From 92e127b2280bce9a81662b6bfe61ad46159e28de Mon Sep 17 00:00:00 2001 From: William Moore Date: Thu, 9 Feb 2023 16:06:39 +0000 Subject: [PATCH] Basic working example --- .gitignore | 24 + index.html | 13 + package-lock.json | 4607 ++++++++++++++++++++++++++++++++++++++++++ package.json | 22 + public/vite.svg | 1 + src/App.css | 41 + src/App.jsx | 34 + src/ImageItem.jsx | 82 + src/Viewer.jsx | 68 + src/assets/react.svg | 1 + src/index.css | 70 + src/main.jsx | 11 + src/util.js | 299 +++ vite.config.js | 7 + 14 files changed, 5280 insertions(+) create mode 100644 .gitignore create mode 100644 index.html create mode 100644 package-lock.json create mode 100644 package.json create mode 100644 public/vite.svg create mode 100644 src/App.css create mode 100644 src/App.jsx create mode 100644 src/ImageItem.jsx create mode 100644 src/Viewer.jsx create mode 100644 src/assets/react.svg create mode 100644 src/index.css create mode 100644 src/main.jsx create mode 100644 src/util.js create mode 100644 vite.config.js diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..a547bf3 --- /dev/null +++ b/.gitignore @@ -0,0 +1,24 @@ +# Logs +logs +*.log +npm-debug.log* +yarn-debug.log* +yarn-error.log* +pnpm-debug.log* +lerna-debug.log* + +node_modules +dist +dist-ssr +*.local + +# Editor directories and files +.vscode/* +!.vscode/extensions.json +.idea +.DS_Store +*.suo +*.ntvs* +*.njsproj +*.sln +*.sw? diff --git a/index.html b/index.html new file mode 100644 index 0000000..79c4701 --- /dev/null +++ b/index.html @@ -0,0 +1,13 @@ + + + + + + + Vite + React + + +
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b/public/vite.svg new file mode 100644 index 0000000..e7b8dfb --- /dev/null +++ b/public/vite.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/src/App.css b/src/App.css new file mode 100644 index 0000000..2c5e2ef --- /dev/null +++ b/src/App.css @@ -0,0 +1,41 @@ +#root { + max-width: 1280px; + margin: 0 auto; + padding: 2rem; + text-align: center; +} + +.logo { + height: 6em; + padding: 1.5em; + will-change: filter; +} +.logo:hover { + filter: drop-shadow(0 0 2em #646cffaa); +} +.logo.react:hover { + filter: drop-shadow(0 0 2em #61dafbaa); +} + +@keyframes logo-spin { + from { + transform: rotate(0deg); + } + to { + transform: rotate(360deg); + } +} + +@media (prefers-reduced-motion: no-preference) { + a:nth-of-type(2) .logo { + animation: logo-spin infinite 20s linear; + } +} + +.card { + padding: 2em; +} + +.read-the-docs { + color: #888; +} diff --git a/src/App.jsx b/src/App.jsx new file mode 100644 index 0000000..338f479 --- /dev/null +++ b/src/App.jsx @@ -0,0 +1,34 @@ +/// app.js +import React from "react"; + +import ImageItem from "./ImageItem"; + +// DeckGL react component +export default function App() { + let sources = [ + "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0048A/9846152.zarr/", + "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr", + "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.2/6001240.zarr", + "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/4495402.zarr" + ] + + let items = sources.map((source) => ); + + return ( + + + + + + + + + + + + + {items} + +
Versions3 URLsizeXsizeYsizeZsizeCsizeTAxes
+ ); +} diff --git a/src/ImageItem.jsx b/src/ImageItem.jsx new file mode 100644 index 0000000..66a0e37 --- /dev/null +++ b/src/ImageItem.jsx @@ -0,0 +1,82 @@ +import React from "react"; + +import Viewer from "./Viewer"; +import { loadOmeroMultiscales, open, getNgffAxes } from "./util"; + +// DeckGL react component +export default function ImageItem({ source }) { + let config = { source }; + + const [layers, setLayers] = React.useState([]); + + const [imgInfo, setImageInfo] = React.useState({}); + + React.useEffect(() => { + const fn = async function () { + const node = await open(config.source); + + const attrs = await node.attrs.asObject(); + console.log("attrs", attrs); + const axes = getNgffAxes(attrs.multiscales); + + let layerData = await loadOmeroMultiscales(config, node, attrs); + console.log("layerData", layerData); + + let shape = layerData.loader[0]._data.meta.shape; + + let selections = []; + layerData.channelsVisible.forEach((visible, chIndex) => { + if (visible) { + selections.push( + axes.map((axis, dim) => { + if (axis.type == "time") return 0; + if (axis.name == "z") return parseInt(shape[dim] / 2); + if (axis.name == "c") return chIndex; + return 0; + }) + ); + } + }); + const dims = {}; + axes.forEach((axis, dim) => (dims[axis.name] = shape[dim])); + layerData.selections = selections; + + setLayers([layerData]); + setImageInfo({ + dims: dims, + axes: axes.map((axis) => axis.name).join(""), + version: attrs.multiscales?.