diff --git a/CHANGELOG.md b/CHANGELOG.md index caf4ba6a..950770b6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,12 +4,74 @@ All notable changes to this project will be documented in this file. Dates are d Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog). -#### [v3.9.1](https://github.com/simularium/simularium-viewer/compare/v3.8.2...v3.9.1) +#### [v3.10.3](https://github.com/simularium/simularium-viewer/compare/v3.10.2...v3.10.3) + +- read frameNumber from intView when parsing binary frame [`#502`](https://github.com/simularium/simularium-viewer/pull/502) + +#### [v3.10.2](https://github.com/simularium/simularium-viewer/compare/v3.10.1...v3.10.2) + +> 2 August 2025 + +- need to include types in export [`#501`](https://github.com/simularium/simularium-viewer/pull/501) + +#### [v3.10.1](https://github.com/simularium/simularium-viewer/compare/v3.10.0...v3.10.1) + +> 31 July 2025 + +- clear available agents [`#500`](https://github.com/simularium/simularium-viewer/pull/500) +- add export field to package.json [`#496`](https://github.com/simularium/simularium-viewer/pull/496) +- Bump form-data from 4.0.1 to 4.0.4 [`#498`](https://github.com/simularium/simularium-viewer/pull/498) +- Bump on-headers and compression in /examples [`#497`](https://github.com/simularium/simularium-viewer/pull/497) +- Bump vite from 5.4.18 to 5.4.19 [`#495`](https://github.com/simularium/simularium-viewer/pull/495) +- Bump webpack-dev-server from 5.1.0 to 5.2.1 in /examples [`#494`](https://github.com/simularium/simularium-viewer/pull/494) + +#### [v3.10.0](https://github.com/simularium/simularium-viewer/compare/v3.9.1...v3.10.0) + +> 9 June 2025 + +- Bump vite from 6.2.5 to 6.3.4 in /examples [`#492`](https://github.com/simularium/simularium-viewer/pull/492) +- Bump vite from 5.4.17 to 5.4.18 [`#491`](https://github.com/simularium/simularium-viewer/pull/491) +- Bump http-proxy-middleware from 2.0.7 to 2.0.9 in /examples [`#490`](https://github.com/simularium/simularium-viewer/pull/490) +- Bug Fix: Blood Plasma Simularium Example [`#493`](https://github.com/simularium/simularium-viewer/pull/493) +- Bump vite from 5.4.14 to 5.4.17 [`#487`](https://github.com/simularium/simularium-viewer/pull/487) +- Bump @babel/runtime from 7.26.0 to 7.27.0 [`#486`](https://github.com/simularium/simularium-viewer/pull/486) +- Bump vite from 6.2.3 to 6.2.5 in /examples [`#485`](https://github.com/simularium/simularium-viewer/pull/485) +- Bump @babel/helpers from 7.26.0 to 7.27.0 [`#483`](https://github.com/simularium/simularium-viewer/pull/483) +- add cache logging callback [`#469`](https://github.com/simularium/simularium-viewer/pull/469) +- Bump vite from 6.1.1 to 6.2.3 in /examples [`#482`](https://github.com/simularium/simularium-viewer/pull/482) +- fix key errors [`#464`](https://github.com/simularium/simularium-viewer/pull/464) +- test-bed layout [`#452`](https://github.com/simularium/simularium-viewer/pull/452) +- test-bed file selection update and json response from remote simulator [`#451`](https://github.com/simularium/simularium-viewer/pull/451) +- Revert "prefetching (#442)" [`#460`](https://github.com/simularium/simularium-viewer/pull/460) +- bug fixes [`#455`](https://github.com/simularium/simularium-viewer/pull/455) +- put style sheet in /es when running build [`#456`](https://github.com/simularium/simularium-viewer/pull/456) +- prefetching [`#442`](https://github.com/simularium/simularium-viewer/pull/442) +- Bump vite from 6.0.2 to 6.1.1 in /examples [`#453`](https://github.com/simularium/simularium-viewer/pull/453) +- Bump esbuild from 0.12.29 to 0.25.0 [`#449`](https://github.com/simularium/simularium-viewer/pull/449) +- watch mode for HMR [`#444`](https://github.com/simularium/simularium-viewer/pull/444) +- Bump vitest and @vitest/coverage-v8 [`#448`](https://github.com/simularium/simularium-viewer/pull/448) +- Feature/test app vite [`#433`](https://github.com/simularium/simularium-viewer/pull/433) +- Biosimulators Prototype [`#426`](https://github.com/simularium/simularium-viewer/pull/426) +- Feature/isimulator [`#441`](https://github.com/simularium/simularium-viewer/pull/441) +- Fix/autoconversion [`#438`](https://github.com/simularium/simularium-viewer/pull/438) +- Fix/example build [`#437`](https://github.com/simularium/simularium-viewer/pull/437) + +#### [v3.9.1](https://github.com/simularium/simularium-viewer/compare/v3.9.0...v3.9.1) + +> 19 December 2024 - Bump three to r171 [`#436`](https://github.com/simularium/simularium-viewer/pull/436) - replace Jest with vitest and use "type":"module" [`#431`](https://github.com/simularium/simularium-viewer/pull/431) -- Bounding box toggle