From c7629747c75f67a7b7d558dafec21baced4c8d57 Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Sat, 1 Aug 2026 07:55:33 +0100 Subject: [PATCH 01/15] changing lighting to brighten up node colors --- CHANGELOG.md | 6 ++++++ frontend/src/three/Scene.ts | 16 ++++++++++++++-- frontend/src/three/postprocessing.ts | 5 +++++ 3 files changed, 25 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 746d2f2..4a7fa65 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [3.1.0dev] - unreleased + +### Fixed + +- Node colors rendered washed out/dark in the 3D scene compared to the 2D navigator. The bloom composer was blitting linear color straight to the sRGB canvas (missing `OutputPass`), and the ambient light was left at the pre-r155 intensity that physical lighting divides by PI. + ## [3.0.0] - 2026-07-27 Full rewrite: migrated from R/Shiny to a **FastAPI (Python) backend + Vite / TypeScript / Three.js frontend**. Algorithms (layouts, clustering, topology) ported 1:1 via python-igraph. diff --git a/frontend/src/three/Scene.ts b/frontend/src/three/Scene.ts index ceea4b4..2add002 100644 --- a/frontend/src/three/Scene.ts +++ b/frontend/src/three/Scene.ts @@ -39,12 +39,24 @@ export class Scene { addLights(): void { this.add(this.createPointLight(1)) this.add(this.createPointLight(-1)) - this.add(new THREE.AmbientLight(0xffffff)) + // three r155+ lights are physical: the Lambert BRDF divides irradiance by + // PI, so intensity 1 renders a node at ~32% of its own color. PI is the + // intensity that makes a node read as the color the user picked — same as + // the minimap, which draws the raw hex. + this.add(new THREE.AmbientLight(0xffffff, Math.PI)) } createPointLight(orientation: number): THREE.PointLight { const sphereGeom = new THREE.SphereGeometry() - const lightObject = new THREE.PointLight(0xffffff, 1, 2 * ctx.yBoundMax) + // decay 0: the lights sit a whole viewport away, where inverse-square + // falloff leaves nothing. They only add the top/bottom shading that keeps + // the spheres reading as 3D on top of the flat ambient. + const lightObject = new THREE.PointLight( + 0xffffff, + 0.5, + 2 * ctx.yBoundMax, + 0 + ) lightObject.add( new THREE.Mesh( sphereGeom, diff --git a/frontend/src/three/postprocessing.ts b/frontend/src/three/postprocessing.ts index 3751382..183fe1d 100644 --- a/frontend/src/three/postprocessing.ts +++ b/frontend/src/three/postprocessing.ts @@ -6,6 +6,7 @@ // devices pay zero extra GPU cost with the toggle off. import * as THREE from 'three' import { EffectComposer } from 'three/addons/postprocessing/EffectComposer.js' +import { OutputPass } from 'three/addons/postprocessing/OutputPass.js' import { RenderPass } from 'three/addons/postprocessing/RenderPass.js' import { UnrealBloomPass } from 'three/addons/postprocessing/UnrealBloomPass.js' import { ctx } from './runtime' @@ -50,6 +51,10 @@ function ensureComposer(): void { // (nodes, colored edges) bloom; labels are DOM overlays and unaffected. bloomPass = new UnrealBloomPass(size, 0.35, 0.3, 0.8) composer.addPass(bloomPass) + // Composer buffers are linear; without this the last pass would blit linear + // values straight to an sRGB canvas and the whole scene renders dark. Must + // stay last. + composer.addPass(new OutputPass()) } export function resizePostprocessing(width: number, height: number): void { From c3cc7d730b331826539cc22b30fcbf05b26bcfbc Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Sat, 1 Aug 2026 21:01:03 +0100 Subject: [PATCH 02/15] fix link to old Docker pulls --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 02939a2..dbfe73b 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ -[![Docker Pulls](https://img.shields.io/docker/pulls/pavlopouloslab/arena3dweb.svg)](https://hub.docker.com/r/pavlopouloslab/arena3d) +[![Docker Pulls](https://img.shields.io/docker/pulls/pavlopouloslab/arena3dweb.svg)](https://hub.docker.com/r/pavlopouloslab/arena3dweb) [![Live Demo](https://img.shields.io/badge/demo-online-brightgreen)](https://www.arena3d.org) [![GitHub Repo](https://img.shields.io/badge/GitHub-PavlopoulosLab%2FArena3D-blue)](https://github.com/pavlopoulos-lab/arena3d) From aee08ee14ef13601371e25a2341e3d3e467a98df Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Sat, 1 Aug 2026 21:57:31 +0100 Subject: [PATCH 03/15] feat: edge width --- CHANGELOG.md | 4 + backend/app/models/session.py | 1 + backend/app/services/session.py | 3 + backend/tests/test_session.py | 13 +++ frontend/e2e/edge-width.spec.ts | 148 +++++++++++++++++++++++++++ frontend/src/actions/edge.test.ts | 22 ++-- frontend/src/actions/edge.ts | 22 +++- frontend/src/actions/network.ts | 3 +- frontend/src/actions/session.test.ts | 4 +- frontend/src/actions/session.ts | 3 +- frontend/src/api/client.ts | 1 + frontend/src/three/Edge.ts | 100 ++++++++++++++---- frontend/src/three/constants.ts | 9 ++ frontend/src/three/runtime.ts | 24 ++++- frontend/src/three/three.test.ts | 39 ++++++- frontend/src/ui/edge.ts | 91 +++++++++++++--- frontend/src/ui/help.ts | 37 ++++--- 17 files changed, 453 insertions(+), 71 deletions(-) create mode 100644 frontend/e2e/edge-width.spec.ts diff --git a/CHANGELOG.md b/CHANGELOG.md index 4a7fa65..fc5ac2b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,10 @@ ## [3.1.0dev] - unreleased +### Added + +- Edge weight can now be shown as **edge thickness**, not only opacity. The Edge Actions panel replaces the "Edge Opacity By Weight" checkbox with a "Show Edge Weight As" radio — Nothing / Opacity / Width / Both — plus intra- and inter-layer width sliders for whichever property weight isn't driving. Sessions carry the choice as the independent `edgeOpacityByWeight` and `edgeWidthByWeight` booleans; files written before this default to opacity, so they render unchanged. Thickness needed `Line2` (instanced quads) because WebGL renders every line primitive at exactly 1px regardless of `linewidth`. + ### Fixed - Node colors rendered washed out/dark in the 3D scene compared to the 2D navigator. The bloom composer was blitting linear color straight to the sRGB canvas (missing `OutputPass`), and the ambient light was left at the pre-r155 intensity that physical lighting divides by PI. diff --git a/backend/app/models/session.py b/backend/app/models/session.py index d3a400d..0037330 100644 --- a/backend/app/models/session.py +++ b/backend/app/models/session.py @@ -16,6 +16,7 @@ class SessionImportResponse(BaseModel): universalLabelColor: str direction: bool edgeOpacityByWeight: bool + edgeWidthByWeight: bool scramble_nodes: bool warnings: list[str] = [] diff --git a/backend/app/services/session.py b/backend/app/services/session.py index 5f25fa4..86b9ae6 100644 --- a/backend/app/services/session.py +++ b/backend/app/services/session.py @@ -168,6 +168,9 @@ def normalize_session(data: dict[str, Any]) -> dict[str, Any]: "universalLabelColor": _default(data.get("universalLabelColor"), "#FFFFFF"), "direction": _default(data.get("direction"), False), "edgeOpacityByWeight": _default(data.get("edgeOpacityByWeight"), True), + # Sessions written before edge thickness existed default to off, so + # they keep rendering exactly as they did. + "edgeWidthByWeight": _default(data.get("edgeWidthByWeight"), False), "scramble_nodes": scramble, "warnings": warnings, } diff --git a/backend/tests/test_session.py b/backend/tests/test_session.py index 496ae26..5c161fc 100644 --- a/backend/tests/test_session.py +++ b/backend/tests/test_session.py @@ -40,6 +40,19 @@ def test_defaults_filled_for_minimal_json() -> None: assert s["scramble_nodes"] is True # no node positions given assert s["nodes"][0]["color"] # palette-assigned assert s["layers"][0]["generate_coordinates"] is True + # Pre-thickness sessions render exactly as before: weight drives opacity, + # not width. + assert s["edgeOpacityByWeight"] is True + assert s["edgeWidthByWeight"] is False + + +def test_edge_weight_encoding_flags_round_trip() -> None: + for by_opacity, by_width in [(False, False), (True, False), (False, True), (True, True)]: + s = normalize_session( + {**_minimal(), "edgeOpacityByWeight": by_opacity, "edgeWidthByWeight": by_width} + ) + assert s["edgeOpacityByWeight"] is by_opacity + assert s["edgeWidthByWeight"] is by_width def test_missing_mandatory_object_raises() -> None: diff --git a/frontend/e2e/edge-width.spec.ts b/frontend/e2e/edge-width.spec.ts new file mode 100644 index 0000000..8faa131 --- /dev/null +++ b/frontend/e2e/edge-width.spec.ts @@ -0,0 +1,148 @@ +import { expect, test } from '@playwright/test' + +// Edge weight as thickness. WebGL renders line primitives at a fixed 1px, so +// this is Line2 (instanced quads) rather than THREE.Line — meaning the only +// honest check is what actually reaches the framebuffer. + +// Count pixels the edges cover. Three things are on screen: near-black +// background, mid-grey layer planes, and bright near-grey edges. Only the +// bright band counts — the planes' own pixel count *falls* as thicker edges +// cover them, so any metric including them cancels the effect out. Nodes are +// the saturated pixels and are excluded by the hue test. Retries because the +// render loop is FPS-limited and the headless GPU context can drop and +// restore, leaving most frames' buffers empty. +const EDGE_MIN_BRIGHTNESS = 128 + +async function edgeCoverage(page: import('@playwright/test').Page) { + for (let i = 0; i < 60; i++) { + const sample = await page.evaluate(() => { + const webgl = [...document.querySelectorAll('canvas')].find( + (c) => !c.closest('#minimap') + ) + if (!webgl) return null + return new Promise<{ edge: number; node: number }>((resolve) => { + requestAnimationFrame(() => { + const c = document.createElement('canvas') + c.width = webgl.width + c.height = webgl.height + const g = c.getContext('2d', { willReadFrequently: true })! + g.drawImage(webgl, 0, 0) + const { data } = g.getImageData(0, 0, c.width, c.height) + let edge = 0 + let node = 0 + for (let p = 0; p < data.length; p += 4) { + const r = data[p] + const gr = data[p + 1] + const b = data[p + 2] + const hi = Math.max(r, gr, b) + const lo = Math.min(r, gr, b) + if (hi - lo >= 30) node++ // saturated: node spheres + else if (hi >= 128) edge++ // bright near-grey: edges + } + resolve({ edge, node }) + }) + }) + }) + if (sample && sample.edge > 0) return sample + await page.waitForTimeout(100) + } + throw new Error('no rendered frame captured') +} + +async function loadExample(page: import('@playwright/test').Page) { + await page.goto('/') + await page.waitForFunction( + () => '__arena' in (window as unknown as Record) + ) + await page.getByRole('tab', { name: 'File' }).click() + await page.getByRole('button', { name: 'Load Example' }).click() + await expect(page.locator('#file_status')).toContainText('Loaded network') + await page.getByRole('tab', { name: 'Edge Actions' }).click() +} + +test('weight-as-width thickens edges without touching nodes', async ({ + page, +}) => { + await loadExample(page) + + // Default is Opacity, matching the pre-thickness appearance. + await expect(page.locator('#edgeWeight_opacity')).toBeChecked() + await expect(page.locator('#intraLayerEdgeOpacityWrap')).toBeHidden() + await expect(page.locator('#intraLayerEdgeWidthWrap')).toBeVisible() + const before = await edgeCoverage(page) + + await page.locator('#edgeWeight_width').check() + // Width now comes from weight, so its manual sliders hide and opacity's show. + await expect(page.locator('#intraLayerEdgeWidthWrap')).toBeHidden() + await expect(page.locator('#intraLayerEdgeOpacityWrap')).toBeVisible() + const after = await edgeCoverage(page) + + expect(after.edge).toBeGreaterThan(before.edge * 1.5) + // Node pixels only ever fall, from thicker edges drawing over the spheres — + // width must never add saturated pixels of its own. + expect(after.node).toBeLessThanOrEqual(before.node) +}) + +test('manual width slider thickens edges when weight drives neither', async ({ + page, +}) => { + await loadExample(page) + await page.locator('#edgeWeight_none').check() + const thin = await edgeCoverage(page) + + for (const id of ['#intraLayerEdgeWidth', '#interLayerEdgeWidth']) { + await page.locator(id).fill('6') + await page.locator(id).dispatchEvent('input') + } + const