diff --git a/CHANGELOG.md b/CHANGELOG.md index 39b93620f..93e86ea6b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,7 @@ Note that since we don't clearly distinguish between a public and private interf ## [Unreleased] - Fix empty transforms default in `ShapeFromPly` +- Use morton order for spheres in dot visual with lod-levels - Add `Camera.changed` event and rotation/translation setter/getter - Add `instanceGranularity: 'auto'` as a memory guard - Honor `instanceGranularity` in `Visual.getLoci` diff --git a/src/mol-repr/volume/_spec/dot.spec.ts b/src/mol-repr/volume/_spec/dot.spec.ts new file mode 100644 index 000000000..d1af9efc4 --- /dev/null +++ b/src/mol-repr/volume/_spec/dot.spec.ts @@ -0,0 +1,59 @@ +/** + * Copyright (c) 2026 mol* contributors, licensed under MIT, See LICENSE file for more info. + * + * @author Ludovic Autin + */ + +import { CustomProperties } from '../../../mol-model/custom-property'; +import { Grid, Volume } from '../../../mol-model/volume'; +import { Mat4, Tensor } from '../../../mol-math/linear-algebra'; +import { createVolumeSphereImpostor } from '../dot'; + +function createTestVolume(dimensions: [number, number, number], data: number[]): Volume { + return { + grid: { + transform: { kind: 'matrix', matrix: Mat4.identity() }, + cells: Tensor.create(Tensor.Space(dimensions, [2, 1, 0]), Tensor.Data1(data)), + stats: { min: 0, max: 1, mean: 0.5, sigma: 0.5 }, + } satisfies Grid, + instances: [{ transform: Mat4.identity() }], + sourceData: { kind: 'test', name: 'test', data: {} } as any, + customProperties: new CustomProperties(), + _propertyData: Object.create(null), + _localPropertyData: Object.create(null), + }; +} + +describe('volume dot representation', () => { + it('adds sphere impostor dots in Morton order for LOD sampling', () => { + const volume = createTestVolume([2, 2, 2], [ + 1, 1, + 1, 1, + 1, 1, + 1, 1, + ]); + const spheres = createVolumeSphereImpostor(undefined as any, volume, 0, undefined as any, { + isoValue: Volume.IsoValue.absolute(0.5), + perturbPositions: false, + lodLevels: [{ minDistance: 0, maxDistance: 0, overlap: 0, stride: 0, scaleBias: 3 }], + } as any); + + expect(Array.from(spheres.groupBuffer.ref.value)).toEqual([0, 4, 2, 6, 1, 5, 3, 7]); + }); + + it('adds sphere impostor dots in row-major order when no LOD levels are configured', () => { + const volume = createTestVolume([2, 2, 2], [ + 1, 1, + 1, 1, + 1, 1, + 1, 1, + ]); + const spheres = createVolumeSphereImpostor(undefined as any, volume, 0, undefined as any, { + isoValue: Volume.IsoValue.absolute(0.5), + perturbPositions: false, + lodLevels: [], + } as any); + + expect(Array.from(spheres.groupBuffer.ref.value)).toEqual([0, 1, 2, 3, 4, 5, 6, 7]); + }); +}); diff --git a/src/mol-repr/volume/dot.ts b/src/mol-repr/volume/dot.ts index c0e350c22..671f0c842 100644 --- a/src/mol-repr/volume/dot.ts +++ b/src/mol-repr/volume/dot.ts @@ -67,7 +67,8 @@ export function VolumeSphereImpostorVisual(materialId: number): VolumeVisual, currentProps: PD.Values, newTheme: Theme, currentTheme: Theme) => { state.createGeometry = ( !Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, newVolume.grid.stats) || - newProps.perturbPositions !== currentProps.perturbPositions + newProps.perturbPositions !