From a80088ec0f0fa6d89a4eecbcae21806408424ed3 Mon Sep 17 00:00:00 2001
From: MarcoSchaeferT <schaefer.marco.ms@web.de>
Date: Wed, 20 Feb 2019 09:51:46 +0100
Subject: [PATCH] parser is working + try to get mesh/shape
---
.../reader/ply/parse_data/data-model.ts | 7 +-
src/mol-io/reader/ply/parse_data/field.ts | 9 --
.../reader/ply/parse_data/ply_parser.ts | 41 ++++-
.../shape/formarts/ply/plyData_to_shape.ts | 143 ++++++++++++++++++
src/mol-plugin/state/actions/basic.ts | 12 +-
src/tests/browser/index.html | 51 ++++---
src/tests/browser/render-shape.ts | 2 +-
7 files changed, 219 insertions(+), 46 deletions(-)
delete mode 100644 src/mol-io/reader/ply/parse_data/field.ts
create mode 100644 src/mol-model/shape/formarts/ply/plyData_to_shape.ts
diff --git a/src/mol-io/reader/ply/parse_data/data-model.ts b/src/mol-io/reader/ply/parse_data/data-model.ts
index 36fdb6b1a..e02c061bb 100644
--- a/src/mol-io/reader/ply/parse_data/data-model.ts
+++ b/src/mol-io/reader/ply/parse_data/data-model.ts
@@ -24,11 +24,14 @@ export interface ply_form {
readonly initialHead: ReadonlyArray<string>,
readonly propertyNames: ReadonlyArray<string>,
readonly properties: number[],
+ readonly vertices: number[],
+ readonly colors: number[],
+ readonly normals: number[],
readonly faces: number[],
}
-export function PlyStructure(vertexCount: number, faceCount: number, propertyCount: number, initialHead: string[], propertyNames: string[], properties: number[], faces: number[]): ply_form {
- return {vertexCount, faceCount, propertyCount, initialHead: [...initialHead], propertyNames: [...propertyNames], properties: [...properties], faces: [...faces]};
+export function PlyStructure(vertexCount: number, faceCount: number, propertyCount: number, initialHead: string[], propertyNames: string[], properties: number[], vertices: number[], colors: number[], normals: number[], faces: number[]): ply_form {
+ return {vertexCount, faceCount, propertyCount, initialHead: [...initialHead], propertyNames: [...propertyNames], properties: [...properties], vertices: [...vertices], colors: [...colors], normals: [...normals], faces: [...faces]};
}
export type PlyColumns = { [name: string]: PlyColumn }
diff --git a/src/mol-io/reader/ply/parse_data/field.ts b/src/mol-io/reader/ply/parse_data/field.ts
deleted file mode 100644
index a86e45353..000000000
--- a/src/mol-io/reader/ply/parse_data/field.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import Field from '../../cif/text/field'
-
-export default Field
\ No newline at end of file
diff --git a/src/mol-io/reader/ply/parse_data/ply_parser.ts b/src/mol-io/reader/ply/parse_data/ply_parser.ts
index d2a42e49a..6729c87db 100644
--- a/src/mol-io/reader/ply/parse_data/ply_parser.ts
+++ b/src/mol-io/reader/ply/parse_data/ply_parser.ts
@@ -9,8 +9,15 @@ import { Tokens, TokenBuilder, Tokenizer } from '../../common/text/tokenizer'
import * as Data from './data-model'
import Result from '../../result'
-import { Task, RuntimeContext, chunkedSubtask, } from 'mol-task'
-
+import {Task, RuntimeContext, chunkedSubtask, Progress,} from 'mol-task'
+import * as plyToShape from 'mol-model/shape/formarts/ply/plyData_to_shape'
+import {MyData} from 'mol-model/shape/formarts/ply/plyData_to_shape';
+import {Mesh} from '../../../../mol-geo/geometry/mesh/mesh';
+import {ParamDefinition} from '../../../../mol-util/param-definition';
+import Color = ParamDefinition.Color;
+import {ColorNames} from '../../../../mol-util/color/tables';
+import {ShapeRepresentation} from '../../../../mol-repr/shape/representation';
+//import {init2} from '../../../../tests/browser/render-shape';
@@ -46,6 +53,9 @@ interface State {
initialHead: string[],
properties: number[],
