@vitessce/spatial-utils 3.2.2 → 3.3.0

package/dist-tsc/index.d.ts

@@ -1,4 +1,5 @@
 export { DOMAINS } from "./constants.js";
 export { GLOBAL_LABELS, DEFAULT_CELLS_LAYER, DEFAULT_MOLECULES_LAYER, DEFAULT_NEIGHBORHOODS_LAYER, DEFAULT_RASTER_DOMAIN_TYPE, DEFAULT_RASTER_LAYER_PROPS, DEFAULT_LAYER_TYPE_ORDERING, square, initializeLayerChannels, initializeRasterLayersAndChannels, getSourceFromLoader, isInterleaved, isRgb, getNgffAxes, getNgffAxesForTiff, coordinateTransformationsToMatrix, physicalSizeToMatrix, hexToRgb, getStatsForResolution, canLoadResolution, normalizeCoordinateTransformations } from "./spatial.js";
+export { loadOmeZarr, guessTileSize, ZarritaPixelSource } from "./load-ome-zarr.js";
 export { toRgbUIString, getSingleSelectionStats, getMultiSelectionStats, getPhysicalSizeScalingMatrix, getBoundingCube, abbreviateNumber, filterSelection } from "./layer-controller.js";
 //# sourceMappingURL=index.d.ts.map

package/dist-tsc/index.js

@@ -1,3 +1,4 @@
 export { GLOBAL_LABELS, DEFAULT_CELLS_LAYER, DEFAULT_MOLECULES_LAYER, DEFAULT_NEIGHBORHOODS_LAYER, DEFAULT_RASTER_DOMAIN_TYPE, DEFAULT_RASTER_LAYER_PROPS, DEFAULT_LAYER_TYPE_ORDERING, square, initializeLayerChannels, initializeRasterLayersAndChannels, getSourceFromLoader, isInterleaved, isRgb, getNgffAxes, getNgffAxesForTiff, coordinateTransformationsToMatrix, physicalSizeToMatrix, hexToRgb, getStatsForResolution, canLoadResolution, normalizeCoordinateTransformations, } from './spatial.js';
+export { loadOmeZarr, guessTileSize, ZarritaPixelSource, } from './load-ome-zarr.js';
 export { toRgbUIString, getSingleSelectionStats, getMultiSelectionStats, getPhysicalSizeScalingMatrix, getBoundingCube, abbreviateNumber, filterSelection, } from './layer-controller.js';
 export { DOMAINS, } from './constants.js';

package/dist-tsc/load-ome-zarr.d.ts

@@ -0,0 +1,11 @@
+export function guessTileSize(arr: any): number;
+export function loadOmeZarr(url: any, requestInit: any): Promise<{
+    data: ZarritaPixelSource[];
+    metadata: import("zarrita").Attributes;
+}>;
+export class ZarritaPixelSource extends viv.ZarrPixelSource<any> {
+    constructor(arr: any, labels: any, tileSize: any);
+    _readChunks: boolean;
+}
+import { viv } from "@vitessce/gl";
+//# sourceMappingURL=load-ome-zarr.d.ts.map

package/dist-tsc/load-ome-zarr.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"load-ome-zarr.d.ts","sourceRoot":"","sources":["../src/load-ome-zarr.js"],"names":[],"mappings":"AAkBA,gDAMC;AAiDD;;;GAcC;AA9BD;IACE,kDASC;IADC,qBAAwB;CAE3B"}

package/dist-tsc/load-ome-zarr.js

@@ -0,0 +1,75 @@
+import { viv } from '@vitessce/gl';
+import { open as zarrOpen } from 'zarrita';
+import { zarrOpenRoot, createZarrArrayAdapter } from '@vitessce/zarr-utils';
+function prevPowerOf2(x) {
+    return 2 ** Math.floor(Math.log2(x));
+}
+/*
+ * Helper method to determine whether pixel data is interleaved or not.
+ * > isInterleaved([1, 24, 24]) === false;
+ * > isInterleaved([1, 24, 24, 3]) === true;
+ */
+function isInterleaved(shape) {
+    const lastDimSize = shape[shape.length - 1];
+    return lastDimSize === 3 || lastDimSize === 4;
+}
+export function guessTileSize(arr) {
+    const interleaved = isInterleaved(arr.shape);
+    const [yChunk, xChunk] = arr.chunks.slice(interleaved ? -3 : -2);
+    const size = Math.min(yChunk, xChunk);
+    // deck.gl requirement for power-of-two tile size.
+    return prevPowerOf2(size);
+}
+function isAxis(axisOrLabel) {
+    return typeof axisOrLabel[0] !== 'string';
+}
+async function loadMultiscales(root) {
+    const rootAttrs = (await zarrOpen(root)).attrs;
+    let paths = ['0'];
+    // Default axes used for v0.1 and v0.2.
+    let labels = ['t', 'c', 'z', 'y', 'x'];
+    if ('multiscales' in rootAttrs) {
+        const { datasets, axes } = rootAttrs.multiscales[0];
+        paths = datasets.map(d => d.path);
+        if (axes) {
+            if (isAxis(axes)) {
+                labels = axes.map(axis => axis.name);
+            }
+            else {
+                labels = axes;
+            }
+        }
+    }
+    const data = paths
+        .map(path => zarrOpen(root.resolve(path), { kind: 'array' }));
+    return {
+        data: (await Promise.all(data)),
+        rootAttrs,
+        labels,
+    };
+}
+export class ZarritaPixelSource extends viv.ZarrPixelSource {
+    constructor(arr, labels, tileSize) {
+        super(arr, labels, tileSize);
+        // We prevent reading chunks directly, since Zarrita does not
+        // handle x/y chunk differences the same as zarr.js.
+        // TODO: fix this once fixed in either zarrita getChunk or
+        // in createZarrArrayAdapter.
+        // Reference: https://github.com/hms-dbmi/vizarr/pull/172#issuecomment-1714497516
+        // eslint-disable-next-line no-underscore-dangle
+        this._readChunks = false;
+    }
+}
+// We use our own loadOmeZarr function (instead of viv.loadOmeZarr)
+// to bypass usage of zarr.js which is used in Viv's version.
+export async function loadOmeZarr(url, requestInit) {
+    const root = await zarrOpenRoot(url, requestInit);
+    const { data, rootAttrs, labels } = await loadMultiscales(root);
+    const tileSize = guessTileSize(data[0]);
+    const pyramid = data
+        .map(arr => new ZarritaPixelSource(createZarrArrayAdapter(arr), labels, tileSize));
+    return {
+        data: pyramid,
+        metadata: rootAttrs,
+    };
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/spatial-utils",
-  "version": "3.2.2",
+  "version": "3.3.0",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -17,10 +17,12 @@
   ],
   "dependencies": {
     "lodash-es": "^4.17.21",
+    "zarrita": "0.4.0-next.4",
     "math.gl": "^3.5.6",
     "mathjs": "^9.2.0",
-    "@vitessce/gl": "3.2.2",
-    "@vitessce/utils": "3.2.2"
+    "@vitessce/gl": "3.3.0",
+    "@vitessce/zarr-utils": "3.3.0",
+    "@vitessce/utils": "3.3.0"
   },
   "scripts": {
     "bundle": "pnpm exec vite build -c ../../../scripts/vite.config.js",

