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Commit 79dba8ea authored by Alexander Rose's avatar Alexander Rose
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wip, gpu gaussian density

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src/mol-geo/representation/structure/visual/gaussian-density-point.ts
+ 0
− 1
View file @ 79dba8ea
......@@ -69,7 +69,6 @@ export function GaussianDensityPointVisual(): UnitsVisual<GaussianDensityPointPr
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
if (newProps.readSlices !== currentProps.readSlices) state.createGeometry = true
if (newProps.ignoreCache !== currentProps.ignoreCache) state.createGeometry = true
}
})
......
src/mol-geo/representation/structure/visual/gaussian-density-volume.ts
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− 1
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......@@ -68,7 +68,6 @@ export function GaussianDensityVolumeVisual(): UnitsVisual<GaussianDensityVolume
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
if (newProps.readSlices !== currentProps.readSlices) state.createGeometry = true
if (newProps.ignoreCache !== currentProps.ignoreCache) state.createGeometry = true
}
})
......
src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
+ 0
− 1
View file @ 79dba8ea
......@@ -93,7 +93,6 @@ export function GaussianSurfaceVisual(): UnitsVisual<GaussianSurfaceProps> {
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
if (newProps.readSlices !== currentProps.readSlices) state.createGeometry = true
if (newProps.ignoreCache !== currentProps.ignoreCache) state.createGeometry = true
}
})
......
src/mol-geo/representation/structure/visual/gaussian-surface-wireframe.ts
+ 0
− 1
View file @ 79dba8ea
......@@ -53,7 +53,6 @@ export function GaussianWireframeVisual(): UnitsVisual<GaussianWireframeProps> {
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
if (newProps.readSlices !== currentProps.readSlices) state.createGeometry = true
if (newProps.ignoreCache !== currentProps.ignoreCache) state.createGeometry = true
}
})
......
src/mol-gl/webgl/texture.ts
+ 17
− 4
View file @ 79dba8ea
......@@ -114,7 +114,11 @@ export interface Texture {
readonly internalFormat: number
readonly type: number
define: (x: number, y: number, z: number) => void
readonly width: number
readonly height: number
readonly depth: number
define: (width: number, height: number, depth?: number) => void
load: (image: TextureImage<any>) => void
bind: (id: TextureId) => void
unbind: (id: TextureId) => void
......@@ -151,6 +155,8 @@ export function createTexture(ctx: Context, kind: TextureKind, _format: TextureF
gl.texParameteri(target, gl.TEXTURE_WRAP_T, gl.CLAMP_TO_EDGE);
gl.bindTexture(target, null)
let width = 0, height = 0, depth = 0
let destroyed = false
ctx.textureCount += 1
......@@ -161,7 +167,12 @@ export function createTexture(ctx: Context, kind: TextureKind, _format: TextureF
internalFormat,
type,
define: (width: number, height: number, depth?: number) => {
get width () { return width },
get height () { return height },
get depth () { return depth },
define: (_width: number, _height: number, _depth?: number) => {
width = _width, height = _height, depth = _depth || 0
gl.bindTexture(target, texture)
if (target === gl.TEXTURE_2D) {
// TODO remove cast when webgl2 types are fixed
......@@ -178,11 +189,13 @@ export function createTexture(ctx: Context, kind: TextureKind, _format: TextureF
gl.pixelStorei(gl.UNPACK_ALIGNMENT, 1);
gl.pixelStorei(gl.UNPACK_COLORSPACE_CONVERSION_WEBGL, gl.NONE);
if (target === gl.TEXTURE_2D) {
const { array, width, height } = data as TextureImage<any>;
const { array, width: _width, height: _height } = data as TextureImage<any>
width = _width, height = _height;
// TODO remove cast when webgl2 types are fixed
(gl as WebGLRenderingContext).texImage2D(target, 0, internalFormat, width, height, 0, format, type, array)
} else if (target === (gl as WebGL2RenderingContext).TEXTURE_3D) {
const { array, width, height, depth } = data as TextureVolume<any>;
const { array, width: _width, height: _height, depth: _depth } = data as TextureVolume<any>
width = _width, height = _height, depth = _depth;
(gl as WebGL2RenderingContext).texImage3D(target, 0, internalFormat, width, height, depth, 0, format, type, array)
} else {
throw new Error('unknown texture target')
......
src/mol-math/geometry/gaussian-density.ts
+ 0
− 1
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......@@ -19,7 +19,6 @@ export const DefaultGaussianDensityProps = {
resolution: 1,
radiusOffset: 0,
smoothness: 1.5,
readSlices: false,
useGpu: true,
}
export type GaussianDensityProps = typeof DefaultGaussianDensityProps
......