thick = await edgeCoverage(page) + + expect(thick.edge).toBeGreaterThan(thin.edge * 1.5) +}) + +// Importing a session writes ctx directly (actions/network.ts) and never +// touches the DOM, so the panel has to re-read it on network:loaded. Drive the +// real path: upload JSON -> backend normalises -> buildFromSession -> radio. +test('the radio reflects whichever flag combination a session carries', async ({ + page, +}) => { + await page.goto('/') + await page.waitForFunction( + () => '__arena' in (window as unknown as Record) + ) + + for (const [byOpacity, byWidth, expected] of [ + [false, true, 'edgeWeight_width'], + [true, true, 'edgeWeight_both'], + [false, false, 'edgeWeight_none'], + [true, false, 'edgeWeight_opacity'], + ] as const) { + await page.getByRole('tab', { name: 'File' }).click() + await page.locator('#load_network_file').setInputFiles({ + name: 'session.json', + mimeType: 'application/json', + buffer: Buffer.from( + JSON.stringify({ + layers: [{ name: 'L1' }], + nodes: [ + { name: 'A', layer: 'L1' }, + { name: 'B', layer: 'L1' }, + ], + edges: [{ src: 'A_L1', trg: 'B_L1' }], + edgeOpacityByWeight: byOpacity, + edgeWidthByWeight: byWidth, + }) + ), + }) + await expect(page.locator('#file_status')).toContainText('Session loaded') + + await page.getByRole('tab', { name: 'Edge Actions' }).click() + await expect(page.locator(`#${expected}`)).toBeChecked() + // The slider pair for a weight-driven property stays hidden. + await expect(page.locator('#intraLayerEdgeOpacityWrap')).toBeVisible({ + visible: !byOpacity, + }) + await expect(page.locator('#intraLayerEdgeWidthWrap')).toBeVisible({ + visible: !byWidth, + }) + } +}) diff --git a/frontend/src/actions/edge.test.ts b/frontend/src/actions/edge.test.ts index 5b2a48d..53c8685 100644 --- a/frontend/src/actions/edge.test.ts +++ b/frontend/src/actions/edge.test.ts @@ -5,7 +5,7 @@ import { renderInterLayerEdges, setChannelColor, setChannelVisibility, - setEdgeWidthByWeight, + setEdgeWeightEncoding, setInterLayerEdgeOpacity, toggleInterLayerEdgesRendering, } from './edge' @@ -70,8 +70,8 @@ describe('renderInterLayerEdges', () => { expect(ctx.waitEdgeRenderFlag).toBe(true) }) - it('removes edges when opacity is 0 and width-by-weight is off', () => { - setEdgeWidthByWeight(false) + it('removes edges when opacity is 0 and opacity-by-weight is off', () => { + setEdgeWeightEncoding(false, false) setInterLayerEdgeOpacity(0) renderInterLayerEdges() expect(ctx.interEdgesRemoved).toBe(true) @@ -107,9 +107,11 @@ describe('channels', () => { expect(ctx.channelVisibility['ch1']).toBe(false) }) - it('toggles the right channel when a sibling channel has no arrow', () => { - // ch1 has weight 0 -> opacity 0 -> no arrow drawn; ch2 keeps its arrow. - // The old positional children[j+1] lookup corrupted ch1's line here. + it('toggles the right channel when a sibling channel is too faint to draw', () => { + // ch1 has weight 0, below EDGE_MIN_VISIBLE_OPACITY, so neither its line nor + // its arrow is built at all; ch2 gets both. Children are therefore not a + // fixed line/arrow interleave, which is why lookups go through + // userData.tag — the old positional children[j+1] corrupted ch1 here. ctx.isDirectionEnabled = true ctx.channelColors = { ch1: '#ff0000', ch2: '#00ff00' } ctx.channelVisibility = { ch1: true, ch2: true } @@ -126,10 +128,10 @@ describe('channels', () => { ] setChannelVisibility('ch2', false) const children = ctx.edgeObjects[0].THREE_Object.children - for (const c of children) { - if (c.userData.tag === 'ch2') expect(c.visible).toBe(false) - if (c.userData.tag === 'ch1') expect(c.visible).toBe(true) - } + expect(children.filter((c) => c.userData.tag === 'ch1')).toHaveLength(0) + const ch2 = children.filter((c) => c.userData.tag === 'ch2') + expect(ch2.length).toBeGreaterThan(0) + for (const c of ch2) expect(c.visible).toBe(false) ctx.isDirectionEnabled = false }) }) diff --git a/frontend/src/actions/edge.ts b/frontend/src/actions/edge.ts index 6bce486..767a7e6 100644 --- a/frontend/src/actions/edge.ts +++ b/frontend/src/actions/edge.ts @@ -50,7 +50,7 @@ export function renderInterLayerEdges(): void { function existsConditionToRemoveInterEdges(): boolean { return ( ctx.interLayerEdgesRenderPauseFlag || - (!ctx.edgeWidthByWeight && ctx.interLayerEdgeOpacity === 0) + (!ctx.edgeOpacityByWeight && ctx.interLayerEdgeOpacity === 0) ) } @@ -113,8 +113,14 @@ export function setInterDirectionArrowSize(size: number): void { ctx.renderInterLayerEdgesFlag = true } -export function setEdgeWidthByWeight(flag: boolean): void { - ctx.edgeWidthByWeight = flag +// The Edge Actions radio always picks both flags at once, so take them +// together and redraw once rather than twice. +export function setEdgeWeightEncoding( + byOpacity: boolean, + byWidth: boolean +): void { + ctx.edgeOpacityByWeight = byOpacity + ctx.edgeWidthByWeight = byWidth ctx.renderInterLayerEdgesFlag = true redrawIntraLayerEdges() } @@ -129,6 +135,16 @@ export function setInterLayerEdgeOpacity(opacity: number): void { ctx.renderInterLayerEdgesFlag = true } +export function setIntraLayerEdgeWidth(width: number): void { + ctx.intraLayerEdgeWidth = width + redrawIntraLayerEdges() +} + +export function setInterLayerEdgeWidth(width: number): void { + ctx.interLayerEdgeWidth = width + ctx.renderInterLayerEdgesFlag = true +} + export function setEdgeSelectedColorPriority(flag: boolean): void { ctx.selectedEdgeColorFlag = flag ctx.renderInterLayerEdgesFlag = true diff --git a/frontend/src/actions/network.ts b/frontend/src/actions/network.ts index 01f1ed1..02d569a 100644 --- a/frontend/src/actions/network.ts +++ b/frontend/src/actions/network.ts @@ -238,7 +238,8 @@ export function buildFromSession(s: SessionData): void { // v2 setJSONExtras setLabelColor(s.universalLabelColor) ctx.isDirectionEnabled = Boolean(s.direction) - ctx.edgeWidthByWeight = Boolean(s.edgeOpacityByWeight) + ctx.edgeOpacityByWeight = Boolean(s.edgeOpacityByWeight) + ctx.edgeWidthByWeight = Boolean(s.edgeWidthByWeight) ctx.edgeFileColorPriority = true store.update({ diff --git a/frontend/src/actions/session.test.ts b/frontend/src/actions/session.test.ts index 7a65117..40d855a 100644 --- a/frontend/src/actions/session.test.ts +++ b/frontend/src/actions/session.test.ts @@ -59,6 +59,7 @@ function session(partial: Partial = {}): SessionData { universalLabelColor: '#abcabc', direction: true, edgeOpacityByWeight: false, + edgeWidthByWeight: true, scramble_nodes: false, ...partial, } @@ -92,7 +93,8 @@ describe('buildFromSession', () => { buildFromSession(session()) expect(ctx.labelColor).toBe('#abcabc') expect(ctx.isDirectionEnabled).toBe(true) - expect(ctx.edgeWidthByWeight).toBe(false) + expect(ctx.edgeOpacityByWeight).toBe(false) + expect(ctx.edgeWidthByWeight).toBe(true) expect(ctx.edgeFileColorPriority).toBe(true) }) diff --git a/frontend/src/actions/session.ts b/frontend/src/actions/session.ts index 733c1f6..e3dca90 100644 --- a/frontend/src/actions/session.ts +++ b/frontend/src/actions/session.ts @@ -54,7 +54,8 @@ export function collectSession(): SessionData { edges: collectEdges(), universalLabelColor: ctx.labelColor, direction: ctx.isDirectionEnabled, - edgeOpacityByWeight: ctx.edgeWidthByWeight, + edgeOpacityByWeight: ctx.edgeOpacityByWeight, + edgeWidthByWeight: ctx.edgeWidthByWeight, scramble_nodes: false, } } diff --git a/frontend/src/api/client.ts b/frontend/src/api/client.ts index 49be009..50c247b 100644 --- a/frontend/src/api/client.ts +++ b/frontend/src/api/client.ts @@ -81,6 +81,7 @@ export interface SessionData { universalLabelColor: string direction: boolean edgeOpacityByWeight: boolean + edgeWidthByWeight: boolean scramble_nodes: boolean warnings?: string[] } diff --git a/frontend/src/three/Edge.ts b/frontend/src/three/Edge.ts index 49fd802..e8b2613 100644 --- a/frontend/src/three/Edge.ts +++ b/frontend/src/three/Edge.ts @@ -1,6 +1,14 @@ import * as THREE from 'three' -import { SELECTED_DEFAULT_COLOR } from './constants' -import { ctx } from './runtime' +import { Line2 } from 'three/addons/lines/Line2.js' +import { LineGeometry } from 'three/addons/lines/LineGeometry.js' +import { LineMaterial } from 'three/addons/lines/LineMaterial.js' +import { + EDGE_MIN_VISIBLE_OPACITY, + EDGE_WIDTH_MAX, + EDGE_WIDTH_MIN, + SELECTED_DEFAULT_COLOR, +} from './constants' +import { ctx, disposeObject3D } from './runtime' export interface EdgeOptions { id?: number @@ -89,19 +97,49 @@ export class Edge { } createEdge(points: THREE.Vector3[]): void { - const geometry = new THREE.BufferGeometry().setFromPoints(points) const color = this.decideColor() const opacity = this.decideOpacity() - const material = new THREE.LineBasicMaterial({ + + // Too faint to see: an empty Group keeps every add/remove/traverse call + // site working while costing no geometry, material or draw call. v2 got + // this from alphaTest, which LineMaterial doesn't implement. + if (opacity < EDGE_MIN_VISIBLE_OPACITY) { + this.THREE_Object = new THREE.Group() + return + } + + this.THREE_Object = this.createLine( + points, + color, + opacity, + this.decideWidth() + ) + + if (ctx.isDirectionEnabled) this.createArrow(points, color) + } + + // Thick lines: WebGL renders every line primitive at exactly 1px, so real + // widths need Line2, which expands each segment into an instanced quad. + // worldUnits keeps the width in view space — with this app's window-sized + // orthographic frustum that reads as constant on-screen thickness, and it + // scales correctly into the higher-resolution PNG export. + // ponytail: one material per line, same count as the LineBasicMaterial it + // replaces. Quantise into a shared cache if material churn ever shows up. + createLine( + points: THREE.Vector3[], + color: string, + opacity: number, + width: number + ): Line2 { + const geometry = new LineGeometry().setFromPoints(points) + const material = new LineMaterial({ color: color, - alphaTest: 0.05, transparent: true, opacity: opacity, + linewidth: width, + worldUnits: true, }) - - this.THREE_Object = new THREE.Line(geometry, material) - - if (ctx.isDirectionEnabled && opacity !== 0) this.createArrow(points, color) + return new Line2(geometry, material) } decideColor(i = 0, forExport = false): string { @@ -119,7 +157,7 @@ export class Edge { decideOpacity(i = 0): number { let opacity: number - if (ctx.edgeWidthByWeight) opacity = this.weights[i] + if (ctx.edgeOpacityByWeight) opacity = this.weights[i] else opacity = this.interLayer ? ctx.interLayerEdgeOpacity @@ -127,6 +165,17 @@ export class Edge { return opacity } + // Mirrors decideOpacity. Weights arrive scaled to [0-1] by the backend, so + // they map onto the width range rather than being used raw — a raw weight + // near 0 would be a sub-pixel, invisible line. + decideWidth(i = 0): number { + if (ctx.edgeWidthByWeight) + return ( + EDGE_WIDTH_MIN + this.weights[i] * (EDGE_WIDTH_MAX - EDGE_WIDTH_MIN) + ) + return this.interLayer ? ctx.interLayerEdgeWidth : ctx.intraLayerEdgeWidth + } + createArrow(points: THREE.Vector3[], arrowColor: string): void { const THREE_arrowHelper = this.createArrowHelper(points, arrowColor) const THREE_Group = new THREE.Group() @@ -189,7 +238,8 @@ export class Edge { verticalPush, color, this.channels[i], - opacity + opacity, + this.decideWidth(i) ) } @@ -203,7 +253,8 @@ export class Edge { verticalPush: number, color: string, channelName: string, - opacity: number + opacity: number, + width: number ): THREE.Group { const p3 = p1.clone() const p4 = p2.clone() @@ -223,19 +274,16 @@ export class Edge { else curve = new THREE.CubicBezierCurve3(p1, p3, p4, p2) const curvePoints = curve.getPoints(points) - const curveGeometry = new THREE.BufferGeometry().setFromPoints(curvePoints) - const curveMaterial = new THREE.LineBasicMaterial({ - color: color, - alphaTest: 0.05, - transparent: true, - opacity: opacity, - }) - const curveLine = new THREE.Line(curveGeometry, curveMaterial) + // Same faintness skip as createEdge — leave the channel out of the group + // entirely rather than rasterising an invisible one. + if (opacity < EDGE_MIN_VISIBLE_OPACITY) return curveGroup + + const curveLine = this.createLine(curvePoints, color, opacity, width) curveLine.userData.tag = channelName curveLine.visible = ctx.channelVisibility[channelName] curveGroup.add(curveLine) - if (ctx.isDirectionEnabled && opacity !