fix-up attrs resolution

package.json

@@ -5,17 +5,15 @@
     "@hms-dbmi/viv": "^0.16.0",
     "@material-ui/core": "^4.11.0",
     "@material-ui/icons": "^4.9.1",
-    "@zarrita/core": "^0.0.3",
-    "@zarrita/indexing": "^0.0.3",
-    "@zarrita/storage": "^0.0.2",
     "deck.gl": "^8.9.34",
     "imjoy-rpc": "^0.2.23",
     "jotai": "^1.0.0",
     "just-debounce-it": "^3.1.1",
     "p-map": "^5.5.0",
     "quick-lru": "^6.0.0",
     "react": "^18.2.0",
-    "react-dom": "^18.2.0"
+    "react-dom": "^18.2.0",
+    "zarrita": "^0.4.0-next.14"
   },
   "scripts": {
     "start": "vite",

src/codecs/jpeg2k.ts

@@ -5,8 +5,9 @@
 import { JpxImage } from 'https://cdn.jsdelivr.net/gh/mozilla/pdf.js@30bd5f0/src/core/jpx.js';
 
 export default class Jpeg2k {
-  static codecId: 'jpeg2k';
-  static fromConfig(_: Record<string, any>): Jpeg2k {
+  kind = 'bytes_to_bytes' as const;
+  static codecId = 'jpeg2k';
+  static fromConfig(): Jpeg2k {
     return new Jpeg2k();
   }
   encode(_: Uint8Array): never {

src/io.ts

@@ -102,12 +102,14 @@ function isMultiscales(attrs: zarr.Attributes): attrs is { multiscales: Ome.Mult
 }
 
 export async function createSourceData(config: ImageLayerConfig): Promise<SourceData> {
+  console.log('createSourceData', config);
   const node = await open(config.source);
+  console.log('node', node);
   let data: zarr.Array<zarr.DataType, Readable>[];
   let axes: Ome.Axis[] | undefined;
 
   if (node instanceof zarr.Group) {
-    const attrs = node.attrs;
+    let attrs = resolveAttrs(node.attrs);
 
     if (isOmePlate(attrs)) {
       return loadPlate(config, node, attrs.plate);

src/ome.ts

@@ -16,6 +16,7 @@ import {
   loadMultiscales,
   parseMatrix,
   range,
+  resolveAttrs,
 } from './utils';
 
 export async function loadWell(
@@ -46,7 +47,7 @@ export async function loadWell(
     // Need to get acquisitions metadata from parent Plate
     const platePath = grp.path.replace(`${row}/${col}`, '');
     const plate = await zarr.open(grp.resolve(platePath));
-    const plateAttrs = plate.attrs as { plate: Ome.Plate };
+    const plateAttrs = resolveAttrs(plate.attrs) as { plate: Ome.Plate };
     acquisitions = plateAttrs?.plate?.acquisitions ?? [];
 
     // filter imagePaths by acquisition

src/utils.ts

@@ -53,8 +53,23 @@ export async function open(source: string | Readable) {
 export async function getAttrsOnly<T = unknown>(location: zarr.Location<Readable>, path?: string) {
   const decoder = new TextDecoder();
   if (path) location = location.resolve(path);
-  const bytes = await location.store.get(location.resolve('.zattrs').path);
-  return bytes ? (JSON.parse(decoder.decode(bytes)) as T) : {};
+
+  // zarr meta and attrs are stored in the same file for v3,
+  // so first we can just open the node and get the attrs,
+  // otherwise we need to open the .zattrs file for v2.
+  let attrs = await zarr.open
+    .v3(location)
+    .then((node) => node.attrs)
+    .catch(async (err) => {
+      if (!(err instanceof zarr.NodeNotFoundError)) {
+        throw err;
+      }
+      const v2AttrsLocation = location.resolve('.zattrs');
+      const maybeBytes = await location.store.get(v2AttrsLocation.path);
+      return maybeBytes ? JSON.parse(decoder.decode(maybeBytes)) : {};
+    });
+
+  return resolveAttrs(attrs) as T;
 }
 
 export async function loadMultiscales(grp: zarr.Group<Readable>, multiscales: Ome.Multiscale[]) {
@@ -348,6 +363,9 @@ function getV2DataType(dtype: string) {
 
 type Selection = (number | Omit<Slice, 'indices'> | null)[];
 
+/**
+ * This is needed by @hms-dbmi/viv to get raw data from a Zarr.js style interface.
+ */
 export function createZarrArrayAdapter(arr: zarr.Array<zarr.DataType>): any {
   return new Proxy(arr, {
     get(target, prop) {
@@ -376,3 +394,16 @@ export function createZarrArrayAdapter(arr: zarr.Array<zarr.DataType>): any {
     },
   });
 }
+
+/**
+ * Extracts the OME metadata from the zarr attributes
+ *
+ * TODO: We should use zod to handle this
+ */
+export function resolveAttrs(attrs: zarr.Attributes): zarr.Attributes {
+  if ('ome' in attrs) {
+    // @ts-expect-error - handles v0.5
+    return attrs.ome;
+  }
+  return attrs;
+}