[0]?.version, + }); + }; + + fn(); + }, []); + + let wrapperStyle = { + width: 150, + height: 100, + position: "relative", + }; + + let sizes = ["x", "y", "z", "c", "t"].map((dim) => ( + + {imgInfo?.dims?.[dim]} + + )); + + return ( + + {imgInfo.version} + + source + + {sizes} + {imgInfo.axes} + +
+ +
+ + + ); +} diff --git a/src/Viewer.jsx b/src/Viewer.jsx new file mode 100644 index 0000000..40d56e7 --- /dev/null +++ b/src/Viewer.jsx @@ -0,0 +1,68 @@ + +import React from "react"; +import DeckGL from "@deck.gl/react"; + +import { OrthographicView } from "@deck.gl/core"; +import { MultiscaleImageLayer } from "@vivjs/layers"; + +import { fitBounds } from "./util"; + +// DeckGL react component +export default function Viewer({layersData}) { + + let layers = layersData.map(ld => new MultiscaleImageLayer(ld)); + + const [viewState, setViewState] = React.useState({ + target: [0, 0, 0], + rotationX: 0, + zoom: 1, + }); + + const deckRef = React.useRef(null); + + const onViewStateChange = React.useCallback(({ viewState }) => { + // Save the view state and trigger rerender + setViewState(viewState); + }, []); + + + React.useEffect(() => { + + if (!layersData || layersData.length == 0) { + return; + } + + let shape = layersData[0].loader[0]._data.meta.shape; + const [height, width] = shape.slice(-2); + + const { deck } = deckRef.current; + let targetWidth = deck.width; + let targetHeight = deck.height; + let padding = 0; + // zoom: 0 maps one unit distance to one pixel on screen, and increasing zoom + // by 1 scales the same object to twice as large + // limit initial zoom to 100% + let maxZoom = 0; + + let bounds = fitBounds( + [width, height], + [targetWidth, targetHeight], + maxZoom, + padding + ); + + setViewState(bounds); + + }, [layersData]); + + return ( + + ); +} diff --git a/src/assets/react.svg b/src/assets/react.svg new file mode 100644 index 0000000..6c87de9 --- /dev/null +++ b/src/assets/react.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/src/index.css b/src/index.css new file mode 100644 index 0000000..917888c --- /dev/null +++ b/src/index.css @@ -0,0 +1,70 @@ +:root { + font-family: Inter, Avenir, Helvetica, Arial, sans-serif; + font-size: 16px; + line-height: 24px; + font-weight: 400; + + color-scheme: light dark; + color: rgba(255, 255, 255, 0.87); + background-color: #242424; + + font-synthesis: none; + text-rendering: optimizeLegibility; + -webkit-font-smoothing: antialiased; + -moz-osx-font-smoothing: grayscale; + -webkit-text-size-adjust: 100%; +} + +a { + font-weight: 500; + color: #646cff; + text-decoration: inherit; +} +a:hover { + color: #535bf2; +} + +body { + margin: 0; + display: flex; + place-items: center; + min-width: 320px; + min-height: 100vh; +} + +h1 { + font-size: 3.2em; + line-height: 1.1; +} + +button { + border-radius: 8px; + border: 1px solid transparent; + padding: 0.6em 1.2em; + font-size: 1em; + font-weight: 500; + font-family: inherit; + background-color: #1a1a1a; + cursor: pointer; + transition: border-color 0.25s; +} +button:hover { + border-color: #646cff; +} +button:focus, +button:focus-visible { + outline: 4px auto -webkit-focus-ring-color; +} + +@media (prefers-color-scheme: light) { + :root { + color: #213547; + background-color: #ffffff; + } + a:hover { + color: #747bff; + } + button { + background-color: #f9f9f9; + } +} diff --git a/src/main.jsx b/src/main.jsx new file mode 100644 index 0000000..9b32e15 --- /dev/null +++ b/src/main.jsx @@ -0,0 +1,11 @@ +import React from 'react' +import ReactDOM from 'react-dom' +import App from './App' +import './index.css' + +ReactDOM.render( + + + , + document.getElementById('root') +) diff --git a/src/util.js b/src/util.js new file mode 