From 2dab0013b4d54fe24e1593234357892cb1a2eaf3 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Tue, 8 Oct 2024 10:30:57 -0700 Subject: [PATCH 01/44] use volumeloadercontext --- src/visGeometry/GeometryStore.ts | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/src/visGeometry/GeometryStore.ts b/src/visGeometry/GeometryStore.ts index 0a5d29e6..1e41eeb7 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"; import jsLogger, { ILogger, ILogLevel } from "js-logger"; -import { createVolumeLoader, LoadSpec } from "@aics/volume-viewer"; +import { LoadSpec, VolumeLoaderContext } from "@aics/volume-viewer"; 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, @@ -384,12 +385,23 @@ class GeometryStore { }); } + /** Don't start a volume load worker until we know we need it */ + private getVolumeLoaderContext(): VolumeLoaderContext { + 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(); + } + 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); + const loader = await this.getVolumeLoaderContext().createLoader(url); // TODO onChannelLoaded callback? const volume = await loader.createVolume(new LoadSpec()); model.setImage(volume); From 5e1406622c2773d998465c4612b378133289de07 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Tue, 8 Oct 2024 13:00:13 -0700 Subject: [PATCH 02/44] add volume object w/ observer connection to drawable --- src/visGeometry/VolumeModel.ts | 39 ++++++++++++++++++++++++++-------- 1 file changed, 30 insertions(+), 9 deletions(-) diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index 7d3a84a2..4f13b361 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -14,27 +14,48 @@ 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; public setImage(volumeObject: Volume): void { - this.image = new VolumeDrawable(volumeObject, {}); + this.volume = volumeObject; + this.drawable = new VolumeDrawable(this.volume, {}); + this.volume.addVolumeDataObserver(this); } 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)); + 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) + ); const r = data.cr * 2; - this.image.setScale(new Vector3(r, r, r)); + this.drawable.setScale(new Vector3(r, r, r)); } } public getObject3D(): Object3D | undefined { - return this.image?.sceneRoot; + return this.drawable?.sceneRoot; } public tempGetBoundingBoxObject(): Box3Helper | undefined { - this.image?.setShowBoundingBox(true); - return (this.image?.volumeRendering as TempRayMarchedVolume)?.boxHelper; + this.drawable?.setShowBoundingBox(true); + return (this.drawable?.volumeRendering as TempRayMarchedVolume) + ?.boxHelper; + } + + // METHODS FROM `VolumeDataObserver` in volume-viewer + + onVolumeData(_volume: Volume, channels: number[]): void { + this.drawable?.updateScale(); + this.drawable?.onChannelLoaded(channels); + } + + onVolumeChannelAdded(_volume: Volume, newChannelIndex: number): void { + this.drawable?.onChannelAdded(newChannelIndex); + } + + onVolumeLoadError(_volume: Volume, error: unknown): void { + console.error("Volume load error", error); } } From 84ac658cde03e3a9fc83006506c41c42fa30a526 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Tue, 8 Oct 2024 13:11:30 -0700 Subject: [PATCH 03/44] (try to) enable volume models to set timesteps --- src/visGeometry/VolumeModel.ts | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index 4f13b361..3c7af9a9 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -31,6 +31,11 @@ export default class VolumeModel { ); const r = data.cr * 2; this.drawable.setScale(new Vector3(r, r, r)); + // Volume agent data may use subpoint 0 as time + const time = data.subpoints?.length > 0 ? data.subpoints[0] : 0; + if (this.volume && this.volume.loadSpec.time !== time) { + this.volume.updateRequiredData({ time }); + } } } From 416e92f2b8dab824719f7a0169062c92af784a7d Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 9 Oct 2024 10:38:24 -0700 Subject: [PATCH 04/44] try to load volume data --- src/visGeometry/GeometryStore.ts | 1 + src/visGeometry/VolumeModel.ts | 4 ++++ 2 files changed, 5 insertions(+) diff --git a/src/visGeometry/GeometryStore.ts b/src/visGeometry/GeometryStore.ts index 1e41eeb7..82a97fa4 100644 --- a/src/visGeometry/GeometryStore.ts +++ b/src/visGeometry/GeometryStore.ts @@ -405,6 +405,7 @@ class GeometryStore { // TODO onChannelLoaded callback? const volume = await loader.createVolume(new LoadSpec()); model.setImage(volume); + model.loadInitialData(); return model; } diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index 3c7af9a9..1662c9fe 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -23,6 +23,10 @@ export default class VolumeModel { this.volume.addVolumeDataObserver(this); } + public loadInitialData(): void { + this.volume?.loader?.loadVolumeData(this.volume); + } + public setAgentData(data: AgentData): void { if (this.drawable) { this.drawable.setTranslation(new Vector3(data.x, data.y, data.z)); From 432be1c5452212ca6bffd60ec8de1d7517bfa531 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 9 Oct 2024 10:41:11 -0700 Subject: [PATCH 05/44] show full volume object, not just box; remove box hack --- src/visGeometry/VolumeModel.ts | 15 +++------------ src/visGeometry/index.ts | 6 +++--- 2 files changed, 6 insertions(+), 15 deletions(-) diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index 1662c9fe..3b751137 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -4,12 +4,6 @@ import { Volume, VolumeDrawable } from "@aics/volume-viewer"; 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? @@ -44,13 +38,10 @@ export default class VolumeModel { } public getObject3D(): Object3D | undefined { - return this.drawable?.sceneRoot; - } - - public tempGetBoundingBoxObject(): Box3Helper | undefined { + // TODO showing bounding box for debugging purposes. + // Do we want it on by default in production? this.drawable?.setShowBoundingBox(true); - return (this.drawable?.volumeRendering as TempRayMarchedVolume) - ?.boxHelper; + return this.drawable?.sceneRoot; } // METHODS FROM `VolumeDataObserver` in volume-viewer diff --git a/src/visGeometry/index.ts b/src/visGeometry/index.ts index 0b1c8e1f..67a2b8a6 100644 --- a/src/visGeometry/index.ts +++ b/src/visGeometry/index.ts @@ -1025,9 +1025,9 @@ 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) { + this.tempVolumeGroup.add(volObj); } } else { const meshEntry = entry as MeshGeometry; From 3711c9e6e44b8c8c26e0b5d0799c00f39c595c4b Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 9 Oct 2024 17:46:30 -0700 Subject: [PATCH 06/44] lots of new methods, code to try n get these dang volumes to show up --- src/visGeometry/VolumeModel.ts | 90 ++++++++++++++++++++++++++++------ 1 file changed, 76 insertions(+), 14 deletions(-) diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index 3b751137..f7c8119d 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -1,6 +1,11 @@ -import { Box3Helper, Euler, Object3D, Vector3 } from "three"; +import { Euler, Object3D, Vector3 } from "three"; -import { Volume, VolumeDrawable } from "@aics/volume-viewer"; +import { + Lut, + Volume, + VolumeDrawable, + HasThreeJsContext, +} from "@aics/volume-viewer"; import { AgentData } from "../simularium/types"; @@ -10,6 +15,26 @@ export default class VolumeModel { public cancelled = false; private drawable?: VolumeDrawable; private volume?: Volume; + private channelsEnabled: boolean[] = []; + + 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.volume = volumeObject; @@ -17,10 +42,6 @@ export default class VolumeModel { this.volume.addVolumeDataObserver(this); } - public loadInitialData(): void { - this.volume?.loader?.loadVolumeData(this.volume); - } - public setAgentData(data: AgentData): void { if (this.drawable) { this.drawable.setTranslation(new Vector3(data.x, data.y, data.z)); @@ -29,33 +50,74 @@ export default class VolumeModel { ); const r = data.cr * 2; this.drawable.setScale(new Vector3(r, r, r)); - // Volume agent data may use subpoint 0 as time - const time = data.subpoints?.length > 0 ? data.subpoints[0] : 0; - if (this.volume && this.volume.loadSpec.time !== time) { - this.volume.updateRequiredData({ time }); + // 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) { + 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 { // TODO showing bounding box for debugging purposes. - // Do we want it on by default in production? + // Do we want it on by default in production? Probably not? this.drawable?.setShowBoundingBox(true); return this.drawable?.sceneRoot; } + public onChannelLoaded(vol: Volume, channelIndex: number): void { + if (this.drawable) { + console.log("load", channelIndex); + 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(); + if (this.drawable && channelIndex === 0) { + console.log(this.drawable); + } + } + } + + public onBeforeRender(context: HasThreeJsContext): void { + this.drawable?.onAnimate(context); + } + // METHODS FROM `VolumeDataObserver` in volume-viewer - onVolumeData(_volume: Volume, channels: number[]): void { + public onVolumeData(_volume: Volume, channels: number[]): void { this.drawable?.updateScale(); this.drawable?.onChannelLoaded(channels); } - onVolumeChannelAdded(_volume: Volume, newChannelIndex: number): void { + public onVolumeChannelAdded( + _volume: Volume, + newChannelIndex: number + ): void { this.drawable?.onChannelAdded(newChannelIndex); } - onVolumeLoadError(_volume: Volume, error: unknown): void { + public onVolumeLoadError(_volume: Volume, error: unknown): void { console.error("Volume load error", error); } } From 1c0d2c6dd6a61d4103b4abb6fc46d476b3363937 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 9 Oct 2024 17:47:12 -0700 Subject: [PATCH 07/44] using more of those methods in geometrystore --- src/visGeometry/GeometryStore.ts | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/visGeometry/GeometryStore.ts b/src/visGeometry/GeometryStore.ts index 82a97fa4..cbc36b30 100644 --- a/src/visGeometry/GeometryStore.ts +++ b/src/visGeometry/GeometryStore.ts @@ -386,12 +386,13 @@ class GeometryStore { } /** Don't start a volume load worker until we know we need it */ - private getVolumeLoaderContext(): VolumeLoaderContext { + 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; } @@ -401,9 +402,10 @@ class GeometryStore { // Should this class get a `VolumeLoaderContext` going? const model = new VolumeModel(); this.setGeometryInRegistry(url, model, GeometryDisplayType.VOLUME); - const loader = await this.getVolumeLoaderContext().createLoader(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; From 18118c9de9d5558b53edc69c3ed2b6ce39778c7e Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 9 Oct 2024 17:47:28 -0700 Subject: [PATCH 08/44] doing the stuff that needs doing in `visGeometry` --- src/visGeometry/index.ts | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/visGeometry/index.ts b/src/visGeometry/index.ts index 67a2b8a6..5146312f 100644 --- a/src/visGeometry/index.ts +++ b/src/visGeometry/index.ts @@ -68,6 +68,7 @@ import { } from "./types"; import { checkAndSanitizePath } from "../util"; import ColorHandler from "./ColorHandler"; +import { HasThreeJsContext } from "@aics/volume-viewer"; const MAX_PATH_LEN = 32; const MAX_MESHES = 100000; @@ -999,6 +1000,15 @@ class VisGeometry { this.tempVolumeGroup.remove(this.tempVolumeGroup.children[i]); } + const volRenderContext: HasThreeJsContext = { + camera: this.camera, + // if not for `renderer` already being used for + // `SimulariumRenderer`, we could use `this` below. + renderer: this.threejsrenderer, + // equivalent prop to TrackballControls.scale as far as I can tell? + orthoScale: this.controls.zoomO, + }; + // re-add fibers immediately this.instancedMeshGroup.add(this.fibers.getGroup()); @@ -1027,6 +1037,7 @@ class VisGeometry { } else if (displayType === GeometryDisplayType.VOLUME) { const volObj = entry.geometry.getObject3D(); if (volObj) { + entry.geometry.onBeforeRender(volRenderContext); this.tempVolumeGroup.add(volObj); } } else { From 55289612bcd4fef1795a47a973addea3189c407b Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Thu, 10 Oct 2024 10:36:04 -0700 Subject: [PATCH 09/44] use volume subpoints --- examples/src/simulators/VolumeSimulator.ts | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/examples/src/simulators/VolumeSimulator.ts b/examples/src/simulators/VolumeSimulator.ts index 68ab51af..18a0e1a6 100644 --- a/examples/src/simulators/VolumeSimulator.ts +++ b/examples/src/simulators/VolumeSimulator.ts @@ -30,7 +30,11 @@ 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 From 3923a429173e78c2f20b38ba80d8b0a06a4ae9d1 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Thu, 10 Oct 2024 10:36:46 -0700 Subject: [PATCH 10/44] set resolution and a few other settings properly --- src/visGeometry/VolumeModel.ts | 25 ++++++++++++++++++------- src/visGeometry/index.ts | 9 ++++++++- 2 files changed, 26 insertions(+), 8 