== 0) + if (ctx.isDirectionEnabled) curveGroup = this.createCurvedArrow( curveGroup, curvePoints, @@ -275,6 +323,16 @@ export class Edge { if (this.interLayer) ctx.scene!.remove(this.THREE_Object) else ctx.layers[this.sourceLayerIndex].removeEdge(this.THREE_Object) + // drawEdge() replaces THREE_Object outright, so the old one is + // unreachable: undo snapshots hold this same Edge instance (which will + // point at the new object), and no command retains a THREE_Object. + // Inter-layer edges redraw every frame the scene moves, and Line2's + // interleaved instance buffers are far bigger than the old Line's. + disposeObject3D(this.THREE_Object) + // A hidden inter-layer edge isn't redrawn below, so drop to an empty + // placeholder rather than leaving THREE_Object on disposed buffers. + this.THREE_Object = new THREE.Group() + if (!this.interLayer || (this.interLayer && this.areLayersNotHidden())) this.drawEdge() } diff --git a/frontend/src/three/constants.ts b/frontend/src/three/constants.ts index d23971b..d4075c9 100644 --- a/frontend/src/three/constants.ts +++ b/frontend/src/three/constants.ts @@ -17,6 +17,15 @@ export const CONE_HEIGHT = 15 export const PLANE_WIDTHSEGMENTS = 8 export const PLANE_HEIGHTSEGMENTS = 8 +// Edge thickness, in world units. The scene renders through an orthographic +// camera whose frustum tracks the window, so one world unit is one pixel and +// EDGE_WIDTH_MIN reproduces the old fixed 1px line. +export const EDGE_WIDTH_MIN = 1 +export const EDGE_WIDTH_MAX = 6 +// LineMaterial has no alphaTest, so edges this faint are skipped at build time +// rather than rasterised as invisible quads (v2 relied on alphaTest: 0.05). +export const EDGE_MIN_VISIBLE_OPACITY = 0.05 + // Colors export const LAYER_DEFAULT_COLOR = '#777777' export const SELECTED_LAYER_DEFAULT_COLOR = '#f7f43e' diff --git a/frontend/src/three/runtime.ts b/frontend/src/three/runtime.ts index 3561cf4..69d977c 100644 --- a/frontend/src/three/runtime.ts +++ b/frontend/src/three/runtime.ts @@ -53,9 +53,14 @@ export interface RuntimeContext { selectedEdgeColorFlag: boolean edgeFileColorPriority: boolean isDirectionEnabled: boolean + // The two weight encodings are independent; the Edge Actions radio is just a + // view over this pair (none / opacity / width / both). + edgeOpacityByWeight: boolean edgeWidthByWeight: boolean interLayerEdgeOpacity: number intraLayerEdgeOpacity: number + interLayerEdgeWidth: number + intraLayerEdgeWidth: number interDirectionArrowSize: number intraDirectionArrowSize: number interChannelCurvature: number @@ -121,9 +126,12 @@ export const ctx: RuntimeContext = { selectedEdgeColorFlag: true, edgeFileColorPriority: false, isDirectionEnabled: false, - edgeWidthByWeight: true, + edgeOpacityByWeight: true, + edgeWidthByWeight: false, interLayerEdgeOpacity: 0.4, intraLayerEdgeOpacity: 1, + interLayerEdgeWidth: 1, + intraLayerEdgeWidth: 1, interDirectionArrowSize: 5, intraDirectionArrowSize: 5, interChannelCurvature: 5, @@ -169,9 +177,12 @@ export function resetContext(): void { ctx.selectedEdgeColorFlag = true ctx.edgeFileColorPriority = false ctx.isDirectionEnabled = false - ctx.edgeWidthByWeight = true + ctx.edgeOpacityByWeight = true + ctx.edgeWidthByWeight = false ctx.interLayerEdgeOpacity = 0.4 ctx.intraLayerEdgeOpacity = 1 + ctx.interLayerEdgeWidth = 1 + ctx.intraLayerEdgeWidth = 1 ctx.interDirectionArrowSize = 5 ctx.intraDirectionArrowSize = 5 ctx.interChannelCurvature = 5 @@ -229,7 +240,14 @@ export function snapshotRegistries(): RegistrySnapshot { export function disposeSnapshot(snapshot: RegistrySnapshot): void { const scene = snapshot.scene if (!scene || scene === ctx.scene) return - scene.THREE_Object.traverse((obj) => { + disposeObject3D(scene.THREE_Object) +} + +// Free the GPU buffers of an object and everything under it. Only ever call +// this on objects that nothing else can still reach — see disposeSnapshot's +// contract above, and Edge.redrawEdge, which discards the object it replaces. +export function disposeObject3D(root: THREE.Object3D): void { + root.traverse((obj) => { const mesh = obj as Partial & THREE.Object3D if (mesh.geometry) mesh.geometry.dispose() const materials = Array.isArray(mesh.material) diff --git a/frontend/src/three/three.test.ts b/frontend/src/three/three.test.ts index f127639..dcd385b 100644 --- a/frontend/src/three/three.test.ts +++ b/frontend/src/three/three.test.ts @@ -1,6 +1,8 @@ import { beforeEach, describe, expect, it } from 'vitest' import * as THREE from 'three' +import { Line2 } from 'three/addons/lines/Line2.js' import { Node, Layer, Scene, Edge, ctx, resetContext } from './index' +import { EDGE_WIDTH_MAX, EDGE_WIDTH_MIN } from './constants' beforeEach(() => { resetContext() @@ -132,7 +134,7 @@ describe('Edge', () => { it('draws an intra-layer line and attaches it to the source layer', () => { seedTwoNodeLayer() const e = new Edge({ source: 'A::L', target: 'B::L', weights: [1] }) - expect(e.THREE_Object).toBeInstanceOf(THREE.Line) + expect(e.THREE_Object).toBeInstanceOf(Line2) expect(e.sourceLayerIndex).toBe(0) expect(ctx.layers[0].plane.children).toContain(e.THREE_Object) expect(e.decideColor()).toBe(ctx.edgeDefaultColor) @@ -164,12 +166,41 @@ describe('Edge', () => { expect(e.decideColor(0)).toBe('#123456') }) - it('decideOpacity uses weight when edgeWidthByWeight is on', () => { + it('decideOpacity uses weight when edgeOpacityByWeight is on', () => { seedTwoNodeLayer() const e = new Edge({ source: 'A::L', target: 'B::L', weights: [0.7] }) - ctx.edgeWidthByWeight = true + ctx.edgeOpacityByWeight = true expect(e.decideOpacity(0)).toBe(0.7) - ctx.edgeWidthByWeight = false + ctx.edgeOpacityByWeight = false expect(e.decideOpacity(0)).toBe(ctx.intraLayerEdgeOpacity) }) + + it('decideWidth maps the scaled weight onto the width range', () => { + seedTwoNodeLayer() + const e = new Edge({ source: 'A::L', target: 'B::L', weights: [0.5] }) + ctx.edgeWidthByWeight = true + expect(e.decideWidth(0)).toBe( + EDGE_WIDTH_MIN + 0.5 * (EDGE_WIDTH_MAX - EDGE_WIDTH_MIN) + ) + ctx.edgeWidthByWeight = false + expect(e.decideWidth(0)).toBe(ctx.intraLayerEdgeWidth) + }) + + it('applies the resolved width to the line material', () => { + seedTwoNodeLayer() + ctx.edgeWidthByWeight = false + ctx.intraLayerEdgeWidth = 4 + const e = new Edge({ source: 'A::L', target: 'B::L', weights: [1] }) + const material = (e.THREE_Object as Line2).material + expect(material.linewidth).toBe(4) + expect(material.worldUnits).toBe(true) + }) + + it('skips edges too faint to see instead of building invisible lines', () => { + seedTwoNodeLayer() + ctx.edgeOpacityByWeight = true + const e = new Edge({ source: 'A::L', target: 'B::L', weights: [0.01] }) + expect(e.THREE_Object).not.toBeInstanceOf(Line2) + expect(e.THREE_Object.children).toHaveLength(0) + }) }) diff --git a/frontend/src/ui/edge.ts b/frontend/src/ui/edge.ts index 8c53239..4bb9edb 100644 --- a/frontend/src/ui/edge.ts +++ b/frontend/src/ui/edge.ts @@ -12,9 +12,11 @@ import { toggleDirection, setIntraDirectionArrowSize, setInterDirectionArrowSize, - setEdgeWidthByWeight, + setEdgeWeightEncoding, setIntraLayerEdgeOpacity, setInterLayerEdgeOpacity, + setIntraLayerEdgeWidth, + setInterLayerEdgeWidth, setIntraChannelCurvature, setInterChannelCurvature, setEdgeSelectedColorPriority, @@ -37,9 +39,24 @@ const EDGE_HTML = ` -
- - + +
+
+ + +
+
+ + +
+
+ + +
+
+ + +
@@ -49,6 +66,14 @@ const EDGE_HTML = `
+
+ + +
+
+ + +
@@ -73,6 +98,38 @@ function show(id: string, visible: boolean): void { document.getElementById(id)?.classList.toggle('d-none', !visible) } +// The radio is only a view over ctx.edgeOpacityByWeight/edgeWidthByWeight, +// which are what the session JSON stores. One row per combination, so any +// imported pair maps back onto an option. +const ENCODING_FLAGS: Record = { + none: [false, false], + opacity: [true, false], + width: [false, true], + both: [true, true], +} + +// Point the radio and the slider visibility at whatever ctx currently holds. +// Called on init and after every network/session load, since importing a +// session writes ctx directly (actions/network.ts) and never touches the DOM. +function syncEncodingSliders(): void { + const value = + Object.keys(ENCODING_FLAGS).find( + (k) => + ENCODING_FLAGS[k][0] === ctx.edgeOpacityByWeight && + ENCODING_FLAGS[k][1] === ctx.edgeWidthByWeight + ) ?? 'opacity' + const radio = document.querySelector( + `input[name="edgeWeightEncodingRadio"][value="${value}"]` + ) + if (radio) radio.checked = true + + // A slider is only useful for the encoding weight isn't already driving. + show('intraLayerEdgeOpacityWrap', !ctx.edgeOpacityByWeight) + show('interLayerEdgeOpacityWrap', !ctx.edgeOpacityByWeight) + show('intraLayerEdgeWidthWrap', !ctx.edgeWidthByWeight) + show('interLayerEdgeWidthWrap', !ctx.edgeWidthByWeight) +} + // v2 attachChannelEditList: per channel a color picker + a Hide checkbox. // XSS fix: `ch` is a user-controlled channel name (TSV Channel column) — // escapeHtml() it before interpolating into innerHTML, including inside the @@ -131,17 +188,21 @@ export function initEdgePanel(): void { range('intraDirectionArrowSize', setIntraDirectionArrowSize) range('interDirectionArrowSize', setInterDirectionArrowSize) - // Opacity-by-weight hides the manual opacity sliders (edges.R). - document - .getElementById('edgeWidthByWeight') - ?.addEventListener('change', (e) => { - const byWeight = (e.target as HTMLInputElement).checked - show('intraLayerEdgeOpacityWrap', !byWeight) - show('interLayerEdgeOpacityWrap', !byWeight) - setEdgeWidthByWeight(byWeight) + // Each encoding driven by weight hides its own manual sliders (edges.R did + // this for opacity; width follows the same rule). + for (const radio of document.querySelectorAll( + 'input[name="edgeWeightEncodingRadio"]' + )) { + radio.addEventListener('change', () => { + const [byOpacity, byWidth] = ENCODING_FLAGS[radio.value] + setEdgeWeightEncoding(byOpacity, byWidth) + syncEncodingSliders() }) + } range('intraLayerEdgeOpacity', setIntraLayerEdgeOpacity) range('interLayerEdgeOpacity', setInterLayerEdgeOpacity) + range('intraLayerEdgeWidth', setIntraLayerEdgeWidth) + range('interLayerEdgeWidth', setInterLayerEdgeWidth) range('intraChannelCurvature', setIntraChannelCurvature) range('interChannelCurvature', setInterChannelCurvature) @@ -157,5 +218,9 @@ export function initEdgePanel(): void { setEdgeFileColorPriority((e.target as HTMLInputElement).checked) }) - bus.on('network:loaded', buildChannelEditList) + syncEncodingSliders() + bus.on('network:loaded', () => { + buildChannelEditList() + syncEncodingSliders() // an imported session may carry either flag + }) } diff --git a/frontend/src/ui/help.ts b/frontend/src/ui/help.ts index 26a105d..ea2124a 100644 --- a/frontend/src/ui/help.ts +++ b/frontend/src/ui/help.ts @@ -30,8 +30,9 @@ const HELP_HTML = ` SourceLayer and TargetLayer and 2 optional columns with the headers Weight and Channel. After the file is uploaded, the weight values are - mapped in a [0-1] range and relative opacities are assigned to the respective edges. Edge transparency represents - the weight. The heavier the weight, the higher the opacity. In the case of unweighted graphs, one can skip the + mapped in a [0-1] range and assigned to the respective edges. By default the weight is shown as edge transparency — + the heavier the weight, the higher the opacity — and the Edge Actions panel can show it as edge thickness instead, + or as both at once. In the case of unweighted graphs, one can skip the weight column. The channel column is only used in the case of a multi-edge graphs. The column order in the input file is irrelevant.
In its online version, @@ -121,7 +122,9 @@ Kn Group4 Tn Group7 #4EFB7D Description
Edge attributes: Edge, Weight, Opacity, Color, Channel
Univers Label Color: hex code for the labels
- Enable Direction: boolean + Enable Direction: boolean
+ Weight Encoding: edgeOpacityByWeight and edgeWidthByWeight booleans, independently selecting + whether edge weight drives opacity, thickness, both or neither 

