From 627b2c7bab30bf3bce78972c1e1bc8854e6e3cb2 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Thu, 21 Feb 2019 14:13:02 -0800
Subject: [PATCH] volume parser tweaks and fixes
---
src/mol-io/common/simple-buffer.ts | 8 +++
src/mol-io/reader/ccp4/parser.ts | 41 ++++++-------
src/mol-io/reader/ccp4/schema.ts | 2 +-
src/mol-io/reader/dsn6/parser.ts | 92 +++++++++++++++++-------------
4 files changed, 81 insertions(+), 62 deletions(-)
diff --git a/src/mol-io/common/simple-buffer.ts b/src/mol-io/common/simple-buffer.ts
index 3ecbaecbc..8825388f1 100644
--- a/src/mol-io/common/simple-buffer.ts
+++ b/src/mol-io/common/simple-buffer.ts
@@ -103,4 +103,12 @@ export namespace SimpleBuffer {
}
}
}
+
+ export function flipByteOrderInPlace2(buffer: ArrayBuffer, byteOffset = 0, length?: number) {
+ const intView = new Int16Array(buffer, byteOffset, length)
+ for (let i = 0, n = intView.length; i < n; ++i) {
+ const val = intView[i]
+ intView[i] = ((val & 0xff) << 8) | ((val >> 8) & 0xff)
+ }
+ }
}
\ No newline at end of file
diff --git a/src/mol-io/reader/ccp4/parser.ts b/src/mol-io/reader/ccp4/parser.ts
index 388c22a87..b81f9cca3 100644
--- a/src/mol-io/reader/ccp4/parser.ts
+++ b/src/mol-io/reader/ccp4/parser.ts
@@ -10,16 +10,14 @@ import { ReaderResult as Result } from '../result'
import { FileHandle } from '../../common/file-handle';
import { SimpleBuffer } from 'mol-io/common/simple-buffer';
-export async function readCcp4Header(file: FileHandle) {
+export async function readCcp4Header(file: FileHandle): Promise<{ header: Ccp4Header, littleEndian: boolean }> {
const headerSize = 1024;
const { buffer } = await file.readBuffer(0, headerSize)
- const bin = buffer.buffer
- const dv = new DataView(bin)
// 53 MAP Character string 'MAP ' to identify file type
const MAP = String.fromCharCode(
- dv.getUint8(52 * 4), dv.getUint8(52 * 4 + 1),
- dv.getUint8(52 * 4 + 2), dv.getUint8(52 * 4 + 3)
+ buffer.readUInt8(52 * 4), buffer.readUInt8(52 * 4 + 1),
+ buffer.readUInt8(52 * 4 + 2), buffer.readUInt8(52 * 4 + 3)
)
if (MAP !== 'MAP ') {
throw new Error('ccp4 format error, missing "MAP " string');
@@ -27,15 +25,15 @@ export async function readCcp4Header(file: FileHandle) {
// 54 MACHST Machine stamp indicating machine type which wrote file
// 17 and 17 for big-endian or 68 and 65 for little-endian
- const MACHST = [ dv.getUint8(53 * 4), dv.getUint8(53 * 4 + 1) ]
+ const MACHST = [ buffer.readUInt8(53 * 4), buffer.readUInt8(53 * 4 + 1) ]
let littleEndian = true
// found MRC files that don't have the MACHST stamp set and are big-endian
if (MACHST[0] !== 68 && MACHST[1] !== 65) {
littleEndian = false;
}
- const readInt = (o: number) => dv.getInt32(o * 4, littleEndian)
- const readFloat = (o: number) => dv.getFloat32(o * 4, littleEndian)
+ const readInt = littleEndian ? (o: number) => buffer.readInt32LE(o * 4) : (o: number) => buffer.readInt32BE(o * 4)
+ const readFloat = littleEndian ? (o: number) => buffer.readFloatLE(o * 4) : (o: number) => buffer.readFloatBE(o * 4)
const header: Ccp4Header = {
NC: readInt(0),
@@ -98,15 +96,12 @@ export async function readCcp4Header(file: FileHandle) {
}
function getElementByteSize(mode: number) {
- if (mode === 2) {
- return 4
- } else if (mode === 1) {
- return 2
- } else if (mode === 0) {
- return 1
- } else {
- throw new Error(`ccp4 mode '${mode}' unsupported`);
+ switch (mode) {
+ case 2: return 4
+ case 1: return 2
+ case 0: return 1