package/src/index.js

@@ -21,6 +21,11 @@ export {
   canLoadResolution,
   normalizeCoordinateTransformations,
 } from './spatial.js';
+export {
+  loadOmeZarr,
+  guessTileSize,
+  ZarritaPixelSource,
+} from './load-ome-zarr.js';
 export {
   toRgbUIString,
   getSingleSelectionStats,

package/src/load-ome-zarr.js

@@ -0,0 +1,88 @@
+import { viv } from '@vitessce/gl';
+import { open as zarrOpen } from 'zarrita';
+import { zarrOpenRoot, createZarrArrayAdapter } from '@vitessce/zarr-utils';
+
+function prevPowerOf2(x) {
+  return 2 ** Math.floor(Math.log2(x));
+}
+
+/*
+ * Helper method to determine whether pixel data is interleaved or not.
+ * > isInterleaved([1, 24, 24]) === false;
+ * > isInterleaved([1, 24, 24, 3]) === true;
+ */
+function isInterleaved(shape) {
+  const lastDimSize = shape[shape.length - 1];
+  return lastDimSize === 3 || lastDimSize === 4;
+}
+
+export function guessTileSize(arr) {
+  const interleaved = isInterleaved(arr.shape);
+  const [yChunk, xChunk] = arr.chunks.slice(interleaved ? -3 : -2);
+  const size = Math.min(yChunk, xChunk);
+  // deck.gl requirement for power-of-two tile size.
+  return prevPowerOf2(size);
+}
+
+function isAxis(axisOrLabel) {
+  return typeof axisOrLabel[0] !== 'string';
+}
+
+async function loadMultiscales(root) {
+  const rootAttrs = (await zarrOpen(root)).attrs;
+
+  let paths = ['0'];
+  // Default axes used for v0.1 and v0.2.
+  let labels = ['t', 'c', 'z', 'y', 'x'];
+  if ('multiscales' in rootAttrs) {
+    const { datasets, axes } = rootAttrs.multiscales[0];
+    paths = datasets.map(d => d.path);
+    if (axes) {
+      if (isAxis(axes)) {
+        labels = axes.map(axis => axis.name);
+      } else {
+        labels = axes;
+      }
+    }
+  }
+
+  const data = paths
+    .map(path => zarrOpen(root.resolve(path), { kind: 'array' }));
+  return {
+    data: (await Promise.all(data)),
+    rootAttrs,
+    labels,
+  };
+}
+
+export class ZarritaPixelSource extends viv.ZarrPixelSource {
+  constructor(arr, labels, tileSize) {
+    super(arr, labels, tileSize);
+    // We prevent reading chunks directly, since Zarrita does not
+    // handle x/y chunk differences the same as zarr.js.
+    // TODO: fix this once fixed in either zarrita getChunk or
+    // in createZarrArrayAdapter.
+    // Reference: https://github.com/hms-dbmi/vizarr/pull/172#issuecomment-1714497516
+    // eslint-disable-next-line no-underscore-dangle
+    this._readChunks = false;
+  }
+}
+
+
+// We use our own loadOmeZarr function (instead of viv.loadOmeZarr)
+// to bypass usage of zarr.js which is used in Viv's version.
+export async function loadOmeZarr(url, requestInit) {
+  const root = await zarrOpenRoot(url, requestInit);
+  const { data, rootAttrs, labels } = await loadMultiscales(root);
+  const tileSize = guessTileSize(data[0]);
+  const pyramid = data
+    .map(arr => new ZarritaPixelSource(
+      createZarrArrayAdapter(arr),
+      labels,
+      tileSize,
+    ));
+  return {
+    data: pyramid,
+    metadata: rootAttrs,
+  };
+}