diff --git a/src/apps/render-test/state.ts b/src/apps/render-test/state.ts
index aeaf9c4f135f4318c753efe8301ea8e29e04f3c8..4e6453fdc9f91a71229686cd67ef7d95fe3e0511 100644
--- a/src/apps/render-test/state.ts
+++ b/src/apps/render-test/state.ts
@@ -51,9 +51,9 @@ export default class State {
await Run(structPointRepr.create(struct), log, 100)
structPointRepr.renderObjects.forEach(viewer.add)
- // const structSpacefillRepr = StructureRepresentation(Spacefill)
- // await Run(structSpacefillRepr.create(struct, { detail: 2 }), log, 100)
- // structSpacefillRepr.renderObjects.forEach(viewer.add)
+ const structSpacefillRepr = StructureRepresentation(Spacefill)
+ await Run(structSpacefillRepr.create(struct, { detail: 2 }), log, 100)
+ structSpacefillRepr.renderObjects.forEach(viewer.add)
viewer.requestDraw()
console.log(viewer.stats)
diff --git a/src/mol-geo/color/data.ts b/src/mol-geo/color/data.ts
index 6e32d8d42d94ea7b1f058003e766526e03e1711e..3e98a815c43a27429fef9b8cbe209122d17eff92 100644
--- a/src/mol-geo/color/data.ts
+++ b/src/mol-geo/color/data.ts
@@ -105,5 +105,6 @@ export function createElementInstanceColor(props: ElementInstanceColorProps): El
/** Create color attribute or texture, depending on the mesh */
export function createAttributeOrElementColor(mesh: Mesh, props: AttributeColorProps) {
- return mesh.vertexCount < 4 * mesh.offsetCount ? createAttributeColor(props) : createElementColor(props)
+ // return mesh.vertexCount < 4 * mesh.offsetCount ? createAttributeColor(props) : createElementColor(props)
+ return createAttributeColor(props)
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/point.ts b/src/mol-geo/representation/structure/point.ts
index 7f187d1720a85741123053ea4375eaaad351a227..511bcd018025e1c6f141f8ed54d99304f48fbc6b 100644
--- a/src/mol-geo/representation/structure/point.ts
+++ b/src/mol-geo/representation/structure/point.ts
@@ -19,6 +19,7 @@ import { fillSerial } from 'mol-gl/renderable/util';
import { ColorScale } from '../../color/scale';
import { createUniformSize } from '../../size/data';
import { vdwSizeData } from '../../size/structure/vdw';
+import VertexMap from '../../shape/vertex-map';
export const DefaultPointProps = {
@@ -65,11 +66,12 @@ export default function Point(): UnitsRepresentation<PointProps> {
const size = vdwSizeData({
units,
elementGroup,
- offsetData: {
- primitiveCount: elementCount,
- offsetCount: elementCount + 1,
- offsets: fillSerial(new Uint32Array(elementCount + 1))
- }
+ vertexMap: VertexMap.create(
+ elementCount,
+ elementCount + 1,
+ fillSerial(new Uint32Array(elementCount)),
+ fillSerial(new Uint32Array(elementCount + 1))
+ )
})
console.log(size)
diff --git a/src/mol-geo/representation/structure/spacefill.ts b/src/mol-geo/representation/structure/spacefill.ts
index 39c206cf87be50dbcff62dd7565dacd9cd045463..9a38a8526a8a15b1e1d81b4af45fe0f54ba763e4 100644
--- a/src/mol-geo/representation/structure/spacefill.ts
+++ b/src/mol-geo/representation/structure/spacefill.ts
@@ -60,7 +60,6 @@ export default function Spacefill(): UnitsRepresentation<SpacefillProps> {
const mesh = meshBuilder.getMesh()
// console.log(mesh)
- if (!mesh.offsetBuffer.ref.value) return
const unitCount = units.length
const transformArray = new Float32Array(unitCount * 16)
@@ -100,7 +99,7 @@ export default function Spacefill(): UnitsRepresentation<SpacefillProps> {
instanceCount: unitCount,
indexCount: mesh.triangleCount,
- elementCount: mesh.offsetCount - 1,
+ elementCount: elementCount,
positionCount: mesh.vertexCount
})
renderObjects.push(spheres)
diff --git a/src/mol-geo/shape/mesh.ts b/src/mol-geo/shape/mesh.ts