100644 index 0000000..8ac39f9 --- /dev/null +++ b/src/util.js @@ -0,0 +1,299 @@ +import { + ContainsArrayError, + HTTPStore, + openArray, + openGroup, + ZarrArray, +} from "zarr"; + +export const MAX_CHANNELS = 6; + +export const COLORS = { + cyan: '#00FFFF', + yellow: '#FFFF00', + magenta: '#FF00FF', + red: '#FF0000', + green: '#00FF00', + blue: '#0000FF', + white: '#FFFFFF', +}; +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); + +import { ZarrPixelSource } from "@vivjs/loaders"; + +export function range(length) { + return Array.from({ length }, (_, i) => i); +} + +async function normalizeStore(source) { + let path; + if (typeof source === "string") { + let store; + + // if (source.endsWith('.json')) { + // // import custom store implementation``` + // const [{ ReferenceStore }, json] = await Promise.all([ + // import('reference-spec-reader'), + // fetch(source).then((res) => res.json()), + // ]); + + // store = ReferenceStore.fromJSON(json); + // } else { + const url = new URL(source); + store = new HTTPStore(url.origin); + path = url.pathname.slice(1); + // } + + // Wrap remote stores in a cache + // return { store: new LRUCacheStore(store), path }; + return { store, path }; + } + + return { store: source, path }; +} + +export async function open(source) { + const { store, path } = await normalizeStore(source); + return openGroup(store, path).catch((err) => { + if (err instanceof ContainsArrayError) { + return openArray({ store }); + } + throw err; + }); +} + +async function loadMultiscales(grp, multiscales) { + const { datasets } = multiscales[0] || [{ path: "0" }]; + const nodes = await Promise.all( + datasets.map(({ path }) => grp.getItem(path)) + ); + if (nodes.every((node) => node instanceof ZarrArray)) { + return nodes; + } + throw Error("Multiscales metadata included a path to a group."); +} + +export function getNgffAxes(multiscales) { + // Returns axes in the latest v0.4+ format. + // defaults for v0.1 & v0.2 + const default_axes = [ + { type: "time", name: "t" }, + { type: "channel", name: "c" }, + { type: "space", name: "z" }, + { type: "space", name: "y" }, + { type: "space", name: "x" }, + ]; + function getDefaultType(name) { + if (name === "t") return "time"; + if (name === "c") return "channel"; + return "space"; + } + let axes = default_axes; + // v0.3 & v0.4+ + if (multiscales[0].axes) { + axes = multiscales[0].axes.map((axis) => { + // axis may be string 'x' (v0.3) or object + if (typeof axis === "string") { + return { name: axis, type: getDefaultType(axis) }; + } + const { name, type } = axis; + return { name, type: type ?? getDefaultType(name) }; + }); + } + return axes; +} + +function getNgffAxisLabels(axes) { + return axes.map((axis) => axis.name); +} + +export function isInterleaved(shape) { + const lastDimSize = shape[shape.length - 1]; + return lastDimSize === 3 || lastDimSize === 4; +} + +export function guessTileSize(arr) { + const interleaved = isInterleaved(arr.shape); + const [ySize, xSize] = arr.chunks.slice(interleaved ? -3 : -2); + const size = Math.min(ySize, xSize); + // Needs to be a power of 2 for deck.gl + return 2 ** Math.floor(Math.log2(size)); +} + +export function hexToRGB(hex) { + if (hex.startsWith("#")) hex = hex.slice(1); + const r = parseInt(hex.slice(0, 2), 16); + const g = parseInt(hex.slice(2, 4), 16); + const b = parseInt(hex.slice(4, 6), 16); + return [r, g, b]; +} + +export async function calcDataRange(source, selection) { + if (source.dtype === 'Uint8') return [0, 255]; + const { data } = await source.getRaster({ selection }); + let minVal = Infinity; + let maxVal = -Infinity; + for (let i = 0; i < data.length; i++) { + if (data[i] > maxVal) maxVal = data[i]; + if (data[i] < minVal) minVal = data[i]; + } + if (minVal === maxVal) { + minVal = 0; + maxVal = 1; + } + return [minVal, maxVal]; +} + +export async function calcConstrastLimits( + source, + channelAxis, + visibilities, + defaultSelection +) { + const def = defaultSelection ?? source.shape.map(() => 0); + const csize = source.shape[channelAxis]; + + if (csize !