From 8bdbe950759a70cd8847089e348ff33d208116b3 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Thu, 21 Mar 2019 14:11:51 -0700
Subject: [PATCH] ply provider params for use in plugin
---
src/mol-model-formats/shape/ply.ts | 86 ++++++++++++++-----
src/mol-model/shape/provider.ts | 1 +
src/mol-plugin/state/transforms/model.ts | 1 -
.../state/transforms/representation.ts | 4 +-
4 files changed, 66 insertions(+), 26 deletions(-)
diff --git a/src/mol-model-formats/shape/ply.ts b/src/mol-model-formats/shape/ply.ts
index 4eb687020..e5488ea98 100644
--- a/src/mol-model-formats/shape/ply.ts
+++ b/src/mol-model-formats/shape/ply.ts
@@ -13,10 +13,14 @@ 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';
+import { arrayMax, fillSerial } from 'mol-util/array';
+import { Column } from 'mol-data/db';
+import { ParamDefinition as PD } from 'mol-util/param-definition';
+
+// TODO support 'edge' and 'material' elements, see https://www.mathworks.com/help/vision/ug/the-ply-format.html
async function getPlyMesh(ctx: RuntimeContext, vertex: PlyTable, face: PlyList, groupIds: ArrayLike<number>, mesh?: Mesh) {
- const builderState = MeshBuilder.createState(face.rowCount, face.rowCount, mesh)
+ const builderState = MeshBuilder.createState(vertex.rowCount, vertex.rowCount / 4, mesh)
const { vertices, normals, indices, groups } = builderState
const x = vertex.getProperty('x')
@@ -27,7 +31,7 @@ async function getPlyMesh(ctx: RuntimeContext, vertex: PlyTable, face: PlyList,
const nx = vertex.getProperty('nx')
const ny = vertex.getProperty('ny')
const nz = vertex.getProperty('nz')
- if (!nx || !ny || !nz) throw new Error('missing normal properties')
+ if (!nx || !ny || !nz) throw new Error('missing normal properties') // TODO calculate normals when not provided
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}` })
@@ -46,53 +50,89 @@ async function getPlyMesh(ctx: RuntimeContext, vertex: PlyTable, face: PlyList,
return MeshBuilder.getMesh(builderState);
}
-async function getShape(ctx: RuntimeContext, plyFile: PlyFile, props: {}, shape?: Shape<Mesh>) {
- await ctx.update('async creation of shape from myData')
+function getGrouping(count: number, column?: Column<number>) {
+ const ids = column ? column.toArray({ array: Int32Array }) : fillSerial(new Uint32Array(count))
+ const maxId = arrayMax(ids) // assumes uint ids
+ const map = new Uint32Array(maxId + 1)
+ for (let i = 0, il = ids.length; i < il; ++i) map[ids[i]] = i
+ return { ids, map }
+}
- const vertex = plyFile.getElement('vertex') as PlyTable
- if (!vertex) throw new Error('missing vertex element')
+async function getShape(ctx: RuntimeContext, plyFile: PlyFile, props: PD.Values<PlyShapeParams>, shape?: Shape<Mesh>) {
+ await ctx.update('async creation of shape from ply file')
- const atomid = vertex.getProperty('atomid')
- if (!atomid) throw new Error('missing atomid property')
+ const { vertexProperties: vp } = props
- 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 vertex = plyFile.getElement('vertex') as PlyTable
+ if (!vertex) throw new Error('missing vertex element')
- const red = vertex.getProperty('red')
- const green = vertex.getProperty('green')
- const blue = vertex.getProperty('blue')
+ const red = vertex.getProperty(vp.red)
+ const green = vertex.getProperty(vp.green)
+ const blue = vertex.getProperty(vp.blue)
if (!red || !green || !blue) throw new Error('missing color properties')
const face = plyFile.getElement('face') as PlyList
if (!face) throw new Error('missing face element')
- const mesh = await getPlyMesh(ctx, vertex, face, groupIds, shape && shape.geometry)
- return shape || Shape.create(
+ const { ids, map } = getGrouping(vertex.rowCount, vertex.getProperty(vp.group))
+
+ const mesh = await getPlyMesh(ctx, vertex, face, ids, shape && shape.geometry)
+ return Shape.create(
'test', plyFile, mesh,
(groupId: number) => {
- const idx = groupIdMap[groupId]