deletions(-) diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index f7c8119d..1062a1d9 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -1,10 +1,10 @@ import { Euler, Object3D, Vector3 } from "three"; import { + HasThreeJsContext, Lut, Volume, VolumeDrawable, - HasThreeJsContext, } from "@aics/volume-viewer"; import { AgentData } from "../simularium/types"; @@ -40,6 +40,10 @@ export default class VolumeModel { this.volume = volumeObject; this.drawable = new VolumeDrawable(this.volume, {}); this.volume.addVolumeDataObserver(this); + this.drawable.setBrightness(0.7); + this.drawable.setGamma(0.15, 0.9, 1.0); + this.drawable.setDensity(0.7); + this.drawable.setMaxProjectMode(true); } public setAgentData(data: AgentData): void { @@ -79,7 +83,6 @@ export default class VolumeModel { public onChannelLoaded(vol: Volume, channelIndex: number): void { if (this.drawable) { - console.log("load", channelIndex); const isEnabled = this.channelsEnabled[channelIndex]; this.drawable.setVolumeChannelEnabled(channelIndex, isEnabled); this.drawable.updateScale(); @@ -93,14 +96,22 @@ export default class VolumeModel { } this.drawable.updateLuts(); this.drawable.fuse(); - if (this.drawable && channelIndex === 0) { - console.log(this.drawable); - } } } - public onBeforeRender(context: HasThreeJsContext): void { - this.drawable?.onAnimate(context); + public onBeforeRender( + context: HasThreeJsContext, + width: number, + height: number + ): void { + if (this.drawable) { + this.drawable.setResolution(width, height); + this.drawable.onAnimate(context); + } + } + + public setSize(width: number, height: number): void { + this.drawable?.setResolution(width, height); } // METHODS FROM `VolumeDataObserver` in volume-viewer diff --git a/src/visGeometry/index.ts b/src/visGeometry/index.ts index 5146312f..751ea3a0 100644 --- a/src/visGeometry/index.ts +++ b/src/visGeometry/index.ts @@ -1009,6 +1009,9 @@ class VisGeometry { orthoScale: this.controls.zoomO, }; + const canvasWidth = this.threejsrenderer.domElement.width; + const canvasHeight = this.threejsrenderer.domElement.height; + // re-add fibers immediately this.instancedMeshGroup.add(this.fibers.getGroup()); @@ -1037,7 +1040,11 @@ class VisGeometry { } else if (displayType === GeometryDisplayType.VOLUME) { const volObj = entry.geometry.getObject3D(); if (volObj) { - entry.geometry.onBeforeRender(volRenderContext); + entry.geometry.onBeforeRender( + volRenderContext, + canvasWidth, + canvasHeight + ); this.tempVolumeGroup.add(volObj); } } else { From b7dce62b251d301d674d932227e5a54e59a151be Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Thu, 10 Oct 2024 16:59:36 -0700 Subject: [PATCH 11/44] switch back from max project (fix on volume-viewer side) --- src/visGeometry/VolumeModel.ts | 1 - 1 file changed, 1 deletion(-) diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index 1062a1d9..329bf142 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -43,7 +43,6 @@ export default class VolumeModel { this.drawable.setBrightness(0.7); this.drawable.setGamma(0.15, 0.9, 1.0); this.drawable.setDensity(0.7); - this.drawable.setMaxProjectMode(true); } public setAgentData(data: AgentData): void { From 1a9d4350b8d8c1c051e2f62a5189927a8bcf9788 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Thu, 10 Oct 2024 17:00:14 -0700 Subject: [PATCH 12/44] move ball geometry into volume --- examples/src/simulators/VolumeSimulator.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/src/simulators/VolumeSimulator.ts b/examples/src/simulators/VolumeSimulator.ts index 18a0e1a6..9e0f5a2a 100644 --- a/examples/src/simulators/VolumeSimulator.ts +++ b/examples/src/simulators/VolumeSimulator.ts @@ -42,7 +42,7 @@ export default class VolumeSim implements IClientSimulatorImpl { 1, // type 0, // x 0, // y - 6, // z + 3, // z 0, // rx 0, // ry 0, // rz From 1bbcfd94f4cf0e7f34ffe2c4b040383d16603f99 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Thu, 10 Oct 2024 18:38:34 -0700 Subject: [PATCH 13/44] trying to get ortho camera to work --- src/visGeometry/VolumeModel.ts | 11 +++++++---- src/visGeometry/index.ts | 8 +++++++- 2 files changed, 14 insertions(+), 5 deletions(-) diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index 329bf142..1377d822 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -74,9 +74,6 @@ export default class VolumeModel { } public getObject3D(): Object3D | undefined { - // TODO showing bounding box for debugging purposes. - // Do we want it on by default in production? Probably not? - this.drawable?.setShowBoundingBox(true); return this.drawable?.sceneRoot; } @@ -101,9 +98,15 @@ export default class VolumeModel { public onBeforeRender( context: HasThreeJsContext, width: number, - height: number + height: number, + orthoScale: number | undefined ): void { if (this.drawable) { + const isOrtho = orthoScale !== undefined; + this.drawable.setIsOrtho(isOrtho); + if (isOrtho) { + this.drawable.setOrthoScale(orthoScale); + } this.drawable.setResolution(width, height); this.drawable.onAnimate(context); } diff --git a/src/visGeometry/index.ts b/src/visGeometry/index.ts index 751ea3a0..f94f28ba 100644 --- a/src/visGeometry/index.ts +++ b/src/visGeometry/index.ts @@ -1040,10 +1040,16 @@ class VisGeometry { } else if (displayType === GeometryDisplayType.VOLUME) { const volObj = entry.geometry.getObject3D(); if (volObj) { + const isOrtho = (this.camera as OrthographicCamera) + .isOrthographicCamera; + const orthoScale = isOrtho + ? this.camera.zoom + : undefined; entry.geometry.onBeforeRender( volRenderContext, canvasWidth, - canvasHeight + canvasHeight, + orthoScale ); this.tempVolumeGroup.add(volObj); } From d2b8e724d776148f1598c56a89437ec2f72506c8 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Thu, 10 Oct 2024 22:58:22 -0700 Subject: [PATCH 14/44] remove orthoscale context prop --- src/visGeometry/index.ts | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/visGeometry/index.ts b/src/visGeometry/index.ts index f94f28ba..c1f1377e 100644 --- a/src/visGeometry/index.ts +++ b/src/visGeometry/index.ts @@ -1005,8 +1005,6 @@ class VisGeometry { // if not for `renderer` already being used for // `SimulariumRenderer`, we could use `this` below. renderer: this.threejsrenderer, - // equivalent prop to TrackballControls.scale as far as I can tell? - orthoScale: this.controls.zoomO, }; const canvasWidth = this.threejsrenderer.domElement.width; @@ -1043,7 +1041,7 @@ class VisGeometry { const isOrtho = (this.camera as OrthographicCamera) .isOrthographicCamera; const orthoScale = isOrtho - ? this.camera.zoom + ? 1 / this.camera.zoom : undefined; entry.geometry.onBeforeRender( volRenderContext, From 0033592aea8069aea7e26b41c6748c87591ff5bf Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Thu, 10 Oct 2024 22:59:33 -0700 Subject: [PATCH 15/44] rename: `tempVolumeGroup` -> `volumeGroup` --- src/visGeometry/index.ts | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/visGeometry/index.ts b/src/visGeometry/index.ts index c1f1377e..9298c6c7 100644 --- a/src/visGeometry/index.ts +++ b/src/visGeometry/index.ts @@ -153,7 +153,7 @@ 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[]; @@ -220,9 +220,9 @@ 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.resetBounds(DEFAULT_VOLUME_DIMENSIONS); @@ -996,8 +996,8 @@ 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 volRenderContext: HasThreeJsContext = { @@ -1049,7 +1049,7 @@ class VisGeometry { canvasHeight, orthoScale ); - this.tempVolumeGroup.add(volObj); + this.volumeGroup.add(volObj); } } else { const meshEntry = entry as MeshGeometry; @@ -1082,7 +1082,7 @@ 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, @@ -1094,7 +1094,7 @@ class VisGeometry { this.boundingBoxMesh.visible = true; this.tickMarksMesh.visible = true; 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 From b9f30b7381b110bb379a17630757077c70ceaa38 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Mon, 21 Oct 2024 13:18:49 -0700 Subject: [PATCH 16/44] update volume-viewer interface; try (fail) to get ortho volumes to work --- src/visGeometry/VolumeModel.ts | 31 +++++++++++++++++++------------ src/visGeometry/index.ts | 19 ++++++------------- 2 files changed, 25 insertions(+), 25 deletions(-) diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index 1377d822..21d0fce5 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -1,11 +1,13 @@ -import { Euler, Object3D, Vector3 } from "three"; - import { - HasThreeJsContext, - Lut, - Volume, - VolumeDrawable, -} from "@aics/volume-viewer"; + Euler, + Object3D, + OrthographicCamera, + PerspectiveCamera, + Vector3, + WebGLRenderer, +} from "three"; + +import { Lut, Volume, VolumeDrawable } from "@aics/volume-viewer"; import { AgentData } from "../simularium/types"; @@ -77,7 +79,7 @@ export default class VolumeModel { return this.drawable?.sceneRoot; } - public onChannelLoaded(vol: Volume, channelIndex: number): void { + public onChannelLoaded(_vol: Volume, channelIndex: number): void { if (this.drawable) { const isEnabled = this.channelsEnabled[channelIndex]; this.drawable.setVolumeChannelEnabled(channelIndex, isEnabled); @@ -95,11 +97,10 @@ export default class VolumeModel { } } - public onBeforeRender( - context: HasThreeJsContext, + public setViewportSize( width: number, height: number, - orthoScale: number | undefined + orthoScale?: number ): void { if (this.drawable) { const isOrtho = orthoScale !== undefined; @@ -108,10 +109,16 @@ export default class VolumeModel { this.drawable.setOrthoScale(orthoScale); } this.drawable.setResolution(width, height); - this.drawable.onAnimate(context); } } + 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); } diff --git a/src/visGeometry/index.ts b/src/visGeometry/index.ts index f94f28ba..b65c8cb3 100644 --- a/src/visGeometry/index.ts +++ b/src/visGeometry/index.ts @@ -68,7 +68,6 @@ import { } from "./types"; import { checkAndSanitizePath } from "../util"; import ColorHandler from "./ColorHandler"; -import { HasThreeJsContext } from "@aics/volume-viewer"; const MAX_PATH_LEN = 32; const MAX_MESHES = 100000; @@ -1000,15 +999,6 @@ class VisGeometry { this.tempVolumeGroup.remove(this.tempVolumeGroup.children[i]); } - const volRenderContext: HasThreeJsContext = { - camera: this.camera, - // if not for `renderer` already being used for - // `SimulariumRenderer`, we could use `this` below. - renderer: this.threejsrenderer, - // equivalent prop to TrackballControls.scale as far as I can tell? - orthoScale: this.controls.zoomO, - }; - const canvasWidth = this.threejsrenderer.domElement.width; const canvasHeight = this.threejsrenderer.domElement.height; @@ -1043,14 +1033,17 @@ class VisGeometry { const isOrtho = (this.camera as OrthographicCamera) .isOrthographicCamera; const orthoScale = isOrtho - ? this.camera.zoom + ? 0.5 / this.camera.zoom : undefined; - entry.geometry.onBeforeRender( - volRenderContext, + entry.geometry.setViewportSize( canvasWidth, canvasHeight, orthoScale ); + entry.geometry.onBeforeRender( + this.threejsrenderer, + this.camera + ); this.tempVolumeGroup.add(volObj); } } else { From 547f8c041ee1dd04df3e9a27ce3de342e57e56c4 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Mon, 21 Oct 2024 15:55:44 -0700 Subject: [PATCH 17/44] experiment with how to get `orthoScale` right --- src/visGeometry/VolumeModel.ts | 11 ++++++++--- src/visGeometry/index.ts | 2 +- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index 21d0fce5..9a732454 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -18,6 +18,7 @@ export default class VolumeModel { private drawable?: VolumeDrawable; private volume?: Volume; private channelsEnabled: boolean[] = []; + private scale = 1; private setEnabledChannels(channels: number[]): void { if (!this.volume || !this.drawable) { @@ -53,8 +54,10 @@ export default class VolumeModel { this.drawable.setRotation( new Euler(data.xrot, data.yrot, data.zrot) ); - const r = data.cr * 2; - this.drawable.setScale(new Vector3(r, r, r)); + 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 @@ -106,7 +109,9 @@ export default class VolumeModel { const isOrtho = orthoScale !== undefined; this.drawable.setIsOrtho(isOrtho); if (isOrtho) { - this.drawable.setOrthoScale(orthoScale); + this.drawable.setOrthoScale( + (orthoScale * this.scale) / (height / width) + ); } this.drawable.setResolution(width, height); } diff --git a/src/visGeometry/index.ts b/src/visGeometry/index.ts index d4139cf8..eaaa338f 100644 --- a/src/visGeometry/index.ts +++ b/src/visGeometry/index.ts @@ -1033,7 +1033,7 @@ class VisGeometry { const isOrtho = (this.camera as OrthographicCamera) .isOrthographicCamera; const orthoScale = isOrtho - ? 0.5 / this.camera.zoom + ? 