From 78753f606151cdcba56cba7bcc2357666906170a Mon Sep 17 00:00:00 2001 From: Skyler Moosman <8845503+TheMooseman@users.noreply.github.com> Date: Wed, 12 Jun 2024 14:45:50 -0700 Subject: [PATCH 1/2] feat: add neuroglancer url demo (#19) * add neuroglancer url demo * update readme * export functions, add contact sheet and image series * try to fix up URL creation * remove useless stuff * contact sheet works, woo! * sliders are replaced * some comments --- .prettierrc | 8 + apps/neuroglancer-url/README.md | 12 + apps/neuroglancer-url/package.json | 42 +++ apps/neuroglancer-url/public/demo.html | 35 ++ apps/neuroglancer-url/src/contact-sheet.ts | 125 +++++++ apps/neuroglancer-url/src/data.ts | 349 ++++++++++++++++++++ apps/neuroglancer-url/src/demo.ts | 145 ++++++++ apps/neuroglancer-url/src/image-series.ts | 107 ++++++ apps/neuroglancer-url/src/types.ts | 51 +++ apps/neuroglancer-url/src/url-elem-maker.ts | 112 +++++++ apps/neuroglancer-url/src/utils.ts | 213 ++++++++++++ apps/neuroglancer-url/tsconfig.json | 5 + pnpm-lock.yaml | 9 + 13 files changed, 1213 insertions(+) create mode 100644 .prettierrc create mode 100644 apps/neuroglancer-url/README.md create mode 100644 apps/neuroglancer-url/package.json create mode 100644 apps/neuroglancer-url/public/demo.html create mode 100644 apps/neuroglancer-url/src/contact-sheet.ts create mode 100644 apps/neuroglancer-url/src/data.ts create mode 100644 apps/neuroglancer-url/src/demo.ts create mode 100644 apps/neuroglancer-url/src/image-series.ts create mode 100644 apps/neuroglancer-url/src/types.ts create mode 100644 apps/neuroglancer-url/src/url-elem-maker.ts create mode 100644 apps/neuroglancer-url/src/utils.ts create mode 100644 apps/neuroglancer-url/tsconfig.json diff --git a/.prettierrc b/.prettierrc new file mode 100644 index 0000000..7c0342a --- /dev/null +++ b/.prettierrc @@ -0,0 +1,8 @@ +{ + "printWidth": 120, + "trailingComma": "es5", + "tabWidth": 4, + "singleQuote": true, + "semi": true, + "singleAttributePerLine": true +} diff --git a/apps/neuroglancer-url/README.md b/apps/neuroglancer-url/README.md new file mode 100644 index 0000000..517d44e --- /dev/null +++ b/apps/neuroglancer-url/README.md @@ -0,0 +1,12 @@ +## Neuroglancer URL Generator + +This is a demo for generating Neuroglancer URLs like the python POC [here](https://github.com/AllenInstitute/ome_zarr_converter/blob/main/src/ome_zarr_converter/neuroglancer/utils.py). + +### How to build / run +1. `pnpm build` from the root directory of this project +2. `pnpm install` in this directory +3. `pnpm run demo` in this directory - this will produce `dst/neuroglancer-url.html` +4. navigate to `dst/neuroglancer-url.html` and open it in your browser + +### The Code + -- TBD -- \ No newline at end of file diff --git a/apps/neuroglancer-url/package.json b/apps/neuroglancer-url/package.json new file mode 100644 index 0000000..33d82d2 --- /dev/null +++ b/apps/neuroglancer-url/package.json @@ -0,0 +1,42 @@ +{ + "name": "@alleninstitute/neuroglancer-url-demo", + "version": "0.0.1", + "contributors": [ + { + "name": "Lane Sawyer", + "email": "lane.sawyer@alleninstitute.org" + }, + { + "name": "James Gerstenberger", + "email": "james.gerstenberger@alleninstitute.org" + }, + { + "name": "Noah Shepard", + "email": "noah.shepard@alleninstitute.org" + }, + { + "name": "Skyler Moosman", + "email": "skyler.moosman@alleninstitute.org" + }, + { + "name": "Su Li", + "email": "su.li@alleninstitute.org" + } + ], + "license": "TBD", + "type": "module", + "main": "lib/index.js", + "types": "lib/index.d.ts", + "private": true, + "scripts": { + "preinstall": "npx only-allow pnpm", + "demo": "esbuild src/demo.ts --bundle --outfile=dst/demo.js && cp public/* dst/", + "typecheck": "tsc --noEmit" + }, + "devDependencies": { + "esbuild": "^0.19.12", + "typescript": "^5.3.3" + }, + "dependencies": { + } +} \ No newline at end of file diff --git a/apps/neuroglancer-url/public/demo.html b/apps/neuroglancer-url/public/demo.html new file mode 100644 index 0000000..8b27db8 --- /dev/null +++ b/apps/neuroglancer-url/public/demo.html @@ -0,0 +1,35 @@ + + + +
+
+
+
+ + +
+

+
+
+

NG URLS

+

Contact Sheets

+

Image Series

+ + + diff --git a/apps/neuroglancer-url/src/contact-sheet.ts b/apps/neuroglancer-url/src/contact-sheet.ts new file mode 100644 index 0000000..16a5391 --- /dev/null +++ b/apps/neuroglancer-url/src/contact-sheet.ts @@ -0,0 +1,125 @@ +import { neuroglancerUrl, finalizeConfig, getImageLayer, getShaderCode, urlFromConfig } from './utils'; + +export function getContactSheetUrl( + srcUrl: string, + imgName: string, + omeZarrShape: number[], + xMm: number, + yMm: number, + zMm: number, + redMin: number, + redMax: number, + greenMin: number, + greenMax: number, + blueMin: number, + blueMax: number, + crossSectionScale: number = 0.5 +): string { + const config = getContactSheetConfig( + srcUrl, + imgName, + omeZarrShape, + xMm, + yMm, + zMm, + redMin, + redMax, + greenMin, + greenMax, + blueMin, + blueMax, + crossSectionScale + ); + + console.log(config); + return urlFromConfig(neuroglancerUrl, config); +} + +function getContactSheetConfig( + srcUrl: string, + imgName: string, + omeZarrShape: number[], + xMm: number, + yMm: number, + zMm: number, + redMin: number, + redMax: number, + greenMin: number, + greenMax: number, + blueMin: number, + blueMax: number, + crossSectionScale: number = 0.5 +): Record { + const [shaderCode, shaderControls] = getShaderCode(redMin, redMax, greenMin, greenMax, blueMin, blueMax); + + const source = createSourceGrid(srcUrl, omeZarrShape, xMm, yMm, zMm); + + const imgLayer = getImageLayer(imgName, source, shaderCode, shaderControls); + + const config = finalizeConfig(imgLayer, imgName, xMm, yMm, zMm); + + config['layout'] = 'xy'; + config['velocity'] = { z: { velocity: -10, atBoundary: 'reverse' } }; + + const nz = omeZarrShape[omeZarrShape.length - 3]; + const sqrtNz = Math.round(Math.sqrt(nz)); + const ny = omeZarrShape[omeZarrShape.length - 2]; + const nx = omeZarrShape[omeZarrShape.length - 1]; + config['position'] = [(nx * sqrtNz) / 2, (ny * sqrtNz) / 2, -(nz - 1)]; + config['crossSectionScale'] = crossSectionScale; + + return config; +} + +function createSourceGrid(srcUrl: string, omeZarrShape: number[], xMm: number, yMm: number, zMm: number): any[] { + const nz = omeZarrShape[omeZarrShape.length - 3]; + const ny = omeZarrShape[omeZarrShape.length - 2]; + const nx = omeZarrShape[omeZarrShape.length - 1]; + const sqrtNz = Math.ceil(Math.sqrt(nz)); + const izToDxDy: { [key: number]: [number, number] } = {}; + let dx = 0; + let dy = 0; + for (let iz = 0; iz < nz; iz++) { + izToDxDy[iz] = [dx, dy]; + dx++; + if (dx >= sqrtNz) { + dy++; + dx = 0; + } + } + + const dimensions = { + 'c^': [1, ''], + z: [0.001 * zMm, 'm'], + y: [0.001 * yMm, 'm'], + x: [0.001 * xMm, 'm'], + }; + + const srcList = []; + for (let iz = 0; iz < nz; iz++) { + const src = { url: srcUrl }; + const [dx, dy] = izToDxDy[iz]; + const matrix = [ + [1, 0, 0, 0, 0], + [0, -1, 0, 0, -1 * iz], + [0, 0, 1, 0, dy * ny], + [0, 0, 0, 1, dx * nx], + ]; + // @ts-expect-error + src['transform'] = { + outputDimensions: dimensions, + matrix: matrix, + }; + + // @ts-expect-error + src['subsources'] = { + default: true, + }; + // @ts-expect-error + src['enableDefaultSubsources'] = false; + + srcList.push(src); + } + + return srcList; +} diff --git a/apps/neuroglancer-url/src/data.ts b/apps/neuroglancer-url/src/data.ts new file mode 100644 index 0000000..40311c0 --- /dev/null +++ b/apps/neuroglancer-url/src/data.ts @@ -0,0 +1,349 @@ +import type { NGData } from "./types"; + +export const data: NGData[] = [ + { + "function": "get_image_series_grid_url", + "params": { + "src_config_list": [ + { + "blue_max": 4095.0, + "blue_min": 0.0, + "green_max": 7261.0, + "green_min": 0.0, + "img_name": "1125628029 (40_512_512)", + "ome_zarr_shape": [ + 3, + 142, + 29998, + 39998 + ], + "red_max": 1261.0, + "red_min": 0.0, + "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1125628029", + "x_mm": 0.00035, + "y_mm": 0.00035, + "z_mm": 0.1 + }, + { + "blue_max": 4095.0, + "blue_min": 0.0, + "green_max": 1304.0, + "green_min": 0.0, + "img_name": "1145081396 (40_512_512)", + "ome_zarr_shape": [ + 3, + 142, + 11998, + 15998 + ], + "red_max": 1344.0, + "red_min": 0.0, + "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1145081396", + "x_mm": 0.000875, + "y_mm": 0.000875, + "z_mm": 0.1 + }, + { + "blue_max": 4095.0, + "blue_min": 0.0, + "green_max": 4045.0, + "green_min": 0.0, + "img_name": "1182837942 (40_512_512)", + "ome_zarr_shape": [ + 3, + 142, + 29998, + 39998 + ], + "red_max": 864.0, + "red_min": 0.0, + "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1182837942", + "x_mm": 0.00035, + "y_mm": 0.00035, + "z_mm": 0.1 + }, + { + "blue_max": 4095.0, + "blue_min": 0.0, + "green_max": 3013.0, + "green_min": 0.0, + "img_name": "1240649363 (40_512_512)", + "ome_zarr_shape": [ + 3, + 142, + 29998, + 39998 + ], + "red_max": 1356.0, + "red_min": 0.0, + "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1240649363", + "x_mm": 0.00035, + "y_mm": 0.00035, + "z_mm": 0.1 + } + ] + }, + "type": "Multiple image series; coronal projection", + "url": 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+ } + ] \ No newline at end of file diff --git a/apps/neuroglancer-url/src/demo.ts b/apps/neuroglancer-url/src/demo.ts new file mode 100644 index 0000000..bc5737e --- /dev/null +++ b/apps/neuroglancer-url/src/demo.ts @@ -0,0 +1,145 @@ +import type { ImageSeriesData, NGData, RegularData } from './types'; +import { getNeuroglancerUrl } from './utils'; +import { data } from './data'; +import { getContactSheetUrl } from './contact-sheet'; +import { makeContactSheetElems, makeImageSeriesElems, makeNgUrlElems } from './url-elem-maker'; + +interface NeuroglancerUrl { + srcUrl: string; + imgName: string; + xMm: number; + yMm: number; + zMm: number; + redMin: number; + redMax: number; + greenMin: number; + greenMax: number; + blueMin: number; + blueMax: number; + crossSectionScale?: number; + layout?: string; +} + +const jsonFormat = { + input: { + srcUrl: '', + imgName: '', + xMm: 0, + yMm: 0, + zMm: 0, + redMin: 0, + redMax: 255, + greenMin: 0, + greenMax: 255, + blueMin: 0, + blueMax: 255, + crossSectionScale: 50.0, + layout: '4panel', + }, + output: 'neuroglancer.com/urlstuff', +}; + +const defaultNeuroglancerUrl: NeuroglancerUrl = { + srcUrl: '', + imgName: '', + xMm: 0, + yMm: 0, + zMm: 0, + redMin: 0, + redMax: 255, + greenMin: 0, + greenMax: 255, + blueMin: 0, + blueMax: 255, + crossSectionScale: 50.0, + layout: '4panel', +}; +function demoTime() { + let imageSeries: ImageSeriesData[] = []; + let contactSheets: RegularData[] = []; + let ngURLs: RegularData[] = []; + + data.forEach((item) => { + switch (item.function) { + case 'get_image_series_grid_url': + imageSeries.push(item as ImageSeriesData); + break; + case 'get_contact_sheet_url': + contactSheets.push(item as RegularData); + break; + case 'get_neuroglancer_url': + ngURLs.push(item as RegularData); + break; + } + }); + + const argEl = document.getElementById('urlArgEl'); + const btnEl = document.getElementById('urlBtn'); + const outUrl = document.getElementById('goodUrl'); + const copyBtn = document.getElementById('copyBtn'); + const ngUrlParent = document.getElementById('ngUrls'); + const contactParent = document.getElementById('contacts'); + const imageParent = document.getElementById('imageSeries'); + if (argEl && btnEl && outUrl && copyBtn && ngUrlParent && contactParent && imageParent) { + const fields = document.createElement('ol'); + const fieldItems = Object.entries(defaultNeuroglancerUrl).map(([name, val]) => { + const listEl = document.createElement('li'); + const pEl = document.createElement('p'); + const text = document.createElement('input'); + text.type = 'text'; + text.value = val; + // @ts-expect-error + text.onchange = (e) => (defaultNeuroglancerUrl[name] = val); + + pEl.innerText = name; + listEl.id = name; + + listEl.appendChild(pEl); + listEl.appendChild(text); + fields.appendChild(listEl); + }); + argEl.appendChild(fields); + btnEl.addEventListener('click', (e) => { + const { + srcUrl, + imgName, + xMm, + yMm, + zMm, + redMin, + redMax, + greenMin, + greenMax, + blueMin, + blueMax, + crossSectionScale, + layout, + } = defaultNeuroglancerUrl; + outUrl.innerText = getNeuroglancerUrl( + srcUrl, + imgName, + xMm, + yMm, + zMm, + redMin, + redMax, + greenMin, + greenMax, + blueMin, + blueMax, + crossSectionScale, + layout + ); + }); + copyBtn.addEventListener('click', () => { + navigator.clipboard.writeText(outUrl.innerText); + }); + + // These URLs are example URLs that acted as test cases for my formatting + makeNgUrlElems(ngURLs, ngUrlParent); + makeContactSheetElems(contactSheets, contactParent); + makeImageSeriesElems(imageSeries, imageParent); + } +} + +demoTime(); diff --git a/apps/neuroglancer-url/src/image-series.ts b/apps/neuroglancer-url/src/image-series.ts new file mode 100644 index 0000000..8a00801 --- /dev/null +++ b/apps/neuroglancer-url/src/image-series.ts @@ -0,0 +1,107 @@ +import type { NeuroglancerConfig } from './types'; +import { urlFromConfig, getShaderCode, getSourceConfig, getImageLayer, neuroglancerUrl } from './utils'; + +export function getImageSeriesGridUrl(srcConfigList: NeuroglancerConfig[]): string { + const config = getImgGridConfig(srcConfigList); + const baseUrl = neuroglancerUrl; + const url = urlFromConfig(baseUrl, config); + return url; +} + +function getImgGridConfig(srcConfigList: NeuroglancerConfig[]): Record { + const xMm = srcConfigList[0].x_mm; + const yMm = srcConfigList[0].y_mm; + const zMm = srcConfigList[0].z_mm; + + const imgLayerList = srcConfigList.map((config) => getSingleImgLayer(config)); + + const nLayers = srcConfigList.length; + const nSide = Math.ceil(Math.sqrt(nLayers)); + + if (imgLayerList.length < nSide ** 2) { + imgLayerList.push(getBlankImgLayer(srcConfigList[0])); + } + + const dimensions = { + x: [0.001 * xMm, 'm'], + y: [0.001 * yMm, 'm'], + z: [0.001 * zMm, 'm'], + }; + + const config: Record = {}; + config.dimensions = dimensions; + config.crossSectionScale = 50.0; + config.projectionScale = 40000; + config.selectedLayer = { + visible: true, + layer: imgLayerList[0].name, + }; + config.layers = imgLayerList; + + const layout: Record = {}; + layout.type = 'row'; + const rowChildren = []; + let thisRow: Record = {}; + imgLayerList.forEach((img) => { + if (!('type' in thisRow)) { + thisRow.type = 'column'; + thisRow.children = []; + } + const thisCol = { + type: 'viewer', + layers: [img.name], + layout: 'xy', + }; + thisRow.children.push(thisCol); + if (thisRow.children.length >= nSide) { + rowChildren.push(thisRow); + thisRow = {}; + } + }); + + if (Object.keys(thisRow).length > 0) { + while (thisRow.children.length < nSide) { + const dummy = { + type: 'viewer', + layers: ['blank'], + layout: 'xy', + }; + thisRow.children.push(dummy); + } + rowChildren.push(thisRow); + } + + layout.children = rowChildren; + config.layout = layout; + + return config; +} + +function getSingleImgLayer(srcConfig: NeuroglancerConfig): Record { + const [shaderCode, shaderControls] = getShaderCode( + srcConfig.red_min, + srcConfig.red_max, + srcConfig.green_min, + srcConfig.green_max, + srcConfig.blue_min, + srcConfig.blue_max + ); + + const source = getSourceConfig(srcConfig.src_url, srcConfig.x_mm, srcConfig.y_mm, srcConfig.z_mm); + + const imgLayer = getImageLayer(srcConfig.img_name, source, shaderCode, shaderControls); + + return imgLayer; +} + +function getBlankImgLayer(srcConfig: NeuroglancerConfig): Record { + const shaderCode: string = ` + void main() { emitRGB(vec3(0, 0, 0)); } + `; + + const source = getSourceConfig(srcConfig.src_url, srcConfig.x_mm, srcConfig.y_mm, srcConfig.z_mm); + + const imgLayer = getImageLayer('blank', source, shaderCode, {}); + + return imgLayer; +} diff --git a/apps/neuroglancer-url/src/types.ts b/apps/neuroglancer-url/src/types.ts new file mode 100644 index 0000000..a706c0f --- /dev/null +++ b/apps/neuroglancer-url/src/types.ts @@ -0,0 +1,51 @@ +export type NeuroglancerConfig = { + red_min: number; + red_max: number; + green_min: number; + green_max: number; + blue_min: number; + blue_max: number; + img_name: string; + x_mm: number; + y_mm: number; + z_mm: number; + src_url: string; + cross_section_scale?: number; + layout?: string; + ome_zarr_shape?: number[]; +}; +export type ImageSeriesConfig = NeuroglancerConfig & { + ome_zarr_shape: number[]; + src_url: string; +}; +export type ContactSheetConfig = NeuroglancerConfig & { + ome_zarr_shape: number[]; +}; +export type NGFunc = 'get_contact_sheet_url' | 'get_neuroglancer_url' | 'get_image_series_grid_url'; + +export type NGData = { + function: NGFunc; + params: + | { + src_config_list: NeuroglancerConfig[]; + } + | NeuroglancerConfig; + type: string; + url: string; +}; + +export type ImageSeriesData = { + function: NGFunc; + params: { + src_config_list: NeuroglancerConfig[]; + }; + type: string; + url: string; +}; + +export type RegularData = { + function: NGFunc; + params: NeuroglancerConfig; + type: string; + url: string; +}; diff --git a/apps/neuroglancer-url/src/url-elem-maker.ts b/apps/neuroglancer-url/src/url-elem-maker.ts new file mode 100644 index 0000000..f7d6610 --- /dev/null +++ b/apps/neuroglancer-url/src/url-elem-maker.ts @@ -0,0 +1,112 @@ +import { getContactSheetUrl } from './contact-sheet'; +import { getImageSeriesGridUrl } from './image-series'; +import type { ImageSeriesData, RegularData } from './types'; +import { getNeuroglancerUrl } from './utils'; + +export function makeImageSeriesElems(imageSeries: ImageSeriesData[], parent: HTMLElement) { + imageSeries.forEach((item, idx) => { + const configs = item.params.src_config_list; + const elem = document.createElement('p'); + const url = getImageSeriesGridUrl(configs); + elem.innerText = url; + elem.style.maxWidth = '500px'; + elem.style.textWrap = 'nowrap'; + elem.style.overflow = 'hidden'; + elem.style.textOverflow = 'ellipsis'; + parent.appendChild(elem); + console.log(url.length, imageSeries[idx].url.length); + }); +} + +export function makeNgUrlElems(ngUrls: RegularData[], parent: HTMLElement) { + ngUrls.forEach((item, idx) => { + const params = item.params; + const { + blue_max, + blue_min, + green_max, + green_min, + img_name, + red_max, + red_min, + src_url, + x_mm, + y_mm, + z_mm, + cross_section_scale, + layout, + ome_zarr_shape, + } = params; + const elem = document.createElement('p'); + const url = getNeuroglancerUrl( + src_url, + img_name, + x_mm, + y_mm, + z_mm, + red_min, + red_max, + green_min, + green_max, + blue_min, + blue_max, + cross_section_scale, + layout + ); + elem.innerText = url; + elem.style.maxWidth = '500px'; + elem.style.textWrap = 'nowrap'; + elem.style.overflow = 'hidden'; + elem.style.textOverflow = 'ellipsis'; + parent.appendChild(elem); + console.log(url.length, ngUrls[idx].url.length); + }); +} + +export function makeContactSheetElems(contactSheets: RegularData[], parent: HTMLElement) { + contactSheets.forEach((item, idx) => { + const params = item.params; + const { + blue_max, + blue_min, + green_max, + green_min, + img_name, + red_max, + red_min, + src_url, + x_mm, + y_mm, + z_mm, + cross_section_scale, + layout, + ome_zarr_shape, + } = params; + if (ome_zarr_shape) { + const elem = document.createElement('p'); + const url = getContactSheetUrl( + src_url, + img_name, + ome_zarr_shape, + x_mm, + y_mm, + z_mm, + red_min, + red_max, + green_min, + green_max, + blue_min, + blue_max, + cross_section_scale ?? 0.5 + ); + + elem.innerText = url; + elem.style.maxWidth = '500px'; + elem.style.textWrap = 'nowrap'; + elem.style.overflow = 'hidden'; + elem.style.textOverflow = 'ellipsis'; + parent.appendChild(elem); + console.log(url.length, contactSheets[idx].url.length); + } + }); +} diff --git a/apps/neuroglancer-url/src/utils.ts b/apps/neuroglancer-url/src/utils.ts new file mode 100644 index 0000000..fdbefa0 --- /dev/null +++ b/apps/neuroglancer-url/src/utils.ts @@ -0,0 +1,213 @@ +/* + The code here and the code that utilizes this is partially adapted from + https://github.com/AllenInstitute/ome_zarr_converter/blob/main/src/ome_zarr_converter/neuroglancer/utils.py +*/ +export function finalizeConfig( + imgLayer: Record, + imgName: string, + xMm: number, + yMm: number, + zMm: number, + crossSectionScale: number = 50.0, + layout: string = '4panel' +): Record { + const dimensions = { + x: [0.001 * xMm, 'm'], + y: [0.001 * yMm, 'm'], + z: [0.001 * zMm, 'm'], + }; + + const config: Record = {}; + config.dimensions = dimensions; + config.crossSectionScale = crossSectionScale; + config.projectionScale = 40000; // affects initial zoom of 3D view; larger is more zoomed out + config.selectedLayer = { visible: true, layer: imgName }; + config.layout = layout; + config.layers = [imgLayer]; + + return config; +} + +export const neuroglancerUrl = 'https://neuroglancer-demo.appspot.com/'; + +export function getSourceConfig(srcUrl: string, xMm: number, yMm: number, zMm: number): Record { + const source: Record = {}; + source.url = srcUrl; + source.transform = { + outputDimensions: { + 'c^': [1, ''], + z: [0.001 * zMm, 'm'], + y: [0.001 * yMm, 'm'], + x: [0.001 * xMm, 'm'], + }, + }; + return source; +} + +export function getImageLayer( + layerName: string, + source: any, + shaderCode: string, + shaderControls: any +): Record { + const layer: Record = {}; + layer.type = 'image'; + layer.tab = 'rendering'; + layer.shader = shaderCode; + layer.shaderControls = shaderControls; + layer.source = source; + layer.channelDimensions = { 'c^': [1, ''] }; + layer.name = layerName; + layer.opacity = 1; + return layer; +} + +type NeuroglancerControls = { + red_min: number; + red_max: number; + green_min: number; + green_max: number; + blue_min: number; + blue_max: number; +}; + +export function getShaderCode( + redMin: number, + redMax: number, + greenMin: number, + greenMax: number, + blueMin: number, + blueMax: number +): [string, NeuroglancerControls] { + const redMinStr = parseFloat(redMin.toString()); + const redMaxStr = parseFloat(redMax.toString()); + const greenMinStr = parseFloat(greenMin.toString()); + const greenMaxStr = parseFloat(greenMax.toString()); + const blueMinStr = parseFloat(blueMin.toString()); + const blueMaxStr = parseFloat(blueMax.toString()); + + let code = ''; + code += ` + #uicontrol invlerp red_scale(range=[${redMinStr},${2 * redMaxStr}], channel=0)`; + + code += ` + #uicontrol invlerp green_scale(range=[${greenMinStr}, ${2 * greenMaxStr}], channel=1)`; + + code += ` + #uicontrol invlerp blue_scale(range=[${blueMinStr}, ${2 * blueMaxStr}], channel=2)`; + + code += ` + #uicontrol bool red_visible checkbox(default=true); + #uicontrol bool green_visible checkbox(default=true); + #uicontrol bool blue_visible checkbox(default=true); + `; + + code += ` + void main() { + float r; + float r_scale=red_scale(); + if(!red_visible || (r_scale<=0.0) ){ + r=0.0; + } + else{ + r=r_scale; + } + if(r>1.0)r=1.0; + + float g; + float g_scale=green_scale(); + if(!green_visible || (g_scale<=0.0)){ + g=0.0; + } + else{ + g=g_scale; + } + if(g>1.0)g=1.0; + + float b; + float b_scale=blue_scale(); + if(!blue_visible || (b_scale<=0.0)){ + b=0.0; + } + else{ + b=b_scale; + } + if(b>1.0)b=1.0; + + emitRGB(vec3(r,g,b)); + } + `; + + const controls: NeuroglancerControls = { + red_min: redMin, + red_max: redMax, + green_min: greenMin, + green_max: greenMax, + blue_min: blueMin, + blue_max: blueMax, + }; + + return [code, controls]; +} + +export function getNeuroglancerConfig( + srcUrl: string, + imgName: string, + xMm: number, + yMm: number, + zMm: number, + redMin: number, + redMax: number, + greenMin: number, + greenMax: number, + blueMin: number, + blueMax: number, + crossSectionScale: number = 50.0, + layout: string = '4panel' +): Record { + const [shaderCode, shaderControls] = getShaderCode(redMin, redMax, greenMin, greenMax, blueMin, blueMax); + + const source = getSourceConfig(srcUrl, xMm, yMm, zMm); + + const imgLayer = getImageLayer(imgName, source, shaderCode, shaderControls); + + return finalizeConfig(imgLayer, imgName, xMm, yMm, zMm, crossSectionScale, layout); +} + +export function urlFromConfig(url: string, config: Record): string { + return encodeURI(`${url}#!${JSON.stringify(config)}`); +} + +export function getNeuroglancerUrl( + srcUrl: string, + imgName: string, + xMm: number, + yMm: number, + zMm: number, + redMin: number, + redMax: number, + greenMin: number, + greenMax: number, + blueMin: number, + blueMax: number, + crossSectionScale: number = 50.0, + layout: string = '4panel' +): string { + const config = getNeuroglancerConfig( + srcUrl, + imgName, + xMm, + yMm, + zMm, + redMin, + redMax, + greenMin, + greenMax, + blueMin, + blueMax, + crossSectionScale, + layout + ); + + return urlFromConfig(neuroglancerUrl, config); +} diff --git a/apps/neuroglancer-url/tsconfig.json b/apps/neuroglancer-url/tsconfig.json new file mode 100644 index 0000000..e5bee2e --- /dev/null +++ b/apps/neuroglancer-url/tsconfig.json @@ -0,0 +1,5 @@ +{ + "extends": "../tsconfig.json", + "include": ["./src/**/*", "../common/src/**/*"] + +} \ No newline at end of file diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 0767af5..cc34308 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -133,6 +133,15 @@ importers: specifier: ^5.3.3 version: 5.3.3 + apps/neuroglancer-url: + devDependencies: + esbuild: + specifier: ^0.19.12 + version: 0.19.12 + typescript: + specifier: ^5.3.3 + version: 5.3.3 + apps/omezarr-viewer: dependencies: '@alleninstitute/vis-geometry': From b244c4682a18e9c6034e1da2adf7d877d24c4f4d Mon Sep 17 00:00:00 2001 From: Lane Sawyer Date: Tue, 18 Jun 2024 11:45:10 -0700 Subject: [PATCH 2/2] chore: Formatting (#26) * Install prettier for packages * Run pretttier for packages * Prettier all the things! --- .prettierrc | 12 +- LICENSE.md | 50 +- README.md | 9 +- apps/common/package.json | 55 +- .../src/loaders/ome-zarr/fetchSlice.worker.ts | 26 +- .../src/loaders/ome-zarr/sliceWorkerPool.ts | 30 +- apps/common/src/loaders/ome-zarr/zarr-data.ts | 322 +- apps/common/src/loaders/scatterplot/data.ts | 68 +- .../scatterplot/scatterbrain-loader.ts | 52 +- apps/common/src/typed-array.ts | 2 +- apps/layers/package.json | 126 +- apps/layers/public/demo.html | 24 +- apps/layers/readme.md | 15 +- apps/layers/src/app.tsx | 76 +- .../src/data-renderers/annotation-renderer.ts | 115 +- .../dynamicGridSlideRenderer.ts | 137 +- .../layers/src/data-renderers/lineRenderer.ts | 52 +- .../src/data-renderers/mesh-renderer.ts | 64 +- .../simpleAnnotationRenderer.ts | 66 +- apps/layers/src/data-renderers/types.ts | 34 +- apps/layers/src/data-renderers/utils.ts | 8 +- .../src/data-renderers/volumeSliceRenderer.ts | 180 +- .../annotation/annotation-codec.ts | 4 +- .../annotation/annotation-grid.ts | 32 +- .../annotation/annotation-to-mesh.ts | 67 +- .../annotation/fetch-annotation.ts | 4 +- .../src/data-sources/annotation/types.ts | 4 +- .../src/data-sources/ome-zarr/planar-slice.ts | 26 +- .../src/data-sources/ome-zarr/slice-grid.ts | 27 +- .../data-sources/scatterplot/dynamic-grid.ts | 42 +- apps/layers/src/data-sources/types.ts | 16 +- apps/layers/src/demo.ts | 471 +- apps/layers/src/types.ts | 96 +- apps/layers/src/ui/annotation-grid.tsx | 34 +- apps/layers/src/ui/contact-sheet.tsx | 97 +- apps/layers/src/ui/scatterplot-ui.tsx | 60 +- apps/layers/src/ui/slice-ui.tsx | 117 +- apps/layers/tsconfig.json | 13 +- apps/neuroglancer-url/README.md | 4 +- apps/neuroglancer-url/package.json | 77 +- apps/neuroglancer-url/public/demo.html | 2 +- apps/neuroglancer-url/src/data.ts | 602 +- apps/neuroglancer-url/tsconfig.json | 3 +- apps/omezarr-viewer/README.md | 19 +- apps/omezarr-viewer/package.json | 96 +- apps/omezarr-viewer/public/tissuecyte.html | 16 +- apps/omezarr-viewer/public/versa.html | 17 +- apps/omezarr-viewer/src/annotation/path.ts | 196 +- apps/omezarr-viewer/src/camera.ts | 17 +- .../src/components/color-map.ts | 132 +- apps/omezarr-viewer/src/image-renderer.ts | 134 +- apps/omezarr-viewer/src/slice-renderer.ts | 505 +- apps/omezarr-viewer/src/tissuecyte.ts | 899 +- apps/omezarr-viewer/src/versa-renderer.ts | 610 +- apps/omezarr-viewer/src/versa.ts | 1091 +- apps/omezarr-viewer/tsconfig.json | 8 +- apps/scatterplot/README.md | 6 +- apps/scatterplot/package.json | 88 +- apps/scatterplot/public/demo.html | 19 +- apps/scatterplot/src/demo.ts | 329 +- apps/scatterplot/src/renderer.ts | 192 +- apps/scatterplot/tsconfig.json | 20 +- apps/tsconfig.json | 35 +- docs/authenticating.md | 2 + docs/examples.md | 2 + docs/publishing.md | 2 + package.json | 7 +- packages/geometry/package.json | 98 +- packages/geometry/src/BoundingBox.ts | 210 +- packages/geometry/src/Rectangle2D.ts | 70 +- packages/geometry/src/box2D.ts | 42 +- packages/geometry/src/box3D.ts | 38 +- packages/geometry/src/index.ts | 32 +- packages/geometry/src/interval.ts | 136 +- packages/geometry/src/line.ts | 6 +- packages/geometry/src/spatialIndexing/tree.ts | 2 +- .../geometry/src/tests/Rectangle2D.test.ts | 92 +- packages/geometry/src/tests/box2D.test.ts | 188 +- packages/geometry/src/tests/box3D.test.ts | 2 +- packages/geometry/src/tests/interval.test.ts | 120 +- packages/geometry/src/tests/line.test.ts | 30 +- packages/geometry/src/tests/vec2.test.ts | 270 +- packages/geometry/src/tests/vec3.test.ts | 262 +- packages/geometry/src/tests/vec4.test.ts | 2 +- packages/geometry/src/vec5.ts | 10 +- packages/geometry/src/vector.ts | 326 +- packages/geometry/tsconfig.json | 35 +- packages/scatterbrain/package.json | 110 +- packages/scatterbrain/src/dataset-cache.ts | 535 +- packages/scatterbrain/src/index.ts | 8 +- .../scatterbrain/src/layers/buffer-pair.ts | 3 +- packages/scatterbrain/src/layers/layer-2D.ts | 74 +- packages/scatterbrain/src/layers/types.ts | 33 +- packages/scatterbrain/src/render-queue.ts | 363 +- .../src/test/render-cache.test.ts | 273 +- .../src/test/render-queue.test.ts | 268 +- packages/scatterbrain/src/test/test-utils.ts | 21 +- packages/scatterbrain/tsconfig.json | 33 +- pnpm-lock.yaml | 9433 ++++++++++------- pnpm-workspace.yaml | 8 +- tsconfig.base.json | 20 +- 101 files changed, 11291 insertions(+), 9625 deletions(-) diff --git a/.prettierrc b/.prettierrc index 7c0342a..f429b83 100644 --- a/.prettierrc +++ b/.prettierrc @@ -1,8 +1,8 @@ { - "printWidth": 120, - "trailingComma": "es5", - "tabWidth": 4, - "singleQuote": true, - "semi": true, - "singleAttributePerLine": true + "printWidth": 120, + "trailingComma": "es5", + "tabWidth": 4, + "singleQuote": true, + "semi": true, + "singleAttributePerLine": true } diff --git a/LICENSE.md b/LICENSE.md index 1863975..53b3297 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,33 +1,33 @@ -Allen Institute Software License – This software license is the 2-clause BSD -license plus clause a third clause that prohibits redistribution and use for -commercial purposes without further permission. +Allen Institute Software License – This software license is the 2-clause BSD +license plus clause a third clause that prohibits redistribution and use for +commercial purposes without further permission. -Copyright © 2019. Allen Institute. All rights reserved. +Copyright © 2019. Allen Institute. All rights reserved. -Redistribution and use in source and binary forms, with or without +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: -1. Redistributions of source code must retain the above copyright notice, this -list of conditions and the following disclaimer. +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. -2. Redistributions in binary form must reproduce the above copyright notice, -this list of conditions and the following disclaimer in the documentation -and/or other materials provided with the distribution. +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. -3. Redistributions and use for commercial purposes are not permitted without -the Allen Institute’s written permission. For purposes of this license, -commercial purposes are the incorporation of the Allen Institute's software -into anything for which you will charge fees or other compensation or use of -the software to perform a commercial service for a third party. Contact -terms@alleninstitute.org for commercial licensing opportunities. +3. Redistributions and use for commercial purposes are not permitted without + the Allen Institute’s written permission. For purposes of this license, + commercial purposes are the incorporation of the Allen Institute's software + into anything for which you will charge fees or other compensation or use of + the software to perform a commercial service for a third party. Contact + terms@alleninstitute.org for commercial licensing opportunities. -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND -ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE -FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/README.md b/README.md index 46b41b9..a9a0ba7 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,22 @@ # Allen Institute Vis + This repository contains a collection of packages for building scalable visualization tools at the Allen Institute. It houses the `vis-[package name]` packages on the Allen Institute GitHub organization's NPM package registry. # Available Packages -- `vis-geometry`: A collection of vector functions for 2D and 3D geometry -- `scatterbrain`: A collection of useful utitilites used to build our big-data, scalable, scatterplot tool "Scatterbrain" in the Brain Knowledge Platform + +- `vis-geometry`: A collection of vector functions for 2D and 3D geometry +- `scatterbrain`: A collection of useful utitilites used to build our big-data, scalable, scatterplot tool "Scatterbrain" in the Brain Knowledge Platform # Examples + See the `apps` directory for example projects using the packages. Over time, these examples will become simpler as the base tooling becomes more mature. For details on running or adding new examples, see the `docs/examples.md` file. # Contributing + Contributions are welcome! We're currently breaking apart the Scattebrain component into smaller, more manageable packages. If you have a package that you think would be useful to others, please open a PR. # Using the Libraries + See the `docs/using-packages.md` file for information on how to use the packages in your own projects. diff --git a/apps/common/package.json b/apps/common/package.json index 2772f5a..5542b7f 100644 --- a/apps/common/package.json +++ b/apps/common/package.json @@ -3,35 +3,34 @@ "version": "0.0.1", "HEY": "NOTE! DO not use this package directly - its just for sharing code between our little apps", "contributors": [ - { - "name": "Lane Sawyer", - "email": "lane.sawyer@alleninstitute.org" - }, - { - "name": "James Gerstenberger", - "email": "james.gerstenberger@alleninstitute.org" - }, - { - "name": "Noah Shepard", - "email": "noah.shepard@alleninstitute.org" - }, - { - "name": "Skyler Moosman", - "email": "skyler.moosman@alleninstitute.org" - }, - { - "name": "Su Li", - "email": "su.li@alleninstitute.org" - } + { + "name": "Lane Sawyer", + "email": "lane.sawyer@alleninstitute.org" + }, + { + "name": "James Gerstenberger", + "email": "james.gerstenberger@alleninstitute.org" + }, + { + "name": "Noah Shepard", + "email": "noah.shepard@alleninstitute.org" + }, + { + "name": "Skyler Moosman", + "email": "skyler.moosman@alleninstitute.org" + }, + { + "name": "Su Li", + "email": "su.li@alleninstitute.org" + } ], "private": true, "dependencies": { - "@alleninstitute/vis-geometry": "workspace:*", - "@alleninstitute/vis-scatterbrain": "workspace:*", - "@types/lodash": "^4.14.202", - "lodash": "^4.17.21", - "regl": "^2.1.0", - "zarr": "^0.6.2" - + "@alleninstitute/vis-geometry": "workspace:*", + "@alleninstitute/vis-scatterbrain": "workspace:*", + "@types/lodash": "^4.14.202", + "lodash": "^4.17.21", + "regl": "^2.1.0", + "zarr": "^0.6.2" } - } \ No newline at end of file +} diff --git a/apps/common/src/loaders/ome-zarr/fetchSlice.worker.ts b/apps/common/src/loaders/ome-zarr/fetchSlice.worker.ts index 41b0072..655c445 100644 --- a/apps/common/src/loaders/ome-zarr/fetchSlice.worker.ts +++ b/apps/common/src/loaders/ome-zarr/fetchSlice.worker.ts @@ -1,16 +1,15 @@ - // a web-worker which fetches slices of data, decodes them, and returns the result as a flat float32 array, using transferables -import type { NestedArray, TypedArray } from 'zarr' -import { getSlice, type ZarrDataset, type ZarrRequest } from "./zarr-data"; +import type { NestedArray, TypedArray } from 'zarr'; +import { getSlice, type ZarrDataset, type ZarrRequest } from './zarr-data'; const ctx = self; type ZarrSliceRequest = { id: string; - type: 'ZarrSliceRequest' - metadata: ZarrDataset - req: ZarrRequest, - layerIndex: number -} + type: 'ZarrSliceRequest'; + metadata: ZarrDataset; + req: ZarrRequest; + layerIndex: number; +}; function isSliceRequest(payload: any): payload is ZarrSliceRequest { return typeof payload === 'object' && payload['type'] === 'ZarrSliceRequest'; } @@ -18,13 +17,10 @@ ctx.onmessage = (msg: MessageEvent) => { const { data } = msg; if (isSliceRequest(data)) { const { metadata, req, layerIndex, id } = data; - getSlice(metadata, req, layerIndex).then((result: { - shape: number[], - buffer: NestedArray - }) => { + getSlice(metadata, req, layerIndex).then((result: { shape: number[]; buffer: NestedArray }) => { const { shape, buffer } = result; const R = new Float32Array(buffer.flatten()); - ctx.postMessage({ type: 'slice', id, shape, data: R }, { transfer: [R.buffer] }) - }) + ctx.postMessage({ type: 'slice', id, shape, data: R }, { transfer: [R.buffer] }); + }); } -} \ No newline at end of file +}; diff --git a/apps/common/src/loaders/ome-zarr/sliceWorkerPool.ts b/apps/common/src/loaders/ome-zarr/sliceWorkerPool.ts index 0f4302a..905bb3c 100644 --- a/apps/common/src/loaders/ome-zarr/sliceWorkerPool.ts +++ b/apps/common/src/loaders/ome-zarr/sliceWorkerPool.ts @@ -1,5 +1,5 @@ -import { uniqueId } from "lodash"; -import type { ZarrDataset, ZarrRequest } from "./zarr-data"; +import { uniqueId } from 'lodash'; +import type { ZarrDataset, ZarrRequest } from './zarr-data'; type PromisifiedMessage = { requestCacheKey: string; @@ -8,15 +8,15 @@ type PromisifiedMessage = { promise?: Promise | undefined; }; type ExpectedResultSlice = { - type: 'slice', + type: 'slice'; id: string; } & Slice; type Slice = { data: Float32Array; - shape: number[] -} + shape: number[]; +}; function isExpectedResult(obj: any): obj is ExpectedResultSlice { - return (typeof obj === 'object' && 'type' in obj && obj.type === 'slice') + return typeof obj === 'object' && 'type' in obj && obj.type === 'slice'; } export class SliceWorkerPool { private workers: Worker[]; @@ -26,7 +26,7 @@ export class SliceWorkerPool { this.workers = new Array(size); for (let i = 0; i < size; i++) { this.workers[i] = new Worker(new URL('./fetchSlice.worker.ts', import.meta.url), { type: 'module' }); - this.workers[i].onmessage = (msg) => this.handleResponse(msg) + this.workers[i].onmessage = (msg) => this.handleResponse(msg); } this.promises = {}; this.which = 0; @@ -37,14 +37,14 @@ export class SliceWorkerPool { if (isExpectedResult(payload)) { const prom = this.promises[payload.id]; if (prom) { - const { data, shape } = payload + const { data, shape } = payload; prom.resolve({ data, shape }); - delete this.promises[payload.id] + delete this.promises[payload.id]; } } } private roundRobin() { - this.which = (this.which + 1) % this.workers.length + this.which = (this.which + 1) % this.workers.length; } requestSlice(dataset: ZarrDataset, req: ZarrRequest, layerIndex: number) { const reqId = uniqueId('rq'); @@ -57,7 +57,13 @@ export class SliceWorkerPool { reject, promise: undefined, // ill get added to the map once I am fully defined! }; - this.workers[this.which].postMessage({ id: reqId, type: 'ZarrSliceRequest', metadata: dataset, req, layerIndex }); + this.workers[this.which].postMessage({ + id: reqId, + type: 'ZarrSliceRequest', + metadata: dataset, + req, + layerIndex, + }); this.roundRobin(); }); this.promises[reqId].promise = eventually; @@ -72,4 +78,4 @@ export function getSlicePool() { slicePool = new SliceWorkerPool(16); } return slicePool; -} \ No newline at end of file +} diff --git a/apps/common/src/loaders/ome-zarr/zarr-data.ts b/apps/common/src/loaders/ome-zarr/zarr-data.ts index a48664d..9229752 100644 --- a/apps/common/src/loaders/ome-zarr/zarr-data.ts +++ b/apps/common/src/loaders/ome-zarr/zarr-data.ts @@ -1,238 +1,236 @@ // lets make some easy to understand utils to access .zarr data stored in an s3 bucket somewhere -import { HTTPStore, NestedArray, type TypedArray, openArray, openGroup, slice } from "zarr"; -import { some } from "lodash"; -import { Box2D, type Interval, Vec2, type box2D, limit, type vec2 } from "@alleninstitute/vis-geometry"; -import type { AxisAlignedPlane } from "../../../../omezarr-viewer/src/versa-renderer"; +import { HTTPStore, NestedArray, type TypedArray, openArray, openGroup, slice } from 'zarr'; +import { some } from 'lodash'; +import { Box2D, type Interval, Vec2, type box2D, limit, type vec2 } from '@alleninstitute/vis-geometry'; +import type { AxisAlignedPlane } from '../../../../omezarr-viewer/src/versa-renderer'; // documentation for ome-zarr datasets (from which these types are built) // can be found here: // https://ngff.openmicroscopy.org/latest/#multiscale-md // export type ZarrDataset = Awaited>; type AxisDesc = { - name: string; // x or y or z or time or ? - type: string; // space or time or ? - unit: string; // see list of possible units: https://ngff.openmicroscopy.org/latest/#axes-md + name: string; // x or y or z or time or ? + type: string; // space or time or ? + unit: string; // see list of possible units: https://ngff.openmicroscopy.org/latest/#axes-md }; // todo, there are other types of coordinate transforms... type ScaleTransform = { - type: "scale"; - scale: ReadonlyArray; + type: 'scale'; + scale: ReadonlyArray; }; function isScaleTransform(trn: unknown): trn is ScaleTransform { - if (typeof trn === "object" && trn !== null) { - const scaleTransform = trn as ScaleTransform; - return scaleTransform.type === "scale" && scaleTransform.scale !== undefined; - } - return false; + if (typeof trn === 'object' && trn !== null) { + const scaleTransform = trn as ScaleTransform; + return scaleTransform.type === 'scale' && scaleTransform.scale !== undefined; + } + return false; } type DatasetDesc = { - path: string; - coordinateTransformations: ReadonlyArray; + path: string; + coordinateTransformations: ReadonlyArray; }; type DatasetWithShape = DatasetDesc & { - shape: number[]; + shape: number[]; }; type ZarrAttr = { - axes: ReadonlyArray; - datasets: ReadonlyArray; + axes: ReadonlyArray; + datasets: ReadonlyArray; }; type ZarrAttrs = { - multiscales: ReadonlyArray; + multiscales: ReadonlyArray; }; async function getRawInfo(store: HTTPStore) { - const group = await openGroup(store); - // TODO HACK ALERT: I am once again doing the thing that I hate, in which I promise to my friend Typescript that - // the junk I just pulled out of this internet file is exactly what I expect it to be: :fingers_crossed: - return group.attrs.asObject() as Promise; + const group = await openGroup(store); + // TODO HACK ALERT: I am once again doing the thing that I hate, in which I promise to my friend Typescript that + // the junk I just pulled out of this internet file is exactly what I expect it to be: :fingers_crossed: + return group.attrs.asObject() as Promise; } async function mapAsync(arr: ReadonlyArray, fn: (t: T, index: number) => Promise) { - return Promise.all(arr.map((v, i) => fn(v, i))); + return Promise.all(arr.map((v, i) => fn(v, i))); } // return the mapping from path (aka resolution group???) to the dimensional shape of the data async function loadMetadata(store: HTTPStore, attrs: ZarrAttrs) { - const addShapeToDesc = async (d: DatasetDesc) => ({ - ...d, - shape: (await openArray({ store, mode: "r", path: d.path })).shape, - }); - return { - url: store.url, - multiscales: await mapAsync(attrs.multiscales, async (attr) => ({ - ...attr, - datasets: await mapAsync(attr.datasets, addShapeToDesc), - })), - }; + const addShapeToDesc = async (d: DatasetDesc) => ({ + ...d, + shape: (await openArray({ store, mode: 'r', path: d.path })).shape, + }); + return { + url: store.url, + multiscales: await mapAsync(attrs.multiscales, async (attr) => ({ + ...attr, + datasets: await mapAsync(attr.datasets, addShapeToDesc), + })), + }; } -type OmeDimension = "x" | "y" | "z" | "t" | "c"; +type OmeDimension = 'x' | 'y' | 'z' | 't' | 'c'; const uvTable = { - xy: { u: "x", v: "y" }, - xz: { u: "x", v: "z" }, - yz: { u: "y", v: "z" }, + xy: { u: 'x', v: 'y' }, + xz: { u: 'x', v: 'z' }, + yz: { u: 'y', v: 'z' }, } as const; const sliceDimension = { - xy: "z", - xz: "y", - yz: "x", + xy: 'z', + xz: 'y', + yz: 'x', } as const; export function uvForPlane(plane: AxisAlignedPlane) { - return uvTable[plane]; + return uvTable[plane]; } export function sliceDimensionForPlane(plane: AxisAlignedPlane) { - return sliceDimension[plane]; + return sliceDimension[plane]; } export type ZarrRequest = Record; export function pickBestScale( - dataset: ZarrDataset, - plane: { - u: OmeDimension; - v: OmeDimension; - }, - relativeView: box2D, // a box in data-unit-space - // in the plane given above - displayResolution: vec2 + dataset: ZarrDataset, + plane: { + u: OmeDimension; + v: OmeDimension; + }, + relativeView: box2D, // a box in data-unit-space + // in the plane given above + displayResolution: vec2 ) { - const datasets = dataset.multiscales[0].datasets; - const axes = dataset.multiscales[0].axes; - const realSize = sizeInUnits(plane, axes, datasets[0])! + const datasets = dataset.multiscales[0].datasets; + const axes = dataset.multiscales[0].axes; + const realSize = sizeInUnits(plane, axes, datasets[0])!; - const vxlPitch = (size: vec2) => Vec2.div(realSize, size); - // size, in dataspace, of a pixel 1/res - const pxPitch = Vec2.div(Box2D.size(relativeView), displayResolution); - const dstToDesired = (a: vec2, goal: vec2) => { - const diff = Vec2.sub(a, goal); - if (diff[0] * diff[1] > 0) { - // the res (a) is higher than our goal - - // weight this heavily to prefer smaller than the goal - return 1000 * Vec2.length(Vec2.sub(a, goal)); - } - return Vec2.length(Vec2.sub(a, goal)); - } - // we assume the datasets are ordered... hmmm TODO - const choice = datasets.reduce( - (bestSoFar, cur) => - dstToDesired(vxlPitch(planeSizeInVoxels(plane, axes, bestSoFar)!), pxPitch) > - dstToDesired(vxlPitch(planeSizeInVoxels(plane, axes, cur)!), pxPitch) - ? cur - : bestSoFar, - datasets[0] - ); - return choice ?? datasets[datasets.length - 1]; + const vxlPitch = (size: vec2) => Vec2.div(realSize, size); + // size, in dataspace, of a pixel 1/res + const pxPitch = Vec2.div(Box2D.size(relativeView), displayResolution); + const dstToDesired = (a: vec2, goal: vec2) => { + const diff = Vec2.sub(a, goal); + if (diff[0] * diff[1] > 0) { + // the res (a) is higher than our goal - + // weight this heavily to prefer smaller than the goal + return 1000 * Vec2.length(Vec2.sub(a, goal)); + } + return Vec2.length(Vec2.sub(a, goal)); + }; + // we assume the datasets are ordered... hmmm TODO + const choice = datasets.reduce( + (bestSoFar, cur) => + dstToDesired(vxlPitch(planeSizeInVoxels(plane, axes, bestSoFar)!), pxPitch) > + dstToDesired(vxlPitch(planeSizeInVoxels(plane, axes, cur)!), pxPitch) + ? cur + : bestSoFar, + datasets[0] + ); + return choice ?? datasets[datasets.length - 1]; } function indexFor(dim: OmeDimension, axes: readonly AxisDesc[]) { - return axes.findIndex((axe) => axe.name === dim); + return axes.findIndex((axe) => axe.name === dim); } export function sizeInUnits( - plane: AxisAlignedPlane | { - u: OmeDimension; - v: OmeDimension; - }, - axes: readonly AxisDesc[], - dataset: DatasetWithShape + plane: + | AxisAlignedPlane + | { + u: OmeDimension; + v: OmeDimension; + }, + axes: readonly AxisDesc[], + dataset: DatasetWithShape ): vec2 | undefined { - plane = typeof plane === 'string' ? uvForPlane(plane) : plane - const vxls = planeSizeInVoxels(plane, axes, dataset); + plane = typeof plane === 'string' ? uvForPlane(plane) : plane; + const vxls = planeSizeInVoxels(plane, axes, dataset); - if (vxls === undefined) return undefined; - let size: vec2 = vxls; - // now, just apply the correct transforms, if they exist... + if (vxls === undefined) return undefined; + let size: vec2 = vxls; + // now, just apply the correct transforms, if they exist... - dataset.coordinateTransformations.forEach((trn) => { - if (isScaleTransform(trn)) { - // try to apply it! - const uIndex = indexOfDimension(axes, plane.u); - const vIndex = indexOfDimension(axes, plane.v); - size = Vec2.mul(size, [trn.scale[uIndex], trn.scale[vIndex]]); - } - }); - return size; + dataset.coordinateTransformations.forEach((trn) => { + if (isScaleTransform(trn)) { + // try to apply it! + const uIndex = indexOfDimension(axes, plane.u); + const vIndex = indexOfDimension(axes, plane.v); + size = Vec2.mul(size, [trn.scale[uIndex], trn.scale[vIndex]]); + } + }); + return size; } -export function sizeInVoxels( - dim: OmeDimension, - axes: readonly AxisDesc[], - dataset: DatasetWithShape -) { - const uI = indexFor(dim, axes); - if (uI === -1) return undefined +export function sizeInVoxels(dim: OmeDimension, axes: readonly AxisDesc[], dataset: DatasetWithShape) { + const uI = indexFor(dim, axes); + if (uI === -1) return undefined; - return dataset.shape[uI] + return dataset.shape[uI]; } export function planeSizeInVoxels( - plane: { - u: OmeDimension; - v: OmeDimension; - }, - axes: readonly AxisDesc[], - dataset: DatasetWithShape + plane: { + u: OmeDimension; + v: OmeDimension; + }, + axes: readonly AxisDesc[], + dataset: DatasetWithShape ): vec2 | undefined { - // first - u&v must not refer to the same dimension, - // and both should exist in the axes... - const { u, v } = plane; - if (u === v) return undefined; - const uI = indexFor(u, axes); - const vI = indexFor(v, axes); + // first - u&v must not refer to the same dimension, + // and both should exist in the axes... + const { u, v } = plane; + if (u === v) return undefined; + const uI = indexFor(u, axes); + const vI = indexFor(v, axes); - if (uI === -1 || vI === -1) return undefined; + if (uI === -1 || vI === -1) return undefined; - return [dataset.shape[uI], dataset.shape[vI]] as const; + return [dataset.shape[uI], dataset.shape[vI]] as const; } // feel free to freak out if the request is over or under determined or whatever function buildQuery(r: Readonly, axes: readonly AxisDesc[], shape: number[]) { - const ordered = axes.map((a) => r[a.name as OmeDimension]); - // if any are undefined, throw up - if (some(ordered, (a) => a === undefined)) { - throw new Error("request does not match expected dimensions of ome-zarr dataset!"); - } - - return ordered.map((d, i) => { - const bounds = { min: 0, max: shape[i] }; - if (d === null) { - return d; - } else if (typeof d === "number") { - return limit(bounds, d); + const ordered = axes.map((a) => r[a.name as OmeDimension]); + // if any are undefined, throw up + if (some(ordered, (a) => a === undefined)) { + throw new Error('request does not match expected dimensions of ome-zarr dataset!'); } - return slice(limit(bounds, d.min), limit(bounds, d.max)); - }); + + return ordered.map((d, i) => { + const bounds = { min: 0, max: shape[i] }; + if (d === null) { + return d; + } else if (typeof d === 'number') { + return limit(bounds, d); + } + return slice(limit(bounds, d.min), limit(bounds, d.max)); + }); } function dieIfMalformed(r: ZarrRequest) { - // deal with me later - // TODO + // deal with me later + // TODO } export async function explain(z: ZarrDataset) { - console.dir(z); - const store = new HTTPStore(z.url); - for (const d of z.multiscales[0].datasets) { - openArray({ store, path: d.path, mode: "r" }).then((arr) => { - console.dir(arr); - }); - } + console.dir(z); + const store = new HTTPStore(z.url); + for (const d of z.multiscales[0].datasets) { + openArray({ store, path: d.path, mode: 'r' }).then((arr) => { + console.dir(arr); + }); + } } export function indexOfDimension(axes: readonly AxisDesc[], dim: OmeDimension) { - return axes.findIndex((ax) => ax.name === dim); + return axes.findIndex((ax) => ax.name === dim); } export async function getSlice(metadata: ZarrDataset, r: ZarrRequest, layerIndex: number) { - dieIfMalformed(r); - // put the request in native order - const store = new HTTPStore(metadata.url); - const scene = metadata.multiscales[0]; - const { axes } = scene; - const level = scene.datasets[layerIndex] ?? scene.datasets[scene.datasets.length - 1]; - const arr = await openArray({ store, path: level.path, mode: "r" }); - const result = await arr.get(buildQuery(r, axes, level.shape)); - if (typeof result == "number") { - throw new Error("oh noes, slice came back all weird"); - } - return { - shape: result.shape, - buffer: result, - }; + dieIfMalformed(r); + // put the request in native order + const store = new HTTPStore(metadata.url); + const scene = metadata.multiscales[0]; + const { axes } = scene; + const level = scene.datasets[layerIndex] ?? scene.datasets[scene.datasets.length - 1]; + const arr = await openArray({ store, path: level.path, mode: 'r' }); + const result = await arr.get(buildQuery(r, axes, level.shape)); + if (typeof result == 'number') { + throw new Error('oh noes, slice came back all weird'); + } + return { + shape: result.shape, + buffer: result, + }; } export async function load(url: string) { - const store = new HTTPStore(url); - return loadMetadata(store, await getRawInfo(store)); + const store = new HTTPStore(url); + return loadMetadata(store, await getRawInfo(store)); } diff --git a/apps/common/src/loaders/scatterplot/data.ts b/apps/common/src/loaders/scatterplot/data.ts index 68e273b..3d2320a 100644 --- a/apps/common/src/loaders/scatterplot/data.ts +++ b/apps/common/src/loaders/scatterplot/data.ts @@ -1,10 +1,17 @@ - // todo rename this file -import { Box2D, visitBFS, type box2D, type vec2 } from "@alleninstitute/vis-geometry"; -import { fetchColumn, type ColumnData, type ColumnRequest, type ColumnarNode, type ColumnarTree, type SlideViewDataset, type loadDataset } from "./scatterbrain-loader"; -import REGL from 'regl' -export type Dataset = ReturnType +import { Box2D, visitBFS, type box2D, type vec2 } from '@alleninstitute/vis-geometry'; +import { + fetchColumn, + type ColumnData, + type ColumnRequest, + type ColumnarNode, + type ColumnarTree, + type SlideViewDataset, + type loadDataset, +} from './scatterbrain-loader'; +import REGL from 'regl'; +export type Dataset = ReturnType; export type RenderSettings = { dataset: Dataset; view: box2D; @@ -12,53 +19,66 @@ export type RenderSettings = { pointSize: number; target: REGL.Framebuffer2D | null; regl: REGL.Regl; -} +}; function isVisible(view: box2D, sizeLimit: number, tree: ColumnarTree) { const { bounds } = tree.content; return Box2D.size(bounds)[0] > sizeLimit && !!Box2D.intersection(view, tree.content.bounds); } export function getVisibleItems(dataset: Dataset, view: box2D, sizeLimit: number) { - const hits: ColumnarTree[] = [] + const hits: ColumnarTree[] = []; let tree = 'slides' in dataset ? Object.values(dataset.slides)[0].tree : dataset.tree; - visitBFS(tree, + visitBFS( + tree, (t: ColumnarTree) => t.children, - (tree) => { hits.push(tree) }, - (tree) => isVisible(view, sizeLimit, tree)); + (tree) => { + hits.push(tree); + }, + (tree) => isVisible(view, sizeLimit, tree) + ); return hits; } export function getVisibleItemsInSlide(dataset: SlideViewDataset, slide: string, view: box2D, sizeLimit: number) { const theSlide = dataset.slides[slide]; if (!theSlide) { - console.log('nope', Object.keys(dataset.slides)) - return [] + console.log('nope', Object.keys(dataset.slides)); + return []; } - const hits: ColumnarTree[] = [] + const hits: ColumnarTree[] = []; const tree = theSlide.tree; - visitBFS(tree, + visitBFS( + tree, (t: ColumnarTree) => t.children, - (tree) => { hits.push(tree) }, - (tree) => isVisible(view, sizeLimit, tree)); + (tree) => { + hits.push(tree); + }, + (tree) => isVisible(view, sizeLimit, tree) + ); return hits; } function toReglBuffer(c: ColumnData, regl: REGL.Regl) { return { type: 'vbo', - data: regl.buffer(c) + data: regl.buffer(c), } as const; } -function fetchAndUpload(settings: { dataset: Dataset, regl: REGL.Regl }, node: ColumnarNode, req: ColumnRequest, signal?: AbortSignal | undefined) { +function fetchAndUpload( + settings: { dataset: Dataset; regl: REGL.Regl }, + node: ColumnarNode, + req: ColumnRequest, + signal?: AbortSignal | undefined +) { const { dataset, regl } = settings; - return fetchColumn(node, dataset, req, signal).then(cd => toReglBuffer(cd, regl)) + return fetchColumn(node, dataset, req, signal).then((cd) => toReglBuffer(cd, regl)); } export function fetchItem(item: ColumnarTree, settings: RenderSettings, signal?: AbortSignal) { const { dataset, colorBy } = settings; - const position = () => fetchAndUpload(settings, item.content, { type: 'METADATA', name: dataset.spatialColumn }, signal); - const color = () => fetchAndUpload(settings, item.content, colorBy, signal) + const position = () => + fetchAndUpload(settings, item.content, { type: 'METADATA', name: dataset.spatialColumn }, signal); + const color = () => fetchAndUpload(settings, item.content, colorBy, signal); return { position, - color - } as const + color, + } as const; } - diff --git a/apps/common/src/loaders/scatterplot/scatterbrain-loader.ts b/apps/common/src/loaders/scatterplot/scatterbrain-loader.ts index 7e868d5..fcddd2b 100644 --- a/apps/common/src/loaders/scatterplot/scatterbrain-loader.ts +++ b/apps/common/src/loaders/scatterplot/scatterbrain-loader.ts @@ -1,6 +1,6 @@ -import { Box2D, Box3D, Vec3, type box, type box3D, type vec2, type vec3 } from "@alleninstitute/vis-geometry"; -import { MakeTaggedBufferView, type TaggedTypedArray, type WebGLSafeBasicType } from "../../typed-array"; -import type REGL from "regl"; +import { Box2D, Box3D, Vec3, type box, type box3D, type vec2, type vec3 } from '@alleninstitute/vis-geometry'; +import { MakeTaggedBufferView, type TaggedTypedArray, type WebGLSafeBasicType } from '../../typed-array'; +import type REGL from 'regl'; type volumeBound = { lx: number; @@ -68,7 +68,7 @@ export type SlideColumnarMetadata = Omit +type VectorConstraint = ReadonlyArray; export type ColumnarNode = { url: string; name: string; @@ -79,8 +79,8 @@ export type ColumnarNode = { }; export type ColumnarTree = { content: ColumnarNode; - children: ReadonlyArray> -} + children: ReadonlyArray>; +}; // adapted from Potree createChildAABB // note that if you do not do indexing in precisely the same order @@ -135,14 +135,14 @@ function convertTree2D( children: n.children !== undefined && n.children.length > 0 ? n.children.map((c) => - convertTree2D( - c, - getChildBoundsUsingPotreeIndexing(bounds, getRelativeIndex(safeName, sanitizeName(c.file))), - depth + 1, - metadataPath, - genePath - ) - ) + convertTree2D( + c, + getChildBoundsUsingPotreeIndexing(bounds, getRelativeIndex(safeName, sanitizeName(c.file))), + depth + 1, + metadataPath, + genePath + ) + ) : [], }; } @@ -185,7 +185,7 @@ function loadSlideViewDataset(metadata: SlideColumnarMetadata, _datasetUrl: stri const slideBounds = Box3D.create([box.lx, box.ly, box.lz], [box.ux, box.uy, box.uz]); return { tree: convertTree2D(slide.tree.root, slideBounds, 0, metadataFileEndpoint, geneFileEndpoint), - id: (slide.featureTypeValueReferenceId), + id: slide.featureTypeValueReferenceId, }; }); return { @@ -226,13 +226,7 @@ export function loadDataset(metadata: ColumnarMetadata, datasetUrl: string) { geneUrl: metadata.geneFileEndpoint, columnInfo, spatialColumn: metadata.spatialColumn, - tree: convertTree2D( - metadata.root, - rootBounds, - 0, - metadata.metadataFileEndpoint, - metadata.geneFileEndpoint - ), + tree: convertTree2D(metadata.root, rootBounds, 0, metadata.metadataFileEndpoint, metadata.geneFileEndpoint), }; } @@ -246,15 +240,15 @@ type QuantitativeColumn = { }; export type ColumnRequest = MetadataColumn | QuantitativeColumn; export type ColumnBuffer = { - type: 'vbo', - data: REGL.Buffer -} + type: 'vbo'; + data: REGL.Buffer; +}; export type ColumnData = TaggedTypedArray & { elements: number; // per vector entry - for example 'xy' would have elements: 2 }; export async function loadScatterbrainJson(url: string) { // obviously, we should check or something - return fetch(url).then(stuff => stuff.json() as unknown as ColumnarMetadata) + return fetch(url).then((stuff) => stuff.json() as unknown as ColumnarMetadata); } export async function fetchColumn( @@ -268,11 +262,13 @@ export async function fetchColumn( const getGeneUrl = (columnName: string) => `${dataset.geneUrl}${columnName}/${referenceIdForEmbedding}/${node.name}.bin`; if (column.type === 'QUANTITATIVE') { - const buff = await fetch(getGeneUrl(column.name), { signal: signal ?? null }).then((resp) => resp.arrayBuffer()); + const buff = await fetch(getGeneUrl(column.name), { signal: signal ?? null }).then((resp) => + resp.arrayBuffer() + ); return { ...MakeTaggedBufferView('float', buff), elements: 1 }; } const info = dataset.columnInfo[column.name]; const buff = await fetch(getColumnUrl(column.name), { signal: signal ?? null }).then((resp) => resp.arrayBuffer()); return { ...MakeTaggedBufferView(info.type, buff), elements: info.elements }; -} \ No newline at end of file +} diff --git a/apps/common/src/typed-array.ts b/apps/common/src/typed-array.ts index 40af16d..ef008cb 100644 --- a/apps/common/src/typed-array.ts +++ b/apps/common/src/typed-array.ts @@ -88,4 +88,4 @@ export function MakeTaggedBufferView(type: WebGLSafeBasicType, buffer: ArrayBuff throw new Error(`unsupported type requested: ${unreachable}`); } } -} \ No newline at end of file +} diff --git a/apps/layers/package.json b/apps/layers/package.json index 150d506..229f921 100644 --- a/apps/layers/package.json +++ b/apps/layers/package.json @@ -1,67 +1,67 @@ { - "name": "@alleninstitute/layer-demo", - "version": "0.0.1", - "contributors": [ - { - "name": "Lane Sawyer", - "email": "lane.sawyer@alleninstitute.org" + "name": "@alleninstitute/layer-demo", + "version": "0.0.1", + "contributors": [ + { + "name": "Lane Sawyer", + "email": "lane.sawyer@alleninstitute.org" + }, + { + "name": "James Gerstenberger", + "email": "james.gerstenberger@alleninstitute.org" + }, + { + "name": "Noah Shepard", + "email": "noah.shepard@alleninstitute.org" + }, + { + "name": "Skyler Moosman", + "email": "skyler.moosman@alleninstitute.org" + }, + { + "name": "Su Li", + "email": "su.li@alleninstitute.org" + } + ], + "license": "TBD", + "type": "module", + "main": "lib/index.js", + "types": "lib/index.d.ts", + "private": true, + "scripts": { + "preinstall": "npx only-allow pnpm", + "typecheck": "tsc --noEmit", + "start": "parcel public/demo.html" }, - { - "name": "James Gerstenberger", - "email": "james.gerstenberger@alleninstitute.org" + "devDependencies": { + "@parcel/packager-ts": "^2.12.0", + "@parcel/transformer-typescript-types": "^2.12.0", + "@types/file-saver": "^2.0.7", + "@types/react": "^18.3.0", + "@types/react-dom": "^18.3.0", + "esbuild": "^0.19.12", + "parcel": "2.12.0", + "typescript": "^5.3.3" }, - { - "name": "Noah Shepard", - "email": "noah.shepard@alleninstitute.org" - }, - { - "name": "Skyler Moosman", - "email": "skyler.moosman@alleninstitute.org" - }, - { - "name": "Su Li", - "email": "su.li@alleninstitute.org" + "dependencies": { + "@alleninstitute/vis-geometry": "workspace:*", + "@alleninstitute/vis-scatterbrain": "workspace:*", + "@czi-sds/components": "^20.0.1", + "@emotion/css": "^11.11.2", + "@emotion/react": "^11.11.4", + "@emotion/styled": "^11.11.5", + "@mui/base": "5.0.0-beta.40", + "@mui/icons-material": "^5.15.15", + "@mui/lab": "5.0.0-alpha.170", + "@mui/material": "^5.15.15", + "@types/lodash": "^4.14.202", + "file-saver": "^2.0.5", + "json5": "^2.2.3", + "kiwi-schema": "^0.5.0", + "lodash": "^4.17.21", + "regl": "^2.1.0", + "react": "^18.3.0", + "react-dom": "^18.3.0", + "zarr": "^0.6.2" } - ], - "license": "TBD", - "type": "module", - "main": "lib/index.js", - "types": "lib/index.d.ts", - "private": true, - "scripts": { - "preinstall": "npx only-allow pnpm", - "typecheck": "tsc --noEmit", - "start": "parcel public/demo.html" - }, - "devDependencies": { - "@parcel/packager-ts": "^2.12.0", - "@parcel/transformer-typescript-types": "^2.12.0", - "@types/file-saver": "^2.0.7", - "@types/react": "^18.3.0", - "@types/react-dom": "^18.3.0", - "esbuild": "^0.19.12", - "parcel": "2.12.0", - "typescript": "^5.3.3" - }, - "dependencies": { - "@alleninstitute/vis-geometry": "workspace:*", - "@alleninstitute/vis-scatterbrain": "workspace:*", - "@czi-sds/components": "^20.0.1", - "@emotion/css": "^11.11.2", - "@emotion/react": "^11.11.4", - "@emotion/styled": "^11.11.5", - "@mui/base": "5.0.0-beta.40", - "@mui/icons-material": "^5.15.15", - "@mui/lab": "5.0.0-alpha.170", - "@mui/material": "^5.15.15", - "@types/lodash": "^4.14.202", - "file-saver": "^2.0.5", - "json5": "^2.2.3", - "kiwi-schema": "^0.5.0", - "lodash": "^4.17.21", - "regl": "^2.1.0", - "react": "^18.3.0", - "react-dom": "^18.3.0", - "zarr": "^0.6.2" - } -} \ No newline at end of file +} diff --git a/apps/layers/public/demo.html b/apps/layers/public/demo.html index bde8af2..6dceb31 100644 --- a/apps/layers/public/demo.html +++ b/apps/layers/public/demo.html @@ -1,11 +1,17 @@ - + - - - - - - + + + + - \ No newline at end of file + diff --git a/apps/layers/readme.md b/apps/layers/readme.md index 6b4b782..80b874c 100644 --- a/apps/layers/readme.md +++ b/apps/layers/readme.md @@ -1,5 +1,7 @@ # Layered Rendering Example App + ## Run it + 1. download/clone this repository. 2. in the root directory (vis/) run `pnpm install` 3. run `pnpm build` @@ -8,12 +10,17 @@ 6. navigate to the running app (default `localhost://1234`) ## Why? + the goal of this (rather complicated) example app is not to show off a cool app - rather its goal is to show that we can build complexity by composing simple, focused modules. As we (the AIBS Apps team) have developed ABC-Atlas, we've tried to make sure our visualization code stays general, and that each part does as little as possible. The result is that it was fairly easy to combine those components into this new app, which mixes a (terrible) UI, scatter-plot rendering, polygon-mesh rendering (for annotations) and multi-channel volumetric rendering into independent layers. Although each of these data types appear different, our caching, fetching, visibility determination, and render-scheduling code is the same regardless of the datatype to be rendered. All that is required is to fill in a simple interface, and provide a low-level "renderer" plugin in order to add a new "layer" type. + ## Demo Script + ### Programmatic Configuration + After starting the app in a browser, you'll be greeted by a blank screen. We're going to demonstrate programmatic access to the features of this demo. The goal here is not to make users invoke command-line arguments, but rather just an easy way for interested parties to "peak under the hood". All the visualizations are configured here via simple json objects - it would not be a stretch to read these configuration options at initialization-time via URL parameters for example. Open your browser's developer tools via ctrl+shift+i, ctrl+opt+i, or F12, and go to the developer console tab. This console is a running REPL environment with direct access to the demo. You can explore what features are available by typing "demo." at which point you should be given some auto-complete options, corresponding to the methods available on the demo object. The first thing we should take a look at is `demo.addLayer`, which accepts a configuration object for some data to be viewed as a layer in the app. A list of pre-constructed objects is provided in the `examples` object. lets run `examples.reconstructed` to take a peek:
+ ```{ "type": "ScatterPlotGridConfig", "colorBy": { @@ -23,22 +30,26 @@ Open your browser's developer tools via ctrl+shift+i, ctrl+opt+i, or F12, and go "url": "https://.../4STCSZBXHYOI0JUUA3M/ScatterBrain.json" } ``` + note - the above config has been slightly altered here for readability! Some things to observe about this config object:
+ 1. its simple json 2. the "type" tag tells the app what fields to expect next. 3. this data is a grid of scatter-plots (slide view!), its colored by a quantitative feature (gene #88). 4. lastly - do not take this structure too seriously! I made up all the layer-config types in a hurry, and we can easily make new ones, compose existing ones, or change anything at all! ### Explore a few layers + Lets continue by adding one layer: `demo.addLayer(examples.reconstructed)`
now, we should be able to navigate the (previously blank) view with the mouse, and we can watch the data load as it becomes visible (and thus, worth fetching & caching). Note also that the UI populates, with very simple (ugly?) controls to change settings, in this case only the gene by which to color can be edited. This ui took about 60 seconds to write, and I would not hesitate to throw it away. -Lets add a second layer: `demo.addLayer(examples.structureAnnotation)`
+Lets add a second layer: `demo.addLayer(examples.structureAnnotation)`
This data is the CCF annotations (the regions to which the scatterplot data is registered), and should line up with the scatterplot grid. This layer type has only a few simple options for altering the opacity of the polygons.
