Changed package structure to no langer have deck.gl as dependency

packages/file-types/spatial-zarr/package.json

@@ -26,25 +26,27 @@
     "dist-tsc"
   ],
   "scripts": {
-    "bundle": "pnpm exec vite build -c ../../../scripts/vite.config.mjs",
+    "bundle": "pnpm exec vite build -c ../../../scripts/vite.config2.mjs",
     "test": "pnpm exec vitest --run"
   },
   "dependencies": {
     "@vitessce/abstract": "workspace:*",
     "@vitessce/error": "workspace:*",
-    "@vitessce/gl": "workspace:*",
     "@vitessce/spatial-utils": "workspace:*",
     "@vitessce/image-utils": "workspace:*",
     "@vitessce/zarr": "workspace:*",
     "@vitessce/config": "workspace:*",
     "@vitessce/globals": "workspace:*",
+    "@math.gl/core": "catalog:",
     "d3-array": "catalog:",
     "lodash-es": "catalog:",
-    "zarrita": "catalog:",
     "apache-arrow": "catalog:",
     "parquet-wasm": "catalog:",
     "ol": "^10.2.1"
   },
+  "peerDependencies": {
+    "zarrita": "catalog:"
+  },
   "devDependencies": {
     "@vitessce/types": "workspace:*",
     "@zarrita/storage": "catalog:"

packages/file-types/spatial-zarr/src/ome-loaders/OmeZarrAsObsSegmentationsLoader.js

@@ -1,8 +1,8 @@
 import { CoordinationLevel as CL } from '@vitessce/config';
 import { LoaderResult } from '@vitessce/abstract';
-import { GLSL_COLORMAP_DEFAULT } from '@vitessce/gl';
-import OmeZarrLoader from './OmeZarrLoader.js';
 
+import OmeZarrLoader from './OmeZarrLoader.js';
+const GLSL_COLORMAP_DEFAULT = 'plasma';
 export default class OmeZarrAsObsSegmentationsLoader extends OmeZarrLoader {
   async load() {
     const { obsTypesFromChannelNames } = this.options || {};

packages/file-types/spatial-zarr/src/spatialdata-loaders/SpatialDataObsSegmentationsLoader.js

@@ -5,12 +5,12 @@ import { CoordinationLevel as CL } from '@vitessce/config';
 import {
   coordinateTransformationsToMatrixForSpatialData,
 } from '@vitessce/spatial-utils';
-import { GLSL_COLORMAP_DEFAULT, math } from '@vitessce/gl';
+import { Vector2 } from '@math.gl/core';
 import {
   OLD_SHAPES_DEFAULT_AXES,
   OLD_SHAPES_DEFAULT_COORDINATE_TRANSFORMATIONS,
 } from './old-defaults.js';
-
+const GLSL_COLORMAP_DEFAULT = 'plasma';
 function getGeometryPath(path) {
   return `${path}/geometry`;
 }
@@ -63,7 +63,7 @@ export default class SpatialDataObsSegmentationsLoader extends AbstractTwoStepLo
 
       // Apply transformation matrix to the coordinates
       const transformedCoords = polygons.map(polygon => polygon.map((coord) => {
-        const transformed = new math.Vector2(coord[0], coord[1])
+        const transformed = new Vector2(coord[0], coord[1])
           .transformAsPoint(modelMatrix);
         return [transformed[0], transformed[1]];
       }));

packages/file-types/spatial-zarr/src/spatialdata-loaders/SpatialDataObsSpotsLoader.js

@@ -6,7 +6,7 @@ import { CoordinationLevel as CL } from '@vitessce/config';
 import {
   coordinateTransformationsToMatrixForSpatialData,
 } from '@vitessce/spatial-utils';
-import { math } from '@vitessce/gl';
+import { Vector2 } from '@math.gl/core';
 import {
   OLD_SHAPES_DEFAULT_AXES,
   OLD_SHAPES_DEFAULT_COORDINATE_TRANSFORMATIONS,
@@ -86,7 +86,7 @@ export default class SpatialDataObsSpotsLoader extends AbstractTwoStepLoader {
       for (let i = 0; i < this.locations.shape[1]; i++) {
         const xCoord = this.locations.data[0][i];
         const yCoord = this.locations.data[1][i];
-        const transformed = new math.Vector2(xCoord, yCoord)
+        const transformed = new Vector2(xCoord, yCoord)
           .transformAsPoint(modelMatrix);
         // eslint-disable-next-line prefer-destructuring
         this.locations.data[0][i] = transformed[0];

