[ENH] Begin adding stim_file option to Events (task events)

brainlife · Aug 16, 2023 · b7f6171 · b7f6171 · dlevitas · Aug 16, 2023
1 parent cc0a2ee
commit b7f6171
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Showing 8 changed files with 52 additions and 11 deletions.
diff --git a/handler/convert.js b/handler/convert.js
diff --git a/handler/convert.ts b/handler/convert.ts
@@ -233,6 +233,11 @@ async.forEachOf(info.objects, (o, idx, next_o)=>{
             const headers = Object.keys(events.eventsBIDS[0]) //take first index value to see which columns user selected
             events.content = headers.join("\t")+"\n";
             events.eventsBIDS.forEach(rec=>{
+                if(rec.stim_file) {
+                    if(!rec.stim_file.startsWith("/stimuli/")) {
+                        rec.stim_file = "/stimuli/" + rec.stim_file
+                    }
+                }
                 const row = [];
                 headers.forEach(key=>{
                     row.push(rec[key]);

diff --git a/handler/ezBIDS_core/ezBIDS_core.py b/handler/ezBIDS_core/ezBIDS_core.py
@@ -254,7 +254,7 @@ def generate_dataset_description(DATA_DIR, bids_compliant):
         {
             "DOI": "n/a",
             "URL": "https://brainlife.io/ezbids/",
-            "Version": "n/a"
+            "Version": "1.0.0"
         }
     ]
 
@@ -2430,7 +2430,8 @@ def extract_series_info(dataset_list_unique_series):
             "responseTime2": None,
             "responseTimeUnit": "sec",
             "values": None,
-            "HED": None
+            "HED": None,
+            "stim_file": None
         },
         "loaded": False,
         "sampleValues": {},

diff --git a/ui/src/Events.vue b/ui/src/Events.vue
@@ -203,6 +203,18 @@
             </td>
         </tr>
 
+        <tr>
+            <th>stim_file</th>
+            <td>
+                <columnSelecter v-model="columns.stim_file" :columnKeys="ezbids.columnKeys" :sampleValues="events.sampleValues"/>
+
+                <p>
+                    Represents the location of the stimulus file (such as an image, video, or audio file) presented at the given onset time. There are no restrictions on the file formats of the stimuli files, but they should be stored in the /stimuli directory (under the root directory of the dataset; with OPTIONAL subdirectories). The values under the stim_file column correspond to a path relative to /stimuli. For example images/cat03.jpg will be translated to /stimuli/images/cat03.jpg. See <a href="https://bids-specification.readthedocs.io/en/stable/99-appendices/03-hed.html">BIDS Specification / Appendix 3</a>
+                </p>
+                <br>
+            </td>
+        </tr>        
+
         </table>
 
         <!--

diff --git a/ui/src/Objects.vue b/ui/src/Objects.vue
@@ -181,6 +181,7 @@
                                 <el-table-column v-if="item.eventsBIDS[0].response_time" prop="response_time" label="response_time" />
                                 <el-table-column v-if="item.eventsBIDS[0].value" prop="value" label="value" />
                                 <el-table-column v-if="item.eventsBIDS[0].HED" prop="HED" label="HED" />
+                                <el-table-column v-if="item.eventsBIDS[0].stim_file" prop="stim_file" label="stim_file" />
                             </el-table>
                         </el-form-item>
                         <br>

diff --git a/ui/src/lib.ts b/ui/src/lib.ts
@@ -93,6 +93,7 @@ export function createEventsTSV(ezbids : IEzbids, events : IEvents) {
                 if(events.columns.trialType) rec.trial_type = event[events.columns.trialType];
                 if(events.columns.value) rec.value = event[events.columns.value];
                 if(events.columns.HED) rec.HED = event[events.columns.HED];
+                if(events.columns.stim_file) rec.stim_file = event[events.columns.stim_file];
 
                 (item.eventsBIDS as IBIDSEvent[]).push(rec);
 

diff --git a/ui/src/libUnsafe.ts b/ui/src/libUnsafe.ts
@@ -1045,7 +1045,9 @@ export function mapEventColumns(ezbids_events, events) {
 
             values: null,
 
-            HED: null
+            HED: null,
+
+            stim_file: null
         }
     }
 }
diff --git a/ui/src/store/index.ts b/ui/src/store/index.ts
@@ -58,12 +58,23 @@ import {
 // export type GenericSchema = { [key: string]: GenericRule | GenericSchema }
 // export type SchemaTypeLike = AnyOf | SchemaType
 
+export interface ContainerObject {
+    Type: string;
+    Tag: string;
+}
 
-export interface DatasetDescriptionObject {
-    Name: string,
-    Version: string,
-    Description: string,
-    CodeURL: string,
+export interface GeneratedByObject {
+    Name: string;
+    Version: string;
+    Description: string;
+    CodeURL: string;
+    Container: [ContainerObject];
+}
+
+export interface SourceDatasetObject {
+    DOI: string;
+    URL: string;
+    Version: string;
 }
 
 export interface DatasetDescription {
@@ -80,8 +91,8 @@ export interface DatasetDescription {
     EthicsApprovals: string[];
     ReferencesAndLinks: string[];
     DatasetDOI: string;
-    GeneratedBy: [DatasetDescriptionObject];
-    SourceDatasets: string[];
+    GeneratedBy: [GeneratedByObject];
+    SourceDatasets: [SourceDatasetObject];
 }
 
 export interface PatientInfo {
@@ -141,6 +152,7 @@ export interface IBIDSEvent {
     response_time?: number;
     value?: string|number;
     HED?: string;
+    stim_file?: string;
 }
 
 export interface IObjectItem {
@@ -356,6 +368,8 @@ const state = {
             value: null,
 
             HED: null,
+
+            stim_file: null,
         },
 
         trialTypes: {