Lets add another layer: `demo.addLayer(examples.tissuecyte396)`
This should load up a contact-sheet style view, with 142 slices. You should note that the slices are not expected to line up with those in the other two layers (the slide-view scatterplot) - the data in each are in different coordinate systems. Perhaps obviously, the whole point of having multiple layers in one view would be to observe interesting relationships between them, and in a (non-demo) app, it would be important to allow configurations to specify mappings / transforms / etc. to get things to "line up". You should also see some double-post, "invlerp" sliders that control how the raw channels of information get mapped to visible-light color. You should be able to move the min & max for each channel, although do note that there seems to be very little data in the 3rd channel, mapped to the color blue. ### Take a picture -At the top left of the UI, you might notice a little 📸 button. This will take a low-resolution snapshot of the current view. If you'd like to be a little patient, enter the dev console again, and run `demo.requestSnapshot(10000)` which, depending on the aspect ratio of your browser window, will (slowly!) capture an ~80 million pixel image of the current screen - the main reason its slow is because, to properly serve that higher resolution, the rendering system must fetch many, many chunks of high-resolution data to render. Note that making changes to the UI during the snapshot process may cause those changes to take partial effect in the final snapshot output. This is a well understood class of bugs that are easy to address when planning to "do software correctly" - however this is a quick demo so I took a bunch of shortcuts! \ No newline at end of file + +At the top left of the UI, you might notice a little 📸 button. This will take a low-resolution snapshot of the current view. If you'd like to be a little patient, enter the dev console again, and run `demo.requestSnapshot(10000)` which, depending on the aspect ratio of your browser window, will (slowly!) capture an ~80 million pixel image of the current screen - the main reason its slow is because, to properly serve that higher resolution, the rendering system must fetch many, many chunks of high-resolution data to render. Note that making changes to the UI during the snapshot process may cause those changes to take partial effect in the final snapshot output. This is a well understood class of bugs that are easy to address when planning to "do software correctly" - however this is a quick demo so I took a bunch of shortcuts! diff --git a/apps/layers/src/app.tsx b/apps/layers/src/app.tsx index cf57847..9e033e8 100644 --- a/apps/layers/src/app.tsx +++ b/apps/layers/src/app.tsx @@ -7,38 +7,52 @@ import { ScatterplotUI } from './ui/scatterplot-ui'; import { Button } from '@czi-sds/components'; export function AppUi(props: { demo: Demo }) { - const {demo}=props; - return (
- - - - - -
) + const { demo } = props; + return ( +
+ + + + + +
+ ); } function LayerUi(props: { demo: Demo }) { - const {demo}=props; - const layer = demo.layers[demo.selectedLayer]; - if(layer){ - switch(layer.type){ - case 'annotationGrid': - return - case 'volumeGrid': - return - case 'volumeSlice': - return - case 'scatterplot': - case 'scatterplotGrid': - return - default: - return null; + const { demo } = props; + const layer = demo.layers[demo.selectedLayer]; + if (layer) { + switch (layer.type) { + case 'annotationGrid': + return ; + case 'volumeGrid': + return ; + case 'volumeSlice': + return ; + case 'scatterplot': + case 'scatterplotGrid': + return ; + default: + return null; + } } - } - return ; + return ; } diff --git a/apps/layers/src/data-renderers/annotation-renderer.ts b/apps/layers/src/data-renderers/annotation-renderer.ts index 5f9ba44..f899933 100644 --- a/apps/layers/src/data-renderers/annotation-renderer.ts +++ b/apps/layers/src/data-renderers/annotation-renderer.ts @@ -1,14 +1,14 @@ -import type REGL from "regl"; -import type { RenderCallback } from "./types"; -import { Box2D, Vec2, type box2D, type vec2, type vec4 } from "@alleninstitute/vis-geometry"; -import type { AnnotationMesh, GPUAnnotationMesh } from "src/data-sources/annotation/types"; -import type { buildLoopRenderer, buildMeshRenderer } from "./mesh-renderer"; -import type { OptionalTransform } from "src/data-sources/types"; -import { AsyncDataCache, beginLongRunningFrame, type FrameLifecycle } from "@alleninstitute/vis-scatterbrain"; -import { fetchAnnotation } from "src/data-sources/annotation/fetch-annotation"; -import { MeshFromAnnotation } from "src/data-sources/annotation/annotation-to-mesh"; -import { type Camera } from "../../../omezarr-viewer/src/camera"; -import type { AnnotationGrid } from "src/data-sources/annotation/annotation-grid"; +import type REGL from 'regl'; +import type { RenderCallback } from './types'; +import { Box2D, Vec2, type box2D, type vec2, type vec4 } from '@alleninstitute/vis-geometry'; +import type { AnnotationMesh, GPUAnnotationMesh } from 'src/data-sources/annotation/types'; +import type { buildLoopRenderer, buildMeshRenderer } from './mesh-renderer'; +import type { OptionalTransform } from 'src/data-sources/types'; +import { AsyncDataCache, beginLongRunningFrame, type FrameLifecycle } from '@alleninstitute/vis-scatterbrain'; +import { fetchAnnotation } from 'src/data-sources/annotation/fetch-annotation'; +import { MeshFromAnnotation } from 'src/data-sources/annotation/annotation-to-mesh'; +import { type Camera } from '../../../omezarr-viewer/src/camera'; +import type { AnnotationGrid } from 'src/data-sources/annotation/annotation-grid'; type SlideId = string; @@ -21,12 +21,12 @@ type SlideAnnotations = { export type LoopRenderer = ReturnType; export type MeshRenderer = ReturnType; -export type CacheContentType = { type: 'mesh', data: GPUAnnotationMesh } +export type CacheContentType = { type: 'mesh'; data: GPUAnnotationMesh }; type Settings = { regl: REGL.Regl; - loopRenderer: LoopRenderer, - meshRenderer: MeshRenderer, - stencilMeshRenderer: MeshRenderer, + loopRenderer: LoopRenderer; + meshRenderer: MeshRenderer; + stencilMeshRenderer: MeshRenderer; camera: Camera; viewport: REGL.BoundingBox; target: REGL.Framebuffer | null; @@ -42,7 +42,7 @@ type Settings = { }; function isMesh(obj: object | undefined): obj is CacheContentType { - return !!(obj && 'type' in obj && obj.type === 'mesh') + return !!(obj && 'type' in obj && obj.type === 'mesh'); } function fetchAnnotationsForSlide( item: SlideAnnotations, @@ -53,21 +53,28 @@ function fetchAnnotationsForSlide( const toCacheEntry = (m: AnnotationMesh | undefined): CacheContentType | undefined => m ? { - type: 'mesh', data: { - points: regl.buffer(m.points), - annotation: m - } - } + type: 'mesh', + data: { + points: regl.buffer(m.points), + annotation: m, + }, + } : undefined; const getMesh = () => { - return fetchAnnotation(item).then((anno) => anno ? MeshFromAnnotation(anno) : undefined).then(toCacheEntry) + return fetchAnnotation(item) + .then((anno) => (anno ? MeshFromAnnotation(anno) : undefined)) + .then(toCacheEntry); }; return { mesh: getMesh }; } type RProps = Parameters>[0]; -function renderSlideAnnotations(item: SlideAnnotations, settings: Settings, columns: Record) { +function renderSlideAnnotations( + item: SlideAnnotations, + settings: Settings, + columns: Record +) { const { camera, viewport, target, regl, loopRenderer, meshRenderer, stencilMeshRenderer } = settings; // const { view } = camera.projection === 'webImage' ? flipY(camera) : camera const { view } = camera; @@ -127,46 +134,58 @@ function renderSlideAnnotations(item: SlideAnnotations, settings: Settings, colu export type RenderSettings = { camera: Camera; - regl: REGL.Regl + regl: REGL.Regl; cache: AsyncDataCache; renderers: { - loopRenderer: LoopRenderer, - meshRenderer: MeshRenderer, - stencilMeshRenderer: MeshRenderer, - }, - callback: RenderCallback, - concurrentTasks?: number, - queueInterval?: number, - cpuLimit?: number, -} - + loopRenderer: LoopRenderer; + meshRenderer: MeshRenderer; + stencilMeshRenderer: MeshRenderer; + }; + callback: RenderCallback; + concurrentTasks?: number; + queueInterval?: number; + cpuLimit?: number; +}; export function renderAnnotationGrid( - target: REGL.Framebuffer2D | null, grid: AnnotationGrid, settings: RenderSettings): FrameLifecycle { + target: REGL.Framebuffer2D | null, + grid: AnnotationGrid, + settings: RenderSettings +): FrameLifecycle { const { dataset, annotationBaseUrl, levelFeature, stroke, fill } = grid; - const { regl, cache, camera: { view, screen }, renderers: { loopRenderer, meshRenderer, stencilMeshRenderer }, callback } = settings; + const { + regl, + cache, + camera: { view, screen }, + renderers: { loopRenderer, meshRenderer, stencilMeshRenderer }, + callback, + } = settings; let { camera, concurrentTasks, queueInterval, cpuLimit } = settings; - concurrentTasks = concurrentTasks ? Math.abs(concurrentTasks) : 5 - queueInterval = queueInterval ? Math.abs(queueInterval) : 33 - cpuLimit = cpuLimit ? Math.abs(cpuLimit) : undefined + concurrentTasks = concurrentTasks ? Math.abs(concurrentTasks) : 5; + queueInterval = queueInterval ? Math.abs(queueInterval) : 33; + cpuLimit = cpuLimit ? Math.abs(cpuLimit) : undefined; const items: SlideAnnotations[] = []; const rowSize = Math.floor(Math.sqrt(Object.keys(dataset.slides).length)); Object.keys(dataset.slides).forEach((slideId, i) => { - const gridIndex: vec2 = [i % rowSize, Math.floor(i / rowSize)] + const gridIndex: vec2 = [i % rowSize, Math.floor(i / rowSize)]; const { bounds } = dataset; - const offset = Vec2.mul(gridIndex, Box2D.size(bounds)) - const realBounds = Box2D.translate(bounds, offset) + const offset = Vec2.mul(gridIndex, Box2D.size(bounds)); + const realBounds = Box2D.translate(bounds, offset); if (Box2D.intersection(view, realBounds)) { items.push({ - annotationBaseUrl, gridFeature: slideId, levelFeature, bounds, toModelSpace: { + annotationBaseUrl, + gridFeature: slideId, + levelFeature, + bounds, + toModelSpace: { offset, - scale: [1, 1] - } - }) + scale: [1, 1], + }, + }); } - }) + }); const frame = beginLongRunningFrame( concurrentTasks, queueInterval, @@ -187,7 +206,7 @@ export function renderAnnotationGrid( width: screen[0], height: screen[1], }, - camera + camera, }, fetchAnnotationsForSlide, renderSlideAnnotations, diff --git a/apps/layers/src/data-renderers/dynamicGridSlideRenderer.ts b/apps/layers/src/data-renderers/dynamicGridSlideRenderer.ts index 8076319..c4f1e35 100644 --- a/apps/layers/src/data-renderers/dynamicGridSlideRenderer.ts +++ b/apps/layers/src/data-renderers/dynamicGridSlideRenderer.ts @@ -1,77 +1,118 @@ -import { beginLongRunningFrame, type AsyncDataCache } from "@alleninstitute/vis-scatterbrain"; -import type REGL from "regl"; -import { buildRenderer as buildScatterplotRenderer } from "../../../scatterplot/src/renderer"; -import { Box2D, Vec2, type vec2 } from "@alleninstitute/vis-geometry"; -import { fetchItem, getVisibleItemsInSlide } from "Common/loaders/scatterplot/data"; -import type { ColumnRequest, ColumnarTree } from "Common/loaders/scatterplot/scatterbrain-loader"; -import { applyOptionalTrn } from "./utils"; -import type { DynamicGrid, DynamicGridSlide } from "../data-sources/scatterplot/dynamic-grid"; -import type { RenderCallback } from "./types"; -import { type Camera } from "../../../omezarr-viewer/src/camera"; +import { beginLongRunningFrame, type AsyncDataCache } from '@alleninstitute/vis-scatterbrain'; +import type REGL from 'regl'; +import { buildRenderer as buildScatterplotRenderer } from '../../../scatterplot/src/renderer'; +import { Box2D, Vec2, type vec2 } from '@alleninstitute/vis-geometry'; +import { fetchItem, getVisibleItemsInSlide } from 'Common/loaders/scatterplot/data'; +import type { ColumnRequest, ColumnarTree } from 'Common/loaders/scatterplot/scatterbrain-loader'; +import { applyOptionalTrn } from './utils'; +import type { DynamicGrid, DynamicGridSlide } from '../data-sources/scatterplot/dynamic-grid'; +import type { RenderCallback } from './types'; +import { type Camera } from '../../../omezarr-viewer/src/camera'; type CacheContentType = { - type: 'vbo', + type: 'vbo'; data: REGL.Buffer; -} +}; -type Renderer = ReturnType +type Renderer = ReturnType; export type RenderSettings = { camera: Camera; cache: AsyncDataCache; - renderer: Renderer, - regl: REGL.Regl, - callback: RenderCallback, - concurrentTasks?: number, - queueInterval?: number, - cpuLimit?: number, -} -const cacheKey = (reqKey: string, item: ColumnarTree, settings: { colorBy: ColumnRequest }) => `${reqKey}:${item.content.name}:${settings.colorBy.name}|${settings.colorBy.type}` -export function renderSlide(target: REGL.Framebuffer2D | null, slide: DynamicGridSlide, settings: RenderSettings) { - const { cache, camera: { view, screen }, renderer, callback, regl } = settings; + renderer: Renderer; + regl: REGL.Regl; + callback: RenderCallback; + concurrentTasks?: number; + queueInterval?: number; + cpuLimit?: number; +}; +const cacheKey = (reqKey: string, item: ColumnarTree, settings: { colorBy: ColumnRequest }) => + `${reqKey}:${item.content.name}:${settings.colorBy.name}|${settings.colorBy.type}`; +export function renderSlide( + target: REGL.Framebuffer2D | null, + slide: DynamicGridSlide, + settings: RenderSettings +) { + const { + cache, + camera: { view, screen }, + renderer, + callback, + regl, + } = settings; let { camera, concurrentTasks, queueInterval, cpuLimit } = settings; - concurrentTasks = concurrentTasks ? Math.abs(concurrentTasks) : 5 - queueInterval = queueInterval ? Math.abs(queueInterval) : 33 - cpuLimit = cpuLimit ? Math.abs(cpuLimit) : undefined + concurrentTasks = concurrentTasks ? Math.abs(concurrentTasks) : 5; + queueInterval = queueInterval ? Math.abs(queueInterval) : 33; + cpuLimit = cpuLimit ? Math.abs(cpuLimit) : undefined; const { dataset, colorBy, pointSize } = slide; const unitsPerPixel = Vec2.div(Box2D.size(view), screen); - camera = { ...camera, view: applyOptionalTrn(camera.view, slide.toModelSpace, true) } + camera = { ...camera, view: applyOptionalTrn(camera.view, slide.toModelSpace, true) }; // camera = camera.projection === 'webImage' ? flipY(camera) : camera; - const items = getVisibleItemsInSlide(slide.dataset, slide.slideId, settings.camera.view, 10 * unitsPerPixel[0]) + const items = getVisibleItemsInSlide(slide.dataset, slide.slideId, settings.camera.view, 10 * unitsPerPixel[0]); // make the frame, return some junk - return beginLongRunningFrame(concurrentTasks, queueInterval, items, cache, - { view, dataset, target, colorBy, regl, pointSize }, fetchItem, renderer, callback, + return beginLongRunningFrame( + concurrentTasks, + queueInterval, + items, + cache, + { view, dataset, target, colorBy, regl, pointSize }, + fetchItem, + renderer, + callback, cacheKey, - cpuLimit); + cpuLimit + ); } -export function renderDynamicGrid(target: REGL.Framebuffer2D | null, grid: DynamicGrid, settings: RenderSettings) { - const { cache, camera: { view, screen }, renderer, callback, regl } = settings; +export function renderDynamicGrid( + target: REGL.Framebuffer2D | null, + grid: DynamicGrid, + settings: RenderSettings +) { + const { + cache, + camera: { view, screen }, + renderer, + callback, + regl, + } = settings; let { camera, concurrentTasks, queueInterval, cpuLimit } = settings; - concurrentTasks = concurrentTasks ? Math.abs(concurrentTasks) : 5 - queueInterval = queueInterval ? Math.abs(queueInterval) : 33 - cpuLimit = cpuLimit ? Math.abs(cpuLimit) : undefined - const items: ColumnarTree[] = [] + concurrentTasks = concurrentTasks ? Math.abs(concurrentTasks) : 5; + queueInterval = queueInterval ? Math.abs(queueInterval) : 33; + cpuLimit = cpuLimit ? Math.abs(cpuLimit) : undefined; + const items: ColumnarTree[] = []; const { dataset, pointSize } = grid; const unitsPerPixel = Vec2.div(Box2D.size(view), screen); const rowSize = Math.floor(Math.sqrt(Object.keys(dataset.slides).length)); - camera = { ...camera, view: applyOptionalTrn(camera.view, grid.toModelSpace, true) } + camera = { ...camera, view: applyOptionalTrn(camera.view, grid.toModelSpace, true) }; Object.keys(dataset.slides).forEach((slideId, i) => { const slide = dataset.slides[slideId]; - const gridIndex: vec2 = [i % rowSize, Math.floor(i / rowSize)] + const gridIndex: vec2 = [i % rowSize, Math.floor(i / rowSize)]; const { bounds } = dataset; - const offset = Vec2.mul(gridIndex, Box2D.size(bounds)) - const realBounds = Box2D.translate(bounds, offset) + const offset = Vec2.mul(gridIndex, Box2D.size(bounds)); + const realBounds = Box2D.translate(bounds, offset); if (Box2D.intersection(view, realBounds)) { - items.push(...getVisibleItemsInSlide(grid.dataset, slide.id, settings.camera.view, 10 * unitsPerPixel[0]).map(t => ({ ...t, offset }))) + items.push( + ...getVisibleItemsInSlide(grid.dataset, slide.id, settings.camera.view, 10 * unitsPerPixel[0]).map( + (t) => ({ ...t, offset }) + ) + ); } - }) - const { colorBy } = grid + }); + const { colorBy } = grid; // make the frame, return some junk - return beginLongRunningFrame(concurrentTasks, queueInterval, items, cache, - { view, dataset, target, colorBy, regl, pointSize }, fetchItem, renderer, callback, + return beginLongRunningFrame( + concurrentTasks, + queueInterval, + items, + cache, + { view, dataset, target, colorBy, regl, pointSize }, + fetchItem, + renderer, + callback, cacheKey, - cpuLimit); -} \ No newline at end of file + cpuLimit + ); +} diff --git a/apps/layers/src/data-renderers/lineRenderer.ts b/apps/layers/src/data-renderers/lineRenderer.ts index 50a3bf5..49fd6d7 100644 --- a/apps/layers/src/data-renderers/lineRenderer.ts +++ b/apps/layers/src/data-renderers/lineRenderer.ts @@ -1,18 +1,24 @@ -import type { box2D, vec2, vec4 } from '@alleninstitute/vis-geometry' -import REGL, { type AttributeConfig } from 'regl' -import type { ColumnData } from 'Common/loaders/scatterplot/scatterbrain-loader' -import type { TaggedFloat32Array } from 'Common/typed-array' +import type { box2D, vec2, vec4 } from '@alleninstitute/vis-geometry'; +import REGL, { type AttributeConfig } from 'regl'; +import type { ColumnData } from 'Common/loaders/scatterplot/scatterbrain-loader'; +import type { TaggedFloat32Array } from 'Common/typed-array'; -type Attrs = { pos: REGL.AttributeConfig } -type Unis = { view: vec4, color: vec4 } -type Props = { target: REGL.Framebuffer2D | null, view: vec4, color: vec4, pos: REGL.AttributeConfig | REGL.BufferData, count: number } +type Attrs = { pos: REGL.AttributeConfig }; +type Unis = { view: vec4; color: vec4 }; +type Props = { + target: REGL.Framebuffer2D | null; + view: vec4; + color: vec4; + pos: REGL.AttributeConfig | REGL.BufferData; + count: number; +}; const frag = ` precision highp float; uniform vec4 color; void main(){ gl_FragColor = color; -}` +}`; const vert = ` precision highp float; attribute vec2 pos; @@ -23,7 +29,7 @@ void main(){ vec2 unit = (pos-view.xy)/size; vec2 clip = 2.0*(unit-0.5); gl_Position = vec4(clip.x,clip.y,0,1); -}` +}`; export function buildLineRenderer(regl: REGL.Regl) { const cmd = regl({ frag, @@ -39,12 +45,12 @@ export function buildLineRenderer(regl: REGL.Regl) { enable: false, }, depth: { - enable: false + enable: false, }, count: regl.prop('count'), primitive: 'line strip', - framebuffer: regl.prop('target') - }) + framebuffer: regl.prop('target'), + }); return (points: Float32Array, color: vec4, view: box2D, target: REGL.Framebuffer2D | null) => { const { minCorner, maxCorner } = view; cmd({ @@ -52,24 +58,28 @@ export function buildLineRenderer(regl: REGL.Regl) { color, view: [...minCorner, ...maxCorner], pos: points, - count: points.length / 2 - }) - } + count: points.length / 2, + }); + }; } export type Path = { id: number; color: vec4; bounds: box2D; points: Array; -} +}; export function buildPathRenderer(regl: REGL.Regl) { const cmd = buildLineRenderer(regl); - return (item: Path, settings: { view: box2D, target: REGL.Framebuffer2D | null }, tasks: Record) => { - const pos = tasks['position'] - const { view, target } = settings + return ( + item: Path, + settings: { view: box2D; target: REGL.Framebuffer2D | null }, + tasks: Record + ) => { + const pos = tasks['position']; + const { view, target } = settings; if (pos && 'type' in pos && pos.type === 'float') { cmd(pos.data, item.color, view, target); } - } -} \ No newline at end of file + }; +} diff --git a/apps/layers/src/data-renderers/mesh-renderer.ts b/apps/layers/src/data-renderers/mesh-renderer.ts index 1a4440c..04ab333 100644 --- a/apps/layers/src/data-renderers/mesh-renderer.ts +++ b/apps/layers/src/data-renderers/mesh-renderer.ts @@ -95,39 +95,39 @@ export function buildMeshRenderer(regl: REGL.Regl, mode: 'draw-stencil' | 'use-s }, ...(mode === 'draw-stencil' ? { - colorMask: [false, false, false, false], - stencil: { - enable: true, - mask: -1, - func: { - cmp: 'always', - mask: -1, - ref: 0, - }, - op: { - fail: 'invert', // cmp is always - thus never fails... - zfail: 'invert', - zpass: 'invert', - }, - }, - } + colorMask: [false, false, false, false], + stencil: { + enable: true, + mask: -1, + func: { + cmp: 'always', + mask: -1, + ref: 0, + }, + op: { + fail: 'invert', // cmp is always - thus never fails... + zfail: 'invert', + zpass: 'invert', + }, + }, + } : { - // use-stencil - stencil: { - enable: true, - mask: 0, - func: { - cmp: 'lequal', - mask: -1, - ref: 1, - }, - op: { - fail: 'keep', - zfail: 'keep', - zpass: 'keep', - }, - }, - }), + // use-stencil + stencil: { + enable: true, + mask: 0, + func: { + cmp: 'lequal', + mask: -1, + ref: 1, + }, + op: { + fail: 'keep', + zfail: 'keep', + zpass: 'keep', + }, + }, + }), }); return ( ...batches: { diff --git a/apps/layers/src/data-renderers/simpleAnnotationRenderer.ts b/apps/layers/src/data-renderers/simpleAnnotationRenderer.ts index 4ebdc6e..f389d74 100644 --- a/apps/layers/src/data-renderers/simpleAnnotationRenderer.ts +++ b/apps/layers/src/data-renderers/simpleAnnotationRenderer.ts @@ -1,40 +1,40 @@ - -import type REGL from "regl"; -import { beginLongRunningFrame, type AsyncDataCache } from "@alleninstitute/vis-scatterbrain"; -import type { RenderCallback } from "./types"; -import type { ColumnData } from "Common/loaders/scatterplot/scatterbrain-loader"; -import { Box2D, type box2D } from "@alleninstitute/vis-geometry"; -import type { Path, buildPathRenderer } from "./lineRenderer"; -import { flatten } from "lodash"; -import type { OptionalTransform } from "../data-sources/types"; -import type { Camera } from "../../../omezarr-viewer/src/camera"; +import type REGL from 'regl'; +import { beginLongRunningFrame, type AsyncDataCache } from '@alleninstitute/vis-scatterbrain'; +import type { RenderCallback } from './types'; +import type { ColumnData } from 'Common/loaders/scatterplot/scatterbrain-loader'; +import { Box2D, type box2D } from '@alleninstitute/vis-geometry'; +import type { Path, buildPathRenderer } from './lineRenderer'; +import { flatten } from 'lodash'; +import type { OptionalTransform } from '../data-sources/types'; +import type { Camera } from '../../../omezarr-viewer/src/camera'; type Renderer = ReturnType; export type SimpleAnnotation = { - paths: Array -} & OptionalTransform + paths: Array; +} & OptionalTransform; export type RenderSettings = { camera: Camera; cache: AsyncDataCache; - renderer: Renderer, - callback: RenderCallback, - regl: REGL.Regl, - concurrentTasks?: number, - queueInterval?: number, - cpuLimit?: number, -} + renderer: Renderer; + callback: RenderCallback; + regl: REGL.Regl; + concurrentTasks?: number; + queueInterval?: number; + cpuLimit?: number; +}; function getVisibleStrokes(camera: Camera, layer: SimpleAnnotation) { - return layer.paths.filter((p) => !!Box2D.intersection(camera.view, p.bounds)) + return layer.paths.filter((p) => !!Box2D.intersection(camera.view, p.bounds)); } function requestsForPath(p: Path) { return { - 'position': () => Promise.resolve({ - type: 'float', - data: new Float32Array(flatten(p.points)) - }) - } + position: () => + Promise.resolve({ + type: 'float', + data: new Float32Array(flatten(p.points)), + }), + }; } export function renderAnnotationLayer( target: REGL.Framebuffer2D | null, @@ -42,17 +42,19 @@ export function renderAnnotationLayer( settings: RenderSettings ) { const { camera, cache, renderer, callback } = settings; - const items = getVisibleStrokes(camera, layer) - return beginLongRunningFrame( - 5, 33, - items, cache, + const items = getVisibleStrokes(camera, layer); + return beginLongRunningFrame( + 5, + 33, + items, + cache, { view: camera.view, - target + target, }, requestsForPath, renderer, callback, (rq: string, path: Path) => `${rq}_${path.id}_${path.points.length}` - ) -} \ No newline at end of file + ); +} diff --git a/apps/layers/src/data-renderers/types.ts b/apps/layers/src/data-renderers/types.ts index 7bec7f8..2f6fc4f 100644 --- a/apps/layers/src/data-renderers/types.ts +++ b/apps/layers/src/data-renderers/types.ts @@ -1,44 +1,36 @@ - // generic rendering of renderable things... -import type { Interval, box2D, vec2, vec4 } from "@alleninstitute/vis-geometry"; -import type { NormalStatus } from "@alleninstitute/vis-scatterbrain"; -import type { ZarrDataset } from "Common/loaders/ome-zarr/zarr-data"; -import type { SlideViewDataset, ColumnRequest } from "Common/loaders/scatterplot/scatterbrain-loader"; -import type { AxisAlignedPlane } from "../../../omezarr-viewer/src/slice-renderer"; - - - +import type { Interval, box2D, vec2, vec4 } from '@alleninstitute/vis-geometry'; +import type { NormalStatus } from '@alleninstitute/vis-scatterbrain'; +import type { ZarrDataset } from 'Common/loaders/ome-zarr/zarr-data'; +import type { SlideViewDataset, ColumnRequest } from 'Common/loaders/scatterplot/scatterbrain-loader'; +import type { AxisAlignedPlane } from '../../../omezarr-viewer/src/slice-renderer'; type ChannelSettings = { gamut: Interval; index: number; -} +}; export type ColorMapping = { R: ChannelSettings; G: ChannelSettings; B: ChannelSettings; -} - - - +}; type Path = { points: vec2[]; bounds: box2D; color: vec4; -} +}; type Drawing = { paths: readonly Path[]; // todo more later... -} +}; export type AnnotationLayer = { - type: "AnnotationLayer" + type: 'AnnotationLayer'; dimensions: 2; drawing: Drawing; -} +}; export type TwoDimensional = { - dimensions: 2 + dimensions: 2; }; -export type RenderCallback = (event: { status: NormalStatus } | { status: 'error', error: unknown }) => void; - +export type RenderCallback = (event: { status: NormalStatus } | { status: 'error'; error: unknown }) => void; diff --git a/apps/layers/src/data-renderers/utils.ts b/apps/layers/src/data-renderers/utils.ts index 51b73aa..45dbe4d 100644 --- a/apps/layers/src/data-renderers/utils.ts +++ b/apps/layers/src/data-renderers/utils.ts @@ -1,6 +1,6 @@ -import { Box2D, Vec2, type box2D, type vec2 } from "@alleninstitute/vis-geometry"; +import { Box2D, Vec2, type box2D, type vec2 } from '@alleninstitute/vis-geometry'; -export function applyOptionalTrn(box:box2D, trn:undefined | {offset:vec2}, inv:boolean=false){ +export function applyOptionalTrn(box: box2D, trn: undefined | { offset: vec2 }, inv: boolean = false) { // todo scale... - return trn ? Box2D.translate(box,Vec2.scale(trn.offset, inv?-1:1)) : box; -} \ No newline at end of file + return trn ? Box2D.translate(box, Vec2.scale(trn.offset, inv ? -1 : 1)) : box; +} diff --git a/apps/layers/src/data-renderers/volumeSliceRenderer.ts b/apps/layers/src/data-renderers/volumeSliceRenderer.ts index b30d41c..f234059 100644 --- a/apps/layers/src/data-renderers/volumeSliceRenderer.ts +++ b/apps/layers/src/data-renderers/volumeSliceRenderer.ts @@ -1,33 +1,53 @@ -import type REGL from "regl"; -import { beginLongRunningFrame, type AsyncDataCache } from "@alleninstitute/vis-scatterbrain"; -import type { RenderCallback } from "./types"; -import { cacheKeyFactory, getVisibleTiles, requestsForTile, type AxisAlignedPlane, type buildVersaRenderer, type VoxelSliceRenderSettings, type VoxelTile } from "../../../omezarr-viewer/src/versa-renderer"; -import { pickBestScale, sizeInUnits, sizeInVoxels, sliceDimensionForPlane, uvForPlane } from "Common/loaders/ome-zarr/zarr-data"; -import { applyOptionalTrn } from "./utils"; -import { Box2D, Vec2, type vec2 } from "@alleninstitute/vis-geometry"; -import type { AxisAlignedZarrSlice } from "../data-sources/ome-zarr/planar-slice"; -import type { AxisAlignedZarrSliceGrid } from "../data-sources/ome-zarr/slice-grid"; -import { type Camera } from "../../../omezarr-viewer/src/camera"; +import type REGL from 'regl'; +import { beginLongRunningFrame, type AsyncDataCache } from '@alleninstitute/vis-scatterbrain'; +import type { RenderCallback } from './types'; +import { + cacheKeyFactory, + getVisibleTiles, + requestsForTile, + type AxisAlignedPlane, + type buildVersaRenderer, + type VoxelSliceRenderSettings, + type VoxelTile, +} from '../../../omezarr-viewer/src/versa-renderer'; +import { + pickBestScale, + sizeInUnits, + sizeInVoxels, + sliceDimensionForPlane, + uvForPlane, +} from 'Common/loaders/ome-zarr/zarr-data'; +import { applyOptionalTrn } from './utils'; +import { Box2D, Vec2, type vec2 } from '@alleninstitute/vis-geometry'; +import type { AxisAlignedZarrSlice } from '../data-sources/ome-zarr/planar-slice'; +import type { AxisAlignedZarrSliceGrid } from '../data-sources/ome-zarr/slice-grid'; +import { type Camera } from '../../../omezarr-viewer/src/camera'; type Renderer = ReturnType; -type CacheContentType = { type: 'texture2D', data: REGL.Texture2D }; +type CacheContentType = { type: 'texture2D'; data: REGL.Texture2D }; export type RenderSettings = { camera: Camera; cache: AsyncDataCache; - renderer: Renderer, - callback: RenderCallback, - regl: REGL.Regl, - concurrentTasks?: number, - queueInterval?: number, - cpuLimit?: number, -} - + renderer: Renderer; + callback: RenderCallback; + regl: REGL.Regl; + concurrentTasks?: number; + queueInterval?: number; + cpuLimit?: number; +}; -function preferCachedEntries(grid: AxisAlignedZarrSliceGrid, settings: VoxelSliceRenderSettings, offset: vec2, cache: AsyncDataCache, camera: Camera, location: { - plane: AxisAlignedPlane, - planeIndex: number -}) { +function preferCachedEntries( + grid: AxisAlignedZarrSliceGrid, + settings: VoxelSliceRenderSettings, + offset: vec2, + cache: AsyncDataCache, + camera: Camera, + location: { + plane: AxisAlignedPlane; + planeIndex: number; + } +) { const { plane, planeIndex } = location; const idealTiles = getVisibleTiles(camera, plane, planeIndex, grid.dataset, offset); const fakes: VoxelTile[] = []; @@ -35,37 +55,46 @@ function preferCachedEntries(grid: AxisAl for (const tile of idealTiles.tiles) { const isCached = (t: VoxelTile) => { const requests = requestsForTile(t, settings); - const cacheKeys = Object.keys(requests).map(rq => cacheKeyFactory(rq, t, settings)) - return cache.areKeysAllCached(cacheKeys) - } + const cacheKeys = Object.keys(requests).map((rq) => cacheKeyFactory(rq, t, settings)); + return cache.areKeysAllCached(cacheKeys); + }; if (!isCached(tile)) { // search a different layer for a stand-in in this area... feels pretty slow... // for now just stick with the most low-res layer... - const lowerLOD = getVisibleTiles({ ...camera, view: tile.realBounds, screen: [1, 1] }, plane, planeIndex, grid.dataset, offset); - fakes.push(...lowerLOD.tiles) + const lowerLOD = getVisibleTiles( + { ...camera, view: tile.realBounds, screen: [1, 1] }, + plane, + planeIndex, + grid.dataset, + offset + ); + fakes.push(...lowerLOD.tiles); } } - return { fake: fakes, ideal: idealTiles } + return { fake: fakes, ideal: idealTiles }; } // todo: write a helper function that makes much smarter descisions about // what (already cached) tiles to use for this frame, given the view, the dataset, // and the cache (and the cache-key-factory...) -export function renderGrid(target: REGL.Framebuffer2D | null, grid: AxisAlignedZarrSliceGrid, settings: RenderSettings) { +export function renderGrid( + target: REGL.Framebuffer2D | null, + grid: AxisAlignedZarrSliceGrid, + settings: RenderSettings +) { const { cache, renderer, callback, regl } = settings; let { camera, concurrentTasks, queueInterval, cpuLimit } = settings; - const { dataset, gamut, plane, slices } = grid + const { dataset, gamut, plane, slices } = grid; const { axes } = dataset.multiscales[0]; - concurrentTasks = concurrentTasks ? Math.abs(concurrentTasks) : 5 - queueInterval = queueInterval ? Math.abs(queueInterval) : 33 - cpuLimit = cpuLimit ? Math.abs(cpuLimit) : undefined + concurrentTasks = concurrentTasks ? Math.abs(concurrentTasks) : 5; + queueInterval = queueInterval ? Math.abs(queueInterval) : 33; + cpuLimit = cpuLimit ? Math.abs(cpuLimit) : undefined; const rowSize = Math.floor(Math.sqrt(slices)); const allItems: VoxelTile[] = []; - const smokeAndMirrors: VoxelTile[] = [] + const smokeAndMirrors: VoxelTile[] = []; const best = pickBestScale(dataset, uvForPlane(plane), camera.view, camera.screen); - const renderSettings = - { + const renderSettings = { dataset, gamut, regl, @@ -73,61 +102,75 @@ export function renderGrid(target: REGL.F target, view: camera.view, viewport: { - x: 0, y: 0, + x: 0, + y: 0, width: camera.screen[0], - height: camera.screen[1] + height: camera.screen[1], }, }; for (let i = 0; i < slices; i++) { - const gridIndex: vec2 = [i % rowSize, Math.floor(i / rowSize)] + const gridIndex: vec2 = [i % rowSize, Math.floor(i / rowSize)]; let param = i / slices; - const slice: AxisAlignedZarrSlice = { ...grid, type: 'AxisAlignedZarrSlice', planeParameter: param } - const curCam = { ...camera, view: applyOptionalTrn(camera.view, slice.toModelSpace, true) } + const slice: AxisAlignedZarrSlice = { ...grid, type: 'AxisAlignedZarrSlice', planeParameter: param }; + const curCam = { ...camera, view: applyOptionalTrn(camera.view, slice.toModelSpace, true) }; const dim = sizeInVoxels(sliceDimensionForPlane(plane), axes, best); const realSize = sizeInUnits(plane, axes, best)!; - const offset = Vec2.mul(gridIndex, realSize) - // the bounds of this slice might not even be in view! + const offset = Vec2.mul(gridIndex, realSize); + // the bounds of this slice might not even be in view! // if we did this a bit different... we could know from the index, without having to conditionally test... TODO if (Box2D.intersection(curCam.view, Box2D.translate(Box2D.create([0, 0], realSize), offset))) { - const planeIndex = Math.round(param * (dim ?? 0)) + const planeIndex = Math.round(param * (dim ?? 0)); const { fake, ideal } = preferCachedEntries(grid, renderSettings, offset, cache, curCam, { plane, - planeIndex + planeIndex, }); // get all the items for the lowest level of detail: - smokeAndMirrors.push(...fake) - allItems.push(...ideal.tiles) - + smokeAndMirrors.push(...fake); + allItems.push(...ideal.tiles); } - } - const frame = beginLongRunningFrame(concurrentTasks, queueInterval, + const frame = beginLongRunningFrame( + concurrentTasks, + queueInterval, [...smokeAndMirrors, ...allItems], cache, - renderSettings, requestsForTile, renderer, callback, cacheKeyFactory, cpuLimit) + renderSettings, + requestsForTile, + renderer, + callback, + cacheKeyFactory, + cpuLimit + ); return frame; } -export function renderSlice(target: REGL.Framebuffer2D | null, slice: AxisAlignedZarrSlice, settings: RenderSettings) { +export function renderSlice( + target: REGL.Framebuffer2D | null, + slice: AxisAlignedZarrSlice, + settings: RenderSettings +) { const { cache, renderer, callback, regl } = settings; let { camera, concurrentTasks, queueInterval, cpuLimit } = settings; - const { dataset, planeParameter, gamut, plane } = slice - concurrentTasks = concurrentTasks ? Math.abs(concurrentTasks) : 5 - queueInterval = queueInterval ? Math.abs(queueInterval) : 33 - cpuLimit = cpuLimit ? Math.abs(cpuLimit) : undefined + const { dataset, planeParameter, gamut, plane } = slice; + concurrentTasks = concurrentTasks ? Math.abs(concurrentTasks) : 5; + queueInterval = queueInterval ? Math.abs(queueInterval) : 33; + cpuLimit = cpuLimit ? Math.abs(cpuLimit) : undefined; const desiredResolution = camera.screen; // convert planeParameter to planeIndex - which requires knowing the bounds of the appropriate dimension - camera = { ...camera, view: applyOptionalTrn(camera.view, slice.toModelSpace, true) } + camera = { ...camera, view: applyOptionalTrn(camera.view, slice.toModelSpace, true) }; const best = pickBestScale(dataset, uvForPlane(plane), camera.view, desiredResolution); const axes = dataset.multiscales[0].axes; const dim = sizeInVoxels(sliceDimensionForPlane(plane), axes, best); - const planeIndex = Math.round(planeParameter * (dim ?? 0)) + const planeIndex = Math.round(planeParameter * (dim ?? 0)); const items = getVisibleTiles({ ...camera, screen: desiredResolution }, plane, planeIndex, dataset); - const frame = beginLongRunningFrame(concurrentTasks, queueInterval, - items.tiles, cache, + const frame = beginLongRunningFrame( + concurrentTasks, + queueInterval, + items.tiles, + cache, { dataset, gamut, @@ -136,10 +179,17 @@ export function renderSlice(target: REGL. target, view: items.view, viewport: { - x: 0, y: 0, + x: 0, + y: 0, width: camera.screen[0], - height: camera.screen[1] + height: camera.screen[1], }, - }, requestsForTile, renderer, callback, cacheKeyFactory, cpuLimit); + }, + requestsForTile, + renderer, + callback, + cacheKeyFactory, + cpuLimit + ); return frame; -} \ No newline at end of file +} diff --git a/apps/layers/src/data-sources/annotation/annotation-codec.ts b/apps/layers/src/data-sources/annotation/annotation-codec.ts index ca73315..fd04f57 100644 --- a/apps/layers/src/data-sources/annotation/annotation-codec.ts +++ b/apps/layers/src/data-sources/annotation/annotation-codec.ts @@ -1,4 +1,4 @@ -import type { AnnotationCodec } from "./annotation-schema-type"; +import type { AnnotationCodec } from './annotation-schema-type'; import { parseSchema, compileSchema } from 'kiwi-schema'; export const AnnotationSchema = ` @@ -41,4 +41,4 @@ export function getAnnotationCodec() { } } return codec; -} \ No newline at end of file +} diff --git a/apps/layers/src/data-sources/annotation/annotation-grid.ts b/apps/layers/src/data-sources/annotation/annotation-grid.ts index 2ee8d95..1bfb1fb 100644 --- a/apps/layers/src/data-sources/annotation/annotation-grid.ts +++ b/apps/layers/src/data-sources/annotation/annotation-grid.ts @@ -1,5 +1,5 @@ -import type { vec4 } from "@alleninstitute/vis-geometry"; -import type { SlideViewDataset } from "Common/loaders/scatterplot/scatterbrain-loader"; +import type { vec4 } from '@alleninstitute/vis-geometry'; +import type { SlideViewDataset } from 'Common/loaders/scatterplot/scatterbrain-loader'; export type AnnotationGridConfig = { type: 'AnnotationGridConfig'; @@ -7,26 +7,26 @@ export type AnnotationGridConfig = { annotationUrl: string; levelFeature: string; stroke: { - overrideColor?: vec4, - opacity: number, + overrideColor?: vec4; + opacity: number; }; fill: { - overrideColor?: vec4, - opacity: number + overrideColor?: vec4; + opacity: number; }; -} +}; export type AnnotationGrid = { - type: 'AnnotationGrid', + type: 'AnnotationGrid'; dataset: SlideViewDataset; annotationBaseUrl: string; levelFeature: string; stroke: { - overrideColor?: vec4, - opacity: number, - width: number, - }, + overrideColor?: vec4; + opacity: number; + width: number; + }; fill: { - overrideColor?: vec4, - opacity: number - } -} \ No newline at end of file + overrideColor?: vec4; + opacity: number; + }; +}; diff --git a/apps/layers/src/data-sources/annotation/annotation-to-mesh.ts b/apps/layers/src/data-sources/annotation/annotation-to-mesh.ts index bcb8e2a..49280c2 100644 --- a/apps/layers/src/data-sources/annotation/annotation-to-mesh.ts +++ b/apps/layers/src/data-sources/annotation/annotation-to-mesh.ts @@ -6,27 +6,28 @@ function groupLoops(path: Path) { // collect each closed polygon from the path - because path commands are very flexible, // there could be multiple overlapping polygons in a single path! const { commands } = path; - const closed = commands?.reduce( - (loops: PathCommand[][], command) => { - const curLoop = loops[loops.length - 1]; - switch (command.type) { - case 'ClosePolygon': - curLoop.push(command); - // start a new loop - loops.push([]); - break; - case 'LineTo': - case 'MoveTo': - case 'CurveTo': - curLoop.push(command); - break; - default: - break; - } - return loops; - }, - [[]] as PathCommand[][] - ) ?? [] + const closed = + commands?.reduce( + (loops: PathCommand[][], command) => { + const curLoop = loops[loops.length - 1]; + switch (command.type) { + case 'ClosePolygon': + curLoop.push(command); + // start a new loop + loops.push([]); + break; + case 'LineTo': + case 'MoveTo': + case 'CurveTo': + curLoop.push(command); + break; + default: + break; + } + return loops; + }, + [[]] as PathCommand[][] + ) ?? []; return closed.filter((loop) => loop.length > 0); } // helper function for computing a bounding box of a bunch of uncertain stuff in a reasonably performant way @@ -71,17 +72,16 @@ function closedPolygon(loop: PathCommand[]) { default: } return acc; - }, initialState) + }, initialState); } function onlyDefined(collection: ReadonlyArray): ReadonlyArray { return collection.reduce((defined, cur) => { - return cur !== undefined ? [...defined, cur] : defined + return cur !== undefined ? [...defined, cur] : defined; }, [] as ReadonlyArray); } // intersection stuff: - type line = { a: vec2; b: vec2 }; /** @@ -175,11 +175,10 @@ export function findFirstHit(annotation: AnnotationMesh, p: vec2): AnnotationPol return undefined; } - - export function MeshFromAnnotation(annotation: Annotation): AnnotationMesh | undefined { const groups = - annotation.closedPolygons?.map((path) => ({ path, loops: onlyDefined(groupLoops(path).map(closedPolygon)) })) ?? []; + annotation.closedPolygons?.map((path) => ({ path, loops: onlyDefined(groupLoops(path).map(closedPolygon)) })) ?? + []; if (groups.length < 1) { return { @@ -210,7 +209,7 @@ export function MeshFromAnnotation(annotation: Annotation): AnnotationMesh | und if (group.loops.length < 1) continue; for (const loop of group.loops) { - if (!loop) continue + if (!loop) continue; const closedLoop: ClosedLoop = { start: outIndex / 2, @@ -229,9 +228,11 @@ export function MeshFromAnnotation(annotation: Annotation): AnnotationMesh | und }); } - return totalBounds === undefined ? undefined : { - bounds: totalBounds, - closedPolygons, - points, - }; + return totalBounds === undefined + ? undefined + : { + bounds: totalBounds, + closedPolygons, + points, + }; } diff --git a/apps/layers/src/data-sources/annotation/fetch-annotation.ts b/apps/layers/src/data-sources/annotation/fetch-annotation.ts index eae8fdc..040a773 100644 --- a/apps/layers/src/data-sources/annotation/fetch-annotation.ts +++ b/apps/layers/src/data-sources/annotation/fetch-annotation.ts @@ -1,4 +1,4 @@ -import { getAnnotationCodec } from "./annotation-codec"; +import { getAnnotationCodec } from './annotation-codec'; export async function fetchAnnotation(payload: { annotationBaseUrl: string; @@ -28,4 +28,4 @@ export async function fetchAnnotation(payload: { /* empty */ } return undefined; -} \ No newline at end of file +} diff --git a/apps/layers/src/data-sources/annotation/types.ts b/apps/layers/src/data-sources/annotation/types.ts index ff05454..79dd954 100644 --- a/apps/layers/src/data-sources/annotation/types.ts +++ b/apps/layers/src/data-sources/annotation/types.ts @@ -1,5 +1,5 @@ -import type { vec4, box2D } from "@alleninstitute/vis-geometry"; -import type REGL from "regl"; +import type { vec4, box2D } from '@alleninstitute/vis-geometry'; +import type REGL from 'regl'; export type ClosedLoop = { start: number; diff --git a/apps/layers/src/data-sources/ome-zarr/planar-slice.ts b/apps/layers/src/data-sources/ome-zarr/planar-slice.ts index b3c9d83..4f44565 100644 --- a/apps/layers/src/data-sources/ome-zarr/planar-slice.ts +++ b/apps/layers/src/data-sources/ome-zarr/planar-slice.ts @@ -1,38 +1,38 @@ -import { load, type ZarrDataset } from "Common/loaders/ome-zarr/zarr-data"; -import type { AxisAlignedPlane } from "../../../../omezarr-viewer/src/versa-renderer"; -import type { ColorMapping } from "../../data-renderers/types"; -import type { OptionalTransform, Simple2DTransform } from "../types"; +import { load, type ZarrDataset } from 'Common/loaders/ome-zarr/zarr-data'; +import type { AxisAlignedPlane } from '../../../../omezarr-viewer/src/versa-renderer'; +import type { ColorMapping } from '../../data-renderers/types'; +import type { OptionalTransform, Simple2DTransform } from '../types'; export type ZarrSliceConfig = { - type: 'zarrSliceConfig', + type: 'zarrSliceConfig'; url: string; plane: AxisAlignedPlane; planeParameter: number; // [0:1] eg. if if plane is 'xy' and parameter is 0.5, then we want the slice from the middle of the z-axis gamut: ColorMapping; rotation?: number; trn?: Simple2DTransform | undefined; -} +}; export type AxisAlignedZarrSlice = { - type: 'AxisAlignedZarrSlice' + type: 'AxisAlignedZarrSlice'; dataset: ZarrDataset; plane: AxisAlignedPlane; planeParameter: number; gamut: ColorMapping; rotation: number; -} & OptionalTransform +} & OptionalTransform; function assembleZarrSlice(config: ZarrSliceConfig, dataset: ZarrDataset): AxisAlignedZarrSlice { - const { rotation, trn } = config + const { rotation, trn } = config; return { ...config, type: 'AxisAlignedZarrSlice', dataset, toModelSpace: trn, - rotation: rotation ?? 0 - } + rotation: rotation ?? 0, + }; } export function createZarrSlice(config: ZarrSliceConfig): Promise { const { url } = config; return load(url).then((dataset) => { - return assembleZarrSlice(config, dataset) - }) + return assembleZarrSlice(config, dataset); + }); } diff --git a/apps/layers/src/data-sources/ome-zarr/slice-grid.ts b/apps/layers/src/data-sources/ome-zarr/slice-grid.ts index 588cedc..cca49c9 100644 --- a/apps/layers/src/data-sources/ome-zarr/slice-grid.ts +++ b/apps/layers/src/data-sources/ome-zarr/slice-grid.ts @@ -1,40 +1,39 @@ -import { load, type ZarrDataset } from "Common/loaders/ome-zarr/zarr-data"; -import type { AxisAlignedPlane } from "../../../../omezarr-viewer/src/versa-renderer"; -import type { ColorMapping } from "../../data-renderers/types"; -import type { OptionalTransform, Simple2DTransform } from "../types"; - +import { load, type ZarrDataset } from 'Common/loaders/ome-zarr/zarr-data'; +import type { AxisAlignedPlane } from '../../../../omezarr-viewer/src/versa-renderer'; +import type { ColorMapping } from '../../data-renderers/types'; +import type { OptionalTransform, Simple2DTransform } from '../types'; export type ZarrSliceGridConfig = { - type: 'ZarrSliceGridConfig', + type: 'ZarrSliceGridConfig'; url: string; plane: AxisAlignedPlane; slices: number; // divide this volume into this many slices, and arrange them in a grid. gamut: ColorMapping; rotation?: number; trn?: Simple2DTransform | undefined; -} +}; export type AxisAlignedZarrSliceGrid = { - type: 'AxisAlignedZarrSliceGrid' + type: 'AxisAlignedZarrSliceGrid'; dataset: ZarrDataset; plane: AxisAlignedPlane; slices: number; gamut: ColorMapping; rotation: number; -} & OptionalTransform +} & OptionalTransform; function assembleZarrSliceGrid(config: ZarrSliceGridConfig, dataset: ZarrDataset): AxisAlignedZarrSliceGrid { - const { rotation, trn } = config + const { rotation, trn } = config; return { ...config, type: 'AxisAlignedZarrSliceGrid', dataset, toModelSpace: trn, - rotation: rotation ?? 0 - } + rotation: rotation ?? 0, + }; } export function createZarrSliceGrid(config: ZarrSliceGridConfig): Promise { const { url } = config; return load(url).then((dataset) => { - return assembleZarrSliceGrid(config, dataset) - }) + return assembleZarrSliceGrid(config, dataset); + }); } diff --git a/apps/layers/src/data-sources/scatterplot/dynamic-grid.ts b/apps/layers/src/data-sources/scatterplot/dynamic-grid.ts index 1d2e5da..be7ba2c 100644 --- a/apps/layers/src/data-sources/scatterplot/dynamic-grid.ts +++ b/apps/layers/src/data-sources/scatterplot/dynamic-grid.ts @@ -1,41 +1,45 @@ -import { isSlideViewData, loadDataset, loadScatterbrainJson, type ColumnRequest, type ColumnarMetadata, type SlideViewDataset } from "Common/loaders/scatterplot/scatterbrain-loader"; -import type { OptionalTransform, Simple2DTransform } from "../types"; +import { + isSlideViewData, + loadDataset, + loadScatterbrainJson, + type ColumnRequest, + type ColumnarMetadata, + type SlideViewDataset, +} from 'Common/loaders/scatterplot/scatterbrain-loader'; +import type { OptionalTransform, Simple2DTransform } from '../types'; export type ScatterplotGridConfig = { type: 'ScatterPlotGridConfig'; colorBy: ColumnRequest; url: string; trn?: Simple2DTransform | undefined; -} +}; export type ScatterPlotGridSlideConfig = { type: 'ScatterPlotGridSlideConfig'; slideId: string; colorBy: ColumnRequest; url: string; trn?: Simple2DTransform | undefined; -} +}; export type DynamicGridSlide = { - type: 'DynamicGridSlide' + type: 'DynamicGridSlide'; dataset: SlideViewDataset; slideId: string; colorBy: ColumnRequest; pointSize: number; } & OptionalTransform; - export type DynamicGrid = { - type: 'DynamicGrid' + type: 'DynamicGrid'; dataset: SlideViewDataset; colorBy: ColumnRequest; pointSize: number; } & OptionalTransform; - - // create the real deal from the config function assembleSlideConfig(config: ScatterPlotGridSlideConfig, dataset: SlideViewDataset): DynamicGridSlide { - const { colorBy, slideId, trn } = config + const { colorBy, slideId, trn } = config; return { type: 'DynamicGridSlide', colorBy, @@ -43,36 +47,36 @@ function assembleSlideConfig(config: ScatterPlotGridSlideConfig, dataset: SlideV slideId, pointSize: 4, toModelSpace: trn, - } + }; } -export function createSlideDataset(config: ScatterPlotGridSlideConfig,): Promise { - const { url } = config +export function createSlideDataset(config: ScatterPlotGridSlideConfig): Promise { + const { url } = config; return loadScatterbrainJson(url).then((metadata) => { if (isSlideViewData(metadata)) { const dataset = loadDataset(metadata, url) as SlideViewDataset; - return assembleSlideConfig(config, dataset) + return assembleSlideConfig(config, dataset); } return undefined; }); } function assembleGridConfig(config: ScatterplotGridConfig, dataset: SlideViewDataset): DynamicGrid { - const { colorBy, trn } = config + const { colorBy, trn } = config; return { type: 'DynamicGrid', colorBy, dataset, pointSize: 4, toModelSpace: trn, - } + }; } export function createGridDataset(config: ScatterplotGridConfig): Promise { - const { url } = config + const { url } = config; return loadScatterbrainJson(url).then((metadata) => { if (isSlideViewData(metadata)) { const dataset = loadDataset(metadata, url) as SlideViewDataset; - return assembleGridConfig(config, dataset) + return assembleGridConfig(config, dataset); } return undefined; }); -} \ No newline at end of file +} diff --git a/apps/layers/src/data-sources/types.ts b/apps/layers/src/data-sources/types.ts index c9a796d..3eb4605 100644 --- a/apps/layers/src/data-sources/types.ts +++ b/apps/layers/src/data-sources/types.ts @@ -1,14 +1,16 @@ -import type { vec2 } from "@alleninstitute/vis-geometry"; +import type { vec2 } from '@alleninstitute/vis-geometry'; export type MaybePromise = T | Promise; // we'd like to be able to configure a layer with a simple payload export type Simple2DTransform = { offset: vec2; scale: vec2; -} +}; export type OptionalTransform = { - toModelSpace?: { - offset: vec2; - scale: vec2; - } | undefined -} \ No newline at end of file + toModelSpace?: + | { + offset: vec2; + scale: vec2; + } + | undefined; +}; diff --git a/apps/layers/src/demo.ts b/apps/layers/src/demo.ts index edba0fe..60be4f6 100644 --- a/apps/layers/src/demo.ts +++ b/apps/layers/src/demo.ts @@ -1,28 +1,56 @@ -import { Box2D, Vec2, type box2D, type vec2 } from "@alleninstitute/vis-geometry"; -import { type ColumnRequest } from "Common/loaders/scatterplot/scatterbrain-loader"; -import REGL from "regl"; -import { AsyncDataCache, ReglLayer2D, type FrameLifecycle, type NormalStatus } from "@alleninstitute/vis-scatterbrain"; -import { buildRenderer } from "../../scatterplot/src/renderer"; -import { buildImageRenderer } from "../../omezarr-viewer/src/image-renderer"; -import { renderDynamicGrid, renderSlide, type RenderSettings as SlideRenderSettings } from "./data-renderers/dynamicGridSlideRenderer"; -import { renderGrid, renderSlice, type RenderSettings as SliceRenderSettings } from "./data-renderers/volumeSliceRenderer"; -import { renderAnnotationLayer, type RenderSettings as AnnotationRenderSettings, type SimpleAnnotation } from "./data-renderers/simpleAnnotationRenderer"; -import { buildPathRenderer } from "./data-renderers/lineRenderer"; -import { buildVersaRenderer, type AxisAlignedPlane } from "../../omezarr-viewer/src/versa-renderer"; -import type { ColorMapping, RenderCallback } from "./data-renderers/types"; -import { createZarrSlice, type AxisAlignedZarrSlice, type ZarrSliceConfig } from "./data-sources/ome-zarr/planar-slice"; -import { createGridDataset, createSlideDataset, type DynamicGrid, type DynamicGridSlide, type ScatterPlotGridSlideConfig, type ScatterplotGridConfig } from "./data-sources/scatterplot/dynamic-grid"; -import type { OptionalTransform } from "./data-sources/types"; -import type { CacheEntry, AnnotationLayer, Layer } from "./types"; -import { AppUi } from "./app"; -import { createRoot } from "react-dom/client"; -import { createZarrSliceGrid, type AxisAlignedZarrSliceGrid, type ZarrSliceGridConfig } from "./data-sources/ome-zarr/slice-grid"; -import { renderAnnotationGrid, type LoopRenderer, type MeshRenderer, type RenderSettings as AnnotationGridRenderSettings } from "./data-renderers/annotation-renderer"; -import { buildLoopRenderer, buildMeshRenderer } from "./data-renderers/mesh-renderer"; -import type { Camera } from "../../omezarr-viewer/src/camera"; -import { saveAs } from 'file-saver' -import type { AnnotationGrid, AnnotationGridConfig } from "./data-sources/annotation/annotation-grid"; -import { sizeInUnits } from "Common/loaders/ome-zarr/zarr-data"; +import { Box2D, Vec2, type box2D, type vec2 } from '@alleninstitute/vis-geometry'; +import { type ColumnRequest } from 'Common/loaders/scatterplot/scatterbrain-loader'; +import REGL from 'regl'; +import { AsyncDataCache, ReglLayer2D, type FrameLifecycle, type NormalStatus } from '@alleninstitute/vis-scatterbrain'; +import { buildRenderer } from '../../scatterplot/src/renderer'; +import { buildImageRenderer } from '../../omezarr-viewer/src/image-renderer'; +import { + renderDynamicGrid, + renderSlide, + type RenderSettings as SlideRenderSettings, +} from './data-renderers/dynamicGridSlideRenderer'; +import { + renderGrid, + renderSlice, + type RenderSettings as SliceRenderSettings, +} from './data-renderers/volumeSliceRenderer'; +import { + renderAnnotationLayer, + type RenderSettings as AnnotationRenderSettings, + type SimpleAnnotation, +} from './data-renderers/simpleAnnotationRenderer'; +import { buildPathRenderer } from './data-renderers/lineRenderer'; +import { buildVersaRenderer, type AxisAlignedPlane } from '../../omezarr-viewer/src/versa-renderer'; +import type { ColorMapping, RenderCallback } from './data-renderers/types'; +import { createZarrSlice, type AxisAlignedZarrSlice, type ZarrSliceConfig } from './data-sources/ome-zarr/planar-slice'; +import { + createGridDataset, + createSlideDataset, + type DynamicGrid, + type DynamicGridSlide, + type ScatterPlotGridSlideConfig, + type ScatterplotGridConfig, +} from './data-sources/scatterplot/dynamic-grid'; +import type { OptionalTransform } from './data-sources/types'; +import type { CacheEntry, AnnotationLayer, Layer } from './types'; +import { AppUi } from './app'; +import { createRoot } from 'react-dom/client'; +import { + createZarrSliceGrid, + type AxisAlignedZarrSliceGrid, + type ZarrSliceGridConfig, +} from './data-sources/ome-zarr/slice-grid'; +import { + renderAnnotationGrid, + type LoopRenderer, + type MeshRenderer, + type RenderSettings as AnnotationGridRenderSettings, +} from './data-renderers/annotation-renderer'; +import { buildLoopRenderer, buildMeshRenderer } from './data-renderers/mesh-renderer'; +import type { Camera } from '../../omezarr-viewer/src/camera'; +import { saveAs } from 'file-saver'; +import type { AnnotationGrid, AnnotationGridConfig } from './data-sources/annotation/annotation-grid'; +import { sizeInUnits } from 'Common/loaders/ome-zarr/zarr-data'; const KB = 1000; const MB = 1000 * KB; @@ -44,7 +72,7 @@ function destroyer(item: CacheEntry) { break; default: // @ts-expect-error - console.error(item.data, 'implement a destroyer for this case!') + console.error(item.data, 'implement a destroyer for this case!'); break; } } @@ -55,7 +83,7 @@ function appendPoint(layer: AnnotationLayer, p: vec2) { const path = layer.data.paths[layer.data.paths.length - 1]; if (path) { path.points.push(p); - path.bounds = Box2D.union(path.bounds, Box2D.create(p, p)) + path.bounds = Box2D.union(path.bounds, Box2D.create(p, p)); } } function startStroke(layer: AnnotationLayer, p: vec2) { @@ -63,26 +91,23 @@ function startStroke(layer: AnnotationLayer, p: vec2) { bounds: Box2D.create(p, p), color: [1, 0, 0, 1], id: Math.random(), - points: [p] - }) + points: [p], + }); } export class Demo { - - - camera: Camera; - layers: Layer[] + layers: Layer[]; regl: REGL.Regl; selectedLayer: number; canvas: HTMLCanvasElement; - mouse: 'up' | 'down' - mode: 'draw' | 'pan' + mouse: 'up' | 'down'; + mode: 'draw' | 'pan'; mousePos: vec2; cache: AsyncDataCache; imgRenderer: ReturnType; plotRenderer: ReturnType; sliceRenderer: ReturnType; - pathRenderer: ReturnType + pathRenderer: ReturnType; loopRenderer: LoopRenderer; meshRenderer: MeshRenderer; stencilMeshRenderer: MeshRenderer; @@ -90,11 +115,11 @@ export class Demo { private redrawRequested: number = 0; constructor(canvas: HTMLCanvasElement, regl: REGL.Regl) { this.canvas = canvas; - this.mouse = 'up' + this.mouse = 'up'; this.regl = regl; - this.mousePos = [0, 0] + this.mousePos = [0, 0]; this.layers = []; - this.mode = 'pan' + this.mode = 'pan'; this.selectedLayer = 0; this.pathRenderer = buildPathRenderer(regl); this.plotRenderer = buildRenderer(regl); @@ -110,8 +135,8 @@ export class Demo { this.camera = { view: Box2D.create([0, 0], [(10 * w) / h, 10]), screen: [w, h], - projection: 'webImage' - } + projection: 'webImage', + }; this.initHandlers(canvas); // each entry in the cache is about 250 kb - so 4000 means we get 1GB of data this.cache = new AsyncDataCache(destroyer, sizeOf, 4000); @@ -120,7 +145,7 @@ export class Demo { if (i >= 0 && i < this.layers.length) { this.selectedLayer = i; if (this.layers[i].type !