From 299f3baf7b03a90f15a72818d754620277296c14 Mon Sep 17 00:00:00 2001
From: MarcoSchaeferT <schaefer.marco.ms@web.de>
Date: Thu, 14 Feb 2019 17:59:29 +0100
Subject: [PATCH] parsing ply-file to ply-data-structure is working
---
src/apps/structure-info/volume.ts | 1 -
src/mol-io/reader/cif/text/parser.ts | 1 -
src/mol-io/reader/common/text/tokenizer.ts | 1 -
.../reader/ply/parse_data/data-model.ts | 17 +-
.../reader/ply/parse_data/ply_parser.ts | 161 ++++++++++++------
src/mol-io/reader/ply/read_data/data.ts | 2 +-
src/mol-plugin/state/actions/basic.ts | 3 +-
7 files changed, 119 insertions(+), 67 deletions(-)
diff --git a/src/apps/structure-info/volume.ts b/src/apps/structure-info/volume.ts
index f74a5440e..2faaf7086 100644
--- a/src/apps/structure-info/volume.ts
+++ b/src/apps/structure-info/volume.ts
@@ -35,7 +35,6 @@ function print(data: Volume) {
console.log(data.volume.cell);
console.log(data.volume.dataStats);
console.log(data.volume.fractionalBox);
- console.log("\n\n Hello 12156421231 \n\n");
}
async function doMesh(data: Volume, filename: string) {
diff --git a/src/mol-io/reader/cif/text/parser.ts b/src/mol-io/reader/cif/text/parser.ts
index 4fa0605e8..3ee75e270 100644
--- a/src/mol-io/reader/cif/text/parser.ts
+++ b/src/mol-io/reader/cif/text/parser.ts
@@ -60,7 +60,6 @@ interface TokenizerState {
* Eat everything until a whitespace/newline occurs.
*/
function eatValue(state: TokenizerState) {
- console.log("hello");
while (state.position < state.length) {
switch (state.data.charCodeAt(state.position)) {
case 9: // \t
diff --git a/src/mol-io/reader/common/text/tokenizer.ts b/src/mol-io/reader/common/text/tokenizer.ts
index 601309348..60f14c1b1 100644
--- a/src/mol-io/reader/common/text/tokenizer.ts
+++ b/src/mol-io/reader/common/text/tokenizer.ts
@@ -85,7 +85,6 @@ export namespace Tokenizer {
/** Sets the current token start to current position and moves to the next line. */
export function markLine(state: Tokenizer) {
state.tokenStart = state.position;
- console.log("hello");
eatLine(state);
}
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 293f4b762..36fdb6b1a 100644
--- a/src/mol-io/reader/ply/parse_data/data-model.ts
+++ b/src/mol-io/reader/ply/parse_data/data-model.ts
@@ -4,33 +4,34 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { CifField as CsvColumn } from '../../cif/data-model'
+import { CifField as PlyColumn } from '../../cif/data-model'
-export { CsvColumn }
+export { PlyColumn }
export interface PlyFile {
readonly name?: string,
readonly PLY_File: ply_form
}
-export function CsvFile(PLY_File: ply_form, name?: string): PlyFile {
+export function PlyFile(PLY_File: ply_form, name?: string): PlyFile {
return { name, PLY_File };
}
export interface ply_form {
- readonly rowCount: number,
readonly vertexCount: number,
readonly faceCount: number,
readonly propertyCount: number,
readonly initialHead: ReadonlyArray<string>,
- getColumn(name: string): CsvColumn | undefined
+ readonly propertyNames: ReadonlyArray<string>,
+ readonly properties: number[],
+ readonly faces: number[],
}
-export function CsvTable(rowCount: number, vertexCount: number, faceCount: number, propertyCount: number, initialHead: string[], columns: CsvColumns): ply_form {
- return { rowCount, vertexCount, faceCount, propertyCount, initialHead: [...initialHead], getColumn(name) { return columns[name]; } };
+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 type CsvColumns = { [name: string]: CsvColumn }
+export type PlyColumns = { [name: string]: PlyColumn }
// export namespace CsvTable {
// export function empty(name: string): Table {
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 31a91deb0..d2a42e49a 100644
--- a/src/mol-io/reader/ply/parse_data/ply_parser.ts
+++ b/src/mol-io/reader/ply/parse_data/ply_parser.ts
@@ -7,18 +7,23 @@
// import { Column } from 'mol-data/db'
import { Tokens, TokenBuilder, Tokenizer } from '../../common/text/tokenizer'
import * as Data from './data-model'
-import Field from './field'
+
import Result from '../../result'
import { Task, RuntimeContext, chunkedSubtask, } from 'mol-task'
+
+
+
const enum PlyTokenType {
Value = 0,
Comment = 1,
End = 2,
- property = 3
+ property = 3,
+ element = 4
}
+
interface State {
data: string;
tokenizer: Tokenizer,
