diff --git a/src/servers/volume/common/binary-schema.ts b/src/servers/volume/common/binary-schema.ts
index 8ce1b47007f50177248f128924d75f617a8daf22..3bd0b10cc276d19f6fee996b42e398d0bb473913 100644
--- a/src/servers/volume/common/binary-schema.ts
+++ b/src/servers/volume/common/binary-schema.ts
@@ -7,6 +7,7 @@
*/
import * as UTF8 from 'mol-io/common/utf8'
+import { SimpleBuffer } from 'mol-io/common/simple-buffer';
export type Bool = { kind: 'bool' }
export type Int = { kind: 'int' }
@@ -105,7 +106,7 @@ export function encode(element: Element, src: any): Buffer {
return write(element, src);
}
-function decodeElement(e: Element, buffer: Buffer, offset: number, target: { value: any }) {
+function decodeElement(e: Element, buffer: SimpleBuffer, offset: number, target: { value: any }) {
switch (e.kind) {
case 'bool': target.value = !!buffer.readInt8(offset); offset += 1; break;
case 'int': target.value = buffer.readInt32LE(offset); offset += 4; break;
@@ -147,7 +148,7 @@ function decodeElement(e: Element, buffer: Buffer, offset: number, target: { val
return offset;
}
-export function decode<T>(element: Element, buffer: Buffer, offset?: number) {
+export function decode<T>(element: Element, buffer: SimpleBuffer, offset?: number) {
const target = { value: void 0 as any };
decodeElement(element, buffer, offset! | 0, target);
return target.value as T;
diff --git a/src/servers/volume/common/data-format.ts b/src/servers/volume/common/data-format.ts
index f1fdeda83277dd145831667fdad3dd4f476bd7af..0492ab16ce2bda7263a578e26d5db4a1bdd1cef3 100644
--- a/src/servers/volume/common/data-format.ts
+++ b/src/servers/volume/common/data-format.ts
@@ -6,8 +6,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import * as File from './file'
import * as Schema from './binary-schema'
+import { FileHandle } from 'mol-io/common/file-handle';
export type ValueType = 'float32' | 'int8' | 'int16'
@@ -121,12 +121,12 @@ export function encodeHeader(header: Header) {
return Schema.encode(headerSchema, header);
}
-export async function readHeader(file: number): Promise<{ header: Header, dataOffset: number }> {
- let { buffer } = await File.readBuffer(file, 0, 4 * 4096);
+export async function readHeader(file: FileHandle): Promise<{ header: Header, dataOffset: number }> {
+ let { buffer } = await file.readBuffer(0, 4 * 4096);
const headerSize = buffer.readInt32LE(0);
if (headerSize > buffer.byteLength - 4) {
- buffer = (await File.readBuffer(file, 0, headerSize + 4)).buffer;
+ buffer = (await file.readBuffer(0, headerSize + 4)).buffer;
}
const header = Schema.decode<Header>(headerSchema, buffer, 4);
diff --git a/src/servers/volume/common/file.ts b/src/servers/volume/common/file.ts
index 6b83f00cef7e225de8dde078e257698fc17eb162..8067b9eaf87419a1f0919a99c243c0c6e8f546dd 100644
--- a/src/servers/volume/common/file.ts
+++ b/src/servers/volume/common/file.ts
@@ -9,6 +9,8 @@
import * as fs from 'fs'
import * as path from 'path'
import * as DataFormat from './data-format'
+import { FileHandle } from 'mol-io/common/file-handle';
+import { SimpleBuffer } from 'mol-io/common/simple-buffer';
export const IsNativeEndianLittle = new Uint16Array(new Uint8Array([0x12, 0x34]).buffer)[0] === 0x3412;
@@ -29,43 +31,6 @@ export async function openRead(filename: string) {
});
}
-export function readBuffer(file: number, position: number, sizeOrBuffer: Buffer | number, size?: number, byteOffset?: number): Promise<{ bytesRead: number, buffer: Buffer }> {
- return new Promise((res, rej) => {
- if (typeof sizeOrBuffer === 'number') {
- let buff = new Buffer(new ArrayBuffer(sizeOrBuffer));
- fs.read(file, buff, 0, sizeOrBuffer, position, (err, bytesRead, buffer) => {
- if (err) {
- rej(err);
- return;
- }
- res({ bytesRead, buffer });
