/** * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info. * * @author David Sehnal * @author Alexander Rose */ import { ParamDefinition as PD } from '../../mol-util/param-definition'; import { Grid, Volume } from '../../mol-model/volume'; import { VisualContext } from '../visual'; import { Theme, ThemeRegistryContext } from '../../mol-theme/theme'; import { Mesh } from '../../mol-geo/geometry/mesh/mesh'; import { computeMarchingCubesMesh, computeMarchingCubesLines } from '../../mol-geo/util/marching-cubes/algorithm'; import { VolumeVisual, VolumeRepresentation, VolumeRepresentationProvider, VolumeKey } from './representation'; import { LocationIterator } from '../../mol-geo/util/location-iterator'; import { NullLocation } from '../../mol-model/location'; import { VisualUpdateState } from '../util'; import { Lines } from '../../mol-geo/geometry/lines/lines'; import { RepresentationContext, RepresentationParamsGetter, Representation } from '../representation'; import { PickingId } from '../../mol-geo/geometry/picking'; import { EmptyLoci, Loci } from '../../mol-model/loci'; import { Interval } from '../../mol-data/int'; import { Tensor, Vec2, Vec3 } from '../../mol-math/linear-algebra'; import { fillSerial } from '../../mol-util/array'; import { createVolumeTexture2d, eachVolumeLoci, getVolumeTexture2dLayout } from './util'; import { TextureMesh } from '../../mol-geo/geometry/texture-mesh/texture-mesh'; import { extractIsosurface } from '../../mol-gl/compute/marching-cubes/isosurface'; import { WebGLContext } from '../../mol-gl/webgl/context'; import { CustomPropertyDescriptor } from '../../mol-model/custom-property'; import { Texture } from '../../mol-gl/webgl/texture'; import { BaseGeometry } from '../../mol-geo/geometry/base'; import { ValueCell } from '../../mol-util/value-cell'; export const VolumeIsosurfaceParams = { isoValue: Volume.IsoValueParam }; export type VolumeIsosurfaceParams = typeof VolumeIsosurfaceParams export type VolumeIsosurfaceProps = PD.Values function gpuSupport(webgl: WebGLContext) { return webgl.extensions.colorBufferFloat && webgl.extensions.textureFloat && webgl.extensions.drawBuffers; } const Padding = 1; function suitableForGpu(volume: Volume, webgl: WebGLContext) { // small volumes are about as fast or faster on CPU vs integrated GPU if (volume.grid.cells.data.length < Math.pow(10, 3)) return false; // the GPU is much more memory contraint, especially true for integrated GPUs, // fallback to CPU for large volumes const gridDim = volume.grid.cells.space.dimensions as Vec3; const { powerOfTwoSize } = getVolumeTexture2dLayout(gridDim, Padding); return powerOfTwoSize <= webgl.maxTextureSize / 2; } export function IsosurfaceVisual(materialId: number, volume: Volume, key: number, props: PD.Values, webgl?: WebGLContext) { if (props.tryUseGpu && webgl && gpuSupport(webgl) && suitableForGpu(volume, webgl)) { return IsosurfaceTextureMeshVisual(materialId); } return IsosurfaceMeshVisual(materialId); } function getLoci(volume: Volume, props: VolumeIsosurfaceProps) { return Volume.Isosurface.Loci(volume, props.isoValue); } function getIsosurfaceLoci(pickingId: PickingId, volume: Volume, key: number, props: VolumeIsosurfaceProps, id: number) { const { objectId, groupId } = pickingId; if (id === objectId) { const granularity = Volume.PickingGranularity.get(volume); if (granularity === 'volume') { return Volume.Loci(volume); } else if (granularity === 'object') { return Volume.Isosurface.Loci(volume, props.isoValue); } else { return Volume.Cell.Loci(volume, Interval.ofSingleton(groupId as Volume.CellIndex)); } } return EmptyLoci; } export function eachIsosurface(loci: Loci, volume: Volume, key: number, props: VolumeIsosurfaceProps, apply: (interval: Interval) => boolean) { return eachVolumeLoci(loci, volume, { isoValue: props.isoValue }, apply); } // export async function createVolumeIsosurfaceMesh(ctx: VisualContext, volume: Volume, key: number, theme: Theme, props: VolumeIsosurfaceProps, mesh?: Mesh) { ctx.runtime.update({ message: 'Marching cubes...' }); const ids = fillSerial(new Int32Array(volume.grid.cells.data.length)); const surface = await computeMarchingCubesMesh({ isoLevel: Volume.IsoValue.toAbsolute(props.isoValue, volume.grid.stats).absoluteValue, scalarField: volume.grid.cells, idField: Tensor.create(volume.grid.cells.space, Tensor.Data1(ids)) }, mesh).runAsChild(ctx.runtime); const