1 / this.camera.zoom : undefined; entry.geometry.setViewportSize( canvasWidth, From f21b65bb7c6a13ec8d65b80d48e1e44c9886c57b Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 23 Oct 2024 11:41:07 -0700 Subject: [PATCH 18/44] FIX orthographic volumes AT LAST --- src/visGeometry/VolumeModel.ts | 4 +--- src/visGeometry/index.ts | 3 ++- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index 9a732454..8556fcb5 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -109,9 +109,7 @@ export default class VolumeModel { const isOrtho = orthoScale !== undefined; this.drawable.setIsOrtho(isOrtho); if (isOrtho) { - this.drawable.setOrthoScale( - (orthoScale * this.scale) / (height / width) - ); + this.drawable.setOrthoScale(orthoScale); } this.drawable.setResolution(width, height); } diff --git a/src/visGeometry/index.ts b/src/visGeometry/index.ts index eaaa338f..e4a2b602 100644 --- a/src/visGeometry/index.ts +++ b/src/visGeometry/index.ts @@ -1033,7 +1033,8 @@ class VisGeometry { const isOrtho = (this.camera as OrthographicCamera) .isOrthographicCamera; const orthoScale = isOrtho - ? 1 / this.camera.zoom + ? (this.camera as OrthographicCamera).top / + this.camera.zoom : undefined; entry.geometry.setViewportSize( canvasWidth, From 7fa5e28169d86a8fd05723e8256b95ee128a362e Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 23 Oct 2024 11:44:45 -0700 Subject: [PATCH 19/44] make camera type testing nicer --- src/visGeometry/index.ts | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/src/visGeometry/index.ts b/src/visGeometry/index.ts index e4a2b602..c506a3fd 100644 --- a/src/visGeometry/index.ts +++ b/src/visGeometry/index.ts @@ -106,6 +106,11 @@ 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 { @@ -1030,11 +1035,8 @@ class VisGeometry { } else if (displayType === GeometryDisplayType.VOLUME) { const volObj = entry.geometry.getObject3D(); if (volObj) { - const isOrtho = (this.camera as OrthographicCamera) - .isOrthographicCamera; - const orthoScale = isOrtho - ? (this.camera as OrthographicCamera).top / - this.camera.zoom + const orthoScale = isOrthographicCamera(this.camera) + ? this.camera.top / this.camera.zoom : undefined; entry.geometry.setViewportSize( canvasWidth, From 9b507cf2bc482f637f790f82dc5db66a7881df33 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Thu, 7 Nov 2024 10:10:43 -0800 Subject: [PATCH 20/44] replace volume-viewer branch dependency with proper npm dep --- package-lock.json | 22 ++++++++++++++++++---- package.json | 2 +- 2 files changed, 19 insertions(+), 5 deletions(-) diff --git a/package-lock.json b/package-lock.json index a2194896..8e66f898 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,7 +9,7 @@ "version": "3.8.4", "license": "MIT", "dependencies": { - "@aics/volume-viewer": "allen-cell-animated/volume-viewer#simularium-volumes", + "@aics/volume-viewer": "^3.12.0", "@babel/plugin-transform-runtime": "^7.23.6", "@babel/runtime": "^7.23.6", "@fortawesome/fontawesome-free": "^5.15.2", @@ -87,18 +87,26 @@ } }, "node_modules/@aics/volume-viewer": { - "version": "3.11.1", - "resolved": "git+ssh://git@github.com/allen-cell-animated/volume-viewer.git#a6efd4a7f2272a58ee4481a3f24be39bf626847c", + "version": "3.12.0", + "resolved": "https://registry.npmjs.org/@aics/volume-viewer/-/volume-viewer-3.12.0.tgz", + "integrity": "sha512-Xll1tYyxpkJzIA8R+W2S2FeDi0BCnorLlSfhx1oG7i1PwSabgM1+GFxlTdR1M3h4BTlKcxlM8RxvS0uFPPMVOw==", "license": "MIT", "dependencies": { "@babel/runtime": "^7.25.6", "geotiff": "^2.0.5", "serialize-error": "^11.0.3", - "three": "^0.144.0", + "three": "^0.162.0", + "throttled-queue": "^2.1.4", "tweakpane": "^3.1.9", "zarrita": "^0.3.2" } }, + "node_modules/@aics/volume-viewer/node_modules/three": { + "version": "0.162.0", + "resolved": "https://registry.npmjs.org/three/-/three-0.162.0.tgz", + "integrity": "sha512-xfCYj4RnlozReCmUd+XQzj6/5OjDNHBy5nT6rVwrOKGENAvpXe2z1jL+DZYaMu4/9pNsjH/4Os/VvS9IrH7IOQ==", + "license": "MIT" + }, "node_modules/@ampproject/remapping": { "version": "2.3.0", "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz", @@ -17191,6 +17199,12 @@ "integrity": "sha512-R8AXPuqfjfRJKkYoTQcTK7A6i3AdO9++2n8ubya/GTU+fEHhYKu1ZooRSCPkx69jbnzT7dD/xEo6eROQTt2lJw==", "license": "MIT" }, + "node_modules/throttled-queue": { + "version": "2.1.4", + "resolved": "https://registry.npmjs.org/throttled-queue/-/throttled-queue-2.1.4.tgz", + "integrity": "sha512-YGdk8sdmr4ge3g+doFj/7RLF5kLM+Mi7DEciu9PHxnMJZMeVuZeTj31g4VE7ekUffx/IdbvrtOCiz62afg0mkg==", + "license": "MIT" + }, "node_modules/through": { "version": "2.3.8", "resolved": "https://registry.npmjs.org/through/-/through-2.3.8.tgz", diff --git a/package.json b/package.json index 2d50eca6..922c6109 100644 --- a/package.json +++ b/package.json @@ -89,7 +89,7 @@ "react-dom": "^18.2.0" }, "dependencies": { - "@aics/volume-viewer": "allen-cell-animated/volume-viewer#simularium-volumes", + "@aics/volume-viewer": "^3.12.0", "@babel/plugin-transform-runtime": "^7.23.6", "@babel/runtime": "^7.23.6", "@fortawesome/fontawesome-free": "^5.15.2", From ff87ac35d29710dacaa9c342d455dcb96d0ce11b Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Fri, 17 Jan 2025 17:38:59 -0800 Subject: [PATCH 21/44] bump @types/three --- package-lock.json | 8 ++++---- package.json | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/package-lock.json b/package-lock.json index e3ed64db..21cc8ce1 100644 --- a/package-lock.json +++ b/package-lock.json @@ -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", @@ -3073,9 +3073,9 @@ "license": "MIT" }, "node_modules/@types/three": { - "version": "0.170.0", - "resolved": "https://registry.npmjs.org/@types/three/-/three-0.170.0.tgz", - "integrity": "sha512-CUm2uckq+zkCY7ZbFpviRttY+6f9fvwm6YqSqPfA5K22s9w7R4VnA3rzJse8kHVvuzLcTx+CjNCs2NYe0QFAyg==", + "version": "0.171.0", + "resolved": "https://registry.npmjs.org/@types/three/-/three-0.171.0.tgz", + "integrity": "sha512-oLuT1SAsT+CUg/wxUTFHo0K3NtJLnx9sJhZWQJp/0uXqFpzSk1hRHmvWvpaAWSfvx2db0lVKZ5/wV0I0isD2mQ==", "dev": true, "license": "MIT", "dependencies": { diff --git a/package.json b/package.json index 8a075a7d..baf59d9f 100644 --- a/package.json +++ b/package.json @@ -55,7 +55,7 @@ "@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", From 8b2edd21431a9f1f03941087ef36c9595c89b100 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Fri, 17 Jan 2025 17:39:16 -0800 Subject: [PATCH 22/44] fix volume simulator import --- examples/src/simulators/VolumeSimulator.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/src/simulators/VolumeSimulator.ts b/examples/src/simulators/VolumeSimulator.ts index 9e0f5a2a..c2111867 100644 --- a/examples/src/simulators/VolumeSimulator.ts +++ b/examples/src/simulators/VolumeSimulator.ts @@ -1,4 +1,4 @@ -import { GeometryDisplayType } from "../../../src"; +import { GeometryDisplayType } from "@aics/simularium-viewer"; import { IClientSimulatorImpl, ClientMessageEnum, From d3f590bd646a44f3aa51dcd9f4a1f6130af0ec8d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 01:29:15 +0000 Subject: [PATCH 23/44] Bump vite from 5.4.14 to 5.4.17 Bumps [vite](https://github.com/vitejs/vite/tree/HEAD/packages/vite) from 5.4.14 to 5.4.17. - [Release notes](https://github.com/vitejs/vite/releases) - [Changelog](https://github.com/vitejs/vite/blob/v5.4.17/packages/vite/CHANGELOG.md) - [Commits](https://github.com/vitejs/vite/commits/v5.4.17/packages/vite) --- updated-dependencies: - dependency-name: vite dependency-version: 5.4.17 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- package-lock.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index 06859e5d..d61ec789 100644 --- a/package-lock.json +++ b/package-lock.json @@ -13753,9 +13753,9 @@ } }, "node_modules/vite": { - "version": "5.4.14", - "resolved": "https://registry.npmjs.org/vite/-/vite-5.4.14.tgz", - "integrity": "sha512-EK5cY7Q1D8JNhSaPKVK4pwBFvaTmZxEnoKXLG/U9gmdDcihQGNzFlgIvaxezFR4glP1LsuiedwMBqCXH3wZccA==", + "version": "5.4.17", + "resolved": "https://registry.npmjs.org/vite/-/vite-5.4.17.tgz", + "integrity": "sha512-5+VqZryDj4wgCs55o9Lp+p8GE78TLVg0lasCH5xFZ4jacZjtqZa6JUw9/p0WeAojaOfncSM6v77InkFPGnvPvg==", "dev": true, "license": "MIT", "dependencies": { From 9aeedfdf834c2f8a746190800914114af6ac6705 Mon Sep 17 00:00:00 2001 From: Cameron Fraser Date: Wed, 23 Apr 2025 16:48:40 -0700 Subject: [PATCH 24/44] update vole-core dependency --- package-lock.json | 101 +++++++++++-------------------- package.json | 2 +- src/visGeometry/GeometryStore.ts | 2 +- src/visGeometry/VolumeModel.ts | 2 +- 4 files changed, 38 insertions(+), 69 deletions(-) diff --git a/package-lock.json b/package-lock.json index 7ab67448..4f57ed3c 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,7 +9,7 @@ "version": "3.9.1", "license": "MIT", "dependencies": { - "@aics/volume-viewer": "^3.12.2", + "@aics/vole-core": "^3.14.1", "@babel/plugin-transform-runtime": "^7.23.6", "@babel/runtime": "^7.23.6", "@fortawesome/fontawesome-free": "^5.15.2", @@ -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": "3.14.1", + "resolved": "https://registry.npmjs.org/@aics/vole-core/-/vole-core-3.14.1.tgz", + "integrity": "sha512-CtLwx3x0wg7Rf/NGYGTjrvulVtDMZrCXGjqyEp3sUk1UIFPq/4yzID5lWMJYFfLfKx0bactCvE72NZuUE5tKyQ==", "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": "^0.4.0" } }, - "node_modules/@aics/volume-viewer/node_modules/three": { - "version": "0.162.0", - "resolved": "https://registry.npmjs.org/three/-/three-0.162.0.tgz", - "integrity": "sha512-xfCYj4RnlozReCmUd+XQzj6/5OjDNHBy5nT6rVwrOKGENAvpXe2z1jL+DZYaMu4/9pNsjH/4Os/VvS9IrH7IOQ==", - "license": "MIT" - }, "node_modules/@ampproject/remapping": { "version": "2.3.0", "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz", @@ -2878,9 +2872,9 @@ } }, "node_modules/@petamoriken/float16": { - "version": "3.9.0", - "resolved": "https://registry.npmjs.org/@petamoriken/float16/-/float16-3.9.0.tgz", - "integrity": "sha512-rYUZ+VFjPHD0NT2JYKj64NxXxrV642IiyaUxxorTEj0S3hT7B5Ixezyc9Fn+XvSk0ETEBp5VWjGIErzh0ug0Xw==", + "version": "3.9.2", + "resolved": "https://registry.npmjs.org/@petamoriken/float16/-/float16-3.9.2.tgz", + "integrity": "sha512-VgffxawQde93xKxT3qap3OH+meZf7VaSB5Sqd4Rqc+FP5alWbpOyan/7tRbOAvynjpG3GpdtAuGU/NdhQpmrog==", "license": "MIT" }, "node_modules/@pkgjs/parseargs": { @@ -3937,40 +3931,16 @@ "license": "Apache-2.0", "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": "sha512-Q61d9MYX6dsK1DLltEpwx4mJWCZHj0TXiaEN4QpxNDtToa/EoyytP/pYHPypO4GXBscZooJ6eZkKT5FMx9PVfg==", - "dependencies": { - "@zarrita/core": "^0.0.3", - "@zarrita/storage": "^0.0.2", - "@zarrita/typedarray": "^0.0.1" - } - }, "node_modules/@zarrita/storage": { - "version": "0.0.2", - "resolved": "https://registry.npmjs.org/@zarrita/storage/-/storage-0.0.2.tgz", - "integrity": "sha512-uFt4abAoiOYLroalNDAnVaQxA17zGKrQ0waYKmTVm+bNonz8ggKZP+0FqMhgUZITGChqoANHuYTazbuU5AFXWA==", + "version": "0.1.1", + "resolved": "https://registry.npmjs.org/@zarrita/storage/-/storage-0.1.1.tgz", + "integrity": "sha512-6/NUCvpzsIxfxeMv59jRTl/bOZg3GZfMP6iR8EIqrTaaE0S2jLL/ceX1OxcFBKnuA8/Z2YmgX4SFBHwFGrCcsw==", + "license": "MIT", "dependencies": { "reference-spec-reader": "^0.2.0", - "unzipit": "^1.3.6" + "unzipit": "^1.4.3" } }, - "node_modules/@zarrita/typedarray": { - "version": "0.0.1", - "resolved": "https://registry.npmjs.org/@zarrita/typedarray/-/typedarray-0.0.1.tgz", - "integrity": "sha512-ZdvNjYP1bEuQXoSTVkemV99w42jHYrJ3nh9golCLd4MVBlrVbfZo4wWgBslU4JZUaDikhFSH+GWMDgAq/rI32g==" - }, "node_modules/acorn": { "version": "8.14.0", "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.14.0.tgz", @@ -6708,7 +6678,6 @@ "version": "0.8.2", "resolved": "https://registry.npmjs.org/fflate/-/fflate-0.8.2.tgz", "integrity": "sha512-cPJU47OaAoCbg0pBvzsgpTPhmhqI5eJjh/JIu8tPj5q+T7iLvW/JAYUqmE7KOB4R1ZyEhzBaIQpQpardBF5z8A==", - "dev": true, "license": "MIT" }, "node_modules/file-entry-cache": { @@ -9577,12 +9546,12 @@ "license": "MIT" }, "node_modules/numcodecs": { - "version": "0.2.2", - "resolved": "https://registry.npmjs.org/numcodecs/-/numcodecs-0.2.2.tgz", - "integrity": "sha512-Y5K8mv80yb4MgVpcElBkUeMZqeE4TrovxRit/dTZvoRl6YkB6WEjY+fiUjGCblITnt3T3fmrDg8yRWu0gOLjhQ==", + "version": "0.3.2", + "resolved": "https://registry.npmjs.org/numcodecs/-/numcodecs-0.3.2.tgz", + "integrity": "sha512-6YSPnmZgg0P87jnNhi3s+FVLOcIn3y+1CTIgUulA3IdASzK9fJM87sUFkpyA+be9GibGRaST2wCgkD+6U+fWKw==", "license": "MIT", - "engines": { - "node": ">=12" + "dependencies": { + "fflate": "^0.8.0" } }, "node_modules/nwsapi": { @@ -10127,9 +10096,9 @@ } }, "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": { @@ -14146,9 +14115,9 @@ } }, "node_modules/web-worker": { - "version": "1.3.0", - "resolved": "https://registry.npmjs.org/web-worker/-/web-worker-1.3.0.tgz", - "integrity": "sha512-BSR9wyRsy/KOValMgd5kMyr3JzpdeoR9KVId8u5GVlTTAtNChlsE4yTxeY7zMdNSyOmoKBv8NH2qeRY9Tg+IaA==", + "version": "1.5.0", + "resolved": "https://registry.npmjs.org/web-worker/-/web-worker-1.5.0.tgz", + "integrity": "sha512-RiMReJrTAiA+mBjGONMnjVDP2u3p9R1vkcGz6gDIrOMT3oGuYwX2WRMYI9ipkphSuE5XKEhydbhNEJh4NY9mlw==", "license": "Apache-2.0" }, "node_modules/webidl-conversions": { @@ -14545,9 +14514,9 @@ } }, "node_modules/xml-utils": { - "version": "1.10.1", - "resolved": "https://registry.npmjs.org/xml-utils/-/xml-utils-1.10.1.tgz", - "integrity": "sha512-Dn6vJ1Z9v1tepSjvnCpwk5QqwIPcEFKdgnjqfYOABv1ngSofuAhtlugcUC3ehS1OHdgDWSG6C5mvj+Qm15udTQ==", + "version": "1.10.2", + "resolved": "https://registry.npmjs.org/xml-utils/-/xml-utils-1.10.2.tgz", + "integrity": "sha512-RqM+2o1RYs6T8+3DzDSoTRAUfrvaejbVHcp3+thnAtDKo8LskR+HomLajEy5UjTz24rpka7AxVBRR3g2wTUkJA==", "license": "CC0-1.0" }, "node_modules/xmlchars": { @@ -14647,13 +14616,13 @@ } }, "node_modules/zarrita": { - "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": "0.4.0", + "resolved": "https://registry.npmjs.org/zarrita/-/zarrita-0.4.0.tgz", + "integrity": "sha512-MK2uustzUF0PooWl6HVUfTares/nmaq5NwRZux/L3npvkSX6Qdpd7w/NOW2cF9EI35yqggoHNi3Nlxyq1YT5eQ==", + "license": "MIT", "dependencies": { - "@zarrita/core": "^0.0.3", - "@zarrita/indexing": "^0.0.3", - "@zarrita/storage": "^0.0.2" + "@zarrita/storage": "^0.1.0", + "numcodecs": "^0.3.2" } }, "node_modules/zstddec": { diff --git a/package.json b/package.json index 78b5cd56..4c8acd37 100644 --- a/package.json +++ b/package.json @@ -93,7 +93,7 @@ "react-dom": "^18.2.0" }, "dependencies": { - "@aics/volume-viewer": "^3.12.2", + "@aics/vole-core": "^3.14.1", "@babel/plugin-transform-runtime": "^7.23.6", "@babel/runtime": "^7.23.6", "@fortawesome/fontawesome-free": "^5.15.2", diff --git a/src/visGeometry/GeometryStore.ts b/src/visGeometry/GeometryStore.ts index ed6f771e..b06e5832 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 { LoadSpec, VolumeLoaderContext } from "@aics/volume-viewer"; +import { LoadSpec, VolumeLoaderContext } from "@aics/vole-core"; import { BufferGeometry, Object3D, diff --git a/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index 8556fcb5..cdb8204f 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -7,7 +7,7 @@ import { WebGLRenderer, } from "three"; -import { Lut, Volume, VolumeDrawable } from "@aics/volume-viewer"; +import { Lut, Volume, VolumeDrawable } from "@aics/vole-core"; import { AgentData } from "../simularium/types"; From 55699e563c7f1693bfee21fb292efb41797b2eeb Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 25 Apr 2025 21:16:40 +0000 Subject: [PATCH 25/44] Bump http-proxy-middleware from 2.0.7 to 2.0.9 in /examples Bumps [http-proxy-middleware](https://github.com/chimurai/http-proxy-middleware) from 2.0.7 to 2.0.9. - [Release notes](https://github.com/chimurai/http-proxy-middleware/releases) - [Changelog](https://github.com/chimurai/http-proxy-middleware/blob/v2.0.9/CHANGELOG.md) - [Commits](https://github.com/chimurai/http-proxy-middleware/compare/v2.0.7...v2.0.9) --- updated-dependencies: - dependency-name: http-proxy-middleware dependency-version: 2.0.9 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- examples/package-lock.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/examples/package-lock.json b/examples/package-lock.json index bfdb1b95..6f3869b3 100644 --- a/examples/package-lock.json +++ b/examples/package-lock.json @@ -3569,9 +3569,9 @@ } }, "node_modules/http-proxy-middleware": { - "version": "2.0.7", - "resolved": "https://registry.npmjs.org/http-proxy-middleware/-/http-proxy-middleware-2.0.7.tgz", - "integrity": "sha512-fgVY8AV7qU7z/MmXJ/rxwbrtQH4jBQ9m7kp3llF0liB7glmFeVZFBepQb32T3y8n8k2+AEYuMPCpinYW+/CuRA==", + "version": "2.0.9", + "resolved": "https://registry.npmjs.org/http-proxy-middleware/-/http-proxy-middleware-2.0.9.tgz", + "integrity": "sha512-c1IyJYLYppU574+YI7R4QyX2ystMtVXZwIdzazUIPIJsHuWNd+mho2j+bKoHftndicGj9yh+xjd+l0yj7VeT1Q==", "dev": true, "license": "MIT", "dependencies": { From b4df8122bcf894470603214b5bcb83348dfb649e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 25 Apr 2025 21:16:46 +0000 Subject: [PATCH 26/44] Bump vite from 5.4.17 to 5.4.18 Bumps [vite](https://github.com/vitejs/vite/tree/HEAD/packages/vite) from 5.4.17 to 5.4.18. - [Release notes](https://github.com/vitejs/vite/releases) - [Changelog](https://github.com/vitejs/vite/blob/v5.4.18/packages/vite/CHANGELOG.md) - [Commits](https://github.com/vitejs/vite/commits/v5.4.18/packages/vite) --- updated-dependencies: - dependency-name: vite dependency-version: 5.4.18 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- package-lock.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index 9a57ceb8..ddfed2bf 100644 --- a/package-lock.json +++ b/package-lock.json @@ -13753,9 +13753,9 @@ } }, "node_modules/vite": { - "version": "5.4.17", - "resolved": "https://registry.npmjs.org/vite/-/vite-5.4.17.tgz", - "integrity": "sha512-5+VqZryDj4wgCs55o9Lp+p8GE78TLVg0lasCH5xFZ4jacZjtqZa6JUw9/p0WeAojaOfncSM6v77InkFPGnvPvg==", + "version": "5.4.18", + "resolved": "https://registry.npmjs.org/vite/-/vite-5.4.18.tgz", + "integrity": "sha512-1oDcnEp3lVyHCuQ2YFelM4Alm2o91xNoMncRm1U7S+JdYfYOvbiGZ3/CxGttrOu2M/KcGz7cRC2DoNUA6urmMA==", "dev": true, "license": "MIT", "dependencies": { From a69bb87d025df1fb8cac47e29924a807627a0c7a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 30 Apr 2025 19:19:05 +0000 Subject: [PATCH 27/44] Bump vite from 6.2.5 to 6.3.4 in /examples Bumps [vite](https://github.com/vitejs/vite/tree/HEAD/packages/vite) from 6.2.5 to 6.3.4. - [Release notes](https://github.com/vitejs/vite/releases) - [Changelog](https://github.com/vitejs/vite/blob/main/packages/vite/CHANGELOG.md) - [Commits](https://github.com/vitejs/vite/commits/v6.3.4/packages/vite) --- updated-dependencies: - dependency-name: vite dependency-version: 6.3.4 dependency-type: direct:development ... Signed-off-by: dependabot[bot] --- examples/package-lock.json | 267 +++++++++++++++++++++++++------------ examples/package.json | 2 +- 2 files changed, 180 insertions(+), 89 deletions(-) diff --git a/examples/package-lock.json b/examples/package-lock.json index bfdb1b95..82461c60 100644 --- a/examples/package-lock.json +++ b/examples/package-lock.json @@ -20,7 +20,7 @@ "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" @@ -990,9 +990,9 @@ } }, "node_modules/@rollup/rollup-android-arm-eabi": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-android-arm-eabi/-/rollup-android-arm-eabi-4.34.8.tgz", - "integrity": "sha512-q217OSE8DTp8AFHuNHXo0Y86e1wtlfVrXiAlwkIvGRQv9zbc6mE3sjIVfwI8sYUyNxwOg0j/Vm1RKM04JcWLJw==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-android-arm-eabi/-/rollup-android-arm-eabi-4.40.1.tgz", + "integrity": "sha512-kxz0YeeCrRUHz3zyqvd7n+TVRlNyTifBsmnmNPtk3hQURUyG9eAB+usz6DAwagMusjx/zb3AjvDUvhFGDAexGw==", "cpu": [ "arm" ], @@ -1004,9 +1004,9 @@ ] }, "node_modules/@rollup/rollup-android-arm64": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-android-arm64/-/rollup-android-arm64-4.34.8.tgz", - "integrity": "sha512-Gigjz7mNWaOL9wCggvoK3jEIUUbGul656opstjaUSGC3eT0BM7PofdAJaBfPFWWkXNVAXbaQtC99OCg4sJv70Q==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-android-arm64/-/rollup-android-arm64-4.40.1.tgz", + "integrity": "sha512-PPkxTOisoNC6TpnDKatjKkjRMsdaWIhyuMkA4UsBXT9WEZY4uHezBTjs6Vl4PbqQQeu6oION1w2voYZv9yquCw==", "cpu": [ "arm64" ], @@ -1018,9 +1018,9 @@ ] }, "node_modules/@rollup/rollup-darwin-arm64": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-darwin-arm64/-/rollup-darwin-arm64-4.34.8.tgz", - "integrity": "sha512-02rVdZ5tgdUNRxIUrFdcMBZQoaPMrxtwSb+/hOfBdqkatYHR3lZ2A2EGyHq2sGOd0Owk80oV3snlDASC24He3Q==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-darwin-arm64/-/rollup-darwin-arm64-4.40.1.tgz", + "integrity": "sha512-VWXGISWFY18v/0JyNUy4A46KCFCb9NVsH+1100XP31lud+TzlezBbz24CYzbnA4x6w4hx+NYCXDfnvDVO6lcAA==", "cpu": [ "arm64" ], @@ -1032,9 +1032,9 @@ ] }, "node_modules/@rollup/rollup-darwin-x64": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-darwin-x64/-/rollup-darwin-x64-4.34.8.tgz", - "integrity": "sha512-qIP/elwR/tq/dYRx3lgwK31jkZvMiD6qUtOycLhTzCvrjbZ3LjQnEM9rNhSGpbLXVJYQ3rq39A6Re0h9tU2ynw==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-darwin-x64/-/rollup-darwin-x64-4.40.1.tgz", + "integrity": "sha512-nIwkXafAI1/QCS7pxSpv/ZtFW6TXcNUEHAIA9EIyw5OzxJZQ1YDrX+CL6JAIQgZ33CInl1R6mHet9Y/UZTg2Bw==", "cpu": [ "x64" ], @@ -1046,9 +1046,9 @@ ] }, "node_modules/@rollup/rollup-freebsd-arm64": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-freebsd-arm64/-/rollup-freebsd-arm64-4.34.8.tgz", - "integrity": "sha512-IQNVXL9iY6NniYbTaOKdrlVP3XIqazBgJOVkddzJlqnCpRi/yAeSOa8PLcECFSQochzqApIOE1GHNu3pCz+BDA==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-freebsd-arm64/-/rollup-freebsd-arm64-4.40.1.tgz", + "integrity": "sha512-BdrLJ2mHTrIYdaS2I99mriyJfGGenSaP+UwGi1kB9BLOCu9SR8ZpbkmmalKIALnRw24kM7qCN0IOm6L0S44iWw==", "cpu": [ "arm64" ], @@ -1060,9 +1060,9 @@ ] }, "node_modules/@rollup/rollup-freebsd-x64": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-freebsd-x64/-/rollup-freebsd-x64-4.34.8.tgz", - "integrity": "sha512-TYXcHghgnCqYFiE3FT5QwXtOZqDj5GmaFNTNt3jNC+vh22dc/ukG2cG+pi75QO4kACohZzidsq7yKTKwq/Jq7Q==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-freebsd-x64/-/rollup-freebsd-x64-4.40.1.tgz", + "integrity": "sha512-VXeo/puqvCG8JBPNZXZf5Dqq7BzElNJzHRRw3vjBE27WujdzuOPecDPc/+1DcdcTptNBep3861jNq0mYkT8Z6Q==", "cpu": [ "x64" ], @@ -1074,9 +1074,9 @@ ] }, "node_modules/@rollup/rollup-linux-arm-gnueabihf": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm-gnueabihf/-/rollup-linux-arm-gnueabihf-4.34.8.tgz", - "integrity": "sha512-A4iphFGNkWRd+5m3VIGuqHnG3MVnqKe7Al57u9mwgbyZ2/xF9Jio72MaY7xxh+Y87VAHmGQr73qoKL9HPbXj1g==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm-gnueabihf/-/rollup-linux-arm-gnueabihf-4.40.1.tgz", + "integrity": "sha512-ehSKrewwsESPt1TgSE/na9nIhWCosfGSFqv7vwEtjyAqZcvbGIg4JAcV7ZEh2tfj/IlfBeZjgOXm35iOOjadcg==", "cpu": [ "arm" ], @@ -1088,9 +1088,9 @@ ] }, "node_modules/@rollup/rollup-linux-arm-musleabihf": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm-musleabihf/-/rollup-linux-arm-musleabihf-4.34.8.tgz", - "integrity": "sha512-S0lqKLfTm5u+QTxlFiAnb2J/2dgQqRy/XvziPtDd1rKZFXHTyYLoVL58M/XFwDI01AQCDIevGLbQrMAtdyanpA==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm-musleabihf/-/rollup-linux-arm-musleabihf-4.40.1.tgz", + "integrity": "sha512-m39iO/aaurh5FVIu/F4/Zsl8xppd76S4qoID8E+dSRQvTyZTOI2gVk3T4oqzfq1PtcvOfAVlwLMK3KRQMaR8lg==", "cpu": [ "arm" ], @@ -1102,9 +1102,9 @@ ] }, "node_modules/@rollup/rollup-linux-arm64-gnu": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm64-gnu/-/rollup-linux-arm64-gnu-4.34.8.tgz", - "integrity": "sha512-jpz9YOuPiSkL4G4pqKrus0pn9aYwpImGkosRKwNi+sJSkz+WU3anZe6hi73StLOQdfXYXC7hUfsQlTnjMd3s1A==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm64-gnu/-/rollup-linux-arm64-gnu-4.40.1.tgz", + "integrity": "sha512-Y+GHnGaku4aVLSgrT0uWe2o2Rq8te9hi+MwqGF9r9ORgXhmHK5Q71N757u0F8yU1OIwUIFy6YiJtKjtyktk5hg==", "cpu": [ "arm64" ], @@ -1116,9 +1116,9 @@ ] }, "node_modules/@rollup/rollup-linux-arm64-musl": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm64-musl/-/rollup-linux-arm64-musl-4.34.8.tgz", - "integrity": "sha512-KdSfaROOUJXgTVxJNAZ3KwkRc5nggDk+06P6lgi1HLv1hskgvxHUKZ4xtwHkVYJ1Rep4GNo+uEfycCRRxht7+Q==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm64-musl/-/rollup-linux-arm64-musl-4.40.1.tgz", + "integrity": "sha512-jEwjn3jCA+tQGswK3aEWcD09/7M5wGwc6+flhva7dsQNRZZTe30vkalgIzV4tjkopsTS9Jd7Y1Bsj6a4lzz8gQ==", "cpu": [ "arm64" ], @@ -1130,9 +1130,9 @@ ] }, "node_modules/@rollup/rollup-linux-loongarch64-gnu": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-loongarch64-gnu/-/rollup-linux-loongarch64-gnu-4.34.8.tgz", - "integrity": "sha512-NyF4gcxwkMFRjgXBM6g2lkT58OWztZvw5KkV2K0qqSnUEqCVcqdh2jN4gQrTn/YUpAcNKyFHfoOZEer9nwo6uQ==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-loongarch64-gnu/-/rollup-linux-loongarch64-gnu-4.40.1.tgz", + "integrity": "sha512-ySyWikVhNzv+BV/IDCsrraOAZ3UaC8SZB67FZlqVwXwnFhPihOso9rPOxzZbjp81suB1O2Topw+6Ug3JNegejQ==", "cpu": [ "loong64" ], @@ -1144,9 +1144,9 @@ ] }, "node_modules/@rollup/rollup-linux-powerpc64le-gnu": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-powerpc64le-gnu/-/rollup-linux-powerpc64le-gnu-4.34.8.tgz", - "integrity": "sha512-LMJc999GkhGvktHU85zNTDImZVUCJ1z/MbAJTnviiWmmjyckP5aQsHtcujMjpNdMZPT2rQEDBlJfubhs3jsMfw==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-powerpc64le-gnu/-/rollup-linux-powerpc64le-gnu-4.40.1.tgz", + "integrity": "sha512-BvvA64QxZlh7WZWqDPPdt0GH4bznuL6uOO1pmgPnnv86rpUpc8ZxgZwcEgXvo02GRIZX1hQ0j0pAnhwkhwPqWg==", "cpu": [ "ppc64" ], @@ -1158,9 +1158,23 @@ ] }, "node_modules/@rollup/rollup-linux-riscv64-gnu": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-riscv64-gnu/-/rollup-linux-riscv64-gnu-4.34.8.tgz", - "integrity": "sha512-xAQCAHPj8nJq1PI3z8CIZzXuXCstquz7cIOL73HHdXiRcKk8Ywwqtx2wrIy23EcTn4aZ2fLJNBB8d0tQENPCmw==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-riscv64-gnu/-/rollup-linux-riscv64-gnu-4.40.1.tgz", + "integrity": "sha512-EQSP+8+1VuSulm9RKSMKitTav89fKbHymTf25n5+Yr6gAPZxYWpj3DzAsQqoaHAk9YX2lwEyAf9S4W8F4l3VBQ==", + "cpu": [ + "riscv64" + ], + "dev": true, + "license": "MIT", + "optional": true, + "os": [ + "linux" + ] + }, + "node_modules/@rollup/rollup-linux-riscv64-musl": { + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-riscv64-musl/-/rollup-linux-riscv64-musl-4.40.1.tgz", + "integrity": "sha512-n/vQ4xRZXKuIpqukkMXZt9RWdl+2zgGNx7Uda8NtmLJ06NL8jiHxUawbwC+hdSq1rrw/9CghCpEONor+l1e2gA==", "cpu": [ "riscv64" ], @@ -1172,9 +1186,9 @@ ] }, "node_modules/@rollup/rollup-linux-s390x-gnu": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-s390x-gnu/-/rollup-linux-s390x-gnu-4.34.8.tgz", - "integrity": "sha512-DdePVk1NDEuc3fOe3dPPTb+rjMtuFw89gw6gVWxQFAuEqqSdDKnrwzZHrUYdac7A7dXl9Q2Vflxpme15gUWQFA==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-s390x-gnu/-/rollup-linux-s390x-gnu-4.40.1.tgz", + "integrity": "sha512-h8d28xzYb98fMQKUz0w2fMc1XuGzLLjdyxVIbhbil4ELfk5/orZlSTpF/xdI9C8K0I8lCkq+1En2RJsawZekkg==", "cpu": [ "s390x" ], @@ -1186,9 +1200,9 @@ ] }, "node_modules/@rollup/rollup-linux-x64-gnu": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-x64-gnu/-/rollup-linux-x64-gnu-4.34.8.tgz", - "integrity": "sha512-8y7ED8gjxITUltTUEJLQdgpbPh1sUQ0kMTmufRF/Ns5tI9TNMNlhWtmPKKHCU0SilX+3MJkZ0zERYYGIVBYHIA==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-x64-gnu/-/rollup-linux-x64-gnu-4.40.1.tgz", + "integrity": "sha512-XiK5z70PEFEFqcNj3/zRSz/qX4bp4QIraTy9QjwJAb/Z8GM7kVUsD0Uk8maIPeTyPCP03ChdI+VVmJriKYbRHQ==", "cpu": [ "x64" ], @@ -1200,9 +1214,9 @@ ] }, "node_modules/@rollup/rollup-linux-x64-musl": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-x64-musl/-/rollup-linux-x64-musl-4.34.8.tgz", - "integrity": "sha512-SCXcP0ZpGFIe7Ge+McxY5zKxiEI5ra+GT3QRxL0pMMtxPfpyLAKleZODi1zdRHkz5/BhueUrYtYVgubqe9JBNQ==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-x64-musl/-/rollup-linux-x64-musl-4.40.1.tgz", + "integrity": "sha512-2BRORitq5rQ4Da9blVovzNCMaUlyKrzMSvkVR0D4qPuOy/+pMCrh1d7o01RATwVy+6Fa1WBw+da7QPeLWU/1mQ==", "cpu": [ "x64" ], @@ -1214,9 +1228,9 @@ ] }, "node_modules/@rollup/rollup-win32-arm64-msvc": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-win32-arm64-msvc/-/rollup-win32-arm64-msvc-4.34.8.tgz", - "integrity": "sha512-YHYsgzZgFJzTRbth4h7Or0m5O74Yda+hLin0irAIobkLQFRQd1qWmnoVfwmKm9TXIZVAD0nZ+GEb2ICicLyCnQ==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-win32-arm64-msvc/-/rollup-win32-arm64-msvc-4.40.1.tgz", + "integrity": "sha512-b2bcNm9Kbde03H+q+Jjw9tSfhYkzrDUf2d5MAd1bOJuVplXvFhWz7tRtWvD8/ORZi7qSCy0idW6tf2HgxSXQSg==", "cpu": [ "arm64" ], @@ -1228,9 +1242,9 @@ ] }, "node_modules/@rollup/rollup-win32-ia32-msvc": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-win32-ia32-msvc/-/rollup-win32-ia32-msvc-4.34.8.tgz", - "integrity": "sha512-r3NRQrXkHr4uWy5TOjTpTYojR9XmF0j/RYgKCef+Ag46FWUTltm5ziticv8LdNsDMehjJ543x/+TJAek/xBA2w==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-win32-ia32-msvc/-/rollup-win32-ia32-msvc-4.40.1.tgz", + "integrity": "sha512-DfcogW8N7Zg7llVEfpqWMZcaErKfsj9VvmfSyRjCyo4BI3wPEfrzTtJkZG6gKP/Z92wFm6rz2aDO7/JfiR/whA==", "cpu": [ "ia32" ], @@ -1242,9 +1256,9 @@ ] }, "node_modules/@rollup/rollup-win32-x64-msvc": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/@rollup/rollup-win32-x64-msvc/-/rollup-win32-x64-msvc-4.34.8.tgz", - "integrity": "sha512-U0FaE5O1BCpZSeE6gBl3c5ObhePQSfk9vDRToMmTkbhCOgW4jqvtS5LGyQ76L1fH8sM0keRp4uDTsbjiUyjk0g==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/@rollup/rollup-win32-x64-msvc/-/rollup-win32-x64-msvc-4.40.1.tgz", + "integrity": "sha512-ECyOuDeH3C1I8jH2MK1RtBJW+YPMvSfT0a5NN0nHfQYnDSJ6tUiZH3gzwVP5/Kfh/+Tt7tpWVF9LXNTnhTJ3kA==", "cpu": [ "x64" ], @@ -1378,9 +1392,9 @@ } }, "node_modules/@types/estree": { - "version": "1.0.6", - "resolved": "https://registry.npmjs.org/@types/estree/-/estree-1.0.6.tgz", - "integrity": "sha512-AYnb1nQyY49te+VRAVgmzfcgjYS91mY5P0TKUDCLEM+gNnA+3T6rWITXRLYCpahpqSQbN5cE+gHpnPyXjHWxcw==", + "version": "1.0.7", + "resolved": "https://registry.npmjs.org/@types/estree/-/estree-1.0.7.tgz", + "integrity": "sha512-w28IoSUCJpidD/TGviZwwMJckNESJZXFu7NBZ5YJ4mEUnNraUn9Pm8HSZm/jDF1pDWYKspWE7oVphigUPRakIQ==", "dev": true, "license": "MIT" }, @@ -4914,13 +4928,13 @@ } }, "node_modules/rollup": { - "version": "4.34.8", - "resolved": "https://registry.npmjs.org/rollup/-/rollup-4.34.8.tgz", - "integrity": "sha512-489gTVMzAYdiZHFVA/ig/iYFllCcWFHMvUHI1rpFmkoUtRlQxqh6/yiNqnYibjMZ2b/+FUQwldG+aLsEt6bglQ==", + "version": "4.40.1", + "resolved": "https://registry.npmjs.org/rollup/-/rollup-4.40.1.tgz", + "integrity": "sha512-C5VvvgCCyfyotVITIAv+4efVytl5F7wt+/I2i9q9GZcEXW9BP52YYOXC58igUi+LFZVHukErIIqQSWwv/M3WRw==", "dev": true, "license": "MIT", "dependencies": { - "@types/estree": "1.0.6" + "@types/estree": "1.0.7" }, "bin": { "rollup": "dist/bin/rollup" @@ -4930,25 +4944,26 @@ "npm": ">=8.0.0" }, "optionalDependencies": { - "@rollup/rollup-android-arm-eabi": "4.34.8", - "@rollup/rollup-android-arm64": "4.34.8", - "@rollup/rollup-darwin-arm64": "4.34.8", - "@rollup/rollup-darwin-x64": "4.34.8", - "@rollup/rollup-freebsd-arm64": "4.34.8", - "@rollup/rollup-freebsd-x64": "4.34.8", - "@rollup/rollup-linux-arm-gnueabihf": "4.34.8", - "@rollup/rollup-linux-arm-musleabihf": "4.34.8", - "@rollup/rollup-linux-arm64-gnu": "4.34.8", - "@rollup/rollup-linux-arm64-musl": "4.34.8", - "@rollup/rollup-linux-loongarch64-gnu": "4.34.8", - "@rollup/rollup-linux-powerpc64le-gnu": "4.34.8", - "@rollup/rollup-linux-riscv64-gnu": "4.34.8", - "@rollup/rollup-linux-s390x-gnu": "4.34.8", - "@rollup/rollup-linux-x64-gnu": "4.34.8", - "@rollup/rollup-linux-x64-musl": "4.34.8", - "@rollup/rollup-win32-arm64-msvc": "4.34.8", - "@rollup/rollup-win32-ia32-msvc": "4.34.8", - "@rollup/rollup-win32-x64-msvc": "4.34.8", + "@rollup/rollup-android-arm-eabi": "4.40.1", + "@rollup/rollup-android-arm64": "4.40.1", + "@rollup/rollup-darwin-arm64": "4.40.1", + "@rollup/rollup-darwin-x64": "4.40.1", + "@rollup/rollup-freebsd-arm64": "4.40.1", + "@rollup/rollup-freebsd-x64": "4.40.1", + "@rollup/rollup-linux-arm-gnueabihf": "4.40.1", + "@rollup/rollup-linux-arm-musleabihf": "4.40.1", + "@rollup/rollup-linux-arm64-gnu": "4.40.1", + "@rollup/rollup-linux-arm64-musl": "4.40.1", + "@rollup/rollup-linux-loongarch64-gnu": "4.40.1", + "@rollup/rollup-linux-powerpc64le-gnu": "4.40.1", + "@rollup/rollup-linux-riscv64-gnu": "4.40.1", + "@rollup/rollup-linux-riscv64-musl": "4.40.1", + "@rollup/rollup-linux-s390x-gnu": "4.40.1", + "@rollup/rollup-linux-x64-gnu": "4.40.1", + "@rollup/rollup-linux-x64-musl": "4.40.1", + "@rollup/rollup-win32-arm64-msvc": "4.40.1", + "@rollup/rollup-win32-ia32-msvc": "4.40.1", + "@rollup/rollup-win32-x64-msvc": "4.40.1", "fsevents": "~2.3.2" } }, @@ -5634,6 +5649,51 @@ "dev": true, "license": "MIT" }, + "node_modules/tinyglobby": { + "version": "0.2.13", + "resolved": "https://registry.npmjs.org/tinyglobby/-/tinyglobby-0.2.13.tgz", + "integrity": "sha512-mEwzpUgrLySlveBwEVDMKk5B57bhLPYovRfPAXD5gA/98Opn0rCDj3GtLwFvCvH5RK9uPCExUROW5NjDwvqkxw==", + "dev": true, + "license": "MIT", + "dependencies": { + "fdir": "^6.4.4", + "picomatch": "^4.0.2" + }, + "engines": { + "node": ">=12.0.0" + }, + "funding": { + "url": "https://github.com/sponsors/SuperchupuDev" + } + }, + "node_modules/tinyglobby/node_modules/fdir": { + "version": "6.4.4", + "resolved": "https://registry.npmjs.org/fdir/-/fdir-6.4.4.tgz", + "integrity": "sha512-1NZP+GK4GfuAv3PqKvxQRDMjdSRZjnkq7KfhlNrCNNlZ0ygQFpebfrnfnq/W7fpUnAv9aGWmY1zKx7FYL3gwhg==", + "dev": true, + "license": "MIT", + "peerDependencies": { + "picomatch": "^3 || ^4" + }, + "peerDependenciesMeta": { + "picomatch": { + "optional": true + } + } + }, + "node_modules/tinyglobby/node_modules/picomatch": { + "version": "4.0.2", + "resolved": "https://registry.npmjs.org/picomatch/-/picomatch-4.0.2.tgz", + "integrity": "sha512-M7BAV6Rlcy5u+m6oPhAPFgJTzAioX/6B0DxyvDlo9l8+T3nLKbrczg2WLUyzd45L8RqfUMyGPzekbMvX2Ldkwg==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">=12" + }, + "funding": { + "url": "https://github.com/sponsors/jonschlinkert" + } + }, "node_modules/to-regex-range": { "version": "5.0.1", "resolved": "https://registry.npmjs.org/to-regex-range/-/to-regex-range-5.0.1.tgz", @@ -5811,15 +5871,18 @@ } }, "node_modules/vite": { - "version": "6.2.5", - "resolved": "https://registry.npmjs.org/vite/-/vite-6.2.5.tgz", - "integrity": "sha512-j023J/hCAa4pRIUH6J9HemwYfjB5llR2Ps0CWeikOtdR8+pAURAk0DoJC5/mm9kd+UgdnIy7d6HE4EAvlYhPhA==", + "version": "6.3.4", + "resolved": "https://registry.npmjs.org/vite/-/vite-6.3.4.tgz", + "integrity": "sha512-BiReIiMS2fyFqbqNT/Qqt4CVITDU9M9vE+DKcVAsB+ZV0wvTKd+3hMbkpxz1b+NmEDMegpVbisKiAZOnvO92Sw==", "dev": true, "license": "MIT", "dependencies": { "esbuild": "^0.25.0", + "fdir": "^6.4.4", + "picomatch": "^4.0.2", "postcss": "^8.5.3", - "rollup": "^4.30.1" + "rollup": "^4.34.9", + "tinyglobby": "^0.2.13" }, "bin": { "vite": "bin/vite.js" @@ -5882,6 +5945,34 @@ } } }, + "node_modules/vite/node_modules/fdir": { + "version": "6.4.4", + "resolved": "https://registry.npmjs.org/fdir/-/fdir-6.4.4.tgz", + "integrity": "sha512-1NZP+GK4GfuAv3PqKvxQRDMjdSRZjnkq7KfhlNrCNNlZ0ygQFpebfrnfnq/W7fpUnAv9aGWmY1zKx7FYL3gwhg==", + "dev": true, + "license": "MIT", + "peerDependencies": { + "picomatch": "^3 || ^4" + }, + "peerDependenciesMeta": { + "picomatch": { + "optional": true + } + } + }, + "node_modules/vite/node_modules/picomatch": { + "version": "4.0.2", + "resolved": "https://registry.npmjs.org/picomatch/-/picomatch-4.0.2.tgz", + "integrity": "sha512-M7BAV6Rlcy5u+m6oPhAPFgJTzAioX/6B0DxyvDlo9l8+T3nLKbrczg2WLUyzd45L8RqfUMyGPzekbMvX2Ldkwg==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">=12" + }, + "funding": { + "url": "https://github.com/sponsors/jonschlinkert" + } + }, "node_modules/watchpack": { "version": "2.4.2", "resolved": "https://registry.npmjs.org/watchpack/-/watchpack-2.4.2.tgz", diff --git a/examples/package.json b/examples/package.json index b98edab4..d38891ce 100644 --- a/examples/package.json +++ b/examples/package.json @@ -26,7 +26,7 @@ "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" From 6cbd7a10762623cc46383ee09832114d459bf37a Mon Sep 17 00:00:00 2001 From: Alli <111383930+ascibisz@users.noreply.github.com> Date: Thu, 8 May 2025 15:58:20 -0700 Subject: [PATCH 28/44] Bug Fix: Blood Plasma Simularium Example (#493) * fix URL with two back slashes * move URL into helper function with comment --- src/visGeometry/GeometryStore.ts | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/src/visGeometry/GeometryStore.ts b/src/visGeometry/GeometryStore.ts index be3902a6..5ac9a0b2 100644 --- a/src/visGeometry/GeometryStore.ts +++ b/src/visGeometry/GeometryStore.ts @@ -74,6 +74,18 @@ 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(); @@ -221,7 +233,7 @@ 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/${pdbID}-assembly1.cif`; + actualUrl = GeometryStore.getPdbUrlFromSanitizedPdbId(pdbID, true); } return fetch(actualUrl) .then((response) => { @@ -229,7 +241,10 @@ class GeometryStore { return response.text(); } else if (pdbID) { // try again as pdb - actualUrl = `https://files.rcsb.org/download/${pdbID}.pdb1`; + actualUrl = GeometryStore.getPdbUrlFromSanitizedPdbId( + pdbID, + false + ); return fetch(actualUrl).then((response) => { if (!response.ok) { // error will be caught by the function that calls this From 5de80fe35a834177d049fda2f1fb8497c24a4d66 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 9 Jun 2025 16:21:31 +0000 Subject: [PATCH 29/44] Bump webpack-dev-server from 5.1.0 to 5.2.1 in /examples Bumps [webpack-dev-server](https://github.com/webpack/webpack-dev-server) from 5.1.0 to 5.2.1. - [Release notes](https://github.com/webpack/webpack-dev-server/releases) - [Changelog](https://github.com/webpack/webpack-dev-server/blob/master/CHANGELOG.md) - [Commits](https://github.com/webpack/webpack-dev-server/compare/v5.1.0...v5.2.1) --- updated-dependencies: - dependency-name: webpack-dev-server dependency-version: 5.2.1 dependency-type: direct:development ... Signed-off-by: dependabot[bot] --- examples/package-lock.json | 316 ++++++++++++++++++++++--------------- examples/package.json | 2 +- 2 files changed, 186 insertions(+), 132 deletions(-) diff --git a/examples/package-lock.json b/examples/package-lock.json index 692164dc..d025c1f5 100644 --- a/examples/package-lock.json +++ b/examples/package-lock.json @@ -23,7 +23,7 @@ "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" } }, "..": { @@ -2105,18 +2105,29 @@ "node": ">= 0.8" } }, - "node_modules/call-bind": { - "version": "1.0.7", - "resolved": "https://registry.npmjs.org/call-bind/-/call-bind-1.0.7.tgz", - "integrity": "sha512-GHTSNSYICQ7scH7sZ+M2rFopRoLh8t2bLSW6BbgrtLsahOIB5iyAVJf9GjWK3cYTDaMj4XdBpM1cA6pIS0Kv2w==", + "node_modules/call-bind-apply-helpers": { + "version": "1.0.2", + "resolved": "https://registry.npmjs.org/call-bind-apply-helpers/-/call-bind-apply-helpers-1.0.2.tgz", + "integrity": "sha512-Sp1ablJ0ivDkSzjcaJdxEunN5/XvksFJ2sMBFfq6x0ryhQV/2b/KwFe21cMpmHtPOSij8K99/wSfoEuTObmuMQ==", "dev": true, "license": "MIT", "dependencies": { - "es-define-property": "^1.0.0", "es-errors": "^1.3.0", - "function-bind": "^1.1.2", - "get-intrinsic": "^1.2.4", - "set-function-length": "^1.2.1" + "function-bind": "^1.1.2" + }, + "engines": { + "node": ">= 