 {
@@ -197,7 +200,8 @@ Kn	        Group4	        Tn	        Group7	        #4EFB7D
     ],
     "universalLabelColor": "#FFFFFF",
     "direction": false,
-    "edgeOpacityByWeight": true
+    "edgeOpacityByWeight": true,
+    "edgeWidthByWeight": false
 }

@@ -605,7 +609,7 @@ Kn Group4 Tn Group7 #4EFB7D style="float:left;width:320px;height:auto;max-width:100%;margin:5px;margin-right:20px;"> 1. This option highlights the selected edges.
2. This option toggles gives priority to the edge color that it is set on file. If - it is not checked and the network has multiple edges then the channel menu 11 is + it is not checked and the network has multiple edges then the channel menu 13 is visible.
3. This option toggles the graph direction from the source node to target node (first figure).
@@ -613,19 +617,24 @@ Kn Group4 Tn Group7 #4EFB7D (3) is enabled.
5. This slider change the inter-layer arrow sizes. This is visible only if option (3) is enabled.
- 6. This option gives priority on any uploaded/imported values of edge - Weights, which are being mapped in the [0-1] range and are assigned on edge opacities. If this option is - unchecked, the edge opacity is decided through options (7) for intra-layer and (8) for inter-layer edges, respectively.
- 7. If option (6) is unchecked, the intra-layer edge + 6. These options decide how uploaded/imported edge Weights, which are + mapped in the [0-1] range, are shown. Opacity assigns them to edge opacities (the heavier the weight, the + more opaque the edge) and Width assigns them to edge thickness (the heavier the weight, the thicker the + edge); Both applies them together, and Nothing ignores the weights entirely. Whichever property is + not driven by weight is set manually through the sliders below.
+ 7. If weight is not assigned to opacity, the intra-layer edge opacity is decided through this slider.
- 8. If option (6) is unchecked, the inter-layer edge + 8. If weight is not assigned to opacity, the inter-layer edge opacity is decided through this slider.
- 9. If the graph is multi-edge then this slider is visible and control the + 9. If weight is not assigned to width, the intra-layer edge + thickness is decided through this slider.
+ 10. If weight is not assigned to width, the inter-layer edge + thickness is decided through this slider.
+ 11. If the graph is multi-edge then this slider is visible and control the curvature of the intra-layer edges.
- 10. If the graph is multi-edge then this slider is visible and control the + 12. If the graph is multi-edge then this slider is visible and control the curvature of the inter-layer edges.
- 11. If the graph that is uploaded is multi-edge then then the channel menu (a + 13. If the graph that is uploaded is multi-edge then then the channel menu (a grid of n x 3) is created, where n is the number of channels and 3 are the available columns for From 7ca536dd3088fbc4233c6cd73e9e7a167a6224bc Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Sat, 1 Aug 2026 22:08:35 +0100 Subject: [PATCH 04/15] hide curvature options when one channel --- frontend/e2e/edge-width.spec.ts | 39 +++++++++++++++++++++++++++++---- frontend/src/ui/edge.ts | 25 +++++++++++++++------ frontend/src/ui/help.ts | 2 +- 3 files changed, 54 insertions(+), 12 deletions(-) diff --git a/frontend/e2e/edge-width.spec.ts b/frontend/e2e/edge-width.spec.ts index 8faa131..46f3485 100644 --- a/frontend/e2e/edge-width.spec.ts +++ b/frontend/e2e/edge-width.spec.ts @@ -11,8 +11,6 @@ import { expect, test } from '@playwright/test' // the saturated pixels and are excluded by the hue test. Retries because the // render loop is FPS-limited and the headless GPU context can drop and // restore, leaving most frames' buffers empty. -const EDGE_MIN_BRIGHTNESS = 128 - async function edgeCoverage(page: import('@playwright/test').Page) { for (let i = 0; i < 60; i++) { const sample = await page.evaluate(() => { @@ -87,7 +85,7 @@ test('manual width slider thickens edges when weight drives neither', async ({ page, }) => { await loadExample(page) - await page.locator('#edgeWeight_none').check() + await page.locator('#edgeWeight_neither').check() const thin = await edgeCoverage(page) for (const id of ['#intraLayerEdgeWidth', '#interLayerEdgeWidth']) { @@ -99,6 +97,39 @@ test('manual width slider thickens edges when weight drives neither', async ({ expect(thick.edge).toBeGreaterThan(thin.edge * 1.5) }) +// Curvature only bends channel curves, which single-edge networks never build. +test('channel curvature sliders appear only for multi-edge networks', async ({ + page, +}) => { + await loadExample(page) // figure2A_data.tsv has no Channel column + await expect(page.locator('#intraChannelCurvatureWrap')).toBeHidden() + await expect(page.locator('#interChannelCurvatureWrap')).toBeHidden() + + await page.getByRole('tab', { name: 'File' }).click() + await page.locator('#load_network_file').setInputFiles({ + name: 'channels.json', + mimeType: 'application/json', + buffer: Buffer.from( + JSON.stringify({ + layers: [{ name: 'L1' }], + nodes: [ + { name: 'A', layer: 'L1' }, + { name: 'B', layer: 'L1' }, + ], + edges: [ + { src: 'A_L1', trg: 'B_L1', channel: 'ppi' }, + { src: 'A_L1', trg: 'B_L1', channel: 'coexpression' }, + ], + }) + ), + }) + await expect(page.locator('#file_status')).toContainText('Session loaded') + + await page.getByRole('tab', { name: 'Edge Actions' }).click() + await expect(page.locator('#intraChannelCurvatureWrap')).toBeVisible() + await expect(page.locator('#interChannelCurvatureWrap')).toBeVisible() +}) + // Importing a session writes ctx directly (actions/network.ts) and never // touches the DOM, so the panel has to re-read it on network:loaded. Drive the // real path: upload JSON -> backend normalises -> buildFromSession -> radio. @@ -113,7 +144,7 @@ test('the radio reflects whichever flag combination a session carries', async ({ for (const [byOpacity, byWidth, expected] of [ [false, true, 'edgeWeight_width'], [true, true, 'edgeWeight_both'], - [false, false, 'edgeWeight_none'], + [false, false, 'edgeWeight_neither'], [true, false, 'edgeWeight_opacity'], ] as const) { await page.getByRole('tab', { name: 'File' }).click() diff --git a/frontend/src/ui/edge.ts b/frontend/src/ui/edge.ts index 4bb9edb..0ab1a5b 100644 --- a/frontend/src/ui/edge.ts +++ b/frontend/src/ui/edge.ts @@ -41,10 +41,6 @@ const EDGE_HTML = `

