From d7ba4d88f719b588491be9b32e4f0862cebb49ae Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Thu, 4 Apr 2019 14:35:07 -0700
Subject: [PATCH] wip, gaussian unit surface texture-mesh
---
src/mol-geo/geometry/geometry.ts | 2 +-
.../compute/histogram-pyramid/reduction.ts | 2 +-
.../compute/marching-cubes/isosurface.ts | 6 +-
.../shader/marching-cubes/isosurface.frag | 4 +-
src/mol-repr/structure/representation.ts | 4 +
.../representation/molecular-surface.ts | 9 ++-
src/mol-repr/structure/units-visual.ts | 22 +++++-
.../structure/visual/gaussian-surface-mesh.ts | 79 ++++++++++++++++---
.../structure/visual/util/gaussian.ts | 11 ++-
9 files changed, 114 insertions(+), 25 deletions(-)
diff --git a/src/mol-geo/geometry/geometry.ts b/src/mol-geo/geometry/geometry.ts
index 98393c607..3497025ba 100644
--- a/src/mol-geo/geometry/geometry.ts
+++ b/src/mol-geo/geometry/geometry.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
diff --git a/src/mol-gl/compute/histogram-pyramid/reduction.ts b/src/mol-gl/compute/histogram-pyramid/reduction.ts
index 5515dcb19..5a9fb03a1 100644
--- a/src/mol-gl/compute/histogram-pyramid/reduction.ts
+++ b/src/mol-gl/compute/histogram-pyramid/reduction.ts
@@ -12,7 +12,7 @@ import { Texture, createTexture } from 'mol-gl/webgl/texture';
import { ShaderCode } from 'mol-gl/shader-code';
import { ValueCell } from 'mol-util';
import { GLRenderingContext } from 'mol-gl/webgl/compat';
-import { printTexture, QuadSchema, QuadValues } from '../util';
+import { QuadSchema, QuadValues } from '../util';
import { Vec2 } from 'mol-math/linear-algebra';
import { getHistopyramidSum } from './sum';
diff --git a/src/mol-gl/compute/marching-cubes/isosurface.ts b/src/mol-gl/compute/marching-cubes/isosurface.ts
index dcc4f3d3e..8f3310497 100644
--- a/src/mol-gl/compute/marching-cubes/isosurface.ts
+++ b/src/mol-gl/compute/marching-cubes/isosurface.ts
@@ -13,7 +13,7 @@ import { ShaderCode } from 'mol-gl/shader-code';
import { ValueCell } from 'mol-util';
import { GLRenderingContext } from 'mol-gl/webgl/compat';
import { Vec3, Vec2, Mat4 } from 'mol-math/linear-algebra';
-import { QuadSchema, QuadValues, readTexture } from '../util';
+import { QuadSchema, QuadValues } from '../util';
import { HistogramPyramid } from '../histogram-pyramid/reduction';
import { getTriIndices } from './tables';
@@ -138,8 +138,8 @@ export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Tex
pr.render()
gl.disable(gl.SCISSOR_TEST)
- const vgt = readTexture(ctx, vertexGroupTexture, pyramidTex.width, height)
- console.log('vertexGroupTexture', vgt.array.subarray(0, 4 * count))
+ // const vgt = readTexture(ctx, vertexGroupTexture, pyramidTex.width, height)
+ // console.log('vertexGroupTexture', vgt.array.subarray(0, 4 * count))
// const vt = readTexture(ctx, verticesTex, pyramidTex.width, height)
// console.log('vt', vt)
diff --git a/src/mol-gl/shader/marching-cubes/isosurface.frag b/src/mol-gl/shader/marching-cubes/isosurface.frag
index 23939b15d..c43d1ba67 100644
--- a/src/mol-gl/shader/marching-cubes/isosurface.frag
+++ b/src/mol-gl/shader/marching-cubes/isosurface.frag
@@ -186,7 +186,7 @@ void main(void) {
float t = (uIsoValue - v0) / (v0 - v1);
// t = -0.5;
- gl_FragColor.xyz = b0 + t * (b0 - b1);
+ gl_FragColor.xyz = (uGridTransform * vec4(b0 + t * (b0 - b1), 1.0)).xyz;
gl_FragColor.w = decodeFloatRGB(d0.rgb); // group id
// normals from gradients
@@ -201,4 +201,6 @@ void main(void) {
v1 - voxel((b1 + c4) / uGridDim).a
));
gl_FragData[1].xyz = -normalize((v0 * n0 + v1 * n1) / max(v0 + v1, EPS));