src/mol-math/geometry/gaussian-density/gpu.ts
+ 180
− 196
View file @ 79dba8ea
......@@ -21,143 +21,48 @@ import { createFramebuffer } from 'mol-gl/webgl/framebuffer';
import { createTexture, Texture, TextureAttachment } from 'mol-gl/webgl/texture';
import { GLRenderingContext } from 'mol-gl/webgl/compat';
let webglContext: Context
function getWebGLContext() {
if (webglContext) return webglContext
const canvas = document.createElement('canvas')
const gl = getGLContext(canvas, {
alpha: true,
antialias: false,
depth: false,
preserveDrawingBuffer: true
})
if (!gl) throw new Error('Could not create a WebGL rendering context')
webglContext = createContext(gl)
return webglContext
}
export async function GaussianDensityGPU(ctx: RuntimeContext, position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps): Promise<DensityData> {
// TODO allow passing a context via props
const webgl = getWebGLContext()
if (webgl.maxDrawBuffers > 0) {
console.log('GaussianDensityMultiDrawBuffer')
const { texture, scale, bbox, dim } = await GaussianDensityMultiDrawBuffer(ctx, webgl, position, box, radius, props)
console.time('gpu gaussian density 3d texture read')
const field = fieldFromTexture3d(webgl, texture, dim)
console.timeEnd('gpu gaussian density 3d texture read')
const idData = field.space.create()
const idField = Tensor.create(field.space, idData)
const transform = Mat4.identity()
Mat4.fromScaling(transform, scale)
Mat4.setTranslation(transform, bbox.min)
const renderTarget = createRenderTarget(webgl, dim[0], dim[1])
return { field, idField, transform, renderTarget, bbox, gridDimension: dim }
} else {
console.log('GaussianDensitySingleDrawBuffer')
return GaussianDensitySingleDrawBuffer(ctx, webgl, position, box, radius, props)
}
}
async function prepareGaussianDensityData(ctx: RuntimeContext, position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps) {
const { resolution, radiusOffset } = props
const { indices, x, y, z } = position
const n = OrderedSet.size(indices)
const positions = new Float32Array(n * 3)
const radii = new Float32Array(n)
let maxRadius = 0
for (let i = 0; i < n; ++i) {
const j = OrderedSet.getAt(indices, i);
positions[i * 3] = x[j]
positions[i * 3 + 1] = y[j]
positions[i * 3 + 2] = z[j]
const r = radius(j) + radiusOffset
if (maxRadius < r) maxRadius = r
radii[i] = r
if (i % 10000 === 0 && ctx.shouldUpdate) {
await ctx.update({ message: 'preparing density data', current: i, max: n })
}
}
const pad = maxRadius * 2 + resolution
const expandedBox = Box3D.expand(Box3D.empty(), box, Vec3.create(pad, pad, pad));
const extent = Vec3.sub(Vec3.zero(), expandedBox.max, expandedBox.min)
const delta = getDelta(expandedBox, resolution)
const dim = Vec3.zero()
Vec3.ceil(dim, Vec3.mul(dim, extent, delta))
console.log('grid dim gpu', dim)
return { drawCount: n, positions, radii, delta, expandedBox, dim }
}
function getGaussianDensityRenderObject(webgl: Context, drawCount: number, positions: Float32Array, radii: Float32Array, box: Box3D, dimensions: Vec3, smoothness: number) {
const extent = Vec3.sub(Vec3.zero(), box.max, box.min)
const values: GaussianDensityValues = {
drawCount: ValueCell.create(drawCount),
instanceCount: ValueCell.create(1),
aRadius: ValueCell.create(radii),
aPosition: ValueCell.create(positions),
uCurrentSlice: ValueCell.create(0),
uCurrentX: ValueCell.create(0),
uCurrentY: ValueCell.create(0),
uBboxMin: ValueCell.create(box.min),
uBboxMax: ValueCell.create(box.max),
uBboxSize: ValueCell.create(extent),
uGridDim: ValueCell.create(dimensions),
uAlpha: ValueCell.create(smoothness),
const useMultiDraw = webgl.maxDrawBuffers > 0
dDrawBuffers: ValueCell.create(Math.min(8, webgl.maxDrawBuffers)),
}
const state: RenderableState = {
visible: true,
depthMask: false
}
console.time('gpu gaussian density render')
const { texture, scale, bbox, dim } = useMultiDraw ?