-
- - -
@@ -57,6 +53,10 @@ const EDGE_HTML = `
+
+ + +
@@ -74,11 +74,11 @@ const EDGE_HTML = `
-
+
-
+
@@ -102,10 +102,10 @@ function show(id: string, visible: boolean): void { // which are what the session JSON stores. One row per combination, so any // imported pair maps back onto an option. const ENCODING_FLAGS: Record = { - none: [false, false], opacity: [true, false], width: [false, true], both: [true, true], + neither: [false, false], } // Point the radio and the slider visibility at whatever ctx currently holds. @@ -130,6 +130,15 @@ function syncEncodingSliders(): void { show('interLayerEdgeWidthWrap', !ctx.edgeWidthByWeight) } +// Curvature only ever reaches Edge.createChannels, which is skipped entirely +// for single-edge networks — so on those the sliders move nothing. The help +// text already described them as multi-edge only; this makes that true. +function syncChannelControls(): void { + const multiEdge = (store.get().network?.channels ?? []).length > 0 + show('intraChannelCurvatureWrap', multiEdge) + show('interChannelCurvatureWrap', multiEdge) +} + // v2 attachChannelEditList: per channel a color picker + a Hide checkbox. // XSS fix: `ch` is a user-controlled channel name (TSV Channel column) — // escapeHtml() it before interpolating into innerHTML, including inside the @@ -219,8 +228,10 @@ export function initEdgePanel(): void { }) syncEncodingSliders() + syncChannelControls() bus.on('network:loaded', () => { buildChannelEditList() syncEncodingSliders() // an imported session may carry either flag + syncChannelControls() // and may or may not be multi-edge }) } diff --git a/frontend/src/ui/help.ts b/frontend/src/ui/help.ts index ea2124a..3b3bcea 100644 --- a/frontend/src/ui/help.ts +++ b/frontend/src/ui/help.ts @@ -620,7 +620,7 @@ Kn Group4 Tn Group7 #4EFB7D 6. These options decide how uploaded/imported edge Weights, which are mapped in the [0-1] range, are shown. Opacity assigns them to edge opacities (the heavier the weight, the more opaque the edge) and Width assigns them to edge thickness (the heavier the weight, the thicker the - edge); Both applies them together, and Nothing ignores the weights entirely. Whichever property is + edge); Both applies them together, and Neither ignores the weights entirely. Whichever property is not driven by weight is set manually through the sliders below.
7. If weight is not assigned to opacity, the intra-layer edge opacity is decided through this slider.
From 8b5748567cc811d296e18bf02cf9ee55183d9b3e Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Sun, 9 Aug 2026 11:13:01 +0100 Subject: [PATCH 05/15] edgeResolution to fix choppy curved lines --- .serena/project.yml | 133 +++++++++++++++++++------------ CHANGELOG.md | 1 + frontend/src/actions/screen.ts | 10 ++- frontend/src/three/Edge.ts | 16 ++-- frontend/src/three/runtime.ts | 9 +++ frontend/src/three/three.test.ts | 15 +++- 6 files changed, 125 insertions(+), 59 deletions(-) diff --git a/.serena/project.yml b/.serena/project.yml index acca853..45f6836 100644 --- a/.serena/project.yml +++ b/.serena/project.yml @@ -1,43 +1,6 @@ -# the name by which the project can be referenced within Serena +# the name by which the project can be referenced within Serena/when chatting with the LLM. project_name: "Arena3Dweb" - -# list of languages for which language servers are started; choose from: -# al angular ansible bash clojure -# cpp cpp_ccls crystal csharp csharp_omnisharp -# dart elixir elm erlang fortran -# fsharp go groovy haskell haxe -# hlsl html java json julia -# kotlin lean4 lua luau markdown -# matlab msl nix ocaml pascal -# perl php php_phpactor powershell python -# python_jedi python_ty r rego ruby -# ruby_solargraph rust scala scss solidity -# svelte swift systemverilog terraform toml -# typescript typescript_vts vue yaml zig -# (This list may be outdated. For the current list, see values of Language enum here: -# https://github.com/oraios/serena/blob/main/src/solidlsp/ls_config.py -# For some languages, there are alternative language servers, e.g. csharp_omnisharp, ruby_solargraph.) -# Note: -# - For C, use cpp -# - For JavaScript, use typescript -# - For Angular projects, use angular (subsumes typescript+html; requires `npm install` in the project root) -# - For Svelte projects, use svelte (subsumes typescript/javascript for .svelte projects; requires npm) -# - For SCSS / Sass / plain CSS, use scss (some-sass-language-server handles all three) -# - For Free Pascal/Lazarus, use pascal -# Special requirements: -# Some languages require additional setup/installations. -# See here for details: https://oraios.github.io/serena/01-about/020_programming-languages.html#language-servers -# When using multiple languages, the first language server that supports a given file will be used for that file. -# The first language is the default language and the respective language server will be used as a fallback. -# Note that when using the JetBrains backend, language servers are not used and this list is correspondingly ignored. -# R dropped: legacy code being deleted through the v3 migration, and its LSP -# (R `languageserver` package) isn't installed — its failure aborted the whole -# language-server manager. Active dev is TS (frontend) + Python (backend). -languages: -- typescript -- python - # the encoding used by text files in the project # For a list of possible encodings, see https://docs.python.org/3.11/library/codecs.html#standard-encodings encoding: "utf-8" @@ -59,23 +22,19 @@ ignore_all_files_in_gitignore: true # advanced configuration option allowing to configure language server-specific options. # Maps the language key to the options. -# Have a look at the docstring of the constructors of the LS implementations within solidlsp (e.g., for C# or PHP) to see which options are available. -# No documentation on options means no options are available. +# The settings are considered only if the project is trusted (see global configuration to define trusted projects). +# See https://oraios.github.io/serena/02-usage/050_configuration.html#language-server-specific-settings ls_specific_settings: {} -# list of additional workspace folder paths for cross-package reference support (e.g. in monorepos). -# Paths can be absolute or relative to the project root. -# Each folder is registered as an LSP workspace folder, enabling language servers to discover -# symbols and references across package boundaries. -# Currently supported for: TypeScript. -# Example: -# additional_workspace_folders: -# - ../sibling-package -# - ../shared-lib -additional_workspace_folders: [] - # list of additional paths to ignore in this project. # Same syntax as gitignore, so you can use * and **. +# Important: quote patterns that start with `*`, otherwise YAML treats them as aliases. +# Example: +# ignored_paths: +# - "examples/**" +# - ".worktrees/**" +# - "**/bin/**" +# - "**/obj/**" # Note: global ignored_paths from serena_config.yml are also applied additively. ignored_paths: [] @@ -135,3 +94,75 @@ read_only_memory_patterns: [] # Extends the list from the global configuration, merging the two lists. # Example: ["_archive/.*", "_episodes/.*"] ignored_memory_patterns: [] + +# list of additional workspace folder paths for cross-package reference support. +# Paths can be absolute or relative to the project root. +# Each folder is registered as an LSP workspace folder, enabling language servers to discover +# symbols and references across package boundaries, but these folders are not indexed by Serena, +# i.e. the respective symbols will not be found using Serena's symbol search tools. +# Example: +# additional_workspace_folders: +# - ../sibling-package +# - ../shared-lib +ls_additional_workspace_folders: [] + +# list of language servers to start when using the LSP backend; choose from: +# ada al angular ansible bash +# bsl clojure cpp cpp_ccls crystal +# csharp csharp_omnisharp cue dart elixir +# elm erlang fortran fsharp gdscript +# go groovy haskell haxe hlsl +# html java json julia kotlin +# latex lean4 lua luau markdown +# matlab msl nextflow nix ocaml +# pascal perl php php_phpactor php_phpantom +# powershell python python_basedpyright python_jedi python_pyrefly +# python_ty qml r rego ruby +# ruby_solargraph rust scala scss solidity +# svelte swift systemverilog terraform toml +# typescript typescript_vts vue yaml zig +# (This list may be outdated; generated with scripts/print_language_list.py; +# For the current list, see values of the LanguageServerId enum here: +# https://github.com/oraios/serena/blob/main/src/solidlsp/ls_config.py) +# For some languages, there are several alternative language servers, e.g. csharp_omnisharp, ruby_solargraph.) +# Note: +# - For C, use cpp +# - For JavaScript, use typescript +# - For Angular projects, use angular (subsumes typescript+html; requires `npm install` in the project root) +# - For Svelte projects, use svelte (subsumes typescript/javascript for .svelte projects; requires npm) +# - For SCSS / Sass / plain CSS, use scss (some-sass-language-server handles all three) +# - For Free Pascal/Lazarus, use pascal +# Special requirements: +# Some language servers require additional setup/installations. +# See here for details: https://oraios.github.io/serena/01-about/020_programming-languages.html#language-servers +# When using multiple language servers, the first language server that supports a given file will be used for that file. +# The first language server is the default language and the respective language server will be used as a fallback. +# Note that when using the JetBrains backend, language servers are not used and this list is correspondingly ignored. +language_servers: +- typescript +- python + +# list of workspace folder paths (LSP backend only). +# These folders will be used to build up Serena's symbol index. +# Paths must be within the project root and should thus be relative to the project root. +# Furthermore, the paths should not be filtered by ignore settings. +# Default setting: The entire project root folder (".") is considered. +# In (large) monorepos, this can be used to index only subfolders of the project root, e.g. +# ls_workspace_folders: +# - "./subproject1" +# - "./subproject2" +ls_workspace_folders: +- . + +# optional shell command to run before the language backend (LSP or JetBrains) is initialised. +# the command runs in the project root directory and is only executed if the project is trusted +# (see trusted_project_path_patterns in the global configuration). +# serena waits for the command to exit: a non-zero exit code is logged as an error but does not +# abort activation. a per-project timeout (activation_command_timeout, default 180s) is the safety +# backstop for non-terminating commands; on expiry the process is killed and activation continues. +# example: activation_command: "npx nx run-many -t build" +activation_command: + +# maximum time in seconds to wait for activation_command to complete before killing it (default 180s). +# must be a positive number. +activation_command_timeout: 180.0 diff --git a/CHANGELOG.md b/CHANGELOG.md index fc5ac2b..f25d1da 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ ### Fixed +- Curved channel edges rendered as dotted lines with beads at the curve points once thickness landed. `LineMaterial`'s `worldUnits` mode assumes a perspective camera — its fragment shader traces a view ray from the camera origin and discards anything farther than half a width from the segment, which under this app's orthographic camera discards along the whole segment. Widths are now screen-space, sized against a shared resolution uniform kept on the frustum size (so the numbers still mean world units), retargeted on resize and for the PNG export. - Node colors rendered washed out/dark in the 3D scene compared to the 2D navigator. The bloom composer was blitting linear color straight to the sRGB canvas (missing `OutputPass`), and the ambient light was left at the pre-r155 intensity that physical lighting divides by PI. ## [3.0.0] - 2026-07-27 diff --git a/frontend/src/actions/screen.ts b/frontend/src/actions/screen.ts index 4412f4e..3ae40fd 100644 --- a/frontend/src/actions/screen.ts +++ b/frontend/src/actions/screen.ts @@ -2,7 +2,7 @@ // Port of v2 www/js/object_actions/screen.js. Shiny sync calls dropped. import * as THREE from 'three' -import { ctx } from '../three' +import { ctx, edgeResolution } from '../three' import { onBackgroundColor, renderFrame, @@ -40,6 +40,9 @@ export function setWindowBounds(): void { ctx.yBoundMax = window.innerHeight / 2 ctx.zBoundMin = -window.innerHeight / 2.5 ctx.zBoundMax = window.innerHeight / 2.5 + // Every edge LineMaterial shares this uniform; keep it on the frustum size + // so screen-space linewidths keep reading as world units. + edgeResolution.set(window.innerWidth, window.innerHeight) } export function setCamera(): void { @@ -127,7 +130,12 @@ export function exportSceneImage(): boolean { }) renderer.setSize(Math.round(w * scale), Math.round(h * scale), false) renderer.setClearColor(ctx.renderer.getClearColor(new THREE.Color()), 1) + // Edge linewidths are screen-space against the shared frustum-sized + // resolution; point it at the export frustum for this render so widths + // scale with the PNG, then hand it back to the live view. + edgeResolution.set(w, h) renderer.render(ctx.scene.THREE_Object, camera) + edgeResolution.set(2 * ctx.xBoundMax, 2 * ctx.yBoundMax) // Composite onto a 2D canvas so the DOM-overlay labels can be drawn on top. const out = document.createElement('canvas') diff --git a/frontend/src/three/Edge.ts b/frontend/src/three/Edge.ts index e8b2613..336da9e 100644 --- a/frontend/src/three/Edge.ts +++ b/frontend/src/three/Edge.ts @@ -8,7 +8,7 @@ import { EDGE_WIDTH_MIN, SELECTED_DEFAULT_COLOR, } from './constants' -import { ctx, disposeObject3D } from './runtime' +import { ctx, disposeObject3D, edgeResolution } from './runtime' export interface EdgeOptions { id?: number @@ -120,9 +120,11 @@ export class Edge { // Thick lines: WebGL renders every line primitive at exactly 1px, so real // widths need Line2, which expands each segment into an instanced quad. - // worldUnits keeps the width in view space — with this app's window-sized - // orthographic frustum that reads as constant on-screen thickness, and it - // scales correctly into the higher-resolution PNG export. + // Widths are screen-space (LineMaterial's worldUnits shader assumes a + // perspective view ray and breaks curved lines into dots under this app's + // orthographic camera) — with the frustum-sized resolution uniform below, + // linewidth is effectively world units, constant on screen and scaled + // correctly into the higher-resolution PNG export. // ponytail: one material per line, same count as the LineBasicMaterial it // replaces. Quantise into a shared cache if material churn ever shows up. createLine( @@ -137,8 +139,12 @@ export class Edge { transparent: true, opacity: opacity, linewidth: width, - worldUnits: true, }) + // Screen-space widths, sized against the shared frustum-tracking + // resolution (see runtime.edgeResolution) so linewidth stays in world + // units. Assign the uniform's value directly: the `resolution` setter + // copies, and we need every edge to share the one mutable Vector2. + material.uniforms.resolution.value = edgeResolution return new Line2(geometry, material) } diff --git a/frontend/src/three/runtime.ts b/frontend/src/three/runtime.ts index 69d977c..8d33118 100644 --- a/frontend/src/three/runtime.ts +++ b/frontend/src/three/runtime.ts @@ -12,6 +12,7 @@ import type { Scene } from './Scene' import type * as THREE from 'three' +import { Vector2 } from 'three' import type { Layer } from './Layer' import type { Node } from './Node' import type { Edge } from './Edge' @@ -97,6 +98,14 @@ export interface RuntimeContext { const winW = typeof window !== 'undefined' ? window.innerWidth : 800 const winH = typeof window !