== 'annotationLayer') { - this.mode = 'pan' + this.mode = 'pan'; } } } @@ -145,7 +170,7 @@ export class Demo { setSlice(param: number) { const layer = this.layers[this.selectedLayer]; if (layer && layer.type === 'volumeSlice') { - layer.data = { ...layer.data, planeParameter: param } + layer.data = { ...layer.data, planeParameter: param }; this.uiChange(); } } @@ -173,40 +198,50 @@ export class Demo { addDynamicGrid(config: ScatterplotGridConfig) { return createGridDataset(config).then((data) => { if (data) { - const [w, h] = this.camera.screen + const [w, h] = this.camera.screen; const layer = new ReglLayer2D>( - this.regl, this.imgRenderer, renderDynamicGrid, [w, h] + this.regl, + this.imgRenderer, + renderDynamicGrid, + [w, h] ); this.layers.push({ type: 'scatterplotGrid', data, - render: layer + render: layer, }); - this.camera = { ...this.camera, view: data.dataset.bounds } + this.camera = { ...this.camera, view: data.dataset.bounds }; this.uiChange(); } - }) + }); } selectLayer(layer: number) { this.selectedLayer = Math.min(this.layers.length - 1, Math.max(0, layer)); const yay = this.layers[this.selectedLayer]; - console.log('selected:', yay.data) + console.log('selected:', yay.data); this.uiChange(); } deleteSelectedLayer() { - const removed = this.layers.splice(this.selectedLayer, 1) - removed.forEach(l => l.render.destroy()) + const removed = this.layers.splice(this.selectedLayer, 1); + removed.forEach((l) => l.render.destroy()); this.uiChange(); } - addLayer(config: ScatterplotGridConfig | ZarrSliceConfig | ZarrSliceGridConfig | ScatterPlotGridSlideConfig | AnnotationGridConfig) { + addLayer( + config: + | ScatterplotGridConfig + | ZarrSliceConfig + | ZarrSliceGridConfig + | ScatterPlotGridSlideConfig + | AnnotationGridConfig + ) { switch (config.type) { case 'AnnotationGridConfig': return this.addAnnotationGrid(config); case 'ScatterPlotGridConfig': return this.addDynamicGrid(config); case 'ScatterPlotGridSlideConfig': - return this.addScatterplot(config) + return this.addScatterplot(config); case 'ZarrSliceGridConfig': return this.addVolumeGrid(config); case 'zarrSliceConfig': @@ -214,63 +249,75 @@ export class Demo { } } addAnnotation(data: SimpleAnnotation) { - const [w, h] = this.camera.screen + const [w, h] = this.camera.screen; this.layers.push({ type: 'annotationLayer', data, render: new ReglLayer2D( - this.regl, this.imgRenderer, renderAnnotationLayer, [w, h] - ) - }) + this.regl, + this.imgRenderer, + renderAnnotationLayer, + [w, h] + ), + }); this.uiChange(); } addEmptyAnnotation() { - const [w, h] = this.camera.screen + const [w, h] = this.camera.screen; this.layers.push({ type: 'annotationLayer', data: { - paths: [] + paths: [], }, render: new ReglLayer2D( - this.regl, this.imgRenderer, renderAnnotationLayer, [w, h] - ) - }) + this.regl, + this.imgRenderer, + renderAnnotationLayer, + [w, h] + ), + }); this.uiChange(); } private addScatterplot(config: ScatterPlotGridSlideConfig) { return createSlideDataset(config).then((data) => { if (data) { - const [w, h] = this.camera.screen + const [w, h] = this.camera.screen; const layer = new ReglLayer2D>( - this.regl, this.imgRenderer, renderSlide, [w, h] + this.regl, + this.imgRenderer, + renderSlide, + [w, h] ); this.layers.push({ type: 'scatterplot', data, - render: layer + render: layer, }); - this.camera = { ...this.camera, view: data.dataset.bounds } + this.camera = { ...this.camera, view: data.dataset.bounds }; this.uiChange(); } - }) - - + }); } private addVolumeSlice(config: ZarrSliceConfig) { - const [w, h] = this.camera.screen + const [w, h] = this.camera.screen; return createZarrSlice(config).then((data) => { - const layer = new ReglLayer2D, 'target'>>( - this.regl, this.imgRenderer, renderSlice, [w, h] - ); + const layer = new ReglLayer2D< + AxisAlignedZarrSlice & OptionalTransform, + Omit, 'target'> + >(this.regl, this.imgRenderer, renderSlice, [w, h]); this.layers.push({ type: 'volumeSlice', data, - render: layer + render: layer, }); - const s = sizeInUnits(data.plane, data.dataset.multiscales[0].axes, data.dataset.multiscales[0].datasets[0]) - this.camera = { ...this.camera, view: Box2D.create([0, 0], s!) } + const s = sizeInUnits( + data.plane, + data.dataset.multiscales[0].axes, + data.dataset.multiscales[0].datasets[0] + ); + this.camera = { ...this.camera, view: Box2D.create([0, 0], s!) }; this.uiChange(); - }) + }); } private addAnnotationGrid(config: AnnotationGridConfig) { return createSlideDataset({ @@ -281,40 +328,46 @@ export class Demo { }).then((data) => { if (data) { const { stroke, fill, levelFeature, annotationUrl } = config; - const [w, h] = this.camera.screen + const [w, h] = this.camera.screen; const grid: AnnotationGrid = { dataset: data?.dataset, levelFeature, annotationBaseUrl: annotationUrl, - stroke: { ...stroke, width: 1 }, fill, + stroke: { ...stroke, width: 1 }, + fill, type: 'AnnotationGrid', - } + }; this.layers.push({ type: 'annotationGrid', data: grid, render: new ReglLayer2D, 'target'>>( - this.regl, this.imgRenderer, renderAnnotationGrid, [w, h]) - }) + this.regl, + this.imgRenderer, + renderAnnotationGrid, + [w, h] + ), + }); // look at it! - this.camera = { ...this.camera, view: data.dataset.bounds } + this.camera = { ...this.camera, view: data.dataset.bounds }; this.uiChange(); } - }) + }); } private addVolumeGrid(config: ZarrSliceGridConfig) { - const [w, h] = this.camera.screen + const [w, h] = this.camera.screen; return createZarrSliceGrid(config).then((data) => { const layer = new ReglLayer2D, 'target'>>( - this.regl, this.imgRenderer, renderGrid, [w, h] + this.regl, + this.imgRenderer, + renderGrid, + [w, h] ); this.layers.push({ type: 'volumeGrid', data: data, - render: layer + render: layer, }); - - - }) + }); } async requestSnapshot(pxWidth: number) { // TODO: using a canvas to build a png is very fast (the browser does it for us) @@ -326,7 +379,10 @@ export class Demo { const aspect = screen[1] / screen[0]; const h = w * aspect; // make it be upside down! - const pixels = await this.takeSnapshot({ view, screen: [w, h], projection: projection === 'webImage' ? 'cartesian' : 'webImage' }, this.layers) + const pixels = await this.takeSnapshot( + { view, screen: [w, h], projection: projection === 'webImage' ? 'cartesian' : 'webImage' }, + this.layers + ); // create an offscreen canvas... const cnvs = new OffscreenCanvas(w, h); const imgData = new ImageData(new Uint8ClampedArray(pixels.buffer), w, h); @@ -339,10 +395,9 @@ export class Demo { // render each layer, in order, given a snapshot buffer // once done, regl.read the whole thing, turn it to a png return new Promise((resolve, reject) => { - - const [width, height] = camera.screen + const [width, height] = camera.screen; const target = this.regl.framebuffer(width, height); - this.regl.clear({ framebuffer: target, color: [0, 0, 0, 1], depth: 1 }) + this.regl.clear({ framebuffer: target, color: [0, 0, 0, 1], depth: 1 }); const renderers = { volumeSlice: this.sliceRenderer, scatterplot: this.plotRenderer, @@ -352,59 +407,78 @@ export class Demo { annotationGrid: { loopRenderer: this.loopRenderer, meshRenderer: this.meshRenderer, - stencilMeshRenderer: this.stencilMeshRenderer - } - } + stencilMeshRenderer: this.stencilMeshRenderer, + }, + }; - - const layerPromises: Array<() => FrameLifecycle> = [] - const nextLayerWhenFinished: RenderCallback = (e: { status: NormalStatus } | { status: 'error', error: unknown }) => { + const layerPromises: Array<() => FrameLifecycle> = []; + const nextLayerWhenFinished: RenderCallback = ( + e: { status: NormalStatus } | { status: 'error'; error: unknown } + ) => { const { status } = e; switch (status) { case 'cancelled': - reject('one of the layer tasks was cancelled') + reject('one of the layer tasks was cancelled'); break; case 'progress': if (Math.random() > 0.7) { - console.log('...') + console.log('...'); } break; case 'finished': case 'finished_synchronously': // start the next layer - const next = layerPromises.shift() + const next = layerPromises.shift(); if (!next) { // do the final read! - const bytes = this.regl.read({ framebuffer: target }) + const bytes = this.regl.read({ framebuffer: target }); resolve(bytes); } else { // do the next layer next(); } } - } + }; const settings = { - cache: this.cache, camera, callback: nextLayerWhenFinished, regl: this.regl - } + cache: this.cache, + camera, + callback: nextLayerWhenFinished, + regl: this.regl, + }; for (const layer of layers) { switch (layer.type) { case 'volumeGrid': - layerPromises.push(() => renderGrid(target, layer.data, { ...settings, renderer: renderers[layer.type] })) + layerPromises.push(() => + renderGrid(target, layer.data, { ...settings, renderer: renderers[layer.type] }) + ); break; case 'annotationGrid': - layerPromises.push(() => renderAnnotationGrid(target, layer.data, { ...settings, renderers: renderers[layer.type] })); + layerPromises.push(() => + renderAnnotationGrid(target, layer.data, { ...settings, renderers: renderers[layer.type] }) + ); break; case 'volumeSlice': - layerPromises.push(() => renderSlice(target, layer.data, { ...settings, renderer: renderers[layer.type] })); + layerPromises.push(() => + renderSlice(target, layer.data, { ...settings, renderer: renderers[layer.type] }) + ); break; case 'scatterplot': - layerPromises.push(() => renderSlide(target, layer.data, { ...settings, renderer: renderers[layer.type] })); + layerPromises.push(() => + renderSlide(target, layer.data, { ...settings, renderer: renderers[layer.type] }) + ); break; case 'annotationLayer': - layerPromises.push(() => renderAnnotationLayer(target, layer.data, { ...settings, renderer: renderers[layer.type] })) + layerPromises.push(() => + renderAnnotationLayer(target, layer.data, { ...settings, renderer: renderers[layer.type] }) + ); break; case 'scatterplotGrid': - layerPromises.push(() => renderDynamicGrid(target, layer.data, { ...settings, renderer: renderers[layer.type] })) + layerPromises.push(() => + renderDynamicGrid(target, layer.data, { + ...settings, + renderer: renderers[layer.type], + }) + ); break; } } @@ -413,11 +487,11 @@ export class Demo { if (first) { first(); } - }) + }); } private doReRender() { const { cache, camera } = this; - const drawOnProgress: RenderCallback = (e: { status: NormalStatus } | { status: 'error', error: unknown }) => { + const drawOnProgress: RenderCallback = (e: { status: NormalStatus } | { status: 'error'; error: unknown }) => { const { status } = e; switch (status) { case 'finished': @@ -427,10 +501,13 @@ export class Demo { this.requestReRender(); break; } - } + }; const settings = { - cache, camera, callback: drawOnProgress, regl: this.regl - } + cache, + camera, + callback: drawOnProgress, + regl: this.regl, + }; const renderers = { volumeSlice: this.sliceRenderer, scatterplot: this.plotRenderer, @@ -440,9 +517,9 @@ export class Demo { annotationGrid: { loopRenderer: this.loopRenderer, meshRenderer: this.meshRenderer, - stencilMeshRenderer: this.stencilMeshRenderer - } - } + stencilMeshRenderer: this.stencilMeshRenderer, + }, + }; for (const layer of this.layers) { // TODO all cases are identical - dry it up! if (layer.type === 'scatterplot') { @@ -452,24 +529,27 @@ export class Demo { ...settings, renderer: renderers[layer.type], - } - }) + }, + }); } else if (layer.type === 'volumeSlice') { layer.render.onChange({ data: layer.data, settings: { ...settings, renderer: renderers[layer.type], - } - }) + }, + }); } else if (layer.type === 'annotationLayer') { - layer.render.onChange({ - data: layer.data, - settings: { - ...settings, - renderer: renderers[layer.type], - } - }, this.mode === 'pan') // dont cancel while drawing + layer.render.onChange( + { + data: layer.data, + settings: { + ...settings, + renderer: renderers[layer.type], + }, + }, + this.mode === 'pan' + ); // dont cancel while drawing } else if (layer.type === 'volumeGrid') { layer.render.onChange({ data: layer.data, @@ -478,8 +558,8 @@ export class Demo { concurrentTasks: 3, cpuLimit: 25, renderer: renderers[layer.type], - } - }) + }, + }); } else if (layer.type === 'annotationGrid') { layer.render.onChange({ data: layer.data, @@ -487,8 +567,8 @@ export class Demo { ...settings, concurrentTasks: 2, renderers: renderers[layer.type], - } - }) + }, + }); } else if (layer.type === 'scatterplotGrid') { layer.render.onChange({ data: layer.data, @@ -497,8 +577,8 @@ export class Demo { concurrentTasks: 3, cpuLimit: 25, renderer: renderers[layer.type], - } - }) + }, + }); } } } @@ -507,7 +587,7 @@ export class Demo { this.redrawRequested = window.requestAnimationFrame(() => { this.doReRender(); this.redrawRequested = 0; - }) + }); } this.requestReRender(); } @@ -516,13 +596,13 @@ export class Demo { this.refreshRequested = window.requestAnimationFrame(() => { this.refreshScreen(); this.refreshRequested = 0; - uiroot?.render(AppUi({ demo: this })) - }) + uiroot?.render(AppUi({ demo: this })); + }); } } - mouseButton(click: "up" | "down", pos: vec2) { + mouseButton(click: 'up' | 'down', pos: vec2) { this.mouse = click; - const curLayer = this.layers[this.selectedLayer] + const curLayer = this.layers[this.selectedLayer]; if (click === 'down' && curLayer && curLayer.type === 'annotationLayer') { startStroke(curLayer, this.toDataspace(pos)); } @@ -535,9 +615,9 @@ export class Demo { return Vec2.add(view.minCorner, c); } mouseMove(delta: vec2, pos: vec2) { - const curLayer = this.layers[this.selectedLayer] + const curLayer = this.layers[this.selectedLayer]; if (this.mode === 'pan') { - if (this.mouse === "down") { + if (this.mouse === 'down') { // drag the view const { screen, view } = this.camera; const p = Vec2.div(delta, [this.canvas.clientWidth, this.canvas.clientHeight]); @@ -546,8 +626,8 @@ export class Demo { this.onCameraChanged(); } } else if (curLayer && curLayer.type === 'annotationLayer') { - if (this.mouse === "down") { - appendPoint(curLayer, this.toDataspace(pos)) + if (this.mouse === 'down') { + appendPoint(curLayer, this.toDataspace(pos)); this.onCameraChanged(); } } @@ -566,10 +646,10 @@ export class Demo { } private initHandlers(canvas: HTMLCanvasElement) { canvas.onmousedown = (e: MouseEvent) => { - this.mouseButton("down", [e.offsetX, canvas.clientHeight - e.offsetY]); + this.mouseButton('down', [e.offsetX, canvas.clientHeight - e.offsetY]); }; canvas.onmouseup = (e: MouseEvent) => { - this.mouseButton("up", [e.offsetX, canvas.clientHeight - e.offsetY]); + this.mouseButton('up', [e.offsetX, canvas.clientHeight - e.offsetY]); }; canvas.onmousemove = (e: MouseEvent) => { // account for gl-origin vs. screen origin: @@ -586,7 +666,8 @@ export class Demo { this.mode = this.mode === 'draw' ? 'pan' : 'draw'; this.uiChange(); } - } if (e.key === 'd') { + } + if (e.key === 'd') { // start a new drawing! if (this.layers.length === 0 || (layer && layer.type !== 'annotationLayer')) { this.addEmptyAnnotation(); @@ -595,41 +676,39 @@ export class Demo { this.uiChange(); } } - } + }; } refreshScreen() { const flipBox = (box: box2D): box2D => { const { minCorner, maxCorner } = box; return { minCorner: [minCorner[0], maxCorner[1]], maxCorner: [maxCorner[0], minCorner[1]] }; - } - const flipped = Box2D.toFlatArray(flipBox(this.camera.view)) - this.regl.clear({ framebuffer: null, color: [0, 0, 0, 1], depth: 1 }) + }; + const flipped = Box2D.toFlatArray(flipBox(this.camera.view)); + this.regl.clear({ framebuffer: null, color: [0, 0, 0, 1], depth: 1 }); for (const layer of this.layers) { - const src = layer.render.getRenderResults('prev') + const src = layer.render.getRenderResults('prev'); if (src.bounds) { this.imgRenderer({ box: Box2D.toFlatArray(src.bounds), img: src.texture, target: null, - view: flipped - }) + view: flipped, + }); } // annotations are often transparent and dont do well... - if ( - layer.render.renderingInProgress() && layer.type !== 'annotationGrid') { + if (layer.render.renderingInProgress() && layer.type !== 'annotationGrid') { // draw our incoming frame overtop the old! - const cur = layer.render.getRenderResults('cur') + const cur = layer.render.getRenderResults('cur'); if (cur.bounds) { this.imgRenderer({ box: Box2D.toFlatArray(cur.bounds), img: cur.texture, target: null, - view: flipped - }) + view: flipped, + }); } } - } } } @@ -644,92 +723,92 @@ function demoTime(thing: HTMLCanvasElement) { thing.height = thing.clientHeight; const offscreen = thing; - const gl = offscreen.getContext("webgl", { + const gl = offscreen.getContext('webgl', { alpha: true, preserveDrawingBuffer: true, antialias: true, premultipliedAlpha: true, }); if (!gl) { - throw new Error('WebGL not supported!') + throw new Error('WebGL not supported!'); } const regl = REGL({ gl, - extensions: ["ANGLE_instanced_arrays", "OES_texture_float", "WEBGL_color_buffer_float"], + extensions: ['ANGLE_instanced_arrays', 'OES_texture_float', 'WEBGL_color_buffer_float'], }); theDemo = new Demo(thing, regl); window['demo'] = theDemo; setupExampleData(); - uiroot.render(AppUi({ demo: theDemo })) - + uiroot.render(AppUi({ demo: theDemo })); } function setupExampleData() { // add a bunch of pre-selected layers to the window object for selection during demo time window.examples = {}; const prep = (key: string, thing: any) => { window.examples[key] = thing; - } + }; prep('structureAnnotation', structureAnnotation); prep('tissuecyte396', tissuecyte396); - prep('slide32', oneSlide) - prep('versa1', versa1) + prep('slide32', oneSlide); + prep('versa1', versa1); prep('reconstructed', reconstructed); - prep('tissuecyte', tissueCyteSlice) - + prep('tissuecyte', tissueCyteSlice); } -const slide32 = 'MQ1B9QBZFIPXQO6PETJ' -const colorByGene: ColumnRequest = { name: '88', type: 'QUANTITATIVE' } -const merfish = 'https://bkp-2d-visualizations-stage.s3.amazonaws.com/wmb_slide_view_02142024-20240223021524/DTVLE1YGNTJQMWVMKEU/ScatterBrain.json' -const ccf = 'https://neuroglancer-vis-prototype.s3.amazonaws.com/mouse3/230524_transposed_1501/avg_template/' -const tissuecyte = "https://tissuecyte-visualizations.s3.amazonaws.com/data/230105/tissuecyte/1111175209/green/" -const tenx = 'https://bkp-2d-visualizations-stage.s3.amazonaws.com/wmb_tenx_01172024_stage-20240128193624/488I12FURRB8ZY5KJ8T/ScatterBrain.json' -const scottpoc = 'https://tissuecyte-ome-zarr-poc.s3.amazonaws.com/40_128_128/1145081396' -const pretend = { min: 0, max: 500 } +const slide32 = 'MQ1B9QBZFIPXQO6PETJ'; +const colorByGene: ColumnRequest = { name: '88', type: 'QUANTITATIVE' }; +const merfish = + 'https://bkp-2d-visualizations-stage.s3.amazonaws.com/wmb_slide_view_02142024-20240223021524/DTVLE1YGNTJQMWVMKEU/ScatterBrain.json'; +const ccf = 'https://neuroglancer-vis-prototype.s3.amazonaws.com/mouse3/230524_transposed_1501/avg_template/'; +const tissuecyte = 'https://tissuecyte-visualizations.s3.amazonaws.com/data/230105/tissuecyte/1111175209/green/'; +const tenx = + 'https://bkp-2d-visualizations-stage.s3.amazonaws.com/wmb_tenx_01172024_stage-20240128193624/488I12FURRB8ZY5KJ8T/ScatterBrain.json'; +const scottpoc = 'https://tissuecyte-ome-zarr-poc.s3.amazonaws.com/40_128_128/1145081396'; +const pretend = { min: 0, max: 500 }; const reconstructed: ScatterplotGridConfig = { colorBy: colorByGene, type: 'ScatterPlotGridConfig', url: 'https://bkp-2d-visualizations-stage.s3.amazonaws.com/wmb_ccf_04112024-20240419205547/4STCSZBXHYOI0JUUA3M/ScatterBrain.json', -} +}; const oneSlide: ScatterPlotGridSlideConfig = { colorBy: colorByGene, slideId: slide32, type: 'ScatterPlotGridSlideConfig', url: 'https://bkp-2d-visualizations-stage.s3.amazonaws.com/wmb_ccf_04112024-20240419205547/4STCSZBXHYOI0JUUA3M/ScatterBrain.json', -} +}; const tissuecyte396: ZarrSliceGridConfig = { type: 'ZarrSliceGridConfig', gamut: { R: { index: 0, gamut: { max: 600, min: 0 } }, G: { index: 1, gamut: { max: 500, min: 0 } }, - B: { index: 2, gamut: { max: 400, min: 0 } } + B: { index: 2, gamut: { max: 400, min: 0 } }, }, plane: 'xy', slices: 142, - url: scottpoc -} + url: scottpoc, +}; const tissueCyteSlice: ZarrSliceConfig = { type: 'zarrSliceConfig', gamut: { R: { index: 0, gamut: { max: 600, min: 0 } }, G: { index: 1, gamut: { max: 500, min: 0 } }, - B: { index: 2, gamut: { max: 400, min: 0 } } + B: { index: 2, gamut: { max: 400, min: 0 } }, }, plane: 'xy', planeParameter: 0.5, - url: scottpoc -} + url: scottpoc, +}; const versa1: ZarrSliceGridConfig = { - url: "https://neuroglancer-vis-prototype.s3.amazonaws.com/VERSA/scratch/0500408166/", + url: 'https://neuroglancer-vis-prototype.s3.amazonaws.com/VERSA/scratch/0500408166/', type: 'ZarrSliceGridConfig', gamut: { R: { index: 0, gamut: { max: 20, min: 0 } }, G: { index: 1, gamut: { max: 20, min: 0 } }, - B: { index: 2, gamut: { max: 20, min: 0 } } + B: { index: 2, gamut: { max: 20, min: 0 } }, }, plane: 'xy', slices: 4, -} +}; const structureAnnotation: AnnotationGridConfig = { type: 'AnnotationGridConfig', url: 'https://bkp-2d-visualizations-stage.s3.amazonaws.com/wmb_ccf_04112024-20240419205547/4STCSZBXHYOI0JUUA3M/ScatterBrain.json', @@ -740,9 +819,9 @@ const structureAnnotation: AnnotationGridConfig = { overrideColor: [1, 0, 0, 1] as const, }, fill: { - opacity: 0.7 - } -} + opacity: 0.7, + }, +}; const uiroot = createRoot(document.getElementById('sidebar')!); -demoTime(document.getElementById('glCanvas') as HTMLCanvasElement) \ No newline at end of file +demoTime(document.getElementById('glCanvas') as HTMLCanvasElement); diff --git a/apps/layers/src/types.ts b/apps/layers/src/types.ts index 7c754c7..2aa76af 100644 --- a/apps/layers/src/types.ts +++ b/apps/layers/src/types.ts @@ -1,64 +1,72 @@ -import type { box2D } from "@alleninstitute/vis-geometry"; -import type REGL from "regl"; -import { type RenderSettings as SlideRenderSettings } from "./data-renderers/dynamicGridSlideRenderer"; -import { type RenderSettings as SliceRenderSettings } from "./data-renderers/volumeSliceRenderer"; -import { type RenderSettings as AnnotationRenderSettings, type SimpleAnnotation } from "./data-renderers/simpleAnnotationRenderer"; -import type { AxisAlignedZarrSlice } from "./data-sources/ome-zarr/planar-slice"; -import type { DynamicGrid, DynamicGridSlide } from "./data-sources/scatterplot/dynamic-grid"; -import type { AxisAlignedZarrSliceGrid } from "./data-sources/ome-zarr/slice-grid"; -import type { RenderSettings as AnnotationGridRenderSettings, CacheContentType as GpuMesh } from "./data-renderers/annotation-renderer"; -import type { AnnotationGrid } from "./data-sources/annotation/annotation-grid"; -import type { ReglLayer2D } from "@alleninstitute/vis-scatterbrain"; +import type { box2D } from '@alleninstitute/vis-geometry'; +import type REGL from 'regl'; +import { type RenderSettings as SlideRenderSettings } from './data-renderers/dynamicGridSlideRenderer'; +import { type RenderSettings as SliceRenderSettings } from './data-renderers/volumeSliceRenderer'; +import { + type RenderSettings as AnnotationRenderSettings, + type SimpleAnnotation, +} from './data-renderers/simpleAnnotationRenderer'; +import type { AxisAlignedZarrSlice } from './data-sources/ome-zarr/planar-slice'; +import type { DynamicGrid, DynamicGridSlide } from './data-sources/scatterplot/dynamic-grid'; +import type { AxisAlignedZarrSliceGrid } from './data-sources/ome-zarr/slice-grid'; +import type { + RenderSettings as AnnotationGridRenderSettings, + CacheContentType as GpuMesh, +} from './data-renderers/annotation-renderer'; +import type { AnnotationGrid } from './data-sources/annotation/annotation-grid'; +import type { ReglLayer2D } from '@alleninstitute/vis-scatterbrain'; // note: right now, all layers should be considered 2D, and WebGL only... export type Image = { - texture: REGL.Framebuffer2D + texture: REGL.Framebuffer2D; bounds: box2D | undefined; // if undefined, it means we allocated the texture, but its empty and should not be used (except to fill it) -} +}; type ColumnBuffer = { type: 'vbo'; data: REGL.Buffer; -} -export type CacheEntry = { - type: 'texture2D'; - data: REGL.Texture2D -} | ColumnBuffer - | GpuMesh - - - +}; +export type CacheEntry = + | { + type: 'texture2D'; + data: REGL.Texture2D; + } + | ColumnBuffer + | GpuMesh; export type ScatterPlotLayer = { - type: 'scatterplot' - data: DynamicGridSlide, - render: ReglLayer2D> + type: 'scatterplot'; + data: DynamicGridSlide; + render: ReglLayer2D>; }; export type ScatterPlotGridLayer = { - type: 'scatterplotGrid' - data: DynamicGrid, - render: ReglLayer2D> + type: 'scatterplotGrid'; + data: DynamicGrid; + render: ReglLayer2D>; }; export type VolumetricSliceLayer = { - type: 'volumeSlice' - data: AxisAlignedZarrSlice, - render: ReglLayer2D> + type: 'volumeSlice'; + data: AxisAlignedZarrSlice; + render: ReglLayer2D>; }; export type AnnotationLayer = { - type: 'annotationLayer', - data: SimpleAnnotation, - render: ReglLayer2D -} + type: 'annotationLayer'; + data: SimpleAnnotation; + render: ReglLayer2D; +}; export type VolumetricGridLayer = { type: 'volumeGrid'; data: AxisAlignedZarrSliceGrid; - render: ReglLayer2D> -} + render: ReglLayer2D>; +}; export type SlideViewAnnotations = { - type: 'annotationGrid', - data: AnnotationGrid, - render: ReglLayer2D> -} + type: 'annotationGrid'; + data: AnnotationGrid; + render: ReglLayer2D>; +}; export type Layer = - ScatterPlotLayer | ScatterPlotGridLayer - | VolumetricSliceLayer | VolumetricGridLayer - | SlideViewAnnotations | AnnotationLayer \ No newline at end of file + | ScatterPlotLayer + | ScatterPlotGridLayer + | VolumetricSliceLayer + | VolumetricGridLayer + | SlideViewAnnotations + | AnnotationLayer; diff --git a/apps/layers/src/ui/annotation-grid.tsx b/apps/layers/src/ui/annotation-grid.tsx index 2e51622..5d10113 100644 --- a/apps/layers/src/ui/annotation-grid.tsx +++ b/apps/layers/src/ui/annotation-grid.tsx @@ -2,21 +2,21 @@ import React from 'react'; import type { Demo } from 'src/demo'; import { InputSlider } from '@czi-sds/components'; export function AnnotationGrid(props: { demo: Demo }) { - const { demo } = props; - // control the gamut with some sliders - const l = demo.layers[demo.selectedLayer]; - if (l && l.type === 'annotationGrid') { - return ( - { - demo.setOpacity('fill', value as number); - }} - /> - ); - } - return null; + const { demo } = props; + // control the gamut with some sliders + const l = demo.layers[demo.selectedLayer]; + if (l && l.type === 'annotationGrid') { + return ( + { + demo.setOpacity('fill', value as number); + }} + /> + ); + } + return null; } diff --git a/apps/layers/src/ui/contact-sheet.tsx b/apps/layers/src/ui/contact-sheet.tsx index 3f66202..a57e04e 100644 --- a/apps/layers/src/ui/contact-sheet.tsx +++ b/apps/layers/src/ui/contact-sheet.tsx @@ -2,48 +2,57 @@ import React from 'react'; import type { Demo } from 'src/demo'; import { InputSlider, Button } from '@czi-sds/components'; export function ContactSheetUI(props: { demo: Demo }) { - const { demo } = props; - // control the gamut with some sliders - const l = demo.layers[demo.selectedLayer]; - if (l && l.type === 'volumeGrid') { - return ( -
- - { - demo.setGamutChannel('R', value as number[]); - }} - /> - { - demo.setGamutChannel('G', value as number[]); - }} - /> - { - demo.setGamutChannel('B', value as number[]); - }} - /> - - - -
- ); - } - return null; + const { demo } = props; + // control the gamut with some sliders + const l = demo.layers[demo.selectedLayer]; + if (l && l.type === 'volumeGrid') { + return ( +
+ + { + demo.setGamutChannel('R', value as number[]); + }} + /> + { + demo.setGamutChannel('G', value as number[]); + }} + /> + { + demo.setGamutChannel('B', value as number[]); + }} + /> + + + +
+ ); + } + return null; } diff --git a/apps/layers/src/ui/scatterplot-ui.tsx b/apps/layers/src/ui/scatterplot-ui.tsx index e38524a..53d8e06 100644 --- a/apps/layers/src/ui/scatterplot-ui.tsx +++ b/apps/layers/src/ui/scatterplot-ui.tsx @@ -2,34 +2,34 @@ import React from 'react'; import type { Demo } from 'src/demo'; import { InputSlider } from '@czi-sds/components'; export function ScatterplotUI(props: { demo: Demo }) { - const { demo } = props; - // control the gamut with some sliders - const l = demo.layers[demo.selectedLayer]; - if ((l && l.type === 'scatterplot') || l.type === 'scatterplotGrid') { - return ( -
- - { - demo.setPointSize(value as number); - }} - /> - - { - demo.setColorByIndex(value as number); - }} - /> -
- ); - } - return null; + const { demo } = props; + // control the gamut with some sliders + const l = demo.layers[demo.selectedLayer]; + if ((l && l.type === 'scatterplot') || l.type === 'scatterplotGrid') { + return ( +
+ + { + demo.setPointSize(value as number); + }} + /> + + { + demo.setColorByIndex(value as number); + }} + /> +
+ ); + } + return null; } diff --git a/apps/layers/src/ui/slice-ui.tsx b/apps/layers/src/ui/slice-ui.tsx index b2a42f7..f1154bf 100644 --- a/apps/layers/src/ui/slice-ui.tsx +++ b/apps/layers/src/ui/slice-ui.tsx @@ -2,58 +2,67 @@ import React from 'react'; import type { Demo } from 'src/demo'; import { InputSlider, Button } from '@czi-sds/components'; export function SliceViewLayer(props: { demo: Demo }) { - const { demo } = props; - // control the gamut with some sliders - const l = demo.layers[demo.selectedLayer]; - if (l && l.type === 'volumeSlice') { - return ( -
- - { - demo.setGamutChannel('R', value as number[]); - }} - /> - { - demo.setGamutChannel('G', value as number[]); - }} - /> - { - demo.setGamutChannel('B', value as number[]); - }} - /> - - { - demo.setSlice(value as number); - }} - /> - - - -
- ); - } - return null; + const { demo } = props; + // control the gamut with some sliders + const l = demo.layers[demo.selectedLayer]; + if (l && l.type === 'volumeSlice') { + return ( +
+ + { + demo.setGamutChannel('R', value as number[]); + }} + /> + { + demo.setGamutChannel('G', value as number[]); + }} + /> + { + demo.setGamutChannel('B', value as number[]); + }} + /> + + { + demo.setSlice(value as number); + }} + /> + + + +
+ ); + } + return null; } diff --git a/apps/layers/tsconfig.json b/apps/layers/tsconfig.json index 8fb771d..19a8384 100644 --- a/apps/layers/tsconfig.json +++ b/apps/layers/tsconfig.json @@ -1,14 +1,11 @@ { "extends": "../tsconfig.json", - "include": ["./src/**/*", "../common/src/**/*", - "../scatterplot/src/**/*", - "../omezarr-viewer/src/**/*"], - "compilerOptions": { + "include": ["./src/**/*", "../common/src/**/*", "../scatterplot/src/**/*", "../omezarr-viewer/src/**/*"], + "compilerOptions": { "jsx": "react", "baseUrl": "./", "paths": { - "Common/*":["../common/src/*"] + "Common/*": ["../common/src/*"] } - } - -} \ No newline at end of file + } +} diff --git a/apps/neuroglancer-url/README.md b/apps/neuroglancer-url/README.md index 517d44e..481592b 100644 --- a/apps/neuroglancer-url/README.md +++ b/apps/neuroglancer-url/README.md @@ -3,10 +3,12 @@ This is a demo for generating Neuroglancer URLs like the python POC [here](https://github.com/AllenInstitute/ome_zarr_converter/blob/main/src/ome_zarr_converter/neuroglancer/utils.py). ### How to build / run + 1. `pnpm build` from the root directory of this project 2. `pnpm install` in this directory 3. `pnpm run demo` in this directory - this will produce `dst/neuroglancer-url.html` 4. navigate to `dst/neuroglancer-url.html` and open it in your browser ### The Code - -- TBD -- \ No newline at end of file + +-- TBD -- diff --git a/apps/neuroglancer-url/package.json b/apps/neuroglancer-url/package.json index 33d82d2..0f3d7b3 100644 --- a/apps/neuroglancer-url/package.json +++ b/apps/neuroglancer-url/package.json @@ -1,42 +1,41 @@ { - "name": "@alleninstitute/neuroglancer-url-demo", - "version": "0.0.1", - "contributors": [ - { - "name": "Lane Sawyer", - "email": "lane.sawyer@alleninstitute.org" + "name": "@alleninstitute/neuroglancer-url-demo", + "version": "0.0.1", + "contributors": [ + { + "name": "Lane Sawyer", + "email": "lane.sawyer@alleninstitute.org" + }, + { + "name": "James Gerstenberger", + "email": "james.gerstenberger@alleninstitute.org" + }, + { + "name": "Noah Shepard", + "email": "noah.shepard@alleninstitute.org" + }, + { + "name": "Skyler Moosman", + "email": "skyler.moosman@alleninstitute.org" + }, + { + "name": "Su Li", + "email": "su.li@alleninstitute.org" + } + ], + "license": "TBD", + "type": "module", + "main": "lib/index.js", + "types": "lib/index.d.ts", + "private": true, + "scripts": { + "preinstall": "npx only-allow pnpm", + "demo": "esbuild src/demo.ts --bundle --outfile=dst/demo.js && cp public/* dst/", + "typecheck": "tsc --noEmit" }, - { - "name": "James Gerstenberger", - "email": "james.gerstenberger@alleninstitute.org" + "devDependencies": { + "esbuild": "^0.19.12", + "typescript": "^5.3.3" }, - { - "name": "Noah Shepard", - "email": "noah.shepard@alleninstitute.org" - }, - { - "name": "Skyler Moosman", - "email": "skyler.moosman@alleninstitute.org" - }, - { - "name": "Su Li", - "email": "su.li@alleninstitute.org" - } - ], - "license": "TBD", - "type": "module", - "main": "lib/index.js", - "types": "lib/index.d.ts", - "private": true, - "scripts": { - "preinstall": "npx only-allow pnpm", - "demo": "esbuild src/demo.ts --bundle --outfile=dst/demo.js && cp public/* dst/", - "typecheck": "tsc --noEmit" - }, - "devDependencies": { - "esbuild": "^0.19.12", - "typescript": "^5.3.3" - }, - "dependencies": { - } -} \ No newline at end of file + "dependencies": {} +} diff --git a/apps/neuroglancer-url/public/demo.html b/apps/neuroglancer-url/public/demo.html index 8b27db8..7461435 100644 --- a/apps/neuroglancer-url/public/demo.html +++ b/apps/neuroglancer-url/public/demo.html @@ -1,4 +1,4 @@ - +
diff --git a/apps/neuroglancer-url/src/data.ts b/apps/neuroglancer-url/src/data.ts index 40311c0..f82b5e8 100644 --- a/apps/neuroglancer-url/src/data.ts +++ b/apps/neuroglancer-url/src/data.ts @@ -1,349 +1,309 @@ -import type { NGData } from "./types"; +import type { NGData } from './types'; export const data: NGData[] = [ { - "function": "get_image_series_grid_url", - "params": { - "src_config_list": [ - { - "blue_max": 4095.0, - "blue_min": 0.0, - "green_max": 7261.0, - "green_min": 0.0, - "img_name": "1125628029 (40_512_512)", - "ome_zarr_shape": [ - 3, - 142, - 29998, - 39998 + function: 'get_image_series_grid_url', + params: { + src_config_list: [ + { + blue_max: 4095.0, + blue_min: 0.0, + green_max: 7261.0, + green_min: 0.0, + img_name: '1125628029 (40_512_512)', + ome_zarr_shape: [3, 142, 29998, 39998], + red_max: 1261.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1125628029', + x_mm: 0.00035, + y_mm: 0.00035, + z_mm: 0.1, + }, + { + blue_max: 4095.0, + blue_min: 0.0, + green_max: 1304.0, + green_min: 0.0, + img_name: '1145081396 (40_512_512)', + ome_zarr_shape: [3, 142, 11998, 15998], + red_max: 1344.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1145081396', + x_mm: 0.000875, + y_mm: 0.000875, + z_mm: 0.1, + }, + { + blue_max: 4095.0, + blue_min: 0.0, + green_max: 4045.0, + green_min: 0.0, + img_name: '1182837942 (40_512_512)', + ome_zarr_shape: [3, 142, 29998, 39998], + red_max: 864.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1182837942', + x_mm: 0.00035, + y_mm: 0.00035, + z_mm: 0.1, + }, + { + blue_max: 4095.0, + blue_min: 0.0, + green_max: 3013.0, + green_min: 0.0, + img_name: '1240649363 (40_512_512)', + ome_zarr_shape: [3, 142, 29998, 39998], + red_max: 1356.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1240649363', + x_mm: 0.00035, + y_mm: 0.00035, + z_mm: 0.1, + }, ], - "red_max": 1261.0, - "red_min": 0.0, - "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1125628029", - "x_mm": 0.00035, - "y_mm": 0.00035, - "z_mm": 0.1 - }, - { - "blue_max": 4095.0, - "blue_min": 0.0, - "green_max": 1304.0, - "green_min": 0.0, - "img_name": "1145081396 (40_512_512)", - "ome_zarr_shape": [ - 3, - 142, - 11998, - 15998 - ], - "red_max": 1344.0, - "red_min": 0.0, - "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1145081396", - "x_mm": 0.000875, - "y_mm": 0.000875, - "z_mm": 0.1 - }, - { - "blue_max": 4095.0, - "blue_min": 0.0, - "green_max": 4045.0, - "green_min": 0.0, - "img_name": "1182837942 (40_512_512)", - "ome_zarr_shape": [ - 3, - 142, - 29998, - 39998 - ], - "red_max": 864.0, - "red_min": 0.0, - "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1182837942", - "x_mm": 0.00035, - "y_mm": 0.00035, - "z_mm": 0.1 - }, - { - "blue_max": 4095.0, - "blue_min": 0.0, - "green_max": 3013.0, - "green_min": 0.0, - "img_name": "1240649363 (40_512_512)", - "ome_zarr_shape": [ - 3, - 142, - 29998, - 39998 - ], - "red_max": 1356.0, - "red_min": 0.0, - "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1240649363", - "x_mm": 0.00035, - "y_mm": 0.00035, - "z_mm": 0.1 - } - ] - }, - "type": "Multiple image series; coronal projection", - "url": 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"https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2057.142857142857146%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221125628029%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%224panel%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D14522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D14522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201261.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%207261.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1125628029%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221125628029%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D" + function: 'get_neuroglancer_url', + params: { + blue_max: 4095.0, + blue_min: 0.0, + cross_section_scale: 57.142857142857146, + green_max: 7261.0, + green_min: 0.0, + img_name: '1125628029 (40_128_128)', + layout: '4panel', + red_max: 1261.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1125628029', + x_mm: 0.00035, + y_mm: 0.00035, + z_mm: 0.1, + }, + type: 'Single image series; all three planes', + url: 'https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2057.142857142857146%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221125628029%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%224panel%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D14522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D14522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201261.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%207261.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1125628029%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221125628029%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D', }, { - "function": "get_neuroglancer_url", - "params": { - "blue_max": 4095.0, - "blue_min": 0.0, - "cross_section_scale": 37.714285714285715, - "green_max": 7261.0, - "green_min": 0.0, - "img_name": "1125628029 (40_128_128)", - "layout": "xy", - "red_max": 1261.0, - "red_min": 0.0, - "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1125628029", - "x_mm": 0.00035, - "y_mm": 0.00035, - "z_mm": 0.1 - }, - "type": "Single image series; coronal projection", - "url": "https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2037.714285714285715%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221125628029%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%22xy%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D14522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D14522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201261.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%207261.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1125628029%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221125628029%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D" + function: 'get_neuroglancer_url', + params: { + blue_max: 4095.0, + blue_min: 0.0, + cross_section_scale: 37.714285714285715, + green_max: 7261.0, + green_min: 0.0, + img_name: '1125628029 (40_128_128)', + layout: 'xy', + red_max: 1261.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1125628029', + x_mm: 0.00035, + y_mm: 0.00035, + z_mm: 0.1, + }, + type: 'Single image series; coronal projection', + url: 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+ function: 'get_contact_sheet_url', + params: { + blue_max: 4095.0, + blue_min: 0.0, + cross_section_scale: 576.0, + green_max: 7261.0, + green_min: 0.0, + img_name: '1125628029 (40_128_128)', + ome_zarr_shape: [3, 142, 29998, 39998], + red_max: 1261.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1125628029', + x_mm: 0.00035, + y_mm: 0.00035, + z_mm: 0.1, + }, + type: 'Single image series; contact sheet', + url: 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+ function: 'get_neuroglancer_url', + params: { + blue_max: 4095.0, + blue_min: 0.0, + cross_section_scale: 22.857142857142858, + green_max: 1304.0, + green_min: 0.0, + img_name: '1145081396 (40_128_128)', + layout: '4panel', + red_max: 1344.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1145081396', + x_mm: 0.000875, + y_mm: 0.000875, + z_mm: 0.1, + }, + type: 'Single image series; all three planes', + url: 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}, { - "function": "get_neuroglancer_url", - "params": { - "blue_max": 4095.0, - "blue_min": 0.0, - "cross_section_scale": 15.085714285714287, - "green_max": 1304.0, - "green_min": 0.0, - "img_name": "1145081396 (40_128_128)", - "layout": "xy", - "red_max": 1344.0, - "red_min": 0.0, - "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1145081396", - "x_mm": 0.000875, - "y_mm": 0.000875, - "z_mm": 0.1 - }, - "type": "Single image series; coronal projection", - "url": "https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2015.085714285714287%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221145081396%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%22xy%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2688.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2688.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D2608.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D2608.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201344.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%201304.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1145081396%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221145081396%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D" + function: 'get_neuroglancer_url', + params: { + blue_max: 4095.0, + blue_min: 0.0, + cross_section_scale: 15.085714285714287, + green_max: 1304.0, + green_min: 0.0, + img_name: '1145081396 (40_128_128)', + layout: 'xy', + red_max: 1344.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1145081396', + x_mm: 0.000875, + y_mm: 0.000875, + z_mm: 0.1, + }, + type: 'Single image series; coronal projection', + url: 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+ function: 'get_contact_sheet_url', + params: { + blue_max: 4095.0, + blue_min: 0.0, + cross_section_scale: 230.4, + green_max: 1304.0, + green_min: 0.0, + img_name: '1145081396 (40_128_128)', + ome_zarr_shape: [3, 142, 11998, 15998], + red_max: 1344.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1145081396', + x_mm: 0.000875, + y_mm: 0.000875, + z_mm: 0.1, + }, + type: 'Single image series; contact sheet', + url: 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"https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2057.142857142857146%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221182837942%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%224panel%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D1728.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D1728.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D8090.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D8090.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%20864.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%204045.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1182837942%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221182837942%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D" + function: 'get_neuroglancer_url', + params: { + blue_max: 4095.0, + blue_min: 0.0, + cross_section_scale: 57.142857142857146, + green_max: 4045.0, + green_min: 0.0, + img_name: '1182837942 (40_128_128)', + layout: '4panel', + red_max: 864.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1182837942', + x_mm: 0.00035, + y_mm: 0.00035, + z_mm: 0.1, + }, + type: 'Single image series; all three planes', + url: 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}, { - "function": "get_neuroglancer_url", - "params": { - "blue_max": 4095.0, - "blue_min": 0.0, - "cross_section_scale": 37.714285714285715, - "green_max": 4045.0, - "green_min": 0.0, - "img_name": "1182837942 (40_128_128)", - "layout": "xy", - "red_max": 864.0, - "red_min": 0.0, - "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1182837942", - "x_mm": 0.00035, - "y_mm": 0.00035, - "z_mm": 0.1 - }, - "type": "Single image series; coronal projection", - "url": "https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2037.714285714285715%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221182837942%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%22xy%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D1728.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D1728.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D8090.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D8090.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%20864.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%204045.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1182837942%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221182837942%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D" + function: 'get_neuroglancer_url', + params: { + blue_max: 4095.0, + blue_min: 0.0, + cross_section_scale: 37.714285714285715, + green_max: 4045.0, + green_min: 0.0, + img_name: '1182837942 (40_128_128)', + layout: 'xy', + red_max: 864.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1182837942', + x_mm: 0.00035, + y_mm: 0.00035, + z_mm: 0.1, + }, + type: 'Single image series; coronal projection', + url: 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+ function: 'get_contact_sheet_url', + params: { + blue_max: 4095.0, + blue_min: 0.0, + cross_section_scale: 576.0, + green_max: 4045.0, + green_min: 0.0, + img_name: '1182837942 (40_128_128)', + ome_zarr_shape: [3, 142, 29998, 39998], + red_max: 864.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1182837942', + x_mm: 0.00035, + y_mm: 0.00035, + z_mm: 0.1, + }, + type: 'Single image series; contact sheet', + url: 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+ function: 'get_neuroglancer_url', + params: { + blue_max: 4095.0, + blue_min: 0.0, + cross_section_scale: 57.142857142857146, + green_max: 3013.0, + green_min: 0.0, + img_name: '1240649363 (40_128_128)', + layout: '4panel', + red_max: 1356.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1240649363', + x_mm: 0.00035, + y_mm: 0.00035, + z_mm: 0.1, + }, + type: 'Single image series; all three planes', + url: 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}, { - "function": "get_neuroglancer_url", - "params": { - "blue_max": 4095.0, - "blue_min": 0.0, - "cross_section_scale": 37.714285714285715, - "green_max": 3013.0, - "green_min": 0.0, - "img_name": "1240649363 (40_128_128)", - "layout": "xy", - "red_max": 1356.0, - "red_min": 0.0, - "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1240649363", - "x_mm": 0.00035, - "y_mm": 0.00035, - "z_mm": 0.1 - }, - "type": "Single image series; coronal projection", - "url": "https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2037.714285714285715%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221240649363%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%22xy%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2712.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2712.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D6026.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D6026.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201356.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%203013.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1240649363%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221240649363%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D" + function: 'get_neuroglancer_url', + params: { + blue_max: 4095.0, + blue_min: 0.0, + cross_section_scale: 37.714285714285715, + green_max: 3013.0, + green_min: 0.0, + img_name: '1240649363 (40_128_128)', + layout: 'xy', + red_max: 1356.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1240649363', + x_mm: 0.00035, + y_mm: 0.00035, + z_mm: 0.1, + }, + type: 'Single image series; coronal projection', + url: 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- } - ] \ No newline at end of file + function: 'get_contact_sheet_url', + params: { + blue_max: 4095.0, + blue_min: 0.0, + cross_section_scale: 576.0, + green_max: 3013.0, + green_min: 0.0, + img_name: '1240649363 (40_128_128)', + ome_zarr_shape: [3, 142, 29998, 39998], + red_max: 1356.0, + red_min: 0.0, + src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1240649363', + x_mm: 0.00035, + y_mm: 0.00035, + z_mm: 0.1, + }, + type: 'Single image series; contact sheet', + url: 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+ }, +]; diff --git a/apps/neuroglancer-url/tsconfig.json b/apps/neuroglancer-url/tsconfig.json index e5bee2e..0f20604 100644 --- a/apps/neuroglancer-url/tsconfig.json +++ b/apps/neuroglancer-url/tsconfig.json @@ -1,5 +1,4 @@ { "extends": "../tsconfig.json", "include": ["./src/**/*", "../common/src/**/*"] - -} \ No newline at end of file +} diff --git a/apps/omezarr-viewer/README.md b/apps/omezarr-viewer/README.md index 1a525dd..a7e14d8 100644 --- a/apps/omezarr-viewer/README.md +++ b/apps/omezarr-viewer/README.md @@ -1,8 +1,11 @@ ## Ome-Zarr Viewer Demo a very minimal demo to show how one might use the scatterbrain package to render volumetric images contained in an OME-zarr "File". Note that the datasets in the demos (there are 2) are hard-coded to some data in public S3 buckets. + ### Versa + to run the versa demo, assuming you've just cloned this repository: + 1. run `pnpm build` from the root directory 2. run `pnpm install` in this (apps/omezarr-viewer/) directory 3. run `pnpm run versa` in this directory @@ -12,21 +15,25 @@ to run the versa demo, assuming you've just cloned this repository: The app will load, and immediately begin requesting chunks from the versa dataset - you should be able to pan and zoom with the scroll-Wheel / mouse, and you should see a very basic set of UI controls. The versa dataset is a multi-channel "sequence of images" modality - so a list of available slices will be displayed, allowing the user to click on one to view it. RGB channels can be manipulated individually. #### For developers + if you are interested in the code - you can start at the top: versa.ts contains the top-level glue code (its rather... demo-y! apologies for that - you should understand that this area of code is not "the point" - its just a short, easy-to-write harness for the good stuff) that makes the whole thing run. The interesting parts are probably in the neighborhood of `renderFrameHelper(...)`. The pattern we're looking for is:
+ 1. get the chunks of data (or rather, handles to that data) which are in view with `getVisibleTiles` 2. create a frame to render those tiles, using the current view & other settings, using `beginLongRunningFrame` 3. now you have an object (we call it a frame) that represents rendering progress - you can cancel the frame, put it in a list, create a promise to do something when its over, whatever you like! the point is that it is a first class entity which lets you abstract away a great deal of uncertainty and complexity. As long as you targeted a private render target, nothing else that happens in the app can have any impact on the image being rendered by this frame. 4. Still reading? you might be interested in the "plugin-style" renderer which actually renders chunks of ome-zarr data - take a look at `versa-renderer.ts` which contain the "strategy" components of rendering: -
- a. given a "camera" and a dataset, get me all the tasks (in our case, chunks of images) for what is in view: `getVisibleTiles` - b. given a handle to a "chunk" fetch the chunk and associate it with how it will be used during rendering: `requestsForTile()` - c. given fully-fetched data for a tile, render it! `buildVersaRenderer` - in this case we use [REgl](https://github.com/regl-project/regl/blob/master/API.md), an excellent WebGL abstraction layer, but the point of this plug-ability is that any user of the scatterbrain components may use whatever low-level rendering system (or data format) they prefer! +
