Add attrs util. Remove generic axes util.

src/io.ts

@@ -14,7 +14,6 @@ import {
   COLORS,
   CYMRGB,
   getAxisLabels,
-  getAxisLabelsFromMultiscales,
   guessTileSize,
   hexToRGB,
   loadMultiscales,
@@ -108,7 +107,6 @@ function loadMultiChannel(config: MultichannelConfig, data: ZarrPixelSource<stri
 export async function createSourceData(config: ImageLayerConfig): Promise<SourceData> {
   const node = await open(config.source);
   let data: ZarrArray[];
-  let axis_labels;
 
   if (node instanceof ZarrGroup) {
     const attrs = (await node.attrs.asObject()) as Ome.Attrs;
@@ -141,12 +139,15 @@ export async function createSourceData(config: ImageLayerConfig): Promise<Source
     }
 
     data = await loadMultiscales(node, attrs.multiscales);
-    axis_labels = getAxisLabelsFromMultiscales(attrs);
+    if (!config.axis_labels) {
+      // Update config axis_labels if present in multiscales
+      config.axis_labels = attrs.multiscales[0].axes;
+    }
   } else {
     data = [node];
   }
 
-  const labels = getAxisLabels(data[0], axis_labels || config.axis_labels);
+  const labels = getAxisLabels(data[0], config.axis_labels);
   const tileSize = guessTileSize(data[0]);
   const loader = data.map((d) => new ZarrPixelSource(d, labels, tileSize));
   const [base] = loader;

src/ome.ts

@@ -2,7 +2,7 @@ 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, getAxisLabelsFromMultiscales, guessTileSize, range, parseMatrix } from './utils';
+import { join, loadMultiscales, guessTileSize, range, parseMatrix, attrs } from './utils';
 
 export async function loadWell(config: ImageLayerConfig, grp: ZarrGroup, wellAttrs: Ome.Well): Promise<SourceData> {
   // Can filter Well fields by URL query ?acquisition=ID
@@ -28,7 +28,7 @@ export async function loadWell(config: ImageLayerConfig, grp: ZarrGroup, wellAtt
     // Need to get acquisitions metadata from parent Plate
     const plateUrl = grp.store.url.replace(`${row}/${col}`, '');
     const plate = await openGroup(new HTTPStore(plateUrl));
-    const plateAttrs = (await plate.attrs.asObject()) as { plate: Ome.Plate };
+    const plateAttrs = await attrs<{ plate: Ome.Plate }>(plate);
     acquisitions = plateAttrs?.plate?.acquisitions ?? [];
 
     // filter imagePaths by acquisition
@@ -42,7 +42,7 @@ export async function loadWell(config: ImageLayerConfig, grp: ZarrGroup, wellAtt
   const rows = Math.ceil(imgPaths.length / cols);
 
   // Use first image for rendering settings, resolutions etc.
-  const imgAttrs = (await grp.getItem(imgPaths[0]).then((g) => g.attrs.asObject())) as Ome.Attrs;
+  const imgAttrs = await attrs<Ome.Attrs>(grp, imgPaths[0]);
   if (!('omero' in imgAttrs)) {
     throw Error('Path for image is not valid.');
   }
@@ -51,7 +51,7 @@ export async function loadWell(config: ImageLayerConfig, grp: ZarrGroup, wellAtt
   // Create loader for every Image.
   const promises = imgPaths.map((p) => grp.getItem(join(p, resolution)));
   const data = (await Promise.all(promises)) as ZarrArray[];
-  const axis_labels = getOmeAxisLabels(imgAttrs);
+  const axis_labels = getOmeAxisLabels(imgAttrs.multiscales);
   const meta = parseOmeroMeta(imgAttrs.omero, axis_labels);
 
   const tileSize = guessTileSize(data[0]);
@@ -119,13 +119,13 @@ export async function loadPlate(config: ImageLayerConfig, grp: ZarrGroup, plateA
   const wellPaths = plateAttrs.wells.map((well) => well.path);
 