+ mat3 normalMatrix = transpose(inverse(mat3(uGridTransform)));
+ gl_FragData[1].xyz = normalMatrix * gl_FragData[1].xyz;
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/representation.ts b/src/mol-repr/structure/representation.ts
index 183cd297c..427ab0c0f 100644
--- a/src/mol-repr/structure/representation.ts
+++ b/src/mol-repr/structure/representation.ts
@@ -15,6 +15,7 @@ import { Lines } from 'mol-geo/geometry/lines/lines';
import { DirectVolume } from 'mol-geo/geometry/direct-volume/direct-volume';
import { Spheres } from 'mol-geo/geometry/spheres/spheres';
import { StructureUnitTransforms } from 'mol-model/structure/structure/util/unit-transforms';
+import { TextureMesh } from 'mol-geo/geometry/texture-mesh/texture-mesh';
export interface StructureRepresentationState extends Representation.State {
unitTransforms: StructureUnitTransforms | null
@@ -56,6 +57,9 @@ export type StructureLinesParams = typeof StructureLinesParams
export const StructureDirectVolumeParams = { ...DirectVolume.Params, ...StructureParams }
export type StructureDirectVolumeParams = typeof StructureDirectVolumeParams
+export const StructureTextureMeshParams = { ...TextureMesh.Params, ...StructureParams }
+export type StructureTextureMeshParams = typeof StructureTextureMeshParams
+
export { ComplexRepresentation } from './complex-representation'
export { UnitsRepresentation } from './units-representation'
export { ComplexVisual } from './complex-visual'
diff --git a/src/mol-repr/structure/representation/molecular-surface.ts b/src/mol-repr/structure/representation/molecular-surface.ts
index 4cef6716d..b3c5c7915 100644
--- a/src/mol-repr/structure/representation/molecular-surface.ts
+++ b/src/mol-repr/structure/representation/molecular-surface.ts
@@ -1,10 +1,10 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { GaussianSurfaceVisual, GaussianSurfaceParams } from '../visual/gaussian-surface-mesh';
+import { GaussianSurfaceMeshVisual, GaussianSurfaceTextureMeshVisual, GaussianSurfaceParams } from '../visual/gaussian-surface-mesh';
import { UnitsRepresentation } from '../units-representation';
import { GaussianWireframeVisual, GaussianWireframeParams } from '../visual/gaussian-surface-wireframe';
import { ParamDefinition as PD } from 'mol-util/param-definition';
@@ -14,7 +14,8 @@ import { ThemeRegistryContext } from 'mol-theme/theme';
import { Structure } from 'mol-model/structure';
const MolecularSurfaceVisuals = {
- 'gaussian-surface': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, GaussianSurfaceParams>) => UnitsRepresentation('Gaussian surface', ctx, getParams, GaussianSurfaceVisual),
+ 'gaussian-surface-mesh': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, GaussianSurfaceParams>) => UnitsRepresentation('Gaussian surface', ctx, getParams, GaussianSurfaceMeshVisual),
+ 'gaussian-surface-texture-mesh': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, GaussianSurfaceParams>) => UnitsRepresentation('Gaussian surface', ctx, getParams, GaussianSurfaceTextureMeshVisual),
'gaussian-wireframe': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, GaussianWireframeParams>) => UnitsRepresentation('Gaussian wireframe', ctx, getParams, GaussianWireframeVisual),
}
type MolecularSurfaceVisualName = keyof typeof MolecularSurfaceVisuals
@@ -23,7 +24,7 @@ const MolecularSurfaceVisualOptions = Object.keys(MolecularSurfaceVisuals).map(n
export const MolecularSurfaceParams = {
...GaussianSurfaceParams,
...GaussianWireframeParams,
- visuals: PD.MultiSelect<MolecularSurfaceVisualName>(['gaussian-surface'], MolecularSurfaceVisualOptions),