+ a. given a "camera" and a dataset, get me all the tasks (in our case, chunks of images) for what is in view: `getVisibleTiles` + b. given a handle to a "chunk" fetch the chunk and associate it with how it will be used during rendering: `requestsForTile()` + c. given fully-fetched data for a tile, render it! `buildVersaRenderer` - in this case we use [REgl](https://github.com/regl-project/regl/blob/master/API.md), an excellent WebGL abstraction layer, but the point of this plug-ability is that any user of the scatterbrain components may use whatever low-level rendering system (or data format) they prefer! + ### Tissuecyte + to run the Tissuecyte demo, assuming you've just cloned this repository: + 1. run `pnpm build` from the root directory 2. run `pnpm install` in this (apps/omezarr-viewer/) directory 3. run `pnpm run tissuecyte` in this directory 4. navigate to apps/omezarr-viewer/dst/ using your File browser / finder, and open `tissuecyte.html` in your browser. - -The app will load, and immediately begin requesting chunks from the tissuecyte dataset - you should be able to pan and zoom with the scrollwheel / mouse, and you should see a very basic set of UI controls. The tissuecyte dataset is a "Volume" mode dataset - you get a single channel (gray-scale), and you can scroll through slices of the volume with Alt+Scroll, or use the slider in the UI. Note that in both demos, very little work was done to provide a "production ready" experience - the screen will go black in places where data it needs to render is not yet available, it may be flickery. In particular, the limit on cache memory is quite low, so delays while waiting for data to be (re) downloaded are to be expected. \ No newline at end of file +The app will load, and immediately begin requesting chunks from the tissuecyte dataset - you should be able to pan and zoom with the scrollwheel / mouse, and you should see a very basic set of UI controls. The tissuecyte dataset is a "Volume" mode dataset - you get a single channel (gray-scale), and you can scroll through slices of the volume with Alt+Scroll, or use the slider in the UI. Note that in both demos, very little work was done to provide a "production ready" experience - the screen will go black in places where data it needs to render is not yet available, it may be flickery. In particular, the limit on cache memory is quite low, so delays while waiting for data to be (re) downloaded are to be expected. diff --git a/apps/omezarr-viewer/package.json b/apps/omezarr-viewer/package.json index 4abed12..9eed628 100644 --- a/apps/omezarr-viewer/package.json +++ b/apps/omezarr-viewer/package.json @@ -1,52 +1,52 @@ { - "name": "@alleninstitute/vis-omezarr-demo", - "version": "0.0.1", - "contributors": [ - { - "name": "Lane Sawyer", - "email": "lane.sawyer@alleninstitute.org" + "name": "@alleninstitute/vis-omezarr-demo", + "version": "0.0.1", + "contributors": [ + { + "name": "Lane Sawyer", + "email": "lane.sawyer@alleninstitute.org" + }, + { + "name": "James Gerstenberger", + "email": "james.gerstenberger@alleninstitute.org" + }, + { + "name": "Noah Shepard", + "email": "noah.shepard@alleninstitute.org" + }, + { + "name": "Skyler Moosman", + "email": "skyler.moosman@alleninstitute.org" + }, + { + "name": "Su Li", + "email": "su.li@alleninstitute.org" + } + ], + "license": "TBD", + "type": "module", + "main": "lib/index.js", + "types": "lib/index.d.ts", + "private": true, + "scripts": { + "preinstall": "npx only-allow pnpm", + "typecheck": "tsc --noEmit", + "demo": "esbuild src/demo.ts --bundle --outfile=dst/demo.js && cp public/* dst/", + "versa": "esbuild src/versa.ts --bundle --outfile=dst/versa.js && cp public/* dst/", + "tissuecyte": "esbuild src/tissuecyte.ts --bundle --outfile=dst/tissuecyte.js && cp public/* dst/", + "test": "jest --config=jest.config.cjs --watch" }, - { - "name": "James Gerstenberger", - "email": "james.gerstenberger@alleninstitute.org" + "devDependencies": { + "esbuild": "^0.19.12", + "typescript": "^5.3.3" }, - { - "name": "Noah Shepard", - "email": "noah.shepard@alleninstitute.org" - }, - { - "name": "Skyler Moosman", - "email": "skyler.moosman@alleninstitute.org" - }, - { - "name": "Su Li", - "email": "su.li@alleninstitute.org" + "dependencies": { + "@alleninstitute/vis-geometry": "workspace:*", + "@alleninstitute/vis-scatterbrain": "workspace:*", + "@types/lodash": "^4.14.202", + "@zhobo63/imgui-ts": "^0.1.43", + "lodash": "^4.17.21", + "regl": "^2.1.0", + "zarr": "^0.6.2" } - ], - "license": "TBD", - "type": "module", - "main": "lib/index.js", - "types": "lib/index.d.ts", - "private": true, - "scripts": { - "preinstall": "npx only-allow pnpm", - "typecheck": "tsc --noEmit", - "demo": "esbuild src/demo.ts --bundle --outfile=dst/demo.js && cp public/* dst/", - "versa": "esbuild src/versa.ts --bundle --outfile=dst/versa.js && cp public/* dst/", - "tissuecyte": "esbuild src/tissuecyte.ts --bundle --outfile=dst/tissuecyte.js && cp public/* dst/", - "test": "jest --config=jest.config.cjs --watch" - }, - "devDependencies": { - "esbuild": "^0.19.12", - "typescript": "^5.3.3" - }, - "dependencies": { - "@alleninstitute/vis-geometry": "workspace:*", - "@alleninstitute/vis-scatterbrain": "workspace:*", - "@types/lodash": "^4.14.202", - "@zhobo63/imgui-ts": "^0.1.43", - "lodash": "^4.17.21", - "regl": "^2.1.0", - "zarr": "^0.6.2" - } -} \ No newline at end of file +} diff --git a/apps/omezarr-viewer/public/tissuecyte.html b/apps/omezarr-viewer/public/tissuecyte.html index 5cd56e5..1f15c28 100644 --- a/apps/omezarr-viewer/public/tissuecyte.html +++ b/apps/omezarr-viewer/public/tissuecyte.html @@ -1,8 +1,14 @@ - + - - - - + + + + diff --git a/apps/omezarr-viewer/public/versa.html b/apps/omezarr-viewer/public/versa.html index 9821564..8c25eb8 100644 --- a/apps/omezarr-viewer/public/versa.html +++ b/apps/omezarr-viewer/public/versa.html @@ -1,7 +1,10 @@ - - - - - - - + + + + + + + diff --git a/apps/omezarr-viewer/src/annotation/path.ts b/apps/omezarr-viewer/src/annotation/path.ts index f0ff00e..1bb5aa2 100644 --- a/apps/omezarr-viewer/src/annotation/path.ts +++ b/apps/omezarr-viewer/src/annotation/path.ts @@ -1,99 +1,97 @@ -import type { vec2, vec4 } from "@alleninstitute/vis-geometry" - -export type Point = { - point: vec2; - pressure?: number; -} -// type SLLNode = { -// item: T; -// next: SLLNode | null; -// } -// type SLL = { -// head: SLLNode|null; -// tail: SLLNode|null; -// length -// } -export type Pen = { - color: vec4; - strokeWidth: number; -} -export type PathAnnotation = { - path: Point[]; - pen: Pen; -} - -// make a set of handlers that make a thing drawable... - - -// how would we generify drawing on top of something... -export type DrawingHost = { - updateCurrentStroke: (point: Point) => void; - newStroke: (point: Point) => void; - // endStroke? - currentTool: () => Pen | 'camera'; - pan: (screenDelta: vec2) => void; - screenToDataSpace: (screen: vec2) => vec2; - screenWidthToDataWidth: (w: number) => number; -} - -export function initDrawableInterface(surface: HTMLElement, host: DrawingHost) { - let buttonDown: boolean = false; - let curPointerId: number | null; - - surface.onpointermove = (ev: PointerEvent) => { - if (buttonDown && ev.pointerId === curPointerId) { - if (host.currentTool() == 'camera') { - // pan that camera! - host.pan([ev.movementX, ev.movementY]) - } else { - // draw with our current pen... hmmmm - host.updateCurrentStroke({ - point: host.screenToDataSpace([ev.x, ev.y]), - pressure: ev.pressure - }) - } - } - } - surface.onpointerdown = (ev: PointerEvent) => { - if (curPointerId === null) { - curPointerId = ev.pointerId; - buttonDown = true; - if (host.currentTool() !== 'camera') { - host.newStroke({ - point: host.screenToDataSpace([ev.x, ev.y]), - pressure: ev.pressure - }) - } - } - } - surface.onpointerup = (ev: PointerEvent) => { - if (curPointerId === ev.pointerId) { - curPointerId = null; - buttonDown = false; - } - } - - - return () => { - // cleanup! - // todo! - } -} - -// export function beginDrawing(pen: Pen, p: vec2, pressure?: number): PathAnnotation { -// return { -// pen, -// path: [{ -// point: p, -// pressure: pressure ?? 1.0 -// }] -// } -// } -// export function continueDrawing(annotation: PathAnnotation, p: vec2, pressure?: number): PathAnnotation { -// return { -// ...annotation, path: [...annotation.path, { -// point: p, -// pressure: pressure ?? 1.0 -// }] -// } -// } +import type { vec2, vec4 } from '@alleninstitute/vis-geometry'; + +export type Point = { + point: vec2; + pressure?: number; +}; +// type SLLNode = { +// item: T; +// next: SLLNode | null; +// } +// type SLL = { +// head: SLLNode|null; +// tail: SLLNode|null; +// length +// } +export type Pen = { + color: vec4; + strokeWidth: number; +}; +export type PathAnnotation = { + path: Point[]; + pen: Pen; +}; + +// make a set of handlers that make a thing drawable... + +// how would we generify drawing on top of something... +export type DrawingHost = { + updateCurrentStroke: (point: Point) => void; + newStroke: (point: Point) => void; + // endStroke? + currentTool: () => Pen | 'camera'; + pan: (screenDelta: vec2) => void; + screenToDataSpace: (screen: vec2) => vec2; + screenWidthToDataWidth: (w: number) => number; +}; + +export function initDrawableInterface(surface: HTMLElement, host: DrawingHost) { + let buttonDown: boolean = false; + let curPointerId: number | null; + + surface.onpointermove = (ev: PointerEvent) => { + if (buttonDown && ev.pointerId === curPointerId) { + if (host.currentTool() == 'camera') { + // pan that camera! + host.pan([ev.movementX, ev.movementY]); + } else { + // draw with our current pen... hmmmm + host.updateCurrentStroke({ + point: host.screenToDataSpace([ev.x, ev.y]), + pressure: ev.pressure, + }); + } + } + }; + surface.onpointerdown = (ev: PointerEvent) => { + if (curPointerId === null) { + curPointerId = ev.pointerId; + buttonDown = true; + if (host.currentTool() !== 'camera') { + host.newStroke({ + point: host.screenToDataSpace([ev.x, ev.y]), + pressure: ev.pressure, + }); + } + } + }; + surface.onpointerup = (ev: PointerEvent) => { + if (curPointerId === ev.pointerId) { + curPointerId = null; + buttonDown = false; + } + }; + + return () => { + // cleanup! + // todo! + }; +} + +// export function beginDrawing(pen: Pen, p: vec2, pressure?: number): PathAnnotation { +// return { +// pen, +// path: [{ +// point: p, +// pressure: pressure ?? 1.0 +// }] +// } +// } +// export function continueDrawing(annotation: PathAnnotation, p: vec2, pressure?: number): PathAnnotation { +// return { +// ...annotation, path: [...annotation.path, { +// point: p, +// pressure: pressure ?? 1.0 +// }] +// } +// } diff --git a/apps/omezarr-viewer/src/camera.ts b/apps/omezarr-viewer/src/camera.ts index 5cda0b2..a73dfb5 100644 --- a/apps/omezarr-viewer/src/camera.ts +++ b/apps/omezarr-viewer/src/camera.ts @@ -1,9 +1,8 @@ -import type { box2D, vec2 } from "@alleninstitute/vis-geometry" - -// a basic camera, for viewing slices -export type Camera = { - readonly view: box2D; // a view in 'data space' - readonly screen: vec2; // what that view projects to in display space, aka pixels - readonly projection: 'webImage' | 'cartesian' -} - +import type { box2D, vec2 } from '@alleninstitute/vis-geometry'; + +// a basic camera, for viewing slices +export type Camera = { + readonly view: box2D; // a view in 'data space' + readonly screen: vec2; // what that view projects to in display space, aka pixels + readonly projection: 'webImage' | 'cartesian'; +}; diff --git a/apps/omezarr-viewer/src/components/color-map.ts b/apps/omezarr-viewer/src/components/color-map.ts index 280f09c..41aa90b 100644 --- a/apps/omezarr-viewer/src/components/color-map.ts +++ b/apps/omezarr-viewer/src/components/color-map.ts @@ -1,66 +1,66 @@ -// an IM-gui widget for controlling the display of a single channel - -// an IM-gui widget for controlling the display of a single channel -import type { Interval } from "@alleninstitute/vis-geometry"; -import { ImGui } from "@zhobo63/imgui-ts"; -import type { ImTuple2 } from "@zhobo63/imgui-ts/src/bind-imgui"; -import { ImGuiColorEditFlags, ImGuiSliderFlags, ImVec4 } from "@zhobo63/imgui-ts/src/imgui"; - -// assumes its mid-frame of an IMGui.newFrame() when called! - -export function colorMapWidget( - channel: string, - mutable: { - useMe: boolean; - color: ImVec4; - gamut: Interval; - index: number; - }, - numChannels: number -) { - const channelChoices = new Array(numChannels).map((n) => n.toFixed(0)); - const getter = (data: string[], index: number, out: [string]) => { - out[0] = data[index]; - return false; - }; - let changed = false; - const { gamut, color } = mutable; - let index = mutable.index; - const range: ImTuple2 = [gamut.min, gamut.max]; - if ( - ImGui.Checkbox("", (b?: boolean) => { - mutable.useMe = b ?? mutable.useMe; - return mutable.useMe; - }) - ) { - changed = true; - } - ImGui.SameLine(); - ImGui.ColorButton(" ", color, ImGuiColorEditFlags.NoAlpha); - ImGui.SameLine(); - ImGui.PushItemWidth(10); - if ( - ImGui.DragInt( - `${channel}_options`, - (i?: number) => { - index = i ?? index; - return index; - }, - 0.2, - 0, - numChannels - 1, - "%i" - ) - ) { - changed = true; - mutable.index = index; - } - ImGui.PopItemWidth(); - - ImGui.SameLine(); - if (ImGui.SliderFloat2(channel, range, 0, 9999, "%3f", ImGuiSliderFlags.Logarithmic)) { - mutable.gamut = { min: range[0], max: range[1] }; - changed = true; - } - return { changed, ...mutable }; -} +// an IM-gui widget for controlling the display of a single channel + +// an IM-gui widget for controlling the display of a single channel +import type { Interval } from '@alleninstitute/vis-geometry'; +import { ImGui } from '@zhobo63/imgui-ts'; +import type { ImTuple2 } from '@zhobo63/imgui-ts/src/bind-imgui'; +import { ImGuiColorEditFlags, ImGuiSliderFlags, ImVec4 } from '@zhobo63/imgui-ts/src/imgui'; + +// assumes its mid-frame of an IMGui.newFrame() when called! + +export function colorMapWidget( + channel: string, + mutable: { + useMe: boolean; + color: ImVec4; + gamut: Interval; + index: number; + }, + numChannels: number +) { + const channelChoices = new Array(numChannels).map((n) => n.toFixed(0)); + const getter = (data: string[], index: number, out: [string]) => { + out[0] = data[index]; + return false; + }; + let changed = false; + const { gamut, color } = mutable; + let index = mutable.index; + const range: ImTuple2 = [gamut.min, gamut.max]; + if ( + ImGui.Checkbox('', (b?: boolean) => { + mutable.useMe = b ?? mutable.useMe; + return mutable.useMe; + }) + ) { + changed = true; + } + ImGui.SameLine(); + ImGui.ColorButton(' ', color, ImGuiColorEditFlags.NoAlpha); + ImGui.SameLine(); + ImGui.PushItemWidth(10); + if ( + ImGui.DragInt( + `${channel}_options`, + (i?: number) => { + index = i ?? index; + return index; + }, + 0.2, + 0, + numChannels - 1, + '%i' + ) + ) { + changed = true; + mutable.index = index; + } + ImGui.PopItemWidth(); + + ImGui.SameLine(); + if (ImGui.SliderFloat2(channel, range, 0, 9999, '%3f', ImGuiSliderFlags.Logarithmic)) { + mutable.gamut = { min: range[0], max: range[1] }; + changed = true; + } + return { changed, ...mutable }; +} diff --git a/apps/omezarr-viewer/src/image-renderer.ts b/apps/omezarr-viewer/src/image-renderer.ts index 0984187..0133cb7 100644 --- a/apps/omezarr-viewer/src/image-renderer.ts +++ b/apps/omezarr-viewer/src/image-renderer.ts @@ -1,67 +1,67 @@ -import type { vec2, vec4 } from "@alleninstitute/vis-geometry"; -import REGL, { type Framebuffer2D } from "regl"; - -type Props = { - target: Framebuffer2D | null; - box: vec4; - view: vec4; - // viewport: REGL.BoundingBox; - img: REGL.Texture2D | REGL.Framebuffer2D; -}; -export function buildImageRenderer(regl: REGL.Regl) { - const cmd = regl< - { view: vec4; box: vec4; img: REGL.Texture2D | REGL.Framebuffer2D }, - { pos: REGL.BufferData }, - Props - >({ - vert: ` precision highp float; - attribute vec2 pos; - - uniform vec4 view; - uniform vec4 box; - varying vec2 texCoord; - - void main(){ - vec2 tileSize = box.zw-box.xy; - texCoord = pos; - vec2 obj = (pos.xy*tileSize+box.xy); - vec2 p = (obj-view.xy)/(view.zw-view.xy); - // now, to clip space - p = (p*2.0)-1.0; - gl_Position = vec4(p.x,p.y,0.0,1.0); - }`, - frag: ` - precision highp float; - - uniform sampler2D img; - // its more direct to do 3 separate channels... - varying vec2 texCoord; - void main(){ - - gl_FragColor =texture2D(img, texCoord); - }`, - framebuffer: regl.prop("target"), - attributes: { - pos: [0, 0, 1, 0, 1, 1, 0, 1], - }, - depth: { - enable: false, - }, - uniforms: { - box: regl.prop("box"), - view: regl.prop("view"), - img: regl.prop("img"), - }, - blend: { - enable: true, - func: { - src: "src alpha", - dst: "one minus src alpha", - }, - }, - count: 4, - primitive: "triangle fan", - // ... more! - }); - return cmd; -} +import type { vec2, vec4 } from '@alleninstitute/vis-geometry'; +import REGL, { type Framebuffer2D } from 'regl'; + +type Props = { + target: Framebuffer2D | null; + box: vec4; + view: vec4; + // viewport: REGL.BoundingBox; + img: REGL.Texture2D | REGL.Framebuffer2D; +}; +export function buildImageRenderer(regl: REGL.Regl) { + const cmd = regl< + { view: vec4; box: vec4; img: REGL.Texture2D | REGL.Framebuffer2D }, + { pos: REGL.BufferData }, + Props + >({ + vert: ` precision highp float; + attribute vec2 pos; + + uniform vec4 view; + uniform vec4 box; + varying vec2 texCoord; + + void main(){ + vec2 tileSize = box.zw-box.xy; + texCoord = pos; + vec2 obj = (pos.xy*tileSize+box.xy); + vec2 p = (obj-view.xy)/(view.zw-view.xy); + // now, to clip space + p = (p*2.0)-1.0; + gl_Position = vec4(p.x,p.y,0.0,1.0); + }`, + frag: ` + precision highp float; + + uniform sampler2D img; + // its more direct to do 3 separate channels... + varying vec2 texCoord; + void main(){ + + gl_FragColor =texture2D(img, texCoord); + }`, + framebuffer: regl.prop('target'), + attributes: { + pos: [0, 0, 1, 0, 1, 1, 0, 1], + }, + depth: { + enable: false, + }, + uniforms: { + box: regl.prop('box'), + view: regl.prop('view'), + img: regl.prop('img'), + }, + blend: { + enable: true, + func: { + src: 'src alpha', + dst: 'one minus src alpha', + }, + }, + count: 4, + primitive: 'triangle fan', + // ... more! + }); + return cmd; +} diff --git a/apps/omezarr-viewer/src/slice-renderer.ts b/apps/omezarr-viewer/src/slice-renderer.ts index 91473d0..7575c04 100644 --- a/apps/omezarr-viewer/src/slice-renderer.ts +++ b/apps/omezarr-viewer/src/slice-renderer.ts @@ -1,255 +1,250 @@ -import REGL from "regl"; -import { - type ZarrDataset, - type ZarrRequest, - getSlice, - indexOfDimension, - pickBestScale, - sizeInUnits, - planeSizeInVoxels, -} from "Common/loaders/ome-zarr/zarr-data";; -import { Box2D, type Interval, Vec2, type box2D, type vec2, type vec4 } from "@alleninstitute/vis-geometry"; -import type { Camera } from "./camera"; - -type Props = { - tile: vec4; - view: vec4; - gamut: vec2; - viewport: REGL.BoundingBox; - img: REGL.Texture2D; - rot: number; - target: REGL.Framebuffer2D | null; -}; -export function buildVolumeSliceRenderer(regl: REGL.Regl) { - const cmd = regl< - { view: vec4; tile: vec4; img: REGL.Texture2D; gamut: vec2; rot: number }, - { pos: REGL.BufferData }, - Props - >({ - vert: ` precision highp float; - attribute vec2 pos; - - uniform vec4 view; - uniform vec4 tile; - uniform float rot; - varying vec2 texCoord; - - vec2 rotateObj(vec2 obj, float radians){ - return obj; - // mat2 R = mat2( - // vec2(cos(radians),-sin(radians)), - // vec2(-sin(radians),cos(radians)) - // ); - // return R*obj; - } - vec2 rotateTextureCoordinates(vec2 tx, float radians){ - vec2 xy = tx-vec2(0.5,0.5); - mat2 R = mat2( - vec2(cos(radians),-sin(radians)), - vec2(-sin(radians),cos(radians)) - ); - return ((R*xy)+vec2(0.5,0.5)); - } - void main(){ - vec2 tileSize = (tile.zw-tile.xy); - texCoord = rotateTextureCoordinates(pos,rot); - vec2 obj = rotateObj((pos.xy*tileSize+tile.xy),rot); - vec2 p = (obj-view.xy)/(view.zw-view.xy); - // now, to clip space - p = (p*2.0)-1.0; - - gl_Position = vec4(p.x,p.y,0.0,1.0); - }`, - frag: ` - precision highp float; - uniform sampler2D img; - uniform vec2 gamut; - varying vec2 texCoord; - void main(){ - float span = gamut.y-gamut.x; - float lum = texture2D(img, texCoord).r/span-gamut.x; - gl_FragColor = vec4(lum,lum,lum, 1.0); - }`, - attributes: { - pos: [0, 0, 1, 0, 1, 1, 0, 1], - }, - uniforms: { - rot: regl.prop("rot"), - tile: regl.prop("tile"), - view: regl.prop("view"), - img: regl.prop("img"), - gamut: regl.prop("gamut"), - }, - depth: { - enable: false, - }, - framebuffer: regl.prop("target"), - count: 4, - // viewport: regl.prop("viewport"), - primitive: "triangle fan", - // ... more! - }); - - return (item: VoxelTile, settings: VoxelSliceRenderSettings, tasks: Record) => { - const { view, viewport, gamut, target } = settings; - const { bounds } = item; - const img = tasks[LUMINANCE]; - if (!img || !('type' in img && img.type === 'texture2D')) return; // we cant render if the data for the positions is missing! - cmd({ - view: [...view.minCorner, ...view.maxCorner], - tile: [...bounds.minCorner, ...bounds.maxCorner], - // viewport, - gamut: [gamut.min, gamut.max], - img: img.data, - rot: settings.rotation, - target, - }); - }; -} -type Bfr = { type: 'texture2D', data: REGL.Texture2D }; - -type Tile = { bounds: box2D }; -export type VoxelSliceRenderSettings = { - regl: REGL.Regl; - target: REGL.Framebuffer2D | null; - dataset: ZarrDataset; - view: box2D; - gamut: Interval; - rotation: number; - viewport: REGL.BoundingBox; -}; -export type AxisAlignedPlane = "xy" | "yz" | "xz"; -export type VoxelTile = { - plane: AxisAlignedPlane; - bounds: box2D; // in voxels, in the plane - planeIndex: number; - layerIndex: number; - // time and channel are always = 0, for now -}; - -function toZarrRequest(tile: VoxelTile): ZarrRequest { - const { plane, planeIndex, bounds } = tile; - const { minCorner: min, maxCorner: max } = bounds; - const u = { min: min[0], max: max[0] }; - const v = { min: min[1], max: max[1] }; - switch (plane) { - case "xy": - return { - x: u, - y: v, - t: 0, - c: 0, - z: planeIndex, - }; - case "xz": - return { - x: u, - z: v, - t: 0, - c: 0, - y: planeIndex, - }; - case "yz": - return { - y: u, - z: v, - t: 0, - c: 0, - x: planeIndex, - }; - } -} -export function cacheKeyFactory(col: string, item: VoxelTile, settings: VoxelSliceRenderSettings) { - return `${JSON.stringify(item)}_${col}`; -} -const LUMINANCE = "luminance"; -export function requestsForTile(tile: VoxelTile, settings: VoxelSliceRenderSettings, signal?: AbortSignal) { - const { dataset, regl } = settings; - - return { - luminance: async () => { - // console.log("req: ", tile); - const vxl = await getSlice(dataset, toZarrRequest(tile), tile.layerIndex); - // TODO: cancel? - const { shape, buffer } = vxl; - // upload the data to a webgl texture - // draw that texture to the screen with our command - // console.log("upload new tile: ", cacheKeyFactory("lum", tile, settings)); - const tex = regl.texture({ - data: new Float32Array(buffer.flatten()), - width: shape[1], - height: shape[0], // TODO this swap is sus - format: "luminance", - }); - return { type: 'texture2D', data: tex }; - }, - }; -} - -function getAllTiles(idealTilePx: vec2, layerSize: vec2) { - // return the set of all our "tiles" of this layer, given the tilePx size - const tiles: box2D[] = []; - for (let x = 0; x < layerSize[0]; x += idealTilePx[0]) { - for (let y = 0; y < layerSize[1]; y += idealTilePx[1]) { - const xy: vec2 = [x, y]; - tiles.push(Box2D.create(xy, Vec2.min(Vec2.add(xy, idealTilePx), layerSize))); - } - } - return tiles; -} -const uvTable = { - xy: { u: "x", v: "y" }, - xz: { u: "x", v: "z" }, - yz: { u: "y", v: "z" }, -} as const; -const sliceDimension = { - xy: "z", - xz: "y", - yz: "x", -} as const; - -export function getVisibleTiles( - camera: Camera, - plane: AxisAlignedPlane, - sliceParam: number, - dataset: ZarrDataset -): { layer: number; view: box2D; tiles: VoxelTile[] } { - const { axes, datasets } = dataset.multiscales[0]; - const sliceSize = sizeInUnits(uvTable[plane], axes, datasets[0])!; - - const zIndex = indexOfDimension(axes, sliceDimension[plane]); - const thingy = pickBestScale( - dataset, - uvTable[plane], - camera.view, - camera.screen - ); - const thickness = thingy.shape[zIndex]; - const planeIndex = Math.floor(thickness * sliceParam); - // TODO: open the array, look at its chunks, use that size for the size of the tiles I request! - const layerIndex = dataset.multiscales[0].datasets.indexOf(thingy); - const size = planeSizeInVoxels(uvTable[plane], dataset.multiscales[0].axes, thingy); - const realSize = sizeInUnits(uvTable[plane], dataset.multiscales[0].axes, thingy); - if (!size || !realSize) return { layer: layerIndex, view: Box2D.create([0, 0], [1, 1]), tiles: [] }; - const scale = Vec2.div(realSize, size); - // to go from a voxel-box to a real-box (easier than you think, as both have an origin at 0,0, because we only support scale...) - const vxlToReal = (vxl: box2D) => Box2D.scale(vxl, scale); - const realToVxl = (real: box2D) => Box2D.scale(real, Vec2.div(size, realSize)); - - // find the tiles, in voxels, to request... - const allTiles = getAllTiles([256, 256], size); - const inView = allTiles.filter((tile) => !!Box2D.intersection(camera.view, vxlToReal(tile))); - // camera.view is in a made up dataspace, where 1=height of the current dataset - // thus, we have to convert it into a voxel-space camera for intersections - const voxelView = realToVxl(camera.view); - return { - layer: layerIndex, - view: voxelView, - tiles: inView.map((uv) => ({ - plane, - bounds: uv, - planeIndex, - layerIndex, - })), - }; -} +import REGL from 'regl'; +import { + type ZarrDataset, + type ZarrRequest, + getSlice, + indexOfDimension, + pickBestScale, + sizeInUnits, + planeSizeInVoxels, +} from 'Common/loaders/ome-zarr/zarr-data'; +import { Box2D, type Interval, Vec2, type box2D, type vec2, type vec4 } from '@alleninstitute/vis-geometry'; +import type { Camera } from './camera'; + +type Props = { + tile: vec4; + view: vec4; + gamut: vec2; + viewport: REGL.BoundingBox; + img: REGL.Texture2D; + rot: number; + target: REGL.Framebuffer2D | null; +}; +export function buildVolumeSliceRenderer(regl: REGL.Regl) { + const cmd = regl< + { view: vec4; tile: vec4; img: REGL.Texture2D; gamut: vec2; rot: number }, + { pos: REGL.BufferData }, + Props + >({ + vert: ` precision highp float; + attribute vec2 pos; + + uniform vec4 view; + uniform vec4 tile; + uniform float rot; + varying vec2 texCoord; + + vec2 rotateObj(vec2 obj, float radians){ + return obj; + // mat2 R = mat2( + // vec2(cos(radians),-sin(radians)), + // vec2(-sin(radians),cos(radians)) + // ); + // return R*obj; + } + vec2 rotateTextureCoordinates(vec2 tx, float radians){ + vec2 xy = tx-vec2(0.5,0.5); + mat2 R = mat2( + vec2(cos(radians),-sin(radians)), + vec2(-sin(radians),cos(radians)) + ); + return ((R*xy)+vec2(0.5,0.5)); + } + void main(){ + vec2 tileSize = (tile.zw-tile.xy); + texCoord = rotateTextureCoordinates(pos,rot); + vec2 obj = rotateObj((pos.xy*tileSize+tile.xy),rot); + vec2 p = (obj-view.xy)/(view.zw-view.xy); + // now, to clip space + p = (p*2.0)-1.0; + + gl_Position = vec4(p.x,p.y,0.0,1.0); + }`, + frag: ` + precision highp float; + uniform sampler2D img; + uniform vec2 gamut; + varying vec2 texCoord; + void main(){ + float span = gamut.y-gamut.x; + float lum = texture2D(img, texCoord).r/span-gamut.x; + gl_FragColor = vec4(lum,lum,lum, 1.0); + }`, + attributes: { + pos: [0, 0, 1, 0, 1, 1, 0, 1], + }, + uniforms: { + rot: regl.prop('rot'), + tile: regl.prop('tile'), + view: regl.prop('view'), + img: regl.prop('img'), + gamut: regl.prop('gamut'), + }, + depth: { + enable: false, + }, + framebuffer: regl.prop('target'), + count: 4, + // viewport: regl.prop("viewport"), + primitive: 'triangle fan', + // ... more! + }); + + return (item: VoxelTile, settings: VoxelSliceRenderSettings, tasks: Record) => { + const { view, viewport, gamut, target } = settings; + const { bounds } = item; + const img = tasks[LUMINANCE]; + if (!img || !('type' in img && img.type === 'texture2D')) return; // we cant render if the data for the positions is missing! + cmd({ + view: [...view.minCorner, ...view.maxCorner], + tile: [...bounds.minCorner, ...bounds.maxCorner], + // viewport, + gamut: [gamut.min, gamut.max], + img: img.data, + rot: settings.rotation, + target, + }); + }; +} +type Bfr = { type: 'texture2D'; data: REGL.Texture2D }; + +type Tile = { bounds: box2D }; +export type VoxelSliceRenderSettings = { + regl: REGL.Regl; + target: REGL.Framebuffer2D | null; + dataset: ZarrDataset; + view: box2D; + gamut: Interval; + rotation: number; + viewport: REGL.BoundingBox; +}; +export type AxisAlignedPlane = 'xy' | 'yz' | 'xz'; +export type VoxelTile = { + plane: AxisAlignedPlane; + bounds: box2D; // in voxels, in the plane + planeIndex: number; + layerIndex: number; + // time and channel are always = 0, for now +}; + +function toZarrRequest(tile: VoxelTile): ZarrRequest { + const { plane, planeIndex, bounds } = tile; + const { minCorner: min, maxCorner: max } = bounds; + const u = { min: min[0], max: max[0] }; + const v = { min: min[1], max: max[1] }; + switch (plane) { + case 'xy': + return { + x: u, + y: v, + t: 0, + c: 0, + z: planeIndex, + }; + case 'xz': + return { + x: u, + z: v, + t: 0, + c: 0, + y: planeIndex, + }; + case 'yz': + return { + y: u, + z: v, + t: 0, + c: 0, + x: planeIndex, + }; + } +} +export function cacheKeyFactory(col: string, item: VoxelTile, settings: VoxelSliceRenderSettings) { + return `${JSON.stringify(item)}_${col}`; +} +const LUMINANCE = 'luminance'; +export function requestsForTile(tile: VoxelTile, settings: VoxelSliceRenderSettings, signal?: AbortSignal) { + const { dataset, regl } = settings; + + return { + luminance: async () => { + // console.log("req: ", tile); + const vxl = await getSlice(dataset, toZarrRequest(tile), tile.layerIndex); + // TODO: cancel? + const { shape, buffer } = vxl; + // upload the data to a webgl texture + // draw that texture to the screen with our command + // console.log("upload new tile: ", cacheKeyFactory("lum", tile, settings)); + const tex = regl.texture({ + data: new Float32Array(buffer.flatten()), + width: shape[1], + height: shape[0], // TODO this swap is sus + format: 'luminance', + }); + return { type: 'texture2D', data: tex }; + }, + }; +} + +function getAllTiles(idealTilePx: vec2, layerSize: vec2) { + // return the set of all our "tiles" of this layer, given the tilePx size + const tiles: box2D[] = []; + for (let x = 0; x < layerSize[0]; x += idealTilePx[0]) { + for (let y = 0; y < layerSize[1]; y += idealTilePx[1]) { + const xy: vec2 = [x, y]; + tiles.push(Box2D.create(xy, Vec2.min(Vec2.add(xy, idealTilePx), layerSize))); + } + } + return tiles; +} +const uvTable = { + xy: { u: 'x', v: 'y' }, + xz: { u: 'x', v: 'z' }, + yz: { u: 'y', v: 'z' }, +} as const; +const sliceDimension = { + xy: 'z', + xz: 'y', + yz: 'x', +} as const; + +export function getVisibleTiles( + camera: Camera, + plane: AxisAlignedPlane, + sliceParam: number, + dataset: ZarrDataset +): { layer: number; view: box2D; tiles: VoxelTile[] } { + const { axes, datasets } = dataset.multiscales[0]; + const sliceSize = sizeInUnits(uvTable[plane], axes, datasets[0])!; + + const zIndex = indexOfDimension(axes, sliceDimension[plane]); + const thingy = pickBestScale(dataset, uvTable[plane], camera.view, camera.screen); + const thickness = thingy.shape[zIndex]; + const planeIndex = Math.floor(thickness * sliceParam); + // TODO: open the array, look at its chunks, use that size for the size of the tiles I request! + const layerIndex = dataset.multiscales[0].datasets.indexOf(thingy); + const size = planeSizeInVoxels(uvTable[plane], dataset.multiscales[0].axes, thingy); + const realSize = sizeInUnits(uvTable[plane], dataset.multiscales[0].axes, thingy); + if (!size || !realSize) return { layer: layerIndex, view: Box2D.create([0, 0], [1, 1]), tiles: [] }; + const scale = Vec2.div(realSize, size); + // to go from a voxel-box to a real-box (easier than you think, as both have an origin at 0,0, because we only support scale...) + const vxlToReal = (vxl: box2D) => Box2D.scale(vxl, scale); + const realToVxl = (real: box2D) => Box2D.scale(real, Vec2.div(size, realSize)); + + // find the tiles, in voxels, to request... + const allTiles = getAllTiles([256, 256], size); + const inView = allTiles.filter((tile) => !!Box2D.intersection(camera.view, vxlToReal(tile))); + // camera.view is in a made up dataspace, where 1=height of the current dataset + // thus, we have to convert it into a voxel-space camera for intersections + const voxelView = realToVxl(camera.view); + return { + layer: layerIndex, + view: voxelView, + tiles: inView.map((uv) => ({ + plane, + bounds: uv, + planeIndex, + layerIndex, + })), + }; +} diff --git a/apps/omezarr-viewer/src/tissuecyte.ts b/apps/omezarr-viewer/src/tissuecyte.ts index a4057f0..e4d3179 100644 --- a/apps/omezarr-viewer/src/tissuecyte.ts +++ b/apps/omezarr-viewer/src/tissuecyte.ts @@ -1,482 +1,499 @@ // I am the scatterplot demo // -import { ImGui, ImGui_Impl } from "@zhobo63/imgui-ts"; -import REGL from "regl"; +import { ImGui, ImGui_Impl } from '@zhobo63/imgui-ts'; +import REGL from 'regl'; import { - type ZarrDataset, - explain, - getSlice, - indexOfDimension, - load, - pickBestScale, - sizeInUnits, - planeSizeInVoxels, -} from "Common/loaders/ome-zarr/zarr-data"; -import { AsyncDataCache, type FrameLifecycle, beginLongRunningFrame } from "@alleninstitute/vis-scatterbrain"; + type ZarrDataset, + explain, + getSlice, + indexOfDimension, + load, + pickBestScale, + sizeInUnits, + planeSizeInVoxels, +} from 'Common/loaders/ome-zarr/zarr-data'; +import { AsyncDataCache, type FrameLifecycle, beginLongRunningFrame } from '@alleninstitute/vis-scatterbrain'; -import { Box2D, type Interval, Vec2, type box2D, type vec2 } from "@alleninstitute/vis-geometry"; -import type { Camera } from "./camera"; -import { buildImageRenderer } from "./image-renderer"; -import { ImVec2, ImVec4 } from "@zhobo63/imgui-ts/src/imgui"; -import { colorMapWidget } from "./components/color-map"; -import { initDrawableInterface } from "./annotation/path"; +import { Box2D, type Interval, Vec2, type box2D, type vec2 } from '@alleninstitute/vis-geometry'; +import type { Camera } from './camera'; +import { buildImageRenderer } from './image-renderer'; +import { ImVec2, ImVec4 } from '@zhobo63/imgui-ts/src/imgui'; +import { colorMapWidget } from './components/color-map'; +import { initDrawableInterface } from './annotation/path'; import { - type AxisAlignedPlane, - type VoxelSliceRenderSettings, - type VoxelTile, - buildVolumeSliceRenderer, - cacheKeyFactory, - getVisibleTiles, - requestsForTile, -} from "./slice-renderer"; + type AxisAlignedPlane, + type VoxelSliceRenderSettings, + type VoxelTile, + buildVolumeSliceRenderer, + cacheKeyFactory, + getVisibleTiles, + requestsForTile, +} from './slice-renderer'; const creepy = - "https://aind-open-data.s3.amazonaws.com/SmartSPIM_644106_2022-12-09_12-12-39_stitched_2022-12-16_16-55-11/processed/OMEZarr/Ex_488_Em_525.zarr"; -const tissuecyte = "https://tissuecyte-visualizations.s3.amazonaws.com/data/230105/tissuecyte/1111175209/green/"; + 'https://aind-open-data.s3.amazonaws.com/SmartSPIM_644106_2022-12-09_12-12-39_stitched_2022-12-16_16-55-11/processed/OMEZarr/Ex_488_Em_525.zarr'; +const tissuecyte = 'https://tissuecyte-visualizations.s3.amazonaws.com/data/230105/tissuecyte/1111175209/green/'; // const versa = "https://neuroglancer-vis-prototype.s3.amazonaws.com/VERSA/scratch/0500408166/"; // const b = "https://neuroglancer-vis-prototype.s3.amazonaws.com/VERSA/ome_zarr/20231207.1/1282139033/"; // const scott = "https://neuroglancer-vis-prototype.s3.amazonaws.com/VERSA/ome_zarr/20231204/1197986710/"; const file = tissuecyte; -type Channel = "R" | "G" | "B"; // we can support 3 visual channels at once +type Channel = 'R' | 'G' | 'B'; // we can support 3 visual channels at once type ChannelColorSettings = { - gamut: Interval; - index: number; + gamut: Interval; + index: number; }; class TissuecyteDemo { - mouse: "up" | "down"; - mousePos: vec2; - camera: Camera; - channels: Record; - plane: AxisAlignedPlane; - sliceParameter: number; - canvas: HTMLCanvasElement; - curFrame: FrameLifecycle | null; - rotation: number; - cache: AsyncDataCache; - regl: REGL.Regl; - dataset: ZarrDataset; - screenRenderer: ReturnType; - renderer: ReturnType; - screenBuffer: { bounds: box2D; fbo: REGL.Framebuffer2D }; - datasets: string[]; - constructor( - canvas: HTMLCanvasElement, - dataset: ZarrDataset, - regl: REGL.Regl, - cache: AsyncDataCache, - urls: string[] - ) { - const [w, h] = [canvas.clientWidth, canvas.clientHeight]; - this.datasets = urls; + mouse: 'up' | 'down'; + mousePos: vec2; + camera: Camera; + channels: Record; + plane: AxisAlignedPlane; + sliceParameter: number; + canvas: HTMLCanvasElement; + curFrame: FrameLifecycle | null; + rotation: number; + cache: AsyncDataCache; + regl: REGL.Regl; + dataset: ZarrDataset; + screenRenderer: ReturnType; + renderer: ReturnType; + screenBuffer: { bounds: box2D; fbo: REGL.Framebuffer2D }; + datasets: string[]; + constructor( + canvas: HTMLCanvasElement, + dataset: ZarrDataset, + regl: REGL.Regl, + cache: AsyncDataCache, + urls: string[] + ) { + const [w, h] = [canvas.clientWidth, canvas.clientHeight]; + this.datasets = urls; - const sliceSize = sizeInUnits({ u: "x", v: "y" }, dataset.multiscales[0].axes, dataset.multiscales[0].datasets[0])!; - this.camera = { - view: Box2D.create([0, 0], [(sliceSize[1] * w) / h, sliceSize[1]]), - screen: [w, h], - }; - this.screenBuffer = { bounds: this.camera.view, fbo: regl.framebuffer(w, h) }; - this.dataset = dataset; - this.regl = regl; - this.plane = "yz"; - this.mouse = "up"; - this.cache = cache; - this.sliceParameter = 0.5; - this.mousePos = [0, 0]; - this.channels = { - R: { - gamut: { min: 0, max: 2500 }, - index: 0, - }, - // G: { - // gamut: { min: 0, max: 0.21 }, - // index: 1, - // }, - // B: { - // gamut: { min: 0, max: 0.21 }, - // index: 2, - // }, - }; - this.canvas = canvas; - this.curFrame = null; - this.rotation = (3 * Math.PI) / 2; - this.renderer = buildVolumeSliceRenderer(regl); - this.screenRenderer = buildImageRenderer(regl); - const loop = () => { - this.refreshScreen(); - window.requestAnimationFrame(loop); - }; - window.requestAnimationFrame(loop); - } - setupEventHandlers() { - const canvas = this.canvas; - } - - private upsideDown(v: box2D) { - const { minCorner, maxCorner } = v; - return Box2D.create([minCorner[0], maxCorner[1]], [maxCorner[0], minCorner[1]]); - } - private renderFrame() { - const { camera, plane, sliceParameter, dataset, cache, regl, channels, renderer } = this; - const { layer, view, tiles } = getVisibleTiles(camera, plane, sliceParameter, dataset); - // erase our buffer that holds the render'd dataset image - which lets the UI - // re-render itself independantly - regl.clear({ color: [0, 0, 0, 0], depth: 1, framebuffer: this.screenBuffer.fbo }); - - // get the lowest-resolution view of the current slice - the idea being that we keep - // it cached, and always draw it UNDER the actual layer we want to see, based on our zoom. - // this prevents a flickering black frame when we zoom in to a new, higher resolution layer - const { - layer: baseLayer, - view: baseView, - tiles: baseTiles, - } = getVisibleTiles({ ...camera, screen: [1, 1] }, plane, sliceParameter, dataset); - if (layer === baseLayer) { - this.curFrame = this.renderFrameHelper(baseView, baseTiles); - // if the layer we WANT is actually the lowest res layer, then we're done here and now! - return; + const sliceSize = sizeInUnits( + { u: 'x', v: 'y' }, + dataset.multiscales[0].axes, + dataset.multiscales[0].datasets[0] + )!; + this.camera = { + view: Box2D.create([0, 0], [(sliceSize[1] * w) / h, sliceSize[1]]), + screen: [w, h], + }; + this.screenBuffer = { bounds: this.camera.view, fbo: regl.framebuffer(w, h) }; + this.dataset = dataset; + this.regl = regl; + this.plane = 'yz'; + this.mouse = 'up'; + this.cache = cache; + this.sliceParameter = 0.5; + this.mousePos = [0, 0]; + this.channels = { + R: { + gamut: { min: 0, max: 2500 }, + index: 0, + }, + // G: { + // gamut: { min: 0, max: 0.21 }, + // index: 1, + // }, + // B: { + // gamut: { min: 0, max: 0.21 }, + // index: 2, + // }, + }; + this.canvas = canvas; + this.curFrame = null; + this.rotation = (3 * Math.PI) / 2; + this.renderer = buildVolumeSliceRenderer(regl); + this.screenRenderer = buildImageRenderer(regl); + const loop = () => { + this.refreshScreen(); + window.requestAnimationFrame(loop); + }; + window.requestAnimationFrame(loop); + } + setupEventHandlers() { + const canvas = this.canvas; } - const baseSettings = { - view: baseView, - dataset, - regl, - target: this.screenBuffer.fbo, - viewport: { - x: 0, - y: 0, - width: this.canvas.clientWidth, - height: this.canvas.clientHeight, - }, - rotation: this.rotation, - gamut: this.channels.R.gamut, - // gamut: channels, - }; - const cached = baseTiles.reduce( - (count, cur) => (cache.isCached(cacheKeyFactory("luminance", cur, baseSettings)) ? 1 + count : count), - 0 - ); - if (cached === 0) { - this.curFrame = this.renderFrameHelper(view, tiles); - return; + private upsideDown(v: box2D) { + const { minCorner, maxCorner } = v; + return Box2D.create([minCorner[0], maxCorner[1]], [maxCorner[0], minCorner[1]]); } - const frame = beginLongRunningFrame( - 3, - 33, - baseTiles, - cache, - baseSettings, - requestsForTile, - renderer, - (event) => { - switch (event.status) { - case "error": - throw event.error; // error boundary might catch this - case "progress": - break; - case "finished_synchronously": - case "finished": - console.log("finished base-layer... start real frame!"); - this.curFrame = this.renderFrameHelper(view, tiles); - break; - case "begun": - break; - case "cancelled": - this.curFrame = this.renderFrameHelper(view, tiles); - break; - default: + private renderFrame() { + const { camera, plane, sliceParameter, dataset, cache, regl, channels, renderer } = this; + const { layer, view, tiles } = getVisibleTiles(camera, plane, sliceParameter, dataset); + // erase our buffer that holds the render'd dataset image - which lets the UI + // re-render itself independantly + regl.clear({ color: [0, 0, 0, 0], depth: 1, framebuffer: this.screenBuffer.fbo }); + + // get the lowest-resolution view of the current slice - the idea being that we keep + // it cached, and always draw it UNDER the actual layer we want to see, based on our zoom. + // this prevents a flickering black frame when we zoom in to a new, higher resolution layer + const { + layer: baseLayer, + view: baseView, + tiles: baseTiles, + } = getVisibleTiles({ ...camera, screen: [1, 1] }, plane, sliceParameter, dataset); + if (layer === baseLayer) { + this.curFrame = this.renderFrameHelper(baseView, baseTiles); + // if the layer we WANT is actually the lowest res layer, then we're done here and now! + return; } - }, - cacheKeyFactory - ); - frame.cancelFrame(); - } - // not my fav thing to do - but renderFrame and renderFrame helper are tightly linked - // to accomplish our smoke&mirrors to avoid flickering as tiles load in - - // the both make assumptions about state, and the contents of buffers. do not - // call either of them! - private renderFrameHelper(view: box2D, visibleTiles: VoxelTile[]) { - const { camera, dataset, cache, regl, channels, renderer } = this; - this.screenBuffer.bounds = camera.view; - regl.clear({ depth: 1, framebuffer: this.screenBuffer.fbo }); - // const gamut = { - // R: channels.R.gamut, - // G: channels.G.gamut, - // B: channels.B.gamut, - // }; - const frame = beginLongRunningFrame( - 3, - 33, - visibleTiles, - cache, - { - rotation: this.rotation, - gamut: this.channels.R.gamut, - view: view, - dataset, - regl, - target: this.screenBuffer.fbo, - viewport: { - x: 0, - y: 0, - width: this.canvas.clientWidth, - height: this.canvas.clientHeight, - }, - // gamut: channels, - }, - requestsForTile, - renderer, - (event) => { - switch (event.status) { - case "error": - throw event.error; // error boundary might catch this - case "progress": - this.refreshScreen(); - break; - case "finished_synchronously": - case "finished": - this.curFrame = null; - this.refreshScreen(); - break; - case "begun": - this.refreshScreen(); - break; - case "cancelled": - break; - default: + const baseSettings = { + view: baseView, + dataset, + regl, + target: this.screenBuffer.fbo, + viewport: { + x: 0, + y: 0, + width: this.canvas.clientWidth, + height: this.canvas.clientHeight, + }, + rotation: this.rotation, + gamut: this.channels.R.gamut, + // gamut: channels, + }; + + const cached = baseTiles.reduce( + (count, cur) => (cache.isCached(cacheKeyFactory('luminance', cur, baseSettings)) ? 1 + count : count), + 0 + ); + if (cached === 0) { + this.curFrame = this.renderFrameHelper(view, tiles); + return; } - }, - cacheKeyFactory - ); - return frame; - } - refreshScreen() { - const now = performance.now(); - this.regl._refresh(); - this.regl.clear({ depth: 1, color: [0, 0, 0, 1], framebuffer: null }); + const frame = beginLongRunningFrame( + 3, + 33, + baseTiles, + cache, + baseSettings, + requestsForTile, + renderer, + (event) => { + switch (event.status) { + case 'error': + throw event.error; // error boundary might catch this + case 'progress': + break; + case 'finished_synchronously': + case 'finished': + console.log('finished base-layer... start real frame!'); + this.curFrame = this.renderFrameHelper(view, tiles); + break; + case 'begun': + break; + case 'cancelled': + this.curFrame = this.renderFrameHelper(view, tiles); + break; + default: + } + }, + cacheKeyFactory + ); + frame.cancelFrame(); + } + // not my fav thing to do - but renderFrame and renderFrame helper are tightly linked + // to accomplish our smoke&mirrors to avoid flickering as tiles load in - + // the both make assumptions about state, and the contents of buffers. do not + // call either of them! + private renderFrameHelper(view: box2D, visibleTiles: VoxelTile[]) { + const { camera, dataset, cache, regl, channels, renderer } = this; + this.screenBuffer.bounds = camera.view; + regl.clear({ depth: 1, framebuffer: this.screenBuffer.fbo }); + // const gamut = { + // R: channels.R.gamut, + // G: channels.G.gamut, + // B: channels.B.gamut, + // }; + const frame = beginLongRunningFrame( + 3, + 33, + visibleTiles, + cache, + { + rotation: this.rotation, + gamut: this.channels.R.gamut, + view: view, + dataset, + regl, + target: this.screenBuffer.fbo, + viewport: { + x: 0, + y: 0, + width: this.canvas.clientWidth, + height: this.canvas.clientHeight, + }, + // gamut: channels, + }, + requestsForTile, + renderer, + (event) => { + switch (event.status) { + case 'error': + throw event.error; // error boundary might catch this + case 'progress': + this.refreshScreen(); + break; + case 'finished_synchronously': + case 'finished': + this.curFrame = null; + this.refreshScreen(); + break; + case 'begun': + this.refreshScreen(); + break; + case 'cancelled': + break; + default: + } + }, + cacheKeyFactory + ); + return frame; + } + refreshScreen() { + const now = performance.now(); + this.regl._refresh(); + this.regl.clear({ depth: 1, color: [0, 0, 0, 1], framebuffer: null }); - this.screenRenderer([ - { - box: Box2D.toFlatArray(this.screenBuffer.bounds), - img: this.screenBuffer.fbo, - target: null, - view: Box2D.toFlatArray(this.upsideDown(this.camera.view)), - }, - ]); + this.screenRenderer([ + { + box: Box2D.toFlatArray(this.screenBuffer.bounds), + img: this.screenBuffer.fbo, + target: null, + view: Box2D.toFlatArray(this.upsideDown(this.camera.view)), + }, + ]); - this.drawUI(now); + this.drawUI(now); - this.regl._refresh(); - } + this.regl._refresh(); + } - drawUI(time: number) { - let drawAgain = false; - const effects: Array<() => void> = []; - // imgui wants mutable access to stuff... which is pretty weird - imAccess is nice, but all the vector-style updaters are nasty - try { - ImGui_Impl.NewFrame(time); - ImGui.NewFrame(); - ImGui.Begin("Settings"); - ImGui_Impl.ClearBuffer(new ImVec4(0.2, 0.2, 0.2, 1)); - // ImGui_Impl.ClearBuffer(new ImVec4(0, 0, 0, 0)); - // TODO: count the available channels that we could use for color! - Object.entries(this.channels).forEach(([channel, settings]) => { - const result = colorMapWidget( - channel, - { - gamut: settings.gamut, - color: new ImGui.Vec4(channel === "R" ? 255 : 0, channel === "G" ? 255 : 0, channel === "B" ? 255 : 0, 255), - useMe: true, - index: settings.index, - }, - 3 - ); - if (result.changed) { - this.channels[channel as Channel].gamut = result.gamut; - this.channels[channel as Channel].index = result.index; - drawAgain = true; - } - }); - const highlight = new ImVec4(0, 0.25, 0.65, 1.0); - const regular = new ImVec4(0.2, 0.2, 0.2, 1.0); - // for (const thumb of this.sliceThumbs) { - // if ( - // // here we dig deep into the guts of a regl-managed texture... not super safe, and regl's types are not really set up for this: - // ImGui.ImageButton( - // // @ts-expect-error - // thumb?.color[0]?._texture?.texture ?? null, - // new ImVec2(this.thumbWidth, THUMB_SIZE), - // new ImVec2(0, 0), - // new ImVec2(1, 1), - // // draw a little box around the selected slice: - // this.sliceIndex === this.sliceThumbs.indexOf(thumb) ? 3 : 0, - // this.sliceIndex === this.sliceThumbs.indexOf(thumb) ? highlight : regular - // ) - // ) { - // drawAgain = true; - // effects.push(() => this.setSlice(this.sliceThumbs.indexOf(thumb))); - // } - // ImGui.SameLine(); - // } - let p = this.sliceParameter; - if ( - ImGui.DragFloat( - "slice", - (v?: number) => { - p = v ?? p; - return p; - }, - 0.005, - 0.0, - 1.0, - "%4f" - ) - ) { - effects.push(() => (this.sliceParameter = p)); - drawAgain = true; - } - ImGui.End(); - ImGui.EndFrame(); - ImGui.Render(); + drawUI(time: number) { + let drawAgain = false; + const effects: Array<() => void> = []; + // imgui wants mutable access to stuff... which is pretty weird - imAccess is nice, but all the vector-style updaters are nasty + try { + ImGui_Impl.NewFrame(time); + ImGui.NewFrame(); + ImGui.Begin('Settings'); + ImGui_Impl.ClearBuffer(new ImVec4(0.2, 0.2, 0.2, 1)); + // ImGui_Impl.ClearBuffer(new ImVec4(0, 0, 0, 0)); + // TODO: count the available channels that we could use for color! + Object.entries(this.channels).forEach(([channel, settings]) => { + const result = colorMapWidget( + channel, + { + gamut: settings.gamut, + color: new ImGui.Vec4( + channel === 'R' ? 255 : 0, + channel === 'G' ? 255 : 0, + channel === 'B' ? 255 : 0, + 255 + ), + useMe: true, + index: settings.index, + }, + 3 + ); + if (result.changed) { + this.channels[channel as Channel].gamut = result.gamut; + this.channels[channel as Channel].index = result.index; + drawAgain = true; + } + }); + const highlight = new ImVec4(0, 0.25, 0.65, 1.0); + const regular = new ImVec4(0.2, 0.2, 0.2, 1.0); + // for (const thumb of this.sliceThumbs) { + // if ( + // // here we dig deep into the guts of a regl-managed texture... not super safe, and regl's types are not really set up for this: + // ImGui.ImageButton( + // // @ts-expect-error + // thumb?.color[0]?._texture?.texture ?? null, + // new ImVec2(this.thumbWidth, THUMB_SIZE), + // new ImVec2(0, 0), + // new ImVec2(1, 1), + // // draw a little box around the selected slice: + // this.sliceIndex === this.sliceThumbs.indexOf(thumb) ? 3 : 0, + // this.sliceIndex === this.sliceThumbs.indexOf(thumb) ? highlight : regular + // ) + // ) { + // drawAgain = true; + // effects.push(() => this.setSlice(this.sliceThumbs.indexOf(thumb))); + // } + // ImGui.SameLine(); + // } + let p = this.sliceParameter; + if ( + ImGui.DragFloat( + 'slice', + (v?: number) => { + p = v ?? p; + return p; + }, + 0.005, + 0.0, + 1.0, + '%4f' + ) + ) { + effects.push(() => (this.sliceParameter = p)); + drawAgain = true; + } + ImGui.End(); + ImGui.EndFrame(); + ImGui.Render(); - ImGui_Impl.RenderDrawData(ImGui.GetDrawData()); - effects.forEach((fx) => fx()); - if (drawAgain) { - window.setTimeout(() => this.rerender(), 5); - } - } catch (err) { - console.warn(err); + ImGui_Impl.RenderDrawData(ImGui.GetDrawData()); + effects.forEach((fx) => fx()); + if (drawAgain) { + window.setTimeout(() => this.rerender(), 5); + } + } catch (err) { + console.warn(err); + } } - } - rerender() { - if (this.curFrame !== null) { - this.curFrame.cancelFrame(); + rerender() { + if (this.curFrame !== null) { + this.curFrame.cancelFrame(); + } + this.renderFrame(); + } + mouseButton(click: 'up' | 'down') { + this.mouse = click; } - this.renderFrame(); - } - mouseButton(click: "up" | "down") { - this.mouse = click; - } - mouseMove(delta: vec2) { - if (this.mouse === "down") { - // drag the view - const { screen, view } = this.camera; - const p = Vec2.div(delta, [this.canvas.clientWidth, this.canvas.clientHeight]); - const c = Vec2.mul(p, Box2D.size(view)); - this.camera = { view: Box2D.translate(view, c), screen }; - this.rerender(); + mouseMove(delta: vec2) { + if (this.mouse === 'down') { + // drag the view + const { screen, view } = this.camera; + const p = Vec2.div(delta, [this.canvas.clientWidth, this.canvas.clientHeight]); + const c = Vec2.mul(p, Box2D.size(view)); + this.camera = { view: Box2D.translate(view, c), screen }; + this.rerender(); + } + this.mousePos = Vec2.add(this.mousePos, delta); + } + changeSlice(delta: number) { + this.sliceParameter += delta; + this.rerender(); } - this.mousePos = Vec2.add(this.mousePos, delta); - } - changeSlice(delta: number) { - this.sliceParameter += delta; - this.rerender(); - } - changeGamut(delta: number) { - this.channels.R.gamut = { min: this.channels.R.gamut.min, max: this.channels.R.gamut.max * delta }; - this.rerender(); - } - zoom(scale: number) { - const { view, screen } = this.camera; - const m = Box2D.midpoint(view); - this.camera = { - view: Box2D.translate(Box2D.scale(Box2D.translate(view, Vec2.scale(m, -1)), [scale, scale]), m), - screen, - }; - this.rerender(); - } - nextAxis() { - this.plane = this.plane == "xy" ? "xz" : this.plane === "xz" ? "yz" : "xy"; - this.rerender(); - } - rotateTiles() { - this.rotation += Math.PI / 2; - this.rerender(); - } + changeGamut(delta: number) { + this.channels.R.gamut = { min: this.channels.R.gamut.min, max: this.channels.R.gamut.max * delta }; + this.rerender(); + } + zoom(scale: number) { + const { view, screen } = this.camera; + const m = Box2D.midpoint(view); + this.camera = { + view: Box2D.translate(Box2D.scale(Box2D.translate(view, Vec2.scale(m, -1)), [scale, scale]), m), + screen, + }; + this.rerender(); + } + nextAxis() { + this.plane = this.plane == 'xy' ? 'xz' : this.plane === 'xz' ? 'yz' : 'xy'; + this.rerender(); + } + rotateTiles() { + this.rotation += Math.PI / 2; + this.rerender(); + } } function setupEventHandlers(canvas: HTMLCanvasElement, demo: TissuecyteDemo) { - canvas.onmousedown = (e: MouseEvent) => { - if (ImGui.GetIO().WantCaptureMouse) return; - demo.mouseButton("down"); - }; - canvas.onmouseup = (e: MouseEvent) => { - if (ImGui.GetIO().WantCaptureMouse) return; - demo.mouseButton("up"); - }; - canvas.onmousemove = (e: MouseEvent) => { - if (ImGui.GetIO().WantCaptureMouse) return; - // account for gl-origin vs. screen origin: - demo.mouseMove([-e.movementX, -e.movementY]); - }; - canvas.onwheel = (e: WheelEvent) => { - if (e.shiftKey) { - demo.changeGamut(e.deltaY > 0 ? 1.1 : 0.9); - } else if (e.altKey) { - demo.changeSlice(e.deltaY > 0 ? 0.01 : -0.01); - } else { - demo.zoom(e.deltaY > 0 ? 1.1 : 0.9); - } - }; - canvas.onkeydown = (e: KeyboardEvent) => { - switch (e.key) { - case "a": - demo.nextAxis(); - break; - case "r": - demo.rotateTiles(); - break; - default: - } - }; + canvas.onmousedown = (e: MouseEvent) => { + if (ImGui.GetIO().WantCaptureMouse) return; + demo.mouseButton('down'); + }; + canvas.onmouseup = (e: MouseEvent) => { + if (ImGui.GetIO().WantCaptureMouse) return; + demo.mouseButton('up'); + }; + canvas.onmousemove = (e: MouseEvent) => { + if (ImGui.GetIO().WantCaptureMouse) return; + // account for gl-origin vs. screen origin: + demo.mouseMove([-e.movementX, -e.movementY]); + }; + canvas.onwheel = (e: WheelEvent) => { + if (e.shiftKey) { + demo.changeGamut(e.deltaY > 0 ? 1.1 : 0.9); + } else if (e.altKey) { + demo.changeSlice(e.deltaY > 0 ? 0.01 : -0.01); + } else { + demo.zoom(e.deltaY > 0 ? 