From bddee441c90d6eacf9d7a5bbf1326c2efc29baca Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Thu, 19 Sep 2024 18:30:30 -0700 Subject: [PATCH 01/18] add volume-viewer as file dependency --- package-lock.json | 58 +++++++++++++++++++++++++++++++++++++++++++++++ package.json | 1 + 2 files changed, 59 insertions(+) diff --git a/package-lock.json b/package-lock.json index 574241dc..b91d49fb 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,6 +9,7 @@ "version": "3.8.4", "license": "MIT", "dependencies": { + "@aics/volume-viewer": "file:../volume-viewer", "@babel/plugin-transform-runtime": "^7.23.6", "@babel/runtime": "^7.23.6", "@fortawesome/fontawesome-free": "^5.15.2", @@ -74,6 +75,59 @@ "react-dom": "^18.2.0" } }, + "../volume-viewer": { + "version": "3.11.1", + "license": "MIT", + "dependencies": { + "geotiff": "^2.0.5", + "serialize-error": "^11.0.3", + "three": "^0.144.0", + "tweakpane": "^3.1.9", + "zarrita": "^0.3.2" + }, + "devDependencies": { + "@babel/cli": "^7.14.8", + "@babel/core": "^7.14.8", + "@babel/preset-react": "^7.14.5", + "@babel/preset-typescript": "^7.14.5", + "@babel/register": "^7.14.5", + "@tweakpane/core": "^1.1.9", + "@types/chai": "^4.3.12", + "@types/mocha": "^9.1.1", + "@types/three": "^0.144.0", + "@typescript-eslint/eslint-plugin": "^5.30.5", + "@typescript-eslint/parser": "^5.30.5", + "acorn": "^8.7.0", + "babel-loader": "^8.2.2", + "babel-plugin-inline-import": "^3.0.0", + "babel-plugin-inline-import-data-uri": "^1.0.1", + "chai": "^5.1.0", + "clean-webpack-plugin": "^4.0.0-alpha.0", + "copy-webpack-plugin": "^9.0.1", + "cross-env": "^7.0.3", + "documentation": "^14.0.0", + "eslint": "^8.19.0", + "eslint-config-prettier": "^8.5.0", + "eslint-plugin-react": "^7.30.1", + "file-loader": "^6.2.0", + "html-webpack-plugin": "^5.3.2", + "husky": "^7.0.1", + "lil-gui": "^0.19.2", + "lint-staged": "^13.2.1", + "mocha": "^10.3.0", + "prettier": "^2.3.2", + "raw-loader": "^4.0.2", + "react": "^16.14.0", + "react-dom": "^16.14.0", + "rimraf": "^3.0.2", + "ts-node": "^10.9.2", + "typescript": "^4.3.5", + "url-loader": "^4.1.1", + "webpack": "^5.69.1", + "webpack-cli": "^4.9.2", + "webpack-dev-server": "^4.7.4" + } + }, "node_modules/@aashutoshrathi/word-wrap": { "version": "1.2.6", "resolved": "https://registry.npmjs.org/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz", @@ -83,6 +137,10 @@ "node": ">=0.10.0" } }, + "node_modules/@aics/volume-viewer": { + "resolved": "../volume-viewer", + "link": true + }, "node_modules/@ampproject/remapping": { "version": "2.3.0", "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz", diff --git a/package.json b/package.json index c71bebfc..8ce40e65 100644 --- a/package.json +++ b/package.json @@ -87,6 +87,7 @@ "react-dom": "^18.2.0" }, "dependencies": { + "@aics/volume-viewer": "file:../volume-viewer", "@babel/plugin-transform-runtime": "^7.23.6", "@babel/runtime": "^7.23.6", "@fortawesome/fontawesome-free": "^5.15.2", From 8c1d6daee591ed7434c2ee0f16b4f4ee83742395 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Thu, 19 Sep 2024 18:32:09 -0700 Subject: [PATCH 02/18] add volume types w/ basic loading code --- src/visGeometry/GeometryStore.ts | 18 ++++++++++++++++-- src/visGeometry/VolumeModel.ts | 7 +++++++ src/visGeometry/types.ts | 11 +++++++++-- 3 files changed, 32 insertions(+), 4 deletions(-) create mode 100644 src/visGeometry/VolumeModel.ts diff --git a/src/visGeometry/GeometryStore.ts b/src/visGeometry/GeometryStore.ts index ed819389..349c8de5 100644 --- a/src/visGeometry/GeometryStore.ts +++ b/src/visGeometry/GeometryStore.ts @@ -1,6 +1,7 @@ import { forEach } from "lodash"; import { OBJLoader } from "three/examples/jsm/loaders/OBJLoader"; import jsLogger, { ILogger, ILogLevel } from "js-logger"; +import { createVolumeLoader, LoadSpec } from "@aics/volume-viewer"; import { BufferGeometry, Object3D, @@ -23,6 +24,7 @@ import { MeshLoadRequest, } from "./types"; import { MetaballMesh } from "./rendering/MetaballMesh"; +import VolumeModel from "./VolumeModel"; export const DEFAULT_MESH_NAME = "SPHERE"; @@ -68,7 +70,8 @@ class GeometryStore { } if ( displayType === GeometryDisplayType.PDB || - displayType === GeometryDisplayType.OBJ + displayType === GeometryDisplayType.OBJ || + displayType === GeometryDisplayType.VOLUME ) { return false; } @@ -379,6 +382,15 @@ class GeometryStore { }); } + 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 loader = await createVolumeLoader(url); + // TODO onChannelLoaded callback? + const volume = await loader.createVolume(new LoadSpec()); + return new VolumeModel(volume); + } + /** * Load new geometry if necessary, ie this geometry hasn't already * been loaded or attempted and failed to be loaded. @@ -393,7 +405,7 @@ class GeometryStore { private async attemptToLoadGeometry( urlOrPath: string, displayType: GeometryDisplayType - ): Promise { + ): Promise { if (this._cachedAssets.has(urlOrPath)) { // if it's in the cached assets, parse the data // store it in the registry, and return it @@ -432,6 +444,8 @@ class GeometryStore { return await this.fetchPdb(urlOrPath); case GeometryDisplayType.OBJ: return await this.fetchObj(urlOrPath); + case GeometryDisplayType.VOLUME: + return await this.fetchVolume(urlOrPath); default: // will replace geom in registry is sphere throw new Error( diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts new file mode 100644 index 00000000..9354613a --- /dev/null +++ b/src/visGeometry/VolumeModel.ts @@ -0,0 +1,7 @@ +import { Volume } from "@aics/volume-viewer"; + +export default class VolumeModel { + // TODO what to do with this? + public cancelled = false; + constructor(private volume: Volume) {} +} diff --git