TmMolStar/src/mol-geo/geometry/mesh/mesh.ts

/**
 * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 * @author David Sehnal <david.sehnal@gmail.com>
 */

import { ValueCell } from '../../../mol-util'
import { Vec3, Mat4, Mat3 } from '../../../mol-math/linear-algebra'
import { Sphere3D } from '../../../mol-math/geometry'
import { transformPositionArray,/* , transformDirectionArray, getNormalMatrix */
transformDirectionArray} from '../../util';
import { GeometryUtils } from '../geometry';
import { createMarkers } from '../marker-data';
import { TransformData } from '../transform-data';
import { LocationIterator } from '../../util/location-iterator';
import { createColors } from '../color-data';
import { ChunkedArray, hashFnv32a } from '../../../mol-data/util';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { calculateInvariantBoundingSphere, calculateTransformBoundingSphere } from '../../../mol-gl/renderable/util';
import { Theme } from '../../../mol-theme/theme';
import { MeshValues } from '../../../mol-gl/renderable/mesh';
import { Color } from '../../../mol-util/color';
import { BaseGeometry } from '../base';
import { createEmptyOverpaint } from '../overpaint-data';
import { createEmptyTransparency } from '../transparency-data';

export interface Mesh {
    readonly kind: 'mesh',

    /** Number of vertices in the mesh */
    vertexCount: number,
    /** Number of triangles in the mesh */
    triangleCount: number,

    /** Vertex buffer as array of xyz values wrapped in a value cell */
    readonly vertexBuffer: ValueCell<Float32Array>,
    /** Index buffer as array of vertex index triplets wrapped in a value cell */
    readonly indexBuffer: ValueCell<Uint32Array>,
    /** Normal buffer as array of xyz values for each vertex wrapped in a value cell */
    readonly normalBuffer: ValueCell<Float32Array>,
    /** Group buffer as array of group ids for each vertex wrapped in a value cell */
    readonly groupBuffer: ValueCell<Float32Array>,

    /** Bounding sphere of the mesh */
    readonly boundingSphere: Sphere3D
}

export namespace Mesh {
    export function create(vertices: Float32Array, indices: Uint32Array, normals: Float32Array, groups: Float32Array, vertexCount: number, triangleCount: number, mesh?: Mesh): Mesh {
        return mesh ?
            update(vertices, indices, normals, groups, vertexCount, triangleCount, mesh) :
            fromArrays(vertices, indices, normals, groups, vertexCount, triangleCount)
    }

    export function createEmpty(mesh?: Mesh): Mesh {
        const vb = mesh ? mesh.vertexBuffer.ref.value : new Float32Array(0)
        const ib = mesh ? mesh.indexBuffer.ref.value : new Uint32Array(0)
        const nb = mesh ? mesh.normalBuffer.ref.value : new Float32Array(0)
        const gb = mesh ? mesh.groupBuffer.ref.value : new Float32Array(0)
        return create(vb, ib, nb, gb, 0, 0, mesh)
    }

    function hashCode(mesh: Mesh) {
        return hashFnv32a([
            mesh.vertexCount, mesh.triangleCount,
            mesh.vertexBuffer.ref.version, mesh.indexBuffer.ref.version,
            mesh.normalBuffer.ref.version, mesh.groupBuffer.ref.version
        ])
    }

    function fromArrays(vertices: Float32Array, indices: Uint32Array, normals: Float32Array, groups: Float32Array, vertexCount: number, triangleCount: number): Mesh {

        const boundingSphere = Sphere3D()
        let currentHash = -1

        const mesh = {
            kind: 'mesh' as const,
            vertexCount,
            triangleCount,
            vertexBuffer: ValueCell.create(vertices),
            indexBuffer: ValueCell.create(indices),
            normalBuffer: ValueCell.create(normals),
            groupBuffer: ValueCell.create(groups),
            get boundingSphere() {
                const newHash = hashCode(mesh)
                if (newHash !== currentHash) {
                    const b = calculateInvariantBoundingSphere(mesh.vertexBuffer.ref.value, mesh.vertexCount, 1)
                    Sphere3D.copy(boundingSphere, b)
                    currentHash = newHash
                }
                return boundingSphere
            },
        }
        return mesh
    }

    function update(vertices: Float32Array, indices: Uint32Array, normals: Float32Array, groups: Float32Array, vertexCount: number, triangleCount: number, mesh: Mesh) {
        mesh.vertexCount = vertexCount
        mesh.triangleCount = triangleCount
        ValueCell.update(mesh.vertexBuffer, vertices)
        ValueCell.update(mesh.indexBuffer, indices)
        ValueCell.update(mesh.normalBuffer, normals)
        ValueCell.update(mesh.groupBuffer, groups)
        return mesh
    }

