[electrophysiology_browser] Fix EEG data shift (aces#8999)

This resolves the data shift issue by adding the number of valid samples in the last chunk to the index.json, and using it for the calculations which previously assumed all chunks were filled. Closes aces#8992. Has a Loris-MRI counterpart: aces/Loris-MRI#1030 Loosely dependant on aces#8998 (file modifications in common and done at a later time).
jeffersoncasimir · Jan 23, 2024 · be39a57 · be39a57
1 parent 61b7dbf
commit be39a57
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Showing 5 changed files with 103 additions and 49 deletions.
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
@@ -95,12 +95,19 @@ class EEGLabSeriesProvider extends Component<CProps> {
     Promise.race(racers(fetchJSON, chunksURL, '/index.json')).then(
       ({json, url}) => {
         if (json) {
-          const {channelMetadata, shapes, timeInterval, seriesRange} = json;
+          const {
+            channelMetadata,
+            shapes,
+            timeInterval,
+            seriesRange,
+            validSamples,
+          } = json;
           this.store.dispatch(
             setDatasetMetadata({
               chunksURL: url,
               channelMetadata,
               shapes,
+              validSamples,
               timeInterval,
               seriesRange,
               limit,

diff --git a/...lectrophysiology_browser/jsx/react-series-data-viewer/src/series/components/LineChunk.tsx b/...lectrophysiology_browser/jsx/react-series-data-viewer/src/series/components/LineChunk.tsx
@@ -7,25 +7,30 @@ import {Group} from '@visx/group';
 import {colorOrder} from '../../color';
 
 const LineMemo = R.memoizeWith(
-  ({amplitudeScale, filters, channelIndex, traceIndex,
-     chunkIndex, isStacked, DCOffset, numChannels, numChunks}) =>
-    `${amplitudeScale},${filters.join('-')},`
+  ({amplitudeScale, interval, filters,
+     channelIndex, traceIndex, chunkIndex,
+     isStacked, DCOffset, numChannels,
+     numChunks, previousPoint,
+  }) =>
+    `${amplitudeScale},${interval.join('-')},${filters.join('-')},`
     + `${channelIndex}-${traceIndex}-${chunkIndex},`
-    + `${isStacked},${DCOffset},${numChannels},${numChunks}`,
+    + `${isStacked},${DCOffset},${numChannels},`
+    + `${numChunks},${previousPoint}`,
   ({
-     channelIndex,
-     traceIndex,
-     chunkIndex,
-     interval,
-     seriesRange,
-     amplitudeScale,
-     filters,
-     values,
-     isStacked,
-     DCOffset,
-     numChannels,
-     numChunks,
-     ...rest
+    channelIndex,
+    traceIndex,
+    chunkIndex,
+    interval,
+    seriesRange,
+    amplitudeScale,
+    filters,
+    values,
+    isStacked,
+    DCOffset,
+    numChannels,
+    numChunks,
+    previousPoint,
+    ...rest
    }) => {
     const scales = [
       scaleLinear()
@@ -36,12 +41,25 @@ const LineMemo = R.memoizeWith(
         .range([-0.5, 0.5]),
     ];
 
-    const points = values.map((value, i) =>
-      vec2.fromValues(
-        scales[0](
-          interval[0] + (i / values.length) * (interval[1] - interval[0])
-        ),
-        -(scales[1](value) - DCOffset)
+    const points = previousPoint === null
+      ? []
+      : [
+        vec2.fromValues(
+          scales[0](
+            interval[0] - (1 / values.length) * (interval[1] - interval[0])
+          ),
+          -(scales[1](previousPoint) - DCOffset)
+        )
+    ];
+
+    points.push(
+      ...values.map((value, i) =>
+        vec2.fromValues(
+          scales[0](
+            interval[0] + (i / values.length) * (interval[1] - interval[0])
+          ),
+          -(scales[1](value) - DCOffset)
+        )
       )
     );
 
@@ -77,6 +95,7 @@ type CProps = {
   withDCOffset: number,
   numChannels: number,
   numChunks: number,
+  previousPoint: number | null,
 };
 
 /**
@@ -95,22 +114,24 @@ type CProps = {
  * @param root0.withDCOffset
  * @param root0.numChannels
  * @param root0.numChunks
+ * @param root0.previousPoint
  */
 const LineChunk = ({
-   channelIndex,
-   traceIndex,
-   chunkIndex,
-   chunk,
-   seriesRange,
-   amplitudeScale,
-   scales,
-   physioFileID,
-   isHovered,
-   isStacked,
-   withDCOffset,
-   numChannels,
-   numChunks,
-   ...rest
+  channelIndex,
+  traceIndex,
+  chunkIndex,
+  chunk,
+  seriesRange,
+  amplitudeScale,
+  scales,
+  physioFileID,
+  isHovered,
+  isStacked,
+  withDCOffset,
+  numChannels,
+  numChunks,
+  previousPoint,
+  ...rest
  }: CProps) => {
   const {interval, values} = chunk;
 
@@ -133,7 +154,7 @@ const LineChunk = ({
       top={-p0[1]}
     >
       <Group
-        transform={'translate(' + p0[0] + ' 0)' +
+        transform={'translate(' + p0[0] + ' 0) ' +
           'scale(' + chunkLength + ' ' + chunkHeight + ')'
         }
       >
@@ -151,6 +172,7 @@ const LineChunk = ({
           DCOffset={withDCOffset}
           numChannels={numChannels}
           numChunks={numChunks}
+          previousPoint={previousPoint}
         />
       </Group>
     </Group>

diff --git a/...ophysiology_browser/jsx/react-series-data-viewer/src/series/components/SeriesRenderer.tsx b/...ophysiology_browser/jsx/react-series-data-viewer/src/series/components/SeriesRenderer.tsx
@@ -623,7 +623,8 @@ const SeriesRenderer: FunctionComponent<CProps> = ({
           />
         </clipPath>
 