await GaussianDensityMultiDrawBuffer(ctx, webgl, position, box, radius, props) :
await GaussianDensitySingleDrawBuffer(ctx, webgl, position, box, radius, props)
console.timeEnd('gpu gaussian density render')
const renderObject = createGaussianDensityRenderObject(values, state)
console.time('gpu gaussian density read')
const field = useMultiDraw ?
fieldFromTexture3d(webgl, texture, dim) :
fieldFromTexture2d(webgl, texture, dim)
console.timeEnd('gpu gaussian density read')
return renderObject
}
const idData = field.space.create()
const idField = Tensor.create(field.space, idData)
//
const transform = Mat4.identity()
Mat4.fromScaling(transform, scale)
Mat4.setTranslation(transform, bbox.min)
function setRenderingDefaults(gl: GLRenderingContext) {
gl.disable(gl.CULL_FACE)
gl.frontFace(gl.CCW)
gl.cullFace(gl.BACK)
const renderTarget = createRenderTarget(webgl, dim[0], dim[1])
gl.blendFunc(gl.SRC_ALPHA, gl.ONE_MINUS_SRC_ALPHA)
gl.blendEquation(gl.FUNC_ADD)
gl.enable(gl.BLEND)
return { field, idField, transform, renderTarget, bbox, gridDimension: dim }
}
//
async function GaussianDensitySingleDrawBuffer(ctx: RuntimeContext, webgl: Context, position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps): Promise<DensityData> {
const { readSlices, smoothness } = props
async function GaussianDensitySingleDrawBuffer(ctx: RuntimeContext, webgl: Context, position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps) {
const { smoothness } = props
const { drawCount, positions, radii, delta, expandedBox, dim } = await prepareGaussianDensityData(ctx, position, box, radius, props)
const [ dx, dy, dz ] = dim
const renderObject = getGaussianDensityRenderObject(webgl, drawCount, positions, radii, expandedBox, dim, smoothness)
const renderable = createRenderable(webgl, renderObject)
//
// TODO fallback to lower resolution when texture size is not large enough
const maxTexSize = webgl.maxTextureSize
let fboTexDimX = 0
let fboTexDimY = dim[1]
......@@ -172,93 +77,43 @@ async function GaussianDensitySingleDrawBuffer(ctx: RuntimeContext, webgl: Conte
fboTexDimX = dim[0] * dim[2]
}
console.log('dim', dim, 'cols', fboTexCols, 'rows', fboTexRows)
//
const space = Tensor.Space(dim, [2, 1, 0], Float32Array)
const data = space.create()
const field = Tensor.create(space, data)
const idData = space.create()
const idField = Tensor.create(space, idData)
//
const { gl } = webgl
const { uCurrentSlice, uCurrentX, uCurrentY } = renderObject.values
const program = renderable.getProgram('draw')
const renderTarget = createRenderTarget(webgl, fboTexDimX, fboTexDimY)
const framebuffer = createFramebuffer(webgl)
framebuffer.bind()
const texture = createTexture(webgl, 'image-uint8', 'rgba', 'ubyte', 'linear')
texture.define(fboTexDimX, fboTexDimY)
const program = renderable.getProgram('draw')
program.use()
renderTarget.bind()
setRenderingDefaults(gl)
texture.attachFramebuffer(framebuffer, 0)
const slice = new Uint8Array(dim[0] * dim[1] * 4)
console.time('gpu gaussian density slices')
let currCol = 0
let currY = 0
let currX = 0
let j = 0
for (let i = 0; i < dim[2]; ++i) {
for (let i = 0; i < dz; ++i) {
if (currCol >= fboTexCols) {
currCol -= fboTexCols
currY += dim[1]
currY += dy
currX = 0
}
gl.viewport(currX, currY, dim[0], dim[1])
gl.viewport(currX, currY, dx, dy)
ValueCell.update(uCurrentSlice, i)
ValueCell.update(uCurrentX, currX)
ValueCell.update(uCurrentY, currY)
renderable.render('draw')
if (readSlices) {
renderTarget.readBuffer(currX, currY, dim[0], dim[1], slice)
for (let iy = 0; iy < dim[1]; ++iy) {
for (let ix = 0; ix < dim[0]; ++ix) {
data[j] = slice[4 * (iy * dim[0] + ix)] / 255
++j
}
}
}
++currCol
currX += dim[0]
}
console.timeEnd('gpu gaussian density slices')
//
if (!readSlices) {
console.time('gpu gaussian density full')