in tweakpane [`#434`](https://github.com/simularium/simularium-viewer/pull/434) - test-bed fixes [`#432`](https://github.com/simularium/simularium-viewer/pull/432) +- remove happy-dom [`a7ebd57`](https://github.com/simularium/simularium-viewer/commit/a7ebd57b262ad6222420a8960e169b85797a07aa) +- update package-lock [`f43acf6`](https://github.com/simularium/simularium-viewer/commit/f43acf604ea609c6b71d25ccecbad72844d6a241) +- update some test config [`7dde5d4`](https://github.com/simularium/simularium-viewer/commit/7dde5d4e209b5db30c66d7aa08de3e00bb691ba0) + +#### [v3.9.0](https://github.com/simularium/simularium-viewer/compare/v3.8.4...v3.9.0) + +> 6 December 2024 + +- Bounding box toggle in tweakpane [`#434`](https://github.com/simularium/simularium-viewer/pull/434) - testbed file organization [`#429`](https://github.com/simularium/simularium-viewer/pull/429) - fix test bed download button [`#427`](https://github.com/simularium/simularium-viewer/pull/427) - remove pauseOn property [`#425`](https://github.com/simularium/simularium-viewer/pull/425) @@ -22,18 +84,28 @@ Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog). - Bump express from 4.19.2 to 4.21.0 in /examples [`#414`](https://github.com/simularium/simularium-viewer/pull/414) - remove unused references to colorchange interface [`#410`](https://github.com/simularium/simularium-viewer/pull/410) - code cleanup: dragAndDrop and JSON caching code [`#409`](https://github.com/simularium/simularium-viewer/pull/409) +- npm won't install anything until I bump ts-jest [`19fa8f6`](https://github.com/simularium/simularium-viewer/commit/19fa8f6ffdb2ad56fbcee70649098ef54ada4476) +- more package wrangling to fix tests (where was lodash?!) [`efa53fc`](https://github.com/simularium/simularium-viewer/commit/efa53fcf64e770c38fb036b1d5561c62450c8284) +- bump rimraf too, since it was complaining [`bce9f7e`](https://github.com/simularium/simularium-viewer/commit/bce9f7edc9762c10e9c321709d1751e871bf12e7) + +#### [v3.8.4](https://github.com/simularium/simularium-viewer/compare/v3.8.3...v3.8.4) + +> 22 August 2024 + - Feature/session colors [`#400`](https://github.com/simularium/simularium-viewer/pull/400) - export AgentData type properly from /types and / simularium [`#401`](https://github.com/simularium/simularium-viewer/pull/401) - Bump ws from 7.5.9 to 7.5.10 [`#399`](https://github.com/simularium/simularium-viewer/pull/399) - Bump braces from 3.0.2 to 3.0.3 in /examples [`#398`](https://github.com/simularium/simularium-viewer/pull/398) - Bump ws from 8.16.0 to 8.17.1 in /examples [`#397`](https://github.com/simularium/simularium-viewer/pull/397) - convert vis-type to visType at parse time [`#393`](https://github.com/simularium/simularium-viewer/pull/393) + +#### [v3.8.3](https://github.com/simularium/simularium-viewer/compare/v3.8.2...v3.8.3) + +> 13 June 2024 + - Fix/null agent function [`#396`](https://github.com/simularium/simularium-viewer/pull/396) - spread null agent object when parsing frames [`#395`](https://github.com/simularium/simularium-viewer/pull/395) - send selected agent data to front end [`#392`](https://github.com/simularium/simularium-viewer/pull/392) -- remove happy-dom [`a7ebd57`](https://github.com/simularium/simularium-viewer/commit/a7ebd57b262ad6222420a8960e169b85797a07aa) -- update package-lock [`f43acf6`](https://github.com/simularium/simularium-viewer/commit/f43acf604ea609c6b71d25ccecbad72844d6a241) -- update some test config [`7dde5d4`](https://github.com/simularium/simularium-viewer/commit/7dde5d4e209b5db30c66d7aa08de3e00bb691ba0) #### [v3.8.2](https://github.com/simularium/simularium-viewer/compare/v3.8.1...v3.8.2) @@ -41,12 +113,17 @@ Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog). - Fix/remove simularium engine specific code [`#391`](https://github.com/simularium/simularium-viewer/pull/391) -#### [v3.8.1](https://github.com/simularium/simularium-viewer/compare/v3.7.4...v3.8.1) +#### [v3.8.1](https://github.com/simularium/simularium-viewer/compare/v3.8.0...v3.8.1) > 3 June 2024 - With octopus, we can assume frame per message [`#390`](https://github.com/simularium/simularium-viewer/pull/390) - update cache setting [`#388`](https://github.com/simularium/simularium-viewer/pull/388) + +#### [v3.8.0](https://github.com/simularium/simularium-viewer/compare/v3.7.4...v3.8.0) + +> 23 May 2024 + - Fix/plotdata [`#386`](https://github.com/simularium/simularium-viewer/pull/386) - Feature/trim cache head [`#381`](https://github.com/simularium/simularium-viewer/pull/381) diff --git a/examples/package-lock.json b/examples/package-lock.json index bfdb1b95..bd7a8880 100644 --- a/examples/package-lock.json +++ b/examples/package-lock.json @@ -20,17 +20,18 @@ "css-loader": "^6.9.1", "html-webpack-plugin": "^5.6.0", "mini-css-extract-plugin": "^2.7.7", - "vite": "^6.2.5", + "vite": "^6.3.4", "webpack": "^5.95.0", "webpack-cli": "^5.1.4", - "webpack-dev-server": "^5.0.4" + "webpack-dev-server": "^5.2.1" } }, "..": { "name": "@aics/simularium-viewer", - "version": "3.9.1", + "version": "3.10.3", "license": "MIT", "dependencies": { + "@aics/vole-core": "^4.2.0", "@babel/plugin-transform-runtime": "^7.23.6", "@babel/runtime": "^7.23.6", "@fortawesome/fontawesome-free": "^5.15.2", @@ -62,7 +63,7 @@ "@types/lodash": "^4.14.175", "@types/react": "^18.2.46", "@types/react-dom": "^18.2.18", - 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"version": "5.1.0", - "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-5.1.0.tgz", - "integrity": "sha512-aQpaN81X6tXie1FoOB7xlMfCsN19pSvRAeYUHOdFWOlhpQ/LlbfTqYwwmEDFV0h8GGuqmCmKmT+pxcUV/Nt2gQ==", + "version": "5.2.1", + "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-5.2.1.tgz", + "integrity": "sha512-ml/0HIj9NLpVKOMq+SuBPLHcmbG+TGIjXRHsYfZwocUBIqEvws8NnS/V9AFQ5FKP+tgn5adwVwRrTEpGL33QFQ==", "dev": true, "license": "MIT", "dependencies": { "@types/bonjour": "^3.5.13", "@types/connect-history-api-fallback": "^1.5.4", "@types/express": "^4.17.21", + "@types/express-serve-static-core": "^4.17.21", "@types/serve-index": "^1.9.4", "@types/serve-static": "^1.15.5", "@types/sockjs": "^0.3.36", @@ -6059,10 +6193,9 @@ "colorette": "^2.0.10", "compression": "^1.7.4", "connect-history-api-fallback": "^2.0.0", - "express": "^4.19.2", + "express": "^4.21.2", "graceful-fs": "^4.2.6", - "html-entities": "^2.4.0", - "http-proxy-middleware": "^2.0.3", + "http-proxy-middleware": "^2.0.7", "ipaddr.js": "^2.1.0", "launch-editor": "^2.6.1", "open": "^10.0.3", @@ -6097,6 +6230,19 @@ } } }, + "node_modules/webpack-dev-server/node_modules/@types/express-serve-static-core": { + "version": "4.19.6", + "resolved": "https://registry.npmjs.org/@types/express-serve-static-core/-/express-serve-static-core-4.19.6.tgz", + "integrity": "sha512-N4LZ2xG7DatVqhCZzOGb1Yi5lMbXSZcmdLDe9EzSndPV2HpWYWzRbaerl2n27irrm94EPpprqa8KpskPT085+A==", + "dev": true, + "license": "MIT", + "dependencies": { + "@types/node": "*", + "@types/qs": "*", + "@types/range-parser": "*", + "@types/send": "*" + } + }, "node_modules/webpack-merge": { "version": "5.10.0", "resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-5.10.0.tgz", diff --git a/examples/package.json b/examples/package.json index b98edab4..96535e17 100644 --- a/examples/package.json +++ b/examples/package.json @@ -26,9 +26,9 @@ "css-loader": "^6.9.1", "html-webpack-plugin": "^5.6.0", "mini-css-extract-plugin": "^2.7.7", - "vite": "^6.2.5", + "vite": "^6.3.4", "webpack": "^5.95.0", "webpack-cli": "^5.1.4", - "webpack-dev-server": "^5.0.4" + "webpack-dev-server": "^5.2.1" } } diff --git a/examples/src/Viewer.tsx b/examples/src/Viewer.tsx index f5717a22..da2c8132 100644 --- a/examples/src/Viewer.tsx +++ b/examples/src/Viewer.tsx @@ -122,7 +122,7 @@ const initialState: ViewerState = { appliedColors: [], }, filePending: null, - selectedFile: "TEST_LIVEMODE_API", + selectedFile: "TEST_VOLUME", simulariumFile: null, clientSimulator: false, serverHealthy: false, @@ -650,7 +650,7 @@ class Viewer extends React.Component { case "TEST_METABALLS": config.clientSimulator = new MetaballSimulator(); break; - + case "TEST_VOLUME": config.clientSimulator = new VolumeSimulator(); break; diff --git a/examples/src/simulators/VolumeSimulator.ts b/examples/src/simulators/VolumeSimulator.ts index 68ab51af..72c86061 100644 --- a/examples/src/simulators/VolumeSimulator.ts +++ b/examples/src/simulators/VolumeSimulator.ts @@ -1,4 +1,5 @@ -import { GeometryDisplayType } from "../../../src"; +import { GeometryDisplayType } from "@aics/simularium-viewer"; +import "@aics/vole-core/es/workers/VolumeLoadWorker.js"; import { IClientSimulatorImpl, ClientMessageEnum, @@ -16,6 +17,7 @@ const DEGREES_TO_RADIANS = 3.14159265 / 180.0; export default class VolumeSim implements IClientSimulatorImpl { agentdata: number[]; size: [number, number, number]; + curFrame: number = 0; constructor() { this.agentdata = [ @@ -30,7 +32,11 @@ export default class VolumeSim implements IClientSimulatorImpl { 0, // ry 0, // rz 10.0, // collision radius - 0, // subpoints + 4, // subpoints + 0, + 0, + 1, + 2, // AGENT 2 (sphere, to test volume-mesh intersection) VisTypes.ID_VIS_TYPE_DEFAULT, // vis type @@ -38,17 +44,33 @@ export default class VolumeSim implements IClientSimulatorImpl { 1, // type 0, // x 0, // y - 6, // z + 3, // z 0, // rx 0, // ry 0, // rz - 5.0, // collision