From b09a0c6959d37cd551a8db0550b78d955ac09051 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 12 Mar 2019 15:56:20 -0700
Subject: [PATCH] use fast number parsers
---
.../reader/ply/parse_data/ply_parser.ts | 71 +++++++------------
1 file changed, 27 insertions(+), 44 deletions(-)
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 a9844ee5d..1a88b09be 100644
--- a/src/mol-io/reader/ply/parse_data/ply_parser.ts
+++ b/src/mol-io/reader/ply/parse_data/ply_parser.ts
@@ -1,14 +1,15 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
+ * @author Schäfer, Marco <marco.schaefer@uni-tuebingen.de>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Tokens, TokenBuilder, Tokenizer } from '../../common/text/tokenizer'
import * as Data from './data-model'
-
import{ ReaderResult } from '../../result'
import {Task, RuntimeContext, chunkedSubtask } from 'mol-task'
+import { parseInt as fastParseInt, parseFloat as fastParseFloat } from '../../common/text/number-parser'
const enum PlyTokenType {
Value = 0,
@@ -18,7 +19,6 @@ const enum PlyTokenType {
element = 4
}
-
interface State {
data: string;
tokenizer: Tokenizer,
@@ -54,7 +54,6 @@ interface State {
}
function State(data: string, runtimeCtx: RuntimeContext, opts: PlyOptions): State {
-
const tokenizer = Tokenizer(data)
return {
data,
@@ -134,7 +133,6 @@ function eatLine (state: Tokenizer) {
}
-
function skipLine(state: Tokenizer) {
while (state.position < state.length) {
const c = state.data.charCodeAt(state.position);
@@ -143,14 +141,13 @@ function skipLine(state: Tokenizer) {
}
}
-function getColumns(state: State, NumberofColumns: number){
+function getColumns(state: State, numberOfColumns: number) {
eatLine(state.tokenizer);
- let tmp = (Tokenizer.getTokenString(state.tokenizer))
- let split = tmp.split(" ", NumberofColumns);
+ let tmp = Tokenizer.getTokenString(state.tokenizer)
+ let split = tmp.split(' ', numberOfColumns);
return split;
}
-
/**
* Move to the next token.
* Returns true when the current char is a newline, i.e. indicating a full record.
@@ -172,8 +169,8 @@ function moveNextInternal(state: State) {
skipLine(tokenizer);
break;
case state.propertyCharCode: // checks all line beginning with 'p'
- state.check = getColumns(state,3);
- if(state.check[0] !== 'ply' && state.faceCount === 0){
+ state.check = getColumns(state, 3);
+ if (state.check[0] !== 'ply' && state.faceCount === 0) {
state.propertyNames.push(state.check[1]);
state.propertyNames.push(state.check[2]);
state.propertyCount++;
@@ -181,38 +178,38 @@ function moveNextInternal(state: State) {
return;
case state.elementCharCode: // checks all line beginning with 'e'
state.check = getColumns(state, 3);
- if(state.check[1] === 'vertex') state.vertexCount= Number(state.check[2]);
- if(state.check[1] === 'face') state.faceCount = Number(state.check[2]);
- if(state.check[0] === 'end_header') state.endHeader = 1;
+ if (state.check[1] === 'vertex') state.vertexCount= Number(state.check[2]);
+ if (state.check[1] === 'face') state.faceCount = Number(state.check[2]);
+ if (state.check[0] === 'end_header') state.endHeader = 1;
return;
default: // for all the other lines
state.tokenType = PlyTokenType.Value;
let return_value = eatValue(tokenizer);
- if(state.endHeader === 1)
- {
- if(state.currentVertex < state.vertexCount){
+ if (state.endHeader === 1) {
+ if (state.currentVertex < state.vertexCount) {
+ // TODO the numbers are parsed twice
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.vertices[state.currentVertex * 3 + state.currentProperty] = fastParseFloat(state.tokenizer.data, state.tokenizer.tokenStart, state.tokenizer.tokenEnd);