renderTarget.getBuffer()
const { array } = renderTarget.image
let idx = 0
let tmpCol = 0
let tmpRow = 0
for (let iz = 0; iz < dim[2]; ++iz) {
if (tmpCol >= fboTexCols ) {
tmpCol = 0
tmpRow += dim[1]
}
for (let iy = 0; iy < dim[1]; ++iy) {
for (let ix = 0; ix < dim[0]; ++ix) {
data[idx] = array[4 * (tmpCol * dim[0] + (iy + tmpRow) * fboTexDimX + ix)] / 255
idx++
}
}
tmpCol++
}
console.timeEnd('gpu gaussian density full')
currX += dx
}
//
const transform = Mat4.identity()
Mat4.fromScaling(transform, Vec3.inverse(Vec3.zero(), delta))
Mat4.setTranslation(transform, expandedBox.min)
framebuffer.destroy() // clean up
return { field, idField, transform, renderTarget, bbox: expandedBox, gridDimension: dim }
return { texture, scale: Vec3.inverse(Vec3.zero(), delta), bbox: expandedBox, dim }
}
async function GaussianDensityMultiDrawBuffer(ctx: RuntimeContext, webgl: Context, position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps) {
......@@ -299,14 +154,12 @@ async function GaussianDensityMultiDrawBuffer(ctx: RuntimeContext, webgl: Contex
gl.viewport(0, 0, dx, dy)
setRenderingDefaults(gl)
//
// z-slices to be render with multi render targets
const dzMulti = Math.floor(dz / drawBuffers) * drawBuffers
// render multi target
const programMulti = renderable.getProgram('draw')
programMulti.use()
console.time('gpu gaussian density 3d texture multi')
for (let i = 0; i < dzMulti; i += drawBuffers) {
ValueCell.update(uCurrentSlice, i)
for (let k = 0; k < drawBuffers; ++k) {
......@@ -314,54 +167,185 @@ async function GaussianDensityMultiDrawBuffer(ctx: RuntimeContext, webgl: Contex
}
renderable.render('draw')
}
console.timeEnd('gpu gaussian density 3d texture multi')
// render single target
ValueCell.updateIfChanged(renderable.values.dDrawBuffers, 1)
renderable.update()
const programSingle = renderable.getProgram('draw')
programSingle.use()
console.time('gpu gaussian density 3d texture single')
for (let i = dzMulti; i < dz; ++i) {
ValueCell.update(uCurrentSlice, i)
texture.attachFramebuffer(framebuffer, 0, i)
renderable.render('draw')
}
console.timeEnd('gpu gaussian density 3d texture single')
// must detach framebuffer attachments before reading is possible
for (let k = 0; k < drawBuffers; ++k) {
texture.detachFramebuffer(framebuffer, k as TextureAttachment)
}
framebuffer.destroy() // clean up
// throw new Error('foo')
framebuffer.destroy() // clean up
return { texture, scale: Vec3.inverse(Vec3.zero(), delta), bbox: expandedBox, dim }
}
//
function fieldFromTexture3d(ctx: Context, texture: Texture, dim: Vec3) {
let webglContext: Context
function getWebGLContext() {
if (webglContext) return webglContext
const canvas = document.createElement('canvas')
const gl = getGLContext(canvas, {
alpha: true,
antialias: false,
depth: false,
preserveDrawingBuffer: true
})
if (!gl) throw new Error('Could not create a WebGL rendering context')
webglContext = createContext(gl)
return webglContext
}
async function prepareGaussianDensityData(ctx: RuntimeContext, position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps) {
const { resolution, radiusOffset } = props
const { indices, x, y, z } = position
const n = OrderedSet.size(indices)
const positions = new Float32Array(n * 3)
const radii = new Float32Array(n)
let maxRadius = 0
for (let i = 0; i < n; ++i) {
const j = OrderedSet.getAt(indices, i);
positions[i * 3] = x[j]
positions[i * 3 + 1] = y[j]
positions[i * 3 + 2] = z[j]
const r = radius(j) + radiusOffset
if (maxRadius < r) maxRadius = r
radii[i] = r
if (i % 10000 === 0 && ctx.shouldUpdate) {
await ctx.update({ message: 'preparing density data', current: i, max: n })
}
}
const pad = maxRadius * 2 + resolution
const expandedBox = Box3D.expand(Box3D.empty(), box, Vec3.create(pad, pad, pad));
const extent = Vec3.sub(Vec3.zero(), expandedBox.max, expandedBox.min)