+ vertices: number[],
+ colors: number[],
+ normals: number[],
faces: number[],
propertyNames: string[],
check: string[],
@@ -80,6 +90,9 @@ function State(data: string, runtimeCtx: RuntimeContext, opts: PlyOptions): Stat
initialHead: [],
properties: [],
+ vertices: [],
+ colors: [],
+ normals:[],
faces: [],
propertyNames: [],
check: [],
@@ -192,6 +205,15 @@ function moveNextInternal(state: State) {
{
if(state.currentVertex < state.vertexCount){
state.properties[state.currentVertex * state.propertyCount + state.currentProperty] = Number(Tokenizer.getTokenString(state.tokenizer));
+ if(state.currentProperty < 3){
+ state.vertices[state.currentVertex * 3 + state.currentProperty] = Number(Tokenizer.getTokenString(state.tokenizer));
+ }
+ if(state.currentProperty >= 3 && state.currentProperty <6){
+ state.colors[state.currentVertex * 3 + state.currentProperty-3] = Number(Tokenizer.getTokenString(state.tokenizer));
+ }
+ if(state.currentProperty >= 6 && state.currentProperty <9){
+ state.normals[state.currentVertex * 3 + state.currentProperty-6] = Number(Tokenizer.getTokenString(state.tokenizer));
+ }
state.currentProperty++;
if(state.currentProperty === state.propertyCount){
state.currentProperty = 0;
@@ -287,16 +309,25 @@ async function handleRecords(state: State): Promise<Data.ply_form> {
}
await readRecordsChunks(state)
- return Data.PlyStructure(state.vertexCount, state.faceCount, state.propertyCount, state.initialHead, state.propertyNames, state.properties, state.faces)
+ return Data.PlyStructure(state.vertexCount, state.faceCount, state.propertyCount, state.initialHead, state.propertyNames, state.properties, state.vertices, state.colors, state.normals, state.faces)
}
async function parseInternal(data: string, ctx: RuntimeContext, opts: PlyOptions): Promise<Result<Data.PlyFile>> {
const state = State(data, ctx, opts);
ctx.update({ message: 'Parsing...', current: 0, max: data.length });
- const table = await handleRecords(state)
- const result = Data.PlyFile(table)
+ const PLYdata = await handleRecords(state)
+ const result = Data.PlyFile(PLYdata)
console.log(result);
+
+ // let Data_for_Shape = plyToShape.collectData_for_Shape(table, datas);
+ //console.log(plyToShape.getShape(state.runtimeCtx, table));
+ let shape = plyToShape.init_ren(PLYdata);
+ console.log("shape"+shape);
+ const script = document.createElement('script');
+ script.src = "../../build/src/mol-model/shape/formarts/ply/plyData_to_shape.js";
+ document.body.appendChild(script);
+
return Result.success(result);
}
diff --git a/src/mol-model/shape/formarts/ply/plyData_to_shape.ts b/src/mol-model/shape/formarts/ply/plyData_to_shape.ts
new file mode 100644
index 000000000..f0d56c015
--- /dev/null
+++ b/src/mol-model/shape/formarts/ply/plyData_to_shape.ts
@@ -0,0 +1,143 @@
+import {ply_form} from '../../../../mol-io/reader/ply/parse_data/data-model';
+import {MyData} from '../../../../../build/src/mol-model/shape/formarts/ply/plyData_to_shape';
+import {Progress, RuntimeContext} from 'mol-task';
+import {Mesh} from '../../../../mol-geo/geometry/mesh/mesh';
+import {MeshBuilder} from '../../../../mol-geo/geometry/mesh/mesh-builder';
+import {Mat4, Vec3} from '../../../../mol-math/linear-algebra/3d';
+import {Sphere} from '../../../../mol-geo/primitive/sphere';
+import {Shape} from '../../shape';
+import {Color} from '../../../../mol-util/color';
+import {Canvas3D} from '../../../../mol-canvas3d/canvas3d';
+import {labelFirst} from '../../../../mol-theme/label';
+import {ColorNames} from '../../../../mol-util/color/tables';
+import {ShapeRepresentation} from '../../../../mol-repr/shape/representation';
+
+
+const parent = document.getElementById('app')!