index fce47eec05ff4ccd62b43378190e7771e2b00330..daab5862beadae5b31a7ac0388058dbd876ca65d 100644
--- a/src/mol-geo/shape/mesh.ts
+++ b/src/mol-geo/shape/mesh.ts
@@ -11,18 +11,24 @@ import Sphere from 'mol-math/geometry/sphere'
import { transformPositionArray } from '../util';
export interface Mesh {
+ /** Number of vertices in the mesh */
vertexCount: number,
+ /** Number of triangles in the mesh */
triangleCount: number,
- offsetCount: number,
+ /** Vertex buffer as array of xyz values wrapped in a value cell */
vertexBuffer: ValueCell<Float32Array>,
+ /** Index buffer as array of vertex index triplets wrapped in a value cell */
indexBuffer: ValueCell<Uint32Array>,
+ /** Normal buffer as array of xyz values for each vertex wrapped in a value cell */
normalBuffer: ValueCell<Float32Array | undefined>,
+ /** Id buffer as array of ids for each vertex wrapped in a value cell */
idBuffer: ValueCell<Float32Array | undefined>,
- offsetBuffer: ValueCell<Uint32Array | undefined>,
+
+ /** Flag indicating if normals are computed for the current set of vertices */
normalsComputed: boolean,
- vertexAnnotation?: ValueCell<ArrayLike<number>>
+ /** Bounding sphere of the mesh */
boundingSphere?: Sphere
}
@@ -84,6 +90,38 @@ export namespace Mesh {
mesh.normalsComputed = false;
// mesh.boundingSphere = void 0;
}
+
+ export function computeBoundingSphere(mesh: Mesh): Task<Mesh> {
+ return Task.create<Mesh>('Mesh (Compute Bounding Sphere)', async ctx => {
+ if (mesh.boundingSphere) {
+ return mesh;
+ }
+ await ctx.update('Computing bounding sphere...');
+
+ const vertices = mesh.vertexBuffer.ref.value;
+ let x = 0, y = 0, z = 0;
+ for (let i = 0, _c = vertices.length; i < _c; i += 3) {
+ x += vertices[i];
+ y += vertices[i + 1];
+ z += vertices[i + 2];
+ }
+ x /= mesh.vertexCount;
+ y /= mesh.vertexCount;
+ z /= mesh.vertexCount;
+ let r = 0;
+ for (let i = 0, _c = vertices.length; i < _c; i += 3) {
+ const dx = x - vertices[i];
+ const dy = y - vertices[i + 1];
+ const dz = z - vertices[i + 2];
+ r = Math.max(r, dx * dx + dy * dy + dz * dz);
+ }
+ mesh.boundingSphere = {
+ center: Vec3.create(x, y, z),
+ radius: Math.sqrt(r)
+ }
+ return mesh;
+ });
+ }
}
// function addVertex(src: Float32Array, i: number, dst: Float32Array, j: number) {
@@ -167,45 +205,4 @@ export namespace Mesh {
// if (iterCount === 0) return Computation.resolve(surface);
// return computation(async ctx => await laplacianSmoothComputation(ctx, surface, iterCount, (1.1 * vertexWeight) / 1.1));
-// }
-
- export function computeBoundingSphere(mesh: Mesh): Task<Mesh> {
- return Task.create<Mesh>('Mesh (Compute Bounding Sphere)', async ctx => {
- if (mesh.boundingSphere) {
- return mesh;
- }
- await ctx.update('Computing bounding sphere...');
-
- const vertices = mesh.vertexBuffer.ref.value;
- let x = 0, y = 0, z = 0;
- for (let i = 0, _c = vertices.length; i < _c; i += 3) {
- x += vertices[i];
- y += vertices[i + 1];
- z += vertices[i + 2];
- }
- x /= mesh.vertexCount;
- y /= mesh.vertexCount;
- z /= mesh.vertexCount;
- let r = 0;
- for (let i = 0, _c = vertices.length; i < _c; i += 3) {
- const dx = x - vertices[i];
- const dy = y - vertices[i + 1];
- const dz = z - vertices[i + 2];
- r = Math.max(r, dx * dx + dy * dy + dz * dz);
- }
- mesh.boundingSphere = {
- center: Vec3.create(x, y, z),
- radius: Math.sqrt(r)
- }
- return mesh;
- });
- }
-
-// export function transform(surface: Surface, t: number[]): Computation<Surface> {
-// return computation<Surface>(async ctx => {
-// ctx.updateProgress('Updating surface...');
-// transformImmediate(surface, t);
-// return surface;
-// });
-// }
-// }