@@ -28,14 +33,26 @@ interface State {
tokens: Tokens[],
fieldCount: number,
- recordCount: number,
columnCount: number,
+ propertyCount: number,
+ vertexCount: number,
+ currentVertex: number,
+ currentProperty: number,
+ currentFace: number,
+ currentFaceElement: number,
+ faceCount: number,
+ endHeader: number,
+
initialHead: string[],
+ properties: number[],
+ faces: number[],
propertyNames: string[],
+ check: string[],
commentCharCode: number,
- propertyCharCode: number
+ propertyCharCode: number,
+ elementCharCode: number
}
function State(data: string, runtimeCtx: RuntimeContext, opts: PlyOptions): State {
@@ -50,14 +67,26 @@ function State(data: string, runtimeCtx: RuntimeContext, opts: PlyOptions): Stat
tokens: [],
fieldCount: 0,
- recordCount: 0,
columnCount: 0,
+ propertyCount: 0,
+ vertexCount: 0,
+ currentVertex: 0,
+ currentProperty: 0,
+ currentFace: 0,
+ currentFaceElement: 0,
+ faceCount: 0,
+ endHeader: 0,
+
initialHead: [],
+ properties: [],
+ faces: [],
propertyNames: [],
+ check: [],
commentCharCode: opts.comment.charCodeAt(0),
- propertyCharCode: opts.property.charCodeAt(0)
+ propertyCharCode: opts.property.charCodeAt(0),
+ elementCharCode: opts.element.charCodeAt(0)
};
}
@@ -75,7 +104,7 @@ function eatValue(state: Tokenizer) {
case 13: // \r
return true;
case 32: // ' ' Delimeter of ply is space (Unicode 32)
- return;
+ return true;
case 9: // \t
case 32: // ' '
break;
@@ -86,37 +115,25 @@ function eatValue(state: Tokenizer) {
}
}
-
-
-function skipWhitespace(state: Tokenizer) {
- let prev = -1;
+function eatLine (state: Tokenizer) {
while (state.position < state.length) {
const c = state.data.charCodeAt(state.position);
+ ++state.position
switch (c) {
- case 9: // '\t'
- //case 32: // ' '
- prev = c;
- ++state.position;
- break;
case 10: // \n
- // handle \r\n
- if (prev !== 13) {
- ++state.lineNumber;
- }
- prev = c;
- ++state.position;
- break;
case 13: // \r
- prev = c;
- ++state.position;
- ++state.lineNumber;
+ return true;
+ case 9: // \t
break;
default:
- return;
+ ++state.tokenEnd;
+ break;
}
}
+
}
+
function skipLine(state: Tokenizer) {
while (state.position < state.length) {
const c = state.data.charCodeAt(state.position);
@@ -125,13 +142,20 @@ function skipLine(state: Tokenizer) {
}
}
+function getColumns(state: State, NumberofColumns: number){
+ eatLine(state.tokenizer);
+ 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.
*/
function moveNextInternal(state: State) {
const tokenizer = state.tokenizer
- //skipWhitespace(tokenizer);
if (tokenizer.position >= tokenizer.length) {
state.tokenType = PlyTokenType.End;
@@ -146,12 +170,45 @@ function moveNextInternal(state: State) {
state.tokenType = PlyTokenType.Comment;
skipLine(tokenizer);
break;
- case state.propertyCharCode:
- state.tokenType = PlyTokenType.property;
- //return eatProperty(tokenizer);
- default:
+ case state.propertyCharCode: // checks all line beginning with 'p'
+ 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++;
+ }
+ 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;
+ return;
+ default: // for all the other lines
state.tokenType = PlyTokenType.Value;
- return eatValue(tokenizer);
+ let return_value = eatValue(tokenizer);
+
+ if(state.endHeader === 1)
+ {
+ if(state.currentVertex < state.vertexCount){
+ state.properties[state.currentVertex * state.propertyCount + state.currentProperty] = Number(Tokenizer.getTokenString(state.tokenizer));
+ state.currentProperty++;
+ 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));
+ state.currentFaceElement++;
+ if(state.currentProperty === 4){
+ state.currentFaceElement = 0;
+ state.currentFace++;
+ }
+ }
+ }
+ return return_value;
}
}
@@ -161,25 +218,24 @@ function moveNextInternal(state: State) {
*/
function moveNext(state: State) {
let newRecord = moveNextInternal(state);
- while (state.tokenType === PlyTokenType.Comment) { // skip comment lines (marco
+ while (state.tokenType === PlyTokenType.Comment) { // skip comment lines (marco)
newRecord = moveNextInternal(state);
}
return newRecord
}
+
+
function readRecordsChunk(chunkSize: number, state: State) {
if (state.tokenType === PlyTokenType.End) return 0
- let newRecord = moveNext(state);
- if (newRecord) ++state.recordCount
-
+ moveNext(state);