+parent.style.width = '100%'
+parent.style.height = '100%'
+
+const canvas = document.createElement('canvas')
+canvas.style.width = '100%'
+canvas.style.height = '100%'
+parent.appendChild(canvas)
+
+const info = document.createElement('div')
+info.style.position = 'absolute'
+info.style.fontFamily = 'sans-serif'
+info.style.fontSize = '24pt'
+info.style.bottom = '20px'
+info.style.right = '20px'
+info.style.color = 'white'
+parent.appendChild(info)
+
+const canvas3d = Canvas3D.create(canvas, parent)
+canvas3d.animate()
+canvas3d.input.move.subscribe(async ({x, y}) => {
+ const pickingId = await canvas3d.identify(x, y)
+ let label = ''
+ if (pickingId) {
+ const { loci } = canvas3d.getLoci(pickingId)
+ label = labelFirst(loci)
+ }
+ info.innerText = label
+})
+
+
+
+
+export interface MyData {
+ centers: number[],
+ colors: string[],
+ labels: string[],
+ transforms: number[]
+}
+
+let data:MyData = {
+ centers: [],
+ colors: [],
+ labels: [],
+ transforms:[]
+}
+
+
+function componentToHex(c) {
+ let hex = c.toString(16);
+ return hex.length == 1 ? "0" + hex : hex;
+}
+
+function rgbToHex(r, g, b) {
+ return "#" + componentToHex(r) + componentToHex(g) + componentToHex(b);
+}
+
+ function collectData_for_Shape(parsedData: ply_form):{centers: number[], colors: string[], labels: string[], transforms: number[]}{
+ // parsedData.data.PLY_File. to access So.format.Ply
+
+ data.centers = parsedData.vertices;
+ let hexColor;
+
+ for(let i=0; i<parsedData.vertexCount; i++){
+ hexColor = rgbToHex(parsedData.colors[i*3+0],parsedData.colors[i*3+1],parsedData.colors[i*3+2]);
+ data.colors[i] = hexColor;
+ data.labels[i] = '';
+ data.transforms[i] = 0;
+ }
+ console.log(data);
+ return data;
+}
+
+
+
+
+ async function getSphereMesh(ctx: RuntimeContext, centers: number[], mesh?: Mesh) {
+ const builderState = MeshBuilder.createState(centers.length * 128, centers.length * 128 / 2, mesh)
+ const t = Mat4.identity()
+ const v = Vec3.zero()
+ const sphere = Sphere(4)
+ builderState.currentGroup = 0
+ for (let i = 0, il = centers.length / 3; i < il; ++i) {
+ // for production, calls to update should be guarded by `if (ctx.shouldUpdate)`
+ await ctx.update({ current: i, max: il, message: `adding sphere ${i}` })
+ builderState.currentGroup = i
+ Mat4.setTranslation(t, Vec3.fromArray(v, centers, i * 3))
+ MeshBuilder.addPrimitive(builderState, t, sphere)
+ }
+ let a = MeshBuilder.getMesh(builderState);
+ //console.log(a);
+ return a
+}
+
+
+export async function getShape(ctx: RuntimeContext, parsedData: ply_form, props: {}, shape?: Shape<Mesh>) {
+ let data:MyData;
+ data = collectData_for_Shape(parsedData)
+ await ctx.update('async creation of shape from myData')
+ const { centers , colors, labels} = data
+ const mesh = await getSphereMesh(ctx, centers, shape && shape.geometry)
+ const groupCount = centers.length / 3
+ return shape || Shape.create(
+ 'test', mesh,
+ (groupId: number) => Color(Number(colors[groupId])), // color: per group, same for instances
+ () => 1, // size: constant
+ (groupId: number, instanceId: number) => labels[instanceId * groupCount + groupId] // label: per group and instance
+ )
+}
+
+const repr = ShapeRepresentation(getShape, Mesh.Utils)
+
+export async function init_ren(myData : ply_form) {
+ // Create shape from myData and add to canvas3d
+ await repr.createOrUpdate({}, myData).run((p: Progress) => console.log(Progress.format(p)))
+ canvas3d.add(repr)
+ canvas3d.resetCamera()
+
+ // Change color after 1s
+ setTimeout(async () => {
+ myData.colors[0] = ColorNames.darkmagenta
+ // Calling `createOrUpdate` with `data` will trigger color and transform update
+ await repr.createOrUpdate({}, myData).run()
+ }, 1000)
+}
+
+
+
diff --git a/src/mol-plugin/state/actions/basic.ts b/src/mol-plugin/state/actions/basic.ts