}
+ throw new Error(`ccp4 mode '${mode}' unsupported`);
}
async function parseInternal(file: FileHandle, size: number, ctx: RuntimeContext): Promise<Ccp4File> {
@@ -115,17 +110,23 @@ async function parseInternal(file: FileHandle, size: number, ctx: RuntimeContext
const { header, littleEndian } = await readCcp4Header(file)
const offset = 256 * 4 + header.NSYMBT
+ const { buffer, bytesRead } = await file.readBuffer(offset, size - offset)
+
const count = header.NC * header.NR * header.NS
const elementByteSize = getElementByteSize(header.MODE)
const byteCount = count * elementByteSize
- const { buffer } = await file.readBuffer(offset, size)
+ if (byteCount !== bytesRead) {
+ console.warn(`byteCount ${byteCount} and bytesRead ${bytesRead} differ`)
+ }
let values
if (header.MODE === 2) {
- values = new Float32Array(buffer, offset, count)
+ values = new Float32Array(buffer.buffer, offset, count)
+ } else if (header.MODE === 1) {
+ values = new Int16Array(buffer.buffer, offset, count)
} else if (header.MODE === 0) {
- values = new Int8Array(buffer, offset, count)
+ values = new Int8Array(buffer.buffer, offset, count)
} else {
throw new Error(`ccp4 mode '${header.MODE}' unsupported`);
}
@@ -136,7 +137,7 @@ async function parseInternal(file: FileHandle, size: number, ctx: RuntimeContext
// if the file was converted by mapmode2to0 - scale the data
// based on uglymol (https://github.com/uglymol/uglymol) by Marcin Wojdyr (wojdyr)
- if (header.userFlag1 -128 && header.userFlag2 === 127) {
+ if (header.userFlag1 === -128 && header.userFlag2 === 127) {
values = new Float32Array(values)
// scaling f(x)=b1*x+b0 such that f(-128)=min and f(127)=max
const b1 = (header.AMAX - header.AMIN) / 255.0
diff --git a/src/mol-io/reader/ccp4/schema.ts b/src/mol-io/reader/ccp4/schema.ts
index 1263b590d..f896f81d7 100644
--- a/src/mol-io/reader/ccp4/schema.ts
+++ b/src/mol-io/reader/ccp4/schema.ts
@@ -115,5 +115,5 @@ export interface Ccp4Header {
*/
export interface Ccp4File {
header: Ccp4Header
- values: Float32Array | Int8Array
+ values: Float32Array | Int16Array | Int8Array
}
\ No newline at end of file
diff --git a/src/mol-io/reader/dsn6/parser.ts b/src/mol-io/reader/dsn6/parser.ts
index 737e7461b..2dcfbe060 100644
--- a/src/mol-io/reader/dsn6/parser.ts
+++ b/src/mol-io/reader/dsn6/parser.ts
@@ -10,6 +10,8 @@ import { ReaderResult as Result } from '../result'
import { FileHandle } from '../../common/file-handle';
import { SimpleBuffer } from 'mol-io/common/simple-buffer';
+export const dsn6HeaderSize = 512;
+
function parseBrixHeader(str: string): Dsn6Header {
return {
xStart: parseInt(str.substr(10, 5)),
@@ -33,61 +35,69 @@ function parseBrixHeader(str: string): Dsn6Header {
}
}
-function parseDsn6Header(int: Int16Array): Dsn6Header {
- const factor = 1 / int[ 17 ]
+function parseDsn6Header(buffer: SimpleBuffer, littleEndian: boolean): Dsn6Header {
+ const readInt = littleEndian ? (o: number) => buffer.readInt16LE(o * 2) : (o: number) => buffer.readInt16BE(o * 2)
+ const factor = 1 / readInt(17)
return {
- xStart: int[ 0 ],
- yStart: int[ 1 ],
- zStart: int[ 2 ],
- xExtent: int[ 3 ],
- yExtent: int[ 4 ],
- zExtent: int[ 5 ],
- xRate: int[ 6 ],
- yRate: int[ 7 ],
- zRate: int[ 8 ],
- xlen: int[ 9 ] * factor,
- ylen: int[ 10 ] * factor,
- zlen: int[ 11 ] * factor,
- alpha: int[ 12 ] * factor,
- beta: int[ 13 ] * factor,
- gamma: int[ 14 ] * factor,
- divisor: int[ 15 ] / 100,