+ const idx = map[groupId]
return Color.fromRgb(red.value(idx), green.value(idx), blue.value(idx))
},
() => 1, // size: constant
(groupId: number) => {
- return atomid.value(groupIdMap[groupId]).toString()
+ return ids[groupId].toString()
}
)
}
export const PlyShapeParams = {
- ...Mesh.Params
+ ...Mesh.Params,
+
+ vertexProperties: PD.Group({
+ group: PD.Select('' as string, [['', '']]),
+ red: PD.Select('red' as string, [['red', 'red']]),
+ green: PD.Select('green' as string, [['green', 'green']]),
+ blue: PD.Select('blue' as string, [['blue', 'blue']]),
+ }, { isExpanded: true }),
}
export type PlyShapeParams = typeof PlyShapeParams
+
+export function getPlyShapeParams(plyFile: PlyFile) {
+ const params = PD.clone(PlyShapeParams)
+ const vertex = plyFile.getElement('vertex') as PlyTable
+ if (vertex) {
+ const options: [string, string][] = [['', '']]
+ for (let i = 0, il = vertex.propertyNames.length; i < il; ++i) {
+ const name = vertex.propertyNames[i]
+ options.push([ name, name ])
+ }
+ const vp = params.vertexProperties.params;
+ (vp.group as PD.Select<string>).options = options;
+ (vp.red as PD.Select<string>).options = options;
+ (vp.green as PD.Select<string>).options = options;
+ (vp.blue as PD.Select<string>).options = options;
+
+ // TODO harcoded as convenience for data provided by MegaMol
+ if (vertex.propertyNames.includes('atomid')) {
+ vp.group.defaultValue = 'atomid'
+ params.vertexProperties.defaultValue.group = 'atomid'
+ }
+ }
+ return params
+}
+
export function shapeFromPly(source: PlyFile, params?: {}) {
- return Task.create<ShapeProvider<PlyFile, Mesh, PlyShapeParams>>('Parse Shape Data', async ctx => {
- console.log('source', source)
+ return Task.create<ShapeProvider<PlyFile, Mesh, PlyShapeParams>>('Shape Provider', async ctx => {
return {
label: 'Mesh',
data: source,
+ params: getPlyShapeParams(source),
getShape,
geometryUtils: Mesh.Utils
}
diff --git a/src/mol-model/shape/provider.ts b/src/mol-model/shape/provider.ts
index 2cd0950db..dea45e8ba 100644
--- a/src/mol-model/shape/provider.ts
+++ b/src/mol-model/shape/provider.ts
@@ -10,6 +10,7 @@ import { Geometry, GeometryUtils } from 'mol-geo/geometry/geometry';
export interface ShapeProvider<D, G extends Geometry, P extends Geometry.Params<G>> {
label: string
data: D
+ params: P
getShape: ShapeGetter<D, G, P>
geometryUtils: GeometryUtils<G>
}
\ No newline at end of file
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index 1a6158d7b..5f890882a 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -339,7 +339,6 @@ function updateStructureFromQuery(query: QueryFn<Sel>, src: Structure, obj: SO.M
return true;
}
-
namespace StructureComplexElement {
export type Types = 'atomic-sequence' | 'water' | 'atomic-het' | 'spheres'
}
diff --git a/src/mol-plugin/state/transforms/representation.ts b/src/mol-plugin/state/transforms/representation.ts
index 0b11a2870..0392341d7 100644
--- a/src/mol-plugin/state/transforms/representation.ts
+++ b/src/mol-plugin/state/transforms/representation.ts
@@ -484,7 +484,7 @@ const ShapeRepresentation3D = PluginStateTransform.BuiltIn({
from: SO.Shape.Provider,
to: SO.Shape.Representation3D,
params: (a, ctx: PluginContext) => {
- return a ? a.data.geometryUtils.Params : BaseGeometry.Params
+ return a ? a.data.params : BaseGeometry.Params
}
})({
canAutoUpdate() {
@@ -492,7 +492,7 @@ const ShapeRepresentation3D = PluginStateTransform.BuiltIn({
},
apply({ a, params }, plugin: PluginContext) {
return Task.create('Shape Representation', async ctx => {
- const props = { ...PD.getDefaultValues(a.data.geometryUtils.Params), params }
+ const props = { ...PD.getDefaultValues(a.data.params), params }
const repr = ShapeRepresentation(a.data.getShape, a.data.geometryUtils)
// TODO set initial state, repr.setState({})
await repr.createOrUpdate(props, a.data.data).runInContext(ctx);
--
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