radius + 1.0, // collision radius 0, // subpoints ]; this.size = [25, 25, 25]; } + updateAgentPos(agentIndex: number, x: number, y: number, z: number) { + const OFFSET_TO_FIRST_AGENT = 15; + const baseIndex = OFFSET_TO_FIRST_AGENT + agentIndex * 11; + this.agentdata[baseIndex + 3] = x; + this.agentdata[baseIndex + 4] = y; + this.agentdata[baseIndex + 5] = z; + } + updateVolumeT(t: number) { + this.agentdata[11] = t; + } + update(_dt: number): VisDataMessage { + this.updateAgentPos(0, 0, 0, 3 * Math.sin(this.curFrame / 10)); + this.updateVolumeT(this.curFrame); + this.curFrame++; + // cycle 200 frames + this.curFrame = this.curFrame % 200; return { msgType: ClientMessageEnum.ID_VIS_DATA_ARRIVE, bundleStart: 0, @@ -56,8 +78,8 @@ export default class VolumeSim implements IClientSimulatorImpl { bundleData: [ { data: this.agentdata, - frameNumber: 0, - time: 0, + frameNumber: this.curFrame, + time: this.curFrame, // in seconds }, ], fileName: "hello world", @@ -69,7 +91,7 @@ export default class VolumeSim implements IClientSimulatorImpl { name: "volume", geometry: { displayType: GeometryDisplayType.VOLUME, - url: "https://animatedcell-test-data.s3.us-west-2.amazonaws.com/variance/1.zarr", + url: "https://s3.us-west-2.amazonaws.com/production.files.allencell.org/982/70e/0ba/ecd/e7a/06a/e41/de6/29a/1af/30/3500007062_20250207_20X_Timelapse-01(P17-G3).ome.zarr", color: "ffff00", }, }, diff --git a/examples/vite.config.ts b/examples/vite.config.ts index 3396521d..36d6a04f 100644 --- a/examples/vite.config.ts +++ b/examples/vite.config.ts @@ -16,7 +16,19 @@ export default { }, }, optimizeDeps: { - include: [], + // vole-core uses a worker imported via local import (e.g. new + // URL('./local-worker.js', import.meta.url)). If vite bundles the worker, + // vole-core will not be able to find it at runtime. We exclude vole-core + // from dependency optimization here. + exclude: ["@aics/vole-core"], + // Have to still optimize all CommonJS dependencies of vole-core. See + // https://vite.dev/config/dep-optimization-options#optimizedeps-exclude + include: [ + "@aics/vole-core > tweakpane", + "@aics/vole-core > geotiff", + "@aics/vole-core > numcodecs", + "@aics/vole-core > throttled-queue", + ], }, server: { open: "examples/src/index.html", @@ -25,4 +37,4 @@ export default { allow: [".."], }, }, -} satisfies UserConfig; \ No newline at end of file +} satisfies UserConfig; diff --git a/package-lock.json b/package-lock.json index d7ede979..da5291ca 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,15 +1,15 @@ { "name": "@aics/simularium-viewer", - "version": "3.9.1", + "version": "3.10.3", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@aics/simularium-viewer", - "version": "3.9.1", + "version": "3.10.3", "license": "MIT", "dependencies": { - "@aics/volume-viewer": "^3.12.2", + "@aics/vole-core": "^4.2.0", "@babel/plugin-transform-runtime": "^7.23.6", "@babel/runtime": "^7.23.6", "@fortawesome/fontawesome-free": "^5.15.2", @@ -41,7 +41,7 @@ "@types/lodash": "^4.14.175", "@types/react": "^18.2.46", "@types/react-dom": "^18.2.18", - "@types/three": "^0.170.0", + "@types/three": "^0.171.0", "@typescript-eslint/eslint-plugin": "~8.15.0", "@typescript-eslint/parser": "~8.15.0", "@vitest/coverage-v8": "^2.1.5", @@ -77,27 +77,21 @@ "react-dom": "^18.2.0" } }, - "node_modules/@aics/volume-viewer": { - "version": "3.12.2", - "resolved": "https://registry.npmjs.org/@aics/volume-viewer/-/volume-viewer-3.12.2.tgz", - "integrity": "sha512-YRL7gYqQcjiudaHyFXPyCqPMKZkUq+pJ4gXTlgEwcNV2ozLei8/xMlJdi6bmvPTDbTyeii2N3mgsJZT2dGXkqw==", + "node_modules/@aics/vole-core": { + "version": "4.2.0", + "resolved": "https://registry.npmjs.org/@aics/vole-core/-/vole-core-4.2.0.tgz", + "integrity": "sha512-UEcQIPWbxi7k592FPW9JJPwMU8Wbj2BLDiGz+ByrMvc4P08sEMMyTtxplOLjgDysKN+gk53AkWp05TQ/4VTVLg==", "license": "MIT", "dependencies": { "@babel/runtime": "^7.25.6", "geotiff": "^2.0.5", "serialize-error": "^11.0.3", - "three": "^0.162.0", + "three": "^0.171.0", "throttled-queue": "^2.1.4", "tweakpane": "^3.1.9", - "zarrita": "^0.3.2" + "zarrita": "^0.5.1" } }, - 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"engines": { - "node": ">=12" + "dependencies": { + "fflate": "^0.8.0" } }, "node_modules/nwsapi": { @@ -10127,9 +10151,9 @@ } }, "node_modules/parse-headers": { - "version": "2.0.5", - "resolved": "https://registry.npmjs.org/parse-headers/-/parse-headers-2.0.5.tgz", - "integrity": "sha512-ft3iAoLOB/MlwbNXgzy43SWGP6sQki2jQvAyBg/zDFAgr9bfNWZIUj42Kw2eJIl8kEi4PbgE6U1Zau/HwI75HA==", + "version": "2.0.6", + "resolved": "https://registry.npmjs.org/parse-headers/-/parse-headers-2.0.6.tgz", + "integrity": "sha512-Tz11t3uKztEW5FEVZnj1ox8GKblWn+PvHY9TmJV5Mll2uHEwRdR/5Li1OlXoECjLYkApdhWy44ocONwXLiKO5A==", "license": "MIT" }, "node_modules/parse-json": { @@ -13930,9 +13954,9 @@ } }, "node_modules/vite": { - "version": "5.4.14", - "resolved": "https://registry.npmjs.org/vite/-/vite-5.4.14.tgz", - "integrity": "sha512-EK5cY7Q1D8JNhSaPKVK4pwBFvaTmZxEnoKXLG/U9gmdDcihQGNzFlgIvaxezFR4glP1LsuiedwMBqCXH3wZccA==", + "version": "5.4.19", + "resolved": "https://registry.npmjs.org/vite/-/vite-5.4.19.tgz", + "integrity": "sha512-qO3aKv3HoQC8QKiNSTuUM1l9o/XX3+c+VTgLHbJWHZGeTPVAg2XwazI9UWzoxjIJCGCV2zU60uqMzjeLZuULqA==", "dev": true, "license": "MIT", "dependencies": { @@ -14146,9 +14170,9 @@ } }, "node_modules/web-worker": { - 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"version": "0.3.2", - "resolved": "https://registry.npmjs.org/zarrita/-/zarrita-0.3.2.tgz", - "integrity": "sha512-Zx9nS28C2tXZhF1BmQkgQGi0M/Z5JiM/KCMa+fEYtr/MnIzyizR4sKRA/sXjDP1iuylILWTJAWWBJD//0ONXCA==", + "version": "0.5.3", + "resolved": "https://registry.npmjs.org/zarrita/-/zarrita-0.5.3.tgz", + "integrity": "sha512-to2JRq9nHwYdhWEwJwytHYdMYC6I0f2vKUAQfYkgrwwy8OjShhwmv4sH9drzyV3sLzdy7XS9N1ipdMA/Qjspow==", + "license": "MIT", "dependencies": { - "@zarrita/core": "^0.0.3", - "@zarrita/indexing": "^0.0.3", - "@zarrita/storage": "^0.0.2" + "@zarrita/storage": "^0.1.2", + "numcodecs": "^0.3.2" } }, "node_modules/zstddec": { diff --git a/package.json b/package.json index 6d8b1d83..d67aaf92 100644 --- a/package.json +++ b/package.json @@ -1,13 +1,13 @@ { "name": "@aics/simularium-viewer", - "version": "3.9.1", + "version": "3.10.3", "description": "An npm package to view simulations.", "main": "es/index.js", "type": "module", "module": "es/index.js", "types": "type-declarations", "scripts": { - "start": "run-p 'processCSS -- --watch' 'transpileES -- --watch' 'generateTypes -- --watch' serve-example", + "start": "npm run run-p 'processCSS -- --watch' 'transpileES -- --watch' 'generateTypes -- --watch' serve-example", "dev": "npm install && npm run build && npm run install-examples && npm run start", "serve-example": "cd examples && npm run serve-example", "install-examples": "npm install && cd examples && npm install", @@ -15,7 +15,7 @@ "generateTypes": "tsc -p tsconfig.base.json --emitDeclarationOnly", "transpileES": "cross-env TS_NODE_PROJECT=tsconfig.es.json BABEL_ENV=es babel src --out-dir es --extensions .ts,.tsx,.js,.jsx --ignore 'src/test'", "processCSS": "postcss src/viewport/index.css --output es/style/style.css", - "copy-build": "copyfiles 'es/**/*' style/* 'type-declarations/**/*' package.json README.md dev-build", + "copy-build": "copyfiles 'es/**/*' 'type-declarations/**/*' package.json README.md dev-build", "gh-build": "npm run processCSS && cd examples && npm run build-example", "lint": "eslint src/**", "test": "vitest run", @@ -28,7 +28,6 @@ }, "files": [ "es", - "style", "type-declarations", "README.md", "package.json" @@ -41,6 +40,15 @@ "type": "git", "url": "https://github.com/simularium/simularium-viewer.git" }, + "exports": { + "./style/style.css": "./es/style/style.css", + ".": { + "import": { + "types": "./type-declarations/index.d.ts", + "default": "./es/index.js" + } + } + }, "author": "", "license": "MIT", "devDependencies": { @@ -57,7 +65,7 @@ "@types/lodash": "^4.14.175", "@types/react": "^18.2.46", "@types/react-dom": "^18.2.18", - "@types/three": "^0.170.0", + "@types/three": "^0.171.0", "@typescript-eslint/eslint-plugin": "~8.15.0", "@typescript-eslint/parser": "~8.15.0", "@vitest/coverage-v8": "^2.1.5", @@ -93,7 +101,7 @@ "react-dom": "^18.2.0" }, "dependencies": { - "@aics/volume-viewer": "^3.12.2", + "@aics/vole-core": "^4.2.0", "@babel/plugin-transform-runtime": "^7.23.6", "@babel/runtime": "^7.23.6", "@fortawesome/fontawesome-free": "^5.15.2", diff --git a/src/simularium/VisData.ts b/src/simularium/VisData.ts index faafd3a3..d9616207 100644 --- a/src/simularium/VisData.ts +++ b/src/simularium/VisData.ts @@ -24,7 +24,7 @@ class VisData { const intView = new Uint32Array(data); const frameData: CachedFrame = { data: data, - frameNumber: floatView[0], + frameNumber: intView[0], time: floatView[1], agentCount: intView[2], size: 0, diff --git a/src/visGeometry/GeometryStore.ts b/src/visGeometry/GeometryStore.ts index 0543b49f..b66eaab8 100644 --- a/src/visGeometry/GeometryStore.ts +++ b/src/visGeometry/GeometryStore.ts @@ -1,7 +1,7 @@ import { forEach } from "lodash"; import { OBJLoader } from "three/examples/jsm/loaders/OBJLoader.js"; import jsLogger, { ILogger, ILogLevel } from "js-logger"; -import { createVolumeLoader, LoadSpec } from "@aics/volume-viewer"; +import { LoadSpec, VolumeLoaderContext } from "@aics/vole-core"; import { BufferGeometry, Object3D, @@ -50,6 +50,7 @@ class GeometryStore { private _geoLoadAttempted: Map; private _cachedAssets: Map; private _registry: Registry; + private volumeLoaderContext?: VolumeLoaderContext; public mlogger: ILogger; public static sphereGeometry: SphereGeometry = new SphereGeometry( 1, @@ -77,6 +78,18 @@ class GeometryStore { return true; }; + private static getPdbUrlFromSanitizedPdbId = ( + pdbId: string, + isCif: boolean + ) => { + // Note: pdbId will have a leading backslash, which was prepended + // in checkAndSanitizePath + if (isCif) { + return `https://files.rcsb.org/download${pdbId}-assembly1.cif`; + } + return `https://files.rcsb.org/download${pdbId}.pdb1`; + }; + constructor(loggerLevel?: ILogLevel) { this._geoLoadAttempted = new Map(); this._cachedAssets = new Map(); @@ -227,47 +240,54 @@ class GeometryStore { // TODO: // Can we confirm that the rcsb.org servers have every id as a cif file? // If so, then we don't need to do this second try and we can always use .cif. - actualUrl = `https://files.rcsb.org/download/${pdbID}-assembly1.cif`; - } - - let data: string; - const response = await fetch(actualUrl); - if (response.ok) { - data = await response.text(); - } else if (pdbID) { - // try again as pdb - actualUrl = `https://files.rcsb.org/download/${pdbID}.pdb1`; - const response = await fetch(actualUrl); - if (!response.ok) { - // error will be caught by the function that calls this - throw new Error( - `Failed to fetch ${pdbModel.filePath} from ${actualUrl}` - ); - } - data = await response.text(); - } else { - // error will be caught by function that calls this - throw new Error(`Failed to fetch ${pdbModel.filePath} from ${url}`); - } - - if (pdbModel.cancelled) { - this._registry.delete(url); - return undefined; - } - pdbModel.parse(data, getFileExtension(actualUrl)); - const pdbEntry = this._registry.get(url); - if (pdbEntry && pdbEntry.geometry === pdbModel) { - this.mlogger.info("Finished downloading pdb: ", url); - return pdbModel; - } else { - // This seems like some kind of terrible error if we get here. - // Alternatively, we could try re-adding the registry entry. - // Or reject. - this.mlogger.warn( - `After download, GeometryStore PDB entry not found for ${url}` - ); - return undefined; + actualUrl = GeometryStore.getPdbUrlFromSanitizedPdbId(pdbID, true); } + return fetch(actualUrl) + .then((response) => { + if (response.ok) { + return response.text(); + } else if (pdbID) { + // try again as pdb + actualUrl = GeometryStore.getPdbUrlFromSanitizedPdbId( + pdbID, + false + ); + return fetch(actualUrl).then((response) => { + if (!response.ok) { + // error will be caught by the function that calls this + throw new Error( + `Failed to fetch ${pdbModel.filePath} from ${actualUrl}` + ); + } + return response.text(); + }); + } else { + // error will be caught by function that calls this + throw new Error( + `Failed to fetch ${pdbModel.filePath} from ${url}` + ); + } + }) + .then((data) => { + if (pdbModel.cancelled) { + this._registry.delete(url); + return Promise.resolve(undefined); + } + pdbModel.parse(data, getFileExtension(actualUrl)); + const pdbEntry = this._registry.get(url); + if (pdbEntry && pdbEntry.geometry === pdbModel) { + this.mlogger.info("Finished downloading pdb: ", url); + return pdbModel; + } else { + // This seems like some kind of terrible error if we get here. + // Alternatively, we could try re-adding the registry entry. + // Or reject. + this.mlogger.warn( + `After download, GeometryStore PDB entry not found for ${url}` + ); + return Promise.resolve(undefined); + } + }); } private prepMeshRegistryForNewObj(meshName: string): void { @@ -384,15 +404,29 @@ class GeometryStore { }); } + /** Don't start a volume load worker until we know we need it */ + private async getVolumeLoaderContext(): Promise { + if (!this.volumeLoaderContext) { + // TODO this is missing optional config properties: + // `maxCacheSize`, `maxActiveRequests`, `maxLowPriorityRequests`. + // Do we want to set our own values for these? + this.volumeLoaderContext = new VolumeLoaderContext(); + await this.volumeLoaderContext.onOpen(); + } + return this.volumeLoaderContext; + } + private async fetchVolume(url: string): Promise { // TODO should this be in a worker? Are we already in a worker here? // Should this class get a `VolumeLoaderContext` going? const model = new VolumeModel(); this.setGeometryInRegistry(url, model, GeometryDisplayType.VOLUME); - const loader = await createVolumeLoader(url); - // TODO onChannelLoaded callback? - const volume = await loader.createVolume(new LoadSpec()); + const context = await this.getVolumeLoaderContext(); + const loader = await context.createLoader(url); + const loadCallback = model.onChannelLoaded.bind(model); + const volume = await loader.createVolume(new LoadSpec(), loadCallback); model.setImage(volume); + model.loadInitialData(); return model; } diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index 7d3a84a2..ca0a4083 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -1,40 +1,147 @@ -import { Box3Helper, Euler, Object3D, Vector3 } from "three"; +import { + Euler, + Object3D, + OrthographicCamera, + PerspectiveCamera, + Vector3, + WebGLRenderer, +} from "three"; -import { Volume, VolumeDrawable } from "@aics/volume-viewer"; +import { Lut, Volume, VolumeDrawable } from "@aics/vole-core"; import { AgentData } from "../simularium/types"; -// TEMPORARY HACK to make things typecheck. TODO remove! -import { VolumeRenderImpl } from "@aics/volume-viewer/es/types/VolumeRenderImpl"; -interface TempRayMarchedVolume extends VolumeRenderImpl { - boxHelper: Box3Helper; -} - export default class VolumeModel { // TODO what to do with this `cancelled` property? Type check fails without it. // When should it be set, if ever; what should it be used for, if anything? public cancelled = false; - private image?: VolumeDrawable; + private drawable?: VolumeDrawable; + private volume?: Volume; + private channelsEnabled: boolean[] = []; + private scale = 1; + + private setEnabledChannels(channels: number[]): void { + if (!this.volume || !this.drawable) { + this.channelsEnabled = []; + return; + } + const { numChannels } = this.volume.imageInfo; + this.channelsEnabled = new Array(numChannels).fill(false); + + for (const channel of channels) { + if (channel < numChannels) { + this.channelsEnabled[channel] = true; + } + } + + for (const [channelIndex, enabled] of this.channelsEnabled.entries()) { + this.drawable.setVolumeChannelEnabled(channelIndex, enabled); + } + } public setImage(volumeObject: Volume): void { - this.image = new VolumeDrawable(volumeObject, {}); + this.volume = volumeObject; + this.drawable = new VolumeDrawable(this.volume, {}); + this.volume.addVolumeDataObserver(this); + this.drawable.setBrightness(0.5); + this.drawable.setGamma(0.15, 0.9, 1.0); + this.drawable.setDensity(0.1); } public setAgentData(data: AgentData): void { - if (this.image) { - this.image.setTranslation(new Vector3(data.x, data.y, data.z)); - this.image.setRotation(new Euler(data.xrot, data.yrot, data.zrot)); - const r = data.cr * 2; - this.image.setScale(new Vector3(r, r, r)); + if (this.drawable) { + this.drawable.setTranslation(new Vector3(data.x, data.y, data.z)); + this.drawable.setRotation( + new Euler(data.xrot, data.yrot, data.zrot) + ); + this.scale = data.cr * 2; + this.drawable.setScale( + new Vector3(this.scale, this.scale, this.scale) + ); + // Always defined if `drawable` is, but ts doesn't know that. + if (this.volume) { + // Volume agent data may use subpoint 0 as time + const numPoints = data.subpoints.length; + const time = numPoints > 0 ? data.subpoints[0] : 0; + if (this.volume.loadSpec.time !== time) { + console.log(`Updating volume to time ${time}`); + this.volume.updateRequiredData({ time }); + } + // If there are more subpoints, they are enabled channel idxes. + // Otherwise, just channel 0 is enabled. + const channels = numPoints > 1 ? data.subpoints.slice(1) : [0]; + this.setEnabledChannels(channels); + } } } + public loadInitialData(): void { + this.volume?.loader?.loadVolumeData(this.volume); + } + public getObject3D(): Object3D | undefined { - return this.image?.sceneRoot; + return this.drawable?.sceneRoot; + } + + public onChannelLoaded(_vol: Volume, channelIndex: number): void { + if (this.drawable) { + const isEnabled = this.channelsEnabled[channelIndex]; + this.drawable.setVolumeChannelEnabled(channelIndex, isEnabled); + this.drawable.updateScale(); + this.drawable.onChannelLoaded([channelIndex]); + if (this.volume) { + const histo = this.volume.getHistogram(channelIndex); + const min = histo.findBinOfPercentile(0.5); + const max = histo.findBinOfPercentile(0.983); + const lut = new Lut().createFromMinMax(min, max); + this.volume.setLut(channelIndex, lut); + } + this.drawable.updateLuts(); + this.drawable.fuse(); + } + } + + public setViewportSize( + width: number, + height: number, + orthoScale?: number + ): void { + if (this.drawable) { + const isOrtho = orthoScale !