const delta = getDelta(expandedBox, resolution)
const dim = Vec3.zero()
Vec3.ceil(dim, Vec3.mul(dim, extent, delta))
console.log('grid dim gpu', dim)
return { drawCount: n, positions, radii, delta, expandedBox, dim }
}
function getGaussianDensityRenderObject(webgl: Context, drawCount: number, positions: Float32Array, radii: Float32Array, box: Box3D, dimensions: Vec3, smoothness: number) {
const extent = Vec3.sub(Vec3.zero(), box.max, box.min)
const values: GaussianDensityValues = {
drawCount: ValueCell.create(drawCount),
instanceCount: ValueCell.create(1),
aRadius: ValueCell.create(radii),
aPosition: ValueCell.create(positions),
uCurrentSlice: ValueCell.create(0),
uCurrentX: ValueCell.create(0),
uCurrentY: ValueCell.create(0),
uBboxMin: ValueCell.create(box.min),
uBboxMax: ValueCell.create(box.max),
uBboxSize: ValueCell.create(extent),
uGridDim: ValueCell.create(dimensions),
uAlpha: ValueCell.create(smoothness),
dDrawBuffers: ValueCell.create(Math.min(8, webgl.maxDrawBuffers)),
}
const state: RenderableState = {
visible: true,
depthMask: false
}
const renderObject = createGaussianDensityRenderObject(values, state)
return renderObject
}
function setRenderingDefaults(gl: GLRenderingContext) {
gl.disable(gl.CULL_FACE)
gl.frontFace(gl.CCW)
gl.cullFace(gl.BACK)
gl.blendFunc(gl.SRC_ALPHA, gl.ONE_MINUS_SRC_ALPHA)
gl.blendEquation(gl.FUNC_ADD)
gl.enable(gl.BLEND)
}
function fieldFromTexture2d(ctx: Context, texture: Texture, dim: Vec3) {
const { gl } = ctx
const [ dx, dy, dz ] = dim
const { width, height } = texture
const fboTexCols = Math.floor(width / dx)
const space = Tensor.Space(dim, [2, 1, 0], Float32Array)
const data = space.create()
const field = Tensor.create(space, data)
const image = new Uint8Array(width * height * 4)
const framebuffer = createFramebuffer(ctx)
framebuffer.bind()
texture.attachFramebuffer(framebuffer, 0)
gl.readPixels(0, 0, width, height, gl.RGBA, gl.UNSIGNED_BYTE, image)
let idx = 0
let tmpCol = 0
let tmpRow = 0
for (let iz = 0; iz < dz; ++iz) {
if (tmpCol >= fboTexCols ) {
tmpCol = 0
tmpRow += dy
}
for (let iy = 0; iy < dy; ++iy) {
for (let ix = 0; ix < dx; ++ix) {
data[idx] = image[4 * (tmpCol * dx + (iy + tmpRow) * width + ix)] / 255
idx++
}
}
tmpCol++
}
framebuffer.destroy()
return field
}
function fieldFromTexture3d(ctx: Context, texture: Texture, dim: Vec3) {
const { gl } = ctx
const { width, height, depth } = texture
const space = Tensor.Space(dim, [2, 1, 0], Float32Array)
const data = space.create()
const field = Tensor.create(space, data)
const slice = new Uint8Array(dx * dy * 4)
const slice = new Uint8Array(width * height * 4)
const framebuffer = createFramebuffer(ctx)
framebuffer.bind()
let j = 0
for (let i = 0; i < dz; ++i) {
for (let i = 0; i < depth; ++i) {
texture.attachFramebuffer(framebuffer, 0, i)
gl.readPixels(0, 0, dx, dy, gl.RGBA, gl.UNSIGNED_BYTE, slice)
for (let iy = 0; iy < dim[1]; ++iy) {
for (let ix = 0; ix < dim[0]; ++ix) {
data[j] = slice[4 * (iy * dim[0] + ix)] / 255
gl.readPixels(0, 0, width, height, gl.RGBA, gl.UNSIGNED_BYTE, slice)
for (let iy = 0; iy < height; ++iy) {
for (let ix = 0; ix < width; ++ix) {
data[j] = slice[4 * (iy * width + ix)] / 255
++j
}
}
......
src/mol-model/structure/structure/unit/gaussian-density.ts
+ 0
− 1
View file @ 79dba8ea
......@@ -16,7 +16,6 @@ export const GaussianDensityParams = {
radiusOffset: NumberParam('Radius Offset', '', 0, 0, 10, 0.1),
smoothness: NumberParam('Smoothness', '', 1.5, 0.5, 2.5, 0.1),
useGpu: BooleanParam('Use GPU', '', true),
readSlices: BooleanParam('Read Slices', '', false),
ignoreCache: BooleanParam('Ignore Cache', '', false),
}
export const DefaultGaussianDensityProps = paramDefaultValues(GaussianDensityParams)
......
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