== currentProps.perturbPositions || + newProps.lodLevels.length > 0 && currentProps.lodLevels.length === 0 ); }, geometryUtils: Spheres.Utils, @@ -128,32 +129,65 @@ export function createVolumeSphereImpostor(ctx: VisualContext, volume: Volume, k const p = Vec3(); const [xn, yn, zn] = space.dimensions; - - const count = Math.ceil((xn * yn * zn) / 10); - const builder = SpheresBuilder.create(count, Math.ceil(count / 2), spheres); - const invert = isoVal < 0; // Precompute basis vectors and largest cell axis length const basis = props.perturbPositions ? getBasis(gridToCartn) : undefined; - for (let z = 0; z < zn; ++z) { - for (let y = 0; y < yn; ++y) { - for (let x = 0; x < xn; ++x) { - const value = space.get(data, x, y, z); - if (!invert && value < isoVal || invert && value > isoVal) continue; + const count = Math.ceil((xn * yn * zn) / 10); + const builder = SpheresBuilder.create(count, Math.ceil(count / 2), spheres); - const cellIdx = space.dataOffset(x, y, z); - if (basis) { - Vec3.set(p, x, y, z); - Vec3.transformMat4(p, p, gridToCartn); - const offset = getRandomOffsetFromBasis(basis); - Vec3.add(p, p, offset); - } else { - Vec3.set(p, x, y, z); - Vec3.transformMat4(p, p, gridToCartn); + const add = (x: number, y: number, z: number) => { + const value = space.get(data, x, y, z); + if (!invert && value < isoVal || invert && value > isoVal) return; + + const cellIdx = space.dataOffset(x, y, z); + Vec3.set(p, x, y, z); + Vec3.transformMat4(p, p, gridToCartn); + if (basis) { + Vec3.add(p, p, getRandomOffsetFromBasis(basis)); + } + builder.add(p[0], p[1], p[2], cellIdx); + }; + + // Morton ordering keeps stride-based LOD sampling spatially balanced. + // Only worthwhile when LOD levels are configured; otherwise use the + // direct row-major path to avoid the extra allocations and sort. + const useMortonOrder = props.lodLevels.length > 0; + + if (useMortonOrder) { + // Recursive octree traversal over the bounding power-of-two cube, + // visiting children in Morton order (octant bit2=x, bit1=y, bit0=z). + // Octants whose origin already exceeds the grid extent are pruned, + // so out-of-range subtrees of non-cube grids cost ~O(log) per skip. + let size = 1; + while (size < xn || size < yn || size < zn) size <<= 1; + + const visit = (x0: number, y0: number, z0: number, s: number): void => { + if (x0 >= xn || y0 >= yn || z0 >= zn) return; + + if (s === 1) { + add(x0, y0, z0); + return; + } + const h = s >> 1; + visit(x0, y0, z0, h); + visit(x0, y0, z0 + h, h); + visit(x0, y0 + h, z0, h); + visit(x0, y0 + h, z0 + h, h); + visit(x0 + h, y0, z0, h); + visit(x0 + h, y0, z0 + h, h); + visit(x0 + h, y0 + h, z0, h); + visit(x0 + h, y0 + h, z0 + h, h); + }; + + visit(0, 0, 0, size); + } else { + for (let z = 0; z < zn; ++z) { + for (let y = 0; y < yn; ++y) { + for (let x = 0; x < xn; ++x) { + add(x, y, z); } - builder.add(p[0], p[1], p[2], cellIdx); } } } @@ -320,6 +354,7 @@ const DotVisuals = { export const DotParams = { ...VolumeSphereParams, ...VolumePointParams, + sizeFactor: PD.Numeric(1, { min: 0, max: 10, step: 0.1 }), visuals: PD.MultiSelect(['sphere'], PD.objectToOptions(DotVisuals)), bumpFrequency: PD.Numeric(1, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory), }; @@ -346,4 +381,4 @@ export const DotRepresentationProvider = VolumeRepresentationProvider({ defaultSizeTheme: { name: 'uniform' }, locationKinds: ['cell-location', 'position-location'], isApplicable: (volume: Volume) => !Volume.isEmpty(volume) && !Volume.Segmentation.get(volume) -}); \ No newline at end of file +});