0.4" + } + }, + "node_modules/call-bound": { + "version": "1.0.4", + "resolved": "https://registry.npmjs.org/call-bound/-/call-bound-1.0.4.tgz", + "integrity": "sha512-+ys997U96po4Kx/ABpBCqhA9EuxJaQWDQg7295H4hBphv3IZg0boBKuwYpt4YXp6MZ5AmZQnU/tyMTlRpaSejg==", + "dev": true, + "license": "MIT", + "dependencies": { + "call-bind-apply-helpers": "^1.0.2", + "get-intrinsic": "^1.3.0" }, "engines": { "node": ">= 0.4" @@ -2543,24 +2554,6 @@ "url": "https://github.com/sponsors/sindresorhus" } }, - "node_modules/define-data-property": { - "version": "1.1.4", - "resolved": "https://registry.npmjs.org/define-data-property/-/define-data-property-1.1.4.tgz", - "integrity": "sha512-rBMvIzlpA8v6E+SJZoo++HAYqsLrkg7MSfIinMPFhmkorw7X+dOXVJQs+QT69zGkzMyfDnIMN2Wid1+NbL3T+A==", - "dev": true, - "license": "MIT", - "dependencies": { - "es-define-property": "^1.0.0", - "es-errors": "^1.3.0", - "gopd": "^1.0.1" - }, - "engines": { - "node": ">= 0.4" - }, - "funding": { - "url": "https://github.com/sponsors/ljharb" - } - }, "node_modules/define-lazy-prop": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/define-lazy-prop/-/define-lazy-prop-3.0.0.tgz", @@ -2706,6 +2699,21 @@ "tslib": "^2.0.3" } }, + "node_modules/dunder-proto": { + "version": "1.0.1", + "resolved": "https://registry.npmjs.org/dunder-proto/-/dunder-proto-1.0.1.tgz", + "integrity": "sha512-KIN/nDJBQRcXw0MLVhZE9iQHmG68qAVIBg9CqmUYjmQIhgij9U5MFvrqkUL5FbtyyzZuOeOt0zdeRe4UY7ct+A==", + "dev": true, + "license": "MIT", + "dependencies": { + "call-bind-apply-helpers": "^1.0.1", + "es-errors": "^1.3.0", + "gopd": "^1.2.0" + }, + "engines": { + "node": ">= 0.4" + } + }, "node_modules/ee-first": { "version": "1.1.1", "resolved": "https://registry.npmjs.org/ee-first/-/ee-first-1.1.1.tgz", @@ -2768,14 +2776,11 @@ } }, "node_modules/es-define-property": { - "version": "1.0.0", - "resolved": "https://registry.npmjs.org/es-define-property/-/es-define-property-1.0.0.tgz", - "integrity": "sha512-jxayLKShrEqqzJ0eumQbVhTYQM27CfT1T35+gCgDFoL82JLsXqTJ76zv6A0YLOgEnLUMvLzsDsGIrl8NFpT2gQ==", + "version": "1.0.1", + "resolved": "https://registry.npmjs.org/es-define-property/-/es-define-property-1.0.1.tgz", + "integrity": "sha512-e3nRfgfUZ4rNGL232gUgX06QNyyez04KdjFrF+LTRoOXmrOgFKDg4BCdsjW8EnT69eqdYGmRpJwiPVYNrCaW3g==", "dev": true, "license": "MIT", - "dependencies": { - "get-intrinsic": "^1.2.4" - }, "engines": { "node": ">= 0.4" } @@ -2797,6 +2802,19 @@ "dev": true, "license": "MIT" }, + "node_modules/es-object-atoms": { + "version": "1.1.1", + "resolved": "https://registry.npmjs.org/es-object-atoms/-/es-object-atoms-1.1.1.tgz", + "integrity": "sha512-FGgH2h8zKNim9ljj7dankFPcICIK9Cp5bm+c2gQSYePhpaG5+esrLODihIorn+Pe6FGJzWhXQotPv73jTaldXA==", + "dev": true, + "license": "MIT", + "dependencies": { + "es-errors": "^1.3.0" + }, + "engines": { + "node": ">= 0.4" + } + }, "node_modules/esbuild": { "version": "0.25.1", "resolved": "https://registry.npmjs.org/esbuild/-/esbuild-0.25.1.tgz", @@ -2930,9 +2948,9 @@ } }, "node_modules/express": { - "version": "4.21.1", - "resolved": "https://registry.npmjs.org/express/-/express-4.21.1.tgz", - "integrity": "sha512-YSFlK1Ee0/GC8QaO91tHcDxJiE/X4FbpAyQWkxAvG6AXCuR65YzK8ua6D9hvi/TzUfZMpc+BwuM1IPw8fmQBiQ==", + "version": "4.21.2", + "resolved": "https://registry.npmjs.org/express/-/express-4.21.2.tgz", + "integrity": "sha512-28HqgMZAmih1Czt9ny7qr6ek2qddF4FclbMzwhCREB6OFfH+rXAnuNCwo1/wFvrtbgsQDb4kSbX9de9lFbrXnA==", "dev": true, "license": "MIT", "dependencies": { @@ -2955,7 +2973,7 @@ "methods": "~1.1.2", "on-finished": "2.4.1", "parseurl": "~1.3.3", - "path-to-regexp": "0.1.10", + "path-to-regexp": "0.1.12", "proxy-addr": "~2.0.7", "qs": "6.13.0", "range-parser": "~1.2.1", @@ -2970,6 +2988,10 @@ }, "engines": { "node": ">= 0.10.0" + }, + "funding": { + "type": "opencollective", + "url": "https://opencollective.com/express" } }, "node_modules/express/node_modules/debug": { @@ -3223,17 +3245,22 @@ } }, "node_modules/get-intrinsic": { - "version": "1.2.4", - "resolved": "https://registry.npmjs.org/get-intrinsic/-/get-intrinsic-1.2.4.tgz", - "integrity": "sha512-5uYhsJH8VJBTv7oslg4BznJYhDoRI6waYCxMmCdnTrcCrHA/fCFKoTFz2JKKE0HdDFUF7/oQuhzumXJK7paBRQ==", + "version": "1.3.0", + "resolved": "https://registry.npmjs.org/get-intrinsic/-/get-intrinsic-1.3.0.tgz", + "integrity": "sha512-9fSjSaos/fRIVIp+xSJlE6lfwhES7LNtKaCBIamHsjr2na1BiABJPo0mOjjz8GJDURarmCPGqaiVg5mfjb98CQ==", "dev": true, "license": "MIT", "dependencies": { + "call-bind-apply-helpers": "^1.0.2", + "es-define-property": "^1.0.1", "es-errors": "^1.3.0", + "es-object-atoms": "^1.1.1", "function-bind": "^1.1.2", - "has-proto": "^1.0.1", - "has-symbols": "^1.0.3", - "hasown": "^2.0.0" + "get-proto": "^1.0.1", + "gopd": "^1.2.0", + "has-symbols": "^1.1.0", + "hasown": "^2.0.2", + "math-intrinsics": "^1.1.0" }, "engines": { "node": ">= 0.4" @@ -3242,6 +3269,20 @@ "url": "https://github.com/sponsors/ljharb" } }, + "node_modules/get-proto": { + "version": "1.0.1", + "resolved": "https://registry.npmjs.org/get-proto/-/get-proto-1.0.1.tgz", + "integrity": "sha512-sTSfBjoXBp89JvIKIefqw7U2CCebsc74kiY6awiGogKtoSGbgjYE/G/+l9sF3MWFPNc9IcoOC4ODfKHfxFmp0g==", + "dev": true, + "license": "MIT", + "dependencies": { + "dunder-proto": "^1.0.1", + "es-object-atoms": "^1.0.0" + }, + "engines": { + "node": ">= 0.4" + } + }, "node_modules/glob-parent": { "version": "6.0.2", "resolved": "https://registry.npmjs.org/glob-parent/-/glob-parent-6.0.2.tgz", @@ -3294,14 +3335,11 @@ } }, "node_modules/gopd": { - "version": "1.1.0", - "resolved": "https://registry.npmjs.org/gopd/-/gopd-1.1.0.tgz", - "integrity": "sha512-FQoVQnqcdk4hVM4JN1eromaun4iuS34oStkdlLENLdpULsuQcTyXj8w7ayhuUfPwEYZ1ZOooOTT6fdA9Vmx/RA==", + "version": "1.2.0", + "resolved": "https://registry.npmjs.org/gopd/-/gopd-1.2.0.tgz", + "integrity": "sha512-ZUKRh6/kUFoAiTAtTYPZJ3hw9wNxx+BIBOijnlG9PnrJsCcSjs1wyyD6vJpaYtgnzDrKYRSqf3OO6Rfa93xsRg==", "dev": true, "license": "MIT", - "dependencies": { - "get-intrinsic": "^1.2.4" - }, "engines": { "node": ">= 0.4" }, @@ -3333,35 +3371,6 @@ "node": ">=8" } }, - "node_modules/has-property-descriptors": { - "version": "1.0.2", - "resolved": "https://registry.npmjs.org/has-property-descriptors/-/has-property-descriptors-1.0.2.tgz", - "integrity": "sha512-55JNKuIW+vq4Ke1BjOTjM2YctQIvCT7GFzHwmfZPGo5wnrgkid0YQtnAleFSqumZm4az3n2BS+erby5ipJdgrg==", - "dev": true, - "license": "MIT", - "dependencies": { - "es-define-property": "^1.0.0" - }, - "funding": { - "url": "https://github.com/sponsors/ljharb" - } - }, - "node_modules/has-proto": { - "version": "1.1.0", - "resolved": "https://registry.npmjs.org/has-proto/-/has-proto-1.1.0.tgz", - "integrity": "sha512-QLdzI9IIO1Jg7f9GT1gXpPpXArAn6cS31R1eEZqz08Gc+uQ8/XiqHWt17Fiw+2p6oTTIq5GXEpQkAlA88YRl/Q==", - "dev": true, - "license": "MIT", - "dependencies": { - "call-bind": "^1.0.7" - }, - "engines": { - "node": ">= 0.4" - }, - "funding": { - "url": "https://github.com/sponsors/ljharb" - } - }, "node_modules/has-symbols": { "version": "1.1.0", "resolved": "https://registry.npmjs.org/has-symbols/-/has-symbols-1.1.0.tgz", @@ -3444,23 +3453,6 @@ "safe-buffer": "~5.1.0" } }, - "node_modules/html-entities": { - "version": "2.5.2", - "resolved": "https://registry.npmjs.org/html-entities/-/html-entities-2.5.2.tgz", - "integrity": "sha512-K//PSRMQk4FZ78Kyau+mZurHn3FH0Vwr+H36eE0rPbeYkRRi9YxceYPhuN60UwWorxyKHhqoAJl2OFKa4BVtaA==", - "dev": true, - "funding": [ - { - "type": "github", - "url": "https://github.com/sponsors/mdevils" - }, - { - "type": "patreon", - "url": "https://patreon.com/mdevils" - } - ], - "license": "MIT" - }, "node_modules/html-minifier-terser": { "version": "6.1.0", "resolved": "https://registry.npmjs.org/html-minifier-terser/-/html-minifier-terser-6.1.0.tgz", @@ -4020,6 +4012,16 @@ "yallist": "^3.0.2" } }, + "node_modules/math-intrinsics": { + "version": "1.1.0", + "resolved": "https://registry.npmjs.org/math-intrinsics/-/math-intrinsics-1.1.0.tgz", + "integrity": "sha512-/IXtbwEk5HTPyEwyKX6hGkYXxM9nbj64B+ilVJnC/R6B0pH5G4V3b0pVbL7DBj4tkhBAppbQUlf6F6Xl9LHu1g==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">= 0.4" + } + }, "node_modules/media-typer": { "version": "0.3.0", "resolved": "https://registry.npmjs.org/media-typer/-/media-typer-0.3.0.tgz", @@ -4274,9 +4276,9 @@ } }, "node_modules/object-inspect": { - "version": "1.13.3", - "resolved": "https://registry.npmjs.org/object-inspect/-/object-inspect-1.13.3.tgz", - "integrity": "sha512-kDCGIbxkDSXE3euJZZXzc6to7fCrKHNI/hSRQnRuQ+BWjFNzZwiFF8fj/6o2t2G9/jTj8PSIYTfCLelLZEeRpA==", + "version": "1.13.4", + "resolved": "https://registry.npmjs.org/object-inspect/-/object-inspect-1.13.4.tgz", + "integrity": "sha512-W67iLl4J2EXEGTbfeHCffrjDfitvLANg0UlX3wFUUSTx92KXRFegMHUVgSqE+wvhAbi4WqjGg9czysTV2Epbew==", "dev": true, "license": "MIT", "engines": { @@ -4452,9 +4454,9 @@ "license": "MIT" }, "node_modules/path-to-regexp": { - "version": "0.1.10", - "resolved": "https://registry.npmjs.org/path-to-regexp/-/path-to-regexp-0.1.10.tgz", - "integrity": "sha512-7lf7qcQidTku0Gu3YDPc8DJ1q7OOucfa/BSsIwjuh56VU7katFvuM8hULfkwB3Fns/rsVF7PwPKVw1sl5KQS9w==", + "version": "0.1.12", + "resolved": "https://registry.npmjs.org/path-to-regexp/-/path-to-regexp-0.1.12.tgz", + "integrity": "sha512-RA1GjUVMnvYFxuqovrEqZoxxW5NUZqbwKtYz/Tt7nXerk0LbLblQmrsgdeOxV5SFHf0UDggjS/bSeOZwt1pmEQ==", "dev": true, "license": "MIT" }, @@ -5262,24 +5264,6 @@ "node": ">= 0.8.0" } }, - "node_modules/set-function-length": { - "version": "1.2.2", - "resolved": "https://registry.npmjs.org/set-function-length/-/set-function-length-1.2.2.tgz", - "integrity": "sha512-pgRc4hJ4/sNjWCSS9AmnS40x3bNMDTknHgL5UaMBTMyJnU90EgWh1Rz+MC9eFu4BuN/UwZjKQuY/1v3rM7HMfg==", - "dev": true, - "license": "MIT", - "dependencies": { - "define-data-property": "^1.1.4", - "es-errors": "^1.3.0", - "function-bind": "^1.1.2", - "get-intrinsic": "^1.2.4", - "gopd": "^1.0.1", - "has-property-descriptors": "^1.0.2" - }, - "engines": { - "node": ">= 0.4" - } - }, "node_modules/setprototypeof": { "version": "1.2.0", "resolved": "https://registry.npmjs.org/setprototypeof/-/setprototypeof-1.2.0.tgz", @@ -5337,16 +5321,73 @@ } }, "node_modules/side-channel": { - "version": "1.0.6", - "resolved": "https://registry.npmjs.org/side-channel/-/side-channel-1.0.6.tgz", - "integrity": "sha512-fDW/EZ6Q9RiO8eFG8Hj+7u/oW+XrPTIChwCOM2+th2A6OblDtYYIpve9m+KvI9Z4C9qSEXlaGR6bTEYHReuglA==", + "version": "1.1.0", + "resolved": "https://registry.npmjs.org/side-channel/-/side-channel-1.1.0.tgz", + "integrity": "sha512-ZX99e6tRweoUXqR+VBrslhda51Nh5MTQwou5tnUDgbtyM0dBgmhEDtWGP/xbKn6hqfPRHujUNwz5fy/wbbhnpw==", "dev": true, "license": "MIT", "dependencies": { - "call-bind": "^1.0.7", "es-errors": "^1.3.0", - "get-intrinsic": "^1.2.4", - "object-inspect": "^1.13.1" + "object-inspect": "^1.13.3", + "side-channel-list": "^1.0.0", + "side-channel-map": "^1.0.1", + "side-channel-weakmap": "^1.0.2" + }, + "engines": { + "node": ">= 0.4" + }, + "funding": { + "url": "https://github.com/sponsors/ljharb" + } + }, + "node_modules/side-channel-list": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/side-channel-list/-/side-channel-list-1.0.0.tgz", + "integrity": "sha512-FCLHtRD/gnpCiCHEiJLOwdmFP+wzCmDEkc9y7NsYxeF4u7Btsn1ZuwgwJGxImImHicJArLP4R0yX4c2KCrMrTA==", + "dev": true, + "license": "MIT", + "dependencies": { + "es-errors": "^1.3.0", + "object-inspect": "^1.13.3" + }, + "engines": { + "node": ">= 0.4" + }, + "funding": { + "url": "https://github.com/sponsors/ljharb" + } + }, + "node_modules/side-channel-map": { + "version": "1.0.1", + "resolved": "https://registry.npmjs.org/side-channel-map/-/side-channel-map-1.0.1.tgz", + "integrity": "sha512-VCjCNfgMsby3tTdo02nbjtM/ewra6jPHmpThenkTYh8pG9ucZ/1P8So4u4FGBek/BjpOVsDCMoLA/iuBKIFXRA==", + "dev": true, + "license": "MIT", + "dependencies": { + "call-bound": "^1.0.2", + "es-errors": "^1.3.0", + "get-intrinsic": "^1.2.5", + "object-inspect": "^1.13.3" + }, + "engines": { + "node": ">= 0.4" + }, + "funding": { + "url": "https://github.com/sponsors/ljharb" + } + }, + "node_modules/side-channel-weakmap": { + "version": "1.0.2", + "resolved": "https://registry.npmjs.org/side-channel-weakmap/-/side-channel-weakmap-1.0.2.tgz", + "integrity": "sha512-WPS/HvHQTYnHisLo9McqBHOJk2FkHO/tlpvldyrnem4aeQp4hai3gythswg6p01oSoTl58rcpiFAjF2br2Ak2A==", + "dev": true, + "license": "MIT", + "dependencies": { + "call-bound": "^1.0.2", + "es-errors": "^1.3.0", + "get-intrinsic": "^1.2.5", + "object-inspect": "^1.13.3", + "side-channel-map": "^1.0.1" }, "engines": { "node": ">= 