index 31f8ee47f..910e614ff 100644
--- a/src/mol-plugin/state/actions/basic.ts
+++ b/src/mol-plugin/state/actions/basic.ts
@@ -14,7 +14,9 @@ import { PluginStateObject } from '../objects';
import { StateTransforms } from '../transforms';
import { Download } from '../transforms/data';
import { StructureRepresentation3DHelpers } from '../transforms/representation';
-import * as data_functions from "mol-io/reader/ply//read_data/data"
+import * as data_functions from 'mol-io/reader/ply/read_data/data'
+
+
// TODO: "structure parser provider"
@@ -86,6 +88,7 @@ export const OpenStructure = StateAction.build({
return state.update(createStructureTree(ctx, data, false));
});
+
export const PLYtest = StateAction.build({
display: { name: 'PLY Test', description: 'nothing ply' },
from: PluginStateObject.Root,
@@ -93,13 +96,12 @@ export const PLYtest = StateAction.build({
})(({ params, state }, ctx: PluginContext) => {
const b = state.build();
const data = b.toRoot().apply(data_functions.ReadFile_ascii, { file: params.file, isBinary: false });
- return state.update(getPLYdata(ctx, data));
+ let tmp = state.update(getPLYdata(ctx, data));
+ return tmp ;
});
function getPLYdata(ctx: PluginContext, b: StateTreeBuilder.To<PluginStateObject.Data.String>, ): StateTree {
- let root = b
- .apply(data_functions.ParsePLY);
- console.log(data_functions.ParsePLY);
+ let root = b.apply(data_functions.ParsePLY);
return root.getTree();
}
diff --git a/src/tests/browser/index.html b/src/tests/browser/index.html
index 5a0851f57..856790048 100644
--- a/src/tests/browser/index.html
+++ b/src/tests/browser/index.html
@@ -1,39 +1,42 @@
<!DOCTYPE html>
<html lang="en">
- <head>
+<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
<title>Mol* Browser Test</title>
<style>
- * {
- margin: 0;
- padding: 0;
- box-sizing: border-box;
- }
- html, body {
- width: 100%;
- height: 100%;
- overflow: hidden;
- }
+ * {
+ margin: 0;
+ padding: 0;
+ box-sizing: border-box;
+ }
+ html, body {
+ width: 100%;
+ height: 100%;
+ overflow: hidden;
+ }
</style>
- </head>
- <body>
- <div id="app"></div>
- <script type="text/javascript">
- function urlQueryParameter (id) {
+</head>
+<body>
+<div id="app"></div>
+<script type="text/javascript">
+ function urlQueryParameter (id) {
if (typeof window === 'undefined') return undefined
const a = new RegExp(`${id}=([^&#=]*)`)
const m = a.exec(window.location.search)
return m ? decodeURIComponent(m[1]) : undefined
- }
-
- const name = urlQueryParameter('name')
- if (name) {
+ }
+ const name = urlQueryParameter('name')
+ if (name) {
const script = document.createElement('script')
script.src = name + '.js'
document.body.appendChild(script)
- }
- </script>
- <script type="text/javascript" src="./render-shape.js"></script>
- </body>
+ }
+</script>
+<script type="text/javascript" >
+ const script = document.createElement('script');
+ script.src = "render-shape.js";
+ document.body.appendChild(script);
+</script>
+</body>
</html>
\ No newline at end of file
diff --git a/src/tests/browser/render-shape.ts b/src/tests/browser/render-shape.ts
index 8020d57fd..5f0de8e1f 100644
--- a/src/tests/browser/render-shape.ts
+++ b/src/tests/browser/render-shape.ts
@@ -18,6 +18,7 @@ import { RuntimeContext, Progress } from 'mol-task';
+
const parent = document.getElementById('app')!
parent.style.width = '100%'
parent.style.height = '100%'
@@ -101,7 +102,6 @@ const repr = ShapeRepresentation(getShape, Mesh.Utils)
export async function init() {
// Create shape from myData and add to canvas3d
await repr.createOrUpdate({}, myData).run((p: Progress) => console.log(Progress.format(p)))
- console.log(repr)
canvas3d.add(repr)
canvas3d.resetCamera()
--
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