packages/file-types/zarr/package.json

@@ -26,7 +26,7 @@
     "dist-tsc"
   ],
   "scripts": {
-    "bundle": "pnpm exec vite build -c ../../../scripts/vite.config.mjs",
+    "bundle": "pnpm exec vite build -c ../../../scripts/vite.config2.mjs",
     "test": "pnpm exec vitest --run"
   },
   "dependencies": {
@@ -41,11 +41,13 @@
     "@vitessce/globals": "workspace:*",
     "d3-array": "catalog:",
     "lodash-es": "catalog:",
-    "zarrita": "catalog:",
     "apache-arrow": "catalog:",
     "parquet-wasm": "catalog:",
     "ol": "^10.2.1"
   },
+  "peerDependencies": {
+    "zarrita": "catalog:"
+  },
   "devDependencies": {
     "@vitessce/types": "workspace:*"
   }

packages/utils/image-utils/package.json

@@ -34,7 +34,8 @@
     "@vitessce/spatial-utils": "workspace:*",
     "@vitessce/utils": "workspace:*",
     "@vitessce/globals": "workspace:*",
-    "@hms-dbmi/viv": "catalog:"
+    "@vivjs/loaders": "^0.16.0",
+    "quickselect": "^2.0.0"
   },
   "devDependencies": {
     "vite": "catalog:",

packages/utils/image-utils/src/ome-tiff-types.ts

@@ -1,4 +1,4 @@
-import type { TiffPixelSource } from '@hms-dbmi/viv';
+import type { TiffPixelSource } from '@vivjs/loaders';
 
 type DimensionOrder = 'XYZCT'
   | 'XYZTC'

packages/utils/image-utils/src/ome-zarr-types.ts

@@ -1,4 +1,4 @@
-import type { ZarrPixelSource } from '@hms-dbmi/viv';
+import type { ZarrPixelSource } from '@vivjs/loaders';
 
 type Channel = {
   channelsVisible: boolean;

packages/utils/spatial-utils/package.json

@@ -26,18 +26,21 @@
     "dist-tsc"
   ],
   "scripts": {
-    "bundle": "pnpm exec vite build -c ../../../scripts/vite.config.mjs",
+    "bundle": "pnpm exec vite build -c ../../../scripts/vite.config2.mjs",
     "test": "pnpm exec vitest --run"
   },
+  "peerDependencies": {
+    "zarrita": "catalog:"
+  },
   "dependencies": {
-    "@vitessce/gl": "workspace:*",
+    "@vivjs/loaders": "^0.16.0",
+    "quickselect": "^2.0.0",
     "@vitessce/utils": "workspace:*",
     "@vitessce/zarr-utils": "workspace:*",
     "@vitessce/constants-internal": "workspace:*",
     "@vitessce/globals": "workspace:*",
     "@vitessce/error": "workspace:*",
     "lodash-es": "catalog:",
-    "zarrita": "catalog:",
     "math.gl": "catalog:",
     "mathjs": "catalog:",
     "internmap": "catalog:"

packages/utils/spatial-utils/src/constants.js

@@ -1,10 +1,36 @@
-import { viv } from '@vitessce/gl';
+export const DTYPE_VALUES = {
+  Uint8: {
+    max: 2 ** 8 - 1,
+  },
+  Uint16: {
+    max: 2 ** 16 - 1,
+  },
+  Uint32: {
+    max: 2 ** 32 - 1,
+  },
+  Float32: {
+    max: 3.4 * 10 ** 38,
+  },
+  Int8: {
+    max: 2 ** (8 - 1) - 1,
+  },
+  Int16: {
+    max: 2 ** (16 - 1) - 1,
+  },
+  Int32: {
+    max: 2 ** (32 - 1) - 1,
+  },
+  // Cast Float64 as 32 bit float point so it can be rendered.
+  Float64: {
+    max: 3.4 * 10 ** 38,
+  }
+};
 
 function getDomains() {
   const domains = {};
   const needMin = ['Int8', 'Int16', 'Int32'];
-  Object.keys(viv.DTYPE_VALUES).forEach((dtype) => {
-    const { max } = viv.DTYPE_VALUES[dtype];
+  Object.keys(DTYPE_VALUES).forEach((dtype) => {
+    const { max } = DTYPE_VALUES[dtype];
     const min = needMin.includes(dtype) ? -(max + 1) : 0;
     domains[dtype] = [min, max];
   });

packages/utils/spatial-utils/src/layer-controller.js

@@ -1,4 +1,4 @@
-import { viv } from '@vitessce/gl';
+import { getChannelStats } from '@vivjs/loaders';
 import { Matrix4 } from 'math.gl';
 