const { tokens, tokenizer } = state;
let counter = 0;
while (state.tokenType === PlyTokenType.Value && counter < chunkSize) {
TokenBuilder.add(tokens[state.fieldCount % state.columnCount], tokenizer.tokenStart, tokenizer.tokenEnd);
++state.fieldCount
- newRecord = moveNext(state);
- if (newRecord) ++state.recordCount
+ moveNext(state);
++counter;
}
return counter;
@@ -190,24 +246,26 @@ function readRecordsChunks(state: State) {
(ctx, state) => ctx.update({ message: 'Parsing...', current: state.tokenizer.position, max: state.data.length }));
}
-function addColumn (state: State) {
+function addHeadEntry (state: State) {
state.initialHead.push(Tokenizer.getTokenString(state.tokenizer))
state.tokens.push(TokenBuilder.create(state.tokenizer, state.data.length / 80))
}
-function init(state: State) { // only for first line to get the columns! (marco)
+
+
+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)
- addColumn(state)
+ addHeadEntry(state)
newRecord = moveNext(state);
}
- addColumn(state)
+ addHeadEntry(state)
newRecord = moveNext(state);
while (!newRecord) {
- addColumn(state)
+ addHeadEntry(state)
newRecord = moveNext(state);
}
- addColumn(state)
+ addHeadEntry(state)
if(state.initialHead[0] !== 'ply'){
console.log("ERROR: this is not a .ply file!")
throw new Error("this is not a .ply file!");
@@ -229,13 +287,7 @@ async function handleRecords(state: State): Promise<Data.ply_form> {
}
await readRecordsChunks(state)
- const columns: Data.CsvColumns = Object.create(null);
- for (let i = 0; i < state.columnCount; ++i) {
- columns[state.initialHead[i]] = Field(state.tokens[i], state.recordCount);
- }
-
-
- return Data.CsvTable(state.recordCount,0,0,0, state.initialHead, columns)
+ return Data.PlyStructure(state.vertexCount, state.faceCount, state.propertyCount, state.initialHead, state.propertyNames, state.properties, state.faces)
}
async function parseInternal(data: string, ctx: RuntimeContext, opts: PlyOptions): Promise<Result<Data.PlyFile>> {
@@ -243,7 +295,7 @@ async function parseInternal(data: string, ctx: RuntimeContext, opts: PlyOptions
ctx.update({ message: 'Parsing...', current: 0, max: data.length });
const table = await handleRecords(state)
- const result = Data.CsvFile(table)
+ const result = Data.PlyFile(table)
console.log(result);
return Result.success(result);
}
@@ -251,10 +303,11 @@ async function parseInternal(data: string, ctx: RuntimeContext, opts: PlyOptions
interface PlyOptions {
comment: string;
property: string;
+ element: string;
}
export function parse(data: string, opts?: Partial<PlyOptions>) {
- const completeOpts = Object.assign({}, { comment: 'c', property: 'p' }, opts)
+ const completeOpts = Object.assign({}, { comment: 'c', property: 'p', element: 'e' }, opts)
return Task.create<Result<Data.PlyFile>>('Parse PLY', async ctx => {
return await parseInternal(data, ctx, completeOpts);
});
diff --git a/src/mol-io/reader/ply/read_data/data.ts b/src/mol-io/reader/ply/read_data/data.ts
index 699353a18..6e0be3ad2 100644
--- a/src/mol-io/reader/ply/read_data/data.ts
+++ b/src/mol-io/reader/ply/read_data/data.ts
@@ -46,7 +46,7 @@ export { ParsePLY }
type ParsePLY = typeof ParsePLY
const ParsePLY = PluginStateTransform.BuiltIn({
name: 'parse-ply',
- display: { name: 'Parse PLY', description: 'Parse OLY from String' },
+ display: { name: 'Parse PLY', description: 'Parse PLY from String' },
from: [SO.Data.String],
to: SO.Format.Ply
})({
diff --git a/src/mol-plugin/state/actions/basic.ts b/src/mol-plugin/state/actions/basic.ts
index 0dd4d57aa..31f8ee47f 100644
--- a/src/mol-plugin/state/actions/basic.ts
+++ b/src/mol-plugin/state/actions/basic.ts
@@ -14,6 +14,7 @@ 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"
// TODO: "structure parser provider"
@@ -84,7 +85,7 @@ export const OpenStructure = StateAction.build({
const data = b.toRoot().apply(StateTransforms.Data.ReadFile, { file: params.file, isBinary: /\.bcif$/i.test(params.file.name) });
return state.update(createStructureTree(ctx, data, false));
});
-import * as data_functions from "../../../mol-io/reader/ply//read_data/data"
+
export const PLYtest = StateAction.build({
display: { name: 'PLY Test', description: 'nothing ply' },
from: PluginStateObject.Root,
--
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