wip, geo

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)

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

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)
 

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)

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

src/mol-geo/shape/point.ts

-/**
- * 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

src/mol-geo/shape/sphere.ts

-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */

src/mol-geo/shape/vertex-map.ts

+/**
+ * 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

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

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

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

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);