== undefined; + this.drawable.setIsOrtho(isOrtho); + if (isOrtho) { + this.drawable.setOrthoScale(orthoScale); + } + this.drawable.setResolution(width, height); + } + } + + public onBeforeRender( + renderer: WebGLRenderer, + camera: PerspectiveCamera | OrthographicCamera + ): void { + this.drawable?.onAnimate(renderer, camera, undefined); + } + + public setSize(width: number, height: number): void { + this.drawable?.setResolution(width, height); + } + + // METHODS FROM `VolumeDataObserver` in volume-viewer + + public onVolumeData(_volume: Volume, channels: number[]): void { + this.drawable?.updateScale(); + this.drawable?.onChannelLoaded(channels); + } + + public onVolumeChannelAdded( + _volume: Volume, + newChannelIndex: number + ): void { + this.drawable?.onChannelAdded(newChannelIndex); } - public tempGetBoundingBoxObject(): Box3Helper | undefined { - this.image?.setShowBoundingBox(true); - return (this.image?.volumeRendering as TempRayMarchedVolume)?.boxHelper; + public onVolumeLoadError(_volume: Volume, error: unknown): void { + console.error("Volume load error", error); } } diff --git a/src/visGeometry/index.ts b/src/visGeometry/index.ts index 2b639c26..5417ca2a 100644 --- a/src/visGeometry/index.ts +++ b/src/visGeometry/index.ts @@ -126,6 +126,11 @@ function removeByName(group: Group, name: string): void { const coordsToVector = ({ x, y, z }: Coordinates3d) => new Vector3(x, y, z); +export const isOrthographicCamera = ( + def: PerspectiveCamera | OrthographicCamera +): def is OrthographicCamera => + def && !!(def as OrthographicCamera).isOrthographicCamera; + type Bounds = readonly [number, number, number, number, number, number]; class VisGeometry { @@ -177,7 +182,7 @@ class VisGeometry { public lightsGroup: Group; public agentPathGroup: Group; public instancedMeshGroup: Group; - public tempVolumeGroup: Group; // TODO remove + public volumeGroup: Group; // TODO remove private supportsWebGL2Rendering: boolean; private lodBias: number; private lodDistanceStops: number[]; @@ -245,9 +250,9 @@ class VisGeometry { this.instancedMeshGroup = new Group(); this.instancedMeshGroup.name = "instanced meshes for agents"; this.scene.add(this.instancedMeshGroup); - this.tempVolumeGroup = new Group(); - this.tempVolumeGroup.name = "volumes"; - this.scene.add(this.tempVolumeGroup); + this.volumeGroup = new Group(); + this.volumeGroup.name = "volumes"; + this.scene.add(this.volumeGroup); this.showBounds = true; this.resetBounds(DEFAULT_VOLUME_DIMENSIONS); @@ -1030,10 +1035,13 @@ class VisGeometry { for (let i = this.instancedMeshGroup.children.length - 1; i >= 0; i--) { this.instancedMeshGroup.remove(this.instancedMeshGroup.children[i]); } - for (let i = this.tempVolumeGroup.children.length - 1; i >= 0; i--) { - this.tempVolumeGroup.remove(this.tempVolumeGroup.children[i]); + for (let i = this.volumeGroup.children.length - 1; i >= 0; i--) { + this.volumeGroup.remove(this.volumeGroup.children[i]); } + const canvasWidth = this.threejsrenderer.domElement.width; + const canvasHeight = this.threejsrenderer.domElement.height; + // re-add fibers immediately this.instancedMeshGroup.add(this.fibers.getGroup()); @@ -1060,9 +1068,21 @@ class VisGeometry { } } } else if (displayType === GeometryDisplayType.VOLUME) { - const volObject = entry.geometry.tempGetBoundingBoxObject(); - if (volObject) { - this.tempVolumeGroup.add(volObject); + const volObj = entry.geometry.getObject3D(); + if (volObj) { + const orthoScale = isOrthographicCamera(this.camera) + ? this.camera.top / this.camera.zoom + : undefined; + entry.geometry.setViewportSize( + canvasWidth, + canvasHeight, + orthoScale + ); + entry.geometry.onBeforeRender( + this.threejsrenderer, + this.camera + ); + this.volumeGroup.add(volObj); } } else { const meshEntry = entry as MeshGeometry; @@ -1095,7 +1115,7 @@ class VisGeometry { this.boundingBoxMesh.visible = false; this.tickMarksMesh.visible = false; this.agentPathGroup.visible = false; - this.tempVolumeGroup.visible = false; + this.volumeGroup.visible = false; this.renderer.render( this.threejsrenderer, this.scene, @@ -1107,7 +1127,7 @@ class VisGeometry { this.boundingBoxMesh.visible = this.showBounds; this.tickMarksMesh.visible = this.showBounds; this.agentPathGroup.visible = true; - this.tempVolumeGroup.visible = true; + this.volumeGroup.visible = true; this.threejsrenderer.autoClear = false; // hide everything except the wireframe and paths, and render with the standard renderer @@ -1908,6 +1928,8 @@ class VisGeometry { } public clearForNewTrajectory(): void { + // only gets called by the parent app by calling + // clearFile on the controller this.legacyRenderer.beginUpdate(this.scene); this.legacyRenderer.endUpdate(this.scene); this.resetMapping(); @@ -1916,7 +1938,7 @@ class VisGeometry { this.visAgentInstances.clear(); this.visAgents = []; this.currentSceneData = nullCachedFrame(); - + this.availableAgentPool = []; this.dehighlight(); }