ def generate_dataset_list(uploaded_files_list, exclude_data):
                 'ConversionSoftware': 'ezBIDS',
                 'ConversionSoftwareVersion': '1.0.0'
             }
-            # if not os.path.exists(json_path):
-            #     with open(json_path, "w") as fp:
-            #         json.dump(json_data, fp, indent=3)
-            #     corresponding_files_list = corresponding_files_list + [json_path]
-            #     json_data = open(json_path)
-            #     json_data = json.load(json_data, strict=False)
 
         # Find ImageModality
         if "Modality" in json_data:
@@ -1288,6 +1282,7 @@ def generate_dataset_list(uploaded_files_list, exclude_data):
     dataset_list = sorted(dataset_list, key=itemgetter("AcquisitionDate",
                                                        "subject",
                                                        "session",
+                                                       "AcquisitionTime",
                                                        "ModifiedSeriesNumber",
                                                        "json_path"))
 
@@ -2635,8 +2630,9 @@ def entity_labels_identification(dataset_list_unique_series, lookup_dic):
 
             # If BIDS naming convention isn't detected, do a more thorough check for certain entities labels
             # task
-            func_rest_keys = ["rest", "rsfmri", "fcmri"]
-            if any(x in re.sub("[^A-Za-z0-9]+", "", sd).lower() for x in func_rest_keys) and not series_entities["task"]:
+            func_rest_keys = ["rest", "rsfmri", "fcmri", "resting"]
+            # if any(x in re.sub("[^A-Za-z0-9]+", "", sd).lower() for x in func_rest_keys) and not series_entities["task"]:
+            if any(x in func_rest_keys for x in sd.split('_')) and not series_entities["task"]:
                 series_entities["task"] = "rest"
             else:
                 match_index = [
@@ -2730,6 +2726,10 @@ def entity_labels_identification(dataset_list_unique_series, lookup_dic):
             else:
                 pass
 
+            # rec (reconstruction)
+            if series_entities['reconstruction'] == 'pointspreadfunctionmodellingtimeofflight':
+                series_entities['reconstruction'] = 'PSTOF'
+
             # Make sure any found entities are allowed for specific datatype/suffix pair
             if unique_dic["type"] != "exclude":
                 datatype = unique_dic["datatype"]

ui/src/Objects.vue

@@ -440,13 +440,6 @@ export default defineComponent({
         return {
             so: null as IObject | null, //selected object
             sess: null as OrganizedSession | null, //selected session for IntendedFor handling
-            showInfo: {} as any,
-            petYaml: petYaml,
-            aslYaml: aslYaml,
-            fields: {},
-            showDialog: false,
-            rules: {},
-            formData: {},
         };
     },
 
@@ -679,10 +672,6 @@ export default defineComponent({
                             'It is required that perfusion m0scan images have IntendedFor set to at least 1 series ID.'
                         );
                     }
-                    // let warningMessage = "It is recommended that these images have IntendedFor set to at least 1 object. This is necessary if you plan on using processing BIDS-apps such as fMRIPrep"
-                    // if (!o.validationWarnings.includes(warningMessage)) {
-                    //     o.validationWarnings.push(warningMessage);
-                    // }
                 }
                 //Ensure other fmap series aren't included in the IntendedFor mapping
                 if (o.IntendedFor.length > 0) {

ui/src/libUnsafe.ts

@@ -557,13 +557,12 @@ export function setIntendedFor($root: IEzbids) {
             // Loop through sections
             sectionIDs.forEach((s: number) => {
                 let section = sesGroup.objects.filter(
-                    (e) => e.analysisResults.section_id === s && !e._exclude && e._type != 'exclude'
+                    (e) => e.analysisResults.section_id === s && !e._exclude && e._type !== 'exclude'
                 );
 
                 section.forEach((obj: IObject) => {
                     //add IntendedFor information
                     if (obj._type.startsWith('fmap/') || obj._type === 'perf/m0scan') {
-                        Object.assign(obj, { IntendedFor: [] });
                         let correspindingSeriesIntendedFor = $root.series[obj.series_idx].IntendedFor;
                         if (correspindingSeriesIntendedFor !== undefined && correspindingSeriesIntendedFor !== null) {
                             correspindingSeriesIntendedFor.forEach((i: number) => {
@@ -575,6 +574,22 @@ export function setIntendedFor($root: IEzbids) {
                                 }
                             });
                         }
+                        if (obj.hasOwnProperty('IntendedFor')) {
+                            if (obj.IntendedFor?.length !== 0) {
+                                obj.IntendedFor?.forEach((e) => {
+                                    let IntendedForObj = section.filter((o) => o.idx === e);
+                                    if (!IntendedForObj.length) {
+                                        let badIndex = obj.IntendedFor?.indexOf(e);
+                                        delete obj.IntendedFor[Object.keys(obj.IntendedFor)[badIndex]];
+                                        if (Object.keys(obj.IntendedFor).length === 0) {
+                                            obj.analysisResults.warnings = [
+                                                'It is recommended that field map (fmap) images have IntendedFor set to at least 1 series ID. This is necessary if you plan on using processing BIDS-apps such as fMRIPrep',
+                                            ];
+                                        }
+                                    }
+                                });
+                            }
+                        }
                     }
 
                     // check B0FieldIdentifier and B0FieldSource information
@@ -1821,7 +1836,6 @@ export function metadataAlerts(
                                         sidecarMetadataValue.includes('none')
                                     ) {
                                         // Required based on contain conditional between BIDS and sequence metadata
-                                        console.log('AAAAAAA', fieldName, sidecarMetadataValue);
                                         requiredFields.push(fieldName);
                                     }
                                 }

ui/src/store/index.ts

@@ -605,10 +605,17 @@ const store = createStore({
                 const bses_idx = b.session_idx;
                 if (ases_idx != bses_idx) return ases_idx - bses_idx;
 
-                const amodseriesnum = a.ModifiedSeriesNumber;
-                const bmodseriesnum = b.ModifiedSeriesNumber;
-                if (amodseriesnum && bmodseriesnum && amodseriesnum != bmodseriesnum)
-                    return amodseriesnum.localeCompare(bmodseriesnum);
+                // Shouldn't use this anymore, use AcquisitionTime instead
+                // const amodseriesnum = a.ModifiedSeriesNumber;
+                // const bmodseriesnum = b.ModifiedSeriesNumber;
+                // if (amodseriesnum && bmodseriesnum && amodseriesnum != bmodseriesnum)
+                //     return amodseriesnum.localeCompare(bmodseriesnum);
+
+                const aAcqTime = a.AcquisitionTime;
+                const bAcqTime = b.AcquisitionTime;
+                if (aAcqTime && bAcqTime) {
+                    return aAcqTime.localeCompare(bAcqTime);
+                }
 
                 const apath = a.items[0].path;
                 const bpath = b.items[0].path;