a/src/visGeometry/types.ts b/src/visGeometry/types.ts index 3eb61f68..29d3a93d 100644 --- a/src/visGeometry/types.ts +++ b/src/visGeometry/types.ts @@ -1,6 +1,7 @@ import { BufferGeometry, Color, Object3D } from "three"; import PDBModel from "./PDBModel"; import { MRTShaders } from "./rendering/MultipassMaterials"; +import VolumeModel from "./VolumeModel"; export interface GeometryInstanceContainer { replaceGeometry: (newGeometry: BufferGeometry, name: string) => void; @@ -35,6 +36,7 @@ export enum GeometryDisplayType { OBJ = "OBJ", SPHERE = "SPHERE", CUBE = "CUBE", + VOLUME = "VOLUME", GIZMO = "GIZMO", SPHERE_GROUP = "SPHERE_GROUP", } @@ -57,11 +59,16 @@ export interface MeshGeometry { | PrimitiveDisplayType; } -export type AgentGeometry = PDBGeometry | MeshGeometry; +export interface VolumeGeometry { + geometry: VolumeModel; + displayType: GeometryDisplayType.VOLUME; +} + +export type AgentGeometry = PDBGeometry | MeshGeometry | VolumeGeometry; export interface GeometryStoreLoadResponse { displayType?: GeometryDisplayType; - geometry: MeshLoadRequest | PDBModel; + geometry: MeshLoadRequest | PDBModel | VolumeModel; errorMessage?: string; } From 47cd0283f9e36441dd149e7a2fb828a2e625a87a Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Mon, 23 Sep 2024 08:34:05 -0700 Subject: [PATCH 03/18] update typescript --- package-lock.json | 12 +++++++----- package.json | 2 +- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/package-lock.json b/package-lock.json index b91d49fb..db79aebd 100644 --- a/package-lock.json +++ b/package-lock.json @@ -68,7 +68,7 @@ "rimraf": "~2.6", "ts-jest": "27.1", "ts-node": "~10.1.0", - "typescript": "~4.3.5" + "typescript": "^5.6.2" }, "peerDependencies": { "react": "^18.2.0", @@ -76,6 +76,7 @@ } }, "../volume-viewer": { + "name": "@aics/volume-viewer", "version": "3.11.1", "license": "MIT", "dependencies": { @@ -16069,16 +16070,17 @@ } }, "node_modules/typescript": { - "version": "4.3.5", - "resolved": "https://registry.npmjs.org/typescript/-/typescript-4.3.5.tgz", - "integrity": "sha512-DqQgihaQ9cUrskJo9kIyW/+g0Vxsk8cDtZ52a3NGh0YNTfpUSArXSohyUGnvbPazEPLu398C0UxmKSOrPumUzA==", + "version": "5.6.2", + "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.6.2.tgz", + "integrity": "sha512-NW8ByodCSNCwZeghjN3o+JX5OFH0Ojg6sadjEKY4huZ52TqbJTJnDo5+Tw98lSy63NZvi4n+ez5m2u5d4PkZyw==", "dev": true, + "license": "Apache-2.0", "bin": { "tsc": "bin/tsc", "tsserver": "bin/tsserver" }, "engines": { - "node": ">=4.2.0" + "node": ">=14.17" } }, "node_modules/uglify-js": { diff --git a/package.json b/package.json index 8ce40e65..f8b5c4db 100644 --- a/package.json +++ b/package.json @@ -80,7 +80,7 @@ "rimraf": "~2.6", "ts-jest": "27.1", "ts-node": "~10.1.0", - "typescript": "~4.3.5" + "typescript": "^5.6.2" }, "peerDependencies": { "react": "^18.2.0", From 75c8a3fdc8f3944b3934200f498cc383fc45ba88 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Tue, 24 Sep 2024 10:30:50 -0700 Subject: [PATCH 04/18] `VolumeSimulator` uses vol type, loads data --- examples/src/simulators/VolumeSimulator.ts | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/examples/src/simulators/VolumeSimulator.ts b/examples/src/simulators/VolumeSimulator.ts index 0542f785..68ab51af 100644 --- a/examples/src/simulators/VolumeSimulator.ts +++ b/examples/src/simulators/VolumeSimulator.ts @@ -68,9 +68,8 @@ export default class VolumeSim implements IClientSimulatorImpl { [0]: { name: "volume", geometry: { - // TODO swap with volume display type when available - displayType: GeometryDisplayType.SPHERE, - url: "", + displayType: GeometryDisplayType.VOLUME, + url: "https://animatedcell-test-data.s3.us-west-2.amazonaws.com/variance/1.zarr", color: "ffff00", }, }, From b24cadee2fba5a7e17f2ff6415e13bc341bbf87f Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Tue, 24 Sep 2024 10:33:46 -0700 Subject: [PATCH 05/18] put models in geo registry properly --- src/visGeometry/GeometryStore.ts | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/src/visGeometry/GeometryStore.ts b/src/visGeometry/GeometryStore.ts index 349c8de5..a0765ab4 100644 --- a/src/visGeometry/GeometryStore.ts +++ b/src/visGeometry/GeometryStore.ts @@ -127,7 +127,10 @@ class GeometryStore { // forEach method for manipulating ThreeJs Mesh objects this._registry.forEach((value) => { const { displayType } = value; - if (displayType !== GeometryDisplayType.PDB) { + if ( + displayType !== GeometryDisplayType.PDB && + displayType !== GeometryDisplayType.VOLUME + ) { const agentGeo = value as MeshGeometry; iteratee(agentGeo); } @@ -388,7 +391,9 @@ class GeometryStore { const loader = await createVolumeLoader(url); // TODO onChannelLoaded callback? const volume = await loader.createVolume(new LoadSpec()); - return new VolumeModel(volume); + const model = new VolumeModel(volume); + this.setGeometryInRegistry(url, model, GeometryDisplayType.VOLUME); + return model; } /** From d99190e4de47ca6eeb3c2d64354a00dcdcc495d9 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 25 Sep 2024 00:13:04 -0700 Subject: [PATCH 06/18] create and register volume model immediately (waiting until it's actually ready causes problems) --- src/visGeometry/GeometryStore.ts | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/visGeometry/GeometryStore.ts b/src/visGeometry/GeometryStore.ts index a0765ab4..0356c48d 100644 --- a/src/visGeometry/GeometryStore.ts +++ b/src/visGeometry/GeometryStore.ts @@ -388,11 +388,12 @@ class GeometryStore { 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 model = new VolumeModel(volume); - this.setGeometryInRegistry(url, model, GeometryDisplayType.VOLUME); + model.setImage(volume); return model; } From 8514e883c96a213459a2b45b496879653eb14c50 