diff --git a/src/mol-gl/shader/gaussian-density.vert b/src/mol-gl/shader/gaussian-density.vert
index c37a821246506455ee3ebed1f100ee7eda9db3ac..2bbc651750d6a67283d8a8ea0126ed4a867bc1d0 100644
--- a/src/mol-gl/shader/gaussian-density.vert
+++ b/src/mol-gl/shader/gaussian-density.vert
@@ -22,7 +22,7 @@ uniform float uCurrentSlice;
void main() {
radius = aRadius;
float scale = max(uBboxSize.z, max(uBboxSize.x, uBboxSize.y));
- gl_PointSize = (radius / scale) * max(uGridDim.x, uGridDim.y) * 3.0;
+ gl_PointSize = (radius / scale) * max(uGridDim.x, uGridDim.y) * 6.0;
position = (aPosition - uBboxMin) / uBboxSize;
gl_Position = vec4(position * 2.0 - 1.0, 1.0);
}
\ No newline at end of file
diff --git a/src/mol-math/geometry/gaussian-density/cpu.ts b/src/mol-math/geometry/gaussian-density/cpu.ts
index 7b9195dd0aacb7a6fe839a5211dec82c504bd4d5..1e1d0cdb35a16c476c17f3071c1f669d847573ad 100644
--- a/src/mol-math/geometry/gaussian-density/cpu.ts
+++ b/src/mol-math/geometry/gaussian-density/cpu.ts
@@ -20,7 +20,17 @@ export async function GaussianDensityCPU(ctx: RuntimeContext, position: Position
const v = Vec3.zero()
const p = Vec3.zero()
- const pad = (radiusOffset + 3) * 3 // TODO calculate max radius
+ let maxRadius = 0
+ for (let i = 0; i < n; ++i) {
+ const r = radius(OrderedSet.getAt(indices, i)) + radiusOffset
+ if (maxRadius < r) maxRadius = r
+
+ if (i % 10000 === 0 && ctx.shouldUpdate) {
+ await ctx.update({ message: 'calculating max radius', 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 min = expandedBox.min
@@ -43,7 +53,7 @@ export async function GaussianDensityCPU(ctx: RuntimeContext, position: Position
const alpha = smoothness
- const _r2 = (radiusOffset + 1.4 * 2)
+ const _r2 = maxRadius * 2
const _radius2 = Vec3.create(_r2, _r2, _r2)
Vec3.mul(_radius2, _radius2, delta)
const updateChunk = Math.ceil(10000 / (_radius2[0] * _radius2[1] * _radius2[2]))
diff --git a/src/mol-math/geometry/gaussian-density/gpu.ts b/src/mol-math/geometry/gaussian-density/gpu.ts
index 34fc6f6ae5ae53665d4967511d6d7fe877e0a909..a0602983c597aa79be38d628b8b0965a221b7a11 100644
--- a/src/mol-math/geometry/gaussian-density/gpu.ts
+++ b/src/mol-math/geometry/gaussian-density/gpu.ts
@@ -6,7 +6,7 @@
*/
import { RuntimeContext } from 'mol-task'
-import { PositionData } from '../common'
+import { PositionData, DensityData } from '../common'
import { Box3D } from '../../geometry'
import { GaussianDensityProps, getDelta } from '../gaussian-density'
import { OrderedSet } from 'mol-data/int'
@@ -18,7 +18,7 @@ import { createRenderable, createGaussianDensityRenderObject } from 'mol-gl/rend
import { createRenderTarget } from 'mol-gl/webgl/render-target'
import { Context, createContext } from 'mol-gl/webgl/context';
-export async function GaussianDensityGPU(ctx: RuntimeContext, position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps) { // }: Promise<DensityData> {
+export async function GaussianDensityGPU(ctx: RuntimeContext, position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps): Promise<DensityData> {
const { resolution, radiusOffset, smoothness, readSlices } = props
const { indices, x, y, z } = position
@@ -27,19 +27,7 @@ export async function GaussianDensityGPU(ctx: RuntimeContext, position: Position
const positions = new Float32Array(n * 3)
const radii = new Float32Array(n)
- const pad = (radiusOffset + 3) * 3 // TODO calculate max radius
- 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(Box3D.expand(Box3D.empty(), box, Vec3.create(pad, pad, pad)), resolution)
- const dim = Vec3.zero()
- Vec3.ceil(dim, Vec3.mul(dim, extent, delta))
- console.log('grid dim', dim)
-
- const _r2 = (radiusOffset + 1.4 * 2)
- const _radius2 = Vec3.create(_r2, _r2, _r2)
- Vec3.mul(_radius2, _radius2, delta)
- const updateChunk = Math.ceil(10000 / (_radius2[0] * _radius2[1] * _radius2[2]))