1.1 : 0.9); + } + }; + canvas.onkeydown = (e: KeyboardEvent) => { + switch (e.key) { + case 'a': + demo.nextAxis(); + break; + case 'r': + demo.rotateTiles(); + break; + default: + } + }; } function setupGui(canvas: HTMLCanvasElement | WebGL2RenderingContext | WebGLRenderingContext) { - ImGui.default().then(() => { - ImGui.CHECKVERSION(); - ImGui.CreateContext(); - const io: ImGui.IO = ImGui.GetIO(); - ImGui.StyleColorsDark(); - io.Fonts.AddFontDefault(); - ImGui_Impl.Init(canvas); - ImGui_Impl.ClearBuffer(new ImVec4(0.2, 0.2, 0.2, 1)); - }); + ImGui.default().then(() => { + ImGui.CHECKVERSION(); + ImGui.CreateContext(); + const io: ImGui.IO = ImGui.GetIO(); + ImGui.StyleColorsDark(); + io.Fonts.AddFontDefault(); + ImGui_Impl.Init(canvas); + ImGui_Impl.ClearBuffer(new ImVec4(0.2, 0.2, 0.2, 1)); + }); } async function demotime() { - const ui = document.getElementById("uiCanvas") as HTMLCanvasElement; - const yay = document.getElementById("glCanvas") as HTMLCanvasElement; - yay.width = 2000; - yay.height = 2000; + const ui = document.getElementById('uiCanvas') as HTMLCanvasElement; + const yay = document.getElementById('glCanvas') as HTMLCanvasElement; + yay.width = 2000; + yay.height = 2000; - const gl = ui.getContext("webgl2", { - alpha: true, - preserveDrawingBuffer: true, - antialias: true, - premultipliedAlpha: true, - }) as WebGL2RenderingContext; + const gl = ui.getContext('webgl2', { + alpha: true, + preserveDrawingBuffer: true, + antialias: true, + premultipliedAlpha: true, + }) as WebGL2RenderingContext; - const regl = REGL({ - canvas: yay, - attributes: { - alpha: true, - preserveDrawingBuffer: true, - antialias: true, - premultipliedAlpha: true, - }, - extensions: ["ANGLE_instanced_arrays", "OES_texture_float", "WEBGL_color_buffer_float"], - }); - ui.height = 2000; - ui.width = 2000; - const canvas: HTMLCanvasElement = regl._gl.canvas as HTMLCanvasElement; - canvas.tabIndex = 3; - setupGui(gl); - const voxelSliceCache: AsyncDataCache = new AsyncDataCache((d: REGL.Texture2D) => { - d.destroy() - }, (_d) => 1, 200); - const zarr = await load(file); - explain(zarr); + const regl = REGL({ + canvas: yay, + attributes: { + alpha: true, + preserveDrawingBuffer: true, + antialias: true, + premultipliedAlpha: true, + }, + extensions: ['ANGLE_instanced_arrays', 'OES_texture_float', 'WEBGL_color_buffer_float'], + }); + ui.height = 2000; + ui.width = 2000; + const canvas: HTMLCanvasElement = regl._gl.canvas as HTMLCanvasElement; + canvas.tabIndex = 3; + setupGui(gl); + const voxelSliceCache: AsyncDataCache = new AsyncDataCache< + string, + string, + REGL.Texture2D + >( + (d: REGL.Texture2D) => { + d.destroy(); + }, + (_d) => 1, + 200 + ); + const zarr = await load(file); + explain(zarr); - const theDemo = new TissuecyteDemo(canvas, zarr, regl, voxelSliceCache, []); + const theDemo = new TissuecyteDemo(canvas, zarr, regl, voxelSliceCache, []); - setupEventHandlers(canvas, theDemo); - theDemo.rerender(); + setupEventHandlers(canvas, theDemo); + theDemo.rerender(); } // since I am just included in a script tag in a raw html document, this is how we start: diff --git a/apps/omezarr-viewer/src/versa-renderer.ts b/apps/omezarr-viewer/src/versa-renderer.ts index 6ce6605..0cb1f43 100644 --- a/apps/omezarr-viewer/src/versa-renderer.ts +++ b/apps/omezarr-viewer/src/versa-renderer.ts @@ -1,303 +1,307 @@ -import REGL, { type Framebuffer2D } from "regl"; -import { type ZarrDataset, type ZarrRequest, getSlice, pickBestScale, sizeInUnits, planeSizeInVoxels, indexOfDimension } from "Common/loaders/ome-zarr/zarr-data"; -import { Box2D, type Interval, Vec2, type box2D, type vec2, type vec4 } from "@alleninstitute/vis-geometry"; -import { omit, slice } from "lodash"; -import type { Camera } from "./camera"; -import type { NestedArray, TypedArray } from "zarr"; -import { getSlicePool } from "Common/loaders/ome-zarr/sliceWorkerPool"; - -type Props = { - target: Framebuffer2D | null; - tile: vec4; - view: vec4; - rotation: number; - Rgamut: vec2; - Ggamut: vec2; - Bgamut: vec2; - viewport: REGL.BoundingBox; - R: REGL.Texture2D; - G: REGL.Texture2D; - B: REGL.Texture2D; -}; -function isTexture(obj: object | undefined): obj is Bfr { - return (obj !== undefined && 'type' in obj && obj.type === 'texture2D') -} -export function buildVersaRenderer(regl: REGL.Regl) { - const cmd = regl< - { - view: vec4; - tile: vec4; - rot: number; - R: REGL.Texture2D; - G: REGL.Texture2D; - B: REGL.Texture2D; - Rgamut: vec2; - Ggamut: vec2; - Bgamut: vec2; - }, - { pos: REGL.BufferData }, - Props - >({ - vert: ` precision highp float; - attribute vec2 pos; - - uniform vec4 view; - uniform vec4 tile; - varying vec2 texCoord; - uniform float rot; - - vec2 rotateObj(vec2 obj, float radians){ - return obj; - } - vec2 rotateTextureCoordinates(vec2 tx, float radians){ - vec2 xy = tx-vec2(0.5,0.5); - mat2 R = mat2( - vec2(cos(radians),-sin(radians)), - vec2(-sin(radians),cos(radians)) - ); - return ((R*xy)+vec2(0.5,0.5)); - } - void main(){ - vec2 tileSize = tile.zw-tile.xy; - texCoord = rotateTextureCoordinates(pos,rot); - vec2 obj = rotateObj((pos.xy*tileSize+tile.xy),rot); - - vec2 p = (obj-view.xy)/(view.zw-view.xy); - // now, to clip space - p = (p*2.0)-1.0; - gl_Position = vec4(p.x,p.y,0.0,1.0); - }`, - frag: ` - precision highp float; - uniform sampler2D R; - uniform sampler2D G; - uniform sampler2D B; // for reasons which are pretty annoying - // its more direct to do 3 separate channels... - uniform vec2 Rgamut; - uniform vec2 Ggamut; - uniform vec2 Bgamut; - - varying vec2 texCoord; - void main(){ - vec3 mins = vec3(Rgamut.x,Ggamut.x,Bgamut.x); - vec3 maxs = vec3(Rgamut.y,Ggamut.y,Bgamut.y); - vec3 span = maxs-mins; - vec3 color = (vec3( - texture2D(R, texCoord).r, - texture2D(G, texCoord).r, - texture2D(B, texCoord).r - )-mins) /span; - - gl_FragColor = vec4(color, 1.0); - }`, - framebuffer: regl.prop("target"), - attributes: { - pos: [0, 0, 1, 0, 1, 1, 0, 1], - }, - uniforms: { - rot: regl.prop("rotation"), - tile: regl.prop("tile"), - view: regl.prop("view"), - R: regl.prop("R"), - G: regl.prop("G"), - B: regl.prop("B"), - Rgamut: regl.prop("Rgamut"), - Ggamut: regl.prop("Ggamut"), - Bgamut: regl.prop("Bgamut"), - }, - depth: { - enable: false, - }, - count: 4, - // viewport: regl.prop("viewport"), - primitive: "triangle fan", - // ... more! - }); - - return (item: VoxelTile, settings: VoxelSliceRenderSettings, channels: Record) => { - const { view, viewport, gamut, target, rotation } = settings; - const { realBounds } = item; - const { R, G, B } = channels; - - if (!isTexture(R) || !isTexture(G) || !isTexture(B)) { - console.log("missing data: ", R, G, B); - return; - } - - cmd({ - target, - rotation, - view: [...view.minCorner, ...view.maxCorner], - tile: [...realBounds.minCorner, ...realBounds.maxCorner], - R: R.data, - G: G.data, - B: B.data, - Rgamut: [gamut.R.gamut.min, gamut.R.gamut.max], - Ggamut: [gamut.G.gamut.min, gamut.G.gamut.max], - Bgamut: [gamut.B.gamut.min, gamut.B.gamut.max], - }); - }; -} -type Bfr = { type: 'texture2D', data: REGL.Texture2D }; - -type Tile = { bounds: box2D }; -export type VoxelSliceRenderSettings = { - regl: REGL.Regl; - dataset: ZarrDataset; - view: box2D; - rotation: number; - gamut: Record<"R" | "G" | "B", { gamut: Interval; index: number }>; - viewport: REGL.BoundingBox; - target: REGL.Framebuffer2D | null; -}; -export type AxisAlignedPlane = "xy" | "yz" | "xz"; -export type VoxelTile = { - plane: AxisAlignedPlane; - realBounds: box2D; - bounds: box2D; // in voxels, in the plane - planeIndex: number; - layerIndex: number; - // time and channel are always = 0, for now -}; - -function toZarrRequest(tile: VoxelTile, channel: number): ZarrRequest { - const { plane, planeIndex, bounds } = tile; - const { minCorner: min, maxCorner: max } = bounds; - const u = { min: min[0], max: max[0] }; - const v = { min: min[1], max: max[1] }; - switch (plane) { - case "xy": - return { - x: u, - y: v, - t: 0, - c: channel, - z: planeIndex, - }; - case "xz": - return { - x: u, - z: v, - t: 0, - c: channel, - y: planeIndex, - }; - case "yz": - return { - y: u, - z: v, - t: 0, - c: channel, - x: planeIndex, - }; - } -} -export function cacheKeyFactory(col: string, item: VoxelTile, settings: VoxelSliceRenderSettings) { - return `${settings.dataset.url}_${JSON.stringify(omit(item, "desiredResolution"))}_ch=${settings.gamut[col as "R" | "G" | "B"].index - }`; -} - -function reqSlice(dataset: ZarrDataset, req: ZarrRequest, layerIndex: number) { - return getSlicePool().requestSlice(dataset, req, layerIndex) -} -const LUMINANCE = "luminance"; -export function requestsForTile(tile: VoxelTile, settings: VoxelSliceRenderSettings, signal?: AbortSignal) { - const { dataset, regl } = settings; - const handleResponse = (vxl: Awaited>) => { - const { shape, data } = vxl; - const r = regl.texture({ - data, - width: shape[1], - height: shape[0], // TODO this swap is sus - format: LUMINANCE, - }); - return r; - }; - // lets hope the browser caches our 3x repeat calls to teh same data... - return { - R: async () => { - const vxl = await reqSlice(dataset, toZarrRequest(tile, settings.gamut.R.index), tile.layerIndex); - return { type: 'texture2D', data: handleResponse(vxl) } - }, - G: async () => { - const vxl = await reqSlice(dataset, toZarrRequest(tile, settings.gamut.G.index), tile.layerIndex); - return { type: 'texture2D', data: handleResponse(vxl) } - }, - B: async () => { - const vxl = await reqSlice(dataset, toZarrRequest(tile, settings.gamut.B.index), tile.layerIndex); - return { type: 'texture2D', data: handleResponse(vxl) } - }, - }; -} - -function getAllTiles(idealTilePx: vec2, layerSize: vec2) { - // return the set of all our "tiles" of this layer, given the tilePx size - const tiles: box2D[] = []; - for (let x = 0; x < layerSize[0]; x += idealTilePx[0]) { - for (let y = 0; y < layerSize[1]; y += idealTilePx[1]) { - const xy: vec2 = [x, y]; - tiles.push(Box2D.create(xy, Vec2.min(Vec2.add(xy, idealTilePx), layerSize))); - } - } - return tiles; -} -const uvTable = { - xy: { u: "x", v: "y" }, - xz: { u: "x", v: "z" }, - yz: { u: "y", v: "z" }, -} as const; -const sliceDimension = { - xy: "z", - xz: "y", - yz: "x", -} as const; - -export function getVisibleTiles( - camera: Camera, - plane: AxisAlignedPlane, - planeIndex: number, - dataset: ZarrDataset, - offset?: vec2 -): { layer: number; view: box2D; tiles: VoxelTile[] } { - // const { axes, datasets } = dataset.multiscales[0]; - // const zIndex = indexOfDimension(axes, sliceDimension[plane]); - const sliceSize = sizeInUnits( - uvTable[plane], - dataset.multiscales[0].axes, - dataset.multiscales[0].datasets[0] - )!; - const layer = pickBestScale( - dataset, - uvTable[plane], - camera.view, - camera.screen - ); - // TODO: open the array, look at its chunks, use that size for the size of the tiles I request! - const layerIndex = dataset.multiscales[0].datasets.indexOf(layer); - - const size = planeSizeInVoxels(uvTable[plane], dataset.multiscales[0].axes, layer); - const realSize = sizeInUnits(uvTable[plane], dataset.multiscales[0].axes, layer); - if (!size || !realSize) return { layer: layerIndex, view: Box2D.create([0, 0], [1, 1]), tiles: [] }; - const scale = Vec2.div(realSize, size); - // to go from a voxel-box to a real-box (easier than you think, as both have an origin at 0,0, because we only support scale...) - const vxlToReal = (vxl: box2D) => Box2D.translate(Box2D.scale(vxl, scale), offset ?? [0, 0]); - // const realToVxl = (real: box2D) => Box2D.scale(real, Vec2.div(size, realSize)); - - // find the tiles, in voxels, to request... - const allTiles = getAllTiles([256, 256], size); - const inView = allTiles.filter((tile) => !!Box2D.intersection(camera.view, vxlToReal(tile))); - // camera.view is in a made up dataspace, where 1=height of the current dataset - // thus, we have to convert it into a voxel-space camera for intersections - // const voxelView = realToVxl(camera.view); - return { - layer: layerIndex, - view: camera.view, - tiles: inView.map((uv) => ({ - plane, - realBounds: vxlToReal(uv), - bounds: uv, - planeIndex, - layerIndex, - })), - }; -} +import REGL, { type Framebuffer2D } from 'regl'; +import { + type ZarrDataset, + type ZarrRequest, + getSlice, + pickBestScale, + sizeInUnits, + planeSizeInVoxels, + indexOfDimension, +} from 'Common/loaders/ome-zarr/zarr-data'; +import { Box2D, type Interval, Vec2, type box2D, type vec2, type vec4 } from '@alleninstitute/vis-geometry'; +import { omit, slice } from 'lodash'; +import type { Camera } from './camera'; +import type { NestedArray, TypedArray } from 'zarr'; +import { getSlicePool } from 'Common/loaders/ome-zarr/sliceWorkerPool'; + +type Props = { + target: Framebuffer2D | null; + tile: vec4; + view: vec4; + rotation: number; + Rgamut: vec2; + Ggamut: vec2; + Bgamut: vec2; + viewport: REGL.BoundingBox; + R: REGL.Texture2D; + G: REGL.Texture2D; + B: REGL.Texture2D; +}; +function isTexture(obj: object | undefined): obj is Bfr { + return obj !== undefined && 'type' in obj && obj.type === 'texture2D'; +} +export function buildVersaRenderer(regl: REGL.Regl) { + const cmd = regl< + { + view: vec4; + tile: vec4; + rot: number; + R: REGL.Texture2D; + G: REGL.Texture2D; + B: REGL.Texture2D; + Rgamut: vec2; + Ggamut: vec2; + Bgamut: vec2; + }, + { pos: REGL.BufferData }, + Props + >({ + vert: ` precision highp float; + attribute vec2 pos; + + uniform vec4 view; + uniform vec4 tile; + varying vec2 texCoord; + uniform float rot; + + vec2 rotateObj(vec2 obj, float radians){ + return obj; + } + vec2 rotateTextureCoordinates(vec2 tx, float radians){ + vec2 xy = tx-vec2(0.5,0.5); + mat2 R = mat2( + vec2(cos(radians),-sin(radians)), + vec2(-sin(radians),cos(radians)) + ); + return ((R*xy)+vec2(0.5,0.5)); + } + void main(){ + vec2 tileSize = tile.zw-tile.xy; + texCoord = rotateTextureCoordinates(pos,rot); + vec2 obj = rotateObj((pos.xy*tileSize+tile.xy),rot); + + vec2 p = (obj-view.xy)/(view.zw-view.xy); + // now, to clip space + p = (p*2.0)-1.0; + gl_Position = vec4(p.x,p.y,0.0,1.0); + }`, + frag: ` + precision highp float; + uniform sampler2D R; + uniform sampler2D G; + uniform sampler2D B; // for reasons which are pretty annoying + // its more direct to do 3 separate channels... + uniform vec2 Rgamut; + uniform vec2 Ggamut; + uniform vec2 Bgamut; + + varying vec2 texCoord; + void main(){ + vec3 mins = vec3(Rgamut.x,Ggamut.x,Bgamut.x); + vec3 maxs = vec3(Rgamut.y,Ggamut.y,Bgamut.y); + vec3 span = maxs-mins; + vec3 color = (vec3( + texture2D(R, texCoord).r, + texture2D(G, texCoord).r, + texture2D(B, texCoord).r + )-mins) /span; + + gl_FragColor = vec4(color, 1.0); + }`, + framebuffer: regl.prop('target'), + attributes: { + pos: [0, 0, 1, 0, 1, 1, 0, 1], + }, + uniforms: { + rot: regl.prop('rotation'), + tile: regl.prop('tile'), + view: regl.prop('view'), + R: regl.prop('R'), + G: regl.prop('G'), + B: regl.prop('B'), + Rgamut: regl.prop('Rgamut'), + Ggamut: regl.prop('Ggamut'), + Bgamut: regl.prop('Bgamut'), + }, + depth: { + enable: false, + }, + count: 4, + // viewport: regl.prop("viewport"), + primitive: 'triangle fan', + // ... more! + }); + + return ( + item: VoxelTile, + settings: VoxelSliceRenderSettings, + channels: Record + ) => { + const { view, viewport, gamut, target, rotation } = settings; + const { realBounds } = item; + const { R, G, B } = channels; + + if (!isTexture(R) || !isTexture(G) || !isTexture(B)) { + console.log('missing data: ', R, G, B); + return; + } + + cmd({ + target, + rotation, + view: [...view.minCorner, ...view.maxCorner], + tile: [...realBounds.minCorner, ...realBounds.maxCorner], + R: R.data, + G: G.data, + B: B.data, + Rgamut: [gamut.R.gamut.min, gamut.R.gamut.max], + Ggamut: [gamut.G.gamut.min, gamut.G.gamut.max], + Bgamut: [gamut.B.gamut.min, gamut.B.gamut.max], + }); + }; +} +type Bfr = { type: 'texture2D'; data: REGL.Texture2D }; + +type Tile = { bounds: box2D }; +export type VoxelSliceRenderSettings = { + regl: REGL.Regl; + dataset: ZarrDataset; + view: box2D; + rotation: number; + gamut: Record<'R' | 'G' | 'B', { gamut: Interval; index: number }>; + viewport: REGL.BoundingBox; + target: REGL.Framebuffer2D | null; +}; +export type AxisAlignedPlane = 'xy' | 'yz' | 'xz'; +export type VoxelTile = { + plane: AxisAlignedPlane; + realBounds: box2D; + bounds: box2D; // in voxels, in the plane + planeIndex: number; + layerIndex: number; + // time and channel are always = 0, for now +}; + +function toZarrRequest(tile: VoxelTile, channel: number): ZarrRequest { + const { plane, planeIndex, bounds } = tile; + const { minCorner: min, maxCorner: max } = bounds; + const u = { min: min[0], max: max[0] }; + const v = { min: min[1], max: max[1] }; + switch (plane) { + case 'xy': + return { + x: u, + y: v, + t: 0, + c: channel, + z: planeIndex, + }; + case 'xz': + return { + x: u, + z: v, + t: 0, + c: channel, + y: planeIndex, + }; + case 'yz': + return { + y: u, + z: v, + t: 0, + c: channel, + x: planeIndex, + }; + } +} +export function cacheKeyFactory(col: string, item: VoxelTile, settings: VoxelSliceRenderSettings) { + return `${settings.dataset.url}_${JSON.stringify(omit(item, 'desiredResolution'))}_ch=${ + settings.gamut[col as 'R' | 'G' | 'B'].index + }`; +} + +function reqSlice(dataset: ZarrDataset, req: ZarrRequest, layerIndex: number) { + return getSlicePool().requestSlice(dataset, req, layerIndex); +} +const LUMINANCE = 'luminance'; +export function requestsForTile(tile: VoxelTile, settings: VoxelSliceRenderSettings, signal?: AbortSignal) { + const { dataset, regl } = settings; + const handleResponse = (vxl: Awaited>) => { + const { shape, data } = vxl; + const r = regl.texture({ + data, + width: shape[1], + height: shape[0], // TODO this swap is sus + format: LUMINANCE, + }); + return r; + }; + // lets hope the browser caches our 3x repeat calls to teh same data... + return { + R: async () => { + const vxl = await reqSlice(dataset, toZarrRequest(tile, settings.gamut.R.index), tile.layerIndex); + return { type: 'texture2D', data: handleResponse(vxl) }; + }, + G: async () => { + const vxl = await reqSlice(dataset, toZarrRequest(tile, settings.gamut.G.index), tile.layerIndex); + return { type: 'texture2D', data: handleResponse(vxl) }; + }, + B: async () => { + const vxl = await reqSlice(dataset, toZarrRequest(tile, settings.gamut.B.index), tile.layerIndex); + return { type: 'texture2D', data: handleResponse(vxl) }; + }, + }; +} + +function getAllTiles(idealTilePx: vec2, layerSize: vec2) { + // return the set of all our "tiles" of this layer, given the tilePx size + const tiles: box2D[] = []; + for (let x = 0; x < layerSize[0]; x += idealTilePx[0]) { + for (let y = 0; y < layerSize[1]; y += idealTilePx[1]) { + const xy: vec2 = [x, y]; + tiles.push(Box2D.create(xy, Vec2.min(Vec2.add(xy, idealTilePx), layerSize))); + } + } + return tiles; +} +const uvTable = { + xy: { u: 'x', v: 'y' }, + xz: { u: 'x', v: 'z' }, + yz: { u: 'y', v: 'z' }, +} as const; +const sliceDimension = { + xy: 'z', + xz: 'y', + yz: 'x', +} as const; + +export function getVisibleTiles( + camera: Camera, + plane: AxisAlignedPlane, + planeIndex: number, + dataset: ZarrDataset, + offset?: vec2 +): { layer: number; view: box2D; tiles: VoxelTile[] } { + // const { axes, datasets } = dataset.multiscales[0]; + // const zIndex = indexOfDimension(axes, sliceDimension[plane]); + const sliceSize = sizeInUnits(uvTable[plane], dataset.multiscales[0].axes, dataset.multiscales[0].datasets[0])!; + const layer = pickBestScale(dataset, uvTable[plane], camera.view, camera.screen); + // TODO: open the array, look at its chunks, use that size for the size of the tiles I request! + const layerIndex = dataset.multiscales[0].datasets.indexOf(layer); + + const size = planeSizeInVoxels(uvTable[plane], dataset.multiscales[0].axes, layer); + const realSize = sizeInUnits(uvTable[plane], dataset.multiscales[0].axes, layer); + if (!size || !realSize) return { layer: layerIndex, view: Box2D.create([0, 0], [1, 1]), tiles: [] }; + const scale = Vec2.div(realSize, size); + // to go from a voxel-box to a real-box (easier than you think, as both have an origin at 0,0, because we only support scale...) + const vxlToReal = (vxl: box2D) => Box2D.translate(Box2D.scale(vxl, scale), offset ?? [0, 0]); + // const realToVxl = (real: box2D) => Box2D.scale(real, Vec2.div(size, realSize)); + + // find the tiles, in voxels, to request... + const allTiles = getAllTiles([256, 256], size); + const inView = allTiles.filter((tile) => !!Box2D.intersection(camera.view, vxlToReal(tile))); + // camera.view is in a made up dataspace, where 1=height of the current dataset + // thus, we have to convert it into a voxel-space camera for intersections + // const voxelView = realToVxl(camera.view); + return { + layer: layerIndex, + view: camera.view, + tiles: inView.map((uv) => ({ + plane, + realBounds: vxlToReal(uv), + bounds: uv, + planeIndex, + layerIndex, + })), + }; +} diff --git a/apps/omezarr-viewer/src/versa.ts b/apps/omezarr-viewer/src/versa.ts index 6fdb8a1..8ee3d61 100644 --- a/apps/omezarr-viewer/src/versa.ts +++ b/apps/omezarr-viewer/src/versa.ts @@ -1,537 +1,554 @@ -// I am the scatterplot demo // -import { ImGui, ImGui_Impl } from "@zhobo63/imgui-ts"; -import REGL from "regl"; -import { - type ZarrDataset, - explain, - getSlice, - indexOfDimension, - load, - pickBestScale, - sizeInUnits, - planeSizeInVoxels, -} from "Common/loaders/ome-zarr/zarr-data"; -import { AsyncDataCache, type FrameLifecycle, beginLongRunningFrame } from "@alleninstitute/vis-scatterbrain"; -import { - type AxisAlignedPlane, - type VoxelSliceRenderSettings, - type VoxelTile, - buildVersaRenderer, - cacheKeyFactory, - getVisibleTiles, - requestsForTile, -} from "./versa-renderer"; -import { Box2D, type Interval, Vec2, type box2D, type vec2 } from "@alleninstitute/vis-geometry"; -import type { Camera } from "./camera"; -import { buildImageRenderer } from "./image-renderer"; -import { ImVec2, ImVec4 } from "@zhobo63/imgui-ts/src/imgui"; -import { colorMapWidget } from "./components/color-map"; -import { initDrawableInterface } from "./annotation/path"; - -const versa = "https://neuroglancer-vis-prototype.s3.amazonaws.com/VERSA/scratch/0500408166/"; -const b = "https://neuroglancer-vis-prototype.s3.amazonaws.com/VERSA/ome_zarr/20231207.1/1282139033/"; -const scott = "https://neuroglancer-vis-prototype.s3.amazonaws.com/VERSA/ome_zarr/20231204/1197986710/"; -const file = scott; -type Channel = "R" | "G" | "B"; // we can support 3 visual channels at once -type ChannelColorSettings = { - gamut: Interval; - index: number; -}; -const THUMB_SIZE = 128; -class VersaDemo { - mouse: "up" | "down"; - mousePos: vec2; - camera: Camera; - channels: Record; - plane: AxisAlignedPlane; - sliceIndex: number; - canvas: HTMLCanvasElement; - curFrame: FrameLifecycle | null; - rotation: number; - cache: AsyncDataCache; - regl: REGL.Regl; - dataset: ZarrDataset; - screenRenderer: ReturnType; - renderer: ReturnType; - screenBuffer: { bounds: box2D; fbo: REGL.Framebuffer2D }; - datasets: string[]; - sliceThumbs: REGL.Framebuffer2D[]; - thumbWidth = 64; - constructor( - canvas: HTMLCanvasElement, - dataset: ZarrDataset, - regl: REGL.Regl, - cache: AsyncDataCache, - urls: string[] - ) { - const [w, h] = [canvas.clientWidth, canvas.clientHeight]; - this.datasets = urls; - const baseSize = sizeInUnits({ u: 'x', v: 'y' }, dataset.multiscales[0].axes, dataset.multiscales[0].datasets[0]) ?? [10, 10] - this.camera = { - view: Box2D.create([0, 0], [(baseSize[1] * w) / h, baseSize[1]]), - screen: [w, h], - }; - this.screenBuffer = { bounds: this.camera.view, fbo: regl.framebuffer(w, h) }; - this.dataset = dataset; - this.regl = regl; - this.sliceIndex = 0; - this.plane = "xy"; - this.mouse = "up"; - this.cache = cache; - - this.mousePos = [0, 0]; - this.channels = { - R: { - gamut: { min: 0, max: 0.21 }, - index: 0, - }, - G: { - gamut: { min: 0, max: 0.21 }, - index: 1, - }, - B: { - gamut: { min: 0, max: 0.21 }, - index: 2, - }, - }; - this.canvas = canvas; - this.curFrame = null; - this.rotation = 0; - this.renderer = buildVersaRenderer(regl); - this.screenRenderer = buildImageRenderer(regl); - const loop = () => { - this.refreshScreen(); - window.requestAnimationFrame(loop); - }; - window.requestAnimationFrame(loop); - this.sliceThumbs = []; - this.initThumbnails(); - } - setupEventHandlers() { - const canvas = this.canvas; - - // initDrawableInterface(canvas, { - - // }) - } - async initThumbnails() { - // TODO cleanupThumbnails(); - const sliceSize = sizeInUnits( - { - u: "x", - v: "y", - }, - this.dataset.multiscales[0].axes, - this.dataset.multiscales[0].datasets[0] - )!; - - const smallestLayer = pickBestScale( - this.dataset, - { - u: "x", - v: "y", - }, - Box2D.create([0, 0], sliceSize), - [1, 1] - ); - const smallestLayerIndex = this.dataset.multiscales[0].datasets.indexOf(smallestLayer); - // how many slices are there? - const indexOfZ = indexOfDimension(this.dataset.multiscales[0].axes, "z"); - if (indexOfZ < 0) return; - // get the size, in real units - const sizeInMM = sizeInUnits({ u: "x", v: "y" }, this.dataset.multiscales[0].axes, smallestLayer)!; - // get the aspect ratio, widen the thumbslices... - const r = sizeInMM[0] / sizeInMM[1]; - this.thumbWidth = THUMB_SIZE * r; - const getSliceTextures = async (z: number) => { - const req = { - c: 0, - t: 0, - x: null, - y: null, - z, - }; - return Promise.all([ - getSlice(this.dataset, { ...req, c: 0 }, smallestLayerIndex), - getSlice(this.dataset, { ...req, c: 1 }, smallestLayerIndex), - getSlice(this.dataset, { ...req, c: 2 }, smallestLayerIndex), - ] as const); - }; - const numSlices = smallestLayer.shape[indexOfZ]; - const unitBox = Box2D.create([0, 0], [1, 1]); - for (let z = 0; z < numSlices; z++) { - const buffers = await getSliceTextures(z); - const [R, G, B] = buffers.map((bfr) => - this.regl.texture({ - width: bfr.shape[1], - height: bfr.shape[0], - data: bfr.buffer.flatten(), - format: "luminance", - }) - ); - - const thumb = this.regl.framebuffer(THUMB_SIZE, THUMB_SIZE); - // now render that to a much smaller texture... - this.renderer( - { plane: "xy", bounds: unitBox, layerIndex: smallestLayerIndex, planeIndex: z }, - { - dataset: this.dataset, - gamut: this.channels, - regl: this.regl, - target: thumb, - view: unitBox, - viewport: { x: 0, y: 0, width: THUMB_SIZE, height: THUMB_SIZE }, - }, - { R, G, B } - ); - this.sliceThumbs.push(thumb); - R.destroy(); - G.destroy(); - B.destroy(); - } - } - private upsideDown(v: box2D) { - const { minCorner, maxCorner } = v; - return Box2D.create([minCorner[0], maxCorner[1]], [maxCorner[0], minCorner[1]]); - } - private renderFrame() { - const { camera, plane, sliceIndex, dataset, cache, regl, channels, renderer } = this; - const { layer, view, tiles } = getVisibleTiles(camera, plane, sliceIndex, dataset); - // erase our buffer that holds the render'd dataset image - which lets the UI - // re-render itself independantly - regl.clear({ color: [0, 0, 0, 0], depth: 1, framebuffer: this.screenBuffer.fbo }); - - // get the lowest-resolution view of the current slice - the idea being that we keep - // it cached, and always draw it UNDER the actual layer we want to see, based on our zoom. - // this prevents a flickering black frame when we zoom in to a new, higher resolution layer - const { - layer: baseLayer, - view: baseView, - tiles: baseTiles, - } = getVisibleTiles({ ...camera, screen: [1, 1] }, plane, sliceIndex, dataset); - if (layer === baseLayer) { - this.curFrame = this.renderFrameHelper(baseView, baseTiles); - // if the layer we WANT is actually the lowest res layer, then we're done here and now! - return; - } - const baseSettings = { - view: baseView, - dataset, - regl, - target: this.screenBuffer.fbo, - viewport: { - x: 0, - y: 0, - width: this.canvas.clientWidth, - height: this.canvas.clientHeight, - }, - gamut: channels, - }; - - const cached = baseTiles.reduce( - (count, cur) => (cache.isCached(cacheKeyFactory("R", cur, baseSettings)) ? 1 + count : count), - 0 - ); - if (cached === 0) { - this.curFrame = this.renderFrameHelper(view, tiles); - return; - } - const frame = beginLongRunningFrame( - 3, - 33, - baseTiles, - cache, - baseSettings, - requestsForTile, - renderer, - (event) => { - switch (event.status) { - case "error": - throw event.error; // error boundary might catch this - case "progress": - break; - case "finished_synchronously": - case "finished": - console.log("finished base-layer... start real frame!"); - this.curFrame = this.renderFrameHelper(view, tiles); - break; - case "begun": - break; - case "cancelled": - this.curFrame = this.renderFrameHelper(view, tiles); - break; - default: - } - }, - cacheKeyFactory - ); - frame.cancelFrame(); - } - // not my fav thing to do - but renderFrame and renderFrame helper are tightly linked - // to accomplish our smoke&mirrors to avoid flickering as tiles load in - - // the both make assumptions about state, and the contents of buffers. do not - // call either of them! - private renderFrameHelper(view: box2D, visibleTiles: VoxelTile[]) { - const { camera, dataset, cache, regl, channels, renderer } = this; - this.screenBuffer.bounds = camera.view; - regl._refresh(); - const gamut = { - R: channels.R.gamut, - G: channels.G.gamut, - B: channels.B.gamut, - }; - const frame = beginLongRunningFrame( - 3, - 33, - visibleTiles, - cache, - { - view: view, - dataset, - regl, - target: this.screenBuffer.fbo, - viewport: { - x: 0, - y: 0, - width: this.canvas.clientWidth, - height: this.canvas.clientHeight, - }, - gamut: channels, - }, - requestsForTile, - renderer, - (event) => { - switch (event.status) { - case "error": - throw event.error; // error boundary might catch this - case "progress": - this.refreshScreen(); - break; - case "finished_synchronously": - case "finished": - this.curFrame = null; - this.refreshScreen(); - break; - case "begun": - this.refreshScreen(); - break; - case "cancelled": - break; - default: - } - }, - cacheKeyFactory - ); - return frame; - } - refreshScreen() { - const now = performance.now(); - this.regl._refresh(); - this.regl.clear({ depth: 1, color: [0, 0, 0, 1], framebuffer: null }); - - this.screenRenderer([ - { - box: Box2D.toFlatArray(this.screenBuffer.bounds), - img: this.screenBuffer.fbo, - target: null, - view: Box2D.toFlatArray(this.upsideDown(this.camera.view)), - }, - ]); - - this.drawUI(now); - - this.regl._refresh(); - } - - drawUI(time: number) { - let drawAgain = false; - const effects: Array<() => void> = []; - // imgui wants mutable access to stuff... which is pretty weird - imAccess is nice, but all the vector-style updaters are nasty - try { - this.regl._gl.bindFramebuffer(this.regl._gl.FRAMEBUFFER, null); - ImGui_Impl.NewFrame(time); - ImGui.NewFrame(); - ImGui.Begin("Settings"); - - // TODO: count the available channels that we could use for color! - Object.entries(this.channels).forEach(([channel, settings]) => { - const result = colorMapWidget( - channel, - { - gamut: settings.gamut, - color: new ImGui.Vec4(channel === "R" ? 255 : 0, channel === "G" ? 255 : 0, channel === "B" ? 255 : 0, 255), - useMe: true, - index: settings.index, - }, - 3 - ); - if (result.changed) { - this.channels[channel as Channel].gamut = result.gamut; - this.channels[channel as Channel].index = result.index; - drawAgain = true; - } - }); - const highlight = new ImVec4(0, 0.25, 0.65, 1.0); - const regular = new ImVec4(0.2, 0.2, 0.2, 1.0); - for (const thumb of this.sliceThumbs) { - if ( - // here we dig deep into the guts of a regl-managed texture... not super safe, and regl's types are not really set up for this: - ImGui.ImageButton( - // @ts-expect-error - thumb?.color[0]?._texture?.texture ?? null, - new ImVec2(this.thumbWidth, THUMB_SIZE), - new ImVec2(0, 0), - new ImVec2(1, 1), - // draw a little box around the selected slice: - this.sliceIndex === this.sliceThumbs.indexOf(thumb) ? 3 : 0, - this.sliceIndex === this.sliceThumbs.indexOf(thumb) ? highlight : regular - ) - ) { - drawAgain = true; - effects.push(() => this.setSlice(this.sliceThumbs.indexOf(thumb))); - } - ImGui.SameLine(); - } - ImGui.End(); - ImGui.EndFrame(); - ImGui.Render(); - - ImGui_Impl.RenderDrawData(ImGui.GetDrawData()); - effects.forEach((fx) => fx()); - if (drawAgain) { - window.setTimeout(() => this.rerender(), 5); - } - } catch (err) { - console.warn(err); - } - } - rerender() { - if (this.curFrame !== null) { - this.curFrame.cancelFrame(); - } - this.renderFrame(); - } - mouseButton(click: "up" | "down") { - this.mouse = click; - } - mouseMove(delta: vec2) { - if (this.mouse === "down") { - // drag the view - const { screen, view } = this.camera; - const p = Vec2.div(delta, [this.canvas.clientWidth, this.canvas.clientHeight]); - const c = Vec2.mul(p, Box2D.size(view)); - this.camera = { view: Box2D.translate(view, c), screen }; - this.rerender(); - } - this.mousePos = Vec2.add(this.mousePos, delta); - } - changeSlice(delta: number) { - this.sliceIndex += delta; - this.rerender(); - } - setSlice(sliceIndex: number) { - this.sliceIndex = sliceIndex; - // this.rerender(); - } - // changeGamut(delta: number) { - // this.gamut = { min: this.gamut.min, max: this.gamut.max * delta }; - // this.rerender(); - // } - zoom(scale: number) { - const { view, screen } = this.camera; - const m = Box2D.midpoint(view); - this.camera = { - view: Box2D.translate(Box2D.scale(Box2D.translate(view, Vec2.scale(m, -1)), [scale, scale]), m), - screen, - }; - this.rerender(); - } - nextAxis() { - this.plane = this.plane == "xy" ? "xz" : this.plane === "xz" ? "yz" : "xy"; - this.rerender(); - } - rotateTiles() { - this.rotation += Math.PI / 2; - this.rerender(); - } -} - -function setupEventHandlers(canvas: HTMLCanvasElement, demo: VersaDemo) { - canvas.onmousedown = (e: MouseEvent) => { - if (ImGui.GetIO().WantCaptureMouse) return; - demo.mouseButton("down"); - }; - canvas.onmouseup = (e: MouseEvent) => { - if (ImGui.GetIO().WantCaptureMouse) return; - demo.mouseButton("up"); - }; - canvas.onmousemove = (e: MouseEvent) => { - if (ImGui.GetIO().WantCaptureMouse) return; - // account for gl-origin vs. screen origin: - demo.mouseMove([-e.movementX, -e.movementY]); - }; - canvas.onwheel = (e: WheelEvent) => { - if (ImGui.GetIO().WantCaptureMouse) return; - if (e.ctrlKey) { - demo.nextAxis(); - } else if (e.altKey) { - demo.changeSlice(e.deltaY > 0 ? 1 : -1); - } else { - demo.zoom(e.deltaY > 0 ? 1.1 : 0.9); - } - }; - canvas.onkeydown = (e: KeyboardEvent) => { - if (ImGui.GetIO().WantCaptureKeyboard) return; - - switch (e.key) { - case "a": - demo.nextAxis(); - break; - case "r": - demo.rotateTiles(); - break; - default: - } - }; -} -function setupGui(canvas: HTMLCanvasElement | WebGL2RenderingContext | WebGLRenderingContext) { - ImGui.default().then(() => { - ImGui.CHECKVERSION(); - ImGui.CreateContext(); - const io: ImGui.IO = ImGui.GetIO(); - ImGui.StyleColorsDark(); - io.Fonts.AddFontDefault(); - ImGui_Impl.Init(canvas); - }); -} -async function demotime() { - const thing = document.getElementById("glCanvas") as HTMLCanvasElement; - thing.width = 2000; - thing.height = 2000; - const gl = thing.getContext("webgl2", { - alpha: true, - preserveDrawingBuffer: true, - antialias: true, - premultipliedAlpha: true, - }) as WebGL2RenderingContext; - const regl = REGL({ - gl, - // attributes: {}, - // extensions: ["ANGLE_instanced_arrays", "OES_texture_float", "WEBGL_color_buffer_float"], - }); - const canvas: HTMLCanvasElement = regl._gl.canvas as HTMLCanvasElement; - setupGui(gl); - const voxelSliceCache: AsyncDataCache = new AsyncDataCache((d: REGL.Texture2D) => { - d.destroy() - }, (_d) => 1, 200); - const zarr = await load(file); - explain(zarr); - - const theDemo = new VersaDemo(canvas, zarr, regl, voxelSliceCache, []); - - setupEventHandlers(canvas, theDemo); - theDemo.rerender(); -} - -// since I am just included in a script tag in a raw html document, this is how we start: -demotime(); +// I am the scatterplot demo // +import { ImGui, ImGui_Impl } from '@zhobo63/imgui-ts'; +import REGL from 'regl'; +import { + type ZarrDataset, + explain, + getSlice, + indexOfDimension, + load, + pickBestScale, + sizeInUnits, + planeSizeInVoxels, +} from 'Common/loaders/ome-zarr/zarr-data'; +import { AsyncDataCache, type FrameLifecycle, beginLongRunningFrame } from '@alleninstitute/vis-scatterbrain'; +import { + type AxisAlignedPlane, + type VoxelSliceRenderSettings, + type VoxelTile, + buildVersaRenderer, + cacheKeyFactory, + getVisibleTiles, + requestsForTile, +} from './versa-renderer'; +import { Box2D, type Interval, Vec2, type box2D, type vec2 } from '@alleninstitute/vis-geometry'; +import type { Camera } from './camera'; +import { buildImageRenderer } from './image-renderer'; +import { ImVec2, ImVec4 } from '@zhobo63/imgui-ts/src/imgui'; +import { colorMapWidget } from './components/color-map'; +import { initDrawableInterface } from './annotation/path'; + +const versa = 'https://neuroglancer-vis-prototype.s3.amazonaws.com/VERSA/scratch/0500408166/'; +const b = 'https://neuroglancer-vis-prototype.s3.amazonaws.com/VERSA/ome_zarr/20231207.1/1282139033/'; +const scott = 'https://neuroglancer-vis-prototype.s3.amazonaws.com/VERSA/ome_zarr/20231204/1197986710/'; +const file = scott; +type Channel = 'R' | 'G' | 'B'; // we can support 3 visual channels at once +type ChannelColorSettings = { + gamut: Interval; + index: number; +}; +const THUMB_SIZE = 128; +class VersaDemo { + mouse: 'up' | 'down'; + mousePos: vec2; + camera: Camera; + channels: Record; + plane: AxisAlignedPlane; + sliceIndex: number; + canvas: HTMLCanvasElement; + curFrame: FrameLifecycle | null; + rotation: number; + cache: AsyncDataCache; + regl: REGL.Regl; + dataset: ZarrDataset; + screenRenderer: ReturnType; + renderer: ReturnType; + screenBuffer: { bounds: box2D; fbo: REGL.Framebuffer2D }; + datasets: string[]; + sliceThumbs: REGL.Framebuffer2D[]; + thumbWidth = 64; + constructor( + canvas: HTMLCanvasElement, + dataset: ZarrDataset, + regl: REGL.Regl, + cache: AsyncDataCache, + urls: string[] + ) { + const [w, h] = [canvas.clientWidth, canvas.clientHeight]; + this.datasets = urls; + const baseSize = sizeInUnits( + { u: 'x', v: 'y' }, + dataset.multiscales[0].axes, + dataset.multiscales[0].datasets[0] + ) ?? [10, 10]; + this.camera = { + view: Box2D.create([0, 0], [(baseSize[1] * w) / h, baseSize[1]]), + screen: [w, h], + }; + this.screenBuffer = { bounds: this.camera.view, fbo: regl.framebuffer(w, h) }; + this.dataset = dataset; + this.regl = regl; + this.sliceIndex = 0; + this.plane = 'xy'; + this.mouse = 'up'; + this.cache = cache; + + this.mousePos = [0, 0]; + this.channels = { + R: { + gamut: { min: 0, max: 0.21 }, + index: 0, + }, + G: { + gamut: { min: 0, max: 0.21 }, + index: 1, + }, + B: { + gamut: { min: 0, max: 0.21 }, + index: 2, + }, + }; + this.canvas = canvas; + this.curFrame = null; + this.rotation = 0; + this.renderer = buildVersaRenderer(regl); + this.screenRenderer = buildImageRenderer(regl); + const loop = () => { + this.refreshScreen(); + window.requestAnimationFrame(loop); + }; + window.requestAnimationFrame(loop); + this.sliceThumbs = []; + this.initThumbnails(); + } + setupEventHandlers() { + const canvas = this.canvas; + + // initDrawableInterface(canvas, { + + // }) + } + async initThumbnails() { + // TODO cleanupThumbnails(); + const sliceSize = sizeInUnits( + { + u: 'x', + v: 'y', + }, + this.dataset.multiscales[0].axes, + this.dataset.multiscales[0].datasets[0] + )!; + + const smallestLayer = pickBestScale( + this.dataset, + { + u: 'x', + v: 'y', + }, + Box2D.create([0, 0], sliceSize), + [1, 1] + ); + const smallestLayerIndex = this.dataset.multiscales[0].datasets.indexOf(smallestLayer); + // how many slices are there? + const indexOfZ = indexOfDimension(this.dataset.multiscales[0].axes, 'z'); + if (indexOfZ < 0) return; + // get the size, in real units + const sizeInMM = sizeInUnits({ u: 'x', v: 'y' }, this.dataset.multiscales[0].axes, smallestLayer)!; + // get the aspect ratio, widen the thumbslices... + const r = sizeInMM[0] / sizeInMM[1]; + this.thumbWidth = THUMB_SIZE * r; + const getSliceTextures = async (z: number) => { + const req = { + c: 0, + t: 0, + x: null, + y: null, + z, + }; + return Promise.all([ + getSlice(this.dataset, { ...req, c: 0 }, smallestLayerIndex), + getSlice(this.dataset, { ...req, c: 1 }, smallestLayerIndex), + getSlice(this.dataset, { ...req, c: 2 }, smallestLayerIndex), + ] as const); + }; + const numSlices = smallestLayer.shape[indexOfZ]; + const unitBox = Box2D.create([0, 0], [1, 1]); + for (let z = 0; z < numSlices; z++) { + const buffers = await getSliceTextures(z); + const [R, G, B] = buffers.map((bfr) => + this.regl.texture({ + width: bfr.shape[1], + height: bfr.shape[0], + data: bfr.buffer.flatten(), + format: 'luminance', + }) + ); + + const thumb = this.regl.framebuffer(THUMB_SIZE, THUMB_SIZE); + // now render that to a much smaller texture... + this.renderer( + { plane: 'xy', bounds: unitBox, layerIndex: smallestLayerIndex, planeIndex: z }, + { + dataset: this.dataset, + gamut: this.channels, + regl: this.regl, + target: thumb, + view: unitBox, + viewport: { x: 0, y: 0, width: THUMB_SIZE, height: THUMB_SIZE }, + }, + { R, G, B } + ); + this.sliceThumbs.push(thumb); + R.destroy(); + G.destroy(); + B.destroy(); + } + } + private upsideDown(v: box2D) { + const { minCorner, maxCorner } = v; + return Box2D.create([minCorner[0], maxCorner[1]], [maxCorner[0], minCorner[1]]); + } + private renderFrame() { + const { camera, plane, sliceIndex, dataset, cache, regl, channels, renderer } = this; + const { layer, view, tiles } = getVisibleTiles(camera, plane, sliceIndex, dataset); + // erase our buffer that holds the render'd dataset image - which lets the UI + // re-render itself independantly + regl.clear({ color: [0, 0, 0, 0], depth: 1, framebuffer: this.screenBuffer.fbo }); + + // get the lowest-resolution view of the current slice - the idea being that we keep + // it cached, and always draw it UNDER the actual layer we want to see, based on our zoom. + // this prevents a flickering black frame when we zoom in to a new, higher resolution layer + const { + layer: baseLayer, + view: baseView, + tiles: baseTiles, + } = getVisibleTiles({ ...camera, screen: [1, 1] }, plane, sliceIndex, dataset); + if (layer === baseLayer) { + this.curFrame = this.renderFrameHelper(baseView, baseTiles); + // if the layer we WANT is actually the lowest res layer, then we're done here and now! + return; + } + const baseSettings = { + view: baseView, + dataset, + regl, + target: this.screenBuffer.fbo, + viewport: { + x: 0, + y: 0, + width: this.canvas.clientWidth, + height: this.canvas.clientHeight, + }, + gamut: channels, + }; + + const cached = baseTiles.reduce( + (count, cur) => (cache.isCached(cacheKeyFactory('R', cur, baseSettings)) ? 1 + count : count), + 0 + ); + if (cached === 0) { + this.curFrame = this.renderFrameHelper(view, tiles); + return; + } + const frame = beginLongRunningFrame( + 3, + 33, + baseTiles, + cache, + baseSettings, + requestsForTile, + renderer, + (event) => { + switch (event.status) { + case 'error': + throw event.error; // error boundary might catch this + case 'progress': + break; + case 'finished_synchronously': + case 'finished': + console.log('finished base-layer... start real frame!'); + this.curFrame = this.renderFrameHelper(view, tiles); + break; + case 'begun': + break; + case 'cancelled': + this.curFrame = this.renderFrameHelper(view, tiles); + break; + default: + } + }, + cacheKeyFactory + ); + frame.cancelFrame(); + } + // not my fav thing to do - but renderFrame and renderFrame helper are tightly linked + // to accomplish our smoke&mirrors to avoid flickering as tiles load in - + // the both make assumptions about state, and the contents of buffers. do not + // call either of them! + private renderFrameHelper(view: box2D, visibleTiles: VoxelTile[]) { + const { camera, dataset, cache, regl, channels, renderer } = this; + this.screenBuffer.bounds = camera.view; + regl._refresh(); + const gamut = { + R: channels.R.gamut, + G: channels.G.gamut, + B: channels.B.gamut, + }; + const frame = beginLongRunningFrame( + 3, + 33, + visibleTiles, + cache, + { + view: view, + dataset, + regl, + target: this.screenBuffer.fbo, + viewport: { + x: 0, + y: 0, + width: this.canvas.clientWidth, + height: this.canvas.clientHeight, + }, + gamut: channels, + }, + requestsForTile, + renderer, + (event) => { + switch (event.status) { + case 'error': + throw event.error; // error boundary might catch this + case 'progress': + this.refreshScreen(); + break; + case 'finished_synchronously': + case 'finished': + this.curFrame = null; + this.refreshScreen(); + break; + case 'begun': + this.refreshScreen(); + break; + case 'cancelled': + break; + default: + } + }, + cacheKeyFactory + ); + return frame; + } + refreshScreen() { + const now = performance.now(); + this.regl._refresh(); + this.regl.clear({ depth: 1, color: [0, 0, 0, 1], framebuffer: null }); + + this.screenRenderer([ + { + box: Box2D.toFlatArray(this.screenBuffer.bounds), + img: this.screenBuffer.fbo, + target: null, + view: Box2D.toFlatArray(this.upsideDown(this.camera.view)), + }, + ]); + + this.drawUI(now); + + this.regl._refresh(); + } + + drawUI(time: number) { + let drawAgain = false; + const effects: Array<() => void> = []; + // imgui wants mutable access to stuff... which is pretty weird - imAccess is nice, but all the vector-style updaters are nasty + try { + this.regl._gl.bindFramebuffer(this.regl._gl.FRAMEBUFFER, null); + ImGui_Impl.NewFrame(time); + ImGui.NewFrame(); + ImGui.Begin('Settings'); + + // TODO: count the available channels that we could use for color! + Object.entries(this.channels).forEach(([channel, settings]) => { + const result = colorMapWidget( + channel, + { + gamut: settings.gamut, + color: new ImGui.Vec4( + channel === 'R' ? 255 : 0, + channel === 'G' ? 255 : 0, + channel === 'B' ? 255 : 0, + 255 + ), + useMe: true, + index: settings.index, + }, + 3 + ); + if (result.changed) { + this.channels[channel as Channel].gamut = result.gamut; + this.channels[channel as Channel].index = result.index; + drawAgain = true; + } + }); + const highlight = new ImVec4(0, 0.25, 0.65, 1.0); + const regular = new ImVec4(0.2, 0.2, 0.2, 1.0); + for (const thumb of this.sliceThumbs) { + if ( + // here we dig deep into the guts of a regl-managed texture... not super safe, and regl's types are not really set up for this: + ImGui.ImageButton( + // @ts-expect-error + thumb?.color[0]?._texture?.texture ?? null, + new ImVec2(this.thumbWidth, THUMB_SIZE), + new ImVec2(0, 0), + new ImVec2(1, 1), + // draw a little box around the selected slice: + this.sliceIndex === this.sliceThumbs.indexOf(thumb) ? 3 : 0, + this.sliceIndex === this.sliceThumbs.indexOf(thumb) ? highlight : regular + ) + ) { + drawAgain = true; + effects.push(() => this.setSlice(this.sliceThumbs.indexOf(thumb))); + } + ImGui.SameLine(); + } + ImGui.End(); + ImGui.EndFrame(); + ImGui.Render(); + + ImGui_Impl.RenderDrawData(ImGui.GetDrawData()); + effects.forEach((fx) => fx()); + if (drawAgain) { + window.setTimeout(() => this.rerender(), 5); + } + } catch (err) { + console.warn(err); + } + } + rerender() { + if (this.curFrame !== null) { + this.curFrame.cancelFrame(); + } + this.renderFrame(); + } + mouseButton(click: 'up' | 'down') { + this.mouse = click; + } + mouseMove(delta: vec2) { + if (this.mouse === 'down') { + // drag the view + const { screen, view } = this.camera; + const p = Vec2.div(delta, [this.canvas.clientWidth, this.canvas.clientHeight]); + const c = Vec2.mul(p, Box2D.size(view)); + this.camera = { view: Box2D.translate(view, c), screen }; + this.rerender(); + } + this.mousePos = Vec2.add(this.mousePos, delta); + } + changeSlice(delta: number) { + this.sliceIndex += delta; + this.rerender(); + } + setSlice(sliceIndex: number) { + this.sliceIndex = sliceIndex; + // this.rerender(); + } + // changeGamut(delta: number) { + // this.gamut = { min: this.gamut.min, max: this.gamut.max * delta }; + // this.rerender(); + // } + zoom(scale: number) { + const { view, screen } = this.camera; + const m = Box2D.midpoint(view); + this.camera = { + view: Box2D.translate(Box2D.scale(Box2D.translate(view, Vec2.scale(m, -1)), [scale, scale]), m), + screen, + }; + this.rerender(); + } + nextAxis() { + this.plane = this.plane == 'xy' ? 'xz' : this.plane === 'xz' ? 'yz' : 'xy'; + this.rerender(); + } + rotateTiles() { + this.rotation += Math.PI / 2; + this.rerender(); + } +} + +function setupEventHandlers(canvas: HTMLCanvasElement, demo: VersaDemo) { + canvas.onmousedown = (e: MouseEvent) => { + if (ImGui.GetIO().WantCaptureMouse) return; + demo.mouseButton('down'); + }; + canvas.onmouseup = (e: MouseEvent) => { + if (ImGui.GetIO().WantCaptureMouse) return; + demo.mouseButton('up'); + }; + canvas.onmousemove = (e: MouseEvent) => { + if (ImGui.GetIO().WantCaptureMouse) return; + // account for gl-origin vs. screen origin: + demo.mouseMove([-e.movementX, -e.movementY]); + }; + canvas.onwheel = (e: WheelEvent) => { + if (ImGui.GetIO().WantCaptureMouse) return; + if (e.ctrlKey) { + demo.nextAxis(); + } else if (e.altKey) { + demo.changeSlice(e.deltaY > 0 ? 1 : -1); + } else { + demo.zoom(e.deltaY > 0 ? 1.1 : 0.9); + } + }; + canvas.onkeydown = (e: KeyboardEvent) => { + if (ImGui.GetIO().WantCaptureKeyboard) return; + + switch (e.key) { + case 'a': + demo.nextAxis(); + break; + case 'r': + demo.rotateTiles(); + break; + default: + } + }; +} +function setupGui(canvas: HTMLCanvasElement | WebGL2RenderingContext | WebGLRenderingContext) { + ImGui.default().then(() => { + ImGui.CHECKVERSION(); + ImGui.CreateContext(); + const io: ImGui.IO = ImGui.GetIO(); + ImGui.StyleColorsDark(); + io.Fonts.AddFontDefault(); + ImGui_Impl.Init(canvas); + }); +} +async function demotime() { + const thing = document.getElementById('glCanvas') as HTMLCanvasElement; + thing.width = 2000; + thing.height = 2000; + const gl = thing.getContext('webgl2', { + alpha: true, + preserveDrawingBuffer: true, + antialias: true, + premultipliedAlpha: true, + }) as WebGL2RenderingContext; + const regl = REGL({ + gl, + // attributes: {}, + // extensions: ["ANGLE_instanced_arrays", "OES_texture_float", "WEBGL_color_buffer_float"], + }); + const canvas: HTMLCanvasElement = regl._gl.canvas as HTMLCanvasElement; + setupGui(gl); + const voxelSliceCache: AsyncDataCache = new AsyncDataCache< + string, + string, + REGL.Texture2D + >( + (d: REGL.Texture2D) => { + d.destroy(); + }, + (_d) => 1, + 200 + ); + const zarr = await load(file); + explain(zarr); + + const theDemo = new VersaDemo(canvas, zarr, regl, voxelSliceCache, []); + + setupEventHandlers(canvas, theDemo); + theDemo.rerender(); +} + +// since I am just included in a script tag in a raw html document, this is how we start: +demotime(); diff --git a/apps/omezarr-viewer/tsconfig.json b/apps/omezarr-viewer/tsconfig.json index c0cb85c..0f20604 100644 --- a/apps/omezarr-viewer/tsconfig.json +++ b/apps/omezarr-viewer/tsconfig.json @@ -1,4 +1,4 @@ -{ - "extends": "../tsconfig.json", - "include": ["./src/**/*", "../common/src/**/*"], -} \ No newline at end of file +{ + "extends": "../tsconfig.json", + "include": ["./src/**/*", "../common/src/**/*"] +} diff --git a/apps/scatterplot/README.md b/apps/scatterplot/README.md index df54149..026795a 100644 --- a/apps/scatterplot/README.md +++ b/apps/scatterplot/README.md @@ -1,13 +1,15 @@ ## Scatterplot demo -A demo of rendering a scatterplot using beginLongRunningFrame. The points in the scatterplot are spatially indexed using a quad-tree. The way the quad-tree is organized is based on [link](https://github.com/potree/potree). +A demo of rendering a scatterplot using beginLongRunningFrame. The points in the scatterplot are spatially indexed using a quad-tree. The way the quad-tree is organized is based on [link](https://github.com/potree/potree). specifically, rather than the usual situation in which a parent node in the tree contains a low-resolution replacement for its children's data, all data in all layers of the tree should be considered to be additive; rendering all points in every node of the whole tree at every level would display the original ground truth data. Much like the ome-zarr demo, we can use a few simple tools to allow us to request only the nodes which are currently in view (and take up enough pixels to be worth rendering), and render them as they arrive using the concept of a long-running frame. ### How to build / run + 1. `pnpm build` from the root directory of this project 2. `pnpm install` in this directory 3. `pnpm run demo` in this directory - this will produce `dst/demo.html` 4. navigate to `dev/demo.html` and open it in your browser - its simply a static html page with a single js script import ### The Code - -- under construction come back later -- \ No newline at end of file + +-- under construction come back later -- diff --git a/apps/scatterplot/package.json b/apps/scatterplot/package.json index 22f0124..13cebb6 100644 --- a/apps/scatterplot/package.json +++ b/apps/scatterplot/package.json @@ -1,48 +1,48 @@ { - "name": "@alleninstitute/vis-scatterplot-demo", - "version": "0.0.1", - "contributors": [ - { - "name": "Lane Sawyer", - "email": "lane.sawyer@alleninstitute.org" + "name": "@alleninstitute/vis-scatterplot-demo", + "version": "0.0.1", + "contributors": [ + { + "name": "Lane Sawyer", + "email": "lane.sawyer@alleninstitute.org" + }, + { + "name": "James Gerstenberger", + "email": "james.gerstenberger@alleninstitute.org" + }, + { + "name": "Noah Shepard", + "email": "noah.shepard@alleninstitute.org" + }, + { + "name": "Skyler Moosman", + "email": "skyler.moosman@alleninstitute.org" + }, + { + "name": "Su Li", + "email": "su.li@alleninstitute.org" + } + ], + "license": "TBD", + "type": "module", + "main": "lib/index.js", + "types": "lib/index.d.ts", + "private": true, + "scripts": { + "preinstall": "npx only-allow pnpm", + "demo": "esbuild src/demo.ts --bundle --outfile=dst/demo.js && cp public/* dst/", + "typecheck": "tsc --noEmit" }, - { - "name": "James Gerstenberger", - "email": "james.gerstenberger@alleninstitute.org" + "devDependencies": { + "esbuild": "^0.19.12", + "typescript": "^5.3.3" }, - { - "name": "Noah Shepard", - "email": "noah.shepard@alleninstitute.org" - }, - { - "name": "Skyler Moosman", - "email": "skyler.moosman@alleninstitute.org" - }, - { - "name": "Su Li", - "email": "su.li@alleninstitute.org" + "dependencies": { + "@alleninstitute/vis-geometry": "workspace:*", + "@alleninstitute/vis-scatterbrain": "workspace:*", + "@types/lodash": "^4.14.202", + "@zhobo63/imgui-ts": "^0.1.43", + "lodash": "^4.17.21", + "regl": "^2.1.0" } - ], - "license": "TBD", - "type": "module", - "main": "lib/index.js", - "types": "lib/index.d.ts", - "private": true, - "scripts": { - "preinstall": "npx only-allow pnpm", - "demo": "esbuild src/demo.ts --bundle --outfile=dst/demo.js && cp public/* dst/", - "typecheck": "tsc --noEmit" - }, - "devDependencies": { - "esbuild": "^0.19.12", - "typescript": "^5.3.3" - }, - "dependencies": { - "@alleninstitute/vis-geometry": "workspace:*", - "@alleninstitute/vis-scatterbrain": "workspace:*", - "@types/lodash": "^4.14.202", - "@zhobo63/imgui-ts": "^0.1.43", - "lodash": "^4.17.21", - "regl": "^2.1.0" - } -} \ No newline at end of file +} diff --git a/apps/scatterplot/public/demo.html b/apps/scatterplot/public/demo.html index d5f103e..3ef4680 100644 --- a/apps/scatterplot/public/demo.html +++ b/apps/scatterplot/public/demo.html @@ -1,9 +1,10 @@ - - - - - - - - - \ No newline at end of file + + + + + + + diff --git a/apps/scatterplot/src/demo.ts b/apps/scatterplot/src/demo.ts index 0595a3b..f3f2086 100644 --- a/apps/scatterplot/src/demo.ts +++ b/apps/scatterplot/src/demo.ts @@ -1,157 +1,172 @@ -import { Box2D, Vec2, type box2D, type vec2 } from "@alleninstitute/vis-geometry"; -import { beginLongRunningFrame, AsyncDataCache, type FrameLifecycle } from "@alleninstitute/vis-scatterbrain"; -import { getVisibleItems, type Dataset, type RenderSettings, fetchItem } from 'Common/loaders/scatterplot/data' -import { loadDataset, loadScatterbrainJson, type ColumnarMetadata, type ColumnarTree, type ColumnBuffer } from "Common/loaders/scatterplot/scatterbrain-loader"; -import REGL from "regl"; - -import { buildRenderer } from "./renderer"; -const better = 'https://bkp-2d-visualizations-stage.s3.amazonaws.com/wmb_tenx_01172024_stage-20240128193624/488I12FURRB8ZY5KJ8T/ScatterBrain.json'; -const busted = 'https://bkp-2d-visualizations-stage.s3.amazonaws.com/wmb_tenx_01172024_stage-20240128193624/G4I4GFJXJB9ATZ3PTX1/ScatterBrain.json'; -const KB = 1000; -const MB = 1000 * KB; -class Demo { - camera: { - view: box2D; - screen: vec2; - } - dataset: Dataset | undefined; - regl: REGL.Regl; - canvas: HTMLCanvasElement; - renderer: ReturnType; - mouse: 'up' | 'down' - mousePos: vec2; - cache: AsyncDataCache; - curFrame: FrameLifecycle | null; - constructor(canvas: HTMLCanvasElement, regl: REGL.Regl, url: string) { - const [w, h] = [canvas.clientWidth, canvas.clientHeight]; - this.camera = { - view: Box2D.create([0, 0], [(10 * w) / h, 10]), - screen: [w, h] - } - this.curFrame = null; - this.cache = new AsyncDataCache((entry) => { - entry.data.destroy(); - }, (_data: ColumnBuffer) => 1, 1000); - - loadScatterbrainJson(url).then((metadata) => { - this.dataset = loadDataset(metadata, url) - this.rerender(); - }) - this.renderer = buildRenderer(regl); - this.canvas = canvas; - this.mouse = 'up' - this.regl = regl; - this.mousePos = [0, 0] - } - mouseButton(click: "up" | "down") { - this.mouse = click; - } - mouseMove(delta: vec2) { - if (this.mouse === "down") { - // drag the view - const { screen, view } = this.camera; - const p = Vec2.div(delta, [this.canvas.clientWidth, this.canvas.clientHeight]); - const c = Vec2.mul(p, Box2D.size(view)); - this.camera = { view: Box2D.translate(view, c), screen }; - this.rerender(); - } - this.mousePos = Vec2.add(this.mousePos, delta); - } - zoom(scale: number) { - const { view, screen } = this.camera; - const m = Box2D.midpoint(view); - this.camera = { - view: Box2D.translate(Box2D.scale(Box2D.translate(view, Vec2.scale(m, -1)), [scale, scale]), m), - screen, - }; - this.rerender(); - } - rerender() { - if (this.curFrame) { - this.curFrame.cancelFrame('whatever') - } - this.regl.clear({ color: [0.25, 0.25, 0.25, 1], depth: 1 }) - if (this.dataset) { - // how big is one px in data-units? - const px = Box2D.size(this.camera.view)[0] / this.camera.screen[0] - // lets only draw a box of points if its 90px wide: - const sizeThreshold = 90 * px; - const items = getVisibleItems(this.dataset, this.camera.view, sizeThreshold); - this.curFrame = beginLongRunningFrame, RenderSettings>( - 5, 33, items, this.cache, { - dataset: this.dataset, - view: this.camera.view, - target: null, - colorBy: { - name: '88', - type: 'QUANTITATIVE', - }, - pointSize: 3, - regl: this.regl - }, - fetchItem, - this.renderer, - (event) => { - switch (event.status) { - case "error": - throw event.error; // error boundary might catch this - case "progress": - break; - case "finished_synchronously": - case "finished": - this.curFrame = null; - break; - case "begun": - break; - case "cancelled": - break; - default: - break; - } - }, - (reqKey, item, settings) => `${reqKey}:${item.content.name}`) - } - } -} -let theDemo: Demo; - -function demoTime() { - const thing = document.getElementById("glCanvas") as HTMLCanvasElement; - thing.width = thing.clientWidth; - thing.height = thing.clientHeight; - const gl = thing.getContext("webgl", { - alpha: true, - preserveDrawingBuffer: true, - antialias: true, - premultipliedAlpha: true, - }) as WebGL2RenderingContext; - const regl = REGL({ - gl, - // attributes: {}, - extensions: ["ANGLE_instanced_arrays", "OES_texture_float", "WEBGL_color_buffer_float"], - }); - const canvas: HTMLCanvasElement = regl._gl.canvas as HTMLCanvasElement; - theDemo = new Demo(canvas, regl, better); - - setupEventHandlers(canvas, theDemo); -} - - -function setupEventHandlers(canvas: HTMLCanvasElement, demo: Demo) { - canvas.onmousedown = (e: MouseEvent) => { - demo.mouseButton("down"); - }; - canvas.onmouseup = (e: MouseEvent) => { - demo.mouseButton("up"); - }; - canvas.onmousemove = (e: MouseEvent) => { - // account for gl-origin vs. screen origin: - demo.mouseMove([-e.movementX, e.movementY]); - }; - canvas.onwheel = (e: WheelEvent) => { - demo.zoom(e.deltaY > 0 ? 