Only use nested(store) for correct version of OME-Zarr

hms-dbmi · Mar 31, 2021 · d5a6676 · d5a6676
1 parent 01a051a
commit d5a6676
Show file tree

Hide file tree

Showing 2 changed files with 63 additions and 27 deletions.
diff --git a/src/ome.ts b/src/ome.ts
@@ -2,9 +2,28 @@ import { ZarrPixelSource } from '@hms-dbmi/viv';
 import pMap from 'p-map';
 import { Group as ZarrGroup, HTTPStore, openGroup, ZarrArray } from 'zarr';
 import type { ImageLayerConfig, SourceData } from './state';
-import { join, loadMultiscales, guessTileSize, range, parseMatrix } from './utils';
+import {
+  guessTileSize,
+  join,
+  loadMultiscales,
+  nested,
+  parseMatrix,
+  range
+} from './utils';
 
-export async function loadWell(config: ImageLayerConfig, grp: ZarrGroup, wellAttrs: Ome.Well): Promise<SourceData> {
+// OME-Zarr uses nested chunks since version 0.2
+function isNested(version: String | undefined) : boolean {
+  return version != undefined && version !== "0.1";
+}
+
+export async function loadWell(
+  config: ImageLayerConfig,
+  grp: ZarrGroup,
+  wellAttrs: Ome.Well
+): Promise<SourceData> {
+  if (isNested(wellAttrs.version)) {
+    grp.store = nested(grp.store);
+  }
   // Can filter Well fields by URL query ?acquisition=ID
   const acquisitionId: number | undefined = config.acquisition ? parseInt(config.acquisition) : undefined;
   let acquisitions: Ome.Acquisition[] = [];
@@ -104,7 +123,14 @@ export async function loadWell(config: ImageLayerConfig, grp: ZarrGroup, wellAtt
   return sourceData;
 }
 
-export async function loadPlate(config: ImageLayerConfig, grp: ZarrGroup, plateAttrs: Ome.Plate): Promise<SourceData> {
+export async function loadPlate(
+  config: ImageLayerConfig,
+  grp: ZarrGroup,
+  plateAttrs: Ome.Plate
+): Promise<SourceData> {
+  if (isNested(plateAttrs.version)) {
+    grp.store = nested(grp.store);
+  }
   if (!('columns' in plateAttrs) || !('rows' in plateAttrs)) {
     throw Error(`Plate .zattrs missing columns or rows`);
   }
@@ -193,6 +219,9 @@ export async function loadOmeroMultiscales(
   grp: ZarrGroup,
   attrs: { multiscales: Ome.Multiscale[]; omero: Ome.Omero }
 ): Promise<SourceData> {
+  if (isNested(attrs.multiscales[0]?.version)) {
+    grp.store = nested(grp.store);
+  }
   const { name, opacity = 1, colormap = '' } = config;
   const data = await loadMultiscales(grp, attrs.multiscales);
   const meta = parseOmeroMeta(attrs.omero);

diff --git a/src/utils.ts b/src/utils.ts
@@ -25,37 +25,17 @@ async function normalizeStore(source: string | ZarrArray['store']) {
       const store = await FileReferenceStore.fromUrl(source);
       return { store };
     }
-    const [root, path] = source.split('.zarr');
-    return { store: new HTTPStore(root + '.zarr'), path };
+    // const [root, path] = source.split('.zarr');
+    return { store: new HTTPStore(source), path:'' };
   }
   return { store: source };
 }
 
 export async function open(source: string | ZarrArray['store']) {
   const { store, path } = await normalizeStore(source);
-
-  function nested(store) {
-    const get = (target, key) => {
-      if (key === 'getItem' || key === 'setItem' || key === 'containsItem') {
-        return (path, ...args) => {
-          if (path.endsWith('.zarray') || path.endsWith('.zattrs') || path.endsWith('.zgroup')) {
-            return target[key](path, ...args);
-          }
-          const prefix = path.split('/');
-          const chunkKey = prefix.pop();
-          const newPath = [...prefix, chunkKey.replaceAll('.', '/')].join('/');
-          return target[key](newPath, ...args);
-        }
-      }
-      return Reflect.get(target, key);
-    };
-    return new Proxy(store, { get });
-  }
-  const nested_store = nested(store);
-
-  return openGroup(nested_store, path).catch((err) => {
+  return openGroup(store, path).catch((err) => {
     if (err instanceof ContainsArrayError) {
-      return openArray({ nested_store, path });
+      return openArray({ store, path });
     }
     throw err;
   });
@@ -70,6 +50,33 @@ export async function loadMultiscales(grp: ZarrGroup, multiscales: Ome.Multiscal
   throw Error('Multiscales metadata included a path to a group.');
 }
 
+export function nested(store: ZarrArray['store']) {
+  const get = (target: ZarrArray['store'], key: string | number | symbol) => {
+    if (key === 'getItem' || key === 'containsItem' || key === 'setItem') {
+      return (path: string, ...args: any[]) => {
+        if (path.endsWith('.zarray') || path.endsWith('.zattrs') || path.endsWith('.zgroup')) {
+          if (key === 'setItem') {
+            // TypeScript: setItem() needs 'value'
+            return target[key](path, args[0]);
+          } else {
+            return target[key](path, ...args);
+          }
+        }
+        const prefix = path.split('/');
+        const chunkKey = prefix.pop() as string;
+        const newPath = [...prefix, chunkKey.replaceAll('.', '/')].join('/');
+        if (key === 'setItem') {
+          return target[key](newPath, args[0]);
+        } else {
+          return target[key](newPath, ...args);
+        }
+      }
+    }
+    return Reflect.get(target, key);
+  };
+  return new Proxy(store, { get });
+}
+
 export function hexToRGB(hex: string): number[] {
   if (hex.startsWith('#')) hex = hex.slice(1);
   const r = parseInt(hex.slice(0, 2), 16);