diff --git a/src/mol-geo/util/marching-cubes/algorithm.ts b/src/mol-geo/util/marching-cubes/algorithm.ts
index e9d9e4ad46ee87691bc4c9d34b01dfe8a476b071..d2f524f2c308399cce8f598cd8622c51b007dba8 100644
--- a/src/mol-geo/util/marching-cubes/algorithm.ts
+++ b/src/mol-geo/util/marching-cubes/algorithm.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 David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -12,7 +12,6 @@ import { Index, EdgeIdInfo, CubeEdges, EdgeTable, TriTable } from './tables'
import { defaults } from 'mol-util'
import { MarchinCubesBuilder, MarchinCubesMeshBuilder, MarchinCubesLinesBuilder } from './builder';
import { Lines } from '../../geometry/lines/lines';
-// import { Lines } from '../../geometry/lines/lines';
/**
* The parameters required by the algorithm.
@@ -156,17 +155,38 @@ class MarchingCubesState {
const ret = this.verticesOnEdges[edgeId];
if (ret > 0) return ret - 1;
+ const sf = this.scalarField
+ const sfg = this.scalarFieldGet
+
const edge = CubeEdges[edgeNum];
const a = edge.a, b = edge.b;
const li = a.i + this.i, lj = a.j + this.j, lk = a.k + this.k;
const hi = b.i + this.i, hj = b.j + this.j, hk = b.k + this.k;
- const v0 = this.scalarFieldGet(this.scalarField, li, lj, lk);
- const v1 = this.scalarFieldGet(this.scalarField, hi, hj, hk);
+ const v0 = sfg(sf, li, lj, lk);
+ const v1 = sfg(sf, hi, hj, hk);
const t = (this.isoLevel - v0) / (v0 - v1);
- const id = this.builder.addVertex(li + t * (li - hi), lj + t * (lj - hj), lk + t * (lk - hk));
+ const id = this.builder.addVertex(
+ li + t * (li - hi),
+ lj + t * (lj - hj),
+ lk + t * (lk - hk)
+ );
this.verticesOnEdges[edgeId] = id + 1;
+ const n0x = sfg(sf, Math.max(0, li - 1), lj, lk) - sfg(sf, Math.min(this.nX - 1, li + 1), lj, lk)
+ const n0y = sfg(sf, li, Math.max(0, lj - 1), lk) - sfg(sf, li, Math.min(this.nY - 1, lj + 1), lk)
+ const n0z = sfg(sf, li, lj, Math.max(0, lk - 1)) - sfg(sf, li, lj, Math.min(this.nZ, lk + 1))
+
+ const n1x = sfg(sf, Math.max(0, hi - 1), hj, hk) - sfg(sf, Math.min(this.nX - 1, hi + 1), hj, hk)
+ const n1y = sfg(sf, hi, Math.max(0, hj - 1), hk) - sfg(sf, hi, Math.min(this.nY - 1, hj + 1), hk)
+ const n1z = sfg(sf, hi, hj, Math.max(0, hk - 1)) - sfg(sf, hi, hj, Math.min(this.nZ - 1, hk + 1))
+
+ this.builder.addNormal(
+ n0x + t * (n0x - n1x),
+ n0y + t * (n0y - n1y),
+ n0z + t * (n0z - n1z)
+ )
+
if (this.idField) {
const u = this.idFieldGet!(this.idField, li, lj, lk);
const v = this.idFieldGet!(this.idField, hi, hj, hk)
diff --git a/src/mol-geo/util/marching-cubes/builder.ts b/src/mol-geo/util/marching-cubes/builder.ts
index be7abebb915efd13d1d86f11e3ce866633b09263..8d78d9f32614947573d734bc390fee08b05e9b9d 100644
--- a/src/mol-geo/util/marching-cubes/builder.ts
+++ b/src/mol-geo/util/marching-cubes/builder.ts
@@ -7,7 +7,7 @@
*/
import { ChunkedArray } from '../../../mol-data/util';
-import { ValueCell } from 'mol-util';
+import { ValueCell, noop } from 'mol-util';
import { Mesh } from '../../geometry/mesh/mesh';
import { AllowedContours } from './tables';
import { LinesBuilder } from '../../geometry/lines/lines-builder';
@@ -15,6 +15,7 @@ import { Lines } from '../../geometry/lines/lines';
export interface MarchinCubesBuilder<T> {
addVertex(x: number, y: number, z: number): number
+ addNormal(x: number, y: number, z: number): void
addGroup(group: number): void
addTriangle(vertList: number[], a: number, b: number, c: number, edgeFilter: number): void
get(): T
@@ -24,6 +25,7 @@ export function MarchinCubesMeshBuilder(vertexChunkSize: number, mesh?: Mesh): M
const triangleChunkSize = Math.min(1 << 16, vertexChunkSize * 4)
const vertices = ChunkedArray.create(Float32Array, 3, vertexChunkSize, mesh && mesh.vertexBuffer.ref.value);