+ visuals: PD.MultiSelect<MolecularSurfaceVisualName>(['gaussian-surface-mesh'], MolecularSurfaceVisualOptions),
}
export type MolecularSurfaceParams = typeof MolecularSurfaceParams
export function getMolecularSurfaceParams(ctx: ThemeRegistryContext, structure: Structure) {
diff --git a/src/mol-repr/structure/units-visual.ts b/src/mol-repr/structure/units-visual.ts
index 41b74b4d7..e0b0f76af 100644
--- a/src/mol-repr/structure/units-visual.ts
+++ b/src/mol-repr/structure/units-visual.ts
@@ -7,7 +7,7 @@
import { Unit, Structure } from 'mol-model/structure';
import { RepresentationProps } from '../representation';
import { Visual, VisualContext } from '../visual';
-import { StructureMeshParams, StructurePointsParams, StructureLinesParams, StructureDirectVolumeParams, StructureSpheresParams } from './representation';
+import { StructureMeshParams, StructurePointsParams, StructureLinesParams, StructureDirectVolumeParams, StructureSpheresParams, StructureTextureMeshParams } from './representation';
import { Loci, isEveryLoci, EmptyLoci } from 'mol-model/loci';
import { GraphicsRenderObject, createRenderObject } from 'mol-gl/render-object';
import { deepEqual, ValueCell } from 'mol-util';
@@ -33,6 +33,7 @@ import { Spheres } from 'mol-geo/geometry/spheres/spheres';
import { createUnitsTransform, includesUnitKind } from './visual/util/common';
import { Overpaint } from 'mol-theme/overpaint';
import { Transparency } from 'mol-theme/transparency';
+import { TextureMesh } from 'mol-geo/geometry/texture-mesh/texture-mesh';
export type StructureGroup = { structure: Structure, group: Unit.SymmetryGroup }
@@ -328,7 +329,7 @@ export function UnitsLinesVisual<P extends UnitsLinesParams>(builder: UnitsLines
export const UnitsDirectVolumeParams = { ...StructureDirectVolumeParams, ...UnitsParams }
export type UnitsDirectVolumeParams = typeof UnitsDirectVolumeParams
-export interface UnitsDirectVolumeVisualBuilder<P extends UnitsDirectVolumeParams> extends UnitsVisualGeometryBuilder<P, DirectVolume> { }
+export interface UnitsDirectVolumeVisualBuilder<P extends UnitsDirectVolumeParams> extends UnitsVisualBuilder<P, DirectVolume> { }
export function UnitsDirectVolumeVisual<P extends UnitsDirectVolumeParams>(builder: UnitsDirectVolumeVisualBuilder<P>, materialId: number): UnitsVisual<P> {
return UnitsVisual<DirectVolume, StructureDirectVolumeParams & UnitsParams>({
@@ -339,4 +340,21 @@ export function UnitsDirectVolumeVisual<P extends UnitsDirectVolumeParams>(build
},
geometryUtils: DirectVolume.Utils
}, materialId)
+}
+
+// texture-mesh
+
+export const UnitsTextureMeshParams = { ...StructureTextureMeshParams, ...UnitsParams }
+export type UnitsTextureMeshParams = typeof UnitsTextureMeshParams
+export interface UnitsTextureMeshVisualBuilder<P extends UnitsTextureMeshParams> extends UnitsVisualBuilder<P, TextureMesh> { }
+
+export function UnitsTextureMeshVisual<P extends UnitsTextureMeshParams>(builder: UnitsTextureMeshVisualBuilder<P>, materialId: number): UnitsVisual<P> {
+ return UnitsVisual<TextureMesh, StructureTextureMeshParams & UnitsParams>({
+ ...builder,
+ setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme) => {
+ builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme)
+ if (!SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.createGeometry = true
+ },
+ geometryUtils: TextureMesh.Utils
+ }, materialId)
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
index b2622071a..b817423dd 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -7,14 +7,33 @@