+ let maxRadius = 0
for (let i = 0; i < n; ++i) {
const j = OrderedSet.getAt(indices, i);
@@ -47,13 +35,29 @@ export async function GaussianDensityGPU(ctx: RuntimeContext, position: Position
positions[i * 3] = x[j]
positions[i * 3 + 1] = y[j]
positions[i * 3 + 2] = z[j]
- radii[i] = radius(j) + radiusOffset
+ 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(Box3D.expand(Box3D.empty(), box, Vec3.create(pad, pad, pad)), resolution)
+ const dim = Vec3.zero()
+ Vec3.ceil(dim, Vec3.mul(dim, extent, delta))
+ console.log('grid dim', dim)
+
+ const _r2 = maxRadius * 2
+ const _radius2 = Vec3.create(_r2, _r2, _r2)
+ Vec3.mul(_radius2, _radius2, delta)
+ const updateChunk = Math.ceil(10000 / (_radius2[0] * _radius2[1] * _radius2[2]))
+
//
const values: GaussianDensityValues = {
@@ -86,7 +90,7 @@ export async function GaussianDensityGPU(ctx: RuntimeContext, position: Position
//
// TODO fallback to lower resolution when texture size is not large enough
- const maxTexSize = webgl.maxTextureSize
+ const maxTexSize = 1024 // webgl.maxTextureSize
let fboTexDimX = 0
let fboTexDimY = dim[1]
let fboTexRows = 1
@@ -100,6 +104,8 @@ export async function GaussianDensityGPU(ctx: RuntimeContext, position: Position
fboTexDimX = dim[0] * dim[2]
}
+ console.log('dim', dim, 'cols', fboTexCols, 'rows', fboTexRows)
+
//
const space = Tensor.Space(dim, [2, 1, 0], Float32Array)
@@ -124,7 +130,7 @@ export async function GaussianDensityGPU(ctx: RuntimeContext, position: Position
gl.cullFace(gl.BACK)
gl.depthMask(true)
- gl.clearColor(0, 0, 0, 1)
+ gl.clearColor(0, 0, 0, 0)
gl.clear(gl.COLOR_BUFFER_BIT | gl.DEPTH_BUFFER_BIT)
gl.depthMask(false)
@@ -173,6 +179,7 @@ export async function GaussianDensityGPU(ctx: RuntimeContext, position: Position
if (!readSlices) {
console.time('gpu gaussian density full')
renderTarget.getBuffer()
+ const { array } = renderTarget.image
let idx = 0
let tmpCol = 0
let tmpRow = 0
@@ -183,7 +190,7 @@ export async function GaussianDensityGPU(ctx: RuntimeContext, position: Position
}
for (let iy = 0; iy < dim[1]; ++iy) {
for (let ix = 0; ix < dim[0]; ++ix) {
- data[idx] = renderTarget.image.array[4 * (tmpCol * dim[0] + (iy + tmpRow) * fboTexDimX + ix)] / 255
+ data[idx] = array[4 * (tmpCol * dim[0] + (iy + tmpRow) * fboTexDimX + ix)] / 255
idx++
}
}
@@ -198,7 +205,7 @@ export async function GaussianDensityGPU(ctx: RuntimeContext, position: Position
Mat4.fromScaling(transform, Vec3.inverse(Vec3.zero(), delta))
Mat4.setTranslation(transform, expandedBox.min)
- return { field, idField, transform }
+ return { field, idField, transform, renderTarget, bbox: expandedBox, gridDimension: dim }
}
let webglContext: Context
@@ -206,9 +213,9 @@ function getWebGLContext() {
if (webglContext) return webglContext
const canvas = document.createElement('canvas')
const gl = canvas.getContext('webgl', {
- alpha: false,
- antialias: true,
- depth: true,
+ alpha: true,
+ antialias: false,
+ depth: false,
preserveDrawingBuffer: true
})
if (!gl) throw new Error('Could not create a WebGL rendering context')
diff --git a/src/mol-model/structure/structure/unit/gaussian-density.ts b/src/mol-model/structure/structure/unit/gaussian-density.ts
index 25b06421148d69e2a153ed06c457c69d3cefc224..821a828d9333bb5556d62074ff3b4ff052a47ee8 100644
--- a/src/mol-model/structure/structure/unit/gaussian-density.ts
+++ b/src/mol-model/structure/structure/unit/gaussian-density.ts
@@ -14,7 +14,7 @@ import { NumberParam, paramDefaultValues, BooleanParam } from 'mol-view/paramete
export const GaussianDensityParams = {
resolution: NumberParam('Resolution', '', 1, 0.1, 10, 0.1),
radiusOffset: NumberParam('Radius Offset', '', 0, 0, 10, 0.1),
- smoothness: NumberParam('Smoothness', '', 1.5, 0, 4, 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),