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 25 Sep 2024 00:19:50 -0700 Subject: [PATCH 07/18] try to fit volumes into the render pipeline --- src/visGeometry/index.ts | 44 +++++++++++++++++++++++++++------------- 1 file changed, 30 insertions(+), 14 deletions(-) diff --git a/src/visGeometry/index.ts b/src/visGeometry/index.ts index 35682cb0..9b77b2d5 100644 --- a/src/visGeometry/index.ts +++ b/src/visGeometry/index.ts @@ -35,6 +35,7 @@ import { cloneDeep, noop } from "lodash"; import VisAgent from "./VisAgent"; import VisTypes from "../simularium/VisTypes"; import PDBModel from "./PDBModel"; +import VolumeModel from "./VolumeModel"; import AgentPath from "./agentPath"; import { FrontEndError, ErrorLevel } from "../simularium/FrontEndError"; @@ -151,6 +152,7 @@ class VisGeometry { public lightsGroup: Group; public agentPathGroup: Group; public instancedMeshGroup: Group; + public tempVolumeGroup: Group; // TODO remove private supportsWebGL2Rendering: boolean; private lodBias: number; private lodDistanceStops: number[]; @@ -217,6 +219,9 @@ 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.resetBounds(DEFAULT_VOLUME_DIMENSIONS); @@ -716,7 +721,7 @@ class VisGeometry { public onNewRuntimeGeometryType( geoName: string, displayType: GeometryDisplayType, - data: PDBModel | MeshLoadRequest + data: PDBModel | MeshLoadRequest | VolumeModel ): void { // find all typeIds for this meshName const typeIds = this.getAllTypeIdsForGeometryName(geoName); @@ -990,6 +995,9 @@ 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]); + } // re-add fibers immediately this.instancedMeshGroup.add(this.fibers.getGroup()); @@ -1007,15 +1015,7 @@ class VisGeometry { const meshTypes: GeometryInstanceContainer[] = []; for (const entry of this.geometryStore.registry.values()) { const { displayType } = entry; - if (displayType !== GeometryDisplayType.PDB) { - const meshEntry = entry as MeshGeometry; - if (meshEntry.geometry.instances.instanceCount() > 0) { - meshTypes.push(meshEntry.geometry.instances); - this.instancedMeshGroup.add( - meshEntry.geometry.instances.getMesh() - ); - } - } else { + if (displayType === GeometryDisplayType.PDB) { const pdbEntry = entry as PDBGeometry; for (let i = 0; i < pdbEntry.geometry.numLODs(); ++i) { const lod = pdbEntry.geometry.getLOD(i); @@ -1024,6 +1024,19 @@ class VisGeometry { this.instancedMeshGroup.add(lod.getMesh()); } } + } else if (displayType === GeometryDisplayType.VOLUME) { + const volObject = entry.geometry.tempGetBoundingBoxObject(); + if (volObject) { + this.tempVolumeGroup.add(volObject); + } + } else { + const meshEntry = entry as MeshGeometry; + if (meshEntry.geometry.instances.instanceCount() > 0) { + meshTypes.push(meshEntry.geometry.instances); + this.instancedMeshGroup.add( + meshEntry.geometry.instances.getMesh() + ); + } } } @@ -1047,6 +1060,7 @@ class VisGeometry { this.boundingBoxMesh.visible = false; this.tickMarksMesh.visible = false; this.agentPathGroup.visible = false; + this.tempVolumeGroup.visible = false; this.renderer.render( this.threejsrenderer, this.scene, @@ -1058,6 +1072,7 @@ class VisGeometry { this.boundingBoxMesh.visible = true; this.tickMarksMesh.visible = true; this.agentPathGroup.visible = true; + this.tempVolumeGroup.visible = true; this.threejsrenderer.autoClear = false; // hide everything except the wireframe and paths, and render with the standard renderer @@ -1613,14 +1628,15 @@ class VisGeometry { } const { geometry, displayType } = response; if (geometry && displayType === GeometryDisplayType.PDB) { - const pdbEntry = geometry as PDBModel; - this.addPdbToDrawList(typeId, visAgent, pdbEntry); + this.addPdbToDrawList(typeId, visAgent, geometry); + } else if (displayType === GeometryDisplayType.VOLUME) { + // Hmm... is anyone gonna want to instance a volume? + geometry.setAgentData(agentData); } else { - const meshEntry = geometry as MeshLoadRequest; this.addMeshToDrawList( typeId, visAgent, - meshEntry, + geometry as MeshLoadRequest, agentData ); } From b953816d692552a3b83bbbaf2b38f0f6c19f9acb Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 25 Sep 2024 00:29:51 -0700 Subject: [PATCH 08/18] npm won't install anything until I bump ts-jest --- package-lock.json | 3145 +++++++++++++++++++++++++++------------------ package.json | 4 +- 2 files changed, 1879 insertions(+), 1270 deletions(-) diff --git a/package-lock.json b/package-lock.json index db79aebd..423bf863 100644 --- a/package-lock.json +++ b/package-lock.json @@ -54,7 +54,7 @@ "eslint-config-prettier": "^6.11.0", "eslint-plugin-react": "^7.22.0", "husky": "^1.3.1", - "jest": "^27.1.0", + "jest": "^29.7.0", "lint-staged": "^10.5.4", "npm-run-all": "^4.1.5", "nyc": "~15.0", @@ -66,7 +66,7 @@ "react-dom": "^18.2.0", "regenerator-runtime": "^0.13.7", "rimraf": "~2.6", - "ts-jest": "27.1", + "ts-jest": "^29.2.5", "ts-node": "~10.1.0", "typescript": "^5.6.2" }, @@ -80,6 +80,7 @@ "version": "3.11.1", "license": "MIT", "dependencies": { + "@babel/runtime": "^7.25.6", "geotiff": "^2.0.5", "serialize-error": "^11.0.3", "three": "^0.144.0", @@ -87,11 +88,12 @@ "zarrita": "^0.3.2" }, "devDependencies": { - "@babel/cli": "^7.14.8", - "@babel/core": "^7.14.8", - "@babel/preset-react": "^7.14.5", - "@babel/preset-typescript": "^7.14.5", - "@babel/register": "^7.14.5", + "@babel/cli": "^7.25.6", + "@babel/core": "^7.25.2", + "@babel/plugin-transform-runtime": "^7.25.4", + "@babel/preset-react": "^7.24.7", + "@babel/preset-typescript": "^7.24.7", + "@babel/register": "^7.24.6", "@tweakpane/core": "^1.1.9", "@types/chai": "^4.3.12", "@types/mocha": "^9.1.1", @@ -2005,7 +2007,8 @@ "version": "0.2.3", "resolved": "https://registry.npmjs.org/@bcoe/v8-coverage/-/v8-coverage-0.2.3.tgz", "integrity": "sha512-0hYQ8SB4Db5zvZB4axdMHGwEaQjkZzFjQiN9LVYvIFB2nSUHW9tYpxWriPrWDASIxiaXax83REcLxuSdnGPZtw==", - "dev": true + "dev": true, + "license": "MIT" }, "node_modules/@cnakazawa/watch": { "version": "1.0.4", @@ -2179,20 +2182,21 @@ } }, "node_modules/@jest/console": { - "version": "27.5.1", - "resolved": "https://registry.npmjs.org/@jest/console/-/console-27.5.1.tgz", - "integrity": "sha512-kZ/tNpS3NXn0mlXXXPNuDZnb4c0oZ20r4K5eemM2k30ZC3G0T02nXUvyhf5YdbXWHPEJLc9qGLxEZ216MdL+Zg==", + "version": "29.7.0", + "resolved": "https://registry.npmjs.org/@jest/console/-/console-29.7.0.tgz", + "integrity": "sha512-5Ni4CU7XHQi32IJ398EEP4RrB8eV09sXP2ROqD4bksHrnTree52PsxvX8tpL8LvTZ3pFzXyPbNQReSN41CAhOg==", "dev": true, + "license": "MIT", "dependencies": { - "@jest/types": "^27.5.1", + "@jest/types": "^29.6.3", "@types/node": "*", "chalk": "^4.0.0", - "jest-message-util": "^27.5.1", - "jest-util": "^27.5.1", + "jest-message-util": "^29.7.0", + "jest-util": "^29.7.0", "slash": "^3.0.0" }, "engines": { - "node": "^10.13.0 || ^12.13.0 || ^14.15.0 || >=15.0.0" + "node": "^14.15.0 || ^16.10.0 || >=18.0.0" } }, 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f8b5c4db..fab6e7a6 100644 --- a/package.json +++ b/package.json @@ -66,7 +66,7 @@ "eslint-config-prettier": "^6.11.0", "eslint-plugin-react": "^7.22.0", "husky": "^1.3.1", - "jest": "^27.1.0", + "jest": "^29.7.0", "lint-staged": "^10.5.4", "npm-run-all": "^4.1.5", "nyc": "~15.0", @@ -78,7 +78,7 @@ "react-dom": "^18.2.0", "regenerator-runtime": "^0.13.7", "rimraf": "~2.6", - "ts-jest": "27.1", + "ts-jest": "^29.2.5", "ts-node": "~10.1.0", "typescript": "^5.6.2" }, From 8d6c442628e2c4f510281d062afec72efb84d379 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 25 Sep 2024 00:45:28 -0700 Subject: [PATCH 09/18] more package wrangling to fix tests (where was lodash?!) --- package-lock.json | 585 +++++++++++++++++++++++++++++++++++++++++++++- package.json | 4 +- 2 files changed, 584 insertions(+), 5 deletions(-) diff --git a/package-lock.json b/package-lock.json index 423bf863..3e674964 100644 --- a/package-lock.json +++ b/package-lock.json @@ -18,9 +18,9 @@ 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"entities": "^4.4.0" + }, + "funding": { + "url": "https://github.com/inikulin/parse5?sponsor=1" + } + }, "node_modules/pascalcase": { "version": "0.1.1", "resolved": "https://registry.npmjs.org/pascalcase/-/pascalcase-0.1.1.tgz", @@ -14625,6 +15005,13 @@ "resolved": "https://registry.npmjs.org/react-is/-/react-is-16.13.1.tgz", "integrity": "sha512-24e6ynE2H+OKt4kqsOvNd8kBpV65zoxbA4BVsEOB3ARVWQki/DHzaUoC5KuON/BiccDaCCTZBuOcfZs70kR8bQ==" }, + "node_modules/psl": { + "version": "1.9.0", + "resolved": "https://registry.npmjs.org/psl/-/psl-1.9.0.tgz", + "integrity": "sha512-E/ZsdU4HLs/68gYzgGTkMicWTLPdAftJLfJFlLUAAKZGkStNU72sZjT66SnMDVOfOWY/YAoiD7Jxa9iHvngcag==", + "dev": true, + "license": "MIT" + }, "node_modules/pump": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/pump/-/pump-3.0.0.tgz", @@ -14661,6 +15048,13 @@ ], "license": "MIT" }, + "node_modules/querystringify": { + "version": "2.2.0", + "resolved": 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}, + "node_modules/safer-buffer": { + "version": "2.1.2", + "resolved": "https://registry.npmjs.org/safer-buffer/-/safer-buffer-2.1.2.tgz", + "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg==", + "dev": true, + "license": "MIT" + }, "node_modules/sane": { "version": "4.1.0", "resolved": "https://registry.npmjs.org/sane/-/sane-4.1.0.tgz", @@ -15386,6 +15794,19 @@ "node": ">=0.10.0" } }, + "node_modules/saxes": { + "version": "6.0.0", + "resolved": "https://registry.npmjs.org/saxes/-/saxes-6.0.0.tgz", + "integrity": "sha512-xAg7SOnEhrm5zI3puOOKyy1OMcMlIJZYNJY7xLBwSze0UjhPLnWfj2GF2EpT0jmzaJKIWKHLsaSSajf35bcYnA==", + "dev": true, + "license": "ISC", + "dependencies": { + "xmlchars": "^2.2.0" + }, + "engines": { + "node": ">=v12.22.7" + } + }, "node_modules/scheduler": { "version": "0.23.0", "resolved": "https://registry.npmjs.org/scheduler/-/scheduler-0.23.0.tgz", @@ -16191,6 +16612,13 @@ "url": "https://github.com/sponsors/ljharb" } }, + "node_modules/symbol-tree": { + "version": "3.2.4", + "resolved": "https://registry.npmjs.org/symbol-tree/-/symbol-tree-3.2.4.tgz", + "integrity": "sha512-9QNk5KwDF+Bvz+PyObkmSYjI5ksVUYtjW7AU22r2NKcfLJcXp96hkDWU3+XndOsUb+AQ9QhfzfCT2O+CNWT5Tw==", + "dev": true, + "license": "MIT" + }, "node_modules/table": { "version": "6.8.1", "resolved": "https://registry.npmjs.org/table/-/table-6.8.1.tgz", @@ -16517,6 +16945,45 @@ "node": ">=8.0" } }, + "node_modules/tough-cookie": { + "version": "4.1.4", + "resolved": "https://registry.npmjs.org/tough-cookie/-/tough-cookie-4.1.4.tgz", + "integrity": "sha512-Loo5UUvLD9ScZ6jh8beX1T6sO1w2/MpCRpEP7V280GKMVUQ0Jzar2U3UJPsrdbziLEMMhu3Ujnq//rhiFuIeag==", + "dev": true, + "license": "BSD-3-Clause", + "dependencies": { + "psl": "^1.1.33", + "punycode": "^2.1.1", + "universalify": "^0.2.0", + "url-parse": "^1.5.3" + }, + "engines": { + "node": ">=6" + } + }, + "node_modules/tough-cookie/node_modules/universalify": { + "version": "0.2.0", + "resolved": "https://registry.npmjs.org/universalify/-/universalify-0.2.0.tgz", + "integrity": "sha512-CJ1QgKmNg3CwvAv/kOFmtnEN05f0D/cn9QntgNOQlQF9dgvVTHj3t+8JPdjqawCHk7V/KA+fbUqzZ9XWhcqPUg==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">= 4.0.0" + } + }, + "node_modules/tr46": { + "version": "3.0.0", + "resolved": "https://registry.npmjs.org/tr46/-/tr46-3.0.0.tgz", + "integrity": "sha512-l7FvfAHlcmulp8kr+flpQZmVwtu7nfRV7NZujtN0OqES8EL4O4e0qqzL0DC5gAvx/ZC/9lk6rhcUwYvkBnBnYA==", + "dev": true, + "license": "MIT", + "dependencies": { + "punycode": "^2.1.1" + }, + "engines": { + "node": ">=12" + } + }, "node_modules/ts-jest": { "version": "29.2.5", "resolved": "https://registry.npmjs.org/ts-jest/-/ts-jest-29.2.5.tgz", @@ -17017,6 +17484,17 @@ "deprecated": "Please see https://github.com/lydell/urix#deprecated", "dev": true }, + "node_modules/url-parse": { + "version": "1.5.10", + "resolved": "https://registry.npmjs.org/url-parse/-/url-parse-1.5.10.tgz", + "integrity": "sha512-WypcfiRhfeUP9vvF0j6rw0J3hrWrw6iZv3+22h6iRMJ/8z1Tj6XfLP4DsUix5MhMPnXpiHDoKyoZ/bdCkwBCiQ==", + "dev": true, + "license": "MIT", + "dependencies": { + "querystringify": "^2.1.1", + "requires-port": "^1.0.0" + } + }, "node_modules/use": { "version": "3.1.1", "resolved": "https://registry.npmjs.org/use/-/use-3.1.1.tgz", @@ -17072,6 +17550,19 @@ "spdx-expression-parse": "^3.0.0" } }, + "node_modules/w3c-xmlserializer": { + "version": "4.0.0", + "resolved": "https://registry.npmjs.org/w3c-xmlserializer/-/w3c-xmlserializer-4.0.0.tgz", + "integrity": "sha512-d+BFHzbiCx6zGfz0HyQ6Rg69w9k19nviJspaj4yNscGjrHu94sVP+aRm75yEbCh+r2/yR+7q6hux9LVtbuTGBw==", + "dev": true, + "license": "MIT", + "dependencies": { + "xml-name-validator": "^4.0.0" + }, + "engines": { + "node": ">=14" + } + }, "node_modules/walker": { "version": "1.0.8", "resolved": "https://registry.npmjs.org/walker/-/walker-1.0.8.tgz", @@ -17095,6 +17586,16 @@ "node": ">=10.13.0" } }, + "node_modules/webidl-conversions": { + "version": "7.0.0", + "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-7.0.0.tgz", + "integrity": "sha512-VwddBukDzu71offAQR975unBIGqfKZpM+8ZX6ySk8nYhVoo5CYaZyzt3YBvYtRtO+aoGlqxPg/B87NGVZ/fu6g==", + "dev": true, + "license": "BSD-2-Clause", + "engines": { + "node": ">=12" + } + }, "node_modules/webpack": { "version": "5.90.3", "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.90.3.tgz", @@ -17172,6 +17673,43 @@ "url": "https://opencollective.com/webpack" } }, + "node_modules/whatwg-encoding": { + "version": "2.0.0", + "resolved": "https://registry.npmjs.org/whatwg-encoding/-/whatwg-encoding-2.0.0.tgz", + "integrity": "sha512-p41ogyeMUrw3jWclHWTQg1k05DSVXPLcVxRTYsXUk+ZooOCZLcoYgPZ/HL/D/N+uQPOtcp1me1WhBEaX02mhWg==", + "dev": true, + "license": "MIT", + "dependencies": { + "iconv-lite": "0.6.3" + }, + "engines": { + "node": ">=12" + } + }, + "node_modules/whatwg-mimetype": { + "version": "3.0.0", + "resolved": "https://registry.npmjs.org/whatwg-mimetype/-/whatwg-mimetype-3.0.0.tgz", + "integrity": "sha512-nt+N2dzIutVRxARx1nghPKGv1xHikU7HKdfafKkLNLindmPU/ch3U31NOCGGA/dmPcmb1VlofO0vnKAcsm0o/Q==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">=12" + } + }, + "node_modules/whatwg-url": { + "version": "11.0.0", + "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-11.0.0.tgz", + "integrity": "sha512-RKT8HExMpoYx4igMiVMY83lN6UeITKJlBQ+vR/8ZJ8OCdSiN3RwCq+9gH0+Xzj0+5IrM6i4j/6LuvzbZIQgEcQ==", + "dev": true, + "license": "MIT", + "dependencies": { + "tr46": "^3.0.0", + "webidl-conversions": "^7.0.0" + }, + "engines": { + "node": ">=12" + } + }, "node_modules/which": { "version": "2.0.2", "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz", @@ -17349,6 +17887,45 @@ "typedarray-to-buffer": "^3.1.5" } }, + "node_modules/ws": { + "version": "8.18.0", + "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.0.tgz", + "integrity": "sha512-8VbfWfHLbbwu3+N6OKsOMpBdT4kXPDDB9cJk2bJ6mh9ucxdlnNvH1e+roYkKmN9Nxw2yjz7VzeO9oOz2zJ04Pw==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">=10.0.0" + }, + "peerDependencies": { + "bufferutil": "^4.0.1", + "utf-8-validate": ">=5.0.2" + }, + "peerDependenciesMeta": { + "bufferutil": { + "optional": true + }, + "utf-8-validate": { + "optional": true + } + } + }, + "node_modules/xml-name-validator": { + "version": "4.0.0", + "resolved": "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-4.0.0.tgz", + "integrity": "sha512-ICP2e+jsHvAj2E2lIHxa5tjXRlKDJo4IdvPvCXbXQGdzSfmSpNVyIKMvoZHjDY9DP0zV17iI85o90vRFXNccRw==", + "dev": true, + "license": "Apache-2.0", + "engines": { + "node": ">=12" + } + }, + "node_modules/xmlchars": { + "version": "2.2.0", + "resolved": "https://registry.npmjs.org/xmlchars/-/xmlchars-2.2.0.tgz", + "integrity": "sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw==", + "dev": true, + "license": "MIT" + }, "node_modules/xtend": { "version": "4.0.2", "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz", diff --git a/package.json b/package.json index fab6e7a6..48a603b6 100644 --- a/package.json +++ b/package.json @@ -46,6 +46,7 @@ "@babel/preset-env": "^7.23.5", "@babel/preset-react": "^7.23.3", "@babel/preset-typescript": "^7.23.3", + "@types/dom-webcodecs": "^0.1.11", "@types/jest": "^27.0.1", "@types/lodash": "^4.14.175", "@types/react": "^18.2.46", @@ -67,6 +68,7 @@ "eslint-plugin-react": "^7.22.0", "husky": "^1.3.1", "jest": "^29.7.0", + "jest-environment-jsdom": "^29.7.0", "lint-staged": "^10.5.4", "npm-run-all": "^4.1.5", "nyc": "~15.0", @@ -96,9 +98,9 @@ "@fortawesome/react-fontawesome": "^0.1.14", "@tweakpane/core": "^1.0.8", "@tweakpane/plugin-essentials": "^0.1.4", - "@types/dom-webcodecs": "^0.1.8", "comlink": "^4.3.1", "js-logger": "^1.6.1", + "lodash": "^4.17.21", "mp4-muxer": "^2.2.2", "parse-pdb": "^1.0.0", "si-prefix": "^0.2.0", From 26fd9e49d260349f6dda0aa1ec05a5e0320aec39 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 25 Sep 2024 00:49:11 -0700 Subject: [PATCH 10/18] now at LAST I can bump three and fix my type errors --- package-lock.json | 30 +++++++++++++++++++++--------- package.json | 4 ++-- 2 files changed, 23 insertions(+), 11 deletions(-) diff --git a/package-lock.json b/package-lock.json index 3e674964..5f7bff8e 100644 --- a/package-lock.json +++ b/package-lock.json @@ -24,7 +24,7 @@ "mp4-muxer": "^2.2.2", "parse-pdb": "^1.0.0", "si-prefix": "^0.2.0", - "three": "^0.137.4", + "three": "^0.144.0", "tweakpane": "^3.0.7" }, "devDependencies": { @@ -39,7 +39,7 @@ "@types/lodash": "^4.14.175", "@types/react": "^18.2.46", "@types/react-dom": "^18.2.18", - "@types/three": "^0.137.0", + "@types/three": "^0.144.0", "@typescript-eslint/eslint-plugin": "~4.29.0", "@typescript-eslint/parser": "~4.29.0", "acorn": "^8.7.0", @@ -3410,10 +3410,14 @@ "license": "MIT" }, "node_modules/@types/three": { - "version": "0.137.0", - "resolved": "https://registry.npmjs.org/@types/three/-/three-0.137.0.tgz", - "integrity": "sha512-Xc5EAlfYmgrCLI/VlSVqiRJAtzhWF0Rw2jSq48nqJy+Hcb5sfDOXyfZn1+RNcHyi9l8CeCAXCZygO8IyeOJVEA==", - "dev": true + "version": "0.144.0", + "resolved": "https://registry.npmjs.org/@types/three/-/three-0.144.0.tgz", + "integrity": "sha512-psvEs6q5rLN50jUYZ3D4pZMfxTbdt3A243blt0my7/NcL6chaCZpHe2csbCtx0SOD9fI/XnF3wnVUAYZGqCSYg==", + "dev": true, + "license": "MIT", + "dependencies": { + "@types/webxr": "*" + } }, "node_modules/@types/tough-cookie": { "version": "4.0.5", @@ -3422,6 +3426,13 @@ "dev": true, "license": "MIT" }, + "node_modules/@types/webxr": { + "version": "0.5.20", + "resolved": "https://registry.npmjs.org/@types/webxr/-/webxr-0.5.20.tgz", + "integrity": "sha512-JGpU6qiIJQKUuVSKx1GtQnHJGxRjtfGIhzO2ilq43VZZS//f1h1Sgexbdk+Lq+7569a6EYhOWrUpIruR/1Enmg==", + "dev": true, + "license": "MIT" + }, "node_modules/@types/wicg-file-system-access": { "version": "2020.9.8", "resolved": "https://registry.npmjs.org/@types/wicg-file-system-access/-/wicg-file-system-access-2020.9.8.tgz", @@ -16824,9 +16835,10 @@ "dev": true }, "node_modules/three": { - "version": "0.137.5", - "resolved": "https://registry.npmjs.org/three/-/three-0.137.5.tgz", - "integrity": "sha512-rTyr+HDFxjnN8+N/guZjDgfVxgHptZQpf6xfL/Mo7a5JYIFwK6tAq3bzxYYB4Ae0RosDZlDuP+X5aXDXz+XnHQ==" + "version": "0.144.0", + "resolved": "https://registry.npmjs.org/three/-/three-0.144.0.tgz", + "integrity": "sha512-R8AXPuqfjfRJKkYoTQcTK7A6i3AdO9++2n8ubya/GTU+fEHhYKu1ZooRSCPkx69jbnzT7dD/xEo6eROQTt2lJw==", + "license": "MIT" }, "node_modules/through": { "version": "2.3.8", diff --git a/package.json b/package.json index 48a603b6..2248b08b 100644 --- a/package.json +++ b/package.json @@ -51,7 +51,7 @@ "@types/lodash": "^4.14.175", "@types/react": "^18.2.46", "@types/react-dom": "^18.2.18", - "@types/three": "^0.137.0", + "@types/three": "^0.144.0", "@typescript-eslint/eslint-plugin": "~4.29.0", "@typescript-eslint/parser": "~4.29.0", "acorn": "^8.7.0", @@ -104,7 +104,7 @@ "mp4-muxer": "^2.2.2", "parse-pdb": "^1.0.0", "si-prefix": "^0.2.0", - "three": "^0.137.4", + "three": "^0.144.0", "tweakpane": "^3.0.7" } } From bf87d24e180f10f87fc47cd27f5a7c1a2dd575d7 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 25 Sep 2024 00:54:07 -0700 Subject: [PATCH 11/18] fix new type errors created by fixing old type errors --- src/visGeometry/GeometryStore.ts | 13 ++++++------- src/visGeometry/rendering/HitTestHelper.ts | 4 ++-- src/visGeometry/rendering/LegacyRenderer.ts | 4 ++-- src/visGeometry/rendering/RenderToBuffer.ts | 6 +++--- 4 files changed, 13 insertions(+), 14 deletions(-) diff --git a/src/visGeometry/GeometryStore.ts b/src/visGeometry/GeometryStore.ts index 0356c48d..0a5d29e6 100644 --- a/src/visGeometry/GeometryStore.ts +++ b/src/visGeometry/GeometryStore.ts @@ -6,8 +6,8 @@ import { BufferGeometry, Object3D, Mesh, - SphereBufferGeometry, - BoxBufferGeometry, + SphereGeometry, + BoxGeometry, } from "three"; import { checkAndSanitizePath, getFileExtension } from "../util"; @@ -51,13 +51,12 @@ class GeometryStore { private _cachedAssets: Map; private _registry: Registry; public mlogger: ILogger; - public static sphereGeometry: SphereBufferGeometry = - new SphereBufferGeometry(1, 32, 32); - public static cubeGeometry: BoxBufferGeometry = new BoxBufferGeometry( + public static sphereGeometry: SphereGeometry = new SphereGeometry( 1, - 1, - 1 + 32, + 32 ); + public static cubeGeometry: BoxGeometry = new BoxGeometry(1, 1, 1); private static shouldLoadPrimitive = ( displayType: GeometryDisplayType, diff --git a/src/visGeometry/rendering/HitTestHelper.ts b/src/visGeometry/rendering/HitTestHelper.ts index 27f6c7b9..a6e99268 100644 --- a/src/visGeometry/rendering/HitTestHelper.ts +++ b/src/visGeometry/rendering/HitTestHelper.ts @@ -4,7 +4,7 @@ import { Mesh, NearestFilter, OrthographicCamera, - PlaneBufferGeometry, + PlaneGeometry, RGBAFormat, Scene, ShaderMaterial, @@ -48,7 +48,7 @@ export default class HitTestHelper { } `; this.hitTestMesh = new Mesh( - new PlaneBufferGeometry(2, 2), + new PlaneGeometry(2, 2), new ShaderMaterial({ vertexShader: this.hitTestVertexShader, fragmentShader: this.hitTestFragmentShader, diff --git a/src/visGeometry/rendering/LegacyRenderer.ts b/src/visGeometry/rendering/LegacyRenderer.ts index cf1ce8c9..b08dcb1f 100644 --- a/src/visGeometry/rendering/LegacyRenderer.ts +++ b/src/visGeometry/rendering/LegacyRenderer.ts @@ -7,7 +7,7 @@ import { Material, MeshLambertMaterial, MeshBasicMaterial, - TubeBufferGeometry, + TubeGeometry, Group, LOD, Mesh, @@ -59,7 +59,7 @@ class LegacyRenderer { return; } // expensive - const fibergeometry = new TubeBufferGeometry( + const fibergeometry = new TubeGeometry( visAgent.fiberCurve, 4 * (visAgent.fiberCurve.points.length - 1), // 4 segments per control point scale * 0.5, diff --git a/src/visGeometry/rendering/RenderToBuffer.ts b/src/visGeometry/rendering/RenderToBuffer.ts index db779d1d..10922f18 100644 --- a/src/visGeometry/rendering/RenderToBuffer.ts +++ b/src/visGeometry/rendering/RenderToBuffer.ts @@ -2,7 +2,7 @@ import { IUniform, Mesh, OrthographicCamera, - PlaneBufferGeometry, + PlaneGeometry, Scene, ShaderMaterial, WebGLRenderer, @@ -17,7 +17,7 @@ interface RenderToBufferParams { class RenderToBuffer { public scene: Scene; - public geometry: PlaneBufferGeometry; + public geometry: PlaneGeometry; public material: ShaderMaterial; public camera: OrthographicCamera; public mesh: Mesh; @@ -27,7 +27,7 @@ class RenderToBuffer { // fragmentShader // uniforms this.scene = new Scene(); - this.geometry = new PlaneBufferGeometry(2, 2); + this.geometry = new PlaneGeometry(2, 2); // augment uniforms (and shader source?) this.material = new ShaderMaterial({ From 9348bb05f32e1a183b7941419648b2e7fd26cca4 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 25 Sep 2024 01:04:53 -0700 Subject: [PATCH 12/18] fix more errors from bumping three --- src/visGeometry/index.ts | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/visGeometry/index.ts b/src/visGeometry/index.ts index 9b77b2d5..0b1c8e1f 100644 --- a/src/visGeometry/index.ts +++ b/src/visGeometry/index.ts @@ -1009,7 +1009,7 @@ class VisGeometry { this.setPdbLods(); this.scene.updateMatrixWorld(); - this.scene.autoUpdate = false; + this.scene.matrixAutoUpdate = false; // collect up the meshes that have > 0 instances const meshTypes: GeometryInstanceContainer[] = []; @@ -1081,7 +1081,7 @@ class VisGeometry { this.instancedMeshGroup.visible = true; this.threejsrenderer.autoClear = true; - this.scene.autoUpdate = true; + this.scene.matrixAutoUpdate = true; } } From c023b64a3e3ff2d0115410aa029507e577b2dbd7 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 25 Sep 2024 10:22:03 -0700 Subject: [PATCH 13/18] filling out the `VolumeModel` class --- src/visGeometry/VolumeModel.ts | 34 ++++++++++++++++++++++++++++++++-- 1 file changed, 32 insertions(+), 2 deletions(-) diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index 9354613a..2a91bfc6 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -1,7 +1,37 @@ -import { Volume } from "@aics/volume-viewer"; +import { Box3Helper, Euler, Object3D, Vector3 } from "three"; + +import { Volume, VolumeDrawable } from "@aics/volume-viewer"; + +import { AgentData } from "../simularium/types"; + +// TEMPORARY HACK to make things typecheck +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? public cancelled = false; - constructor(private volume: Volume) {} + private image?: VolumeDrawable; + + public setImage(volumeObject: Volume): void { + this.image = new VolumeDrawable(volumeObject, {}); + } + + 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)); + this.image.setScale(new Vector3(data.cr, data.cr, data.cr)); + } + } + + public getObject3D(): Object3D | undefined { + return this.image?.sceneRoot; + } + + public tempGetBoundingBoxObject(): Box3Helper | undefined { + return (this.image?.volumeRendering as TempRayMarchedVolume)?.boxHelper; + } } From 52e1bbe022a1eaf5f1c68a2dd67a2b19e17eb4b8 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Fri, 27 Sep 2024 15:52:31 -0700 Subject: [PATCH 14/18] you have to turn on the bounding box to see the bounding box --- src/visGeometry/VolumeModel.ts | 1 + 1 file changed, 1 insertion(+) diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index 2a91bfc6..f7ce0312 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -32,6 +32,7 @@ export default class VolumeModel { } public tempGetBoundingBoxObject(): Box3Helper | undefined { + this.image?.setShowBoundingBox(true); return (this.image?.volumeRendering as TempRayMarchedVolume)?.boxHelper; } } From 1540cd0ef6bde74a4b6dbc8410acdd48e79b7670 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Fri, 27 Sep 2024 16:00:08 -0700 Subject: [PATCH 15/18] fix conversion from collision radius to vol scale --- src/visGeometry/VolumeModel.ts | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index f7ce0312..f20b9695 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -23,7 +23,8 @@ export default class VolumeModel { 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)); - this.image.setScale(new Vector3(data.cr, data.cr, data.cr)); + const r = data.cr * 2; + this.image.setScale(new Vector3(r, r, r)); } } From 2ac02c03f2e83763fafc13cee4cf8dbb3001b672 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Thu, 26 Sep 2024 14:33:44 -0700 Subject: [PATCH 16/18] try again to update coverage report (cherry picked from commit f1af28e5821cc758ac3853a6cd046bd6b7afa3dd) --- .github/workflows/coverage.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml index 6c03ecd1..1cd5d4bc 100644 --- a/.github/workflows/coverage.yml +++ b/.github/workflows/coverage.yml @@ -1,4 +1,4 @@ -name: 'coverage' +name: "coverage" on: pull_request: branches: @@ -9,6 +9,6 @@ jobs: if: "!contains(github.event.head_commit.message, '[skip ci]')" steps: - uses: actions/checkout@v1 - - uses: ArtiomTr/jest-coverage-report-action@v1.3 + - uses: ArtiomTr/jest-coverage-report-action@v2.3.1 with: github_token: ${{ secrets.GITHUB_TOKEN }} From d5ad90392649bbcedb8f1802d231a6d2f480762e Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 2 Oct 2024 10:08:20 -0700 Subject: [PATCH 17/18] update some TODOs --- src/visGeometry/VolumeModel.ts | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index f20b9695..7d3a84a2 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -4,14 +4,15 @@ import { Volume, VolumeDrawable } from "@aics/volume-viewer"; import { AgentData } from "../simularium/types"; -// TEMPORARY HACK to make things typecheck +// 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? + // 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; From 59ffb13c6bb07fb9ad37e1dbe1dc9136bbbd8784 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 