== 'undefined' ? window.innerHeight : 800 +// Shared resolution uniform for every edge LineMaterial. Screen-space fat +// lines divide linewidth by this, so it must track the camera frustum size in +// world units: every material references this single Vector2, so resize +// (screen.ts resetScreen) and PNG export retarget all edges by mutating it — +// no scene traversal. worldUnits is not an option: its shader assumes a +// perspective view ray and shreds lines under this app's orthographic camera. +export const edgeResolution = new Vector2(winW, winH) + export const ctx: RuntimeContext = { renderer: null, camera: null, diff --git a/frontend/src/three/three.test.ts b/frontend/src/three/three.test.ts index dcd385b..edf6bfc 100644 --- a/frontend/src/three/three.test.ts +++ b/frontend/src/three/three.test.ts @@ -1,7 +1,15 @@ import { beforeEach, describe, expect, it } from 'vitest' import * as THREE from 'three' import { Line2 } from 'three/addons/lines/Line2.js' -import { Node, Layer, Scene, Edge, ctx, resetContext } from './index' +import { + Node, + Layer, + Scene, + Edge, + ctx, + edgeResolution, + resetContext, +} from './index' import { EDGE_WIDTH_MAX, EDGE_WIDTH_MIN } from './constants' beforeEach(() => { @@ -193,7 +201,10 @@ describe('Edge', () => { const e = new Edge({ source: 'A::L', target: 'B::L', weights: [1] }) const material = (e.THREE_Object as Line2).material expect(material.linewidth).toBe(4) - expect(material.worldUnits).toBe(true) + // Screen-space widths (worldUnits breaks under the orthographic camera), + // sized against the shared frustum-tracking resolution uniform. + expect(material.worldUnits).toBe(false) + expect(material.uniforms.resolution.value).toBe(edgeResolution) }) it('skips edges too faint to see instead of building invisible lines', () => { From ac589c0853cebe87b75a79fb9dec085197898f3a Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Sun, 9 Aug 2026 11:39:14 +0100 Subject: [PATCH 06/15] remove bloom from edges to avoid flashblind, increase curvature upper limit for multi-channel edges --- CHANGELOG.md | 5 +++ frontend/e2e/edge-width.spec.ts | 11 ++++-- frontend/src/actions/screen.ts | 5 ++- frontend/src/three/Edge.ts | 5 +++ frontend/src/three/constants.ts | 5 +++ frontend/src/three/postprocessing.ts | 56 +++++++++++++++++++++++++--- frontend/src/ui/edge.ts | 4 +- 7 files changed, 79 insertions(+), 12 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f25d1da..ed56ad0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,8 +6,13 @@ - Edge weight can now be shown as **edge thickness**, not only opacity. The Edge Actions panel replaces the "Edge Opacity By Weight" checkbox with a "Show Edge Weight As" radio — Nothing / Opacity / Width / Both — plus intra- and inter-layer width sliders for whichever property weight isn't driving. Sessions carry the choice as the independent `edgeOpacityByWeight` and `edgeWidthByWeight` booleans; files written before this default to opacity, so they render unchanged. Thickness needed `Line2` (instanced quads) because WebGL renders every line primitive at exactly 1px regardless of `linewidth`. +### Changed + +- Channel curvature sliders reach much further — intra-layer 10–60 (was 10–20), inter-layer 1–30 (was 1–10) — so the channels of a multi-channel edge can be pulled well apart instead of running nearly parallel. Defaults are unchanged, so existing sessions render exactly as before. + ### Fixed +- Edges no longer glow. Thick edges cover a large share of the screen, and bloom on all of them was blinding against dark backgrounds. Bloom is now selective (three's off-screen bloom-composer pattern): edges render on a dedicated layer that the bloom source masks out, so nodes still glow and edges stay crisp. - Curved channel edges rendered as dotted lines with beads at the curve points once thickness landed. `LineMaterial`'s `worldUnits` mode assumes a perspective camera — its fragment shader traces a view ray from the camera origin and discards anything farther than half a width from the segment, which under this app's orthographic camera discards along the whole segment. Widths are now screen-space, sized against a shared resolution uniform kept on the frustum size (so the numbers still mean world units), retargeted on resize and for the PNG export. - Node colors rendered washed out/dark in the 3D scene compared to the 2D navigator. The bloom composer was blitting linear color straight to the sRGB canvas (missing `OutputPass`), and the ambient light was left at the pre-r155 intensity that physical lighting divides by PI. diff --git a/frontend/e2e/edge-width.spec.ts b/frontend/e2e/edge-width.spec.ts index 46f3485..922d444 100644 --- a/frontend/e2e/edge-width.spec.ts +++ b/frontend/e2e/edge-width.spec.ts @@ -8,9 +8,11 @@ import { expect, test } from '@playwright/test' // background, mid-grey layer planes, and bright near-grey edges. Only the // bright band counts — the planes' own pixel count *falls* as thicker edges // cover them, so any metric including them cancels the effect out. Nodes are -// the saturated pixels and are excluded by the hue test. Retries because the -// render loop is FPS-limited and the headless GPU context can drop and -// restore, leaving most frames' buffers empty. +// the saturated pixels and are excluded by the hue test. Requires bloom off +// (loadExample): glow lifts the whole plane into the bright band, which swamps +// the edges' own pixels. Retries because the render loop is FPS-limited and +// the headless GPU context can drop and restore, leaving most frames' buffers +// empty. async function edgeCoverage(page: import('@playwright/test').Page) { for (let i = 0; i < 60; i++) { const sample = await page.evaluate(() => { @@ -55,6 +57,9 @@ async function loadExample(page: import('@playwright/test').Page) { await page.getByRole('tab', { name: 'File' }).click() await page.getByRole('button', { name: 'Load Example' }).click() await expect(page.locator('#file_status')).toContainText('Loaded network') + // Bloom off so pixel counts measure geometry, not glow. + await page.getByRole('tab', { name: 'Scene Actions' }).click() + await page.locator('#toggleBloom').uncheck() await page.getByRole('tab', { name: 'Edge Actions' }).click() } diff --git a/frontend/src/actions/screen.ts b/frontend/src/actions/screen.ts index 3ae40fd..e5db4db 100644 --- a/frontend/src/actions/screen.ts +++ b/frontend/src/actions/screen.ts @@ -2,7 +2,7 @@ // Port of v2 www/js/object_actions/screen.js. Shiny sync calls dropped. import * as THREE from 'three' -import { ctx, edgeResolution } from '../three' +import { ctx, edgeResolution, NO_BLOOM_LAYER } from '../three' import { onBackgroundColor, renderFrame, @@ -57,6 +57,9 @@ export function setCamera(): void { ) ctx.camera.position.set(0, 0, 100) ctx.camera.lookAt(0, 0, 0) + // Edges sit on NO_BLOOM_LAYER; the normal view still draws them, only the + // bloom source turns the layer off (postprocessing.renderFrame). + ctx.camera.layers.enable(NO_BLOOM_LAYER) } export function resizeRenderer(): void { diff --git a/frontend/src/three/Edge.ts b/frontend/src/three/Edge.ts index 336da9e..82f72c0 100644 --- a/frontend/src/three/Edge.ts +++ b/frontend/src/three/Edge.ts @@ -6,6 +6,7 @@ import { EDGE_MIN_VISIBLE_OPACITY, EDGE_WIDTH_MAX, EDGE_WIDTH_MIN, + NO_BLOOM_LAYER, SELECTED_DEFAULT_COLOR, } from './constants' import { ctx, disposeObject3D, edgeResolution } from './runtime' @@ -77,6 +78,10 @@ export class Edge { if (this.channels.length === 0) this.createEdge(points) else this.createChannels(points) + // Keep every edge out of the bloom source. traverse(), because channels + // and arrows arrive as Groups and layers don't inherit. + this.THREE_Object.traverse((obj) => obj.layers.set(NO_BLOOM_LAYER)) + if (this.interLayer) ctx.scene!.add(this.THREE_Object) else ctx.layers[this.sourceLayerIndex].addEdge(this.THREE_Object) } diff --git a/frontend/src/three/constants.ts b/frontend/src/three/constants.ts index d4075c9..b766b11 100644 --- a/frontend/src/three/constants.ts +++ b/frontend/src/three/constants.ts @@ -26,6 +26,11 @@ export const EDGE_WIDTH_MAX = 6 // rather than rasterised as invisible quads (v2 relied on alphaTest: 0.05). export const EDGE_MIN_VISIBLE_OPACITY = 0.05 +// Render layer holding everything the bloom pass must not see. Edges live here +// (postprocessing.ts renders the bloom source with this layer off): thick lines +// cover much of the screen, and glowing them all washes out dark backgrounds. +export const NO_BLOOM_LAYER = 1 + // Colors export const LAYER_DEFAULT_COLOR = '#777777' export const SELECTED_LAYER_DEFAULT_COLOR = '#f7f43e' diff --git a/frontend/src/three/postprocessing.ts b/frontend/src/three/postprocessing.ts index 183fe1d..6d66cde 100644 --- a/frontend/src/three/postprocessing.ts +++ b/frontend/src/three/postprocessing.ts @@ -8,12 +8,19 @@ import * as THREE from 'three' import { EffectComposer } from 'three/addons/postprocessing/EffectComposer.js' import { OutputPass } from 'three/addons/postprocessing/OutputPass.js' import { RenderPass } from 'three/addons/postprocessing/RenderPass.js' +import { ShaderPass } from 'three/addons/postprocessing/ShaderPass.js' import { UnrealBloomPass } from 'three/addons/postprocessing/UnrealBloomPass.js' +import { NO_BLOOM_LAYER } from './constants' import { ctx } from './runtime' +// Selective bloom (three's webgl_postprocessing_unreal_bloom_selective +// pattern): bloomComposer renders the glow off-screen with NO_BLOOM_LAYER +// masked out, composer draws the full scene and adds that glow on top. let composer: EffectComposer | null = null +let bloomComposer: EffectComposer | null = null let renderPass: RenderPass | null = null let bloomPass: UnrealBloomPass | null = null +let mixPass: ShaderPass | null = null const isMobile = typeof navigator !== 'undefined' && @@ -44,13 +51,43 @@ export function bloomActive(): boolean { function ensureComposer(): void { if (composer || !ctx.renderer) return const size = ctx.renderer.getSize(new THREE.Vector2()) - composer = new EffectComposer(ctx.renderer) renderPass = new RenderPass(new THREE.Scene(), new THREE.Camera()) - composer.addPass(renderPass) - // Subtle accent glow: high threshold so only bright saturated colors - // (nodes, colored edges) bloom; labels are DOM overlays and unaffected. + + // Glow only, rendered off-screen. Subtle accent: high threshold so only + // bright saturated colors (nodes) bloom; labels are DOM overlays and + // unaffected, edges are masked off by layer in renderFrame. + bloomComposer = new EffectComposer(ctx.renderer) + bloomComposer.renderToScreen = false + bloomComposer.addPass(renderPass) bloomPass = new UnrealBloomPass(size, 0.35, 0.3, 0.8) - composer.addPass(bloomPass) + bloomComposer.addPass(bloomPass) + + composer = new EffectComposer(ctx.renderer) + composer.addPass(renderPass) + mixPass = new ShaderPass( + new THREE.ShaderMaterial({ + uniforms: { + baseTexture: { value: null }, + bloomTexture: { value: bloomComposer.renderTarget2.texture }, + }, + vertexShader: ` + varying vec2 vUv; + void main() { + vUv = uv; + gl_Position = projectionMatrix * modelViewMatrix * vec4( position, 1.0 ); + }`, + fragmentShader: ` + uniform sampler2D baseTexture; + uniform sampler2D bloomTexture; + varying vec2 vUv; + void main() { + gl_FragColor = texture2D( baseTexture, vUv ) + texture2D( bloomTexture, vUv ); + }`, + }), + 'baseTexture' + ) + mixPass.needsSwap = true + composer.addPass(mixPass) // Composer buffers are linear; without this the last pass would blit linear // values straight to an sRGB canvas and the whole scene renders dark. Must // stay last. @@ -59,6 +96,7 @@ function ensureComposer(): void { export function resizePostprocessing(width: number, height: number): void { composer?.setSize(width, height) + bloomComposer?.setSize(width, height) bloomPass?.resolution.set(width, height) } @@ -68,10 +106,16 @@ export function renderFrame(): void { if (!ctx.renderer || !ctx.scene || !ctx.camera) return if (userEnabled && backgroundDark) { ensureComposer() - if (composer && renderPass) { + if (composer && bloomComposer && renderPass) { // Scene object is replaced on every network load; re-point per frame. renderPass.scene = ctx.scene.THREE_Object renderPass.camera = ctx.camera + // Edges are drawn normally but must not feed the glow: hide their layer + // for the bloom render only. Edge geometry dominates big networks, so + // this second pass stays cheap. + ctx.camera.layers.disable(NO_BLOOM_LAYER) + bloomComposer.render() + ctx.camera.layers.enable(NO_BLOOM_LAYER) composer.render() return } diff --git a/frontend/src/ui/edge.ts b/frontend/src/ui/edge.ts index 0ab1a5b..4c40cf2 100644 --- a/frontend/src/ui/edge.ts +++ b/frontend/src/ui/edge.ts @@ -76,11 +76,11 @@ const EDGE_HTML = `
- +
- +
From 6440c0131402f6294c8d805d88a2c682fceeceeb Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Sun, 9 Aug 2026 11:55:37 +0100 Subject: [PATCH 07/15] fix e2e runner failing tests --- frontend/e2e/edge-width.spec.ts | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/frontend/e2e/edge-width.spec.ts b/frontend/e2e/edge-width.spec.ts index 922d444..1451d43 100644 --- a/frontend/e2e/edge-width.spec.ts +++ b/frontend/e2e/edge-width.spec.ts @@ -57,9 +57,14 @@ async function loadExample(page: import('@playwright/test').Page) { await page.getByRole('tab', { name: 'File' }).click() await page.getByRole('button', { name: 'Load Example' }).click() await expect(page.locator('#file_status')).toContainText('Loaded network') - // Bloom off so pixel counts measure geometry, not glow. - await page.getByRole('tab', { name: 'Scene Actions' }).click() - await page.locator('#toggleBloom').uncheck() + // Bloom off so pixel counts measure geometry, not glow. Driven on the input + // itself rather than through its tab: uncheck() waits for visibility, and on + // a slow runner the Scene Actions pane isn't shown by the time we get here. + await page.locator('#toggleBloom').evaluate((el) => { + const box = el as HTMLInputElement + box.checked = false + box.dispatchEvent(new Event('change')) + }) await page.getByRole('tab', { name: 'Edge Actions' }).click() } From acec901a436b96fb614b471a4c50cc7a3eba2e91 Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Sun, 9 Aug 2026 12:18:37 +0100 Subject: [PATCH 08/15] bloom only on nodes (instead of no bloom on edges), e2e tsconfig.json --- CHANGELOG.md | 2 +- frontend/e2e/edge-width.spec.ts | 3 ++- frontend/e2e/network-flow.spec.ts | 9 ++++++--- frontend/e2e/tsconfig.json | 11 +++++++++++ frontend/package-lock.json | 18 ++++++++++++++++++ frontend/package.json | 5 +++-- frontend/playwright.config.ts | 4 ++++ frontend/src/actions/screen.ts | 5 +---- frontend/src/three/Edge.ts | 5 ----- frontend/src/three/Node.ts | 4 ++++ frontend/src/three/constants.ts | 9 +++++---- frontend/src/three/postprocessing.ts | 18 ++++++++++-------- frontend/tsconfig.json | 7 +++++-- 13 files changed, 70 insertions(+), 30 deletions(-) create mode 100644 frontend/e2e/tsconfig.json diff --git a/CHANGELOG.md b/CHANGELOG.md index ed56ad0..c240456 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,7 @@ ### Fixed -- Edges no longer glow. Thick edges cover a large share of the screen, and bloom on all of them was blinding against dark backgrounds. Bloom is now selective (three's off-screen bloom-composer pattern): edges render on a dedicated layer that the bloom source masks out, so nodes still glow and edges stay crisp. +- Edges no longer glow. Thick edges cover a large share of the screen, and bloom on all of them was blinding against dark backgrounds. Bloom is now selective (three's off-screen bloom-composer pattern) and reads from node spheres alone, so nodes still glow, edges and layer planes stay crisp, and the extra pass costs a few spheres rather than a second full scene. - Curved channel edges rendered as dotted lines with beads at the curve points once thickness landed. `LineMaterial`'s `worldUnits` mode assumes a perspective camera — its fragment shader traces a view ray from the camera origin and discards anything farther than half a width from the segment, which under this app's orthographic camera discards along the whole segment. Widths are now screen-space, sized against a shared resolution uniform kept on the frustum size (so the numbers still mean world units), retargeted on resize and for the PNG export. - Node colors rendered washed out/dark in the 3D scene compared to the 2D navigator. The bloom composer was blitting linear color straight to the sRGB canvas (missing `OutputPass`), and the ambient light was left at the pre-r155 intensity that physical lighting divides by PI. diff --git a/frontend/e2e/edge-width.spec.ts b/frontend/e2e/edge-width.spec.ts index 1451d43..176e1d4 100644 --- a/frontend/e2e/edge-width.spec.ts +++ b/frontend/e2e/edge-width.spec.ts @@ -36,7 +36,8 @@ async function edgeCoverage(page: import('@playwright/test').Page) { const b = data[p + 2] const hi = Math.max(r, gr, b) const lo = Math.min(r, gr, b) - if (hi - lo >= 30) node++ // saturated: node spheres + if (hi - lo >= 30) + node++ // saturated: node spheres else if (hi >= 128) edge++ // bright near-grey: edges } resolve({ edge, node }) diff --git a/frontend/e2e/network-flow.spec.ts b/frontend/e2e/network-flow.spec.ts index a5492aa..1e0dba8 100644 --- a/frontend/e2e/network-flow.spec.ts +++ b/frontend/e2e/network-flow.spec.ts @@ -13,7 +13,7 @@ async function selectOption( value: string ) { await page.locator(selector).evaluate((el, v) => { - ;(el as HTMLSelectElement).value = v as string + ;(el as HTMLSelectElement).value = v el.dispatchEvent(new Event('change', { bubbles: true })) }, value) } @@ -21,7 +21,8 @@ async function selectOption( type NodeSnapshot = { pos: [number, number, number]; cluster: string } function readNodes() { - return async (): Promise => { + // Runs inside page.evaluate, which accepts a sync function just as happily. + return (): NodeSnapshot[] => { const ctx = ( window as unknown as { __arena: { ctx: { nodeObjects: unknown[] } } } ).