    export function computeNormals(mesh: Mesh) {
        const normals = mesh.normalBuffer.ref.value.length >= mesh.vertexCount * 3
            ? mesh.normalBuffer.ref.value : new Float32Array(mesh.vertexBuffer.ref.value.length);

        const v = mesh.vertexBuffer.ref.value, triangles = mesh.indexBuffer.ref.value;

        if (normals === mesh.normalBuffer.ref.value) {
            for (let i = 0, ii = 3 * mesh.vertexCount; i < ii; i += 3) {
                normals[i] = 0; normals[i + 1] = 0; normals[i + 2] = 0;
            }
        }

        const x = Vec3.zero(), y = Vec3.zero(), z = Vec3.zero(), d1 = Vec3.zero(), d2 = Vec3.zero(), n = Vec3.zero();
        for (let i = 0, ii = 3 * mesh.triangleCount; i < ii; i += 3) {
            const a = 3 * triangles[i], b = 3 * triangles[i + 1], c = 3 * triangles[i + 2];

            Vec3.fromArray(x, v, a);
            Vec3.fromArray(y, v, b);
            Vec3.fromArray(z, v, c);
            Vec3.sub(d1, z, y);
            Vec3.sub(d2, x, y);
            Vec3.cross(n, d1, d2);

            normals[a] += n[0]; normals[a + 1] += n[1]; normals[a + 2] += n[2];
            normals[b] += n[0]; normals[b + 1] += n[1]; normals[b + 2] += n[2];
            normals[c] += n[0]; normals[c + 1] += n[1]; normals[c + 2] += n[2];
        }

        for (let i = 0, ii = 3 * mesh.vertexCount; i < ii; i += 3) {
            const nx = normals[i];
            const ny = normals[i + 1];
            const nz = normals[i + 2];
            const f = 1.0 / Math.sqrt(nx * nx + ny * ny + nz * nz);
            normals[i] *= f; normals[i + 1] *= f; normals[i + 2] *= f;
        }
        ValueCell.update(mesh.normalBuffer, normals);
    }

    export function checkForDuplicateVertices(mesh: Mesh, fractionDigits = 3) {
        const v = mesh.vertexBuffer.ref.value

        const map = new Map<string, number>()
        const hash = (v: Vec3, d: number) => `${v[0].toFixed(d)}|${v[1].toFixed(d)}|${v[2].toFixed(d)}`
        let duplicates = 0

        const a = Vec3.zero()
        for (let i = 0, il = mesh.vertexCount; i < il; ++i) {
            Vec3.fromArray(a, v, i * 3)
            const k = hash(a, fractionDigits)
            const count = map.get(k)
            if (count !== undefined) {
                duplicates += 1
                map.set(k, count + 1)
            } else {
                map.set(k, 1)
            }
        }
        return duplicates
    }

    const tmpMat3 = Mat3.zero()
    export function transform(mesh: Mesh, t: Mat4) {
        const v = mesh.vertexBuffer.ref.value
        transformPositionArray(t, v, 0, mesh.vertexCount)
        if (!Mat4.isTranslationAndUniformScaling(t)) {
            const n = Mat3.directionTransform(tmpMat3, t)
            transformDirectionArray(n, mesh.normalBuffer.ref.value, 0, mesh.vertexCount)
        }
        ValueCell.update(mesh.vertexBuffer, v);
    }

    /**
     * Ensure that each vertices of each triangle have the same group id.
     * Note that normals are copied over and can't be re-created from the new mesh.
     */
    export function uniformTriangleGroup(mesh: Mesh, splitTriangles = true) {
        const { indexBuffer, vertexBuffer, groupBuffer, normalBuffer, triangleCount, vertexCount } = mesh
        const ib = indexBuffer.ref.value
        const vb = vertexBuffer.ref.value
        const gb = groupBuffer.ref.value
        const nb = normalBuffer.ref.value

        // new
        const index = ChunkedArray.create(Uint32Array, 3, 1024, triangleCount)

        // re-use
        const vertex = ChunkedArray.create(Float32Array, 3, 1024, vb)
        vertex.currentIndex = vertexCount * 3
        vertex.elementCount = vertexCount
        const normal = ChunkedArray.create(Float32Array, 3, 1024, nb)
        normal.currentIndex = vertexCount * 3
        normal.elementCount = vertexCount
        const group = ChunkedArray.create(Float32Array, 1, 1024, gb)
        group.currentIndex = vertexCount
        group.elementCount = vertexCount

        const vi = Vec3.zero()
        const vj = Vec3.zero()
        const vk = Vec3.zero()
        const ni = Vec3.zero()
        const nj = Vec3.zero()
        const nk = Vec3.zero()