2 Oct 2024 11:29:43 -0700 Subject: [PATCH 18/18] try out github repo dependency --- package-lock.json | 255 +++++++++++++++++++++++++++++++++++----------- package.json | 2 +- 2 files changed, 194 insertions(+), 63 deletions(-) diff --git a/package-lock.json b/package-lock.json index a124a339..a2194896 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,7 +9,7 @@ "version": "3.8.4", "license": "MIT", "dependencies": { - "@aics/volume-viewer": "file:../volume-viewer", + "@aics/volume-viewer": "allen-cell-animated/volume-viewer#simularium-volumes", "@babel/plugin-transform-runtime": "^7.23.6", "@babel/runtime": "^7.23.6", "@fortawesome/fontawesome-free": "^5.15.2", @@ -77,62 +77,6 @@ "react-dom": "^18.2.0" } }, - "../volume-viewer": { - "name": "@aics/volume-viewer", - "version": "3.11.1", - "license": "MIT", - "dependencies": { - "@babel/runtime": "^7.25.6", - "geotiff": "^2.0.5", - "serialize-error": "^11.0.3", - "three": "^0.144.0", - "tweakpane": "^3.1.9", - "zarrita": "^0.3.2" - }, - "devDependencies": { - "@babel/cli": "^7.25.6", - "@babel/core": "^7.25.2", - "@babel/plugin-transform-runtime": "^7.25.4", - "@babel/preset-react": "^7.24.7", - "@babel/preset-typescript": "^7.24.7", - "@babel/register": "^7.24.6", - "@tweakpane/core": "^1.1.9", - "@types/chai": "^4.3.12", - "@types/mocha": "^9.1.1", - "@types/three": "^0.144.0", - "@typescript-eslint/eslint-plugin": "^5.30.5", - "@typescript-eslint/parser": "^5.30.5", - "acorn": "^8.7.0", - "babel-loader": "^8.2.2", - "babel-plugin-inline-import": "^3.0.0", - "babel-plugin-inline-import-data-uri": "^1.0.1", - "chai": "^5.1.0", - "clean-webpack-plugin": "^4.0.0-alpha.0", - "copy-webpack-plugin": "^9.0.1", - "cross-env": "^7.0.3", - "documentation": "^14.0.0", - "eslint": "^8.19.0", - "eslint-config-prettier": "^8.5.0", - "eslint-plugin-react": "^7.30.1", - "file-loader": "^6.2.0", - "html-webpack-plugin": "^5.3.2", - "husky": "^7.0.1", - "lil-gui": "^0.19.2", - "lint-staged": "^13.2.1", - "mocha": "^10.3.0", - "prettier": "^2.3.2", - "raw-loader": "^4.0.2", - "react": "^16.14.0", - "react-dom": "^16.14.0", - "rimraf": "^3.0.2", - "ts-node": "^10.9.2", - "typescript": "^4.3.5", - "url-loader": "^4.1.1", - "webpack": "^5.69.1", - "webpack-cli": "^4.9.2", - "webpack-dev-server": "^4.7.4" - } - }, "node_modules/@aashutoshrathi/word-wrap": { "version": "1.2.6", "resolved": "https://registry.npmjs.org/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz", @@ -143,8 +87,17 @@ } }, "node_modules/@aics/volume-viewer": { - "resolved": "../volume-viewer", - "link": true + "version": "3.11.1", + "resolved": "git+ssh://git@github.com/allen-cell-animated/volume-viewer.git#a6efd4a7f2272a58ee4481a3f24be39bf626847c", + "license": "MIT", + "dependencies": { + "@babel/runtime": "^7.25.6", + "geotiff": "^2.0.5", + "serialize-error": "^11.0.3", + "three": "^0.144.0", + "tweakpane": "^3.1.9", + "zarrita": "^0.3.2" + } }, "node_modules/@ampproject/remapping": { "version": "2.3.0", @@ -1944,9 +1897,10 @@ "dev": true }, "node_modules/@babel/runtime": { - "version": "7.24.0", - "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.24.0.tgz", - "integrity": "sha512-Chk32uHMg6TnQdvw2e9IlqPpFX/6NLuK0Ys2PqLb7/gL5uFn9mXvK715FGLlOLQrcO4qIkNHkvPGktzzXexsFw==", + "version": "7.25.7", + "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.25.7.tgz", + "integrity": "sha512-FjoyLe754PMiYsFaN5C94ttGiOmBNYTf6pLr4xXHAT5uctHb092PBszndLDR5XA/jghQvn4n7JMHl7dmTgbm9w==", + "license": "MIT", "dependencies": { "regenerator-runtime": "^0.14.0" }, @@ -3241,6 +3195,12 @@ "node": ">= 8" } }, + "node_modules/@petamoriken/float16": { + "version": "3.8.7", + "resolved": "https://registry.npmjs.org/@petamoriken/float16/-/float16-3.8.7.tgz", + "integrity": "sha512-/Ri4xDDpe12NT6Ex/DRgHzLlobiQXEW/hmG08w1wj/YU7hLemk97c+zHQFp0iZQ9r7YqgLEXZR2sls4HxBf9NA==", + "license": "MIT" + }, "node_modules/@sinclair/typebox": { "version": "0.27.8", "resolved": "https://registry.npmjs.org/@sinclair/typebox/-/typebox-0.27.8.tgz", @@ -3932,6 +3892,40 @@ "dev": true, "peer": true }, + "node_modules/@zarrita/core": { + "version": "0.0.3", + "resolved": "https://registry.npmjs.org/@zarrita/core/-/core-0.0.3.tgz", + "integrity": "sha512-fWv51b+xbYnws1pkNDPwJQoDa76aojxplHyMup82u11UAiet3gURMsrrkhM6YbeTgSY1A8oGxDOrvar3SiZpLA==", + "dependencies": { + "@zarrita/storage": "^0.0.2", + "@zarrita/typedarray": "^0.0.1", + "numcodecs": "^0.2.2" + } + }, + "node_modules/@zarrita/indexing": { + "version": "0.0.3", + "resolved": "https://registry.npmjs.org/@zarrita/indexing/-/indexing-0.0.3.tgz", + "integrity": 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"node_modules/geotiff": { + "version": "2.1.3", + "resolved": "https://registry.npmjs.org/geotiff/-/geotiff-2.1.3.tgz", + "integrity": "sha512-PT6uoF5a1+kbC3tHmZSUsLHBp2QJlHasxxxxPW47QIY1VBKpFB+FcDvX+MxER6UzgLQZ0xDzJ9s48B9JbOCTqA==", + "license": "MIT", + "dependencies": { + "@petamoriken/float16": "^3.4.7", + "lerc": "^3.0.0", + "pako": "^2.0.4", + "parse-headers": "^2.0.2", + "quick-lru": "^6.1.1", + "web-worker": "^1.2.0", + "xml-utils": "^1.0.2", + "zstddec": "^0.1.0" + }, + "engines": { + "node": ">=10.19" + } + }, "node_modules/get-caller-file": { "version": "2.0.5", "resolved": "https://registry.npmjs.org/get-caller-file/-/get-caller-file-2.0.5.tgz", @@ -11882,6 +11895,12 @@ "node": ">=6" } }, + "node_modules/lerc": { + "version": "3.0.0", + "resolved": "https://registry.npmjs.org/lerc/-/lerc-3.0.0.tgz", + "integrity": "sha512-Rm4J/WaHhRa93nCN2mwWDZFoRVF18G1f47C+kvQWyHGEZxFpTUi73p7lMVSAndyxGt6lJ2/CFbOcf9ra5p8aww==", + "license": "Apache-2.0" + }, "node_modules/leven": { 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