1.1 : 0.9); - }; -} - - -demoTime(); \ No newline at end of file +import { Box2D, Vec2, type box2D, type vec2 } from '@alleninstitute/vis-geometry'; +import { beginLongRunningFrame, AsyncDataCache, type FrameLifecycle } from '@alleninstitute/vis-scatterbrain'; +import { getVisibleItems, type Dataset, type RenderSettings, fetchItem } from 'Common/loaders/scatterplot/data'; +import { + loadDataset, + loadScatterbrainJson, + type ColumnarMetadata, + type ColumnarTree, + type ColumnBuffer, +} from 'Common/loaders/scatterplot/scatterbrain-loader'; +import REGL from 'regl'; + +import { buildRenderer } from './renderer'; +const better = + 'https://bkp-2d-visualizations-stage.s3.amazonaws.com/wmb_tenx_01172024_stage-20240128193624/488I12FURRB8ZY5KJ8T/ScatterBrain.json'; +const busted = + 'https://bkp-2d-visualizations-stage.s3.amazonaws.com/wmb_tenx_01172024_stage-20240128193624/G4I4GFJXJB9ATZ3PTX1/ScatterBrain.json'; +const KB = 1000; +const MB = 1000 * KB; +class Demo { + camera: { + view: box2D; + screen: vec2; + }; + dataset: Dataset | undefined; + regl: REGL.Regl; + canvas: HTMLCanvasElement; + renderer: ReturnType; + mouse: 'up' | 'down'; + mousePos: vec2; + cache: AsyncDataCache; + curFrame: FrameLifecycle | null; + constructor(canvas: HTMLCanvasElement, regl: REGL.Regl, url: string) { + const [w, h] = [canvas.clientWidth, canvas.clientHeight]; + this.camera = { + view: Box2D.create([0, 0], [(10 * w) / h, 10]), + screen: [w, h], + }; + this.curFrame = null; + this.cache = new AsyncDataCache( + (entry) => { + entry.data.destroy(); + }, + (_data: ColumnBuffer) => 1, + 1000 + ); + + loadScatterbrainJson(url).then((metadata) => { + this.dataset = loadDataset(metadata, url); + this.rerender(); + }); + this.renderer = buildRenderer(regl); + this.canvas = canvas; + this.mouse = 'up'; + this.regl = regl; + this.mousePos = [0, 0]; + } + mouseButton(click: 'up' | 'down') { + this.mouse = click; + } + mouseMove(delta: vec2) { + if (this.mouse === 'down') { + // drag the view + const { screen, view } = this.camera; + const p = Vec2.div(delta, [this.canvas.clientWidth, this.canvas.clientHeight]); + const c = Vec2.mul(p, Box2D.size(view)); + this.camera = { view: Box2D.translate(view, c), screen }; + this.rerender(); + } + this.mousePos = Vec2.add(this.mousePos, delta); + } + zoom(scale: number) { + const { view, screen } = this.camera; + const m = Box2D.midpoint(view); + this.camera = { + view: Box2D.translate(Box2D.scale(Box2D.translate(view, Vec2.scale(m, -1)), [scale, scale]), m), + screen, + }; + this.rerender(); + } + rerender() { + if (this.curFrame) { + this.curFrame.cancelFrame('whatever'); + } + this.regl.clear({ color: [0.25, 0.25, 0.25, 1], depth: 1 }); + if (this.dataset) { + // how big is one px in data-units? + const px = Box2D.size(this.camera.view)[0] / this.camera.screen[0]; + // lets only draw a box of points if its 90px wide: + const sizeThreshold = 90 * px; + const items = getVisibleItems(this.dataset, this.camera.view, sizeThreshold); + this.curFrame = beginLongRunningFrame, RenderSettings>( + 5, + 33, + items, + this.cache, + { + dataset: this.dataset, + view: this.camera.view, + target: null, + colorBy: { + name: '88', + type: 'QUANTITATIVE', + }, + pointSize: 3, + regl: this.regl, + }, + fetchItem, + this.renderer, + (event) => { + switch (event.status) { + case 'error': + throw event.error; // error boundary might catch this + case 'progress': + break; + case 'finished_synchronously': + case 'finished': + this.curFrame = null; + break; + case 'begun': + break; + case 'cancelled': + break; + default: + break; + } + }, + (reqKey, item, settings) => `${reqKey}:${item.content.name}` + ); + } + } +} +let theDemo: Demo; + +function demoTime() { + const thing = document.getElementById('glCanvas') as HTMLCanvasElement; + thing.width = thing.clientWidth; + thing.height = thing.clientHeight; + const gl = thing.getContext('webgl', { + alpha: true, + preserveDrawingBuffer: true, + antialias: true, + premultipliedAlpha: true, + }) as WebGL2RenderingContext; + const regl = REGL({ + gl, + // attributes: {}, + extensions: ['ANGLE_instanced_arrays', 'OES_texture_float', 'WEBGL_color_buffer_float'], + }); + const canvas: HTMLCanvasElement = regl._gl.canvas as HTMLCanvasElement; + theDemo = new Demo(canvas, regl, better); + + setupEventHandlers(canvas, theDemo); +} + +function setupEventHandlers(canvas: HTMLCanvasElement, demo: Demo) { + canvas.onmousedown = (e: MouseEvent) => { + demo.mouseButton('down'); + }; + canvas.onmouseup = (e: MouseEvent) => { + demo.mouseButton('up'); + }; + canvas.onmousemove = (e: MouseEvent) => { + // account for gl-origin vs. screen origin: + demo.mouseMove([-e.movementX, e.movementY]); + }; + canvas.onwheel = (e: WheelEvent) => { + demo.zoom(e.deltaY > 0 ? 1.1 : 0.9); + }; +} + +demoTime(); diff --git a/apps/scatterplot/src/renderer.ts b/apps/scatterplot/src/renderer.ts index fc5a530..127ac0c 100644 --- a/apps/scatterplot/src/renderer.ts +++ b/apps/scatterplot/src/renderer.ts @@ -1,89 +1,103 @@ -import REGL, { type Framebuffer2D } from "regl"; -import type { ColumnBuffer, ColumnarTree } from "Common/loaders/scatterplot/scatterbrain-loader"; -import type { RenderSettings } from "Common/loaders/scatterplot/data"; -import { Box2D, type box2D, type vec2, type vec4 } from "@alleninstitute/vis-geometry"; - -type Props = { - view: vec4; - itemDepth: number; - count: number; - pointSize: number; - position: Float32Array, - color: Float32Array, - offset?: vec2 | undefined, - target: Framebuffer2D | null; -} -export function buildRenderer(regl: REGL.Regl) { - // build the regl command first - const cmd = regl<{ view: vec4, itemDepth: number, offset: vec2, pointSize: number }, { position: Float32Array, color: Float32Array }, Props>({ - vert: ` - precision highp float; - attribute vec2 position; - attribute float color; - - uniform float pointSize; - uniform vec4 view; - uniform float itemDepth; - uniform vec2 offset; - - varying vec4 clr; - - void main(){ - gl_PointSize=pointSize; - vec2 size = view.zw-view.xy; - vec2 pos = ((position+offset)-view.xy)/size; - vec2 clip = (pos*2.0)-1.0; - - // todo: gradients are cool - clr = vec4(mix(vec3(0.3,0,0),vec3(1,1,1),color/15.0),1.0); - - gl_Position = vec4(clip,0.5-color/20.0,1); - }`, - frag: ` - precision highp float; - varying vec4 clr; - void main(){ - // todo: round points with gl_FragCoord - gl_FragColor = clr; - }`, - attributes: { - color: regl.prop('color'), - position: regl.prop('position'), - }, - uniforms: { - itemDepth: regl.prop("itemDepth"), - view: regl.prop("view"), - offset: regl.prop("offset"), - pointSize: regl.prop("pointSize"), - }, - - blend: { - enable: false, - }, - framebuffer: regl.prop('target'), - count: regl.prop('count'), - primitive: "points", - }) - const renderDots = (item: ColumnarTree & { offset?: vec2 | undefined }, settings: RenderSettings, columns: Record) => { - const { color, position } = columns; - const count = item.content.count; - const itemDepth = item.content.depth - if (color && position && 'type' in color && 'type' in position && color.type === 'vbo' && position.type === 'vbo') { - cmd({ - view: Box2D.toFlatArray(settings.view), - count, - itemDepth, - position: position.data, - pointSize: settings.pointSize, - color: color.data, - offset: item.offset ?? [0, 0], - target: settings.target - }) - } else { - // todo freak out! - throw new Error('omg the internet lied to me') - } - - } - return renderDots; -} +import REGL, { type Framebuffer2D } from 'regl'; +import type { ColumnBuffer, ColumnarTree } from 'Common/loaders/scatterplot/scatterbrain-loader'; +import type { RenderSettings } from 'Common/loaders/scatterplot/data'; +import { Box2D, type box2D, type vec2, type vec4 } from '@alleninstitute/vis-geometry'; + +type Props = { + view: vec4; + itemDepth: number; + count: number; + pointSize: number; + position: Float32Array; + color: Float32Array; + offset?: vec2 | undefined; + target: Framebuffer2D | null; +}; +export function buildRenderer(regl: REGL.Regl) { + // build the regl command first + const cmd = regl< + { view: vec4; itemDepth: number; offset: vec2; pointSize: number }, + { position: Float32Array; color: Float32Array }, + Props + >({ + vert: ` + precision highp float; + attribute vec2 position; + attribute float color; + + uniform float pointSize; + uniform vec4 view; + uniform float itemDepth; + uniform vec2 offset; + + varying vec4 clr; + + void main(){ + gl_PointSize=pointSize; + vec2 size = view.zw-view.xy; + vec2 pos = ((position+offset)-view.xy)/size; + vec2 clip = (pos*2.0)-1.0; + + // todo: gradients are cool + clr = vec4(mix(vec3(0.3,0,0),vec3(1,1,1),color/15.0),1.0); + + gl_Position = vec4(clip,0.5-color/20.0,1); + }`, + frag: ` + precision highp float; + varying vec4 clr; + void main(){ + // todo: round points with gl_FragCoord + gl_FragColor = clr; + }`, + attributes: { + color: regl.prop('color'), + position: regl.prop('position'), + }, + uniforms: { + itemDepth: regl.prop('itemDepth'), + view: regl.prop('view'), + offset: regl.prop('offset'), + pointSize: regl.prop('pointSize'), + }, + + blend: { + enable: false, + }, + framebuffer: regl.prop('target'), + count: regl.prop('count'), + primitive: 'points', + }); + const renderDots = ( + item: ColumnarTree & { offset?: vec2 | undefined }, + settings: RenderSettings, + columns: Record + ) => { + const { color, position } = columns; + const count = item.content.count; + const itemDepth = item.content.depth; + if ( + color && + position && + 'type' in color && + 'type' in position && + color.type === 'vbo' && + position.type === 'vbo' + ) { + cmd({ + view: Box2D.toFlatArray(settings.view), + count, + itemDepth, + position: position.data, + pointSize: settings.pointSize, + color: color.data, + offset: item.offset ?? [0, 0], + target: settings.target, + }); + } else { + // todo freak out! + throw new Error('omg the internet lied to me'); + } + }; + return renderDots; +} diff --git a/apps/scatterplot/tsconfig.json b/apps/scatterplot/tsconfig.json index d1537fd..185adba 100644 --- a/apps/scatterplot/tsconfig.json +++ b/apps/scatterplot/tsconfig.json @@ -1,10 +1,10 @@ -{ - "extends": "../tsconfig.json", - "include": ["./src/**/*", "../common/src/**/*"], - "compilerOptions": { - "baseUrl": "./", - "paths": { - "Common/*":["../common/src/*"] - } - } -} \ No newline at end of file +{ + "extends": "../tsconfig.json", + "include": ["./src/**/*", "../common/src/**/*"], + "compilerOptions": { + "baseUrl": "./", + "paths": { + "Common/*": ["../common/src/*"] + } + } +} diff --git a/apps/tsconfig.json b/apps/tsconfig.json index 060e202..fe83fdc 100644 --- a/apps/tsconfig.json +++ b/apps/tsconfig.json @@ -1,20 +1,17 @@ { - "extends": "../tsconfig.base.json", - "compilerOptions": { - "strict": true, - "moduleResolution": "Node", - "module": "ES2022", - "target": "ES2022", - "lib": [ - "es2022", - "DOM" - ], - "declaration": true, - "skipLibCheck": true, - "esModuleInterop": true, - "baseUrl": "./", - "paths": { - "Common/*":["./common/src/*"] - }, - }, -} \ No newline at end of file + "extends": "../tsconfig.base.json", + "compilerOptions": { + "strict": true, + "moduleResolution": "Node", + "module": "ES2022", + "target": "ES2022", + "lib": ["es2022", "DOM"], + "declaration": true, + "skipLibCheck": true, + "esModuleInterop": true, + "baseUrl": "./", + "paths": { + "Common/*": ["./common/src/*"] + } + } +} diff --git a/docs/authenticating.md b/docs/authenticating.md index 8fa9eb3..0330280 100644 --- a/docs/authenticating.md +++ b/docs/authenticating.md @@ -17,6 +17,7 @@ Before you can publish a package, you'll need to get your Personal Access Token ``` ## Authenticating in GitHub Actions or Another CI/CD Pipeline + If you have a CI/CD pipeline outside of GitHub Actions, do the following to authenticate: 1. Follow the instructions for generating a PAT in the previous section. @@ -24,6 +25,7 @@ If you have a CI/CD pipeline outside of GitHub Actions, do the following to auth 2. Add that new token to your pipeline's secrets (e.g. `NODE_AUTH_TOKEN`). 3. Use that secret in your pipeline to set up the token before you do the package install: + ``` npm set "//npm.pkg.github.com/:_authToken=$NODE_AUTH_TOKEN" ``` diff --git a/docs/examples.md b/docs/examples.md index 55a9876..af18733 100644 --- a/docs/examples.md +++ b/docs/examples.md @@ -1,5 +1,7 @@ # Examples + Examples are located in the `apps` directory. ## Adding New Examples + To add a new example, create a new directory in the `apps` directory, copy the `package.json` from another example, and then start building! diff --git a/docs/publishing.md b/docs/publishing.md index 3ae19b2..e2d2832 100644 --- a/docs/publishing.md +++ b/docs/publishing.md @@ -3,6 +3,7 @@ The `vis` project contains multiple packages, each of which is published to the Allen Institute internal GitHub NPM package registry. ## Publishing a New Package + When you have a new package to publish, follow these steps to publish it: 1. Authenticate with GitHub Packages by following the instructions in the [Authenticating with GitHub Packages](authenticating.md) documentation. @@ -24,6 +25,7 @@ When you have a new package to publish, follow these steps to publish it: 4. Verify your package is available. You can see it listed on the [Allen Institute's GitHub NPM package registry](https://github.com/orgs/AllenInstitute/packages) or on the homepage of this repository. ## Updating an Existing Package + When you have changes to an existing package that you want to publish, follow these steps to publish the changes: 1. Authenticate with GitHub Packages by following the instructions in the [Authenticating with GitHub Packages](authenticating.md) documentation. diff --git a/package.json b/package.json index db7ade0..d5007ae 100644 --- a/package.json +++ b/package.json @@ -2,14 +2,17 @@ "name": "@alleninstitute/vis", "scripts": { "preinstall": "npx only-allow pnpm", - "build": "pnpm -r run build", - "watch": "pnpm -r run watch" + "build": "pnpm -r run --no-bail build", + "watch": "pnpm -r run watch", + "fmt": "npx prettier . --write", + "fmt:check": "npx prettier . --check" }, "devDependencies": { "@parcel/packager-ts": "2.12.0", "@parcel/transformer-typescript-types": "2.12.0", "buffer": "^5.5.0||^6.0.0", "parcel": "2.12.0", + "prettier": "3.3.2", "process": "^0.11.10", "typescript": "^5.3.3" } diff --git a/packages/geometry/package.json b/packages/geometry/package.json index a2b0dda..fd1b2fe 100644 --- a/packages/geometry/package.json +++ b/packages/geometry/package.json @@ -1,55 +1,55 @@ { - "name": "@alleninstitute/vis-geometry", - "version": "0.0.2", - "contributors": [ - { - "name": "Lane Sawyer", - "email": "lane.sawyer@alleninstitute.org" + "name": "@alleninstitute/vis-geometry", + "version": "0.0.2", + "contributors": [ + { + "name": "Lane Sawyer", + "email": "lane.sawyer@alleninstitute.org" + }, + { + "name": "James Gerstenberger", + "email": "james.gerstenberger@alleninstitute.org" + }, + { + "name": "Noah Shepard", + "email": "noah.shepard@alleninstitute.org" + }, + { + "name": "Skyler Moosman", + "email": "skyler.moosman@alleninstitute.org" + }, + { + "name": "Su Li", + "email": "su.li@alleninstitute.org" + } + ], + "license": "TBD", + "source": "src/index.ts", + "main": "dist/main.js", + "module": "dist/module.js", + "types": "dist/types.d.ts", + "files": [ + "dist" + ], + "scripts": { + "preinstall": "npx only-allow pnpm", + "typecheck": "tsc --noEmit", + "build": "parcel build --no-cache", + "watch": "parcel watch", + "test": "vitest --watch" }, - { - "name": "James Gerstenberger", - "email": "james.gerstenberger@alleninstitute.org" + "repository": { + "type": "git", + "url": "https://github.com/AllenInstitute/vis.git" }, - { - "name": "Noah Shepard", - "email": "noah.shepard@alleninstitute.org" + "publishConfig": { + "registry": "https://npm.pkg.github.com/AllenInstitute" }, - { - "name": "Skyler Moosman", - "email": "skyler.moosman@alleninstitute.org" - }, - { - "name": "Su Li", - "email": "su.li@alleninstitute.org" + "devDependencies": { + "@parcel/packager-ts": "^2.12.0", + "@parcel/transformer-typescript-types": "^2.12.0", + "parcel": "2.12.0", + "typescript": "^5.3.3", + "vitest": "^1.4.0" } - ], - "license": "TBD", - "source": "src/index.ts", - "main": "dist/main.js", - "module": "dist/module.js", - "types": "dist/types.d.ts", - "files": [ - "dist" - ], - "scripts": { - "preinstall": "npx only-allow pnpm", - "typecheck": "tsc --noEmit", - "build": "parcel build --no-cache", - "watch": "parcel watch", - "test": "vitest --watch" - }, - "repository": { - "type": "git", - "url": "https://github.com/AllenInstitute/vis.git" - }, - "publishConfig": { - "registry": "https://npm.pkg.github.com/AllenInstitute" - }, - "devDependencies": { - "@parcel/packager-ts": "^2.12.0", - "@parcel/transformer-typescript-types": "^2.12.0", - "vitest": "^1.4.0", - "parcel": "2.12.0", - "typescript": "^5.3.3" - } } diff --git a/packages/geometry/src/BoundingBox.ts b/packages/geometry/src/BoundingBox.ts index 295d060..b45aac0 100644 --- a/packages/geometry/src/BoundingBox.ts +++ b/packages/geometry/src/BoundingBox.ts @@ -1,105 +1,105 @@ -import type { VectorLib } from "./vector"; - -type VectorConstraint = ReadonlyArray; -export type box = { - readonly minCorner: V; - readonly maxCorner: V; -}; - -export function BoxClassFactory(lib: VectorLib) { - const create = (low: V, hi: V) => ({ minCorner: low, maxCorner: hi }); - const isValid = (a: box) => { - const diff = lib.sub(a.maxCorner, a.minCorner); - return lib.finite(a.maxCorner) && lib.finite(a.minCorner) && lib.all(diff, (v: number) => v > 0.0); - }; - const union = (a: box, b: box) => ({ - minCorner: lib.min(a.minCorner, b.minCorner), - maxCorner: lib.max(a.maxCorner, b.maxCorner), - }); - const corners = (a: box) => { - const what = a.minCorner.map(() => false); - const next = () => { - for (let i = what.length - 1; i >= 0; i -= 1) { - if (!what[i]) { - what[i] = true; - return true; - } - what[i] = false; - } - return false; - }; - const vals: V[] = []; - const pickValue = (v: boolean, i: number) => (v ? a.maxCorner[i] : a.minCorner[i]); - do { - vals.push(what.map(pickValue) as unknown as V); - } while (next()); - return vals; - }; - const setCorner = (box: box, cornerIndex: number, position: V): box => { - // cornerIndex is based from the generated corners from box.corners - // The corner index corresponds to a binary representation where each bit represents a dimension. - // For example, in a 2D box, [[minX, minY], [minX, maxY], [maxX, minY], [maxX, maxY]] would be [[0,0], [0,1], [1,0], [1,1]] - const binaryIndex = cornerIndex.toString(2).padStart(box.minCorner.length, '0').split('').map(Number); - - const newMinCorner = [...box.minCorner]; - const newMaxCorner = [...box.maxCorner]; - - // And then based on the binaryIndex (dimensions), set the correct value in each corner so the box corner outputs to the intended position - for (let i = 0; i < binaryIndex.length; i += 1) { - if (binaryIndex[i] === 0) { - newMinCorner[i] = position[i]; - } else { - newMaxCorner[i] = position[i]; - } - } - - // Validate that minCorner is actually the minimum and maxCorner is the maximum - for (let i = 0; i < newMinCorner.length; i += 1) { - if (newMinCorner[i] > newMaxCorner[i]) { - [newMinCorner[i], newMaxCorner[i]] = [newMaxCorner[i], newMinCorner[i]]; - } - } - - return { - minCorner: newMinCorner as unknown as V, - maxCorner: newMaxCorner as unknown as V, - }; - }; - const intersection = (a: box, b: box) => { - const result: box = { - minCorner: lib.max(a.minCorner, b.minCorner), - maxCorner: lib.min(a.maxCorner, b.maxCorner), - }; - if (isValid(result)) { - return result; - } - return undefined; - }; - const containsPoint = (box: box, point: V) => { - const greaterThanMin = lib.all(lib.sub(point, box.minCorner), (v) => v > 0.0); - const lessThanMax = lib.all(lib.sub(box.maxCorner, point), (v) => v >= 0.0); - return greaterThanMin && lessThanMax; - }; - - const toFlatArray = (box: box) => [...box.minCorner, ...box.maxCorner] as const; - const size = (b: box) => lib.sub(b.maxCorner, b.minCorner); - const midpoint = (b: box) => lib.scale(lib.add(b.minCorner, b.maxCorner), 0.5); - const map = (box: box, fn: (v: V) => V) => ({ minCorner: fn(box.minCorner), maxCorner: fn(box.maxCorner) }); - const scale = (box: box, s: V) => map(box, (c: V) => lib.mul(s, c)); - const translate = (box: box, offset: V) => map(box, (c: V) => lib.add(c, offset)); - return { - create, // build a box - corners, // get all the corners of the box - setCorner, // set a specific corner of the box to the given position - isValid, // return false if the box has any non-finite points, or has a negative or zero volume/area etc.. - union, // return the smallest box that contains the two given boxes - intersection, // return the intersection of two boxes if it exists - containsPoint, // return true if a point is in a box - note that this is exclusive on the low side, and inclusive on the high side - size, // how big is it? - midpoint, // yup you guessed it, return a vector at the center of a box. - toFlatArray, - scale, - map, - translate, - } as const; -} +import type { VectorLib } from './vector'; + +type VectorConstraint = ReadonlyArray; +export type box = { + readonly minCorner: V; + readonly maxCorner: V; +}; + +export function BoxClassFactory(lib: VectorLib) { + const create = (low: V, hi: V) => ({ minCorner: low, maxCorner: hi }); + const isValid = (a: box) => { + const diff = lib.sub(a.maxCorner, a.minCorner); + return lib.finite(a.maxCorner) && lib.finite(a.minCorner) && lib.all(diff, (v: number) => v > 0.0); + }; + const union = (a: box, b: box) => ({ + minCorner: lib.min(a.minCorner, b.minCorner), + maxCorner: lib.max(a.maxCorner, b.maxCorner), + }); + const corners = (a: box) => { + const what = a.minCorner.map(() => false); + const next = () => { + for (let i = what.length - 1; i >= 0; i -= 1) { + if (!what[i]) { + what[i] = true; + return true; + } + what[i] = false; + } + return false; + }; + const vals: V[] = []; + const pickValue = (v: boolean, i: number) => (v ? a.maxCorner[i] : a.minCorner[i]); + do { + vals.push(what.map(pickValue) as unknown as V); + } while (next()); + return vals; + }; + const setCorner = (box: box, cornerIndex: number, position: V): box => { + // cornerIndex is based from the generated corners from box.corners + // The corner index corresponds to a binary representation where each bit represents a dimension. + // For example, in a 2D box, [[minX, minY], [minX, maxY], [maxX, minY], [maxX, maxY]] would be [[0,0], [0,1], [1,0], [1,1]] + const binaryIndex = cornerIndex.toString(2).padStart(box.minCorner.length, '0').split('').map(Number); + + const newMinCorner = [...box.minCorner]; + const newMaxCorner = [...box.maxCorner]; + + // And then based on the binaryIndex (dimensions), set the correct value in each corner so the box corner outputs to the intended position + for (let i = 0; i < binaryIndex.length; i += 1) { + if (binaryIndex[i] === 0) { + newMinCorner[i] = position[i]; + } else { + newMaxCorner[i] = position[i]; + } + } + + // Validate that minCorner is actually the minimum and maxCorner is the maximum + for (let i = 0; i < newMinCorner.length; i += 1) { + if (newMinCorner[i] > newMaxCorner[i]) { + [newMinCorner[i], newMaxCorner[i]] = [newMaxCorner[i], newMinCorner[i]]; + } + } + + return { + minCorner: newMinCorner as unknown as V, + maxCorner: newMaxCorner as unknown as V, + }; + }; + const intersection = (a: box, b: box) => { + const result: box = { + minCorner: lib.max(a.minCorner, b.minCorner), + maxCorner: lib.min(a.maxCorner, b.maxCorner), + }; + if (isValid(result)) { + return result; + } + return undefined; + }; + const containsPoint = (box: box, point: V) => { + const greaterThanMin = lib.all(lib.sub(point, box.minCorner), (v) => v > 0.0); + const lessThanMax = lib.all(lib.sub(box.maxCorner, point), (v) => v >= 0.0); + return greaterThanMin && lessThanMax; + }; + + const toFlatArray = (box: box) => [...box.minCorner, ...box.maxCorner] as const; + const size = (b: box) => lib.sub(b.maxCorner, b.minCorner); + const midpoint = (b: box) => lib.scale(lib.add(b.minCorner, b.maxCorner), 0.5); + const map = (box: box, fn: (v: V) => V) => ({ minCorner: fn(box.minCorner), maxCorner: fn(box.maxCorner) }); + const scale = (box: box, s: V) => map(box, (c: V) => lib.mul(s, c)); + const translate = (box: box, offset: V) => map(box, (c: V) => lib.add(c, offset)); + return { + create, // build a box + corners, // get all the corners of the box + setCorner, // set a specific corner of the box to the given position + isValid, // return false if the box has any non-finite points, or has a negative or zero volume/area etc.. + union, // return the smallest box that contains the two given boxes + intersection, // return the intersection of two boxes if it exists + containsPoint, // return true if a point is in a box - note that this is exclusive on the low side, and inclusive on the high side + size, // how big is it? + midpoint, // yup you guessed it, return a vector at the center of a box. + toFlatArray, + scale, + map, + translate, + } as const; +} diff --git a/packages/geometry/src/Rectangle2D.ts b/packages/geometry/src/Rectangle2D.ts index b025af7..c2d75c6 100644 --- a/packages/geometry/src/Rectangle2D.ts +++ b/packages/geometry/src/Rectangle2D.ts @@ -1,35 +1,35 @@ -import type { box2D } from "./box2D"; -import { Vec2, type vec2 } from "./vec2"; - -export type rectangle2D = { - center: vec2; - size: vec2; -}; - -export function getMinimumBoundingBox(rect: rectangle2D): box2D { - const { center, size } = rect; - const half = Vec2.scale(size, 0.5); - return { - minCorner: Vec2.sub(center, half), - maxCorner: Vec2.add(center, half), - }; -} -// return a rectangle scaled by scale, with the origin of the scaling at the given point -export const scaleFromPoint = (rect: rectangle2D, scale: number, point: vec2) => { - const centerFromOrigin = Vec2.sub(rect.center, point); - const newCenter = Vec2.add(Vec2.scale(centerFromOrigin, scale), point); - return { - ...rect, - center: newCenter, - size: Vec2.scale(rect.size, scale), - }; -}; - -// linearly interpolate start --> end -export function interpolateRectangles(start: T, end: T, parameter: number): T { - return { - ...start, - center: Vec2.mix(start.center, end.center, parameter), - size: Vec2.mix(start.size, end.size, parameter), - }; -} +import type { box2D } from './box2D'; +import { Vec2, type vec2 } from './vec2'; + +export type rectangle2D = { + center: vec2; + size: vec2; +}; + +export function getMinimumBoundingBox(rect: rectangle2D): box2D { + const { center, size } = rect; + const half = Vec2.scale(size, 0.5); + return { + minCorner: Vec2.sub(center, half), + maxCorner: Vec2.add(center, half), + }; +} +// return a rectangle scaled by scale, with the origin of the scaling at the given point +export const scaleFromPoint = (rect: rectangle2D, scale: number, point: vec2) => { + const centerFromOrigin = Vec2.sub(rect.center, point); + const newCenter = Vec2.add(Vec2.scale(centerFromOrigin, scale), point); + return { + ...rect, + center: newCenter, + size: Vec2.scale(rect.size, scale), + }; +}; + +// linearly interpolate start --> end +export function interpolateRectangles(start: T, end: T, parameter: number): T { + return { + ...start, + center: Vec2.mix(start.center, end.center, parameter), + size: Vec2.mix(start.size, end.size, parameter), + }; +} diff --git a/packages/geometry/src/box2D.ts b/packages/geometry/src/box2D.ts index 7e8ad9c..27e264f 100644 --- a/packages/geometry/src/box2D.ts +++ b/packages/geometry/src/box2D.ts @@ -1,21 +1,21 @@ -import { BoxClassFactory, type box } from "./BoundingBox"; -import type { rectangle2D } from "./Rectangle2D"; -import { type vec2, Vec2 } from "./vec2"; - -export type box2D = box; - -const isBox2D = (maybe: unknown): maybe is box2D => { - if (typeof maybe === "object" && maybe !== null && "minCorner" in maybe && "maxCorner" in maybe) { - if (Array.isArray(maybe.minCorner) && Array.isArray(maybe.maxCorner)) { - return maybe.minCorner.length === 2 && maybe.maxCorner.length === 2; - } - } - - return false; -}; -const boxClass = BoxClassFactory(Vec2); -function toRectangle2D(b: box2D): rectangle2D { - return { center: boxClass.midpoint(b), size: boxClass.size(b) }; -} - -export const Box2D = { isBox2D, toRectangle2D, ...boxClass }; +import { BoxClassFactory, type box } from './BoundingBox'; +import type { rectangle2D } from './Rectangle2D'; +import { type vec2, Vec2 } from './vec2'; + +export type box2D = box; + +const isBox2D = (maybe: unknown): maybe is box2D => { + if (typeof maybe === 'object' && maybe !== null && 'minCorner' in maybe && 'maxCorner' in maybe) { + if (Array.isArray(maybe.minCorner) && Array.isArray(maybe.maxCorner)) { + return maybe.minCorner.length === 2 && maybe.maxCorner.length === 2; + } + } + + return false; +}; +const boxClass = BoxClassFactory(Vec2); +function toRectangle2D(b: box2D): rectangle2D { + return { center: boxClass.midpoint(b), size: boxClass.size(b) }; +} + +export const Box2D = { isBox2D, toRectangle2D, ...boxClass }; diff --git a/packages/geometry/src/box3D.ts b/packages/geometry/src/box3D.ts index 5c300d7..a7a7c9f 100644 --- a/packages/geometry/src/box3D.ts +++ b/packages/geometry/src/box3D.ts @@ -1,19 +1,19 @@ -import { BoxClassFactory, type box } from './BoundingBox'; -import type { vec2 } from './vec2'; -import { type vec3, Vec3 } from './vec3'; - -const isBox3D = (maybe: unknown): maybe is box3D => { - if (typeof maybe === 'object' && maybe !== null && 'minCorner' in maybe && 'maxCorner' in maybe) { - if (Array.isArray(maybe.minCorner) && Array.isArray(maybe.maxCorner)) { - return maybe.minCorner.length === 3 && maybe.maxCorner.length === 3; - } - } - - return false; -}; -export const Box3D = { - ...BoxClassFactory(Vec3), - isBox3D, - xy: (b: box): box => ({ minCorner: Vec3.xy(b.minCorner), maxCorner: Vec3.xy(b.maxCorner) }), -}; -export type box3D = box; +import { BoxClassFactory, type box } from './BoundingBox'; +import type { vec2 } from './vec2'; +import { type vec3, Vec3 } from './vec3'; + +const isBox3D = (maybe: unknown): maybe is box3D => { + if (typeof maybe === 'object' && maybe !== null && 'minCorner' in maybe && 'maxCorner' in maybe) { + if (Array.isArray(maybe.minCorner) && Array.isArray(maybe.maxCorner)) { + return maybe.minCorner.length === 3 && maybe.maxCorner.length === 3; + } + } + + return false; +}; +export const Box3D = { + ...BoxClassFactory(Vec3), + isBox3D, + xy: (b: box): box => ({ minCorner: Vec3.xy(b.minCorner), maxCorner: Vec3.xy(b.maxCorner) }), +}; +export type box3D = box; diff --git a/packages/geometry/src/index.ts b/packages/geometry/src/index.ts index 0b6eb03..48127e3 100644 --- a/packages/geometry/src/index.ts +++ b/packages/geometry/src/index.ts @@ -1,16 +1,16 @@ -export { Vec2 } from "./vec2"; -export type { vec2 } from "./vec2"; -export { Vec3 } from "./vec3"; -export type { vec3 } from "./vec3"; -export { Vec4 } from "./vec4"; -export type { vec4 } from "./vec4"; -export { Vec5 } from "./vec5"; -export type { vec5 } from "./vec5"; -export { Box2D } from "./box2D"; -export type { box2D } from "./box2D"; -export { Box3D } from "./box3D"; -export type { box3D } from "./box3D"; -export { size, within, isFinite, isValid, fixOrder, intersection, limit } from "./interval"; -export type { box } from './BoundingBox'; -export { getMinimumBoundingBox, scaleFromPoint, interpolateRectangles } from './Rectangle2D'; -export { type SpatialTreeInterface, visitBFS } from './spatialIndexing/tree' \ No newline at end of file +export { Vec2 } from './vec2'; +export type { vec2 } from './vec2'; +export { Vec3 } from './vec3'; +export type { vec3 } from './vec3'; +export { Vec4 } from './vec4'; +export type { vec4 } from './vec4'; +export { Vec5 } from './vec5'; +export type { vec5 } from './vec5'; +export { Box2D } from './box2D'; +export type { box2D } from './box2D'; +export { Box3D } from './box3D'; +export type { box3D } from './box3D'; +export { size, within, isFinite, isValid, fixOrder, intersection, limit } from './interval'; +export type { box } from './BoundingBox'; +export { getMinimumBoundingBox, scaleFromPoint, interpolateRectangles } from './Rectangle2D'; +export { type SpatialTreeInterface, visitBFS } from './spatialIndexing/tree'; diff --git a/packages/geometry/src/interval.ts b/packages/geometry/src/interval.ts index 695f4d2..ef2c81e 100644 --- a/packages/geometry/src/interval.ts +++ b/packages/geometry/src/interval.ts @@ -1,68 +1,68 @@ -export type Interval = { - min: number; - max: number; -}; - -/** - * - * @param i the inteval to return the size of - * @returns the size of the interval, aka the distance between its start and end. note this value may be negative - */ -export function size(i: Interval) { - return i.max - i.min; -} -/** - * - * @param i a given VALID interval - * @param x a value - * @returns true iff the x is within (double-inclusive) the interval i - */ -export function within(i: Interval, x: number): boolean { - return i.min <= x && i.max >= x; -} -/** - * - * @param i a given interval - * @returns true iff its min and max values are both finite, non-NaN values - */ -export function isFinite(i: Interval) { - return Number.isFinite(i.min) && Number.isFinite(i.max); -} -/** - * - * @param i - * @param minSize - * @return true iff the given interval i is at least as big as minSize, and min <= max, and isFinite(i) - */ -export function isValid(i: Interval, minSize: number) { - return size(i) >= Math.abs(minSize) && isFinite(i) && i.max >= i.min; -} -/** - * - * @param i an interval - * @return a copy of i, with min&max swapped, if the given i had a negative size - */ -export function fixOrder(i: Interval) { - return { min: Math.min(i.max, i.min), max: Math.max(i.min, i.max) }; -} -/** - * - * @param a a valid interval - * @param b a valid interval - * @return the interval where a and b overlap, or undefined if there is no such interval - */ -export function intersection(a: Interval, b: Interval): Interval | undefined { - const result = { min: Math.max(a.min, b.min), max: Math.min(a.max, b.max) }; - if (size(result) > 0) return result; - - return undefined; -} -/** - * - * @param interval a given VALID interval - * @param x a finite number - * @returns x iff x is within interval (or if interval is invalid), interval.min if x= x; +} +/** + * + * @param i a given interval + * @returns true iff its min and max values are both finite, non-NaN values + */ +export function isFinite(i: Interval) { + return Number.isFinite(i.min) && Number.isFinite(i.max); +} +/** + * + * @param i + * @param minSize + * @return true iff the given interval i is at least as big as minSize, and min <= max, and isFinite(i) + */ +export function isValid(i: Interval, minSize: number) { + return size(i) >= Math.abs(minSize) && isFinite(i) && i.max >= i.min; +} +/** + * + * @param i an interval + * @return a copy of i, with min&max swapped, if the given i had a negative size + */ +export function fixOrder(i: Interval) { + return { min: Math.min(i.max, i.min), max: Math.max(i.min, i.max) }; +} +/** + * + * @param a a valid interval + * @param b a valid interval + * @return the interval where a and b overlap, or undefined if there is no such interval + */ +export function intersection(a: Interval, b: Interval): Interval | undefined { + const result = { min: Math.max(a.min, b.min), max: Math.min(a.max, b.max) }; + if (size(result) > 0) return result; + + return undefined; +} +/** + * + * @param interval a given VALID interval + * @param x a finite number + * @returns x iff x is within interval (or if interval is invalid), interval.min if x> = { bounds: (t: Tree) => box; diff --git a/packages/geometry/src/tests/Rectangle2D.test.ts b/packages/geometry/src/tests/Rectangle2D.test.ts index e1c625e..99e109b 100644 --- a/packages/geometry/src/tests/Rectangle2D.test.ts +++ b/packages/geometry/src/tests/Rectangle2D.test.ts @@ -1,46 +1,46 @@ -import { getMinimumBoundingBox, rectangle2D, scaleFromPoint } from "../Rectangle2D"; -import { Box2D, box2D } from "../box2D"; -import { Vec2, vec2 } from "../vec2"; -import { describe, expect, it, test } from 'vitest' - -function nearlyEqual(a: vec2, b: vec2, epsilon: number) { - return Vec2.maxComponent(Vec2.map(Vec2.sub(a, b), Math.abs)) < epsilon; -} -function boxesVeryClose(a: box2D, b: box2D, epsilon: number) { - return nearlyEqual(a.minCorner, b.minCorner, epsilon) && nearlyEqual(a.maxCorner, b.maxCorner, epsilon); -} -describe("scaleFromPoint", () => { - it("scaling from the center does not move the center!", () => { - const scaled = scaleFromPoint( - { - center: [5, 5], - size: [1, 1], - }, - 100, - [5, 5] - ); - expect(scaled.center).toEqual([5, 5]); - expect(scaled.size).toEqual([100, 100]); - }); - it("scaling from the bottom left corner does not move that corner", () => { - const start: rectangle2D = { - center: [3, 3], - size: [2, 2], - }; // my bottom left corner is 2,2 - const getBottomLeftCornerOfUnrotatedRectangle = (r: rectangle2D) => Vec2.sub(r.center, Vec2.scale(r.size, 0.5)); - const bottomLeft = getBottomLeftCornerOfUnrotatedRectangle(start); // note: this is only correct because rotation is zero - const scaled = scaleFromPoint(start, 100, bottomLeft); - expect(getBottomLeftCornerOfUnrotatedRectangle(scaled)).toEqual(bottomLeft); - expect(scaled.size).toEqual([200, 200]); - }); -}); -describe("getMinimumBoundingBox", () => { - test("that we can get the axis aligned bounding box of a rectangle", () => { - const view: rectangle2D = { - center: [2, 3], - size: [4, 6], - }; - const boundingBox = getMinimumBoundingBox(view); - expect(boundingBox).toStrictEqual(Box2D.create([0, 0], [4, 6])); - }); -}); +import { getMinimumBoundingBox, rectangle2D, scaleFromPoint } from '../Rectangle2D'; +import { Box2D, box2D } from '../box2D'; +import { Vec2, vec2 } from '../vec2'; +import { describe, expect, it, test } from 'vitest'; + +function nearlyEqual(a: vec2, b: vec2, epsilon: number) { + return Vec2.maxComponent(Vec2.map(Vec2.sub(a, b), Math.abs)) < epsilon; +} +function boxesVeryClose(a: box2D, b: box2D, epsilon: number) { + return nearlyEqual(a.minCorner, b.minCorner, epsilon) && nearlyEqual(a.maxCorner, b.maxCorner, epsilon); +} +describe('scaleFromPoint', () => { + it('scaling from the center does not move the center!', () => { + const scaled = scaleFromPoint( + { + center: [5, 5], + size: [1, 1], + }, + 100, + [5, 5] + ); + expect(scaled.center).toEqual([5, 5]); + expect(scaled.size).toEqual([100, 100]); + }); + it('scaling from the bottom left corner does not move that corner', () => { + const start: rectangle2D = { + center: [3, 3], + size: [2, 2], + }; // my bottom left corner is 2,2 + const getBottomLeftCornerOfUnrotatedRectangle = (r: rectangle2D) => Vec2.sub(r.center, Vec2.scale(r.size, 0.5)); + const bottomLeft = getBottomLeftCornerOfUnrotatedRectangle(start); // note: this is only correct because rotation is zero + const scaled = scaleFromPoint(start, 100, bottomLeft); + expect(getBottomLeftCornerOfUnrotatedRectangle(scaled)).toEqual(bottomLeft); + expect(scaled.size).toEqual([200, 200]); + }); +}); +describe('getMinimumBoundingBox', () => { + test('that we can get the axis aligned bounding box of a rectangle', () => { + const view: rectangle2D = { + center: [2, 3], + size: [4, 6], + }; + const boundingBox = getMinimumBoundingBox(view); + expect(boundingBox).toStrictEqual(Box2D.create([0, 0], [4, 6])); + }); +}); diff --git a/packages/geometry/src/tests/box2D.test.ts b/packages/geometry/src/tests/box2D.test.ts index f8757fa..48058f0 100644 --- a/packages/geometry/src/tests/box2D.test.ts +++ b/packages/geometry/src/tests/box2D.test.ts @@ -1,94 +1,94 @@ -import { Box2D } from '../box2D'; -import { Vec2 } from '../vec2'; -import { describe, expect, test } from 'vitest' -describe('box2D', () => { - // Basic box to use throughout the tests - const box = Box2D.create([1, 2], [3, 4]); - - test('create', () => { - expect(box).toStrictEqual({ minCorner: [1, 2], maxCorner: [3, 4] }); - }); - - test('corners', () => { - const corners = Box2D.corners(box); - // Checks that we get them back in this order: - // - bottom left - // - top left - // - bottom right - // - top right - expect(corners).toStrictEqual([ - [1, 2], - [1, 4], - [3, 2], - [3, 4], - ]); - }); - test('map', () => { - expect(Box2D.map(Box2D.create([0, 0], [1, 1]), (v) => Vec2.scale(v, 200))).toStrictEqual( - Box2D.create([0, 0], [200, 200]) - ); - }); - test('isValid', () => { - const validBox = Box2D.isValid(box); - expect(validBox).toBeTruthy(); - - const nanBox = Box2D.isValid(Box2D.create([NaN, NaN], [1, 1])); - expect(nanBox).toBeFalsy(); - - const infinityBox = Box2D.isValid(Box2D.create([Infinity, Infinity], [1, 1])); - expect(infinityBox).toBeFalsy(); - - const noAreaPointBox = Box2D.isValid(Box2D.create([0, 0], [0, 0])); - expect(noAreaPointBox).toBeFalsy(); - - const noAreaLineBox = Box2D.isValid(Box2D.create([0, 0], [0, 100])); - expect(noAreaLineBox).toBeFalsy(); - }); - - test('union', () => { - const union = Box2D.union(box, Box2D.create([3, 3], [5, 5])); - expect(union).toStrictEqual(Box2D.create([1, 2], [5, 5])); - }); - - test('intersection', () => { - const intersection = Box2D.intersection(box, Box2D.create([2, 3], [5, 5])); - expect(intersection).toStrictEqual(Box2D.create([2, 3], [3, 4])); - - const borderIntersection = Box2D.intersection(box, Box2D.create([3, 3], [5, 5])); - expect(borderIntersection).toBeUndefined(); - - const noIntersection = Box2D.intersection(box, Box2D.create([10, 10], [20, 20])); - expect(noIntersection).toBeUndefined(); - }); - - test('containsPoint', () => { - const insidePoint = Box2D.containsPoint(box, [2, 3]); - expect(insidePoint).toBeTruthy(); - - const outsidePoint = Box2D.containsPoint(box, [0, 0]); - expect(outsidePoint).toBeFalsy(); - - // A point on the lower border is not contained within the box - const lowerBorderPoint = Box2D.containsPoint(box, [1, 2]); - expect(lowerBorderPoint).toBeFalsy(); - - // A point on the upper border is contained within the box - const upperBorderPoint = Box2D.containsPoint(box, [3, 4]); - expect(upperBorderPoint).toBeTruthy(); - }); - - test('size', () => { - const size = Box2D.size(box); - expect(size).toStrictEqual([2, 2]); - }); - - test('midpoint', () => { - const midpoint = Box2D.midpoint(box); - expect(midpoint).toStrictEqual([2, 3]); - }); - - test('toFlatArray', () => { - const flatArray = Box2D.toFlatArray(box); - expect(flatArray).toStrictEqual([1, 2, 3, 4]); - }); -}); +import { Box2D } from '../box2D'; +import { Vec2 } from '../vec2'; +import { describe, expect, test } from 'vitest'; +describe('box2D', () => { + // Basic box to use throughout the tests + const box = Box2D.create([1, 2], [3, 4]); + + test('create', () => { + expect(box).toStrictEqual({ minCorner: [1, 2], maxCorner: [3, 4] }); + }); + + test('corners', () => { + const corners = Box2D.corners(box); + // Checks that we get them back in this order: + // - bottom left + // - top left + // - bottom right + // - top right + expect(corners).toStrictEqual([ + [1, 2], + [1, 4], + [3, 2], + [3, 4], + ]); + }); + test('map', () => { + expect(Box2D.map(Box2D.create([0, 0], [1, 1]), (v) => Vec2.scale(v, 200))).toStrictEqual( + Box2D.create([0, 0], [200, 200]) + ); + }); + test('isValid', () => { + const validBox = Box2D.isValid(box); + expect(validBox).toBeTruthy(); + + const nanBox = Box2D.isValid(Box2D.create([NaN, NaN], [1, 1])); + expect(nanBox).toBeFalsy(); + + const infinityBox = Box2D.isValid(Box2D.create([Infinity, Infinity], [1, 1])); + expect(infinityBox).toBeFalsy(); + + const noAreaPointBox = Box2D.isValid(Box2D.create([0, 0], [0, 0])); + expect(noAreaPointBox).toBeFalsy(); + + const noAreaLineBox = Box2D.isValid(Box2D.create([0, 0], [0, 100])); + expect(noAreaLineBox).toBeFalsy(); + }); + + test('union', () => { + const union = Box2D.union(box, Box2D.create([3, 3], [5, 5])); + expect(union).toStrictEqual(Box2D.create([1, 2], [5, 5])); + }); + + test('intersection', () => { + const intersection = Box2D.intersection(box, Box2D.create([2, 3], [5, 5])); + expect(intersection).toStrictEqual(Box2D.create([2, 3], [3, 4])); + + const borderIntersection = Box2D.intersection(box, Box2D.create([3, 3], [5, 5])); + expect(borderIntersection).toBeUndefined(); + + const noIntersection = Box2D.intersection(box, Box2D.create([10, 10], [20, 20])); + expect(noIntersection).toBeUndefined(); + }); + + test('containsPoint', () => { + const insidePoint = Box2D.containsPoint(box, [2, 3]); + expect(insidePoint).toBeTruthy(); + + const outsidePoint = Box2D.containsPoint(box, [0, 0]); + expect(outsidePoint).toBeFalsy(); + + // A point on the lower border is not contained within the box + const lowerBorderPoint = Box2D.containsPoint(box, [1, 2]); + expect(lowerBorderPoint).toBeFalsy(); + + // A point on the upper border is contained within the box + const upperBorderPoint = Box2D.containsPoint(box, [3, 4]); + expect(upperBorderPoint).toBeTruthy(); + }); + + test('size', () => { + const size = Box2D.size(box); + expect(size).toStrictEqual([2, 2]); + }); + + test('midpoint', () => { + const midpoint = Box2D.midpoint(box); + expect(midpoint).toStrictEqual([2, 3]); + }); + + test('toFlatArray', () => { + const flatArray = Box2D.toFlatArray(box); + expect(flatArray).toStrictEqual([1, 2, 3, 4]); + }); +}); diff --git a/packages/geometry/src/tests/box3D.test.ts b/packages/geometry/src/tests/box3D.test.ts index 9264de1..2ec6364 100644 --- a/packages/geometry/src/tests/box3D.test.ts +++ b/packages/geometry/src/tests/box3D.test.ts @@ -1,6 +1,6 @@ import { Box3D } from '../box3D'; import { Vec3 } from '../vec3'; -import { describe, expect, test } from 'vitest' +import { describe, expect, test } from 'vitest'; describe('Box3D', () => { // Basic box to use throughout the tests const box = Box3D.create([1, 2, 3], [3, 4, 5]); diff --git a/packages/geometry/src/tests/interval.test.ts b/packages/geometry/src/tests/interval.test.ts index f6bc796..3d203e5 100644 --- a/packages/geometry/src/tests/interval.test.ts +++ b/packages/geometry/src/tests/interval.test.ts @@ -1,60 +1,60 @@ -import { fixOrder, intersection, Interval, isValid, limit, size, within } from '../interval'; -import { describe, expect, it, test } from 'vitest' -function I(a: number, b: number): Interval { - return { min: a, max: b }; -} -describe('basic interval math', () => { - describe('validity', () => { - it('intervals with zero or negative size are invalid', () => { - expect(isValid(I(3, 3.00001), 0.00002)).toBe(false); - }); - it('intevals with non-finite values are invalid', () => { - expect(isValid(I(3, Number.NaN), 0)).toBeFalsy(); - expect(isValid(I(Number.NEGATIVE_INFINITY, 3), 0)).toBeFalsy(); - expect(isValid(I(Number.NEGATIVE_INFINITY, Number.POSITIVE_INFINITY), 0)).toBeFalsy(); - expect(isValid(I(Number.NEGATIVE_INFINITY, 3), 0)).toBeFalsy(); - expect(isValid(I(0, 1), 0)).toBeTruthy(); - }); - }); - describe('size', () => { - it('size is the signed distance between min and max', () => { - expect(size(I(1, 3))).toBe(2); - expect(size(I(11, -3))).toBe(-14); - expect(size(I(1, 1))).toBe(0); - }); - }); - describe('within', () => { - it('within is inclusive on either side', () => { - expect(within(I(10, 30), 10)).toBeTruthy(); - expect(within(I(10, 30), 30)).toBeTruthy(); - expect(within(I(10, 30), 30.0000001)).toBeFalsy(); - // invalid: should always return false - expect(within(I(30, 10), 15)).toBeFalsy(); - expect(within(I(10, 30), 15)).toBeTruthy(); - }); - }); - describe('fixOrder', () => { - it('fixOrder always returns a valid interval if its given interval was finite', () => { - expect(fixOrder(I(3, 1))).toEqual(I(1, 3)); - expect(fixOrder(I(1, 3))).toEqual(I(1, 3)); - // garbo in garbo out - expect(fixOrder(I(Number.NaN, 3))).toEqual(I(Number.NaN, Number.NaN)); - }); - }); - describe('intersection', () => { - it('intersection is the overlap of two intervals, if they are valid', () => { - expect(intersection(I(1, 4), I(3, 5))).toEqual(I(3, 4)); - expect(intersection(I(4, 1), I(3, 5))).toEqual(undefined); - expect(intersection(I(-1, 2), I(3, 5))).toEqual(undefined); - }); - }); - describe('limit', () => { - it('clamp a value into an interval, if the interval is valid', () => { - expect(limit(I(1, 4), 0)).toEqual(1); - expect(limit(I(1, 4), 50)).toEqual(4); - // given interval is invalid, so dont mess with x - expect(limit(I(4, 1), 200)).toEqual(200); - expect(limit(I(1, 4), 2)).toEqual(2); - }); - }); -}); +import { fixOrder, intersection, Interval, isValid, limit, size, within } from '../interval'; +import { describe, expect, it, test } from 'vitest'; +function I(a: number, b: number): Interval { + return { min: a, max: b }; +} +describe('basic interval math', () => { + describe('validity', () => { + it('intervals with zero or negative size are invalid', () => { + expect(isValid(I(3, 3.00001), 0.00002)).toBe(false); + }); + it('intevals with non-finite values are invalid', () => { + expect(isValid(I(3, Number.NaN), 0)).toBeFalsy(); + expect(isValid(I(Number.NEGATIVE_INFINITY, 3), 0)).toBeFalsy(); + expect(isValid(I(Number.NEGATIVE_INFINITY, Number.POSITIVE_INFINITY), 0)).toBeFalsy(); + expect(isValid(I(Number.NEGATIVE_INFINITY, 3), 0)).toBeFalsy(); + expect(isValid(I(0, 1), 0)).toBeTruthy(); + }); + }); + describe('size', () => { + it('size is the signed distance between min and max', () => { + expect(size(I(1, 3))).toBe(2); + expect(size(I(11, -3))).toBe(-14); + expect(size(I(1, 1))).toBe(0); + }); + }); + describe('within', () => { + it('within is inclusive on either side', () => { + expect(within(I(10, 30), 10)).toBeTruthy(); + expect(within(I(10, 30), 30)).toBeTruthy(); + expect(within(I(10, 30), 30.0000001)).toBeFalsy(); + // invalid: should always return false + expect(within(I(30, 10), 15)).toBeFalsy(); + expect(within(I(10, 30), 15)).toBeTruthy(); + }); + }); + describe('fixOrder', () => { + it('fixOrder always returns a valid interval if its given interval was finite', () => { + expect(fixOrder(I(3, 1))).toEqual(I(1, 3)); + expect(fixOrder(I(1, 3))).toEqual(I(1, 3)); + // garbo in garbo out + expect(fixOrder(I(Number.NaN, 3))).toEqual(I(Number.NaN, Number.NaN)); + }); + }); + describe('intersection', () => { + it('intersection is the overlap of two intervals, if they are valid', () => { + expect(intersection(I(1, 4), I(3, 5))).toEqual(I(3, 4)); + expect(intersection(I(4, 1), I(3, 5))).toEqual(undefined); + expect(intersection(I(-1, 2), I(3, 5))).toEqual(undefined); + }); + }); + describe('limit', () => { + it('clamp a value into an interval, if the interval is valid', () => { + expect(limit(I(1, 4), 0)).toEqual(1); + expect(limit(I(1, 4), 50)).toEqual(4); + // given interval is invalid, so dont mess with x + expect(limit(I(4, 1), 200)).toEqual(200); + expect(limit(I(1, 4), 2)).toEqual(2); + }); + }); +}); diff --git a/packages/geometry/src/tests/line.test.ts b/packages/geometry/src/tests/line.test.ts index b052247..541902a 100644 --- a/packages/geometry/src/tests/line.test.ts +++ b/packages/geometry/src/tests/line.test.ts @@ -9,14 +9,14 @@ describe('line', () => { }); test('lineSegmentsIntersect finds no intersection', () => { - const firstLine: line= { start: [0, 0] , end: [1, 1] }; - const secondLine: line = { start: [1, 0] , end: [2, 1] }; + const firstLine: line = { start: [0, 0], end: [1, 1] }; + const secondLine: line = { start: [1, 0], end: [2, 1] }; expect(lineSegmentsIntersect(firstLine, secondLine)).toBe(0); }); test('lineSegmentsIntersect finds no intersection for segment that starts on the end of another one', () => { - const firstLine: line = { start: [0, 0] , end: [2, 2] }; - const secondLine: line = { start: [2, 2] , end: [2, 4] }; + const firstLine: line = { start: [0, 0], end: [2, 2] }; + const secondLine: line = { start: [2, 2], end: [2, 4] }; expect(lineSegmentsIntersect(firstLine, secondLine)).toBe(0); }); @@ -31,9 +31,9 @@ describe('line', () => { // Test line ---------- // First line / // / - const testLine: line = { start: [0, 1] , end: [2, 1] }; - const firstLine: line = { start: [0, 0] , end: [1, 1] }; - const secondLine: line = { start: [1, 1] , end: [1, 2] }; + const testLine: line = { start: [0, 1], end: [2, 1] }; + const firstLine: line = { start: [0, 0], end: [1, 1] }; + const secondLine: line = { start: [1, 1], end: [1, 2] }; const firstTest = lineSegmentsIntersect(testLine, firstLine); const secondTest = lineSegmentsIntersect(testLine, secondLine); @@ -44,27 +44,27 @@ describe('line', () => { }); test('lineSegmentsIntersect finds no intersection for coincident line segments when start of one is at end of other', () => { - const firstLine: line = { start: [0, 0] , end: [2, 2] }; - const secondLine: line = { start: [2, 2] , end: [3, 3] }; + const firstLine: line = { start: [0, 0], end: [2, 2] }; + const secondLine: line = { start: [2, 2], end: [3, 3] }; expect(lineSegmentsIntersect(firstLine, secondLine)).toBe(0); }); test('lineSegmentsIntersect finds no intersection for collinear line segments', () => { - const firstLine: line = { start: [0, 0] , end: [1, 1] }; - const secondLine: line = { start: [2, 2] , end: [3, 3] }; + const firstLine: line = { start: [0, 0], end: [1, 1] }; + const secondLine: line = { start: [2, 2], end: [3, 3] }; expect(lineSegmentsIntersect(firstLine, secondLine)).toBe(0); }); test('lineSegmentsIntersect finds no intersection for parallel line segments', () => { - const firstLine: line = { start: [0, 0] , end: [1, 1] }; - const secondLine: line = { start: [0, 1] , end: [1, 2] }; + const firstLine: line = { start: [0, 0], end: [1, 1] }; + const secondLine: line = { start: [0, 1], end: [1, 2] }; expect(lineSegmentsIntersect(firstLine, secondLine)).toBe(0); }); // For our purposes, we don't consider colinear and coincident line segments to intersect test('lineSegmentsIntersect finds 0 intersection for coincident & colinear line segments (WARNING: technically incorrect)', () => { - const firstLine: line = { start: [0, 0] , end: [2, 2] }; - const secondLine: line = { start: [1, 1] , end: [3, 3] }; + const firstLine: line = { start: [0, 0], end: [2, 2] }; + const secondLine: line = { start: [1, 1], end: [3, 3] }; expect(lineSegmentsIntersect(firstLine, secondLine)).toBe(0); }); }); diff --git a/packages/geometry/src/tests/vec2.test.ts b/packages/geometry/src/tests/vec2.test.ts index b550699..afecb78 100644 --- a/packages/geometry/src/tests/vec2.test.ts +++ b/packages/geometry/src/tests/vec2.test.ts @@ -1,135 +1,135 @@ -import { Vec2 } from '../vec2'; -import { describe, expect, test } from 'vitest' -describe('vec2', () => { - test('add', () => { - const result = Vec2.add([2, 3], [4, 5]); - expect(result).toStrictEqual([6, 8]); - }); - - test('sub', () => { - const result = Vec2.sub([2, 3], [4, 5]); - expect(result).toStrictEqual([-2, -2]); - }); - - test('mul', () => { - const result = Vec2.mul([2, 3], [4, 5]); - expect(result).toStrictEqual([8, 15]); - }); - - test('div', () => { - const result = Vec2.div([2, 3], [4, 5]); - expect(result).toStrictEqual([0.5, 0.6]); - }); - test('floor', () => { - expect(Vec2.floor([33.999, -21.00001])).toStrictEqual([33, -22]); - }); - test('ceil', () => { - expect(Vec2.ceil([33.999, -21.00001])).toStrictEqual([34, -21]); - }); - - test('min', () => { - const result = Vec2.min([2, 8], [4, 5]); - expect(result).toStrictEqual([2, 5]); - }); - - test('max', () => { - const result = Vec2.max([2, 8], [4, 5]); - expect(result).toStrictEqual([4, 8]); - }); - - test('scale', () => { - const result = Vec2.scale([2, 3], 2); - expect(result).toStrictEqual([4, 6]); - }); - - test('sum', () => { - const result = Vec2.sum([2, 3]); - expect(result).toBe(5); - }); - - test('minComponent', () => { - const result = Vec2.minComponent([2, 3]); - expect(result).toBe(2); - }); - - test('maxComponent', () => { - const result = Vec2.maxComponent([2, 3]); - expect(result).toBe(3); - }); - test('map', () => { - expect(Vec2.map([0, 0], (_v, i) => i)).toStrictEqual([0, 1]); - }); - - test('dot', () => { - const result = Vec2.dot([2, 3], [4, 5]); - expect(result).toBe(23); - - const resultWithNegatives = Vec2.dot([-2, 3], [2, -4]); - expect(resultWithNegatives).toBe(-16); - }); - - test('length', () => { - const result = Vec2.length([2, 3]); - const length = Math.sqrt(2 * 2 + 3 * 3); - - expect(result).toBe(length); - }); - - test('normalize', () => { - const result = Vec2.normalize([2, 3]); - const length = Math.sqrt(2 * 2 + 3 * 3); - expect(result).toStrictEqual([2 / length, 3 / length]); - - const noLength = Vec2.normalize([0, 0]); - expect(noLength).toStrictEqual([NaN, NaN]); - }); - - test('finite', () => { - const result = Vec2.finite([2, 3]); - expect(result).toBeTruthy(); - - const infinityResult = Vec2.finite([Infinity, 2]); - expect(infinityResult).toBeFalsy(); - - const nanResult = Vec2.finite([NaN, 2]); - expect(nanResult).toBeFalsy(); - }); - - test('any', () => { - const result = Vec2.any([2, 3], (num) => num % 2 === 0); - expect(result).toBeTruthy(); - }); - - test('all', () => { - const result = Vec2.all([2, 3], (num) => num % 2 === 0); - expect(result).toBeFalsy(); - - const result2 = Vec2.all([2, 4], (num) => num % 2 === 0); - expect(result2).toBeTruthy(); - }); - - test('exactlyEqual', () => { - const result = Vec2.exactlyEqual([2, 3], [4, 5]); - expect(result).toBeFalsy(); - - const result2 = Vec2.exactlyEqual([2, 3], [2, 3]); - expect(result2).toBeTruthy(); - }); - test('swizzle', () => { - expect(Vec2.swizzle([111, 222], [1, 1])).toStrictEqual([222, 222]); - expect(Vec2.swizzle([111, 222], [0, 1])).toStrictEqual([111, 222]); - // dangerous cases: - expect(Vec2.swizzle([111, 222], [2, 1])).toStrictEqual([undefined, 222]); - }); - test('isVec2', () => { - const result = Vec2.isVec2([2, 3]); - expect(result).toBeTruthy(); - - const nonVec2 = Vec2.isVec2([1, 2, 3]); - expect(nonVec2).toBeFalsy(); - }); - test('det', () => { - const result = Vec2.det([2, 3], [4, 5]); - expect(result).toBe(-2); - }); -}); +import { Vec2 } from '../vec2'; +import { describe, expect, test } from 'vitest'; +describe('vec2', () => { + test('add', () => { + const result = Vec2.add([2, 3], [4, 5]); + expect(result).toStrictEqual([6, 8]); + }); + + test('sub', () => { + const result = Vec2.sub([2, 3], [4, 5]); + expect(result).toStrictEqual([-2, -2]); + }); + + test('mul', () => { + const result = Vec2.mul([2, 3], [4, 5]); + expect(result).toStrictEqual([8, 15]); + }); + + test('div', () => { + const result = Vec2.div([2, 3], [4, 5]); + expect(result).toStrictEqual([0.5, 0.6]); + }); + test('floor', () => { + expect(Vec2.floor([33.999, -21.00001])).toStrictEqual([33, -22]); + }); + test('ceil', () => { + expect(Vec2.ceil([33.999, -21.00001])).toStrictEqual([34, -21]); + }); + + test('min', () => { + const result = Vec2.min([2, 8], [4, 5]); + expect(result).toStrictEqual([2, 5]); + }); + + test('max', () => { + const result = Vec2.max([2, 8], [4, 5]); + expect(result).toStrictEqual([4, 8]); + }); + + test('scale', () => { + const result = Vec2.scale([2, 3], 2); + expect(result).toStrictEqual([4, 6]); + }); + + test('sum', () => { + const result = Vec2.sum([2, 3]); + expect(result).toBe(5); + }); + + test('minComponent', () => { + const result = Vec2.minComponent([2, 3]); + expect(result).toBe(2); + }); + + test('maxComponent', () => { + const result = Vec2.maxComponent([2, 3]); + expect(result).toBe(3); + }); + test('map', () => { + expect(Vec2.map([0, 0], (_v, i) => i)).toStrictEqual([0, 1]); + }); + + test('dot', () => { + const result = Vec2.dot([2, 3], [4, 5]); + expect(result).toBe(23); + + const resultWithNegatives = Vec2.dot([-2, 3], [2, -4]); + expect(resultWithNegatives).toBe(-16); + }); + + test('length', () => { + const result = Vec2.length([2, 3]); + const length = Math.sqrt(2 * 2 + 3 * 3); + + expect(result).toBe(length); + }); + + test('normalize', () => { + const result = Vec2.normalize([2, 3]); + const length = Math.sqrt(2 * 2 + 3 * 3); + expect(result).toStrictEqual([2 / length, 3 / length]); + + const noLength = Vec2.normalize([0, 0]); + expect(noLength).toStrictEqual([NaN, NaN]); + }); + + test('finite', () => { + const result = Vec2.finite([2, 3]); + expect(result).toBeTruthy(); + + const infinityResult = Vec2.finite([Infinity, 2]); + expect(infinityResult).toBeFalsy(); + + const nanResult = Vec2.finite([NaN, 2]); + expect(nanResult).toBeFalsy(); + }); + + test('any', () => { + const result = Vec2.any([2, 3], (num) => num % 2 === 0); + expect(result).toBeTruthy(); + }); + + test('all', () => { + const result = Vec2.all([2, 3], (num) => num % 2 === 0); + expect(result).toBeFalsy(); + + const result2 = Vec2.all([2, 4], (num) => num % 2 === 0); + expect(result2).toBeTruthy(); + }); + + test('exactlyEqual', () => { + const result = Vec2.exactlyEqual([2, 3], [4, 5]); + expect(result).toBeFalsy(); + + const result2 = Vec2.exactlyEqual([2, 3], [2, 3]); + expect(result2).toBeTruthy(); + }); + test('swizzle', () => { + expect(Vec2.swizzle([111, 222], [1, 1])).toStrictEqual([222, 222]); + expect(Vec2.swizzle([111, 222], [0, 1])).toStrictEqual([111, 222]); + // dangerous cases: + expect(Vec2.swizzle([111, 222], [2, 1])).toStrictEqual([undefined, 222]); + }); + test('isVec2', () => { + const result = Vec2.isVec2([2, 3]); + expect(result).toBeTruthy(); + + const nonVec2 = Vec2.isVec2([1, 2, 3]); + expect(nonVec2).toBeFalsy(); + }); + test('det', () => { + const result = Vec2.det([2, 3], [4, 5]); + expect(result).toBe(-2); + }); +}); diff --git a/packages/geometry/src/tests/vec3.test.ts b/packages/geometry/src/tests/vec3.test.ts index e46c767..c986505 100644 --- a/packages/geometry/src/tests/vec3.test.ts +++ b/packages/geometry/src/tests/vec3.test.ts @@ -1,131 +1,131 @@ -import { Vec3 } from '../vec3'; -import { describe, expect, test } from 'vitest' -describe('Vec3', () => { - test('add', () => { - const result = Vec3.add([2, 3, 4], [4, 5, 6]); - expect(result).toStrictEqual([6, 8, 10]); - }); - - test('sub', () => { - const result = Vec3.sub([2, 3, 4], [4, 5, 6]); - expect(result).toStrictEqual([-2, -2, -2]); - }); - - test('mul', () => { - const result = Vec3.mul([2, 3, 4], [4, 5, 6]); - expect(result).toStrictEqual([8, 15, 24]); - }); - - test('div', () => { - const result = Vec3.div([2, 3, 4], [4, 5, 6]); - expect(result).toStrictEqual([0.5, 0.6, 0.6666666666666666]); - }); - - test('min', () => { - const result = Vec3.min([2, 8, 13], [4, 5, 11]); - expect(result).toStrictEqual([2, 5, 11]); - }); - - test('max', () => { - const result = Vec3.max([2, 8, 13], [4, 5, 11]); - expect(result).toStrictEqual([4, 8, 13]); - }); - test('floor', () => { - expect(Vec3.floor([33.999, -21.00001, 1])).toStrictEqual([33, -22, 1]); - }); - test('ceil', () => { - expect(Vec3.ceil([2, 33.999, -21.00001])).toStrictEqual([2, 34, -21]); - }); - test('scale', () => { - const result = Vec3.scale([2, 3, 4], 2); - expect(result).toStrictEqual([4, 6, 8]); - }); - - test('sum', () => { - const result = Vec3.sum([2, 3, 4]); - expect(result).toBe(9); - }); - - test('minComponent', () => { - const result = Vec3.minComponent([2, 3, 4]); - expect(result).toBe(2); - }); - - test('maxComponent', () => { - const result = Vec3.maxComponent([2, 3, 4]); - expect(result).toBe(4); - }); - test('map', () => { - expect(Vec3.map([0, 0, 33], (_v, i) => i)).toStrictEqual([0, 1, 2]); - }); - test('dot', () => { - const result = Vec3.dot([2, 3, 4], [4, 5, 6]); - expect(result).toBe(47); - - const resultWithNegatives = Vec3.dot([-2, 3, 4], [2, -4, 5]); - expect(resultWithNegatives).toBe(4); - }); - - test('length', () => { - const result = Vec3.length([2, 3, 4]); - const length = Math.sqrt(2 * 2 + 3 * 3 + 4 * 4); - - expect(result).toBe(length); - }); - - test('normalize', () => { - const result = Vec3.normalize([2, 3, 4]); - const length = Math.sqrt(2 * 2 + 3 * 3 + 4 * 4); - expect(result).toStrictEqual([2 / length, 3 / length, 4 / length]); - - const noLength = Vec3.normalize([0, 0, 0]); - expect(noLength).toStrictEqual([NaN, NaN, NaN]); - }); - - test('finite', () => { - const result = Vec3.finite([2, 3, 4]); - expect(result).toBeTruthy(); - - const infinityResult = Vec3.finite([Infinity, 2, 3]); - expect(infinityResult).toBeFalsy(); - - const nanResult = Vec3.finite([NaN, 2, 3]); - expect(nanResult).toBeFalsy(); - }); - - test('any', () => { - const result = Vec3.any([2, 3, 4], (num) => num % 2 === 0); - expect(result).toBeTruthy(); - }); - - test('all', () => { - const result = Vec3.all([2, 3, 4], (num) => num % 2 === 0); - expect(result).toBeFalsy(); - - const result2 = Vec3.all([2, 4, 6], (num) => num % 2 === 0); - expect(result2).toBeTruthy(); - }); - - test('exactlyEqual', () => { - const result = Vec3.exactlyEqual([2, 3, 4], [4, 5, 6]); - expect(result).toBeFalsy(); - - const result2 = Vec3.exactlyEqual([2, 3, 4], [2, 3, 4]); - expect(result2).toBeTruthy(); - }); - test('swizzle', () => { - expect(Vec3.swizzle([111, 222, 33], [2, 1, 2])).toStrictEqual([33, 222, 33]); - expect(Vec3.swizzle([111, 222, 33], [0, 1, 0])).toStrictEqual([111, 222, 111]); - // dangerous cases: - expect(Vec3.swizzle([111, 222, 33], [2, 1, 3])).toStrictEqual([33, 222, undefined]); - }); - test('xy', () => { - const result = Vec3.xy([2, 3, 4]); - expect(result).toStrictEqual([2, 3]); - }); - test('isVec3', () => { - expect(Vec3.isVec3([1, 2, 3])).toBeTruthy(); - expect(Vec3.isVec3([1, 2, 2, 3])).toBeFalsy(); - expect(Vec3.isVec3([1, 2])).toBeFalsy(); - }); -}); +import { Vec3 } from '../vec3'; +import { describe, expect, test } from 'vitest'; +describe('Vec3', () => { + test('add', () => { + const result = Vec3.add([2, 3, 4], [4, 5, 6]); + expect(result).toStrictEqual([6, 8, 10]); + }); + + test('sub', () => { + const result = Vec3.sub([2, 3, 4], [4, 5, 6]); + expect(result).toStrictEqual([-2, -2, -2]); + }); + + test('mul', () => { + const result = Vec3.mul([2, 3, 4], [4, 5, 6]); + expect(result).toStrictEqual([8, 15, 24]); + }); + + test('div', () => { + const result = Vec3.div([2, 3, 4], [4, 5, 6]); + expect(result).toStrictEqual([0.5, 0.6, 0.6666666666666666]); + }); + + test('min', () => { + const result = Vec3.min([2, 8, 13], [4, 5, 11]); + expect(result).toStrictEqual([2, 5, 11]); + }); + + test('max', () => { + const result = Vec3.max([2, 8, 13], [4, 5, 11]); + expect(result).toStrictEqual([4, 8, 13]); + }); + test('floor', () => { + expect(Vec3.floor([33.999, -21.00001, 1])).toStrictEqual([33, -22, 1]); + }); + test('ceil', () => { + expect(Vec3.ceil([2, 33.999, -21.00001])).toStrictEqual([2, 34, -21]); + }); + test('scale', () => { + const result = Vec3.scale([2, 3, 4], 2); + expect(result).toStrictEqual([4, 6, 8]); + }); + + test('sum', () => { + const result = Vec3.sum([2, 3, 4]); + expect(result).toBe(9); + }); + + test('minComponent', () => { + const result = Vec3.minComponent([2, 3, 4]); + expect(result).toBe(2); + }); + + test('maxComponent', () => { + const result = Vec3.maxComponent([2, 3, 4]); + expect(result).toBe(4); + }); + test('map', () => { + expect(Vec3.map([0, 0, 33], (_v, i) => i)).toStrictEqual([0, 1, 2]); + }); + test('dot', () => { + const result = Vec3.dot([2, 3, 4], [4, 5, 6]); + expect(result).toBe(47); + + const resultWithNegatives = Vec3.dot([-2, 3, 4], [2, -4, 5]); + expect(resultWithNegatives).toBe(4); + }); + + test('length', () => { + const result = Vec3.length([2, 3, 4]); + const length = Math.sqrt(2 * 2 + 3 * 3 + 4 * 4); + + expect(result).toBe(length); + }); + + test('normalize', () => { + const result = Vec3.normalize([2, 3, 4]); + const length = Math.sqrt(2 * 2 + 3 * 3 + 4 * 4); + expect(result).toStrictEqual([2 / length, 3 / length, 4 / length]); + + const noLength = Vec3.normalize([0, 0, 0]); + expect(noLength).toStrictEqual([NaN, NaN, NaN]); + }); + + test('finite', () => { + const result = Vec3.finite([2, 3, 4]); + expect(result).toBeTruthy(); + + const infinityResult = Vec3.finite([Infinity, 2, 3]); + expect(infinityResult).toBeFalsy(); + + const nanResult = Vec3.finite([NaN, 2, 3]); + expect(nanResult).toBeFalsy(); + }); + + test('any', () => { + const result = Vec3.any([2, 3, 4], (num) => num % 2 === 0); + expect(result).toBeTruthy(); + }); + + test('all', () => { + const result = Vec3.all([2, 3, 4], (num) => num % 2 === 0); + expect(result).toBeFalsy(); + + const result2 = Vec3.all([2, 4, 6], (num) => num % 2 === 0); + expect(result2).toBeTruthy(); + }); + + test('exactlyEqual', () => { + const result = Vec3.exactlyEqual([2, 3, 4], [4, 5, 6]); + expect(result).toBeFalsy(); + + const result2 = Vec3.exactlyEqual([2, 3, 4], [2, 3, 4]); + expect(result2).toBeTruthy(); + }); + test('swizzle', () => { + expect(Vec3.swizzle([111, 222, 33], [2, 1, 2])).toStrictEqual([33, 222, 33]); + expect(Vec3.swizzle([111, 222, 33], [0, 1, 0])).toStrictEqual([111, 222, 111]); + // dangerous cases: + expect(Vec3.swizzle([111, 222, 33], [2, 1, 3])).toStrictEqual([33, 222, undefined]); + }); + test('xy', () => { + const result = Vec3.xy([2, 3, 4]); + expect(result).toStrictEqual([2, 3]); + }); + test('isVec3', () => { + expect(Vec3.isVec3([1, 2, 3])).toBeTruthy(); + expect(Vec3.isVec3([1, 2, 2, 3])).toBeFalsy(); + expect(Vec3.isVec3([1, 2])).toBeFalsy(); + }); +}); diff --git a/packages/geometry/src/tests/vec4.test.ts b/packages/geometry/src/tests/vec4.test.ts index ffcd6a0..e053f90 100644 --- a/packages/geometry/src/tests/vec4.test.ts +++ b/packages/geometry/src/tests/vec4.test.ts @@ -1,5 +1,5 @@ import { Vec4 } from '../vec4'; -import { describe, expect, test } from 'vitest' +import { describe, expect, test } from 'vitest'; describe('Vec4', () => { test('add', () => { const result = Vec4.add([2, 3, 4, 5], [4, 5, 6, 7]); diff --git a/packages/geometry/src/vec5.ts b/packages/geometry/src/vec5.ts index 54bab15..5bcd4d6 100644 --- a/packages/geometry/src/vec5.ts +++ b/packages/geometry/src/vec5.ts @@ -1,5 +1,5 @@ -import { VectorLibFactory } from "./vector"; - -export type vec5 = readonly [number, number, number, number, number]; - -export const Vec5 = VectorLibFactory(); +import { VectorLibFactory } from './vector'; + +export type vec5 = readonly [number, number, number, number, number]; + +export const Vec5 = VectorLibFactory(); diff --git a/packages/geometry/src/vector.ts b/packages/geometry/src/vector.ts index d53f58a..b6671b5 100644 --- a/packages/geometry/src/vector.ts +++ b/packages/geometry/src/vector.ts @@ -1,163 +1,163 @@ -// this is a utility file for producing 'libraries' that provide basic math operations -// on short vectors. The vectors here are readonly tuples of numbers - -// I think vectors are more like numbers than objects, so immutable 'value semantics' makes -// much more sense to me. -// furthermore, I have all the 'methods' that would act on a class of vectors in a separate -// object, more like a module. I like the data to be plain old data - its immutability -// makes it easy to stash in redux, and Pojo's can be serialized (or copied to a web-worker) -// very easily. -// its also, IMHO, very slightly more flexible - these libraries just operate on readonly arrays - -// no need to extend any interfaces, no need to buy into my world view - its easy to just pass in -// a literal array on the fly (eg. add([1,1], someOtherVector)) -// anyway - probably start at the end of this file - -// the type VectorLib and the factory that produces libraries for a given vector type (1d, 2d... 66d etc) -// if you want to see on in action, check out vec2.ts - -type binOp = (a: T, b: T) => T; -type scalarOp = (a: T, scalar: number) => T; -type reduceOp = (a: T) => number; -type unaryOp = (a: T) => T; -type predOp = (a: T) => boolean; -type VectorConstraint = ReadonlyArray; -function componentOpFn(op: binOp): binOp { - return (a: T, b: T) => { - const r: Array = [...a]; - for (let i = 0; i < a.length; i += 1) { - r[i] = op(a[i], b[i]); - } - // its fine - we're trying to present things as though they are readonly, immutable - // static-length arrays of numbers, all in the service of semi-generic vector convenience... - return r as unknown as T; - }; -} -function componentUnaryOpFn(op: unaryOp): unaryOp { - return (a: T) => { - const r: Array = [...a]; - for (let i = 0; i < a.length; i += 1) { - r[i] = op(a[i]); - } - // its fine - we're trying to present things as though they are readonly, immutable - // static-length arrays of numbers, all in the service of semi-generic vector convenience... - return r as unknown as T; - }; -} -function reduceComponentOpFn(op: binOp): reduceOp { - return (a: T) => { - let r: number = a[0]; - for (let i = 1; i < a.length; i += 1) { - r = op(r, a[i]); - } - return r; - }; -} -function scalarOpFn(op: scalarOp): scalarOp { - return (a: T, scalar: number) => { - const r: Array = [...a]; - for (let i = 0; i < a.length; i += 1) { - r[i] = op(a[i], scalar); - } - // its fine - we're trying to present things as though they are readonly, immutable - // static-length arrays of numbers, all in the service of semi-generic vector convenience... - return r as unknown as T; - }; -} - -function allCmp(op: predOp): predOp { - return (a: T) => { - let truth = true; - for (let i = 0; i < a.length; i += 1) { - truth = truth && op(a[i]); - } - return truth; - }; -} -function anyCmp(op: predOp): predOp { - return (a: T) => { - let truth = false; - for (let i = 0; i < a.length; i += 1) { - truth = truth || op(a[i]); - } - return truth; - }; -} - -export type VectorLib = Readonly<{ - add: binOp; - sub: binOp; - mul: binOp; - div: binOp; - min: binOp; - map: (v: T, op: (c: number, index: number) => number) => T; - max: binOp; - minComponent: reduceOp; - maxComponent: reduceOp; - floor: unaryOp; - ceil: unaryOp; - scale: scalarOp; - mix: (a: T, b: T, p: number) => T; - sum: reduceOp; - dot: (a: T, b: T) => number; - length: reduceOp; - normalize: unaryOp; - finite: predOp; - any: (v: T, op: (c: number) => boolean) => boolean; - all: (v: T, op: (c: number) => boolean) => boolean; - exactlyEqual: (a: T, b: T) => boolean; - swizzle: binOp; -}>; -// see the rambling at the top of this file for more details -// TLDR: return a module with functions that perform basic math -// on vectors, where vector means an immutable array of numbers with a known length -// note that this function will generate a library suitable for any length of vector - -// just pass its type (eg. readonly [number,number,number]) as the generic V -export function VectorLibFactory(): VectorLib { - const add = componentOpFn((a, b) => a + b); - const sub = componentOpFn((a, b) => a - b); - const mul = componentOpFn((a, b) => a * b); - const div = componentOpFn((a, b) => a / b); - const min = componentOpFn((a, b) => Math.min(a, b)); - const max = componentOpFn((a, b) => Math.max(a, b)); - const floor = componentUnaryOpFn((a) => Math.floor(a)); - const ceil = componentUnaryOpFn((a) => Math.ceil(a)); - const scale = scalarOpFn((a, b) => a * b); - const mix = (a: V, b: V, p: number) => add(scale(a, 1.0 - p), scale(b, p)); - const sum = reduceComponentOpFn((a, b) => a + b); - const minComponent = reduceComponentOpFn((a, b) => Math.min(a, b)); - const maxComponent = reduceComponentOpFn((a, b) => Math.max(a, b)); - const dot = (a: V, b: V) => sum(mul(a, b)); - const length = (a: V) => Math.sqrt(sum(mul(a, a))); - const normalize = (a: V) => scale(a, 1.0 / length(a)); - const finite = allCmp((a) => Number.isFinite(a)); // no NaNs, no +- Infinities - const any = (vec: V, op: predOp) => anyCmp(op)(vec); - const all = (vec: V, op: predOp) => allCmp(op)(vec); - const exactlyEqual = (a: V, b: V) => all(sub(a, b), (v) => v === 0); - const map = (v: V, fn: (c: number, index: number) => number) => v.map(fn) as unknown as V; - // return a re-indexed vector - for example - // swizzle([33,22,11], [1,1,0])==> [22,22,33] - // note that passing invalid indexes will result in values of undefined in affected components of the result - const swizzle = (v: V, index: V) => index.map((i) => v[i]) as unknown as V; - return { - add, - sub, - mul, - div, - min, - map, - max, - minComponent, - maxComponent, - floor, - ceil, - scale, - mix, - sum, - dot, - length, - normalize, - finite, - any, - all, - exactlyEqual, - swizzle, - }; -} +// this is a utility file for producing 'libraries' that provide basic math operations +// on short vectors. The vectors here are readonly tuples of numbers - +// I think vectors are more like numbers than objects, so immutable 'value semantics' makes +// much more sense to me. +// furthermore, I have all the 'methods' that would act on a class of vectors in a separate +// object, more like a module. I like the data to be plain old data - its immutability +// makes it easy to stash in redux, and Pojo's can be serialized (or copied to a web-worker) +// very easily. +// its also, IMHO, very slightly more flexible - these libraries just operate on readonly arrays - +// no need to extend any interfaces, no need to buy into my world view - its easy to just pass in +// a literal array on the fly (eg. add([1,1], someOtherVector)) +// anyway - probably start at the end of this file - +// the type VectorLib and the factory that produces libraries for a given vector type (1d, 2d... 66d etc) +// if you want to see on in action, check out vec2.ts + +type binOp = (a: T, b: T) => T; +type scalarOp = (a: T, scalar: number) => T; +type reduceOp = (a: T) => number; +type unaryOp = (a: T) => T; +type predOp = (a: T) => boolean; +type VectorConstraint = ReadonlyArray; +function componentOpFn(op: binOp): binOp { + return (a: T, b: T) => { + const r: Array = [...a]; + for (let i = 0; i < a.length; i += 1) { + r[i] = op(a[i], b[i]); + } + // its fine - we're trying to present things as though they are readonly, immutable + // static-length arrays of numbers, all in the service of semi-generic vector convenience... + return r as unknown as T; + }; +} +function componentUnaryOpFn(op: unaryOp): unaryOp { + return (a: T) => { + const r: Array = [...a]; + for (let i = 0; i < a.length; i += 1) { + r[i] = op(a[i]); + } + // its fine - we're trying to present things as though they are readonly, immutable + // static-length arrays of numbers, all in the service of semi-generic vector convenience... + return r as unknown as T; + }; +} +function reduceComponentOpFn(op: binOp): reduceOp { + return (a: T) => { + let r: number = a[0]; + for (let i = 1; i < a.length; i += 1) { + r = op(r, a[i]); + } + return r; + }; +} +function scalarOpFn(op: scalarOp): scalarOp { + return (a: T, scalar: number) => { + const r: Array = [...a]; + for (let i = 0; i < a.length; i += 1) { + r[i] = op(a[i], scalar); + } + // its fine - we're trying to present things as though they are readonly, immutable + // static-length arrays of numbers, all in the service of semi-generic vector convenience... + return r as unknown as T; + }; +} + +function allCmp(op: predOp): predOp { + return (a: T) => { + let truth = true; + for (let i = 0; i < a.length; i += 1) { + truth = truth && op(a[i]); + } + return truth; + }; +} +function anyCmp(op: predOp): predOp { + return (a: T) => { + let truth = false; + for (let i = 0; i < a.length; i += 1) { + truth = truth || op(a[i]); + } + return truth; + }; +} + +export type VectorLib = Readonly<{ + add: binOp; + sub: binOp; + mul: binOp; + div: binOp; + min: binOp; + map: (v: T, op: (c: number, index: number) => number) => T; + max: binOp; + minComponent: reduceOp; + maxComponent: reduceOp; + floor: unaryOp; + ceil: unaryOp; + scale: scalarOp; + mix: (a: T, b: T, p: number) => T; + sum: reduceOp; + dot: (a: T, b: T) => number; + length: reduceOp; + normalize: unaryOp; + finite: predOp; + any: (v: T, op: (c: number) => boolean) => boolean; + all: (v: T, op: (c: number) => boolean) => boolean; + exactlyEqual: (a: T, b: T) => boolean; + swizzle: binOp; +}>; +// see the rambling at the top of this file for more details +// TLDR: return a module with functions that perform basic math +// on vectors, where vector means an immutable array of numbers with a known length +// note that this function will generate a library suitable for any length of vector - +// just pass its type (eg. readonly [number,number,number]) as the generic V +export function VectorLibFactory(): VectorLib { + const add = componentOpFn((a, b) => a + b); + const sub = componentOpFn((a, b) => a - b); + const mul = componentOpFn((a, b) => a * b); + const div = componentOpFn((a, b) => a / b); + const min = componentOpFn((a, b) => Math.min(a, b)); + const max = componentOpFn((a, b) => Math.max(a, b)); + const floor = componentUnaryOpFn((a) => Math.floor(a)); + const ceil = componentUnaryOpFn((a) => Math.ceil(a)); + const scale = scalarOpFn((a, b) => a * b); + const mix = (a: V, b: V, p: number) => add(scale(a, 1.0 - p), scale(b, p)); + const sum = reduceComponentOpFn((a, b) => a + b); + const minComponent = reduceComponentOpFn((a, b) => Math.min(a, b)); + const maxComponent = reduceComponentOpFn((a, b) => Math.max(a, b)); + const dot = (a: V, b: V) => sum(mul(a, b)); + const length = (a: V) => Math.sqrt(sum(mul(a, a))); + const normalize = (a: V) => scale(a, 1.0 / length(a)); + const finite = allCmp((a) => Number.isFinite(a)); // no NaNs, no +- Infinities + const any = (vec: V, op: predOp) => anyCmp(op)(vec); + const all = (vec: V, op: predOp) => allCmp(op)(vec); + const exactlyEqual = (a: V, b: V) => all(sub(a, b), (v) => v === 0); + const map = (v: V, fn: (c: number, index: number) => number) => v.map(fn) as unknown as V; + // return a re-indexed vector - for example + // swizzle([33,22,11], [1,1,0])==> [22,22,33] + // note that passing invalid indexes will result in values of undefined in affected components of the result + const swizzle = (v: V, index: V) => index.map((i) => v[i]) as unknown as V; + return { + add, + sub, + mul, + div, + min, + map, + max, + minComponent, + maxComponent, + floor, + ceil, + scale, + mix, + sum, + dot, + length, + normalize, + finite, + any, + all, + exactlyEqual, + swizzle, + }; +} diff --git a/packages/geometry/tsconfig.json b/packages/geometry/tsconfig.json index da9a8ea..e0b8abd 100644 --- a/packages/geometry/tsconfig.json +++ b/packages/geometry/tsconfig.json @@ -1,22 +1,13 @@ -{ - "extends": "../../tsconfig.base.json", - "compilerOptions": { - "paths": { - "~/*": [ - "./*" - ] - }, - "module": "ES2022", - "target": "ES2022", - "lib": [ - "es2022" - ], - }, - "include": [ - "./src/index.ts" - ], - "exclude": [ - "tests/", - "**/*.test.ts" - ] -} \ No newline at end of file +{ + "extends": "../../tsconfig.base.json", + "compilerOptions": { + "paths": { + "~/*": ["./*"] + }, + "module": "ES2022", + "target": "ES2022", + "lib": ["es2022"] + }, + "include": ["./src/index.ts"], + "exclude": ["tests/", "**/*.test.ts"] +} diff --git a/packages/scatterbrain/package.json b/packages/scatterbrain/package.json index f53f3f3..941b8a9 100644 --- a/packages/scatterbrain/package.json +++ b/packages/scatterbrain/package.json @@ -1,61 +1,61 @@ { - "name": "@alleninstitute/vis-scatterbrain", - "version": "0.0.3", - "contributors": [ - { - "name": "Lane Sawyer", - "email": "lane.sawyer@alleninstitute.org" + "name": "@alleninstitute/vis-scatterbrain", + "version": "0.0.3", + "contributors": [ + { + "name": "Lane Sawyer", + "email": "lane.sawyer@alleninstitute.org" + }, + { + "name": "James Gerstenberger", + "email": "james.gerstenberger@alleninstitute.org" + }, + { + "name": "Noah Shepard", + "email": "noah.shepard@alleninstitute.org" + }, + { + "name": "Skyler Moosman", + "email": "skyler.moosman@alleninstitute.org" + }, + { + "name": "Su Li", + "email": "su.li@alleninstitute.org" + } + ], + "license": "TBD", + "source": "src/index.ts", + "main": "dist/main.js", + "module": "dist/module.js", + "types": "dist/types.d.ts", + "files": [ + "dist" + ], + "scripts": { + "preinstall": "npx only-allow pnpm", + "typecheck": "tsc --noEmit", + "build": "parcel build --no-cache", + "watch": "parcel watch", + "test": "vitest --watch" }, - { - "name": "James Gerstenberger", - "email": "james.gerstenberger@alleninstitute.org" + "repository": { + "type": "git", + "url": "https://github.com/AllenInstitute/vis.git" }, - { - "name": "Noah Shepard", - "email": "noah.shepard@alleninstitute.org" + "publishConfig": { + "registry": "https://npm.pkg.github.com/AllenInstitute" }, - { - "name": "Skyler Moosman", - "email": "skyler.moosman@alleninstitute.org" + "devDependencies": { + "@parcel/packager-ts": "^2.12.0", + "@parcel/transformer-typescript-types": "^2.12.0", + "@types/lodash": "^4.14.202", + "parcel": "2.12.0", + "typescript": "^5.3.3", + "vitest": "^1.4.0" }, - { - "name": "Su Li", - "email": "su.li@alleninstitute.org" + "dependencies": { + "@alleninstitute/vis-geometry": "workspace:*", + "lodash": "^4.17.21", + "regl": "^2.1.0" } - ], - "license": "TBD", - "source": "src/index.ts", - "main": "dist/main.js", - "module": "dist/module.js", - "types": "dist/types.d.ts", - "files": [ - "dist" - ], - "scripts": { - "preinstall": "npx only-allow pnpm", - "typecheck": "tsc --noEmit", - "build": "parcel build --no-cache", - "watch": "parcel watch", - "test": "vitest --watch" - }, - "repository": { - "type": "git", - "url": "https://github.com/AllenInstitute/vis.git" - }, - "publishConfig": { - "registry": "https://npm.pkg.github.com/AllenInstitute" - }, - "devDependencies": { - "@parcel/packager-ts": "^2.12.0", - "@parcel/transformer-typescript-types": "^2.12.0", - "@types/lodash": "^4.14.202", - "parcel": "2.12.0", - "typescript": "^5.3.3", - "vitest": "^1.4.0" - }, - "dependencies": { - "@alleninstitute/vis-geometry": "workspace:*", - "lodash": "^4.17.21", - "regl": "^2.1.0" - } -} \ No newline at end of file +} diff --git a/packages/scatterbrain/src/dataset-cache.ts b/packages/scatterbrain/src/dataset-cache.ts index 447abe3..6cab4c8 100644 --- a/packages/scatterbrain/src/dataset-cache.ts +++ b/packages/scatterbrain/src/dataset-cache.ts @@ -1,260 +1,275 @@ -type MaybePromise = D | Promise; -type RecordKey = string | number | symbol -export interface AsyncCache { - isCached(k: CacheKey): boolean; - getCachedUNSAFE(k: CacheKey): D | undefined; - cacheAndUse(workingSet: Record Promise>, use: (items: Record) => void, cacheKey: (semantic: SemanticKey) => CacheKey): cancelFn | undefined; -} - -type useFn = (items: Record) => void; -type cancelFn = () => void; -type MutablePendingRequest = { - runner: useFn; - awaiting: Map>; - blocking: Set; // these are the cache keys associated with the items in 'ready' - we keep them around to make it easy to make sure we dont delete something we assume we have - // while an outstanding task is waiting on more data - ready: Record; -} -// return true if the request is completely satisfied, false if its still awaiting more entries -function updatePendingRequest(req: MutablePendingRequest, key: SemanticKey, cacheKey: CacheKey, item: D): boolean { - if (req.awaiting.has(cacheKey)) { - const remaningAwaited = req.awaiting.get(cacheKey); - // we just fullfilled one - remove it from awaiting - remaningAwaited?.delete(key); - if ((remaningAwaited?.size ?? 0) < 1) { - req.awaiting.delete(cacheKey); - } - req.blocking.add(cacheKey); - req.ready[key] = item; - } - return req.awaiting.size === 0 -} -type MutableCacheEntry = { - data: MaybePromise; - lastRequestedTimestamp: number; -}; - -/** - * `AsyncDataCache` asynchronous data cache, useful for minimizing network requests by caching the results of - * a network request and returning the cached result if the request has already been made previously - * for a given key. - * - * It is generalizable over any type of data. - * - * @example - * const getMyData = ()=>fetch('https://example.com/data.json'); - * myCache.cache('myKey', getMyData).then((data)=>{console.log('its here now (and we cached it) ', data)}); - * } - - */ -export class AsyncDataCache implements AsyncCache { - private limit: number; - private size: (d: D) => number; - private destroyer: (d: D) => void; - private entries: Map>; - private pendingRequests: Set>; - - /** - * the intended use of this cache is to store resources used for rendering. Because the specific contents are generic, a simple interface must be provided - * to support LRU cache eviction - * occasionally, it can be necessary to manage these resources more explicitly (see https://stackoverflow.com/a/31250301 for a great example) - * @param destroy a function which safely releases the resources owned by an entry in this cache - for normal garbage-collected objects, a no-op function will suffice. - * @param size a function which returns the size of a resource - this is used only in relation to the cacheLimit - * @param cacheLimit a limit (in whatever units are returned by the size() parameter) to place on cache contents - * note that this limit is not a hard limit - old entries are evicted when new data is fetched, but the limit may be exceeded occasionally - * a reasonable implementation may simply return 1 for size, and a desired occupancy count for the limit - */ - constructor(destroy: (data: D) => void, size: (data: D) => number, cacheLimit: number) { - this.size = size; - this.destroyer = destroy; - this.limit = cacheLimit; - this.entries = new Map>(); - this.pendingRequests = new Set>(); - } - private usedSpace() { - // Map uses iterators, so we're in for-loop territory here - let sum = 0; - this.entries.forEach((entry) => (sum += entry.data instanceof Promise ? 0 : this.size(entry.data))); - return sum; - } - private countRequests() { - const reqCounts: Record = {} as Record - for (const req of this.pendingRequests) { - for (const key of [...req.blocking, ...req.awaiting.keys()]) { - if (!reqCounts[key]) { - reqCounts[key] = 0; - } - reqCounts[key] += 1; - } - } - return reqCounts; - } - // if the cache is full, sort candidates which are not currently requested by their last-used timestamps - // evict those items until the cache is no longer full - private evictIfFull() { - // find entries which have 0 pending requests, and are not themselves promises... - let used = this.usedSpace(); - const candidates: { key: CacheKey; data: D; lastRequestedTimestamp: number }[] = []; - if (used > this.limit) { - // its potentially a bit slow to do this: - const counts = this.countRequests(); - this.entries.forEach((entry, key) => { - if (!(entry.data instanceof Promise) && (counts[key] ?? 0) < 1) { - candidates.push({ key, data: entry.data, lastRequestedTimestamp: entry.lastRequestedTimestamp }); - } - }); - const priority = candidates.sort((a, b) => a.lastRequestedTimestamp - b.lastRequestedTimestamp); - for (const evictMe of priority) { - used -= this.size(evictMe.data); - this.destroyer(evictMe.data); - this.entries.delete(evictMe.key); - if (used < this.limit) { - return; - } - } - } - } - - /** - * `isCached` checks if the entry is in the cache with a resolved promise. - * - * @param key The entry key to check for in the cache - * @returns True if the entry in the cache has been resolved, false if there is no entry with that key or the promise is still pending - */ - isCached(key: CacheKey): boolean { - // the key exists, and the value associated is not a promise - return this.entries.has(key) && !(this.entries.get(key)?.data instanceof Promise); - } - - /** - * `areKeysAllCached` checks if all the keys provided are in the cache with resolved promises. - * - * Useful for checking if all the data needed for a particular operation is already in the cache. - * - * @param cacheKeys A list of keys to check for in the cache - * @returns True if all keys are cached, false if any are not in the cache - */ - areKeysAllCached(cacheKeys: readonly CacheKey[]): boolean { - return cacheKeys.every((key) => this.isCached(key)); - } - - /** - * @deprecated to alert (external) users to avoid calling this! - * `getCachedUNSAFE` gets an entry from the cache for the given key (if the promise is resolved). - * because of how eviction works - this method should be considered unsafe! consider the following - * @example - * const entry = cache.getCachedUnsafe('whatever') - * const otherStuff = await fetch('....') - * ... more code - * doSomethingCool(entry, otherStuff) - * - * by the time the caller gets to the doSomethingCool call, the resources bound to the cache entry - * may have been disposed! - * do note that if you use a cache-entry synchronously (no awaits!) after requesting it, you're likely to not - * encounter any issues, however its a much more robust practice to simply refactor like so: - * - * const otherStuff = await fetch('...') - * cache.cacheAndUse({...}, (...args)=>doSomethingCool(otherStuff, ..args), ...) - * - * @param key Entry key to look up in the cache - * @returns The entry (D) if it is present, or undefined if it is not - */ - getCachedUNSAFE(key: CacheKey): D | undefined { - const entry = this.entries.get(key); - if (!entry) return undefined; - - entry.lastRequestedTimestamp = performance.now(); - return entry.data instanceof Promise ? undefined : entry?.data; - } - getNumPendingTasks(): number { - return this.pendingRequests.size; - } - private dataArrived(key: SemanticKey, cacheKey: CacheKey, data: D) { - this.evictIfFull(); // we just got some data - is there room in the cache? - const mutableEntry = this.entries.get(cacheKey); - if (mutableEntry) { - mutableEntry.data = data; - } - const removeUs: MutablePendingRequest[] = [] - for (const req of this.pendingRequests) { - if (updatePendingRequest(req, key, cacheKey, data)) { - req.runner(req.ready); - removeUs.push(req); - } - } - removeUs.forEach(finished => this.pendingRequests.delete(finished)); - } - private prepareCache(semanticKey: SemanticKey, cacheKey: CacheKey, getter: () => Promise) { - let promise: Promise - let entry = this.entries.get(cacheKey); - const data = entry?.data; - // we either return early (data is cached) - // or we initialize promise (either getter() or a pre-existing request for the same cachekey) - // if we dont return early, we hook up a call to dataArrived to promise - if (data) { - if (data instanceof Promise) { - promise = data; - } else { - // we could simply "return data" - // however getCachedUnsafe updates its "last-requested timestamp" - return this.getCachedUNSAFE(cacheKey)! - } - } else { - promise = getter(); - this.entries.set(cacheKey, { - data: promise, - lastRequestedTimestamp: performance.now(), - }) - } - return promise.then((data) => { - this.dataArrived(semanticKey, cacheKey, data); - }) - } - cacheAndUse(workingSet: Record Promise>, use: (items: Record) => void, toCacheKey: (semanticKey: SemanticKey) => CacheKey, taskFinished?: () => void): cancelFn | undefined { - const keys: SemanticKey[] = Object.keys(workingSet) as SemanticKey[] - const req: MutablePendingRequest = { - awaiting: new Map>(), - ready: {} as Record, - runner: use, - blocking: new Set() - } - keys.forEach((k) => { - if (req.awaiting.has(toCacheKey(k))) { - req.awaiting.get(toCacheKey(k))?.add(k); - } else { - req.awaiting.set(toCacheKey(k), new Set([k])) - } - }) - for (const semanticKey of keys) { - const result = this.prepareCache(semanticKey, toCacheKey(semanticKey), workingSet[semanticKey]) - if (result instanceof Promise) { - const prom = taskFinished !== undefined ? result.then(taskFinished) : result; - prom.catch((_reason) => { - // delete the failed entry from the cache - // also remove the entire request it belongs to - this.entries.delete(toCacheKey(semanticKey)); - this.pendingRequests.delete(req); - // note that catches get chained - so any catch handlers that came in with this promise - // still get called - }) - } else { - if (updatePendingRequest(req, semanticKey, toCacheKey(semanticKey), result)) { - use(req.ready); - if (taskFinished !== undefined) { - Promise.resolve().then(taskFinished); // we did the task synchronously... - } - - // early return in the case that everything was cached! - // the only thing this short-circuits is pendingRequests.add(req) - // (because of course it isn't pending, because we just did it!) - return undefined; - } - } - } - this.pendingRequests.add(req); - return () => { - this.pendingRequests.delete(req); - } - } - -} +type MaybePromise = D | Promise; +type RecordKey = string | number | symbol; +export interface AsyncCache { + isCached(k: CacheKey): boolean; + getCachedUNSAFE(k: CacheKey): D | undefined; + cacheAndUse( + workingSet: Record Promise>, + use: (items: Record) => void, + cacheKey: (semantic: SemanticKey) => CacheKey + ): cancelFn | undefined; +} + +type useFn = (items: Record) => void; +type cancelFn = () => void; +type MutablePendingRequest = { + runner: useFn; + awaiting: Map>; + blocking: Set; // these are the cache keys associated with the items in 'ready' - we keep them around to make it easy to make sure we dont delete something we assume we have + // while an outstanding task is waiting on more data + ready: Record; +}; +// return true if the request is completely satisfied, false if its still awaiting more entries +function updatePendingRequest( + req: MutablePendingRequest, + key: SemanticKey, + cacheKey: CacheKey, + item: D +): boolean { + if (req.awaiting.has(cacheKey)) { + const remaningAwaited = req.awaiting.get(cacheKey); + // we just fullfilled one - remove it from awaiting + remaningAwaited?.delete(key); + if ((remaningAwaited?.size ?? 0) < 1) { + req.awaiting.delete(cacheKey); + } + req.blocking.add(cacheKey); + req.ready[key] = item; + } + return req.awaiting.size === 0; +} +type MutableCacheEntry = { + data: MaybePromise; + lastRequestedTimestamp: number; +}; + +/** + * `AsyncDataCache` asynchronous data cache, useful for minimizing network requests by caching the results of + * a network request and returning the cached result if the request has already been made previously + * for a given key. + * + * It is generalizable over any type of data. + * + * @example + * const getMyData = ()=>fetch('https://example.com/data.json'); + * myCache.cache('myKey', getMyData).then((data)=>{console.log('its here now (and we cached it) ', data)}); + * } + + */ +export class AsyncDataCache + implements AsyncCache +{ + private limit: number; + private size: (d: D) => number; + private destroyer: (d: D) => void; + private entries: Map>; + private pendingRequests: Set>; + + /** + * the intended use of this cache is to store resources used for rendering. Because the specific contents are generic, a simple interface must be provided + * to support LRU cache eviction + * occasionally, it can be necessary to manage these resources more explicitly (see https://stackoverflow.com/a/31250301 for a great example) + * @param destroy a function which safely releases the resources owned by an entry in this cache - for normal garbage-collected objects, a no-op function will suffice. + * @param size a function which returns the size of a resource - this is used only in relation to the cacheLimit + * @param cacheLimit a limit (in whatever units are returned by the size() parameter) to place on cache contents + * note that this limit is not a hard limit - old entries are evicted when new data is fetched, but the limit may be exceeded occasionally + * a reasonable implementation may simply return 1 for size, and a desired occupancy count for the limit + */ + constructor(destroy: (data: D) => void, size: (data: D) => number, cacheLimit: number) { + this.size = size; + this.destroyer = destroy; + this.limit = cacheLimit; + this.entries = new Map>(); + this.pendingRequests = new Set>(); + } + private usedSpace() { + // Map uses iterators, so we're in for-loop territory here + let sum = 0; + this.entries.forEach((entry) => (sum += entry.data instanceof Promise ? 0 : this.size(entry.data))); + return sum; + } + private countRequests() { + const reqCounts: Record = {} as Record; + for (const req of this.pendingRequests) { + for (const key of [...req.blocking, ...req.awaiting.keys()]) { + if (!reqCounts[key]) { + reqCounts[key] = 0; + } + reqCounts[key] += 1; + } + } + return reqCounts; + } + // if the cache is full, sort candidates which are not currently requested by their last-used timestamps + // evict those items until the cache is no longer full + private evictIfFull() { + // find entries which have 0 pending requests, and are not themselves promises... + let used = this.usedSpace(); + const candidates: { key: CacheKey; data: D; lastRequestedTimestamp: number }[] = []; + if (used > this.limit) { + // its potentially a bit slow to do this: + const counts = this.countRequests(); + this.entries.forEach((entry, key) => { + if (!(entry.data instanceof Promise) && (counts[key] ?? 0) < 1) { + candidates.push({ key, data: entry.data, lastRequestedTimestamp: entry.lastRequestedTimestamp }); + } + }); + const priority = candidates.sort((a, b) => a.lastRequestedTimestamp - b.lastRequestedTimestamp); + for (const evictMe of priority) { + used -= this.size(evictMe.data); + this.destroyer(evictMe.data); + this.entries.delete(evictMe.key); + if (used < this.limit) { + return; + } + } + } + } + + /** + * `isCached` checks if the entry is in the cache with a resolved promise. + * + * @param key The entry key to check for in the cache + * @returns True if the entry in the cache has been resolved, false if there is no entry with that key or the promise is still pending + */ + isCached(key: CacheKey): boolean { + // the key exists, and the value associated is not a promise + return this.entries.has(key) && !(this.entries.get(key)?.data instanceof Promise); + } + + /** + * `areKeysAllCached` checks if all the keys provided are in the cache with resolved promises. + * + * Useful for checking if all the data needed for a particular operation is already in the cache. + * + * @param cacheKeys A list of keys to check for in the cache + * @returns True if all keys are cached, false if any are not in the cache + */ + areKeysAllCached(cacheKeys: readonly CacheKey[]): boolean { + return cacheKeys.every((key) => this.isCached(key)); + } + + /** + * @deprecated to alert (external) users to avoid calling this! + * `getCachedUNSAFE` gets an entry from the cache for the given key (if the promise is resolved). + * because of how eviction works - this method should be considered unsafe! consider the following + * @example + * const entry = cache.getCachedUnsafe('whatever') + * const otherStuff = await fetch('....') + * ... more code + * doSomethingCool(entry, otherStuff) + * + * by the time the caller gets to the doSomethingCool call, the resources bound to the cache entry + * may have been disposed! + * do note that if you use a cache-entry synchronously (no awaits!) after requesting it, you're likely to not + * encounter any issues, however its a much more robust practice to simply refactor like so: + * + * const otherStuff = await fetch('...') + * cache.cacheAndUse({...}, (...args)=>doSomethingCool(otherStuff, ..args), ...) + * + * @param key Entry key to look up in the cache + * @returns The entry (D) if it is present, or undefined if it is not + */ + getCachedUNSAFE(key: CacheKey): D | undefined { + const entry = this.entries.get(key); + if (!entry) return undefined; + + entry.lastRequestedTimestamp = performance.now(); + return entry.data instanceof Promise ? undefined : entry?.data; + } + getNumPendingTasks(): number { + return this.pendingRequests.size; + } + private dataArrived(key: SemanticKey, cacheKey: CacheKey, data: D) { + this.evictIfFull(); // we just got some data - is there room in the cache? + const mutableEntry = this.entries.get(cacheKey); + if (mutableEntry) { + mutableEntry.data = data; + } + const removeUs: MutablePendingRequest[] = []; + for (const req of this.pendingRequests) { + if (updatePendingRequest(req, key, cacheKey, data)) { + req.runner(req.ready); + removeUs.push(req); + } + } + removeUs.forEach((finished) => this.pendingRequests.delete(finished)); + } + private prepareCache(semanticKey: SemanticKey, cacheKey: CacheKey, getter: () => Promise) { + let promise: Promise; + let entry = this.entries.get(cacheKey); + const data = entry?.data; + // we either return early (data is cached) + // or we initialize promise (either getter() or a pre-existing request for the same cachekey) + // if we dont return early, we hook up a call to dataArrived to promise + if (data) { + if (data instanceof Promise) { + promise = data; + } else { + // we could simply "return data" + // however getCachedUnsafe updates its "last-requested timestamp" + return this.getCachedUNSAFE(cacheKey)!; + } + } else { + promise = getter(); + this.entries.set(cacheKey, { + data: promise, + lastRequestedTimestamp: performance.now(), + }); + } + return promise.then((data) => { + this.dataArrived(semanticKey, cacheKey, data); + }); + } + cacheAndUse( + workingSet: Record Promise>, + use: (items: Record) => void, + toCacheKey: (semanticKey: SemanticKey) => CacheKey, + taskFinished?: () => void + ): cancelFn | undefined { + const keys: SemanticKey[] = Object.keys(workingSet) as SemanticKey[]; + const req: MutablePendingRequest = { + awaiting: new Map>(), + ready: {} as Record, + runner: use, + blocking: new Set(), + }; + keys.forEach((k) => { + if (req.awaiting.has(toCacheKey(k))) { + req.awaiting.get(toCacheKey(k))?.add(k); + } else { + req.awaiting.set(toCacheKey(k), new Set([k])); + } + }); + for (const semanticKey of keys) { + const result = this.prepareCache(semanticKey, toCacheKey(semanticKey), workingSet[semanticKey]); + if (result instanceof Promise) { + const prom = taskFinished !== undefined ? result.then(taskFinished) : result; + prom.catch((_reason) => { + // delete the failed entry from the cache + // also remove the entire request it belongs to + this.entries.delete(toCacheKey(semanticKey)); + this.pendingRequests.delete(req); + // note that catches get chained - so any catch handlers that came in with this promise + // still get called + }); + } else { + if (updatePendingRequest(req, semanticKey, toCacheKey(semanticKey), result)) { + use(req.ready); + if (taskFinished !== undefined) { + Promise.resolve().then(taskFinished); // we did the task synchronously... + } + + // early return in the case that everything was cached! + // the only thing this short-circuits is pendingRequests.add(req) + // (because of course it isn't pending, because we just did it!) + return undefined; + } + } + } + this.pendingRequests.add(req); + return () => { + this.pendingRequests.delete(req); + }; + } +} diff --git a/packages/scatterbrain/src/index.ts b/packages/scatterbrain/src/index.ts index b9ea96b..e4a2f6d 100644 --- a/packages/scatterbrain/src/index.ts +++ b/packages/scatterbrain/src/index.ts @@ -1,4 +1,4 @@ -export { beginLongRunningFrame } from "./render-queue"; -export { AsyncDataCache } from "./dataset-cache"; -export { ReglLayer2D } from './layers/layer-2D' -export * from './layers/buffer-pair' \ No newline at end of file +export { beginLongRunningFrame } from './render-queue'; +export { AsyncDataCache } from './dataset-cache'; +export { ReglLayer2D } from './layers/layer-2D'; +export * from './layers/buffer-pair'; diff --git a/packages/scatterbrain/src/layers/buffer-pair.ts b/packages/scatterbrain/src/layers/buffer-pair.ts index 4698f0e..a744942 100644 --- a/packages/scatterbrain/src/layers/buffer-pair.ts +++ b/packages/scatterbrain/src/layers/buffer-pair.ts @@ -1,8 +1,7 @@ - export type BufferPair = { writeTo: T; readFrom: T; -} +}; export function swapBuffers(doubleBuffer: BufferPair) { const { readFrom, writeTo } = doubleBuffer; return { readFrom: writeTo, writeTo: readFrom }; diff --git a/packages/scatterbrain/src/layers/layer-2D.ts b/packages/scatterbrain/src/layers/layer-2D.ts index ccb5b15..958bc9d 100644 --- a/packages/scatterbrain/src/layers/layer-2D.ts +++ b/packages/scatterbrain/src/layers/layer-2D.ts @@ -1,45 +1,53 @@ - // a helper to render a 2D layer, using regl -import type { Image, ImageRenderer, RenderFn } from "./types"; -import { type BufferPair, swapBuffers } from "./buffer-pair"; -import type REGL from "regl"; -import type { FrameLifecycle, RenderCallback } from "../render-queue"; -import { Box2D, type box2D, type vec2 } from '@alleninstitute/vis-geometry' +import type { Image, ImageRenderer, RenderFn } from './types'; +import { type BufferPair, swapBuffers } from './buffer-pair'; +import type REGL from 'regl'; +import type { FrameLifecycle, RenderCallback } from '../render-queue'; +import { Box2D, type box2D, type vec2 } from '@alleninstitute/vis-geometry'; -type EventType = Parameters[0] -type RequiredSettings = { camera: { view: box2D }, callback: RenderCallback } +type EventType = Parameters[0]; +type RequiredSettings = { camera: { view: box2D }; callback: RenderCallback }; export class ReglLayer2D { private buffers: BufferPair; - private renderFn: RenderFn + private renderFn: RenderFn; private runningFrame: FrameLifecycle | null; private regl: REGL.Regl; - private renderImg: ImageRenderer - constructor(regl: REGL.Regl, imgRenderer: ImageRenderer, renderFn: RenderFn, resolution: vec2) { + private renderImg: ImageRenderer; + constructor( + regl: REGL.Regl, + imgRenderer: ImageRenderer, + renderFn: RenderFn, + resolution: vec2 + ) { this.buffers = { readFrom: { resolution, texture: regl.framebuffer(...resolution), bounds: undefined }, - writeTo: { resolution, texture: regl.framebuffer(...resolution), bounds: undefined } + writeTo: { resolution, texture: regl.framebuffer(...resolution), bounds: undefined }, }; - this.renderImg = imgRenderer + this.renderImg = imgRenderer; this.regl = regl; this.runningFrame = null; this.renderFn = renderFn; } destroy() { - this.runningFrame?.cancelFrame("destroy this layer"); + this.runningFrame?.cancelFrame('destroy this layer'); this.buffers.readFrom.texture.destroy(); this.buffers.writeTo.texture.destroy(); } - renderingInProgress() { return this.runningFrame !