- summand: int[ 16 ],
+ xStart: readInt(0),
+ yStart: readInt(1),
+ zStart: readInt(2),
+ xExtent: readInt(3),
+ yExtent: readInt(4),
+ zExtent: readInt(5),
+ xRate: readInt(6),
+ yRate: readInt(7),
+ zRate: readInt(8),
+ xlen: readInt(9) * factor,
+ ylen: readInt(10) * factor,
+ zlen: readInt(11) * factor,
+ alpha: readInt(12) * factor,
+ beta: readInt(13) * factor,
+ gamma: readInt(14) * factor,
+ divisor: readInt(15) / 100,
+ summand: readInt(16),
sigma: undefined
}
}
-async function parseInternal(file: FileHandle, size: number, ctx: RuntimeContext): Promise<Dsn6File> {
- await ctx.update({ message: 'Parsing DSN6/BRIX file...' });
-
- const { buffer } = await file.readBuffer(0, size)
- const bin = buffer.buffer
-
- const intView = new Int16Array(bin)
- const byteView = new Uint8Array(bin)
- const brixStr = String.fromCharCode.apply(null, byteView.subarray(0, 512))
+export async function readDsn6Header(file: FileHandle): Promise<{ header: Dsn6Header, littleEndian: boolean }> {
+ const { buffer } = await file.readBuffer(0, dsn6HeaderSize)
+ const brixStr = String.fromCharCode.apply(null, buffer) as string
const isBrix = brixStr.startsWith(':-)')
+ const littleEndian = isBrix || buffer.readInt16LE(18 * 2) === 100
+ const header = isBrix ? parseBrixHeader(brixStr) : parseDsn6Header(buffer, littleEndian)
+ return { header, littleEndian }
+}
- if (!isBrix) {
- // for DSN6, swap byte order when big endian
- if (intView[18] !== 100) {
- for (let i = 0, n = intView.length; i < n; ++i) {
- const val = intView[i]
- intView[i] = ((val & 0xff) << 8) | ((val >> 8) & 0xff)
- }
- }
- }
+async function parseInternal(file: FileHandle, size: number, ctx: RuntimeContext): Promise<Dsn6File> {
+ await ctx.update({ message: 'Parsing DSN6/BRIX file...' });
- const header = isBrix ? parseBrixHeader(brixStr) : parseDsn6Header(intView)
+ const { header, littleEndian } = await readDsn6Header(file)
const { divisor, summand } = header
- const values = new Float32Array(header.xExtent * header.yExtent * header.zExtent)
+ const { buffer, bytesRead } = await file.readBuffer(dsn6HeaderSize, size - dsn6HeaderSize)
- let offset = 512
const xBlocks = Math.ceil(header.xExtent / 8)
const yBlocks = Math.ceil(header.yExtent / 8)
const zBlocks = Math.ceil(header.zExtent / 8)
+ const valueCount = header.xExtent * header.yExtent * header.zExtent
+
+ const count = xBlocks * 8 * yBlocks * 8 * zBlocks * 8
+ const elementByteSize = 1
+ const byteCount = count * elementByteSize
+
+ if (byteCount !== bytesRead) {
+ console.warn(`byteCount ${byteCount} and bytesRead ${bytesRead} differ`)
+ }
+
+ const values = new Float32Array(valueCount)
+
+ if (!littleEndian) {
+ // even though the values are one byte they need to be swapped like they are 2
+ SimpleBuffer.flipByteOrderInPlace2(buffer.buffer)
+ }
+ let offset = 0
// loop over blocks
for (let zz = 0; zz < zBlocks; ++zz) {
for (let yy = 0; yy < yBlocks; ++yy) {
@@ -102,7 +112,7 @@ async function parseInternal(file: FileHandle, size: number, ctx: RuntimeContext
// check if remaining slice-part contains values
if (x < header.xExtent && y < header.yExtent && z < header.zExtent) {
const idx = ((((x * header.yExtent) + y) * header.zExtent) + z)
- values[ idx ] = (byteView[ offset ] - summand) / divisor
+ values[idx] = (buffer[offset] - summand) / divisor
++offset
} else {
offset += 8 - i
--
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