0.4" @@ -6131,15 +6172,16 @@ } }, "node_modules/webpack-dev-server": { - "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", @@ -6150,10 +6192,9 @@ "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", @@ -6188,6 +6229,19 @@ } } }, + "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 d38891ce..96535e17 100644 --- a/examples/package.json +++ b/examples/package.json @@ -29,6 +29,6 @@ "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" } } From 0f1226095e2ebe568431f644bc283b7629661a63 Mon Sep 17 00:00:00 2001 From: ascibisz Date: Mon, 9 Jun 2025 17:36:18 -0700 Subject: [PATCH 30/44] 3.10.0 --- CHANGELOG.md | 66 ++++++++++++++++++++++++++++++++++++++++++----- package-lock.json | 4 +-- package.json | 2 +- 3 files changed, 63 insertions(+), 9 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index caf4ba6a..aeb236a5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,12 +4,51 @@ 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) +#### [v3.10.0](https://github.com/simularium/simularium-viewer/compare/v3.9.1...v3.10.0) + +- 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 +61,28 @@ 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 +90,17 @@ 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/package-lock.json b/package-lock.json index ddfed2bf..398501ea 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "@aics/simularium-viewer", - "version": "3.9.1", + "version": "3.10.0", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@aics/simularium-viewer", - "version": "3.9.1", + "version": "3.10.0", "license": "MIT", "dependencies": { "@babel/plugin-transform-runtime": "^7.23.6", diff --git a/package.json b/package.json index 35edc52d..cb8aefaa 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@aics/simularium-viewer", - "version": "3.9.1", + "version": "3.10.0", "description": "An npm package to view simulations.", "main": "es/index.js", "type": "module", From d6edd91f76a90d788af54d940c864b3d7aacec76 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 11 Jun 2025 00:29:02 +0000 Subject: [PATCH 31/44] Bump vite from 5.4.18 to 5.4.19 Bumps [vite](https://github.com/vitejs/vite/tree/HEAD/packages/vite) from 5.4.18 to 5.4.19. - [Release notes](https://github.com/vitejs/vite/releases) - [Changelog](https://github.com/vitejs/vite/blob/v5.4.19/packages/vite/CHANGELOG.md) - [Commits](https://github.com/vitejs/vite/commits/v5.4.19/packages/vite) --- updated-dependencies: - dependency-name: vite dependency-version: 5.4.19 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- package-lock.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index 398501ea..58b007af 100644 --- a/package-lock.json +++ b/package-lock.json @@ -13753,9 +13753,9 @@ } }, "node_modules/vite": { - "version": "5.4.18", - "resolved": "https://registry.npmjs.org/vite/-/vite-5.4.18.tgz", - "integrity": "sha512-1oDcnEp3lVyHCuQ2YFelM4Alm2o91xNoMncRm1U7S+JdYfYOvbiGZ3/CxGttrOu2M/KcGz7cRC2DoNUA6urmMA==", + "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": { From 0561f627f92358da5dd1def65e35a32d72c73c00 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 18 Jul 2025 00:08:41 +0000 Subject: [PATCH 32/44] Bump on-headers and compression in /examples Bumps [on-headers](https://github.com/jshttp/on-headers) and [compression](https://github.com/expressjs/compression). These dependencies needed to be updated together. Updates `on-headers` from 1.0.2 to 1.1.0 - [Release notes](https://github.com/jshttp/on-headers/releases) - [Changelog](https://github.com/jshttp/on-headers/blob/master/HISTORY.md) - [Commits](https://github.com/jshttp/on-headers/compare/v1.0.2...v1.1.0) Updates `compression` from 1.7.5 to 1.8.1 - [Release notes](https://github.com/expressjs/compression/releases) - [Changelog](https://github.com/expressjs/compression/blob/master/HISTORY.md) - [Commits](https://github.com/expressjs/compression/compare/1.7.5...v1.8.1) --- updated-dependencies: - dependency-name: on-headers dependency-version: 1.1.0 dependency-type: indirect - dependency-name: compression dependency-version: 1.8.1 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- examples/package-lock.json | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/examples/package-lock.json b/examples/package-lock.json index d025c1f5..09e5413f 100644 --- a/examples/package-lock.json +++ b/examples/package-lock.json @@ -28,7 +28,7 @@ }, "..": { "name": "@aics/simularium-viewer", - "version": "3.9.1", + "version": "3.10.0", "license": "MIT", "dependencies": { "@babel/plugin-transform-runtime": "^7.23.6", @@ -2275,9 +2275,9 @@ } }, "node_modules/compression": { - "version": "1.7.5", - "resolved": "https://registry.npmjs.org/compression/-/compression-1.7.5.tgz", - "integrity": "sha512-bQJ0YRck5ak3LgtnpKkiabX5pNF7tMUh1BSy2ZBOTh0Dim0BUu6aPPwByIns6/A5Prh8PufSPerMDUklpzes2Q==", + "version": "1.8.1", + "resolved": "https://registry.npmjs.org/compression/-/compression-1.8.1.tgz", + "integrity": "sha512-9mAqGPHLakhCLeNyxPkK4xVo746zQ/czLH1Ky+vkitMnWfWZps8r0qXuwhwizagCRttsL4lfG4pIOvaWLpAP0w==", "dev": true, "license": "MIT", "dependencies": { @@ -2285,7 +2285,7 @@ "compressible": "~2.0.18", "debug": "2.6.9", "negotiator": "~0.6.4", - "on-headers": "~1.0.2", + "on-headers": "~1.1.0", "safe-buffer": "5.2.1", "vary": "~1.1.2" }, @@ -4309,9 +4309,9 @@ } }, "node_modules/on-headers": { - "version": "1.0.2", - "resolved": "https://registry.npmjs.org/on-headers/-/on-headers-1.0.2.tgz", - "integrity": "sha512-pZAE+FJLoyITytdqK0U5s+FIpjN0JP3OzFi/u8Rx+EV5/W+JTWGXG8xFzevE7AjBfDqHv/8vL8qQsIhHnqRkrA==", + "version": "1.1.0", + "resolved": "https://registry.npmjs.org/on-headers/-/on-headers-1.1.0.tgz", + "integrity": "sha512-737ZY3yNnXy37FHkQxPzt4UZ2UWPWiCZWLvFZ4fu5cueciegX0zGPnrlY6bwRg4FdQOe9YU8MkmJwGhoMybl8A==", "dev": true, "license": "MIT", "engines": { From 2a0159afa03d0dfb356dfa27cf5387688a9959a9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 22 Jul 2025 11:53:40 +0000 Subject: [PATCH 33/44] Bump form-data from 4.0.1 to 4.0.4 --- updated-dependencies: - dependency-name: form-data dependency-version: 4.0.4 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- package-lock.json | 113 ++++++++++++++++++++++++++++++++++------------ 1 file changed, 84 insertions(+), 29 deletions(-) diff --git a/package-lock.json b/package-lock.json index 58b007af..91829919 100644 --- a/package-lock.json +++ b/package-lock.json @@ -4630,6 +4630,20 @@ "url": "https://github.com/sponsors/ljharb" } }, + "node_modules/call-bind-apply-helpers": { + "version": "1.0.2", + "resolved": "https://registry.npmjs.org/call-bind-apply-helpers/-/call-bind-apply-helpers-1.0.2.tgz", + "integrity": "sha512-Sp1ablJ0ivDkSzjcaJdxEunN5/XvksFJ2sMBFfq6x0ryhQV/2b/KwFe21cMpmHtPOSij8K99/wSfoEuTObmuMQ==", + "dev": true, + "license": "MIT", + "dependencies": { + "es-errors": "^1.3.0", + "function-bind": "^1.1.2" + }, + "engines": { + "node": ">= 0.4" + } + }, "node_modules/caller-callsite": { "version": "2.0.0", "resolved": "https://registry.npmjs.org/caller-callsite/-/caller-callsite-2.0.0.tgz", @@ -5465,6 +5479,21 @@ "node": ">=0.10.0" } }, + "node_modules/dunder-proto": { + "version": "1.0.1", + "resolved": "https://registry.npmjs.org/dunder-proto/-/dunder-proto-1.0.1.tgz", + "integrity": "sha512-KIN/nDJBQRcXw0MLVhZE9iQHmG68qAVIBg9CqmUYjmQIhgij9U5MFvrqkUL5FbtyyzZuOeOt0zdeRe4UY7ct+A==", + "dev": true, + "license": "MIT", + "dependencies": { + "call-bind-apply-helpers": "^1.0.1", + "es-errors": "^1.3.0", + "gopd": "^1.2.0" + }, + "engines": { + "node": ">= 0.4" + } + }, "node_modules/eastasianwidth": { "version": "0.2.0", "resolved": "https://registry.npmjs.org/eastasianwidth/-/eastasianwidth-0.2.0.tgz", @@ -5619,14 +5648,11 @@ } }, "node_modules/es-define-property": { - "version": "1.0.0", - "resolved": "https://registry.npmjs.org/es-define-property/-/es-define-property-1.0.0.tgz", - "integrity": "sha512-jxayLKShrEqqzJ0eumQbVhTYQM27CfT1T35+gCgDFoL82JLsXqTJ76zv6A0YLOgEnLUMvLzsDsGIrl8NFpT2gQ==", + "version": "1.0.1", + "resolved": "https://registry.npmjs.org/es-define-property/-/es-define-property-1.0.1.tgz", + "integrity": "sha512-e3nRfgfUZ4rNGL232gUgX06QNyyez04KdjFrF+LTRoOXmrOgFKDg4BCdsjW8EnT69eqdYGmRpJwiPVYNrCaW3g==", "dev": true, "license": "MIT", - "dependencies": { - "get-intrinsic": "^1.2.4" - }, "engines": { "node": ">= 0.4" } @@ -5676,9 +5702,9 @@ "license": "MIT" }, "node_modules/es-object-atoms": { - "version": "1.0.0", - "resolved": "https://registry.npmjs.org/es-object-atoms/-/es-object-atoms-1.0.0.tgz", - "integrity": "sha512-MZ4iQ6JwHOBQjahnjwaC1ZtIBH+2ohjamzAO3oaHcXYup7qxjF2fixyH+Q71voWHeOkI2q/TnJao/KfXYIZWbw==", + "version": "1.1.1", + "resolved": "https://registry.npmjs.org/es-object-atoms/-/es-object-atoms-1.1.1.tgz", + "integrity": "sha512-FGgH2h8zKNim9ljj7dankFPcICIK9Cp5bm+c2gQSYePhpaG5+esrLODihIorn+Pe6FGJzWhXQotPv73jTaldXA==", "dev": true, "license": "MIT", "dependencies": { @@ -5689,15 +5715,16 @@ } }, "node_modules/es-set-tostringtag": { - "version": "2.0.3", - "resolved": "https://registry.npmjs.org/es-set-tostringtag/-/es-set-tostringtag-2.0.3.tgz", - "integrity": "sha512-3T8uNMC3OQTHkFUsFq8r/BwAXLHvU/9O9mE0fBc/MY5iq/8H7ncvO947LmYA6ldWw9Uh8Yhf25zu6n7nML5QWQ==", + "version": "2.1.0", + "resolved": "https://registry.npmjs.org/es-set-tostringtag/-/es-set-tostringtag-2.1.0.tgz", + "integrity": "sha512-j6vWzfrGVfyXxge+O0x5sh6cvxAog0a/4Rdd2K36zCMV5eJ+/+tOAngRO8cODMNWbVRdVlmGZQL2YS3yR8bIUA==", "dev": true, "license": "MIT", "dependencies": { - "get-intrinsic": "^1.2.4", + "es-errors": "^1.3.0", + "get-intrinsic": "^1.2.6", "has-tostringtag": "^1.0.2", - "hasown": "^2.0.1" + "hasown": "^2.0.2" }, "engines": { "node": ">= 0.4" @@ -6784,14 +6811,16 @@ } }, "node_modules/form-data": { - "version": "4.0.1", - "resolved": "https://registry.npmjs.org/form-data/-/form-data-4.0.1.tgz", - "integrity": "sha512-tzN8e4TX8+kkxGPK8D5u0FNmjPUjw3lwC9lSLxxoB/+GtsJG91CO8bSWy73APlgAZzZbXEYZJuxjkHH2w+Ezhw==", + "version": "4.0.4", + "resolved": "https://registry.npmjs.org/form-data/-/form-data-4.0.4.tgz", + "integrity": "sha512-KrGhL9Q4zjj0kiUt5OO4Mr/A/jlI2jDYs5eHBpYHPcBEVSiipAvn2Ko2HnPe20rmcuuvMHNdZFp+4IlGTMF0Ow==", "dev": true, "license": "MIT", "dependencies": { "asynckit": "^0.4.0", "combined-stream": "^1.0.8", + "es-set-tostringtag": "^2.1.0", + "hasown": "^2.0.2", "mime-types": "^2.1.12" }, "engines": { @@ -6922,17 +6951,22 @@ } }, "node_modules/get-intrinsic": { - "version": "1.2.4", - "resolved": "https://registry.npmjs.org/get-intrinsic/-/get-intrinsic-1.2.4.tgz", - "integrity": "sha512-5uYhsJH8VJBTv7oslg4BznJYhDoRI6waYCxMmCdnTrcCrHA/fCFKoTFz2JKKE0HdDFUF7/oQuhzumXJK7paBRQ==", + "version": "1.3.0", + "resolved": "https://registry.npmjs.org/get-intrinsic/-/get-intrinsic-1.3.0.tgz", + "integrity": "sha512-9fSjSaos/fRIVIp+xSJlE6lfwhES7LNtKaCBIamHsjr2na1BiABJPo0mOjjz8GJDURarmCPGqaiVg5mfjb98CQ==", "dev": true, "license": "MIT", "dependencies": { + "call-bind-apply-helpers": "^1.0.2", + "es-define-property": "^1.0.1", "es-errors": "^1.3.0", + "es-object-atoms": "^1.1.1", "function-bind": "^1.1.2", - "has-proto": "^1.0.1", - "has-symbols": "^1.0.3", - "hasown": "^2.0.0" + "get-proto": "^1.0.1", + "gopd": "^1.2.0", + "has-symbols": "^1.1.0", + "hasown": "^2.0.2", + "math-intrinsics": "^1.1.0" }, "engines": { "node": ">= 0.4" @@ -6958,6 +6992,20 @@ "node": ">=8.0.0" } }, + "node_modules/get-proto": { + "version": "1.0.1", + "resolved": "https://registry.npmjs.org/get-proto/-/get-proto-1.0.1.tgz", + "integrity": "sha512-sTSfBjoXBp89JvIKIefqw7U2CCebsc74kiY6awiGogKtoSGbgjYE/G/+l9sF3MWFPNc9IcoOC4ODfKHfxFmp0g==", + "dev": true, + "license": "MIT", + "dependencies": { + "dunder-proto": "^1.0.1", + "es-object-atoms": "^1.0.0" + }, + "engines": { + "node": ">= 0.4" + } + }, "node_modules/get-stdin": { "version": "6.0.0", "resolved": "https://registry.npmjs.org/get-stdin/-/get-stdin-6.0.0.tgz", @@ -7104,14 +7152,11 @@ } }, "node_modules/gopd": { - "version": "1.1.0", - "resolved": "https://registry.npmjs.org/gopd/-/gopd-1.1.0.tgz", - "integrity": "sha512-FQoVQnqcdk4hVM4JN1eromaun4iuS34oStkdlLENLdpULsuQcTyXj8w7ayhuUfPwEYZ1ZOooOTT6fdA9Vmx/RA==", + "version": "1.2.0", + "resolved": "https://registry.npmjs.org/gopd/-/gopd-1.2.0.tgz", + "integrity": "sha512-ZUKRh6/kUFoAiTAtTYPZJ3hw9wNxx+BIBOijnlG9PnrJsCcSjs1wyyD6vJpaYtgnzDrKYRSqf3OO6Rfa93xsRg==", "dev": true, "license": "MIT", - "dependencies": { - "get-intrinsic": "^1.2.4" - }, "engines": { "node": ">= 0.4" }, @@ -8943,6 +8988,16 @@ "dev": true, "license": "ISC" }, + "node_modules/math-intrinsics": { + "version": "1.1.0", + "resolved": "https://registry.npmjs.org/math-intrinsics/-/math-intrinsics-1.1.0.tgz", + "integrity": "sha512-/IXtbwEk5HTPyEwyKX6hGkYXxM9nbj64B+ilVJnC/R6B0pH5G4V3b0pVbL7DBj4tkhBAppbQUlf6F6Xl9LHu1g==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">= 0.4" + } + }, "node_modules/memorystream": { "version": "0.3.1", "resolved": "https://registry.npmjs.org/memorystream/-/memorystream-0.3.1.tgz", From 