== null } + renderingInProgress() { + return this.runningFrame !== null; + } getRenderResults(stage: 'prev' | 'cur') { - return stage == 'cur' ? this.buffers.writeTo : this.buffers.readFrom + return stage == 'cur' ? this.buffers.writeTo : this.buffers.readFrom; } - onChange(props: { - readonly data: Readonly; - readonly settings: Readonly - }, cancel: boolean = true) { - + onChange( + props: { + readonly data: Readonly; + readonly settings: Readonly; + }, + cancel: boolean = true + ) { if (cancel && this.runningFrame) { this.runningFrame.cancelFrame(); this.runningFrame = null; @@ -52,20 +60,21 @@ export class ReglLayer2D { img: writeTo.texture, target: readFrom.texture, viewport: { - x: 0, y: 0, width, height + x: 0, + y: 0, + width, + height, }, - view: Box2D.toFlatArray(readFrom.bounds) - }) + view: Box2D.toFlatArray(readFrom.bounds), + }); } - this.regl.clear({ framebuffer: this.buffers.writeTo.texture, color: [0, 0, 0, 0], depth: 1 }) + this.regl.clear({ framebuffer: this.buffers.writeTo.texture, color: [0, 0, 0, 0], depth: 1 }); } const { data, settings } = props; const { camera, callback } = settings; this.buffers.writeTo.bounds = camera.view; - - const wrapCallback: RenderSettings = - { + const wrapCallback: RenderSettings = { ...settings, callback: (ev: EventType) => { const { status } = ev; @@ -75,15 +84,18 @@ export class ReglLayer2D { this.buffers = swapBuffers(this.buffers); // only erase... if we would have cancelled... if (cancel) { - this.regl.clear({ framebuffer: this.buffers.writeTo.texture, color: [0, 0, 0, 0], depth: 1 }) + this.regl.clear({ + framebuffer: this.buffers.writeTo.texture, + color: [0, 0, 0, 0], + depth: 1, + }); } this.runningFrame = null; break; } callback?.(ev); - } + }, }; this.runningFrame = this.renderFn(this.buffers.writeTo.texture, data, wrapCallback); } - } diff --git a/packages/scatterbrain/src/layers/types.ts b/packages/scatterbrain/src/layers/types.ts index 8801f3e..a0c3e47 100644 --- a/packages/scatterbrain/src/layers/types.ts +++ b/packages/scatterbrain/src/layers/types.ts @@ -1,23 +1,26 @@ import type { box2D, vec2, vec4 } from '@alleninstitute/vis-geometry'; -import type { FrameLifecycle } from '../render-queue' -import type REGL from "regl"; +import type { FrameLifecycle } from '../render-queue'; +import type REGL from 'regl'; -export type RenderFn = - (target: REGL.Framebuffer2D | null, thing: Readonly, settings: Readonly) => FrameLifecycle; +export type RenderFn = ( + target: REGL.Framebuffer2D | null, + thing: Readonly, + settings: Readonly +) => FrameLifecycle; export type Image = { - resolution: vec2; - texture: REGL.Framebuffer2D; - bounds: box2D | undefined; // if undefined, it means we allocated the texture, but its empty and should not be used (except to fill it) -} + resolution: vec2; + texture: REGL.Framebuffer2D; + bounds: box2D | undefined; // if undefined, it means we allocated the texture, but its empty and should not be used (except to fill it) +}; type ImageRendererProps = { - target: REGL.Framebuffer2D | null; - box: vec4; - view: vec4; - viewport: REGL.BoundingBox; - img: REGL.Texture2D | REGL.Framebuffer2D; -} + target: REGL.Framebuffer2D | null; + box: vec4; + view: vec4; + viewport: REGL.BoundingBox; + img: REGL.Texture2D | REGL.Framebuffer2D; +}; // a function which renders an axis aligned image to another axis aligned image - no funny buisness -export type ImageRenderer = (props: ImageRendererProps) => void; \ No newline at end of file +export type ImageRenderer = (props: ImageRendererProps) => void; diff --git a/packages/scatterbrain/src/render-queue.ts b/packages/scatterbrain/src/render-queue.ts index 7e79dad..88e8cd1 100644 --- a/packages/scatterbrain/src/render-queue.ts +++ b/packages/scatterbrain/src/render-queue.ts @@ -1,182 +1,181 @@ -import { partial } from 'lodash'; -import { AsyncDataCache } from './dataset-cache'; - -/** - * FrameLifecycle type that defines the functions a user can call to interact with the frame lifecycle. - * - * Currently only supports `cancelFrame` to allow the user to cancel the frame on an ad-hoc basis. - */ -export type FrameLifecycle = { - cancelFrame: (reason?: string) => void; -}; - - -/** - * NormalStatus type that defines the possible non-error statuses for a frame. - * - * `begun` - The frame has started running - * - * `finished` - The frame has finished running - * - * `cancelled` - The frame was cancelled by the user - * - * `finished_synchronously` - The frame finished synchronously - * - * `progress` - The frame is still running and has not finished - */ -export type NormalStatus = 'begun' | 'finished' | 'cancelled' | 'finished_synchronously' | 'progress'; -export type RenderCallback = (event: { status: NormalStatus } | { status: 'error', error: unknown }) => void; -/** - * `beingLongRunningFrame` starts a long-running frame that will render a list of items asynchronously based on - * the provided data, settings, and rendering functions. - * - * The frame will run until all items have been rendered, or until the user cancels the frame. It will update the - * provided cache so that the data is available for other frames that may be running. This function is safe to call - * multiple times in different areas of your code, as it will complete quickly if/when all the data is already cached and available. - * - * You can listen for the status of the frame, allowing you to make decisions based on the progress of the frame. - * - * In addition, you can cancel the frame at any time, which will stop the frame from running and prevent any further - * rendering or data fetching from occurring. - * - * @param maximumInflightAsyncTasks The maximum number of async tasks to run at once. - * @param queueProcessingIntervalMS The length of time to wait between processing the queue in milliseconds. - * @param items An array of generic items to render - * @param mutableCache The asynchronous cache used to store the data - * @param settings Flexible object of settings related to the items that are being rendered - * @param requestsForItem a function which returns a mapping of "columns" to async functions that would fetch the column - * @param render The main render function that will be called once all data is available - * @param lifecycleCallback Callback function so they user can be notified of the status of the frame - * @param cacheKeyForRequest A function for generating a cache key for a given request key, item, and settings. Defaults to the request key if not provided. - * @param queueTimeBudgetMS the maximum ammount of time (milliseconds) to spend rendering before yeilding to allow other work to run - rendering will resume next frame (@param queueProcessingIntervalMS) - * @returns A FrameLifecycle object with a cancelFrame function to allow users to cancel the frame when necessary - */ -export function beginLongRunningFrame( - maximumInflightAsyncTasks: number, - queueProcessingIntervalMS: number, - items: Item[], - mutableCache: AsyncDataCache, - settings: Settings, - requestsForItem: (item: Item, settings: Settings, signal?: AbortSignal) => Record Promise>, - render: (item: Item, settings: Settings, columns: Record) => void, - lifecycleCallback: RenderCallback, - cacheKeyForRequest: (requestKey: string, item: Item, settings: Settings) => string = (key) => key, - queueTimeBudgetMS: number = queueProcessingIntervalMS / 3 -): FrameLifecycle { - const abort = new AbortController(); - const queue: Item[] = []; - const taskCancelCallbacks: Array<() => void> = []; - - const reportNormalStatus = (status: NormalStatus) => { - // we want to report our status, however the flow of events can be confusing - - // our callers anticipate an asynchronous (long running) frame to be started, - // but there are scenarios in which the whole thing is completely synchronous - // callers who are scheduling things may be surprised that their frame finished - // before the code that handles it appears to start. thus, we make the entire lifecycle callback - // system async, to prevent surprises. - Promise.resolve().then(() => lifecycleCallback({ status })); - }; - // when starting a frame, we greedily attempt to render any tasks that are already in the cache - // however, if there is too much overhead (or too many tasks) we would risk hogging the main thread - // thus - obey the limit (its a soft limit) - const startTime = performance.now(); - - for (let i = 0; i < items.length; i += 1) { - const itemToRender = items[i]; - const requestFns = requestsForItem(itemToRender, settings, abort.signal) - const cacheKey = (rq: string) => cacheKeyForRequest(rq, itemToRender, settings) - const cacheKeys = Object.keys(requestFns).map(cacheKey); - - if (mutableCache.areKeysAllCached(cacheKeys)) { - - const result = mutableCache.cacheAndUse( - requestFns, partial(render, itemToRender, settings), cacheKey - ); - if (result !== undefined) { - // this is a problem - the cache reported that all the keys are in the cache, however this result is a cancellation callback, - // which indicates that the item could not be rendered right away, which should be impossible... - // TODO - taskCancelCallbacks.push(result); - } - } else { - // areKeysAllCached returned false - enqueue for later - queue.push(itemToRender) - } - if (performance.now() - startTime > queueTimeBudgetMS) { - // we've used up all our time - enqueue all remaining tasks - if (i < items.length - 1) { - queue.push(...items.slice(i + 1)); - } - break; - } - } - - if (queue.length === 0) { - // we did all the work - it was already cached - reportNormalStatus('finished_synchronously'); - return { cancelFrame: () => { } }; - } - // TODO: Re-examine lifecycle reporting, potentially unify all statuses into a single type - reportNormalStatus('begun'); - if (queue.length !== items.length) { - // We did some work, but there's some left - reportNormalStatus('progress'); - } - const doWorkOnQueue = (intervalId: number) => { - // try our best to cleanup if something goes awry - const startWorkTime = performance.now(); - const cleanupOnError = (err: unknown) => { - // clear the queue and the staging area (inFlight) - taskCancelCallbacks.forEach(cancelMe => cancelMe()); - queue.splice(0, queue.length); - // stop fetching - abort.abort(err); - clearInterval(intervalId); - // pass the error somewhere better: - lifecycleCallback({ status: 'error', error: err }); - }; - while (mutableCache.getNumPendingTasks() < Math.max(maximumInflightAsyncTasks, 1)) { - if (queue.length < 1) { - // we cant add anything to the in-flight staging area, the final task - // is already in flight - if (mutableCache.getNumPendingTasks() < 1) { - // we do want to wait for that last in-flight task to actually finish though: - clearInterval(intervalId); - reportNormalStatus('finished'); - } - return; - } - // We know there are items in the queue because of the check above, so we assert the type exist - const itemToRender = queue.shift()!; - const toCacheKey = (rq: string) => cacheKeyForRequest(rq, itemToRender, settings); - try { - const result = mutableCache.cacheAndUse( - requestsForItem(itemToRender, settings, abort.signal), partial(render, itemToRender, settings), toCacheKey, () => reportNormalStatus('progress') - ); - if (result !== undefined) { - // put this cancel callback in a list where we can invoke if something goes wrong - // note that it is harmless to cancel a task that was completed - taskCancelCallbacks.push(result); - } - } catch (err) { - cleanupOnError(err); - } - if (performance.now() - startWorkTime > queueTimeBudgetMS) { - // used up all our time - leave remaining work for later - break; - } - } - }; - const interval = setInterval(() => doWorkOnQueue(interval), queueProcessingIntervalMS); - - // return a function to allow our caller to cancel the frame - guaranteed that no settings/data will be - // touched/referenced after cancellation, unless the author of render() did some super weird bad things - return { - cancelFrame: (reason?: string) => { - taskCancelCallbacks.forEach(cancelMe => cancelMe()); - abort.abort(new DOMException(reason, 'AbortError')); - clearInterval(interval); - reportNormalStatus('cancelled'); - }, - }; -} +import { partial } from 'lodash'; +import { AsyncDataCache } from './dataset-cache'; + +/** + * FrameLifecycle type that defines the functions a user can call to interact with the frame lifecycle. + * + * Currently only supports `cancelFrame` to allow the user to cancel the frame on an ad-hoc basis. + */ +export type FrameLifecycle = { + cancelFrame: (reason?: string) => void; +}; + +/** + * NormalStatus type that defines the possible non-error statuses for a frame. + * + * `begun` - The frame has started running + * + * `finished` - The frame has finished running + * + * `cancelled` - The frame was cancelled by the user + * + * `finished_synchronously` - The frame finished synchronously + * + * `progress` - The frame is still running and has not finished + */ +export type NormalStatus = 'begun' | 'finished' | 'cancelled' | 'finished_synchronously' | 'progress'; +export type RenderCallback = (event: { status: NormalStatus } | { status: 'error'; error: unknown }) => void; +/** + * `beingLongRunningFrame` starts a long-running frame that will render a list of items asynchronously based on + * the provided data, settings, and rendering functions. + * + * The frame will run until all items have been rendered, or until the user cancels the frame. It will update the + * provided cache so that the data is available for other frames that may be running. This function is safe to call + * multiple times in different areas of your code, as it will complete quickly if/when all the data is already cached and available. + * + * You can listen for the status of the frame, allowing you to make decisions based on the progress of the frame. + * + * In addition, you can cancel the frame at any time, which will stop the frame from running and prevent any further + * rendering or data fetching from occurring. + * + * @param maximumInflightAsyncTasks The maximum number of async tasks to run at once. + * @param queueProcessingIntervalMS The length of time to wait between processing the queue in milliseconds. + * @param items An array of generic items to render + * @param mutableCache The asynchronous cache used to store the data + * @param settings Flexible object of settings related to the items that are being rendered + * @param requestsForItem a function which returns a mapping of "columns" to async functions that would fetch the column + * @param render The main render function that will be called once all data is available + * @param lifecycleCallback Callback function so they user can be notified of the status of the frame + * @param cacheKeyForRequest A function for generating a cache key for a given request key, item, and settings. Defaults to the request key if not provided. + * @param queueTimeBudgetMS the maximum ammount of time (milliseconds) to spend rendering before yeilding to allow other work to run - rendering will resume next frame (@param queueProcessingIntervalMS) + * @returns A FrameLifecycle object with a cancelFrame function to allow users to cancel the frame when necessary + */ +export function beginLongRunningFrame( + maximumInflightAsyncTasks: number, + queueProcessingIntervalMS: number, + items: Item[], + mutableCache: AsyncDataCache, + settings: Settings, + requestsForItem: (item: Item, settings: Settings, signal?: AbortSignal) => Record Promise>, + render: (item: Item, settings: Settings, columns: Record) => void, + lifecycleCallback: RenderCallback, + cacheKeyForRequest: (requestKey: string, item: Item, settings: Settings) => string = (key) => key, + queueTimeBudgetMS: number = queueProcessingIntervalMS / 3 +): FrameLifecycle { + const abort = new AbortController(); + const queue: Item[] = []; + const taskCancelCallbacks: Array<() => void> = []; + + const reportNormalStatus = (status: NormalStatus) => { + // we want to report our status, however the flow of events can be confusing - + // our callers anticipate an asynchronous (long running) frame to be started, + // but there are scenarios in which the whole thing is completely synchronous + // callers who are scheduling things may be surprised that their frame finished + // before the code that handles it appears to start. thus, we make the entire lifecycle callback + // system async, to prevent surprises. + Promise.resolve().then(() => lifecycleCallback({ status })); + }; + // when starting a frame, we greedily attempt to render any tasks that are already in the cache + // however, if there is too much overhead (or too many tasks) we would risk hogging the main thread + // thus - obey the limit (its a soft limit) + const startTime = performance.now(); + + for (let i = 0; i < items.length; i += 1) { + const itemToRender = items[i]; + const requestFns = requestsForItem(itemToRender, settings, abort.signal); + const cacheKey = (rq: string) => cacheKeyForRequest(rq, itemToRender, settings); + const cacheKeys = Object.keys(requestFns).map(cacheKey); + + if (mutableCache.areKeysAllCached(cacheKeys)) { + const result = mutableCache.cacheAndUse(requestFns, partial(render, itemToRender, settings), cacheKey); + if (result !== undefined) { + // this is a problem - the cache reported that all the keys are in the cache, however this result is a cancellation callback, + // which indicates that the item could not be rendered right away, which should be impossible... + // TODO + taskCancelCallbacks.push(result); + } + } else { + // areKeysAllCached returned false - enqueue for later + queue.push(itemToRender); + } + if (performance.now() - startTime > queueTimeBudgetMS) { + // we've used up all our time - enqueue all remaining tasks + if (i < items.length - 1) { + queue.push(...items.slice(i + 1)); + } + break; + } + } + + if (queue.length === 0) { + // we did all the work - it was already cached + reportNormalStatus('finished_synchronously'); + return { cancelFrame: () => {} }; + } + // TODO: Re-examine lifecycle reporting, potentially unify all statuses into a single type + reportNormalStatus('begun'); + if (queue.length !== items.length) { + // We did some work, but there's some left + reportNormalStatus('progress'); + } + const doWorkOnQueue = (intervalId: number) => { + // try our best to cleanup if something goes awry + const startWorkTime = performance.now(); + const cleanupOnError = (err: unknown) => { + // clear the queue and the staging area (inFlight) + taskCancelCallbacks.forEach((cancelMe) => cancelMe()); + queue.splice(0, queue.length); + // stop fetching + abort.abort(err); + clearInterval(intervalId); + // pass the error somewhere better: + lifecycleCallback({ status: 'error', error: err }); + }; + while (mutableCache.getNumPendingTasks() < Math.max(maximumInflightAsyncTasks, 1)) { + if (queue.length < 1) { + // we cant add anything to the in-flight staging area, the final task + // is already in flight + if (mutableCache.getNumPendingTasks() < 1) { + // we do want to wait for that last in-flight task to actually finish though: + clearInterval(intervalId); + reportNormalStatus('finished'); + } + return; + } + // We know there are items in the queue because of the check above, so we assert the type exist + const itemToRender = queue.shift()!; + const toCacheKey = (rq: string) => cacheKeyForRequest(rq, itemToRender, settings); + try { + const result = mutableCache.cacheAndUse( + requestsForItem(itemToRender, settings, abort.signal), + partial(render, itemToRender, settings), + toCacheKey, + () => reportNormalStatus('progress') + ); + if (result !== undefined) { + // put this cancel callback in a list where we can invoke if something goes wrong + // note that it is harmless to cancel a task that was completed + taskCancelCallbacks.push(result); + } + } catch (err) { + cleanupOnError(err); + } + if (performance.now() - startWorkTime > queueTimeBudgetMS) { + // used up all our time - leave remaining work for later + break; + } + } + }; + const interval = setInterval(() => doWorkOnQueue(interval), queueProcessingIntervalMS); + + // return a function to allow our caller to cancel the frame - guaranteed that no settings/data will be + // touched/referenced after cancellation, unless the author of render() did some super weird bad things + return { + cancelFrame: (reason?: string) => { + taskCancelCallbacks.forEach((cancelMe) => cancelMe()); + abort.abort(new DOMException(reason, 'AbortError')); + clearInterval(interval); + reportNormalStatus('cancelled'); + }, + }; +} diff --git a/packages/scatterbrain/src/test/render-cache.test.ts b/packages/scatterbrain/src/test/render-cache.test.ts index 0d6599d..7b9fc75 100644 --- a/packages/scatterbrain/src/test/render-cache.test.ts +++ b/packages/scatterbrain/src/test/render-cache.test.ts @@ -1,17 +1,17 @@ -import { beforeEach, describe, expect, it } from "vitest"; -import { AsyncDataCache } from "../dataset-cache"; -import { fakeFetch } from "./test-utils"; -import { delay, partial, partialRight, uniqueId } from "lodash"; -type Columns = 'color' | 'position' -type vec3 = readonly [number, number, number] -type Data = { pretend: vec3 } +import { beforeEach, describe, expect, it } from 'vitest'; +import { AsyncDataCache } from '../dataset-cache'; +import { fakeFetch } from './test-utils'; +import { delay, partial, partialRight, uniqueId } from 'lodash'; +type Columns = 'color' | 'position'; +type vec3 = readonly [number, number, number]; +type Data = { pretend: vec3 }; type Entry = { resolveMe: () => void; rejectMe: (reason?: any) => void; -} +}; class PromiseFarm { - entries: Map, Entry> + entries: Map, Entry>; staging: Record; constructor() { this.entries = new Map(); @@ -20,11 +20,10 @@ class PromiseFarm { promiseMe(t: T) { const reqId = uniqueId('rq'); const prom = new Promise((resolve, reject) => { - this.staging[reqId] = - { + this.staging[reqId] = { resolveMe: () => resolve(t), - rejectMe: (reason: any) => reject(reason) - } + rejectMe: (reason: any) => reject(reason), + }; }); this.entries.set(prom, this.staging[reqId]); delete this.staging[reqId]; @@ -50,160 +49,170 @@ class PromiseFarm { type SpyOnRenderer = { data: Record; -} +}; function cacheKey(item: { id: number }, rq: Columns) { return `api:4000/${rq}_${item.id}.bin`; } describe('async cache', () => { let mockPromises = new PromiseFarm(); const fetchFakeItem = (id: number, color: vec3, pos: vec3) => { - const c = mockPromises.promiseMe({ pretend: color }) - const p = mockPromises.promiseMe({ pretend: pos }) + const c = mockPromises.promiseMe({ pretend: color }); + const p = mockPromises.promiseMe({ pretend: pos }); return { fetchers: { color: () => c, position: () => p, }, spies: [c, p], - id + id, } as const; - } + }; const fetchTheSameThingTwice = (id: number, color: vec3, _pos: vec3) => { - const c = mockPromises.promiseMe({ pretend: color }) - const c2 = mockPromises.promiseMe({ pretend: [...color] as vec3 }) + const c = mockPromises.promiseMe({ pretend: color }); + const c2 = mockPromises.promiseMe({ pretend: [...color] as vec3 }); return { fetchers: { color: () => c, position: () => c2, }, spies: [c, c2], - id + id, } as const; - } + }; const fetchTheSameThingTwiceOnePromise = (id: number, color: vec3, _pos: vec3) => { - const c = mockPromises.promiseMe({ pretend: color }) + const c = mockPromises.promiseMe({ pretend: color }); return { fetchers: { color: () => c, position: () => c, }, spies: [c, c], - id + id, } as const; - } + }; const resolveFakePromises = async (lies: readonly Promise[]): Promise => { - lies.forEach((p) => { mockPromises.mockResolve(p) }) + lies.forEach((p) => { + mockPromises.mockResolve(p); + }); // because the promises are mega hackified, even though we call resolve, the event system hasn't had a chance to catch up // so - we have to inject a fake wait in here to give all the promises we just resolved a chance to run for realsies - await Promise.resolve() + await Promise.resolve(); return Promise.resolve(); + }; - } - - let cache = new AsyncDataCache((item: Data) => { }, () => 1, 10); - let disposed: Data[] = [] - let rendered: SpyOnRenderer[] = [] // these are just for spying + let cache = new AsyncDataCache( + (item: Data) => {}, + () => 1, + 10 + ); + let disposed: Data[] = []; + let rendered: SpyOnRenderer[] = []; // these are just for spying const render = (data: Record) => { rendered.push({ data }); - } + }; beforeEach(() => { - cache = new AsyncDataCache((item: Data) => { disposed.push(item) }, () => 1, 10); - disposed = [] - rendered = [] - }) + cache = new AsyncDataCache( + (item: Data) => { + disposed.push(item); + }, + () => 1, + 10 + ); + disposed = []; + rendered = []; + }); describe('cacheAndUse', () => { it('calls the use fn once all requested data is available', async () => { - const { fetchers, id, spies } = fetchFakeItem(1, [255, 0, 0], [1, 2, 3]) + const { fetchers, id, spies } = fetchFakeItem(1, [255, 0, 0], [1, 2, 3]); const toCacheKey = partial(cacheKey, { id }); - const result = cache.cacheAndUse(fetchers, render, toCacheKey) + const result = cache.cacheAndUse(fetchers, render, toCacheKey); expect(result).toBeDefined(); // the promises for our fake data never resolve until we tell them to - expect(cache.getNumPendingTasks()).toBe(1) + expect(cache.getNumPendingTasks()).toBe(1); expect(rendered.length).toBe(0); await resolveFakePromises(spies); - expect(cache.getNumPendingTasks()).toBe(0) + expect(cache.getNumPendingTasks()).toBe(0); expect(rendered.length).toBe(1); - }) + }); it('behaves correctly when a fetch fails', async () => { - const { fetchers, id, spies } = fetchFakeItem(1, [255, 0, 0], [1, 2, 3]) + const { fetchers, id, spies } = fetchFakeItem(1, [255, 0, 0], [1, 2, 3]); const toCacheKey = partial(cacheKey, { id }); - const result = cache.cacheAndUse(fetchers, render, toCacheKey) + const result = cache.cacheAndUse(fetchers, render, toCacheKey); expect(result).toBeDefined(); // fail one, resolve the other let boom = false; // this little catch represents passing our deep error up to someone smarter: - spies[0].catch(() => boom = true) + spies[0].catch(() => (boom = true)); - - mockPromises.mockResolve(spies[1]) + mockPromises.mockResolve(spies[1]); // resolve one first so that we can be sure its value lives in the cache - await Promise.resolve() - expect(cache.isCached(toCacheKey('position'))).toBeTruthy() + await Promise.resolve(); + expect(cache.isCached(toCacheKey('position'))).toBeTruthy(); // then reject the other to fail the overall task - mockPromises.mockReject(spies[0], 'fetch failed for reals') + mockPromises.mockReject(spies[0], 'fetch failed for reals'); // so this is pretty gross... // the number of awaits here relates to how many promises are chained together... // todo think of a way to be smarter about this very async test... - await Promise.resolve() - await Promise.resolve() + await Promise.resolve(); + await Promise.resolve(); - expect(cache.getNumPendingTasks()).toBe(0) + expect(cache.getNumPendingTasks()).toBe(0); expect(rendered.length).toBe(0); - expect(boom).toBeTruthy() + expect(boom).toBeTruthy(); // the one that failed of course is missing from the cache - expect(cache.isCached(toCacheKey('color'))).toBeFalsy() - }) + expect(cache.isCached(toCacheKey('color'))).toBeFalsy(); + }); it('evicts data after the soft limit is hit', async () => { // each of our tasks requests two chunks of data // the cache has a limit of 10 items (see beforeEach) - let allKeysSoFar: string[] = [] + let allKeysSoFar: string[] = []; for (let i = 0; i < 5; i++) { - const { fetchers, id, spies } = fetchFakeItem(i, [255, 0, i], [1, 2 * i, 3 * i]) - const toCacheKey = partial(cacheKey, { id }) - const result = cache.cacheAndUse(fetchers, render, toCacheKey) + const { fetchers, id, spies } = fetchFakeItem(i, [255, 0, i], [1, 2 * i, 3 * i]); + const toCacheKey = partial(cacheKey, { id }); + const result = cache.cacheAndUse(fetchers, render, toCacheKey); // store all the cache keys so we can expect them later - allKeysSoFar.push(toCacheKey('color'), toCacheKey('position')) - await resolveFakePromises(spies) + allKeysSoFar.push(toCacheKey('color'), toCacheKey('position')); + await resolveFakePromises(spies); } // so after making 5 requests, we should have a full cache expect(cache.areKeysAllCached(allKeysSoFar)).toBe(true); expect(cache.getNumPendingTasks()).toBe(0); // now request a new thing - this should cause the cache to remove at least one item - const { fetchers, id, spies } = fetchFakeItem(99, [99, 99, 99], [9, 9, 9]) - const toCacheKey = partial(cacheKey, { id }) + const { fetchers, id, spies } = fetchFakeItem(99, [99, 99, 99], [9, 9, 9]); + const toCacheKey = partial(cacheKey, { id }); const result = cache.cacheAndUse(fetchers, render, toCacheKey); - await resolveFakePromises(spies) + await resolveFakePromises(spies); // we would expect the items with id=0 to have been removed, as they are the oldest - expect(cache.isCached(toCacheKey('color'))).toBeTruthy() - expect(cache.isCached(toCacheKey('position'))).toBeTruthy() + expect(cache.isCached(toCacheKey('color'))).toBeTruthy(); + expect(cache.isCached(toCacheKey('position'))).toBeTruthy(); // and the old ones: - expect(cache.isCached(cacheKey({ id: 0 }, 'color'))).toBeFalsy() - expect(cache.isCached(cacheKey({ id: 0 }, 'position'))).toBeFalsy() - }) + expect(cache.isCached(cacheKey({ id: 0 }, 'color'))).toBeFalsy(); + expect(cache.isCached(cacheKey({ id: 0 }, 'position'))).toBeFalsy(); + }); it('does not evict data if it is marked as critical for a pending request', async () => { // almost the same scenario as the previous test, except we're going to intentionally NOT // resolve the task with id=0. Because its still pending, we would like to see that it does not get evicted! // each of our tasks requests two chunks of data // the cache has a limit of 10 items (see beforeEach) - let allKeysSoFar: string[] = [] + let allKeysSoFar: string[] = []; let reallySlowRequest: Promise; for (let i = 0; i < 6; i++) { - const { fetchers, id, spies } = fetchFakeItem(i, [255, 0, i], [1, 2 * i, 3 * i]) - const toCacheKey = partial(cacheKey, { id }) - const result = cache.cacheAndUse(fetchers, render, toCacheKey) + const { fetchers, id, spies } = fetchFakeItem(i, [255, 0, i], [1, 2 * i, 3 * i]); + const toCacheKey = partial(cacheKey, { id }); + const result = cache.cacheAndUse(fetchers, render, toCacheKey); if (i !== 0) { // dont resolve the stuff for the first task! - allKeysSoFar.push(toCacheKey('color'), toCacheKey('position')) - await resolveFakePromises(spies) + allKeysSoFar.push(toCacheKey('color'), toCacheKey('position')); + await resolveFakePromises(spies); } else { - allKeysSoFar.push(toCacheKey('color')) - await resolveFakePromises([spies[0]]) + allKeysSoFar.push(toCacheKey('color')); + await resolveFakePromises([spies[0]]); reallySlowRequest = spies[1]; // intentionally not resolving position! } @@ -213,46 +222,46 @@ describe('async cache', () => { expect(cache.getNumPendingTasks()).toBe(1); // the first task is still pending, because we didn't resolve its position request // now request a new thing - this should cause the cache to remove at least one item - const { fetchers, id, spies } = fetchFakeItem(99, [99, 99, 99], [9, 9, 9]) + const { fetchers, id, spies } = fetchFakeItem(99, [99, 99, 99], [9, 9, 9]); const result = cache.cacheAndUse(fetchers, render, partial(cacheKey, { id })); - await resolveFakePromises(spies) + await resolveFakePromises(spies); - expect(cache.isCached(cacheKey({ id: 99 }, 'color'))).toBeTruthy() - expect(cache.isCached(cacheKey({ id: 99 }, 'position'))).toBeTruthy() + expect(cache.isCached(cacheKey({ id: 99 }, 'color'))).toBeTruthy(); + expect(cache.isCached(cacheKey({ id: 99 }, 'position'))).toBeTruthy(); // we would expect the items with id=0 to have been removed, as they are the oldest, HOWEVER - // we never resolved (position,id:0) so we expect to not have removed - expect(cache.isCached(cacheKey({ id: 0 }, 'color'))).toBeTruthy() // its still in the cache - expect(cache.isCached(cacheKey({ id: 0 }, 'position'))).toBeFalsy() // its never been resolved, so it cant be in the cache (yet) + // we never resolved (position,id:0) so we expect to not have removed + expect(cache.isCached(cacheKey({ id: 0 }, 'color'))).toBeTruthy(); // its still in the cache + expect(cache.isCached(cacheKey({ id: 0 }, 'position'))).toBeFalsy(); // its never been resolved, so it cant be in the cache (yet) - expect(cache.isCached(cacheKey({ id: 1 }, 'color'))).toBeFalsy() - expect(cache.isCached(cacheKey({ id: 1 }, 'position'))).toBeFalsy() + expect(cache.isCached(cacheKey({ id: 1 }, 'color'))).toBeFalsy(); + expect(cache.isCached(cacheKey({ id: 1 }, 'position'))).toBeFalsy(); // finally, resolve that first stalled request, and observe us fulfilling our first render task: - await resolveFakePromises([reallySlowRequest!]) - expect(cache.getNumPendingTasks()).toBe(0) + await resolveFakePromises([reallySlowRequest!]); + expect(cache.getNumPendingTasks()).toBe(0); // expect everything to have been rendered, regardless of all this cache nonsense - expect(rendered.length).toEqual(7) // id=0...5, 99 + expect(rendered.length).toEqual(7); // id=0...5, 99 // spot check the last two rendered things: - rendered[rendered.length - 2].data.color[1] = 99 - rendered[rendered.length - 1].data.position[2] = 0 // 3*(i=0) - }) + rendered[rendered.length - 2].data.color[1] = 99; + rendered[rendered.length - 1].data.position[2] = 0; // 3*(i=0) + }); it('evicts data after the soft limit is hit, while prioritizing Least-recently used entries', async () => { // each of our tasks requests two chunks of data // the cache has a limit of 10 items (see beforeEach) - let allKeysSoFar: string[] = [] - let first: ReturnType & { toCacheKey: (rq: Columns) => string } + let allKeysSoFar: string[] = []; + let first: ReturnType & { toCacheKey: (rq: Columns) => string }; for (let i = 0; i < 5; i++) { - const { fetchers, id, spies } = fetchFakeItem(i, [255, 0, i], [1, 2 * i, 3 * i]) - const toCacheKey = partial(cacheKey, { id }) + const { fetchers, id, spies } = fetchFakeItem(i, [255, 0, i], [1, 2 * i, 3 * i]); + const toCacheKey = partial(cacheKey, { id }); if (i === 0) { - first = { fetchers, id, spies, toCacheKey } + first = { fetchers, id, spies, toCacheKey }; } - const result = cache.cacheAndUse(fetchers, render, toCacheKey) + const result = cache.cacheAndUse(fetchers, render, toCacheKey); // store all the cache keys so we can expect them later - allKeysSoFar.push(toCacheKey('color'), toCacheKey('position')) - await resolveFakePromises(spies) + allKeysSoFar.push(toCacheKey('color'), toCacheKey('position')); + await resolveFakePromises(spies); } // so after making 5 requests, we should have a full cache expect(cache.areKeysAllCached(allKeysSoFar)).toBe(true); @@ -263,21 +272,21 @@ describe('async cache', () => { await resolveFakePromises(again.spies); expect(cache.getNumPendingTasks()).toBe(0); // now request a new thing - this should cause the cache to remove at least one item - const { fetchers, id, spies } = fetchFakeItem(99, [99, 99, 99], [9, 9, 9]) - const toCacheKey = partial(cacheKey, { id }) + const { fetchers, id, spies } = fetchFakeItem(99, [99, 99, 99], [9, 9, 9]); + const toCacheKey = partial(cacheKey, { id }); const result = cache.cacheAndUse(fetchers, render, toCacheKey); - await resolveFakePromises(spies) + await resolveFakePromises(spies); // we would expect the items with id=1 to have been removed (not id=0 because we re-requested it) - expect(cache.isCached(toCacheKey('color'))).toBeTruthy() - expect(cache.isCached(toCacheKey('position'))).toBeTruthy() + expect(cache.isCached(toCacheKey('color'))).toBeTruthy(); + expect(cache.isCached(toCacheKey('position'))).toBeTruthy(); - expect(cache.isCached(cacheKey({ id: 0 }, 'color'))).toBeTruthy() - expect(cache.isCached(cacheKey({ id: 0 }, 'position'))).toBeTruthy() + expect(cache.isCached(cacheKey({ id: 0 }, 'color'))).toBeTruthy(); + expect(cache.isCached(cacheKey({ id: 0 }, 'position'))).toBeTruthy(); // these are gone - they would have been the second oldest (and thus safe) - but we re-requested the id=0 items // so they get updated as having been used most-recently - the idea being they'll be requested again and maybe other things would be better to evict - expect(cache.isCached(cacheKey({ id: 1 }, 'color'))).toBeFalsy() - expect(cache.isCached(cacheKey({ id: 1 }, 'position'))).toBeFalsy() - }) + expect(cache.isCached(cacheKey({ id: 1 }, 'color'))).toBeFalsy(); + expect(cache.isCached(cacheKey({ id: 1 }, 'position'))).toBeFalsy(); + }); it('handles the case in which the same cache-key is requested by multiple semantic-keys within the same task: ', async () => { // a nice edge-case. // real-world version: imagine a 1-channel ome-zarr image, in which the user wants to render with a 3-channel (RGB) shader @@ -286,51 +295,51 @@ describe('async cache', () => { // green: ()=>fetch(http://blah.channel0), // blue: ()=>fetch(http://blah.channel0), // } - // prior to this fix, the cache assumed that any incoming data would map to exactly one (per-task) semantic output - + // prior to this fix, the cache assumed that any incoming data would map to exactly one (per-task) semantic output - // the result would be that the task would resolve itself early, with several keys being undefined - const clr: vec3 = [255, 0, 0] - const { fetchers, id, spies } = fetchTheSameThingTwice(1, clr, [1, 2, 3]) + const clr: vec3 = [255, 0, 0]; + const { fetchers, id, spies } = fetchTheSameThingTwice(1, clr, [1, 2, 3]); // in this case, we want to test what happens when one cache key is associated with multiple semantic keys: - const toCacheKey = () => `http://blah.channel0` - const result = cache.cacheAndUse(fetchers, render, toCacheKey) + const toCacheKey = () => `http://blah.channel0`; + const result = cache.cacheAndUse(fetchers, render, toCacheKey); expect(result).toBeDefined(); - expect(cache.getNumPendingTasks()).toBe(1) + expect(cache.getNumPendingTasks()).toBe(1); expect(rendered.length).toBe(0); // the point of this test is that one promise ends up fullfilling multiple "semantic" entries // thus, we need only resolve one fake promise for the whole thing to be ready (both elements of 'spies' are the same promise) await resolveFakePromises([spies[0]]); - expect(cache.getNumPendingTasks()).toBe(0) + expect(cache.getNumPendingTasks()).toBe(0); expect(rendered.length).toBe(1); // expect that all the parts of the response did show up: const renderedData = rendered[0]; // each entry (position and color) are the same value - which we put in at the beginning of the test (clr) - expect(renderedData.data.color.pretend).toEqual(clr) - expect(renderedData.data.position.pretend).toEqual(clr) - }) + expect(renderedData.data.color.pretend).toEqual(clr); + expect(renderedData.data.position.pretend).toEqual(clr); + }); it('handles the case in which the same cache-key is requested by multiple semantic-keys within the same task (and also the promises beneath are the same promise): ', async () => { // same as above, but internally returns the same promise twice... - const clr: vec3 = [255, 0, 0] - const { fetchers, id, spies } = fetchTheSameThingTwiceOnePromise(1, clr, [1, 2, 3]) + const clr: vec3 = [255, 0, 0]; + const { fetchers, id, spies } = fetchTheSameThingTwiceOnePromise(1, clr, [1, 2, 3]); // in this case, we want to test what happens when one cache key is associated with multiple semantic keys: - const toCacheKey = () => `http://blah.channel0` - const result = cache.cacheAndUse(fetchers, render, toCacheKey) + const toCacheKey = () => `http://blah.channel0`; + const result = cache.cacheAndUse(fetchers, render, toCacheKey); expect(result).toBeDefined(); - expect(cache.getNumPendingTasks()).toBe(1) + expect(cache.getNumPendingTasks()).toBe(1); expect(rendered.length).toBe(0); // the point of this test is that one promise ends up fullfilling multiple "semantic" entries // thus, we need only resolve one fake promise for the whole thing to be ready (both elements of 'spies' are the same promise) await resolveFakePromises([spies[0]]); - expect(cache.getNumPendingTasks()).toBe(0) + expect(cache.getNumPendingTasks()).toBe(0); expect(rendered.length).toBe(1); // expect that all the parts of the response did show up: const renderedData = rendered[0]; // each entry (position and color) are the same value - which we put in at the beginning of the test (clr) - expect(renderedData.data.color.pretend).toEqual(clr) - expect(renderedData.data.position.pretend).toEqual(clr) - }) - }) -}) \ No newline at end of file + expect(renderedData.data.color.pretend).toEqual(clr); + expect(renderedData.data.position.pretend).toEqual(clr); + }); + }); +}); diff --git a/packages/scatterbrain/src/test/render-queue.test.ts b/packages/scatterbrain/src/test/render-queue.test.ts index ae7b134..5a102bb 100644 --- a/packages/scatterbrain/src/test/render-queue.test.ts +++ b/packages/scatterbrain/src/test/render-queue.test.ts @@ -1,129 +1,139 @@ -import { beforeEach, describe, expect, it, vi } from 'vitest' -import delay from 'lodash/delay'; -import { beginLongRunningFrame, type NormalStatus } from '../render-queue'; -import { AsyncDataCache } from '../dataset-cache'; -import { fakeFetch } from './test-utils'; - -type FakeTask = { id: number; color: string }; -type FakeItem = { id: number }; -type FakeSettings = { color: string }; -function cacheKey(item: FakeItem, settings: FakeSettings) { - return `${settings.color}_${item.id}`; -} - -// a few easy tests to start, we can get crazy later -describe('beginLongRunningFrame', () => { - let cache: AsyncDataCache = new AsyncDataCache(() => { }, () => 1, 9999); - let renderSequence: FakeTask[] = []; - function renderPretender(item: FakeItem, settings: FakeSettings, tasks: Record) { - const tsk = tasks[cacheKey(item, settings)]; - if (!tsk) throw new Error('undefined column!'); - renderSequence.push(tsk); - } - const getPretendItemsToRender = (howMany: number) => { - const items: FakeItem[] = []; - for (let i = 0; i < howMany; i += 1) { - items.push({ id: i }); - } - return items; - }; - function rq(item: FakeItem, settings: FakeSettings, signal?: AbortSignal) { - return { - [cacheKey(item, settings)]: () => fakeFetch({ id: item.id, color: settings.color }, signal), - }; - } - // a less wordy fake frame: - const fakeFrame = ( - items: number, - eventHandler: (event: { status: NormalStatus } | { status: 'error'; error: unknown }) => void - ) => - beginLongRunningFrame( - 5, - 33, - getPretendItemsToRender(items), - cache, - { color: 'red' }, - rq, - renderPretender, - eventHandler, - (rq: string, item: FakeItem, settings: FakeSettings) => cacheKey(item, settings), - 9999 - ); - beforeEach(() => { - cache = new AsyncDataCache(() => { }, () => 1, 9999); - renderSequence = []; - }); - it('runs the expected number of tasks', async () => { - let done: () => void; - const testOver = new Promise((resolve, reject) => { - done = () => { resolve() } - }) - const events: string[] = []; - fakeFrame(9, (e) => { - events.push(e.status); // track the events for the test - switch (e.status) { - case 'finished': - done(); // if I dont get called, the test will fail very slowly - break; - default: - break; - } - }); - await testOver; - expect(renderSequence.length).toBe(9); - expect(events.length).toBe(9 + 2); // begin, ... progress x9 ..., finished - expect(events[0]).toEqual('begun'); - expect(events[events.length - 1]).toEqual('finished'); - }); - it('can be cancelled without crash', async () => { - let done: () => void; - const testOver = new Promise((resolve, reject) => { - done = () => resolve() - }) - try { - const frame = fakeFrame(9, (e) => { - expect(renderSequence.length).toBeLessThan(9); - switch (e.status) { - case 'cancelled': - done(); - break; - default: - break; - } - }); - // cancel the fetch after brief delay to simulate cancelling partway through - delay(() => frame.cancelFrame('for testing'), 1); - } catch (err) { - // should not happen! - expect(err).not.toBeDefined(); - } - await testOver; - }); - it('synchronously completes the second frame, because the cache gets warmed up', async () => { - const allEvents: string[] = []; - let done: () => void; - const testOver = new Promise((resolve, reject) => { - done = () => resolve() - }) - fakeFrame(9, (e) => { - allEvents.push(e.status); - if (e.status === 'finished') { - // start the second frame after the first is done for this test: - // eslint-disable-next-line @typescript-eslint/no-shadow - fakeFrame(9, (e) => { - allEvents.push(e.status); - switch (e.status) { - case 'finished_synchronously': - break; - default: - expect(e.status).toBe('finished_synchronously'); - } - done(); - }); - } - }); - await testOver - expect(renderSequence.length).toBe(9 + 9); // two frames, each having 9 tasks - expect(allEvents.length).toBe(9 + 2 + 1); // all of the events of the first frame(begun,progress*9,finished) + 'finished_sync' - }); -}); +import { beforeEach, describe, expect, it, vi } from 'vitest'; +import delay from 'lodash/delay'; +import { beginLongRunningFrame, type NormalStatus } from '../render-queue'; +import { AsyncDataCache } from '../dataset-cache'; +import { fakeFetch } from './test-utils'; + +type FakeTask = { id: number; color: string }; +type FakeItem = { id: number }; +type FakeSettings = { color: string }; +function cacheKey(item: FakeItem, settings: FakeSettings) { + return `${settings.color}_${item.id}`; +} + +// a few easy tests to start, we can get crazy later +describe('beginLongRunningFrame', () => { + let cache: AsyncDataCache = new AsyncDataCache( + () => {}, + () => 1, + 9999 + ); + let renderSequence: FakeTask[] = []; + function renderPretender(item: FakeItem, settings: FakeSettings, tasks: Record) { + const tsk = tasks[cacheKey(item, settings)]; + if (!tsk) throw new Error('undefined column!'); + renderSequence.push(tsk); + } + const getPretendItemsToRender = (howMany: number) => { + const items: FakeItem[] = []; + for (let i = 0; i < howMany; i += 1) { + items.push({ id: i }); + } + return items; + }; + function rq(item: FakeItem, settings: FakeSettings, signal?: AbortSignal) { + return { + [cacheKey(item, settings)]: () => fakeFetch({ id: item.id, color: settings.color }, signal), + }; + } + // a less wordy fake frame: + const fakeFrame = ( + items: number, + eventHandler: (event: { status: NormalStatus } | { status: 'error'; error: unknown }) => void + ) => + beginLongRunningFrame( + 5, + 33, + getPretendItemsToRender(items), + cache, + { color: 'red' }, + rq, + renderPretender, + eventHandler, + (rq: string, item: FakeItem, settings: FakeSettings) => cacheKey(item, settings), + 9999 + ); + beforeEach(() => { + cache = new AsyncDataCache( + () => {}, + () => 1, + 9999 + ); + renderSequence = []; + }); + it('runs the expected number of tasks', async () => { + let done: () => void; + const testOver = new Promise((resolve, reject) => { + done = () => { + resolve(); + }; + }); + const events: string[] = []; + fakeFrame(9, (e) => { + events.push(e.status); // track the events for the test + switch (e.status) { + case 'finished': + done(); // if I dont get called, the test will fail very slowly + break; + default: + break; + } + }); + await testOver; + expect(renderSequence.length).toBe(9); + expect(events.length).toBe(9 + 2); // begin, ... progress x9 ..., finished + expect(events[0]).toEqual('begun'); + expect(events[events.length - 1]).toEqual('finished'); + }); + it('can be cancelled without crash', async () => { + let done: () => void; + const testOver = new Promise((resolve, reject) => { + done = () => resolve(); + }); + try { + const frame = fakeFrame(9, (e) => { + expect(renderSequence.length).toBeLessThan(9); + switch (e.status) { + case 'cancelled': + done(); + break; + default: + break; + } + }); + // cancel the fetch after brief delay to simulate cancelling partway through + delay(() => frame.cancelFrame('for testing'), 1); + } catch (err) { + // should not happen! + expect(err).not.toBeDefined(); + } + await testOver; + }); + it('synchronously completes the second frame, because the cache gets warmed up', async () => { + const allEvents: string[] = []; + let done: () => void; + const testOver = new Promise((resolve, reject) => { + done = () => resolve(); + }); + fakeFrame(9, (e) => { + allEvents.push(e.status); + if (e.status === 'finished') { + // start the second frame after the first is done for this test: + // eslint-disable-next-line @typescript-eslint/no-shadow + fakeFrame(9, (e) => { + allEvents.push(e.status); + switch (e.status) { + case 'finished_synchronously': + break; + default: + expect(e.status).toBe('finished_synchronously'); + } + done(); + }); + } + }); + await testOver; + expect(renderSequence.length).toBe(9 + 9); // two frames, each having 9 tasks + expect(allEvents.length).toBe(9 + 2 + 1); // all of the events of the first frame(begun,progress*9,finished) + 'finished_sync' + }); +}); diff --git a/packages/scatterbrain/src/test/test-utils.ts b/packages/scatterbrain/src/test/test-utils.ts index e5970e0..0aa777d 100644 --- a/packages/scatterbrain/src/test/test-utils.ts +++ b/packages/scatterbrain/src/test/test-utils.ts @@ -1,12 +1,15 @@ -import { delay } from "lodash"; +import { delay } from 'lodash'; export const fakeFetch = (data: FakeTask, signal?: AbortSignal): Promise => new Promise((resolve, reject) => { - delay(() => { - if (signal?.aborted ?? false) { - reject(new DOMException('abort fetch', 'AbortError')); - } else { - resolve(data); - } - }, 100 * Math.random() + 50); - }); \ No newline at end of file + delay( + () => { + if (signal?.aborted ?? false) { + reject(new DOMException('abort fetch', 'AbortError')); + } else { + resolve(data); + } + }, + 100 * Math.random() + 50 + ); + }); diff --git a/packages/scatterbrain/tsconfig.json b/packages/scatterbrain/tsconfig.json index d9869b8..baaee9e 100644 --- a/packages/scatterbrain/tsconfig.json +++ b/packages/scatterbrain/tsconfig.json @@ -1,20 +1,13 @@ -{ - "extends": "../../tsconfig.base.json", - "compilerOptions": { - "paths": { - "~/*": [ - "./*" - ] - }, - "moduleResolution": "Bundler", - "module": "ES2022", - "target": "ES2022", - "lib": [ - "es2022", - "DOM" - ], - }, - "include": [ - "./src/index.ts" - ] -} \ No newline at end of file +{ + "extends": "../../tsconfig.base.json", + "compilerOptions": { + "paths": { + "~/*": ["./*"] + }, + "moduleResolution": "Bundler", + "module": "ES2022", + "target": "ES2022", + "lib": ["es2022", "DOM"] + }, + "include": ["./src/index.ts"] +} diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index cc34308..50f0831 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -1,4067 +1,5382 @@ lockfileVersion: '6.0' settings: - autoInstallPeers: true - excludeLinksFromLockfile: false + autoInstallPeers: true + excludeLinksFromLockfile: false importers: - - .: - devDependencies: - '@parcel/packager-ts': - specifier: 2.12.0 - version: 2.12.0(@parcel/core@2.12.0) - '@parcel/transformer-typescript-types': - specifier: 2.12.0 - version: 2.12.0(@parcel/core@2.12.0)(typescript@5.3.3) - buffer: - specifier: ^5.5.0||^6.0.0 - version: 6.0.3 - parcel: - specifier: 2.12.0 - version: 2.12.0(typescript@5.3.3) - process: - specifier: ^0.11.10 - version: 0.11.10 - typescript: - specifier: ^5.3.3 - version: 5.3.3 - - apps/common: - dependencies: - '@alleninstitute/vis-geometry': - specifier: workspace:* - version: link:../../packages/geometry - '@alleninstitute/vis-scatterbrain': - specifier: workspace:* - version: link:../../packages/scatterbrain - '@types/lodash': - specifier: ^4.14.202 - version: 4.14.202 - lodash: - specifier: ^4.17.21 - version: 4.17.21 - regl: - specifier: ^2.1.0 - version: 2.1.0 - zarr: - specifier: ^0.6.2 - version: 0.6.2 - - apps/layers: - dependencies: - '@alleninstitute/vis-geometry': - specifier: workspace:* - version: link:../../packages/geometry - '@alleninstitute/vis-scatterbrain': - specifier: workspace:* - version: link:../../packages/scatterbrain - '@czi-sds/components': - specifier: ^20.0.1 - version: 20.0.1(@emotion/core@11.0.0)(@emotion/css@11.11.2)(@emotion/react@11.11.4)(@emotion/styled@11.11.5)(@mui/base@5.0.0-beta.40)(@mui/icons-material@5.15.15)(@mui/lab@5.0.0-alpha.170)(@mui/material@5.15.15)(react-dom@18.3.0)(react@18.3.0) - '@emotion/css': - specifier: ^11.11.2 - version: 11.11.2 - '@emotion/react': - specifier: ^11.11.4 - version: 11.11.4(@types/react@18.3.0)(react@18.3.0) - '@emotion/styled': - specifier: ^11.11.5 - version: 11.11.5(@emotion/react@11.11.4)(@types/react@18.3.0)(react@18.3.0) - '@mui/base': - specifier: 5.0.0-beta.40 - version: 5.0.0-beta.40(@types/react@18.3.0)(react-dom@18.3.0)(react@18.3.0) - '@mui/icons-material': - specifier: ^5.15.15 - version: 5.15.15(@mui/material@5.15.15)(@types/react@18.3.0)(react@18.3.0) - '@mui/lab': - specifier: 5.0.0-alpha.170 - version: 5.0.0-alpha.170(@emotion/react@11.11.4)(@emotion/styled@11.11.5)(@mui/material@5.15.15)(@types/react@18.3.0)(react-dom@18.3.0)(react@18.3.0) - '@mui/material': - specifier: ^5.15.15 - version: 5.15.15(@emotion/react@11.11.4)(@emotion/styled@11.11.5)(@types/react@18.3.0)(react-dom@18.3.0)(react@18.3.0) - '@types/lodash': - specifier: ^4.14.202 - version: 4.14.202 - file-saver: - specifier: ^2.0.5 - version: 2.0.5 - json5: - specifier: ^2.2.3 - version: 2.2.3 - kiwi-schema: - specifier: ^0.5.0 - version: 0.5.0 - lodash: - specifier: ^4.17.21 - version: 4.17.21 - react: - specifier: ^18.3.0 - version: 18.3.0 - react-dom: - specifier: ^18.3.0 - version: 18.3.0(react@18.3.0) - regl: - specifier: ^2.1.0 - version: 2.1.0 - zarr: - specifier: ^0.6.2 - version: 0.6.2 - devDependencies: - '@parcel/packager-ts': - specifier: ^2.12.0 - version: 2.12.0(@parcel/core@2.12.0) - '@parcel/transformer-typescript-types': - specifier: ^2.12.0 - version: 2.12.0(@parcel/core@2.12.0)(typescript@5.3.3) - '@types/file-saver': - specifier: ^2.0.7 - version: 2.0.7 - '@types/react': - specifier: ^18.3.0 - version: 18.3.0 - '@types/react-dom': - specifier: ^18.3.0 - version: 18.3.0 - esbuild: - specifier: ^0.19.12 - version: 0.19.12 - parcel: - specifier: 2.12.0 - version: 2.12.0(typescript@5.3.3) - typescript: - specifier: ^5.3.3 - version: 5.3.3 - - apps/neuroglancer-url: - devDependencies: - esbuild: - specifier: ^0.19.12 - version: 0.19.12 - typescript: - specifier: ^5.3.3 - version: 5.3.3 - - apps/omezarr-viewer: - dependencies: - 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