\ No newline at end of file
+// }
\ No newline at end of file
diff --git a/src/mol-geo/shape/point.ts b/src/mol-geo/shape/point.ts
deleted file mode 100644
index 5720e664f898570e2de8b3e8808f8199df111f5f..0000000000000000000000000000000000000000
--- a/src/mol-geo/shape/point.ts
+++ /dev/null
@@ -1,17 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-
-export function countFromModel(model: any) {}
-export function positionFromModel(model: any, array: Float32Array, offset: number) {
-
-}
-export function colorFromModel(model: any, params: any, array: Float32Array, offset: number) {
-
-}
-export function sizeFromModel(model: any, params: any, array: Float32Array, offset: number) {
-
-}
\ No newline at end of file
diff --git a/src/mol-geo/shape/sphere.ts b/src/mol-geo/shape/sphere.ts
deleted file mode 100644
index 54cd72a4b8ba4dcf581d87842432de530588078b..0000000000000000000000000000000000000000
--- a/src/mol-geo/shape/sphere.ts
+++ /dev/null
@@ -1,5 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
diff --git a/src/mol-geo/shape/vertex-map.ts b/src/mol-geo/shape/vertex-map.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e21f0bf00456dc3ee61ee6572991f3c5b36c2f18
--- /dev/null
+++ b/src/mol-geo/shape/vertex-map.ts
@@ -0,0 +1,42 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Mesh } from './mesh';
+
+/** Mapping between vertices and ids */
+interface VertexMap {
+ idCount: number,
+ offsetCount: number,
+ ids: Helpers.NumberArray | undefined
+ offsets: Helpers.NumberArray,
+}
+
+function createOffsets(ids: Helpers.NumberArray | undefined) {
+ return []
+}
+
+namespace VertexMap {
+ export function create(idCount: number, offsetCount: number, ids: Helpers.NumberArray | undefined, offsets: Helpers.NumberArray): VertexMap {
+ return {
+ idCount,
+ offsetCount,
+ ids,
+ offsets
+ }
+ }
+
+ export function fromMesh(mesh: Mesh) {
+ const ids = mesh.idBuffer.ref.value
+ const offsets = createOffsets(ids)
+ return create(mesh.vertexCount, offsets.length, ids, offsets)
+ }
+
+ export function rangeFromId (id: number, vertexMap: VertexMap) {
+ return [0, 0]
+ }
+}
+
+export default VertexMap
\ No newline at end of file
diff --git a/src/mol-geo/size/data.ts b/src/mol-geo/size/data.ts
index fe8be6a3a7fbc2f88a87a29d2c2a11c6d3cd5765..a05726b17e76cdd1d0631db82b516f5526d8e120 100644
--- a/src/mol-geo/size/data.ts
+++ b/src/mol-geo/size/data.ts
@@ -5,17 +5,11 @@
*/
import { ValueCell } from 'mol-util';
+import VertexMap from '../shape/vertex-map';
export type UniformSize = { type: 'uniform', value: number }
export type AttributeSize = { type: 'attribute', value: ValueCell<Float32Array> }
export type SizeData = UniformSize | AttributeSize
-
-export interface OffsetData {
- primitiveCount: number,
- offsetCount: number,
- offsets: Uint32Array
-}
-
export interface UniformSizeProps {
value: number
}
@@ -27,18 +21,17 @@ export function createUniformSize(props: UniformSizeProps): UniformSize {
export interface AttributeSizeProps {
sizeFn: (elementIdx: number) => number
- offsetData: OffsetData
+ vertexMap: VertexMap
}
/** Creates size attribute with size for each element (i.e. shared across indtances/units) */
export function createAttributeSize(props: AttributeSizeProps): AttributeSize {
- const { sizeFn, offsetData } = props
- const { primitiveCount, offsetCount, offsets } = offsetData
- const sizes = new Float32Array(primitiveCount);
- const _offsets = offsets // .ref.value
+ const { sizeFn, vertexMap } = props
+ const { idCount, offsetCount, offsets } = vertexMap
+ const sizes = new Float32Array(idCount);
for (let i = 0, il = offsetCount - 1; i < il; ++i) {