- });
- } else {
- if (size === void 0) {
- rej('readBuffer: Specify size.');
- return;
- }
-
- fs.read(file, sizeOrBuffer, byteOffset ? +byteOffset : 0, size, position, (err, bytesRead, buffer) => {
- if (err) {
- rej(err);
- return;
- }
- res({ bytesRead, buffer });
- });
- }
- })
-}
-
-export function writeBuffer(file: number, position: number, buffer: Buffer, size?: number): Promise<number> {
- return new Promise<number>((res, rej) => {
- fs.write(file, buffer, 0, size !== void 0 ? size : buffer.length, position, (err, written) => {
- if (err) rej(err);
- else res(written);
- })
- })
-}
-
function makeDir(path: string, root?: string): boolean {
let dirs = path.split(/\/|\\/g),
dir = dirs.shift();
@@ -95,19 +60,10 @@ export function createFile(filename: string) {
});
}
-const __emptyFunc = function () { };
-export function close(file: number | undefined) {
- try {
- if (file !== void 0) fs.close(file, __emptyFunc);
- } catch (e) {
-
- }
-}
-
-const smallBuffer = new Buffer(8);
-export async function writeInt(file: number, value: number, position: number) {
+const smallBuffer = SimpleBuffer.fromBuffer(new Buffer(8));
+export async function writeInt(file: FileHandle, value: number, position: number) {
smallBuffer.writeInt32LE(value, 0);
- await writeBuffer(file, position, smallBuffer, 4);
+ await file.writeBuffer(position, smallBuffer, 4);
}
export interface TypedArrayBufferContext {
@@ -144,7 +100,7 @@ export function createTypedArrayBufferContext(size: number, type: DataFormat.Val
};
}
-function flipByteOrder(source: Buffer, target: Uint8Array, byteCount: number, elementByteSize: number, offset: number) {
+function flipByteOrder(source: SimpleBuffer, target: Uint8Array, byteCount: number, elementByteSize: number, offset: number) {
for (let i = 0, n = byteCount; i < n; i += elementByteSize) {
for (let j = 0; j < elementByteSize; j++) {
target[offset + i + elementByteSize - j - 1] = source[offset + i + j];
@@ -152,19 +108,19 @@ function flipByteOrder(source: Buffer, target: Uint8Array, byteCount: number, el
}
}
-export async function readTypedArray(ctx: TypedArrayBufferContext, file: number, position: number, count: number, valueOffset: number, littleEndian?: boolean) {
+export async function readTypedArray(ctx: TypedArrayBufferContext, file: FileHandle, position: number, count: number, valueOffset: number, littleEndian?: boolean) {
let byteCount = ctx.elementByteSize * count;
let byteOffset = ctx.elementByteSize * valueOffset;
- await readBuffer(file, position, ctx.readBuffer, byteCount, byteOffset);
+ await file.readBuffer(position, ctx.readBuffer, byteCount, byteOffset);
if (ctx.elementByteSize > 1 && ((littleEndian !== void 0 && littleEndian !== IsNativeEndianLittle) || !IsNativeEndianLittle)) {
- // fix the endian
+ // fix the endian
flipByteOrder(ctx.readBuffer, ctx.valuesBuffer, byteCount, ctx.elementByteSize, byteOffset);
}
return ctx.values;
}
-export function ensureLittleEndian(source: Buffer, target: Buffer, byteCount: number, elementByteSize: number, offset: number) {
+export function ensureLittleEndian(source: SimpleBuffer, target: SimpleBuffer, byteCount: number, elementByteSize: number, offset: number) {
if (IsNativeEndianLittle) return;
if (!byteCount || elementByteSize <= 1) return;
flipByteOrder(source, target, byteCount, elementByteSize, offset);
diff --git a/src/servers/volume/pack/ccp4.ts b/src/servers/volume/pack/ccp4.ts
index 46ac835bc1d1f6dd33d749d2a0458e8071e41657..f41d2d8a23ca5d7381119ab8db155e3115d90fb3 100644
--- a/src/servers/volume/pack/ccp4.ts
+++ b/src/servers/volume/pack/ccp4.ts
@@ -1,13 +1,16 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Taken/adapted from DensityServer (https://github.com/dsehnal/DensityServer)