        function add(i: number) {
            Vec3.fromArray(vi, vb, i * 3)
            Vec3.fromArray(ni, nb, i * 3)
            ChunkedArray.add3(vertex, vi[0], vi[1], vi[2])
            ChunkedArray.add3(normal, ni[0], ni[1], ni[2])
        }

        function addMid(i: number, j: number) {
            Vec3.fromArray(vi, vb, i * 3)
            Vec3.fromArray(vj, vb, j * 3)
            Vec3.scale(vi, Vec3.add(vi, vi, vj), 0.5)
            Vec3.fromArray(ni, nb, i * 3)
            Vec3.fromArray(nj, nb, j * 3)
            Vec3.scale(ni, Vec3.add(ni, ni, nj), 0.5)
            ChunkedArray.add3(vertex, vi[0], vi[1], vi[2])
            ChunkedArray.add3(normal, ni[0], ni[1], ni[2])
        }

        function addCenter(i: number, j: number, k: number) {
            Vec3.fromArray(vi, vb, i * 3)
            Vec3.fromArray(vj, vb, j * 3)
            Vec3.fromArray(vk, vb, k * 3)
            Vec3.scale(vi, Vec3.add(vi, Vec3.add(vi, vi, vj), vk), 1/3)
            Vec3.fromArray(ni, nb, i * 3)
            Vec3.fromArray(nj, nb, j * 3)
            Vec3.fromArray(nk, nb, k * 3)
            Vec3.scale(ni, Vec3.add(ni, Vec3.add(ni, ni, nj), nk), 1/3)
            ChunkedArray.add3(vertex, vi[0], vi[1], vi[2])
            ChunkedArray.add3(normal, ni[0], ni[1], ni[2])
        }

        function split2(i0: number, i1: number, i2: number, g0: number, g1: number) {
            ++newTriangleCount
            add(i0); addMid(i0, i1); addMid(i0, i2);
            ChunkedArray.add3(index, newVertexCount, newVertexCount + 1, newVertexCount + 2)
            for (let j = 0; j < 3; ++j) ChunkedArray.add(group, g0)
            newVertexCount += 3

            newTriangleCount += 2
            add(i1); add(i2); addMid(i0, i1); addMid(i0, i2);
            ChunkedArray.add3(index, newVertexCount, newVertexCount + 1, newVertexCount + 3)
            ChunkedArray.add3(index, newVertexCount, newVertexCount + 3, newVertexCount + 2)
            for (let j = 0; j < 4; ++j) ChunkedArray.add(group, g1)
            newVertexCount += 4
        }

        let newVertexCount = vertexCount
        let newTriangleCount = 0

        if (splitTriangles) {
            for (let i = 0, il = triangleCount; i < il; ++i) {
                const i0 = ib[i * 3], i1 = ib[i * 3 + 1], i2 = ib[i * 3 + 2]
                const g0 = gb[i0], g1 = gb[i1], g2 = gb[i2]
                if (g0 === g1 && g0 === g2) {
                    ++newTriangleCount
                    ChunkedArray.add3(index, i0, i1, i2)
                } else if (g0 === g1) {
                    split2(i2, i0, i1, g2, g0)
                } else if (g0 === g2) {
                    split2(i1, i2, i0, g1, g2)
                } else if (g1 === g2) {
                    split2(i0, i1, i2, g0, g1)
                } else {
                    newTriangleCount += 2
                    add(i0); addMid(i0, i1); addMid(i0, i2); addCenter(i0, i1, i2);
                    ChunkedArray.add3(index, newVertexCount, newVertexCount + 1, newVertexCount + 3)
                    ChunkedArray.add3(index, newVertexCount, newVertexCount + 3, newVertexCount + 2)
                    for (let j = 0; j < 4; ++j) ChunkedArray.add(group, g0)
                    newVertexCount += 4

                    newTriangleCount += 2
                    add(i1); addMid(i1, i2); addMid(i1, i0); addCenter(i0, i1, i2);
                    ChunkedArray.add3(index, newVertexCount, newVertexCount + 1, newVertexCount + 3)
                    ChunkedArray.add3(index, newVertexCount, newVertexCount + 3, newVertexCount + 2)
                    for (let j = 0; j < 4; ++j) ChunkedArray.add(group, g1)
                    newVertexCount += 4