import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual } from '../representation';
import { VisualUpdateState } from '../../util';
-import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
+import { UnitsMeshVisual, UnitsMeshParams, UnitsTextureMeshParams, UnitsTextureMeshVisual } from '../units-visual';
import { StructureElementIterator, getElementLoci, eachElement } from './util/element';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { Mesh } from 'mol-geo/geometry/mesh/mesh';
import { computeMarchingCubesMesh } from 'mol-geo/util/marching-cubes/algorithm';
import { VisualContext } from 'mol-repr/visual';
import { Theme } from 'mol-theme/theme';
-import { GaussianDensityProps, computeUnitGaussianDensity, GaussianDensityParams } from './util/gaussian';
+import { GaussianDensityProps, computeUnitGaussianDensity, GaussianDensityParams, computeUnitGaussianDensityTexture2d, GaussianDensityTextureProps } from './util/gaussian';
+import { WebGLContext } from 'mol-gl/webgl/context';
+import { TextureMesh } from 'mol-geo/geometry/texture-mesh/texture-mesh';
+import { calcActiveVoxels } from 'mol-gl/compute/marching-cubes/active-voxels';
+import { createHistogramPyramid } from 'mol-gl/compute/histogram-pyramid/reduction';
+import { createIsosurfaceBuffers } from 'mol-gl/compute/marching-cubes/isosurface';
+import { Sphere3D } from 'mol-math/geometry';
+
+export const GaussianSurfaceParams = {
+ ...UnitsMeshParams,
+ ...UnitsTextureMeshParams,
+ ...GaussianDensityParams,
+}
+export type GaussianSurfaceParams = typeof GaussianSurfaceParams
+
+export function getGaussianSurfaceVisual(webgl?: WebGLContext) {
+ return webgl && webgl.extensions.drawBuffers ? GaussianSurfaceTextureMeshVisual : GaussianSurfaceMeshVisual
+}
+
+//
async function createGaussianSurfaceMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, mesh?: Mesh): Promise<Mesh> {
const { smoothness } = props
@@ -31,16 +50,10 @@ async function createGaussianSurfaceMesh(ctx: VisualContext, unit: Unit, structu
Mesh.computeNormalsImmediate(surface)
Mesh.uniformTriangleGroup(surface)
- return surface;
+ return surface
}
-export const GaussianSurfaceParams = {
- ...UnitsMeshParams,
- ...GaussianDensityParams,
-}
-export type GaussianSurfaceParams = typeof GaussianSurfaceParams
-
-export function GaussianSurfaceVisual(materialId: number): UnitsVisual<GaussianSurfaceParams> {
+export function GaussianSurfaceMeshVisual(materialId: number): UnitsVisual<GaussianSurfaceParams> {
return UnitsMeshVisual<GaussianSurfaceParams>({
defaultProps: PD.getDefaultValues(GaussianSurfaceParams),
createGeometry: createGaussianSurfaceMesh,
@@ -54,4 +67,48 @@ export function GaussianSurfaceVisual(materialId: number): UnitsVisual<GaussianS
if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
}
}, materialId)
+}
+
+//
+
+async function createGaussianSurfaceTextureMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityTextureProps, textureMesh?: TextureMesh): Promise<TextureMesh> {
+ if (!ctx.webgl) throw new Error('webgl context required to create gaussian surface texture-mesh')
+ const isoLevel = Math.exp(-props.smoothness)
+
+ const densityTextureData = await computeUnitGaussianDensityTexture2d(unit, props, ctx.webgl).runInContext(ctx.runtime)
+ // console.log(densityTextureData)
+ // console.log('vertexGroupTexture', readTexture(ctx.webgl, densityTextureData.texture))
+ // ctx.webgl.waitForGpuCommandsCompleteSync()
+
+ const activeVoxelsTex = calcActiveVoxels(ctx.webgl, densityTextureData.texture, densityTextureData.gridDimension, isoLevel)