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import * as File from '../common/file'
import * as DataFormat from '../common/data-format'
+import { FileHandle } from 'mol-io/common/file-handle';
+import { readCcp4Header } from 'mol-io/reader/ccp4/parser';
export const enum Mode { Int8 = 0, Int16 = 1, Float32 = 2 }
@@ -40,7 +43,7 @@ export interface SliceBuffer {
export interface Data {
header: Header,
- file: number,
+ file: FileHandle,
slices: SliceBuffer
}
@@ -84,47 +87,24 @@ export function compareHeaders(a: Header, b: Header) {
return true;
}
-function getArray(r: (offset: number) => number, offset: number, count: number) {
- const ret: number[] = [];
- for (let i = 0; i < count; i++) {
- ret[i] = r(offset + i);
- }
- return ret;
-}
-
-async function readHeader(name: string, file: number) {
- const headerSize = 1024;
- const { buffer: data } = await File.readBuffer(file, 0, headerSize);
-
- let littleEndian = true;
-
- let mode = data.readInt32LE(3 * 4);
- if (mode < 0 || mode > 2) {
- littleEndian = false;
- mode = data.readInt32BE(3 * 4, true);
- if (mode < 0 || mode > 2) {
- throw Error('Only CCP4 modes 0, 1, and 2 are supported.');
- }
- }
-
- const readInt = littleEndian ? (o: number) => data.readInt32LE(o * 4) : (o: number) => data.readInt32BE(o * 4);
- const readFloat = littleEndian ? (o: number) => data.readFloatLE(o * 4) : (o: number) => data.readFloatBE(o * 4);
+async function readHeader(name: string, file: FileHandle) {
+ const { header: ccp4Header, littleEndian } = await readCcp4Header(file)
- const origin2k = getArray(readFloat, 49, 3);
- const nxyzStart = getArray(readInt, 4, 3);
+ const origin2k = [ccp4Header.originX, ccp4Header.originY, ccp4Header.originZ];
+ const nxyzStart = [ccp4Header.NCSTART, ccp4Header.NRSTART, ccp4Header.NSSTART];
const header: Header = {
name,
- mode,
- grid: getArray(readInt, 7, 3),
- axisOrder: getArray(readInt, 16, 3).map(i => i - 1),
- extent: getArray(readInt, 0, 3),
+ mode: ccp4Header.MODE,
+ grid: [ccp4Header.NX, ccp4Header.NY, ccp4Header.NZ],
+ axisOrder: [ccp4Header.MAPC, ccp4Header.MAPR, ccp4Header.MAPS].map(i => i - 1),
+ extent: [ccp4Header.NC, ccp4Header.NR, ccp4Header.NS],
origin: origin2k[0] === 0.0 && origin2k[1] === 0.0 && origin2k[2] === 0.0 ? nxyzStart : origin2k,
- spacegroupNumber: readInt(22),
- cellSize: getArray(readFloat, 10, 3),
- cellAngles: getArray(readFloat, 13, 3),
+ spacegroupNumber: ccp4Header.ISPG,
+ cellSize: [ccp4Header.xLength, ccp4Header.yLength, ccp4Header.zLength],
+ cellAngles: [ccp4Header.alpha, ccp4Header.beta, ccp4Header.gamma],
// mean: readFloat(21),
littleEndian,
- dataOffset: headerSize + readInt(23) /* symBytes */
+ dataOffset: 256 * 4 + ccp4Header.NSYMBT /* symBytes */
};
// "normalize" the grid axis order
header.grid = [header.grid[header.axisOrder[0]], header.grid[header.axisOrder[1]], header.grid[header.axisOrder[2]]];
@@ -153,7 +133,8 @@ export async function readSlices(data: Data) {
}
export async function open(name: string, filename: string): Promise<Data> {
- const file = await File.openRead(filename);
+ const descriptor = await File.openRead(filename);
+ const file = FileHandle.fromDescriptor(descriptor)
const header = await readHeader(name, file);
return {
header,
diff --git a/src/servers/volume/pack/data-model.ts b/src/servers/volume/pack/data-model.ts
index 268fdeb5cd9dbb43f7d194f2f4a0d08e069085b8..ef6696b41c460a3026aa82a725a941b4edf82380 100644
--- a/src/servers/volume/pack/data-model.ts
+++ b/src/servers/volume/pack/data-model.ts
@@ -7,6 +7,8 @@
*/
import * as CCP4 from './ccp4'
import * as DataFormat from '../common/data-format'
+import { FileHandle } from 'mol-io/common/file-handle';
+import { SimpleBuffer } from 'mol-io/common/simple-buffer';