- const start = _offsets[i]
- const end = _offsets[i + 1]
+ const start = offsets[i]
+ const end = offsets[i + 1]
const size = sizeFn(i)
for (let i = start, il = end; i < il; ++i) {
sizes[i] = size
diff --git a/src/mol-geo/size/structure/index.ts b/src/mol-geo/size/structure/index.ts
index 20e1a15617b1084aee91f124377a32cb576c7dc8..4ec3dee79cd5467e969fe3cc1679661991cc9274 100644
--- a/src/mol-geo/size/structure/index.ts
+++ b/src/mol-geo/size/structure/index.ts
@@ -5,10 +5,10 @@
*/
import { ElementGroup, Unit } from 'mol-model/structure';
-import { OffsetData } from '../data';
+import VertexMap from '../../shape/vertex-map';
export interface StructureSizeDataProps {
units: ReadonlyArray<Unit>,
elementGroup: ElementGroup,
- offsetData: OffsetData
+ vertexMap: VertexMap
}
\ No newline at end of file
diff --git a/src/mol-geo/size/structure/vdw.ts b/src/mol-geo/size/structure/vdw.ts
index dd4e230b93e5a0d772064e6a00808abd118fde58..522033493e26bcca88abab4cdfdfb8c57792fec1 100644
--- a/src/mol-geo/size/structure/vdw.ts
+++ b/src/mol-geo/size/structure/vdw.ts
@@ -10,13 +10,13 @@ import { StructureSizeDataProps } from '.';
import { createAttributeSize } from '../data';
export function vdwSizeData(props: StructureSizeDataProps) {
- const { units, elementGroup, offsetData } = props
+ const { units, elementGroup, vertexMap } = props
const { type_symbol } = units[0].model.hierarchy.atoms
return createAttributeSize({
sizeFn: (elementIdx: number) => {
const e = OrderedSet.getAt(elementGroup.elements, elementIdx)
return VdwRadius(type_symbol.value(e))
},
- offsetData
+ vertexMap
})
}
\ No newline at end of file
diff --git a/src/mol-geo/util/marching-cubes/algorithm.ts b/src/mol-geo/util/marching-cubes/algorithm.ts
index 015f7f4db104d0fc5a9defef176264e46e62934f..25b266773ce26c0afd7a22332083f915f63aa913 100644
--- a/src/mol-geo/util/marching-cubes/algorithm.ts
+++ b/src/mol-geo/util/marching-cubes/algorithm.ts
@@ -21,7 +21,7 @@ export interface MarchingCubesParameters {
bottomLeft?: ArrayLike<number>,
topRight?: ArrayLike<number>,
- annotationField?: Tensor,
+ idField?: Tensor,
oldSurface?: Mesh
}
@@ -73,20 +73,17 @@ class MarchingCubesComputation {
const os = this.parameters.oldSurface
- let ret: Mesh = {
+ const ret: Mesh = {
vertexCount: this.state.vertexCount,
triangleCount: this.state.triangleCount,
- offsetCount: 0,
vertexBuffer: os ? ValueCell.update(os.vertexBuffer, vb) : ValueCell.create(vb),
indexBuffer: os ? ValueCell.update(os.indexBuffer, ib) : ValueCell.create(ib),
normalBuffer: os ? os.normalBuffer : ValueCell.create(void 0),
- idBuffer: os ? os.idBuffer : ValueCell.create(void 0),
- offsetBuffer: os ? os.offsetBuffer : ValueCell.create(void 0),
- vertexAnnotation: this.state.annotate
- ? os && os.vertexAnnotation
- ? ValueCell.update(os.vertexAnnotation, ChunkedArray.compact(this.state.annotationBuffer))
- : ValueCell.create(ChunkedArray.compact(this.state.annotationBuffer))
- : void 0,
+ idBuffer: this.state.assignIds
+ ? os && os.idBuffer
+ ? ValueCell.update(os.idBuffer, ChunkedArray.compact(this.state.idBuffer) as Float32Array)
+ : ValueCell.create(ChunkedArray.compact(this.state.idBuffer) as Float32Array)
+ : ValueCell.create(void 0),
normalsComputed: false
}
@@ -124,9 +121,9 @@ class MarchingCubesState {
isoLevel: number;
scalarFieldGet: Tensor.Space['get'];
scalarField: Tensor.Data;
- annotationFieldGet?: Tensor.Space['get'];
- annotationField?: Tensor.Data;
- annotate: boolean;
+ idFieldGet?: Tensor.Space['get'];
+ idField?: Tensor.Data;
+ assignIds: boolean;
// two layers of vertex indices. Each vertex has 3 edges associated.