+ // ctx.webgl.waitForGpuCommandsCompleteSync()
+
+ const compacted = createHistogramPyramid(ctx.webgl, activeVoxelsTex)
+ // ctx.webgl.waitForGpuCommandsCompleteSync()
+
+ const gv = createIsosurfaceBuffers(ctx.webgl, activeVoxelsTex, densityTextureData.texture, compacted, densityTextureData.gridDimension, densityTextureData.transform, isoLevel)
+ // ctx.webgl.waitForGpuCommandsCompleteSync()
+
+ // const boundingSphere = Sphere3D.zero()
+ // Sphere3D.addVec3(boundingSphere, boundingSphere, densityTextureData.gridDimension)
+ const boundingSphere = Sphere3D.fromBox3D(Sphere3D(), densityTextureData.bbox)
+ const surface = TextureMesh.create(gv.vertexCount, 1, gv.vertexGroupTexture, gv.normalTexture, boundingSphere, textureMesh)
+
+ // ctx.webgl.waitForGpuCommandsCompleteSync()
+ return surface
+}
+
+export function GaussianSurfaceTextureMeshVisual(materialId: number): UnitsVisual<GaussianSurfaceParams> {
+ return UnitsTextureMeshVisual<GaussianSurfaceParams>({
+ defaultProps: PD.getDefaultValues(GaussianSurfaceParams),
+ createGeometry: createGaussianSurfaceTextureMesh,
+ createLocationIterator: StructureElementIterator.fromGroup,
+ getLoci: getElementLoci,
+ eachLocation: eachElement,
+ setUpdateState: (state: VisualUpdateState, newProps: PD.Values<GaussianSurfaceParams>, currentProps: PD.Values<GaussianSurfaceParams>) => {
+ if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
+ if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
+ if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
+ }
+ }, materialId)
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/util/gaussian.ts b/src/mol-repr/structure/visual/util/gaussian.ts
index 9cee5dcdd..d50d95c8f 100644
--- a/src/mol-repr/structure/visual/util/gaussian.ts
+++ b/src/mol-repr/structure/visual/util/gaussian.ts
@@ -8,7 +8,7 @@ import { Unit, StructureElement, ElementIndex, Structure } from 'mol-model/struc
import { GaussianDensity } from 'mol-math/geometry/gaussian-density';
import { Task } from 'mol-task';
import { ParamDefinition as PD } from 'mol-util/param-definition';
-import { GaussianDensityTexture } from 'mol-math/geometry/gaussian-density/gpu';
+import { GaussianDensityTexture, GaussianDensityTexture2d } from 'mol-math/geometry/gaussian-density/gpu';
import { Texture } from 'mol-gl/webgl/texture';
import { WebGLContext } from 'mol-gl/webgl/context';
import { PhysicalSizeTheme } from 'mol-theme/size/physical';
@@ -68,13 +68,20 @@ export function computeUnitGaussianDensity(unit: Unit, props: GaussianDensityPro
});
}
-export function computeUnitGaussianDensityTexture(unit: Unit, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture) {
+export function computeUnitGaussianDensityTexture(unit: Unit, props: GaussianDensityTextureProps, webgl: WebGLContext, texture?: Texture) {
const { position, radius } = getUnitConformationAndRadius(unit)
return Task.create('Gaussian Density', async ctx => {
return await GaussianDensityTexture(ctx, webgl, position, unit.lookup3d.boundary.box, radius, props, texture);
});
}
+export function computeUnitGaussianDensityTexture2d(unit: Unit, props: GaussianDensityTextureProps, webgl: WebGLContext, texture?: Texture) {
+ const { position, radius } = getUnitConformationAndRadius(unit)
+ return Task.create('Gaussian Density', async ctx => {
+ return await GaussianDensityTexture2d(ctx, webgl, position, unit.lookup3d.boundary.box, radius, props, texture);
+ });
+}
+
//
function getStructureConformationAndRadius(structure: Structure) {
--
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