const FORMAT_VERSION = '1.0.0';
@@ -24,7 +26,7 @@ export interface ValuesInfo {
export interface BlockBuffer {
values: DataFormat.ValueArray[],
- buffers: Buffer[],
+ buffers: SimpleBuffer[],
slicesWritten: number
}
@@ -68,7 +70,7 @@ export interface Kernel {
export interface Context {
/** Output file handle */
- file: number,
+ file: FileHandle,
/** Periodic are x-ray density files that cover the entire grid and have [0,0,0] origin */
isPeriodic: boolean,
@@ -77,9 +79,9 @@ export interface Context {
valueType: DataFormat.ValueType,
blockSize: number,
/** Able to store channels.length * blockSize^3 values. */
- cubeBuffer: Buffer,
+ cubeBuffer: SimpleBuffer,
/** All values are stored in little endian format which might not be the native endian of the system */
- litteEndianCubeBuffer: Buffer,
+ litteEndianCubeBuffer: SimpleBuffer,
kernel: Kernel,
sampling: Sampling[],
diff --git a/src/servers/volume/pack/main.ts b/src/servers/volume/pack/main.ts
index 116be4bb1f030f8546d0f5a8b48aa3566fb0d5a4..a3ccc8b7a8ea2244be386949303e1a6aea1a040c 100644
--- a/src/servers/volume/pack/main.ts
+++ b/src/servers/volume/pack/main.ts
@@ -11,7 +11,7 @@ import * as File from '../common/file'
import * as Data from './data-model'
import * as Sampling from './sampling'
import * as DataFormat from '../common/data-format'
-import * as fs from 'fs'
+import { FileHandle } from 'mol-io/common/file-handle';
export default async function pack(input: { name: string, filename: string }[], blockSize: number, isPeriodic: boolean, outputFilename: string) {
try {
@@ -36,7 +36,7 @@ function updateAllocationProgress(progress: Data.Progress, progressDone: number)
}
/**
- * Pre allocate the disk space to be able to do "random" writes into the entire file.
+ * Pre allocate the disk space to be able to do "random" writes into the entire file.
*/
async function allocateFile(ctx: Data.Context) {
const { totalByteSize, file } = ctx;
@@ -44,7 +44,7 @@ async function allocateFile(ctx: Data.Context) {
const progress: Data.Progress = { current: 0, max: Math.ceil(totalByteSize / buffer.byteLength) };
let written = 0;
while (written < totalByteSize) {
- written += fs.writeSync(file, buffer, 0, Math.min(totalByteSize - written, buffer.byteLength));
+ written += file.writeBufferSync(written, buffer, Math.min(totalByteSize - written, buffer.byteLength));
updateAllocationProgress(progress, 1);
}
}
@@ -66,7 +66,7 @@ function determineBlockSize(data: CCP4.Data, blockSize: number) {
async function writeHeader(ctx: Data.Context) {
const header = DataFormat.encodeHeader(Data.createHeader(ctx));
await File.writeInt(ctx.file, header.byteLength, 0);
- await File.writeBuffer(ctx.file, 4, header);
+ await ctx.file.writeBuffer(4, header);
}
async function create(filename: string, sourceDensities: { name: string, filename: string }[], sourceBlockSize: number, isPeriodic: boolean) {
@@ -81,7 +81,7 @@ async function create(filename: string, sourceDensities: { name: string, filenam
}
process.stdout.write('Initializing... ');
- const files: number[] = [];
+ const files: FileHandle[] = [];
try {
// Step 1a: Read the CCP4 headers
const channels: CCP4.Data[] = [];
@@ -102,18 +102,18 @@ async function create(filename: string, sourceDensities: { name: string, filenam
console.log(`Block size: ${blockSize}`);
- // Step 2: Allocate disk space.
+ // Step 2: Allocate disk space.
process.stdout.write('Allocating... 0%');
await allocateFile(context);
process.stdout.write('\rAllocating... done.\n');
- // Step 3: Process and write the data
+ // Step 3: Process and write the data
process.stdout.write('Writing data... 0%');
await Sampling.processData(context);
process.stdout.write('\rWriting data... done.\n');
// Step 4: Write the header at the start of the file.