   // Use first image as proxy for others.
-  const wellAttrs = (await grp.getItem(wellPaths[0]).then((g) => g.attrs.asObject())) as Ome.Attrs;
+  const wellAttrs = await attrs<Ome.Attrs>(grp, wellPaths[0]);
   if (!('well' in wellAttrs)) {
     throw Error('Path for image is not valid, not a well.');
   }
 
   const imgPath = wellAttrs.well.images[0].path;
-  const imgAttrs = (await grp.getItem(join(wellPaths[0], imgPath)).then((g) => g.attrs.asObject())) as Ome.Attrs;
+  const imgAttrs = await attrs<Ome.Attrs>(grp, join(wellPaths[0], imgPath));
   if (!('omero' in imgAttrs)) {
     throw Error('Path for image is not valid.');
   }
@@ -141,7 +141,7 @@ export async function loadPlate(config: ImageLayerConfig, grp: ZarrGroup, plateA
     { concurrency: 10 }
   );
   const data = await Promise.all(promises);
-  const axis_labels = getOmeAxisLabels(imgAttrs);
+  const axis_labels = getOmeAxisLabels(imgAttrs.multiscales);
   const meta = parseOmeroMeta(imgAttrs.omero, axis_labels);
   const tileSize = guessTileSize(data[0][1]);
   const loaders = data.map((d) => {
@@ -200,7 +200,7 @@ export async function loadOmeroMultiscales(
 ): Promise<SourceData> {
   const { name, opacity = 1, colormap = '' } = config;
   const data = await loadMultiscales(grp, attrs.multiscales);
-  const axis_labels = getOmeAxisLabels(attrs);
+  const axis_labels = getOmeAxisLabels(attrs.multiscales);
   const meta = parseOmeroMeta(attrs.omero, axis_labels);
   const tileSize = guessTileSize(data[0]);
 
@@ -252,8 +252,7 @@ function parseOmeroMeta({ rdefs, channels, name }: Ome.Omero, axis_labels: strin
   };
 }
 
-function getOmeAxisLabels(attrs: Ome.Attrs): [...string[], 'y', 'x'] {
-  let axis_labels = getAxisLabelsFromMultiscales(attrs);
+function getOmeAxisLabels(multiscales: Ome.Multiscale[]): [...string[], 'y', 'x'] {
   const default_axes = ['t', 'c', 'z', 'y', 'x']; // v0.1 & v0.2
-  return (axis_labels || default_axes) as [...string[], 'y', 'x'];
+  return (multiscales[0].axes || default_axes) as [...string[], 'y', 'x'];
 }

src/utils.ts

@@ -19,6 +19,11 @@ export const MAGENTA_GREEN = [COLORS.magenta, COLORS.green];
 export const RGB = [COLORS.red, COLORS.green, COLORS.blue];
 export const CYMRGB = Object.values(COLORS).slice(0, -2);
 
+export async function attrs<T>(grp: ZarrGroup, path?: string) {
+  const g = path ? await grp.getItem(path) : grp;
+  return g.attrs.asObject() as Promise<T>;
+}
+
 async function normalizeStore(source: string | Store) {
   if (typeof source === 'string') {
     let store: AsyncStore<ArrayBuffer>;
@@ -100,12 +105,6 @@ export function getAxisLabels(arr: ZarrArray, axis_labels?: string[]): [...strin
   return axis_labels as [...string[], 'y', 'x'];
 }
 
-export function getAxisLabelsFromMultiscales(attrs) {
-  if ('multiscales' in attrs && attrs.multiscales?.[0]?.axes) {
-    return attrs.multiscales[0].axes;
-  }
-}
-
 export function isInterleaved(shape: number[]) {
   const lastDimSize = shape[shape.length - 1];
   return lastDimSize === 3 || lastDimSize === 4;

types/ome.ts

@@ -1,5 +1,5 @@
 declare module Ome {
-  type Version = '0.1';
+  type Version = '0.1' | '0.2' | '0.3';
 
   interface Channel {
     active: boolean;