__arena.ctx @@ -113,7 +114,9 @@ test('load example → layout → clustered layout → export', async ({ page }) // --- Export session ------------------------------------------------------ await page.getByRole('tab', { name: 'File' }).dispatchEvent('click') const downloadPromise = page.waitForEvent('download') - await page.getByRole('button', { name: 'Save Session' }).dispatchEvent('click') + await page + .getByRole('button', { name: 'Save Session' }) + .dispatchEvent('click') const download = await downloadPromise expect(download.suggestedFilename()).toMatch(/\.json$/) }) diff --git a/frontend/e2e/tsconfig.json b/frontend/e2e/tsconfig.json new file mode 100644 index 0000000..bce0526 --- /dev/null +++ b/frontend/e2e/tsconfig.json @@ -0,0 +1,11 @@ +{ + // The specs live outside the app's tsconfig (which covers src/ only) and run + // in Node, not the browser bundle — hence node types and their own project. + // typescript-eslint resolves each file against its nearest tsconfig.json, so + // this file is what makes typed linting work in e2e/. + "extends": "../tsconfig.json", + "compilerOptions": { + "types": ["node"] + }, + "include": ["."] +} diff --git a/frontend/package-lock.json b/frontend/package-lock.json index 71a493e..3d77d3e 100644 --- a/frontend/package-lock.json +++ b/frontend/package-lock.json @@ -14,6 +14,7 @@ "devDependencies": { "@playwright/test": "^1.61.1", "@types/bootstrap": "^5.2.11", + "@types/node": "^26.2.0", "@types/three": "^0.185.0", "eslint": "^10.6.0", "prettier": "^3.9.4", @@ -623,6 +624,16 @@ "dev": true, "license": "MIT" }, + "node_modules/@types/node": { + "version": "26.2.0", + "resolved": "https://registry.npmjs.org/@types/node/-/node-26.2.0.tgz", + "integrity": "sha512-5IviulTZeRNp2vAJ514cc/HUlY5nZ9fCbq9DMyC52BrhFZACo3nI0R7qBxhQmo/d27NFe96ur/b7Wwxklda+kg==", + "dev": true, + "license": "MIT", + "dependencies": { + "undici-types": "~8.3.0" + } + }, "node_modules/@types/stats.js": { "version": "0.17.4", "resolved": "https://registry.npmjs.org/@types/stats.js/-/stats.js-0.17.4.tgz", @@ -2343,6 +2354,13 @@ "typescript": ">=4.8.4 <6.1.0" } }, + "node_modules/undici-types": { + "version": "8.3.0", + "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-8.3.0.tgz", + "integrity": "sha512-j375ScV60dom+YkPFIfTLcOiPxkN/buHz5GobjLhixFuANaNs3C9l4GmrWqejgXWJ7BbJcFYpTEUkS1Ge8bpZQ==", + "dev": true, + "license": "MIT" + }, "node_modules/uri-js": { "version": "4.4.1", "resolved": "https://registry.npmjs.org/uri-js/-/uri-js-4.4.1.tgz", diff --git a/frontend/package.json b/frontend/package.json index b8c4a62..b63ec7f 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -6,8 +6,8 @@ "dev": "vite", "build": "tsc --noEmit && vite build", "preview": "vite preview", - "lint": "eslint src", - "format": "prettier --write src", + "lint": "eslint src e2e", + "format": "prettier --write src e2e", "test": "vitest", "test:e2e": "playwright test" }, @@ -18,6 +18,7 @@ "devDependencies": { "@playwright/test": "^1.61.1", "@types/bootstrap": "^5.2.11", + "@types/node": "^26.2.0", "@types/three": "^0.185.0", "eslint": "^10.6.0", "prettier": "^3.9.4", diff --git a/frontend/playwright.config.ts b/frontend/playwright.config.ts index 68bf373..79ab670 100644 --- a/frontend/playwright.config.ts +++ b/frontend/playwright.config.ts @@ -7,6 +7,10 @@ export default defineConfig({ testDir: './e2e', fullyParallel: false, retries: process.env.CI ? 2 : 0, + // These drive a WebGL scene, and CI has no GPU — every test renders through + // software GL and lands in the 15-30s range, so the 30s default was passing + // on retries alone. + timeout: 90_000, reporter: [['list']], use: { baseURL: 'http://localhost:5173', diff --git a/frontend/src/actions/screen.ts b/frontend/src/actions/screen.ts index e5db4db..3ae40fd 100644 --- a/frontend/src/actions/screen.ts +++ b/frontend/src/actions/screen.ts @@ -2,7 +2,7 @@ // Port of v2 www/js/object_actions/screen.js. Shiny sync calls dropped. import * as THREE from 'three' -import { ctx, edgeResolution, NO_BLOOM_LAYER } from '../three' +import { ctx, edgeResolution } from '../three' import { onBackgroundColor, renderFrame, @@ -57,9 +57,6 @@ export function setCamera(): void { ) ctx.camera.position.set(0, 0, 100) ctx.camera.lookAt(0, 0, 0) - // Edges sit on NO_BLOOM_LAYER; the normal view still draws them, only the - // bloom source turns the layer off (postprocessing.renderFrame). - ctx.camera.layers.enable(NO_BLOOM_LAYER) } export function resizeRenderer(): void { diff --git a/frontend/src/three/Edge.ts b/frontend/src/three/Edge.ts index 82f72c0..336da9e 100644 --- a/frontend/src/three/Edge.ts +++ b/frontend/src/three/Edge.ts @@ -6,7 +6,6 @@ import { EDGE_MIN_VISIBLE_OPACITY, EDGE_WIDTH_MAX, EDGE_WIDTH_MIN, - NO_BLOOM_LAYER, SELECTED_DEFAULT_COLOR, } from './constants' import { ctx, disposeObject3D, edgeResolution } from './runtime' @@ -78,10 +77,6 @@ export class Edge { if (this.channels.length === 0) this.createEdge(points) else this.createChannels(points) - // Keep every edge out of the bloom source. traverse(), because channels - // and arrows arrive as Groups and layers don't inherit. - this.THREE_Object.traverse((obj) => obj.layers.set(NO_BLOOM_LAYER)) - if (this.interLayer) ctx.scene!.add(this.THREE_Object) else ctx.layers[this.sourceLayerIndex].addEdge(this.THREE_Object) } diff --git a/frontend/src/three/Node.ts b/frontend/src/three/Node.ts index 72bc7ba..db34098 100644 --- a/frontend/src/three/Node.ts +++ b/frontend/src/three/Node.ts @@ -7,6 +7,7 @@ import { DIAMOND_RADIUS, CONE_RADIUS, CONE_HEIGHT, + BLOOM_LAYER, } from './constants' import { ctx } from './runtime' @@ -83,6 +84,9 @@ export class Node { transparent: true, }) this.sphere = new THREE.Mesh(geometry, material) + // Nodes are the only thing that glows. enable(), not set(): the sphere + // stays on layer 0 so the default-masked raycaster still picks it. + this.sphere.layers.enable(BLOOM_LAYER) } initTranslate(x: number, y: number, z: number): void { diff --git a/frontend/src/three/constants.ts b/frontend/src/three/constants.ts index b766b11..6f33aa3 100644 --- a/frontend/src/three/constants.ts +++ b/frontend/src/three/constants.ts @@ -26,10 +26,11 @@ export const EDGE_WIDTH_MAX = 6 // rather than rasterised as invisible quads (v2 relied on alphaTest: 0.05). export const EDGE_MIN_VISIBLE_OPACITY = 0.05 -// Render layer holding everything the bloom pass must not see. Edges live here -// (postprocessing.ts renders the bloom source with this layer off): thick lines -// cover much of the screen, and glowing them all washes out dark backgrounds. -export const NO_BLOOM_LAYER = 1 +// Render layer for the things that glow — node spheres, and nothing else. +// postprocessing.ts renders the bloom source with the camera masked to this +// layer alone, so edges stay crisp (thick lines glowing all over wash out dark +// backgrounds) and that second pass costs a few spheres instead of the scene. +export const BLOOM_LAYER = 1 // Colors export const LAYER_DEFAULT_COLOR = '#777777' diff --git a/frontend/src/three/postprocessing.ts b/frontend/src/three/postprocessing.ts index 6d66cde..8f28ef5 100644 --- a/frontend/src/three/postprocessing.ts +++ b/frontend/src/three/postprocessing.ts @@ -10,12 +10,12 @@ import { OutputPass } from 'three/addons/postprocessing/OutputPass.js' import { RenderPass } from 'three/addons/postprocessing/RenderPass.js' import { ShaderPass } from 'three/addons/postprocessing/ShaderPass.js' import { UnrealBloomPass } from 'three/addons/postprocessing/UnrealBloomPass.js' -import { NO_BLOOM_LAYER } from './constants' +import { BLOOM_LAYER } from './constants' import { ctx } from './runtime' // Selective bloom (three's webgl_postprocessing_unreal_bloom_selective -// pattern): bloomComposer renders the glow off-screen with NO_BLOOM_LAYER -// masked out, composer draws the full scene and adds that glow on top. +// pattern): bloomComposer renders the glow off-screen from BLOOM_LAYER alone, +// composer draws the full scene and adds that glow on top. let composer: EffectComposer | null = null let bloomComposer: EffectComposer | null = null let renderPass: RenderPass | null = null @@ -110,12 +110,14 @@ export function renderFrame(): void { // Scene object is replaced on every network load; re-point per frame. renderPass.scene = ctx.scene.THREE_Object renderPass.camera = ctx.camera - // Edges are drawn normally but must not feed the glow: hide their layer - // for the bloom render only. Edge geometry dominates big networks, so - // this second pass stays cheap. - ctx.camera.layers.disable(NO_BLOOM_LAYER) + // Glow source: node spheres only. Masking the camera to BLOOM_LAYER + // keeps edges and planes out of it — the point of the exercise — and + // makes this second pass a handful of spheres rather than the scene, + // which matters where there's no GPU (CI runs on software GL). + const mask = ctx.camera.layers.mask + ctx.camera.layers.set(BLOOM_LAYER) bloomComposer.render() - ctx.camera.layers.enable(NO_BLOOM_LAYER) + ctx.camera.layers.mask = mask composer.render() return } diff --git a/frontend/tsconfig.json b/frontend/tsconfig.json index 9bb92fc..7db3ec6 100644 --- a/frontend/tsconfig.json +++ b/frontend/tsconfig.json @@ -10,7 +10,10 @@ "sourceMap": true, "noEmit": true, "skipLibCheck": true, - "lib": ["ES2022", "DOM", "DOM.Iterable"] + "lib": ["ES2022", "DOM", "DOM.Iterable"], + // playwright.config.ts reads process.env; @types/node is not picked up + // automatically here, so name it. + "types": ["node"] }, - "include": ["src"] + "include": ["src", "playwright.config.ts"] } From 70665bb96a57854632f44dfc84b629815ac057e2 Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Sun, 9 Aug 2026 12:34:01 +0100 Subject: [PATCH 09/15] accept minimal 2-column edgelist input, nodes default to single layer Co-Authored-By: Claude Fable 5 --- backend/app/config.py | 2 ++ backend/app/routers/network.py | 2 ++ backend/app/services/parser.py | 9 ++++++++- backend/tests/test_network.py | 18 ++++++++++++++++++ 4 files changed, 30 insertions(+), 1 deletion(-) diff --git a/backend/app/config.py b/backend/app/config.py index 28051e8..508d4f9 100644 --- a/backend/app/config.py +++ b/backend/app/config.py @@ -8,6 +8,8 @@ # Input validation MANDATORY_NETWORK_COLUMNS = ["SourceNode", "SourceLayer", "TargetNode", "TargetLayer"] OPTIONAL_NETWORK_COLUMNS = ["Channel", "Weight"] +# Layer assigned to every node when a minimal 2-column edgelist omits the layer columns +DEFAULT_LAYER_NAME = "Layer1" MANDATORY_JSON_OBJECTS = ["layers", "nodes", "edges"] OPTIONAL_JSON_OBJECTS = ["scene", "universalLabelColor", "direction", "edgeOpacityByWeight"] MANDATORY_JSON_NODE_COLUMNS = ["name", "layer"] diff --git a/backend/app/routers/network.py b/backend/app/routers/network.py index d447771..f31bf54 100644 --- a/backend/app/routers/network.py +++ b/backend/app/routers/network.py @@ -11,6 +11,8 @@ @router.post("/api/network", response_model=NetworkModel) async def upload_network(file: UploadFile) -> NetworkModel: + """Parse an uploaded network TSV — the 4-column Arena3D format, or a minimal + 2-column edgelist (SourceNode, TargetNode) whose nodes all land in one default layer.""" raw_bytes = await file.read() # DoS fix: reject oversized uploads before pandas parses the whole file # into memory — MAX_EDGES was only checked *after* the parse completed. diff --git a/backend/app/services/parser.py b/backend/app/services/parser.py index 2fbd241..af9d594 100644 --- a/backend/app/services/parser.py +++ b/backend/app/services/parser.py @@ -34,7 +34,8 @@ def _validate(df: pd.DataFrame) -> None: if not set(config.MANDATORY_NETWORK_COLUMNS).issubset(df.columns): raise NetworkValidationError( "Your network file must contain at least these four columns: " - "SourceNode, SourceLayer, TargetNode, TargetLayer" + "SourceNode, SourceLayer, TargetNode, TargetLayer — or just " + "SourceNode and TargetNode for a minimal edgelist (single layer)." ) # Reject rows with an empty/whitespace mandatory cell — a blank becomes NaN # and would crash EdgeModel construction with a 500 instead of a clean 400. @@ -63,6 +64,12 @@ def parse_network_tsv(text: str) -> NetworkModel: df = pd.read_csv(StringIO(text), sep="\t", dtype=str) except pd.errors.EmptyDataError as e: raise NetworkValidationError("The network file is empty or has no columns.") from e + + # minimal 2-column edgelist: no layer columns -> every node in one default layer + if "SourceLayer" not in df.columns and "TargetLayer" not in df.columns: + df["SourceLayer"] = config.DEFAULT_LAYER_NAME + df["TargetLayer"] = config.DEFAULT_LAYER_NAME + _validate(df) # subset legit columns (mandatory + optional Channel/Weight, in fixed order) diff --git a/backend/tests/test_network.py b/backend/tests/test_network.py index 7467827..28b200d 100644 --- a/backend/tests/test_network.py +++ b/backend/tests/test_network.py @@ -55,6 +55,24 @@ def test_missing_mandatory_column_400() -> None: assert "four columns" in resp.json()["detail"] +def test_two_column_edgelist_single_default_layer() -> None: + body = _post("SourceNode\tTargetNode\nA\tB\nB\tC\n").json() + assert body["layers"] == ["Layer1"] + assert {n["layer"] for n in body["nodes"]} == {"Layer1"} + assert len(body["edges"]) == 2 + + +def test_two_column_edgelist_with_optional_columns() -> None: + body = _post("SourceNode\tTargetNode\tWeight\tChannel\nA\tB\t2\tch1\nB\tC\t4\tch2\n").json() + assert body["layers"] == ["Layer1"] + assert body["channels"] == ["ch1", "ch2"] + + +def test_single_layer_column_still_400() -> None: + resp = _post("SourceNode\tTargetNode\tTargetLayer\nA\tB\tL1\n") + assert resp.status_code == 400 + + def test_non_numeric_weight_400() -> None: tsv = f"{HDR}\tWeight\nA\tL1\tB\tL2\theavy\n" assert _post(tsv).status_code == 400 From 8e8482a0682a066078c9aa5e7ba04b1f5771e910 Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Sun, 9 Aug 2026 12:37:04 +0100 Subject: [PATCH 10/15] document 2-column edgelist format in help, changelog and agent docs; add example file Co-Authored-By: Claude Fable 5 --- AGENTS.md | 2 +- CHANGELOG.md | 2 ++ frontend/public/data/edgelist_2columns.tsv | 13 +++++++++++++ frontend/src/ui/help.ts | 16 +++++++++++++++- 4 files changed, 31 insertions(+), 2 deletions(-) create mode 100644 frontend/public/data/edgelist_2columns.tsv diff --git a/AGENTS.md b/AGENTS.md index 1366145..b1ebd6b 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -80,6 +80,6 @@ Stateless FastAPI — the frontend holds all scene state; the server validates i - **Within frontend**: components emit/subscribe on the `EventBus` and read/write the `store`; the render loop reacts to `ctx` flags (`renderInterLayerEdgesFlag`, label flags, etc.). ### Network Data Model -- Networks upload as TSV with mandatory columns `SourceNode`, `SourceLayer`, `TargetNode`, `TargetLayer` (optional: `Weight`, `Channel`, edge color columns). +- Networks upload as TSV with mandatory columns `SourceNode`, `SourceLayer`, `TargetNode`, `TargetLayer` (optional: `Weight`, `Channel`, edge color columns). A minimal 2-column edgelist (`SourceNode`, `TargetNode`) is also accepted — all nodes land in a single default layer. - Node/edge attribute files add per-node color/size/url/description and per-edge (optionally per-channel) color. - Sessions export/import as JSON with full node/edge/layer/scene state. `POST /api/external` returns a token URL so another app can hand off a session. diff --git a/CHANGELOG.md b/CHANGELOG.md index c240456..04193f7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,8 @@ ### Added +- Network upload accepts a minimal 2-column edgelist (`SourceNode`, `TargetNode` only) — all nodes are spread out in a single default layer named `Layer1`. The optional `Weight` and `Channel` columns still apply. A downloadable example lives in the Help → Examples tab. + - Edge weight can now be shown as **edge thickness**, not only opacity. The Edge Actions panel replaces the "Edge Opacity By Weight" checkbox with a "Show Edge Weight As" radio — Nothing / Opacity / Width / Both — plus intra- and inter-layer width sliders for whichever property weight isn't driving. Sessions carry the choice as the independent `edgeOpacityByWeight` and `edgeWidthByWeight` booleans; files written before this default to opacity, so they render unchanged. Thickness needed `Line2` (instanced quads) because WebGL renders every line primitive at exactly 1px regardless of `linewidth`. ### Changed diff --git a/frontend/public/data/edgelist_2columns.tsv b/frontend/public/data/edgelist_2columns.tsv new file mode 100644 index 0000000..96abeec --- /dev/null +++ b/frontend/public/data/edgelist_2columns.tsv @@ -0,0 +1,13 @@ +SourceNode TargetNode +An Bn +An Cn +Bn Cn +Cn Dn +Dn En +En Fn +Fn Gn +Gn Hn +Hn An +Bn Fn +Cn Gn +Dn Hn diff --git a/frontend/src/ui/help.ts b/frontend/src/ui/help.ts index 3b3bcea..bb4a048 100644 --- a/frontend/src/ui/help.ts +++ b/frontend/src/ui/help.ts @@ -28,6 +28,8 @@ const HELP_HTML = ` 1. The Upload Network option allows the user to upload network data in the Arena3D format. This file consists of 4 mandatory columns with headers SourceNode, TargetNode, SourceLayer and TargetLayer and 2 optional columns with the headers Weight and Channel. + Alternatively, a minimal 2-column edgelist with only the SourceNode and TargetNode headers is + accepted — all its nodes are then spread out in a single default layer (the optional columns still apply). After the file is uploaded, the weight values are mapped in a [0-1] range and assigned to the respective edges. By default the weight is shown as edge transparency — @@ -76,7 +78,14 @@ Hn Group2 In Group3 1 1 Hn Group2 Kn Group4 1 1 Kn Group4 Ln Group4 0.1 1 Kn Group4 Mn Group5 1 1 -An Group1 Nn Group5 1 1 +An Group1 Nn Group5 1 1 + +