- // The header is written last because the sigma/min/max values are computed
+ // The header is written last because the sigma/min/max values are computed
// during step 3.
process.stdout.write('Writing header... ');
await writeHeader(context);
@@ -123,11 +123,11 @@ async function create(filename: string, sourceDensities: { name: string, filenam
const time = getTime() - startedTime;
console.log(`[Done] ${time.toFixed(0)}ms.`);
} finally {
- for (let f of files) File.close(f);
+ for (let f of files) f.close();
// const ff = await File.openRead(filename);
// const hh = await DataFormat.readHeader(ff);
// File.close(ff);
// console.log(hh.header);
}
-}
\ No newline at end of file
+}
\ No newline at end of file
diff --git a/src/servers/volume/pack/sampling.ts b/src/servers/volume/pack/sampling.ts
index e193fb218bba78b243e4ebbcf4d837ec705bd552..9c5cc44c7546201ca4d55b56c71f49253af5c72e 100644
--- a/src/servers/volume/pack/sampling.ts
+++ b/src/servers/volume/pack/sampling.ts
@@ -12,6 +12,7 @@ import * as File from '../common/file'
import * as Downsampling from './downsampling'
import * as Writer from './writer'
import * as DataFormat from '../common/data-format'
+import { FileHandle } from 'mol-io/common/file-handle';
export async function createContext(filename: string, channels: CCP4.Data[], blockSize: number, isPeriodic: boolean): Promise<Data.Context> {
const header = channels[0].header;
@@ -29,7 +30,7 @@ export async function createContext(filename: string, channels: CCP4.Data[], blo
}
const ctx: Data.Context = {
- file: await File.createFile(filename),
+ file: FileHandle.fromDescriptor(await File.createFile(filename)),
isPeriodic,
channels,
valueType,
diff --git a/src/servers/volume/pack/writer.ts b/src/servers/volume/pack/writer.ts
index 6cf357df36f23a3a36e0724d8709c97a511e4c6a..e63750780a0f9241ce105ad9980a7a0887d98fb7 100644
--- a/src/servers/volume/pack/writer.ts
+++ b/src/servers/volume/pack/writer.ts
@@ -19,7 +19,7 @@ export async function writeBlockLayer(ctx: Data.Context, sampling: Data.Sampling
for (let v = 0; v < nV; v++) {
for (let u = 0; u < nU; u++) {
const size = fillCubeBuffer(ctx, sampling, u, v);
- await File.writeBuffer(ctx.file, startOffset + sampling.writeByteOffset, ctx.litteEndianCubeBuffer, size);
+ await ctx.file.writeBuffer(startOffset + sampling.writeByteOffset, ctx.litteEndianCubeBuffer, size);
sampling.writeByteOffset += size;
updateProgress(ctx.progress, 1);
}
@@ -46,7 +46,8 @@ function fillCubeBuffer(ctx: Data.Context, sampling: Data.Sampling, u: number, v
for (let k = offsetK; k < maxK; k++) {
// copying the bytes direct is faster than using buffer.write* functions.