                    newTriangleCount += 2
                    add(i2); addMid(i2, i1); addMid(i2, i0); addCenter(i0, i1, i2);
                    ChunkedArray.add3(index, newVertexCount + 3, newVertexCount + 1, newVertexCount)
                    ChunkedArray.add3(index, newVertexCount + 2, newVertexCount + 3, newVertexCount)
                    for (let j = 0; j < 4; ++j) ChunkedArray.add(group, g2)
                    newVertexCount += 4
                }
            }
        } else {
            for (let i = 0, il = triangleCount; i < il; ++i) {
                const i0 = ib[i * 3], i1 = ib[i * 3 + 1], i2 = ib[i * 3 + 2]
                const g0 = gb[i0], g1 = gb[i1], g2 = gb[i2]
                if (g0 !== g1 || g0 !== g2) {
                    ++newTriangleCount
                    add(i0); add(i1); add(i2)
                    ChunkedArray.add3(index, newVertexCount, newVertexCount + 1, newVertexCount + 2)
                    const g = g1 === g2 ? g1 : g0
                    for (let j = 0; j < 3; ++j) ChunkedArray.add(group, g)
                    newVertexCount += 3
                } else {
                    ++newTriangleCount
                    ChunkedArray.add3(index, i0, i1, i2)
                }
            }
        }

        const newIb = ChunkedArray.compact(index)
        const newVb = ChunkedArray.compact(vertex)
        const newNb = ChunkedArray.compact(normal)
        const newGb = ChunkedArray.compact(group)

        mesh.vertexCount = newVertexCount
        mesh.triangleCount = newTriangleCount

        ValueCell.update(vertexBuffer, newVb) as ValueCell<Float32Array>
        ValueCell.update(groupBuffer, newGb) as ValueCell<Float32Array>
        ValueCell.update(indexBuffer, newIb) as ValueCell<Uint32Array>
        ValueCell.update(normalBuffer, newNb) as ValueCell<Float32Array>

        return mesh
    }

    //

    export const Params = {
        ...BaseGeometry.Params,
        doubleSided: PD.Boolean(false),
        flipSided: PD.Boolean(false),
        flatShaded: PD.Boolean(false),
        ignoreLight: PD.Boolean(false),
    }
    export type Params = typeof Params

    export const Utils: GeometryUtils<Mesh, Params> = {
        Params,
        createEmpty,
        createValues,
        createValuesSimple,
        updateValues,
        updateBoundingSphere,
        createRenderableState: BaseGeometry.createRenderableState,
        updateRenderableState: BaseGeometry.updateRenderableState
    }

    function createValues(mesh: Mesh, transform: TransformData, locationIt: LocationIterator, theme: Theme, props: PD.Values<Params>): MeshValues {
        const { instanceCount, groupCount } = locationIt
        if (instanceCount !== transform.instanceCount.ref.value) {
            throw new Error('instanceCount values in TransformData and LocationIterator differ')
        }

        const color = createColors(locationIt, theme.color)
        const marker = createMarkers(instanceCount * groupCount)
        const overpaint = createEmptyOverpaint()
        const transparency = createEmptyTransparency()

        const counts = { drawCount: mesh.triangleCount * 3, groupCount, instanceCount }

        const invariantBoundingSphere = Sphere3D.clone(mesh.boundingSphere)
        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount)

        return {
            aPosition: mesh.vertexBuffer,
            aNormal: mesh.normalBuffer,
            aGroup: mesh.groupBuffer,
            elements: mesh.indexBuffer,
            boundingSphere: ValueCell.create(boundingSphere),
            invariantBoundingSphere: ValueCell.create(invariantBoundingSphere),
            ...color,
            ...marker,
            ...overpaint,
            ...transparency,
            ...transform,

            ...BaseGeometry.createValues(props, counts),
            dDoubleSided: ValueCell.create(props.doubleSided),
            dFlatShaded: ValueCell.create(props.flatShaded),
            dFlipSided: ValueCell.create(props.flipSided),
            dIgnoreLight: ValueCell.create(props.ignoreLight),
        }
    }

    function createValuesSimple(mesh: Mesh, props: Partial<PD.Values<Params>>, colorValue: Color, sizeValue: number, transform?: TransformData) {
        const s = BaseGeometry.createSimple(colorValue, sizeValue, transform)
        const p = { ...PD.getDefaultValues(Params), ...props }
        return createValues(mesh, s.transform, s.locationIterator, s.theme, p)
    }

    function updateValues(values: MeshValues, props: PD.Values<Params>) {
        BaseGeometry.updateValues(values, props)
        ValueCell.updateIfChanged(values.dDoubleSided, props.doubleSided)
        ValueCell.updateIfChanged(values.dFlatShaded, props.flatShaded)
        ValueCell.updateIfChanged(values.dFlipSided, props.flipSided)
        ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight)
    }

    function updateBoundingSphere(values: MeshValues, mesh: Mesh) {
        const invariantBoundingSphere = Sphere3D.clone(mesh.boundingSphere)
        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value)

        if (!Sphere3D.equals(boundingSphere, values.boundingSphere.ref.value)) {
            ValueCell.update(values.boundingSphere, boundingSphere)
        }
        if (!Sphere3D.equals(invariantBoundingSphere, values.invariantBoundingSphere.ref.value)) {
            ValueCell.update(values.invariantBoundingSphere, invariantBoundingSphere)
        }
    }
}