molstar
Version:
A comprehensive macromolecular library.
57 lines (56 loc) • 2.67 kB
JavaScript
;
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.Dsn6Provider = void 0;
exports.readSlices = readSlices;
const parser_1 = require("../../../../mol-io/reader/dsn6/parser");
const typed_array_1 = require("../../../../mol-io/common/typed-array");
async function readHeader(name, file) {
const { header: dsn6Header, littleEndian } = await (0, parser_1.readDsn6Header)(file);
const header = {
name,
valueType: typed_array_1.TypedArrayValueType.Float32,
grid: [dsn6Header.xRate, dsn6Header.yRate, dsn6Header.zRate].reverse(),
axisOrder: [0, 1, 2].reverse(),
extent: [dsn6Header.xExtent, dsn6Header.yExtent, dsn6Header.zExtent].reverse(),
origin: [dsn6Header.xStart, dsn6Header.yStart, dsn6Header.zStart].reverse(),
spacegroupNumber: 1, // set as P 1, since it is not available in DSN6 files
cellSize: [dsn6Header.xlen, dsn6Header.ylen, dsn6Header.zlen],
cellAngles: [dsn6Header.alpha, dsn6Header.beta, dsn6Header.gamma],
littleEndian,
dataOffset: parser_1.dsn6HeaderSize,
originalHeader: dsn6Header
};
return header;
}
async function readSlices(data) {
// TODO due to the dsn6 data layout we the read file into one big buffer
// to avoid this, either change the sampling algoritm to work with this layout or
// read the data into a collection of buffers that can be access like one big buffer
// => for now not worth putting time in, for big files better use another file format
const { slices, header, file } = data;
if (slices.isFinished) {
return;
}
const { extent, dataOffset, originalHeader } = header;
const sliceCount = extent[2];
const { byteCount } = (0, parser_1.getDsn6Counts)(originalHeader);
if (byteCount > slices.maxBlockBytes) {
throw new Error(`dsn6 file to large, can't read ${byteCount} bytes at once, increase block size or use another file format`);
}
const { buffer } = await file.readBuffer(dataOffset, byteCount);
if (!(slices.values instanceof Float32Array)) {
throw new Error(`dsn6 reader only supports Float32Array for output values`);
}
await (0, parser_1.parseDsn6Values)(originalHeader, buffer, slices.values, header.littleEndian);
slices.slicesRead += sliceCount;
slices.sliceCount = sliceCount;
if (slices.slicesRead >= extent[2]) {
slices.isFinished = true;
}
}
exports.Dsn6Provider = { readHeader, readSlices };