const start = (l * sizeHK + k * sizeH + offsetH) * elementSize;
- src.copy(cubeBuffer, writeOffset, start, start + copyH);
+ // TODO
+ cubeBuffer.set(src.subarray(start, start + copyH), writeOffset)
writeOffset += copyH;
}
}
diff --git a/src/servers/volume/server/api.ts b/src/servers/volume/server/api.ts
index c1046a4875498e357e62f37450109b264161a797..42f028cf0f6890cc38cc70d5626e33c7955eab38 100644
--- a/src/servers/volume/server/api.ts
+++ b/src/servers/volume/server/api.ts
@@ -12,6 +12,7 @@ import * as Data from './query/data-model'
import { ConsoleLogger } from 'mol-util/console-logger'
import * as DataFormat from '../common/data-format'
import ServerConfig from '../server-config'
+import { FileHandle } from 'mol-io/common/file-handle';
export function getOutputFilename(source: string, id: string, { asBinary, box, detail, forcedSamplingLevel }: Data.QueryParams) {
function n(s: string) { return (s || '').replace(/[ \n\t]/g, '').toLowerCase() }
@@ -57,16 +58,16 @@ export async function queryBox(params: Data.QueryParams, outputProvider: () => D
}
async function readHeader(filename: string | undefined, sourceId: string) {
- let file: number | undefined = void 0;
+ let file: FileHandle | undefined;
try {
if (!filename) return void 0;
- file = await File.openRead(filename);
+ file = FileHandle.fromDescriptor(await File.openRead(filename));
const header = await DataFormat.readHeader(file);
return header.header;
} catch (e) {
ConsoleLogger.error(`Info ${sourceId}`, e);
return void 0;
} finally {
- File.close(file);
+ if (file) file.close();
}
}
\ No newline at end of file
diff --git a/src/servers/volume/server/query/data-model.ts b/src/servers/volume/server/query/data-model.ts
index d20c192ce4b1c319fac66eedc57858ab319c9e7d..9df53a9414cd4e7da79d00faffbcc5f63bf93d6a 100644
--- a/src/servers/volume/server/query/data-model.ts
+++ b/src/servers/volume/server/query/data-model.ts
@@ -11,6 +11,7 @@ import * as Coords from '../algebra/coordinate'
import * as Box from '../algebra/box'
import Writer from 'mol-io/writer/writer'
import { SpacegroupCell } from 'mol-math/geometry';
+import { FileHandle } from 'mol-io/common/file-handle';
//////////////////////////////////////
// DATA
@@ -25,7 +26,7 @@ export interface Sampling {
}
export interface DataContext {
- file: number,
+ file: FileHandle,
header: DataFormat.Header,
spacegroup: SpacegroupCell,
dataBox: Box.Fractional,
diff --git a/src/servers/volume/server/query/execute.ts b/src/servers/volume/server/query/execute.ts
index c5d4272dfdbb87975ec80759d5abab86e4cdf6cf..cf62baa880b7e561b04d18d8da6a5f059020fabb 100644
--- a/src/servers/volume/server/query/execute.ts
+++ b/src/servers/volume/server/query/execute.ts
@@ -21,6 +21,7 @@ import encode from './encode'
import { SpacegroupCell } from 'mol-math/geometry';
import { Vec3 } from 'mol-math/linear-algebra';
import { UUID } from 'mol-util';
+import { FileHandle } from 'mol-io/common/file-handle';
export default async function execute(params: Data.QueryParams, outputProvider: () => Data.QueryOutputStream) {
const start = getTime();
@@ -30,16 +31,16 @@ export default async function execute(params: Data.QueryParams, outputProvider:
params.detail = Math.min(Math.max(0, params.detail | 0), ServerConfig.limits.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1);
ConsoleLogger.logId(guid, 'Info', `id=${params.sourceId},encoding=${params.asBinary ? 'binary' : 'text'},detail=${params.detail},${queryBoxToString(params.box)}`);
- let sourceFile: number | undefined = void 0;
+ let sourceFile: FileHandle | undefined;
try {
- sourceFile = await File.openRead(params.sourceFilename);
+ sourceFile = FileHandle.fromDescriptor(await File.openRead(params.sourceFilename));
await _execute(sourceFile, params, guid, outputProvider);
return true;
} catch (e) {
ConsoleLogger.errorId(guid, e);
return false;
} finally {
- File.close(sourceFile);
+ if (sourceFile) sourceFile.close();
ConsoleLogger.logId(guid, 'Time', `${Math.round(getTime() - start)}ms`);
State.pendingQueries--;
}
@@ -80,7 +81,7 @@ function createSampling(header: DataFormat.Header, index: number, dataOffset: nu
}
}
-async function createDataContext(file: number): Promise<Data.DataContext> {
+async function createDataContext(file: FileHandle): Promise<Data.DataContext> {
const { header, dataOffset } = await DataFormat.readHeader(file);
const origin = Coords.fractional(header.origin[0], header.origin[1], header.origin[2]);
@@ -185,7 +186,7 @@ function createQueryContext(data: Data.DataContext, params: Data.QueryParams, gu
}
-async function _execute(file: number, params: Data.QueryParams, guid: string, outputProvider: () => Data.QueryOutputStream) {
+async function _execute(file: FileHandle, params: Data.QueryParams, guid: string, outputProvider: () => Data.QueryOutputStream) {
let output: any = void 0;
try {
// Step 1a: Create data context