feat(zarr): Flatten zarr module, remove XML-parsing (#1462)

* wip * Use DTYPE_LOOKUP for supported dtype types * Use store built on fetch API * bump zarr
visgl · Jun 24, 2021 · 6c5d201 · 6c5d201
1 parent e5daf5b
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diff --git a/modules/zarr/README.md b/modules/zarr/README.md
@@ -1,5 +1,3 @@
-<<<<<<< HEAD:modules/textures/README.md
-
 # @loaders.gl/zarr
 
 [loaders.gl](https://loaders.gl/docs) is a collection of framework-independent 3D and geospatial parsers and encoders.

diff --git a/modules/zarr/package.json b/modules/zarr/package.json
@@ -15,7 +15,7 @@
     "loader",
     "zarr"
   ],
-  "types": "src/index.ts",
+  "types": "src/index.d.ts",
   "main": "dist/es5/index.js",
   "module": "dist/esm/index.js",
   "sideEffects": false,
@@ -30,11 +30,8 @@
     "build-bundle": "webpack --display=minimal --config ../../scripts/webpack/bundle.js"
   },
   "dependencies": {
-    "@loaders.gl/core": "3.0.0-alpha.18",
     "@loaders.gl/worker-utils": "3.0.0-alpha.18",
-    "@luma.gl/constants": "^8.3.0",
-    "fast-xml-parser": "^3.16.0",
-    "zarr": "^0.4.0"
+    "zarr": "^0.5.0"
   },
   "devDependencies": {
     "@loaders.gl/core": "3.0.0-alpha.18"

diff --git a/modules/zarr/src/constants.ts b/modules/zarr/src/constants.ts
diff --git a/modules/zarr/src/index.ts b/modules/zarr/src/index.ts
@@ -1,4 +1,2 @@
 export {loadZarr} from './lib/load-zarr';
-export {loadBioformatsZarr} from './lib/load-bioformats-zarr';
-
 export {default as ZarrPixelSource} from './lib/zarr-pixel-source';
diff --git a/modules/zarr/src/lib/load-bioformats-zarr-helper.ts b/modules/zarr/src/lib/load-bioformats-zarr-helper.ts
diff --git a/modules/zarr/src/lib/load-bioformats-zarr.ts b/modules/zarr/src/lib/load-bioformats-zarr.ts
diff --git a/modules/zarr/src/lib/load-zarr.ts b/modules/zarr/src/lib/load-zarr.ts
@@ -1,44 +1,24 @@
-import type {ZarrArray} from 'zarr';
-import {loadMultiscales, guessTileSize} from './utils/zarr-utils';
+import type {Store} from 'zarr/types/storage/types';
+import {loadMultiscales, guessTileSize, guessLabels, normalizeStore, validLabels} from './utils';
 import ZarrPixelSource from './zarr-pixel-source';
-import type {Labels} from '../types';
 
-interface Channel {
-  active: boolean;
-  color: string;
-  label: string;
-  window: {
-    min?: number;
-    max?: number;
-    start: number;
-    end: number;
-  };
+interface ZarrOptions {
+  labels?: string[];
 }
 
-interface Omero {
-  channels: Channel[];
-  rdefs: {
-    defaultT?: number;
-    defaultZ?: number;
-    model: string;
-  };
-  name?: string;
-}
+export async function loadZarr(root: string | Store, options: ZarrOptions = {}) {
+  const store = normalizeStore(root);
+  const {data, rootAttrs} = await loadMultiscales(store);
+  const tileSize = guessTileSize(data[0]);
 
-interface Multiscale {
-  datasets: {path: string}[];
-  version?: string;
-}
+  // If no labels are provided, inspect the root attributes for the store.
+  // For now, we only infer labels for OME-Zarr.
+  const labels = options.labels ?? guessLabels(rootAttrs);
 
-export interface RootAttrs {
-  omero: Omero;
-  multiscales: Multiscale[];
-}
+  if (!validLabels(labels, data[0].shape)) {
+    throw new Error('Invalid labels for Zarr array dimensions.');
+  }
 
-export async function loadZarr(store: ZarrArray['store']) {
-  const {data, rootAttrs} = await loadMultiscales(store);
-  const labels = ['t', 'c', 'z', 'y', 'x'] as Labels<['t', 'c', 'z']>;
-  const tileSize = guessTileSize(data[0]);
   const pyramid = data.map((arr) => new ZarrPixelSource(arr, labels, tileSize));
   return {
     data: pyramid,