verticesOnEdges: Int32Array;
@@ -134,7 +131,7 @@ class MarchingCubesState {
i: number = 0; j: number = 0; k: number = 0;
vertexBuffer: ChunkedArray<number, 3>;
- annotationBuffer: ChunkedArray<number, 1>;
+ idBuffer: ChunkedArray<number, 1>;
triangleBuffer: ChunkedArray<number, 3>;
vertexCount = 0;
triangleCount = 0;
@@ -164,7 +161,8 @@ class MarchingCubesState {
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), v1 = this.scalarFieldGet(this.scalarField, hi, hj, hk);
+ const v0 = this.scalarFieldGet(this.scalarField, li, lj, lk);
+ const v1 = this.scalarFieldGet(this.scalarField, hi, hj, hk);
const t = (this.isoLevel - v0) / (v0 - v1);
const id = ChunkedArray.add3(
@@ -175,12 +173,12 @@ class MarchingCubesState {
this.verticesOnEdges[edgeId] = id + 1;
- if (this.annotate) {
- const u = this.annotationFieldGet!(this.annotationField!, li, lj, lk);
- const v = this.annotationFieldGet!(this.annotationField!, hi, hj, hk)
+ if (this.assignIds) {
+ const u = this.idFieldGet!(this.idField!, li, lj, lk);
+ const v = this.idFieldGet!(this.idField!, hi, hj, hk)
let a = t < 0.5 ? u : v;
if (a < 0) a = t < 0.5 ? v : u;
- ChunkedArray.add(this.annotationBuffer, a);
+ ChunkedArray.add(this.idBuffer, a);
}
this.vertexCount++;
@@ -194,9 +192,9 @@ class MarchingCubesState {
this.isoLevel = params.isoLevel;
this.scalarFieldGet = params.scalarField.space.get;
this.scalarField = params.scalarField.data;
- if (params.annotationField) {
- this.annotationField = params.annotationField.data;
- this.annotationFieldGet = params.annotationField.space.get;
+ if (params.idField) {
+ this.idField = params.idField.data;
+ this.idFieldGet = params.idField.space.get;
}
let dX = params.topRight![0] - params.bottomLeft![0], dY = params.topRight![1] - params.bottomLeft![1], dZ = params.topRight![2] - params.bottomLeft![2],
@@ -208,8 +206,8 @@ class MarchingCubesState {
this.triangleBuffer = ChunkedArray.create(Uint32Array, 3, triangleBufferSize,
params.oldSurface && params.oldSurface.indexBuffer.ref.value);
- this.annotate = !!params.annotationField;
- if (this.annotate) this.annotationBuffer = ChunkedArray.create(Int32Array, 1, vertexBufferSize);
+ this.assignIds = !!params.idField;
+ if (this.assignIds) this.idBuffer = ChunkedArray.create(Int32Array, 1, vertexBufferSize);
// two layers of vertex indices. Each vertex has 3 edges associated.
this.verticesOnEdges = new Int32Array(3 * this.nX * this.nY * 2);