== visibilities.length) { + throw new Error("provided visibilities don't match number of channels"); + } + + return Promise.all( + visibilities.map(async (isVisible, i) => { + if (!isVisible) return undefined; // don't compute non-visible channels + const selection = [...def]; + selection[channelAxis] = i; + return calcDataRange(source, selection); + }) + ); +} + +export function getDefaultVisibilities(n) { + let visibilities; + if (n <= MAX_CHANNELS) { + // Default to all on if visibilities not specified and less than 6 channels. + visibilities = Array(n).fill(true); + } else { + // If more than MAX_CHANNELS, only make first set on by default. + visibilities = [ + ...Array(MAX_CHANNELS).fill(true), + ...Array(n - MAX_CHANNELS).fill(false), + ]; + } + return visibilities; +} + +export function getDefaultColors(n, visibilities) { + let colors = []; + if (n == 1) { + colors = [COLORS.white]; + } else if (n == 2) { + colors = MAGENTA_GREEN; + } else if (n === 3) { + colors = RGB; + } else if (n <= MAX_CHANNELS) { + colors = CYMRGB.slice(0, n); + } else { + // Default color for non-visible is white + colors = Array(n).fill(COLORS.white); + // Get visible indices + const visibleIndices = visibilities.flatMap((bool, i) => (bool ? i : [])); + // Set visible indices to CYMRGB colors. visibleIndices.length === MAX_CHANNELS from above. + for (const [i, visibleIndex] of visibleIndices.entries()) { + colors[visibleIndex] = CYMRGB[i]; + } + } + return colors.map(hexToRGB); +} + +async function defaultMeta(loader, axis_labels) { + const channel_axis = axis_labels.indexOf("c"); + const channel_count = loader.shape[channel_axis]; + const visibilities = getDefaultVisibilities(channel_count); + const contrast_limits = await calcConstrastLimits( + loader, + channel_axis, + visibilities + ); + const colors = getDefaultColors(channel_count, visibilities); + return { + name: "Image", + names: range(channel_count).map((i) => `channel_${i}`), + colors, + contrastLimits: contrast_limits, + channelsVisible: visibilities, + channel_axis: axis_labels.includes("c") ? axis_labels.indexOf("c") : null, + defaultSelection: axis_labels.map(() => 0), + }; +} + +function parseOmeroMeta({ rdefs, channels, name }, axes) { + const t = rdefs.defaultT ?? 0; + const z = rdefs.defaultZ ?? 0; + + const colors = []; + const contrast_limits = []; + const visibilities = []; + const names = []; + + channels.forEach((c, index) => { + colors.push(hexToRGB(c.color)); + contrast_limits.push([c.window.start, c.window.end]); + visibilities.push(c.active); + names.push(c.label || "" + index); + }); + + const defaultSelection = axes.map((axis) => { + if (axis.type == "time") return t; + if (axis.name == "z") return z; + return 0; + }); + const channel_axis = axes.findIndex((axis) => axis.type === "channel"); + + return { + name, + names, + colors, + contrastLimits: contrast_limits, + channelsVisible: visibilities, + channel_axis, + defaultSelection, + }; +} + +// Scales the real image size to the target viewport. +export function fitBounds( + [width, height], + [targetWidth, targetHeight], + maxZoom, + padding +) { + const scaleX = (targetWidth - padding * 2) / width; + const scaleY = (targetHeight - padding * 2) / height; + const zoom = Math.min(maxZoom, Math.log2(Math.min(scaleX, scaleY))); + return { zoom, target: [width / 2, height / 2] }; +} + +export async function loadOmeroMultiscales(config, zarrGroup, attrs) { + const { name, opacity = 1, colormap = "" } = config; + let data = await loadMultiscales(zarrGroup, attrs.multiscales); + const axes = getNgffAxes(attrs.multiscales); + const axis_labels = getNgffAxisLabels(axes); + const tileSize = guessTileSize(data[0]); + + const loaders = data.map( + (arr) => new ZarrPixelSource(arr, axis_labels, tileSize) + ); + const meta = + "omero" in attrs + ? parseOmeroMeta(attrs.omero, axes) + : await defaultMeta(loaders[0], axis_labels); + + return { + loader: loaders, + axis_labels, + ...meta, + name: meta.name ?? name, + }; +} diff --git a/vite.config.js b/vite.config.js new file mode 100644 index 0000000..b1b5f91 --- /dev/null +++ b/vite.config.js @@ -0,0 +1,7 @@ +import { defineConfig } from 'vite' +import react from '@vitejs/plugin-react' + +// https://vitejs.dev/config/ +export default defineConfig({ + plugins: [react()] +})