+ const normals = ChunkedArray.create(Float32Array, 3, vertexChunkSize, mesh && mesh.normalBuffer.ref.value);
const groups = ChunkedArray.create(Float32Array, 1, vertexChunkSize, mesh && mesh.groupBuffer.ref.value);
const indices = ChunkedArray.create(Uint32Array, 3, triangleChunkSize, mesh && mesh.indexBuffer.ref.value);
@@ -35,6 +37,9 @@ export function MarchinCubesMeshBuilder(vertexChunkSize: number, mesh?: Mesh): M
++vertexCount
return ChunkedArray.add3(vertices, x, y, z );
},
+ addNormal: (x: number, y: number, z: number) => {
+ ChunkedArray.add3(normals, x, y, z );
+ },
addGroup: (group: number) => {
ChunkedArray.add(groups, group);
},
@@ -44,6 +49,7 @@ export function MarchinCubesMeshBuilder(vertexChunkSize: number, mesh?: Mesh): M
},
get: () => {
const vb = ChunkedArray.compact(vertices, true) as Float32Array;
+ const nb = ChunkedArray.compact(normals, true) as Float32Array;
const ib = ChunkedArray.compact(indices, true) as Uint32Array;
const gb = ChunkedArray.compact(groups, true) as Float32Array;
@@ -54,8 +60,8 @@ export function MarchinCubesMeshBuilder(vertexChunkSize: number, mesh?: Mesh): M
vertexBuffer: mesh ? ValueCell.update(mesh.vertexBuffer, vb) : ValueCell.create(vb),
groupBuffer: mesh ? ValueCell.update(mesh.groupBuffer, gb) : ValueCell.create(gb),
indexBuffer: mesh ? ValueCell.update(mesh.indexBuffer, ib) : ValueCell.create(ib),
- normalBuffer: mesh ? mesh.normalBuffer : ValueCell.create(new Float32Array(0)),
- normalsComputed: false
+ normalBuffer: mesh ? ValueCell.update(mesh.normalBuffer, nb) : ValueCell.create(nb),
+ normalsComputed: true
}
}
}
@@ -72,6 +78,7 @@ export function MarchinCubesLinesBuilder(vertexChunkSize: number, lines?: Lines)
addVertex: (x: number, y: number, z: number) => {
return ChunkedArray.add3(vertices, x, y, z);
},
+ addNormal: () => noop,
addGroup: (group: number) => {
ChunkedArray.add(groups, group);
},
diff --git a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
index a538309b830c33b9806f3b58d3a80ee94906330d..d4253e03d599ae818313a955edfc85e5bc3ecb82 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
@@ -47,7 +47,6 @@ async function createGaussianSurfaceMesh(ctx: VisualContext, unit: Unit, structu
const surface = await computeMarchingCubesMesh(params, mesh).runAsChild(ctx.runtime)
Mesh.transformImmediate(surface, transform)
- Mesh.computeNormalsImmediate(surface)
Mesh.uniformTriangleGroup(surface)
return surface
diff --git a/src/mol-repr/structure/visual/molecular-surface-mesh.ts b/src/mol-repr/structure/visual/molecular-surface-mesh.ts
index 24c0e973052c5575d6598f285e0b8e90fd172983..aea6b6de911d54e3b67996e1cb028cf1c9881db8 100644
--- a/src/mol-repr/structure/visual/molecular-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/molecular-surface-mesh.ts
@@ -37,7 +37,6 @@ async function createMolecularSurfaceMesh(ctx: VisualContext, unit: Unit, struct
const surface = await computeMarchingCubesMesh(params, mesh).runAsChild(ctx.runtime)
Mesh.transformImmediate(surface, transform)
- Mesh.computeNormalsImmediate(surface)
Mesh.uniformTriangleGroup(surface)
return surface
diff --git a/src/mol-repr/volume/isosurface.ts b/src/mol-repr/volume/isosurface.ts
index 364e3c42e4afdeac974c990881cff75732d03c3d..224afe6779457f11d03b73c9a9e4806d41d0e752 100644
--- a/src/mol-repr/volume/isosurface.ts
+++ b/src/mol-repr/volume/isosurface.ts
@@ -78,7 +78,6 @@ export async function createVolumeIsosurfaceMesh(ctx: VisualContext, volume: Vol
const transform = VolumeData.getGridToCartesianTransform(volume);
ctx.runtime.update({ message: 'Transforming mesh...' });
Mesh.transformImmediate(surface, transform);
- Mesh.computeNormalsImmediate(surface)
return surface;
}