wip, ply-to-shape groupId mapping

src/mol-model-formats/shape/ply.ts

@@ -13,8 +13,9 @@ import { MeshBuilder } from 'mol-geo/geometry/mesh/mesh-builder';
 import { Mesh } from 'mol-geo/geometry/mesh/mesh';
 import { Shape } from 'mol-model/shape';
 import { ChunkedArray } from 'mol-data/util';
+import { arrayMax } from 'mol-util/array';
 
-async function getPlyMesh(ctx: RuntimeContext, vertex: PlyTable, face: PlyList, mesh?: Mesh) {
+async function getPlyMesh(ctx: RuntimeContext, vertex: PlyTable, face: PlyList, groupIds: ArrayLike<number>, mesh?: Mesh) {
     const builderState = MeshBuilder.createState(face.rowCount, face.rowCount, mesh)
     const { vertices, normals, indices, groups } = builderState
 
@@ -28,15 +29,12 @@ async function getPlyMesh(ctx: RuntimeContext, vertex: PlyTable, face: PlyList,
     const nz = vertex.getProperty('nz')
     if (!nx || !ny || !nz) throw new Error('missing normal properties')
 
-    const atomid = vertex.getProperty('atomid')
-    if (!atomid) throw new Error('missing atomid property')
-
     for (let i = 0, il = vertex.rowCount; i < il; ++i) {
         if (i % 10000 === 0 && ctx.shouldUpdate) await ctx.update({ current: i, max: il, message: `adding vertex ${i}` })
 
         ChunkedArray.add3(vertices, x.value(i), y.value(i), z.value(i))
         ChunkedArray.add3(normals, nx.value(i), ny.value(i), nz.value(i));
-        ChunkedArray.add(groups, atomid.value(i))
+        ChunkedArray.add(groups, groupIds[i])
     }
 
     for (let i = 0, il = face.rowCount; i < il; ++i) {
@@ -57,6 +55,11 @@ async function getShape(ctx: RuntimeContext, plyFile: PlyFile, props: {}, shape?
     const atomid = vertex.getProperty('atomid')
     if (!atomid) throw new Error('missing atomid property')
 
+    const groupIds = atomid.toArray({ array: Int32Array })
+    const maxGroupId = arrayMax(groupIds) // assumes uint group ids
+    const groupIdMap = new Uint32Array(maxGroupId + 1)
+    for (let i = 0, il = groupIds.length; i < il; ++i) groupIdMap[groupIds[i]] = i
+
     const red = vertex.getProperty('red')
     const green = vertex.getProperty('green')
     const blue = vertex.getProperty('blue')
@@ -65,15 +68,16 @@ async function getShape(ctx: RuntimeContext, plyFile: PlyFile, props: {}, shape?
     const face = plyFile.getElement('face') as PlyList
     if (!face) throw new Error('missing face element')
 
-    const mesh = await getPlyMesh(ctx, vertex, face, shape && shape.geometry)
+    const mesh = await getPlyMesh(ctx, vertex, face, groupIds, shape && shape.geometry)
     return shape || Shape.create(
         'test', plyFile, mesh,
         (groupId: number) => {
-            return Color.fromRgb(red.value(groupId), green.value(groupId), blue.value(groupId))
+            const idx = groupIdMap[groupId]
+            return Color.fromRgb(red.value(idx), green.value(idx), blue.value(idx))
         },
         () => 1, // size: constant
         (groupId: number) => {
-            return atomid.value(groupId).toString()
+            return atomid.value(groupIdMap[groupId]).toString()
         }
     )
 }

src/mol-util/array.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>
  */
@@ -9,7 +9,7 @@ import { NumberArray } from './type-helpers';
 // TODO move to mol-math as Vector???
 
 /** Get the maximum value in an array */
-export function arrayMax(array: NumberArray) {
+export function arrayMax(array: ArrayLike<number>) {
     let max = -Infinity
     for (let i = 0, il = array.length; i < il; ++i) {
         if (array[i] > max) max = array[i]
@@ -18,7 +18,7 @@ export function arrayMax(array: NumberArray) {
 }
 
 /** Get the minimum value in an array */
-export function arrayMin(array: NumberArray) {
+export function arrayMin(array: ArrayLike<number>) {
     let min = Infinity
     for (let i = 0, il = array.length; i < il; ++i) {
         if (array[i] < min) min = array[i]
@@ -27,7 +27,7 @@ export function arrayMin(array: NumberArray) {
 }
 
 /** Get the sum of values in an array */
-export function arraySum(array: NumberArray, stride = 1, offset = 0) {
+export function arraySum(array: ArrayLike<number>, stride = 1, offset = 0) {
     const n = array.length
     let sum = 0
     for (let i = offset; i < n; i += stride) {
@@ -37,12 +37,12 @@ export function arraySum(array: NumberArray, stride = 1, offset = 0) {
 }
 
 /** Get the mean of values in an array */
-export function arrayMean(array: NumberArray, stride = 1, offset = 0) {
+export function arrayMean(array: ArrayLike<number>, stride = 1, offset = 0) {
     return arraySum(array, stride, offset) / (array.length / stride)
 }
 
 /** Get the root mean square of values in an array */
-export function arrayRms(array: NumberArray) {
+export function arrayRms(array: ArrayLike<number>) {
     const n = array.length
     let sumSq = 0
     for (let i = 0; i < n; ++i) {