}
- if(state.currentProperty >= 3 && state.currentProperty <6){
- state.colors[state.currentVertex * 3 + state.currentProperty-3] = Number(Tokenizer.getTokenString(state.tokenizer));
+ if (state.currentProperty >= 3 && state.currentProperty < 6) {
+ state.colors[state.currentVertex * 3 + state.currentProperty - 3] = fastParseInt(state.tokenizer.data, state.tokenizer.tokenStart, state.tokenizer.tokenEnd);
}
- if(state.currentProperty >= 6 && state.currentProperty <9){
- state.normals[state.currentVertex * 3 + state.currentProperty-6] = Number(Tokenizer.getTokenString(state.tokenizer));
+ if (state.currentProperty >= 6 && state.currentProperty < 9) {
+ state.normals[state.currentVertex * 3 + state.currentProperty - 6] = fastParseFloat(state.tokenizer.data, state.tokenizer.tokenStart, state.tokenizer.tokenEnd);
}
state.currentProperty++;
- if(state.currentProperty === state.propertyCount){
+ if (state.currentProperty === state.propertyCount) {
state.currentProperty = 0;
state.currentVertex++;
}
return return_value;
}
- if(state.currentFace < state.faceCount && state.currentVertex === state.vertexCount){
- state.faces[state.currentFace * 4 + state.currentFaceElement] = Number(Tokenizer.getTokenString(state.tokenizer));
+ if (state.currentFace < state.faceCount && state.currentVertex === state.vertexCount) {
+ state.faces[state.currentFace * 4 + state.currentFaceElement] = fastParseInt(state.tokenizer.data, state.tokenizer.tokenStart, state.tokenizer.tokenEnd);
state.currentFaceElement++;
- if(state.currentProperty === 4){
+ if (state.currentProperty === 4) {
state.currentFaceElement = 0;
state.currentFace++;
}
@@ -234,8 +231,6 @@ function moveNext(state: State) {
return newRecord
}
-
-
function readRecordsChunk(chunkSize: number, state: State) {
if (state.tokenType === PlyTokenType.End) return 0
@@ -258,13 +253,10 @@ function readRecordsChunks(state: State) {
function addHeadEntry (state: State) {
const head = Tokenizer.getTokenString(state.tokenizer)
- console.log(head)
state.initialHead.push(head)
state.tokens.push(TokenBuilder.create(head, state.data.length / 80))
}
-
-
function init(state: State) { // only for first two lines to get the format and the coding! (marco)
let newRecord = moveNext(state)
while (!newRecord) { // newRecord is only true when a newline occurs (marco)
@@ -278,12 +270,12 @@ function init(state: State) { // only for first two lines to get the format and
newRecord = moveNext(state);
}
addHeadEntry(state)
- if(state.initialHead[0] !== 'ply'){
+ if (state.initialHead[0] !== 'ply') {
console.log('ERROR: this is not a .ply file!')
throw new Error('this is not a .ply file!');
return 0;
}
- if(state.initialHead[2] !== 'ascii'){
+ if (state.initialHead[2] !== 'ascii') {
console.log('ERROR: only ASCII-DECODING is supported!');
throw new Error('only ASCII-DECODING is supported!');
return 0;
@@ -293,7 +285,7 @@ function init(state: State) { // only for first two lines to get the format and
}
async function handleRecords(state: State): Promise<Data.ply_form> {
- if(!init(state)){
+ if (!init(state)) {
console.log('ERROR: parsing file (PLY) failed!')
throw new Error('arsing file (PLY) failed!');
}
@@ -308,15 +300,6 @@ async function parseInternal(data: string, ctx: RuntimeContext, opts: PlyOptions
ctx.update({ message: 'Parsing...', current: 0, max: data.length });
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 ReaderResult.success(result);
}
--
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