molstar
Version:
A comprehensive macromolecular library.
68 lines • 3.69 kB
JavaScript
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { __awaiter, __generator } from "tslib";
import { readCcp4Header, readCcp4Slices, getCcp4DataOffset, getCcp4ValueType } from '../../../../mol-io/reader/ccp4/parser';
import { getCcp4Origin } from '../../../../mol-model-formats/volume/ccp4';
function readHeader(name, file) {
return __awaiter(this, void 0, void 0, function () {
var _a, ccp4Header, littleEndian, header;
return __generator(this, function (_b) {
switch (_b.label) {
case 0: return [4 /*yield*/, readCcp4Header(file)];
case 1:
_a = _b.sent(), ccp4Header = _a.header, littleEndian = _a.littleEndian;
header = {
name: name,
valueType: getCcp4ValueType(ccp4Header),
grid: [ccp4Header.NX, ccp4Header.NY, ccp4Header.NZ],
axisOrder: [ccp4Header.MAPC, ccp4Header.MAPR, ccp4Header.MAPS].map(function (i) { return i - 1; }),
extent: [ccp4Header.NC, ccp4Header.NR, ccp4Header.NS],
origin: getCcp4Origin(ccp4Header),
spacegroupNumber: ccp4Header.ISPG,
cellSize: [ccp4Header.xLength, ccp4Header.yLength, ccp4Header.zLength],
cellAngles: [ccp4Header.alpha, ccp4Header.beta, ccp4Header.gamma],
littleEndian: littleEndian,
dataOffset: getCcp4DataOffset(ccp4Header),
originalHeader: ccp4Header
};
// "normalize" the grid axis order
header.grid = [header.grid[header.axisOrder[0]], header.grid[header.axisOrder[1]], header.grid[header.axisOrder[2]]];
return [2 /*return*/, header];
}
});
});
}
export function readSlices(data) {
return __awaiter(this, void 0, void 0, function () {
var slices, header, extent, originalHeader, sliceSize, sliceByteOffset, sliceCount, sliceByteCount;
return __generator(this, function (_a) {
switch (_a.label) {
case 0:
slices = data.slices, header = data.header;
if (slices.isFinished) {
return [2 /*return*/];
}
extent = header.extent, originalHeader = header.originalHeader;
sliceSize = extent[0] * extent[1];
sliceByteOffset = slices.buffer.elementByteSize * sliceSize * slices.slicesRead;
sliceCount = Math.min(slices.sliceCapacity, extent[2] - slices.slicesRead);
sliceByteCount = slices.buffer.elementByteSize * sliceCount * sliceSize;
return [4 /*yield*/, readCcp4Slices(originalHeader, slices.buffer, data.file, header.dataOffset + sliceByteOffset, sliceByteCount, header.littleEndian)];
case 1:
_a.sent();
slices.slicesRead += sliceCount;
slices.sliceCount = sliceCount;
if (slices.slicesRead >= extent[2]) {
slices.isFinished = true;
}
return [2 /*return*/];
}
});
});
}
export var Ccp4Provider = { readHeader: readHeader, readSlices: readSlices };
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