transform = Grid.getGridToCartesianTransform(volume.grid); Mesh.transform(surface, transform); if (ctx.webgl && !ctx.webgl.isWebGL2) { // 2nd arg means not to split triangles based on group id. Splitting triangles // is too expensive if each cell has its own group id as is the case here. Mesh.uniformTriangleGroup(surface, false); ValueCell.updateIfChanged(surface.varyingGroup, false); } else { ValueCell.updateIfChanged(surface.varyingGroup, true); } surface.setBoundingSphere(Volume.Isosurface.getBoundingSphere(volume, props.isoValue)); return surface; } export const IsosurfaceMeshParams = { ...Mesh.Params, ...TextureMesh.Params, ...VolumeIsosurfaceParams, quality: { ...Mesh.Params.quality, isEssential: false }, tryUseGpu: PD.Boolean(true), }; export type IsosurfaceMeshParams = typeof IsosurfaceMeshParams export function IsosurfaceMeshVisual(materialId: number): VolumeVisual { return VolumeVisual({ defaultProps: PD.getDefaultValues(IsosurfaceMeshParams), createGeometry: createVolumeIsosurfaceMesh, createLocationIterator: (volume: Volume) => LocationIterator(volume.grid.cells.data.length, 1, 1, () => NullLocation), getLoci: getIsosurfaceLoci, eachLocation: eachIsosurface, setUpdateState: (state: VisualUpdateState, volume: Volume, newProps: PD.Values, currentProps: PD.Values) => { if (!Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats)) state.createGeometry = true; }, geometryUtils: Mesh.Utils, mustRecreate: (volumekey: VolumeKey, props: PD.Values, webgl?: WebGLContext) => { return props.tryUseGpu && !!webgl && suitableForGpu(volumekey.volume, webgl); } }, materialId); } // namespace VolumeIsosurfaceTexture { const name = 'volume-isosurface-texture'; export const descriptor = CustomPropertyDescriptor({ name }); export function get(volume: Volume, webgl: WebGLContext) { const { resources } = webgl; const transform = Grid.getGridToCartesianTransform(volume.grid); const gridDimension = Vec3.clone(volume.grid.cells.space.dimensions as Vec3); const { width, height, powerOfTwoSize: texDim } = getVolumeTexture2dLayout(gridDimension, Padding); const gridTexDim = Vec3.create(width, height, 0); const gridTexScale = Vec2.create(width / texDim, height / texDim); // console.log({ texDim, width, height, gridDimension }); if (texDim > webgl.maxTextureSize / 2) { throw new Error('volume too large for gpu isosurface extraction'); } if (!volume._propertyData[name]) { volume._propertyData[name] = resources.texture('image-uint8', 'alpha', 'ubyte', 'linear'); const texture = volume._propertyData[name] as Texture; texture.define(texDim, texDim); // load volume into sub-section of texture texture.load(createVolumeTexture2d(volume, 'data', Padding), true); volume.customProperties.add(descriptor); volume.customProperties.assets(descriptor, [{ dispose: () => texture.destroy() }]); } gridDimension[0] += Padding; gridDimension[1] += Padding; return { texture: volume._propertyData[name] as Texture, transform, gridDimension, gridTexDim, gridTexScale }; } } async function createVolumeIsosurfaceTextureMesh(ctx: VisualContext, volume: Volume, key: number, theme: Theme, props: VolumeIsosurfaceProps, textureMesh?: TextureMesh) { if (!ctx.webgl) throw new Error('webgl context required to create volume isosurface texture-mesh'); if (volume.grid.cells.data.length <= 1) { return TextureMesh.createEmpty(textureMesh); } const { max, min } = volume.grid.stats; const diff = max - min; const value = Volume.IsoValue.toAbsolute(props.isoValue, volume.grid.stats).absoluteValue; const isoLevel = ((value - min) / diff); const { texture, gridDimension, gridTexDim, gridTexScale, transform } = VolumeIsosurfaceTexture.get(volume, ctx.webgl); const axisOrder = volume.grid.cells.space.axisOrderSlowToFast as Vec3; const buffer = textureMesh?.doubleBuffer.get(); const gv = extractIsosurface(ctx.webgl, texture, gridDimension, gridTexDim, gridTexScale, transform, isoLevel, value < 0, false, axisOrder, true, buffer?.vertex, buffer?.group, buffer?.normal); const groupCount = volume.grid.cells.data.length; const boundingSphere = Volume.getBoundingSphere(volume); // getting isosurface bounding-sphere is too expensive here const surface = TextureMesh.create(gv.vertexCount, groupCount, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh); surface.meta.webgl = ctx.webgl; return surface; } export function IsosurfaceTextureMeshVisual(materialId: number): VolumeVisual { return VolumeVisual({ defaultProps: PD.getDefaultValues(IsosurfaceMeshParams), createGeometry: createVolumeIsosurfaceTextureMesh, createLocationIterator: (volume: Volume) => LocationIterator(volume.grid.cells.data.length, 1, 1, () => NullLocation), getLoci: getIsosurfaceLoci, eachLocation: eachIsosurface, setUpdateState: (state: VisualUpdateState, volume: Volume, newProps: PD.Values, currentProps: PD.Values) => { if (!Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats)) state.createGeometry = true; }, geometryUtils: TextureMesh.Utils, mustRecreate: (volumeKey: VolumeKey, props: PD.Values, webgl?: WebGLContext) => { return !props.tryUseGpu || !webgl || !suitableForGpu(volumeKey.volume, webgl); }, dispose: (geometry: TextureMesh) => { geometry.vertexTexture.ref.value.destroy(); geometry.groupTexture.ref.value.destroy(); geometry.normalTexture.ref.value.destroy(); geometry.doubleBuffer.destroy(); } }, materialId); } // export async function createVolumeIsosurfaceWireframe(ctx: VisualContext, volume: Volume, key: number, theme: Theme, props: VolumeIsosurfaceProps, lines?: Lines) { ctx.runtime.update({ message: 'Marching cubes...' }); const ids = fillSerial(new Int32Array(volume.grid.cells.data.length)); const wireframe = await computeMarchingCubesLines({ isoLevel: Volume.IsoValue.toAbsolute(props.isoValue, volume.grid.stats).absoluteValue, scalarField: volume.grid.cells, idField: Tensor.create(volume.grid.cells.space, Tensor.Data1(ids)) }, lines).runAsChild(ctx.runtime); const transform = Grid.getGridToCartesianTransform(volume.grid); Lines.transform(wireframe, transform); wireframe.setBoundingSphere(Volume.Isosurface.getBoundingSphere(volume, props.isoValue)); return wireframe; } export const IsosurfaceWireframeParams = { ...Lines.Params, ...VolumeIsosurfaceParams, quality: { ...Lines.Params.quality, isEssential: false }, sizeFactor: PD.Numeric(3, { min: 0, max: 10, step: 0.1 }), }; export type IsosurfaceWireframeParams = typeof IsosurfaceWireframeParams export function IsosurfaceWireframeVisual(materialId: number): VolumeVisual { return VolumeVisual({ defaultProps: PD.getDefaultValues(IsosurfaceWireframeParams), createGeometry: createVolumeIsosurfaceWireframe, createLocationIterator: (volume: Volume) => LocationIterator(volume.grid.cells.data.length, 1, 1, () => NullLocation), getLoci: getIsosurfaceLoci, eachLocation: eachIsosurface, setUpdateState: (state: VisualUpdateState, volume: Volume, newProps: PD.Values, currentProps: PD.Values) => { if (!Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats)) state.createGeometry = true; }, geometryUtils: Lines.Utils }, materialId); } // const IsosurfaceVisuals = { 'solid': (ctx: RepresentationContext, getParams: RepresentationParamsGetter) => VolumeRepresentation('Isosurface mesh', ctx, getParams, IsosurfaceVisual, getLoci), 'wireframe': (ctx: RepresentationContext, getParams: RepresentationParamsGetter) => VolumeRepresentation('Isosurface wireframe', ctx, getParams, IsosurfaceWireframeVisual, getLoci), }; export const IsosurfaceParams = { ...IsosurfaceMeshParams, ...IsosurfaceWireframeParams, visuals: PD.MultiSelect(['solid'], PD.objectToOptions(IsosurfaceVisuals)), bumpFrequency: PD.Numeric(1, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory), }; export type IsosurfaceParams = typeof IsosurfaceParams export function getIsosurfaceParams(ctx: ThemeRegistryContext, volume: Volume) { const p = PD.clone(IsosurfaceParams); p.isoValue = Volume.createIsoValueParam(Volume.IsoValue.relative(2), volume.grid.stats); return p; } export type IsosurfaceRepresentation = VolumeRepresentation export function IsosurfaceRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter): IsosurfaceRepresentation { return Representation.createMulti('Isosurface', ctx, getParams, Representation.StateBuilder, IsosurfaceVisuals as unknown as Representation.Def); } export const IsosurfaceRepresentationProvider = VolumeRepresentationProvider({ name: 'isosurface', label: 'Isosurface', description: 'Displays a triangulated isosurface of volumetric data.', factory: IsosurfaceRepresentation, getParams: getIsosurfaceParams, defaultValues: PD.getDefaultValues(IsosurfaceParams), defaultColorTheme: { name: 'uniform' }, defaultSizeTheme: { name: 'uniform' }, isApplicable: (volume: Volume) => !Volume.isEmpty(volume) && !Volume.Segmentation.get(volume) });