 // Returns an rgb string for display, and changes the color (arr)
@@ -31,7 +31,7 @@ async function getSingleSelectionStats2D({ loader, selection }) {
   const data = Array.isArray(loader) ? loader[loader.length - 1] : loader;
   const filteredSelection = filterSelection(loader, selection);
   const raster = await data.getRaster({ selection: filteredSelection });
-  const selectionStats = viv.getChannelStats(raster.data);
+  const selectionStats = getChannelStats(raster.data);
   const { domain, contrastLimits: slider } = selectionStats;
   return { domain, slider };
 }
@@ -50,9 +50,9 @@ async function getSingleSelectionStats3D({ loader, selection }) {
   const rasterTop = await lowResSource.getRaster({
     selection: { ...filteredSelection, z: Math.max(0, sizeZ - 1) },
   });
-  const stats0 = viv.getChannelStats(raster0.data);
-  const statsMid = viv.getChannelStats(rasterMid.data);
-  const statsTop = viv.getChannelStats(rasterTop.data);
+  const stats0 = getChannelStats(raster0.data);
+  const statsMid = getChannelStats(rasterMid.data);
+  const statsTop = getChannelStats(rasterTop.data);
   return {
     domain: [
       Math.min(stats0.domain[0], statsMid.domain[0], statsTop.domain[0]),

packages/utils/spatial-utils/src/load-ome-zarr.js

@@ -1,4 +1,4 @@
-import { viv } from '@vitessce/gl';
+import { ZarrPixelSource } from '@vivjs/loaders';
 import { open as zarrOpen } from 'zarrita';
 import { createZarrArrayAdapter } from '@vitessce/zarr-utils';
 import { ZarrNodeNotFoundError } from '@vitessce/error';
@@ -68,7 +68,7 @@ async function loadMultiscales(root) {
   };
 }
 
-export class ZarritaPixelSource extends viv.ZarrPixelSource {
+export class ZarritaPixelSource extends ZarrPixelSource {
   constructor(arr, labels, tileSize) {
     super(arr, labels, tileSize);
     // We prevent reading chunks directly, since Zarrita does not

packages/utils/zarr-utils/package.json

@@ -26,15 +26,15 @@
     "dist-tsc"
   ],
   "scripts": {
-    "bundle": "pnpm exec vite build -c ../../../scripts/vite.config.mjs",
+    "bundle": "pnpm exec vite build -c ../../../scripts/vite.config2.mjs",
     "test": "pnpm exec vitest --run"
   },
   "dependencies": {
-    "zarrita": "catalog:",
     "@zarrita/storage": "catalog:",
     "@vitessce/globals": "workspace:*"
   },
   "devDependencies": {
-    "unzipit": "^1.4.3"
+    "unzipit": "^1.4.3",
+    "zarrita": "catalog:"
   }
 }

packages/utils/zarr-utils/vite.config.mjs

@@ -0,0 +1,30 @@
+import { defineConfig } from 'vite';
+import react from '@vitejs/plugin-react';
+import { serveTestFixtures, svgLoaderForNeuroglancerIcons } from '../../vite.config.mjs';
+
+
+export default defineConfig({
+  base: './',
+  plugins: [
+    react({
+      jsxRuntime: 'classic',
+    }),
+    serveTestFixtures(),
+    svgLoaderForNeuroglancerIcons(),
+  ],
+  define: {
+    // References:
+    // - https://github.com/smnhgn/vite-plugin-package-version/blob/master/src/index.ts#L10
+    // - https://stackoverflow.com/a/70524430
+    'import.meta.env.PACKAGE_VERSION': JSON.stringify(process.env.npm_package_version),
+  },
+  server: {
+    fs: {
+      // Without this, Vite blocks data-URI query parameters,
+      // such as http://localhost:3000/?url=data:,{}
+      strict: false,
+    },
+  },
+});
+
+