-        {channelList.map((channel, i) => {
+        {
+          channelList.map((channel, i) => {
           if (!channelMetadata[channel.index]) {
             return null;
           }
@@ -733,12 +734,12 @@ const SeriesRenderer: FunctionComponent<CProps> = ({
                 : 0;
 
               return (
-                trace.chunks.map((chunk, k) => (
+                trace.chunks.map((chunk, k, chunks) => (
                     <LineChunk
                       channelIndex={channel.index}
                       traceIndex={j}
                       chunkIndex={k}
-                      key={`${k}-${trace.chunks.length}`}
+                      key={`${channel.index}-${k}-${trace.chunks.length}`}
                       chunk={chunk}
                       seriesRange={seriesRange}
                       amplitudeScale={amplitudeScale}
@@ -749,6 +750,11 @@ const SeriesRenderer: FunctionComponent<CProps> = ({
                       withDCOffset={DCOffset}
                       numChannels={numDisplayedChannels}
                       numChunks={numChunks}
+                      previousPoint={
+                        k === 0
+                          ? null
+                          : chunks[k - 1].values.slice(-1)[0]
+                      }
                     />
                 ))
               );

diff --git a/...trophysiology_browser/jsx/react-series-data-viewer/src/series/store/logic/fetchChunks.tsx b/...trophysiology_browser/jsx/react-series-data-viewer/src/series/store/logic/fetchChunks.tsx
@@ -110,7 +110,7 @@ export const createFetchChunksEpic = (fromState: (any) => State) => (
     Rx.map(([, state]) => fromState(state)),
     Rx.debounceTime(UPDATE_DEBOUNCE_TIME),
     Rx.concatMap(({bounds, dataset, channels}) => {
-      const {chunksURL, shapes, timeInterval} = dataset;
+      const {chunksURL, shapes, validSamples, timeInterval} = dataset;
       if (!chunksURL) {
         return of();
       }
@@ -123,19 +123,25 @@ export const createFetchChunksEpic = (fromState: (any) => State) => (
               const shapeChunks =
                 shapes.map((shape) => shape[shape.length - 2]);
 
-              const chunkIntervals : chunkIntervals[] = shapeChunks
+              const valuesPerChunk =
+                shapes.map((shape) => shape[shape.length - 1]);
+
+              const chunkIntervals = shapeChunks
                 .map((numChunks, downsampling) => {
                   const recordingDuration = Math.abs(
                     timeInterval[1] - timeInterval[0]
                   );
 
+                  const filledChunks = (numChunks - 1) +
+                    (validSamples[downsampling] / valuesPerChunk[downsampling]);
+
                   const i0 =
-                    (numChunks *
+                    (filledChunks *
                       Math.floor(bounds.interval[0] - bounds.domain[0])
                     ) / recordingDuration;
 
                   const i1 =
-                    (numChunks *
+                    (filledChunks *
                       Math.ceil(bounds.interval[1] - bounds.domain[0])
                     ) / recordingDuration;
 
@@ -145,7 +151,11 @@ export const createFetchChunksEpic = (fromState: (any) => State) => (
                   ];
 
                   return {
-                    interval: interval,
+                    interval:
+                      [
+                        Math.floor(i0),
+                        Math.min(Math.ceil(i1), filledChunks),
+                      ],
                     numChunks: numChunks,
                     downsampling,
                   };
@@ -164,12 +174,18 @@ export const createFetchChunksEpic = (fromState: (any) => State) => (
               const chunkPromises = R.range(...finestChunks.interval).flatMap(
                 (chunkIndex) => {
                   const numChunks = finestChunks.numChunks;
+
+                  const filledChunks = (numChunks - 1) + (
+                    validSamples[finestChunks.downsampling] /
+                    valuesPerChunk[finestChunks.downsampling]
+                  );
+
                   const chunkInterval = [
                     timeInterval[0] +
-                    (chunkIndex / numChunks) *
+                    (chunkIndex / filledChunks) *
                     (timeInterval[1] - timeInterval[0]),
                     timeInterval[0] +
-                    ((chunkIndex + 1) / numChunks) *
+                    ((chunkIndex + 1) / filledChunks) *
                     (timeInterval[1] - timeInterval[0]),
                   ];
                   if (chunkInterval[0] <= bounds.interval[1]) {

diff --git a/...electrophysiology_browser/jsx/react-series-data-viewer/src/series/store/state/dataset.tsx b/...electrophysiology_browser/jsx/react-series-data-viewer/src/series/store/state/dataset.tsx
@@ -29,6 +29,7 @@ export type Action =
         chunksURL: string,
         channelNames: string[],
         shapes: number[][],
+        validSamples: number[],
         timeInterval: [number, number],
         seriesRange: [number, number],
         limit: number,
@@ -46,6 +47,7 @@ export type State = {
   activeEpoch: number | null,
   physioFileID: number | null,
   shapes: number[][],
+  validSamples: number[],
   timeInterval: [number, number],
   seriesRange: [number, number],
 };
@@ -68,6 +70,7 @@ export const datasetReducer = (
     offsetIndex: 1,
     limit: DEFAULT_MAX_CHANNELS,
     shapes: [],
+    validSamples: [],
     timeInterval: [0, 1],
     seriesRange: [-1, 2],
   },