Example of the minimal 2-column edgelist format (all nodes placed in a single default layer).

+ 
SourceNode	TargetNode
+An	        Bn
+An	        Cn
+Bn	        Cn
+Cn	        Dn
 Kn	        Group4	        On	        Group5	        1       1
 Kn	        Group4	        Pn	        Group5	        12      1
 Kn	        Group4	        Qn	        Group6	        1       1
@@ -258,6 +267,11 @@ Kn	        Group4	        Tn	        Group7	        #4EFB7D
 
   
Example Data

 
+  

+    Minimal 2-column edgelist (single default layer):  

+    A minimal edgelist with only SourceNode and TargetNode columns. 

+  

+  

   

     Random networks with different topologies mapped in 6 layers respectively:  

     The example network in the Arena3D format. 


From db46e9bc40c764c6f4afce3c13a9334f527758a6 Mon Sep 17 00:00:00 2001
From: vagkaratzas 
Date: Sun, 9 Aug 2026 12:46:26 +0100
Subject: [PATCH 11/15] help fixed

---
 frontend/src/ui/help.ts | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/frontend/src/ui/help.ts b/frontend/src/ui/help.ts
index bb4a048..5c1a00a 100644
--- a/frontend/src/ui/help.ts
+++ b/frontend/src/ui/help.ts
@@ -78,7 +78,14 @@ Hn	        Group2	        In	        Group3	        1       1
 Hn	        Group2	        Kn	        Group4	        1       1
 Kn	        Group4	        Ln	        Group4	        0.1     1
 Kn	        Group4	        Mn	        Group5	        1       1
-An	        Group1	        Nn	        Group5	        1       1
+An Group1 Nn Group5 1 1 +Kn Group4 On Group5 1 1 +Kn Group4 Pn Group5 12 1 +Kn Group4 Qn Group6 1 1 +Kn Group4 Rn Group6 1 1 +Kn Group4 Sn Group7 1 1 +Kn Group4 Tn Group7 10 1 +

Example of the minimal 2-column edgelist format (all nodes placed in a single default layer).

SourceNode	TargetNode
@@ -86,13 +93,7 @@ An	        Bn
 An	        Cn
 Bn	        Cn
 Cn	        Dn
-Kn	        Group4	        On	        Group5	        1       1
-Kn	        Group4	        Pn	        Group5	        12      1
-Kn	        Group4	        Qn	        Group6	        1       1
-Kn	        Group4	        Rn	        Group6	        1       1
-Kn	        Group4	        Sn	        Group7	        1       1
-Kn	        Group4	        Tn	        Group7	        10      1
-

+

Example of the Arena3D Upload NODE attributes file format. All columns are ommitable except from Node and Layer ones. Users do not need to mention every node, just the ones of interest.

From 12284ab413421865c9a6b734e827e0798feace57 Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Sun, 9 Aug 2026 13:11:29 +0100 Subject: [PATCH 12/15] uv lock backend versions updated --- CHANGELOG.md | 14 + backend/uv.lock | 728 ++++++++++++++++++++++++++++-------------------- 2 files changed, 440 insertions(+), 302 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 04193f7..5a584a9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,20 @@ - Curved channel edges rendered as dotted lines with beads at the curve points once thickness landed. `LineMaterial`'s `worldUnits` mode assumes a perspective camera — its fragment shader traces a view ray from the camera origin and discards anything farther than half a width from the segment, which under this app's orthographic camera discards along the whole segment. Widths are now screen-space, sized against a shared resolution uniform kept on the frustum size (so the numbers still mean world units), retargeted on resize and for the PNG export. - Node colors rendered washed out/dark in the 3D scene compared to the 2D navigator. The bloom composer was blitting linear color straight to the sRGB canvas (missing `OutputPass`), and the ambient light was left at the pre-r155 intensity that physical lighting divides by PI. +### `Dependencies` + +| Tool | Previous version | New version | +| ------------ | ---------------- | ------------- | +| fastapi | 0.139.0 | 0.141.1 | +| pandas | 3.0.3 | 3.0.5 | +| uvicorn | 0.50.0 | 0.52.1 | +| httpx2 | 2.5.0 | 2.10.0 | +| mypy | 2.1.0 | 2.3.0 | +| pandas-stubs | 3.0.3.260530 | 3.0.5.260730 | +| ruff | 0.15.20 | 0.16.2 | + +Backend dependencies updated to latest via `uv lock --upgrade`; transitives moved with them (notably starlette 1.3.1 → 1.6.0 and websockets 16.0 → 17.0.1). No known vulnerabilities before or after. `pydantic-core` stays at 2.46.4 — pydantic pins it exactly. All 79 backend tests, `ruff check`, and strict `mypy` pass on the new set. + ## [3.0.0] - 2026-07-27 Full rewrite: migrated from R/Shiny to a **FastAPI (Python) backend + Vite / TypeScript / Three.js frontend**. 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8000 &) - run: cd frontend && npm ci && npx playwright install --with-deps chromium - run: cd frontend && npm run test:e2e From 2cfc990ac7c9a6e61564138b5220cad7eb290d23 Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Sun, 9 Aug 2026 13:33:35 +0100 Subject: [PATCH 14/15] frontend packages updates --- CHANGELOG.md | 29 +- frontend/package-lock.json | 994 +++++++++++++++++-------------------- 2 files changed, 476 insertions(+), 547 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5a584a9..0c7b435 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,17 +20,24 @@ ### `Dependencies` -| Tool | Previous version | New version | -| ------------ | ---------------- | ------------- | -| fastapi | 0.139.0 | 0.141.1 | -| pandas | 3.0.3 | 3.0.5 | -| uvicorn | 0.50.0 | 0.52.1 | -| httpx2 | 2.5.0 | 2.10.0 | -| mypy | 2.1.0 | 2.3.0 | -| pandas-stubs | 3.0.3.260530 | 3.0.5.260730 | -| ruff | 0.15.20 | 0.16.2 | - -Backend dependencies updated to latest via `uv lock --upgrade`; transitives moved with them (notably starlette 1.3.1 → 1.6.0 and websockets 16.0 → 17.0.1). No known vulnerabilities before or after. `pydantic-core` stays at 2.46.4 — pydantic pins it exactly. All 79 backend tests, `ruff check`, and strict `mypy` pass on the new set. +| Tool | Previous version | New version | +| ----------------- | ---------------- | ------------ | +| fastapi | 0.139.0 | 0.141.1 | +| pandas | 3.0.3 | 3.0.5 | +| uvicorn | 0.50.0 | 0.52.1 | +| httpx2 | 2.5.0 | 2.10.0 | +| mypy | 2.1.0 | 2.3.0 | +| pandas-stubs | 3.0.3.260530 | 3.0.5.260730 | +| ruff | 0.15.20 | 0.16.2 | +| @playwright/test | 1.61.1 | 1.62.1 | +| @types/three | 0.185.0 | 0.185.4 | +| eslint | 10.6.0 | 10.8.1 | +| prettier | 3.9.4 | 3.9.6 | +| typescript-eslint | 8.62.1 | 8.66.0 | +| vite | 8.1.3 | 8.2.1 | +| vitest | 4.1.9 | 4.1.10 | + +Backend dependencies updated to latest via `uv lock --upgrade`; transitives moved with them (notably starlette 1.3.1 → 1.6.0 and websockets 16.0 → 17.0.1). No known vulnerabilities on either side. `pydantic-core` stays at 2.46.4 — pydantic pins it exactly. TypeScript stays on 6.0.3: 7.0.2 typechecks fine but typescript-eslint 8.x refuses to load against the TS 7 API, so linting breaks; revisit once typescript-eslint ships TS >=7.1 support. 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unreleased +## [3.1.0] - 2026-08-10 ### Added