121596c762576cdf6136ac9b31e08cadf3e0299f Mon Sep 17 00:00:00 2001 From: Joe Heffernan Date: Thu, 31 Jul 2025 10:39:33 -0700 Subject: [PATCH 34/44] add export field to package.json (#496) * add export field to package.json * import stylesheet index.ts * move stylesheet import up one level * don't procses css in vitest * take style directory out of copy-build step * remove top level stylesheet duplication restore exports field --- package.json | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/package.json b/package.json index cb8aefaa..908f07de 100644 --- a/package.json +++ b/package.json @@ -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 +40,10 @@ "type": "git", "url": "https://github.com/simularium/simularium-viewer.git" }, + "exports": { + ".": "./es/index.js", + "./style/style.css": "./es/style/style.css" + }, "author": "", "license": "MIT", "devDependencies": { From 80d054633d9cf497e1056d4219a134ada6aec199 Mon Sep 17 00:00:00 2001 From: Megan Riel-Mehan Date: Thu, 31 Jul 2025 17:29:45 -0700 Subject: [PATCH 35/44] clear available agents (#500) --- src/visGeometry/index.ts | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/visGeometry/index.ts b/src/visGeometry/index.ts index 54260836..1fd2aa31 100644 --- a/src/visGeometry/index.ts +++ b/src/visGeometry/index.ts @@ -1906,6 +1906,8 @@ 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(); @@ -1914,7 +1916,7 @@ class VisGeometry { this.visAgentInstances.clear(); this.visAgents = []; this.currentSceneData = nullCachedFrame(); - + this.availableAgentPool = []; this.dehighlight(); } From baec486e8bdde05a4a6097aa0a3b25ea250df20e Mon Sep 17 00:00:00 2001 From: meganrm Date: Thu, 31 Jul 2025 17:32:15 -0700 Subject: [PATCH 36/44] 3.10.1 --- CHANGELOG.md | 11 +++++++++++ package-lock.json | 4 ++-- package.json | 2 +- 3 files changed, 14 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index aeb236a5..44bcb07b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,8 +4,19 @@ 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). +#### [v3.10.1](https://github.com/simularium/simularium-viewer/compare/v3.10.0...v3.10.1) + +- 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) diff --git a/package-lock.json b/package-lock.json index 91829919..ebf11264 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "@aics/simularium-viewer", - "version": "3.10.0", + "version": "3.10.1", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@aics/simularium-viewer", - "version": "3.10.0", + "version": "3.10.1", "license": "MIT", "dependencies": { "@babel/plugin-transform-runtime": "^7.23.6", diff --git a/package.json b/package.json index 908f07de..dcb9f055 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@aics/simularium-viewer", - "version": "3.10.0", + "version": "3.10.1", "description": "An npm package to view simulations.", "main": "es/index.js", "type": "module", From 746b4b73a2814b6c720291f7239a4096e9c54ca1 Mon Sep 17 00:00:00 2001 From: Megan Riel-Mehan Date: Sat, 2 Aug 2025 14:57:49 -0700 Subject: [PATCH 37/44] need to include types in export (#501) --- package.json | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/package.json b/package.json index dcb9f055..3fc29ef7 100644 --- a/package.json +++ b/package.json @@ -41,8 +41,13 @@ "url": "https://github.com/simularium/simularium-viewer.git" }, "exports": { - ".": "./es/index.js", - "./style/style.css": "./es/style/style.css" + "./style/style.css": "./es/style/style.css", + ".": { + "import": { + "types": "./type-declarations/index.d.ts", + "default": "./es/index.js" + } + } }, "author": "", "license": "MIT", @@ -113,4 +118,4 @@ "three": "^0.171.0", "tweakpane": "^3.0.7" } -} +} \ No newline at end of file From b59b2fb185eaf2ba10bf8df70dd9bd6f1bb05234 Mon Sep 17 00:00:00 2001 From: meganrm Date: Sat, 2 Aug 2025 14:59:24 -0700 Subject: [PATCH 38/44] 3.10.2 --- CHANGELOG.md | 6 ++++++ package-lock.json | 4 ++-- package.json | 4 ++-- 3 files changed, 10 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 44bcb07b..c5b1bdec 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,8 +4,14 @@ 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). +#### [v3.10.2](https://github.com/simularium/simularium-viewer/compare/v3.10.1...v3.10.2) + +- 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) diff --git a/package-lock.json b/package-lock.json index ebf11264..1d593ea5 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "@aics/simularium-viewer", - "version": "3.10.1", + "version": "3.10.2", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@aics/simularium-viewer", - "version": "3.10.1", + "version": "3.10.2", "license": "MIT", "dependencies": { "@babel/plugin-transform-runtime": "^7.23.6", diff --git a/package.json b/package.json index 3fc29ef7..c5f0bc15 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@aics/simularium-viewer", - "version": "3.10.1", + "version": "3.10.2", "description": "An npm package to view simulations.", "main": "es/index.js", "type": "module", @@ -118,4 +118,4 @@ "three": "^0.171.0", "tweakpane": "^3.0.7" } -} \ No newline at end of file +} From 4527126954a8ff2cf700e4e8e052336309cc30d5 Mon Sep 17 00:00:00 2001 From: Alli <111383930+ascibisz@users.noreply.github.com> Date: Fri, 15 Aug 2025 09:14:28 -0700 Subject: [PATCH 39/44] read frameNumber from intView when parsing binary frame (#502) --- src/simularium/VisData.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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, From 6dc215d7707dde3bd5d9420254e53289ad6167e3 Mon Sep 17 00:00:00 2001 From: ascibisz Date: Fri, 15 Aug 2025 09:19:52 -0700 Subject: [PATCH 40/44] 3.10.3 --- CHANGELOG.md | 6 ++++++ package-lock.json | 4 ++-- package.json | 2 +- 3 files changed, 9 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c5b1bdec..950770b6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,8 +4,14 @@ 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). +#### [v3.10.3](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) diff --git a/package-lock.json b/package-lock.json index 1d593ea5..a01a8a16 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "@aics/simularium-viewer", - "version": "3.10.2", + "version": "3.10.3", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@aics/simularium-viewer", - "version": "3.10.2", + "version": "3.10.3", "license": "MIT", "dependencies": { "@babel/plugin-transform-runtime": "^7.23.6", diff --git a/package.json b/package.json index c5f0bc15..440e3755 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@aics/simularium-viewer", - "version": "3.10.2", + "version": "3.10.3", "description": "An npm package to view simulations.", "main": "es/index.js", "type": "module", From 9b9e1cd2ceaab66676e5b63190befda20f01b678 Mon Sep 17 00:00:00 2001 From: Dan Toloudis Date: Tue, 23 Sep 2025 20:05:52 -0700 Subject: [PATCH 41/44] trying to revive this example --- examples/package-lock.json | 3 ++- examples/src/Viewer.tsx | 4 ++-- examples/src/simulators/VolumeSimulator.ts | 1 + package-lock.json | 24 +++++++++++----------- package.json | 4 ++-- 5 files changed, 19 insertions(+), 17 deletions(-) diff --git a/examples/package-lock.json b/examples/package-lock.json index bfdb1b95..e18d4f92 100644 --- a/examples/package-lock.json +++ b/examples/package-lock.json @@ -31,6 +31,7 @@ "version": "3.9.1", "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", - "@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", 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 c2111867..7b78639a 100644 --- a/examples/src/simulators/VolumeSimulator.ts +++ b/examples/src/simulators/VolumeSimulator.ts @@ -1,4 +1,5 @@ import { GeometryDisplayType } from "@aics/simularium-viewer"; +import "@aics/vole-core/es/workers/VolumeLoadWorker.js"; import { IClientSimulatorImpl, ClientMessageEnum, diff --git a/package-lock.json b/package-lock.json index 4f57ed3c..f44b0257 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,7 +9,7 @@ "version": "3.9.1", "license": "MIT", "dependencies": { - "@aics/vole-core": "^3.14.1", + "@aics/vole-core": "^4.2.0", "@babel/plugin-transform-runtime": "^7.23.6", "@babel/runtime": "^7.23.6", "@fortawesome/fontawesome-free": "^5.15.2", @@ -78,9 +78,9 @@ } }, "node_modules/@aics/vole-core": { - "version": "3.14.1", - "resolved": "https://registry.npmjs.org/@aics/vole-core/-/vole-core-3.14.1.tgz", - "integrity": "sha512-CtLwx3x0wg7Rf/NGYGTjrvulVtDMZrCXGjqyEp3sUk1UIFPq/4yzID5lWMJYFfLfKx0bactCvE72NZuUE5tKyQ==", + "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", @@ -89,7 +89,7 @@ "three": "^0.171.0", "throttled-queue": "^2.1.4", "tweakpane": "^3.1.9", - "zarrita": "^0.4.0" + "zarrita": "^0.5.1" } }, "node_modules/@ampproject/remapping": { @@ -3932,9 +3932,9 @@ "peer": true }, "node_modules/@zarrita/storage": { - "version": "0.1.1", - "resolved": "https://registry.npmjs.org/@zarrita/storage/-/storage-0.1.1.tgz", - "integrity": "sha512-6/NUCvpzsIxfxeMv59jRTl/bOZg3GZfMP6iR8EIqrTaaE0S2jLL/ceX1OxcFBKnuA8/Z2YmgX4SFBHwFGrCcsw==", + "version": "0.1.2", + "resolved": "https://registry.npmjs.org/@zarrita/storage/-/storage-0.1.2.tgz", + "integrity": "sha512-zUi3CqeEU6avbE104qm5y4MGZbyxmqxXBIh3jyAJgQ4eQRG7KJ6cCmoD7wS7y/uCTl6nUiG7QU6k8QbyfrFjyg==", "license": "MIT", "dependencies": { "reference-spec-reader": "^0.2.0", @@ -14616,12 +14616,12 @@ } }, "node_modules/zarrita": { - "version": "0.4.0", - "resolved": "https://registry.npmjs.org/zarrita/-/zarrita-0.4.0.tgz", - "integrity": "sha512-MK2uustzUF0PooWl6HVUfTares/nmaq5NwRZux/L3npvkSX6Qdpd7w/NOW2cF9EI35yqggoHNi3Nlxyq1YT5eQ==", + "version": "0.5.3", + "resolved": "https://registry.npmjs.org/zarrita/-/zarrita-0.5.3.tgz", + "integrity": "sha512-to2JRq9nHwYdhWEwJwytHYdMYC6I0f2vKUAQfYkgrwwy8OjShhwmv4sH9drzyV3sLzdy7XS9N1ipdMA/Qjspow==", "license": "MIT", "dependencies": { - "@zarrita/storage": "^0.1.0", + "@zarrita/storage": "^0.1.2", "numcodecs": "^0.3.2" } }, diff --git a/package.json b/package.json index 4c8acd37..ee8e2237 100644 --- a/package.json +++ b/package.json @@ -7,7 +7,7 @@ "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", @@ -93,7 +93,7 @@ "react-dom": "^18.2.0" }, "dependencies": { - "@aics/vole-core": "^3.14.1", + "@aics/vole-core": "^4.2.0", "@babel/plugin-transform-runtime": "^7.23.6", "@babel/runtime": "^7.23.6", "@fortawesome/fontawesome-free": "^5.15.2", From ac0f5fe92d0a368cfe21acd3dbaa8197c527df72 Mon Sep 17 00:00:00 2001 From: Dan Toloudis Date: Tue, 23 Sep 2025 20:12:55 -0700 Subject: [PATCH 42/44] viewer version --- examples/package-lock.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/package-lock.json b/examples/package-lock.json index 7ea2642a..bd7a8880 100644 --- a/examples/package-lock.json +++ b/examples/package-lock.json @@ -28,7 +28,7 @@ }, "..": { "name": "@aics/simularium-viewer", - "version": "3.10.0", + "version": "3.10.3", "license": "MIT", "dependencies": { "@aics/vole-core": "^4.2.0", From a3aea7e24374efc1b7fd3156b6ef709c12a25ff5 Mon Sep 17 00:00:00 2001 From: Dan Toloudis Date: Wed, 24 Sep 2025 15:06:25 -0700 Subject: [PATCH 43/44] fix worker loading! --- examples/vite.config.ts | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) 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; From 50a0a309a0744c1ba6095316dc97d16d46e727fd Mon Sep 17 00:00:00 2001 From: Dan Toloudis Date: Thu, 25 Sep 2025 13:17:30 -0700 Subject: [PATCH 44/44] WIP working toward fixing time series volume playback --- examples/src/simulators/VolumeSimulator.ts | 25 ++++++++++++++++++---- src/visGeometry/VolumeModel.ts | 5 +++-- 2 files changed, 24 insertions(+), 6 deletions(-) diff --git a/examples/src/simulators/VolumeSimulator.ts b/examples/src/simulators/VolumeSimulator.ts index 7b78639a..72c86061 100644 --- a/examples/src/simulators/VolumeSimulator.ts +++ b/examples/src/simulators/VolumeSimulator.ts @@ -17,6 +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 = [ @@ -47,13 +48,29 @@ export default class VolumeSim implements IClientSimulatorImpl { 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, @@ -61,8 +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", @@ -74,7 +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/src/visGeometry/VolumeModel.ts b/src/visGeometry/VolumeModel.ts index cdb8204f..ca0a4083 100644 --- a/src/visGeometry/VolumeModel.ts +++ b/src/visGeometry/VolumeModel.ts @@ -43,9 +43,9 @@ export default class VolumeModel { this.volume = volumeObject; this.drawable = new VolumeDrawable(this.volume, {}); this.volume.addVolumeDataObserver(this); - this.drawable.setBrightness(0.7); + this.drawable.setBrightness(0.5); this.drawable.setGamma(0.15, 0.9, 1.0); - this.drawable.setDensity(0.7); + this.drawable.setDensity(0.1); } public setAgentData(data: AgentData): void { @@ -64,6 +64,7 @@ export default class VolumeModel { 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.