[EEG Browser] Add ability to view annotations in event panel and over…

…laid on signal viewer (#8235) The changes in this PR fill in a few gaps in the code and allow for annotation data to be viewed in the EEG Browser. Annotations are displayed in orange in the Events / Annotation Panel and when selected are shown as an overlay in the signal viewer. Replaces #7828
aces · Nov 24, 2022 · 2ac39b0 · 2ac39b0
1 parent 1d3a4d0
commit 2ac39b0
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Showing 6 changed files with 63 additions and 23 deletions.
diff --git a/modules/electrophysiology_browser/jsx/electrophysiologySessionView.js b/modules/electrophysiology_browser/jsx/electrophysiologySessionView.js
@@ -192,10 +192,10 @@ class ElectrophysiologySessionView extends Component {
       }
       return resp.json();
     })
-        .then((data) => {
+      .then((data) => {
           const database = data.database.map((dbEntry) => ({
             ...dbEntry,
-            // EEG Visualisation urls
+            // EEG Visualization parameters
             chunksURLs:
                 dbEntry
                 && dbEntry.file.chunks_urls.map(
@@ -219,6 +219,9 @@ class ElectrophysiologySessionView extends Component {
                       + '/electrophysiology_browser/file_reader/?file='
                       + group.links[1].file
                 ),
+            annotations:
+                dbEntry
+                && dbEntry.file.annotations,
           }));
 
           this.setState({
@@ -318,6 +321,7 @@ class ElectrophysiologySessionView extends Component {
           chunksURLs,
           epochsURL,
           electrodesURL,
+          annotations,
         } = this.state.database[i];
         const file = this.state.database[i].file;
         const splitPagination = [];
@@ -346,7 +350,8 @@ class ElectrophysiologySessionView extends Component {
           chunksURLs?.[file.splitData?.splitIndex] || chunksURLs
       }
         epochsURL={epochsURL}
-        electrodesURL={electrodesURL}
+                  electrodesURL={electrodesURL}
+                  annotations={annotations}
             >
             <Panel
         id='channel-viewer'

diff --git a/...lectrophysiology_browser/jsx/react-series-data-viewer/src/eeglab/EEGLabSeriesProvider.tsx b/...lectrophysiology_browser/jsx/react-series-data-viewer/src/eeglab/EEGLabSeriesProvider.tsx
@@ -17,6 +17,7 @@ import {setDomain, setInterval} from '../series/store/state/bounds';
 import {updateFilteredEpochs} from '../series/store/logic/filterEpochs';
 import {setElectrodes} from '../series/store/state/montage';
 import {Channel} from '../series/store/types';
+import {AnnotationMetadata} from '../series/store/types';
 
 declare global {
   interface Window {
@@ -28,6 +29,7 @@ type CProps = {
   chunksURL: string,
   epochsURL: string,
   electrodesURL: string,
+  annotations: AnnotationMetadata,
   limit: number,
 };
 
@@ -67,6 +69,7 @@ class EEGLabSeriesProvider extends Component<CProps> {
       chunksURL,
       epochsURL,
       electrodesURL,
+      annotations,
       limit,
     } = props;
 
@@ -106,20 +109,45 @@ class EEGLabSeriesProvider extends Component<CProps> {
           this.store.dispatch(setInterval(timeInterval));
         }
       }
-    ).then(() => Promise.race(racers(fetchText, epochsURL)).then((text) => {
+    ).then(() => Promise.race(racers(fetchText, epochsURL))
+      .then((text) => {
         if (!(typeof text.json === 'string'
           || text.json instanceof String)) return;
+        return tsvParse(
+          text.json.replace('trial_type', 'label'))
+          .map(({onset, duration, label}, i) => ({
+            onset: parseFloat(onset),
+            duration: parseFloat(duration),
+            type: 'Event',
+            label: label,
+            comment: null,
+            channels: 'all',
+          }));
+      }).then(events => {
+        let epochs = events;
+        annotations.instances.map(instance => {
+          const label = annotations.labels
+            .find(label =>
+              label.AnnotationLabelID == instance.AnnotationLabelID
+            ).LabelDescription;
+          epochs.push({
+            onset: parseFloat(instance.Onset),
+            duration: parseFloat(instance.Duration),
+            type: 'Annotation',
+            label: label,
+            comment: null,
+            channels: 'all',
+          });
+        });
+        return epochs;
+      }).then(epochs => {
         this.store.dispatch(
-          setEpochs(tsvParse(
-            text.json.replace('trial_type', 'label'))
-              .map(({onset, duration, label}, i) => ({
-                onset: parseFloat(onset),
-                duration: parseFloat(duration),
-                type: 'Event',
-                label: label,
-                comment: null,
-                channels: 'all',
-              }))
+          setEpochs(
+            epochs
+            .flat()
+            .sort(function(a, b) {
+              return a.onset - b.onset;
+            })
           )
         );
         this.store.dispatch(updateFilteredEpochs());

diff --git a/modules/electrophysiology_browser/jsx/react-series-data-viewer/src/series/store/types.tsx b/modules/electrophysiology_browser/jsx/react-series-data-viewer/src/series/store/types.tsx
@@ -32,6 +32,12 @@ export type Epoch = {
   channels: number[] | "all",
 };
 
+export type AnnotationMetadata = {
+  instances: any[],
+  labels: any[],
+  metadata: any[]
+}
+
 export type RightPanel = 'annotationForm' | 'epochList' | null;
 
 export type Electrode = {

diff --git a/modules/electrophysiology_browser/php/models/electrophysioannotations.class.inc b/modules/electrophysiology_browser/php/models/electrophysioannotations.class.inc
@@ -48,7 +48,7 @@ class ElectrophysioAnnotations
 
         $annotationLabels = $db->pselect(
             'SELECT * FROM physiological_annotation_label',
-            ['PFID' => $this->_physioFileID]
+            []
         );
 
         $this->_data = [

diff --git a/modules/electrophysiology_browser/php/sessions.class.inc b/modules/electrophysiology_browser/php/sessions.class.inc
@@ -477,15 +477,12 @@ class Sessions extends \NDB_Page
             ['PFID' => $physioFileID]
         );
 
-        //Get the annotation data if the output type is derivative
-        //Get the annotation data if the output type is derivative
-        if (strcmp($fileOutput, 'derivative') == 0) {
-            $annotations = new ElectrophysioAnnotations(
-                intval($physioFileID)
-            );
-            $fileSummary['annotations'] = $annotations->getData();
-        }
+        //Get the annotation data
+        $annotations = new ElectrophysioAnnotations(
+            intval($physioFileID)
+        );
 
+        $fileSummary['annotations'] = $annotations->getData();
         $fileSummary['output_type'] = $fileOutput;
         $fileSummary['splitData']   = $physioFileObj->getSplitData(0);
 

diff --git a/modules/electrophysiology_browser/test/electrophysiologyBrowserTest.php b/modules/electrophysiology_browser/test/electrophysiologyBrowserTest.php
@@ -120,6 +120,8 @@ function setUp(): void
             [
                 'SessionID'                 => '999999',
                 'PhysiologicalOutputTypeID' => 22,
+                'InsertedByUser'            => 'Unit Tester',
+                'FilePath'                  => '/path/to/test/file',
                 'FileType'                  => 'testType'
             ]
         );
@@ -128,6 +130,8 @@ function setUp(): void
             [
                 'SessionID'                 => '999997',
                 'PhysiologicalOutputTypeID' => 23,
+                'InsertedByUser'            => 'Unit Tester',
+                'FilePath'                  => '/path/to/test/file2',
                 'FileType'                  => 'testType2'
             ]
         );