Z downsampling

src/ZarrPixelSource.ts

@@ -19,6 +19,7 @@ type VivPixelData = {
 export class ZarrPixelSource implements viv.PixelSource<Array<string>> {
   readonly labels: viv.Labels<Array<string>>;
   readonly tileSize: number;
+  originalSizeZ: number;
   readonly dtype: viv.SupportedDtype;
   readonly #arr: zarr.Array<zarr.NumberDataType | zarr.BigintDataType, zarr.Readable>;
   readonly #transform: (
@@ -43,6 +44,7 @@ export class ZarrPixelSource implements viv.PixelSource<Array<string>> {
     this.#arr = arr;
     this.labels = options.labels;
     this.tileSize = options.tileSize;
+    this.originalSizeZ = this.shape[this.labels.indexOf("z")];
     /**
      * Some `zarrita` data types are not supported by Viv and require casting.
      *
@@ -64,6 +66,10 @@ export class ZarrPixelSource implements viv.PixelSource<Array<string>> {
     }
   }
 
+  setOriginalSizeZ(sizeZ: number) {
+    this.originalSizeZ = sizeZ;
+  }
+
   get #width() {
     const lastIndex = this.shape.length - 1;
     return this.shape[this.labels.indexOf("c") === lastIndex ? lastIndex - 1 : lastIndex];
@@ -103,14 +109,21 @@ export class ZarrPixelSource implements viv.PixelSource<Array<string>> {
     signal?: AbortSignal;
   }): Promise<viv.PixelData> {
     const { x, y, selection, signal } = options;
+    let zarrSelection = buildZarrSelection(selection, {
+      labels: this.labels,
+      slices: {
+        x: zarr.slice(x * this.tileSize, Math.min((x + 1) * this.tileSize, this.#width)),
+        y: zarr.slice(y * this.tileSize, Math.min((y + 1) * this.tileSize, this.#height)),
+      },
+    });
+    // If we know the original sizeZ, adjust the z index of this array to account for downsampling
+    let zIndex = this.labels.indexOf("z");
+    if (this.originalSizeZ > 0 && zarrSelection[zIndex] instanceof Number) {
+      let z = zarrSelection[zIndex] as number;
+      zarrSelection[zIndex] = Math.floor((z * this.shape[zIndex]) / this.originalSizeZ);
+    }
     return this.#fetchData({
-      selection: buildZarrSelection(selection, {
-        labels: this.labels,
-        slices: {
-          x: zarr.slice(x * this.tileSize, Math.min((x + 1) * this.tileSize, this.#width)),
-          y: zarr.slice(y * this.tileSize, Math.min((y + 1) * this.tileSize, this.#height)),
-        },
-      }),
+      selection: zarrSelection,
       signal,
     });
   }

src/ome.ts

@@ -267,6 +267,11 @@ export async function loadOmeMultiscales(
     meta = await defaultMeta(lowresSource, axis_labels);
   }
   const loader = data.map((arr) => new ZarrPixelSource(arr, { labels: axis_labels, tileSize }));
+  // Set originalSizeZ for all ZarrPixelSource arrays so they can adjust for Z downsampling
+  let originalSizeZ = loader[0].shape[axis_labels.indexOf("z")];
+  for (const l of loader) {
+    l.setOriginalSizeZ(originalSizeZ);
+  }
   const labels = await resolveOmeLabelsFromMultiscales(grp);
   return {
     loader: loader,