import {
Tag,
isSequenceDelimitationItemTag,
isItemDelimitationItemTag,
isPixelDataTag
} from './dicomTag';
import {
is32bitVLVR,
isCharSetStringVR,
vrTypes,
} from './dictionary';
import {DataReader} from './dataReader';
import {logger} from '../utils/logger';
import {arrayEquals} from '../utils/array';
// doc imports
/* eslint-disable no-unused-vars */
import {DataElement} from '../dicom/dataElement';
/* eslint-enable no-unused-vars */
/**
* List of DICOM data elements indexed via a 8 character string formed from
* the group and element numbers.
*
* @typedef {Object<string, DataElement>} DataElements
*/
/**
* Get the version of the library.
*
* @returns {string} The version of the library.
*/
export function getDwvVersion() {
return '0.32.2';
}
/**
* Check that an input buffer includes the DICOM prefix 'DICM'
* after the 128 bytes preamble.
* Ref: [DICOM File Meta]{@link https://dicom.nema.org/dicom/2013/output/chtml/part10/chapter_7.html#sect_7.1}
*
* @param {ArrayBuffer} buffer The buffer to check.
* @returns {boolean} True if the buffer includes the prefix.
*/
export function hasDicomPrefix(buffer) {
const prefixArray = new Uint8Array(buffer, 128, 4);
const stringReducer = function (previous, current) {
return previous += String.fromCharCode(current);
};
return prefixArray.reduce(stringReducer, '') === 'DICM';
}
// Zero-width space (u200B)
// @ts-ignore
const ZWS = String.fromCharCode('u200B');
/**
* Clean string: remove zero-width space ending and trim.
* Warning: no tests are done on the input, will fail if
* null or undefined or not string.
* (exported for tests only)
*
* @param {string} inputStr The string to clean.
* @returns {string} The cleaned string.
*/
export function cleanString(inputStr) {
let res = inputStr;
// get rid of ending zero-width space
const lastIndex = inputStr.length - 1;
if (inputStr[lastIndex] === ZWS) {
res = inputStr.substring(0, lastIndex);
}
// trim spaces
res = res.trim();
// return
return res;
}
/**
* Get the utfLabel (used by the TextDecoder) from a character set term
* References:
* - DICOM [Value Encoding]{@link http://dicom.nema.org/dicom/2013/output/chtml/part05/chapter_6.html}
* - DICOM [Specific Character Set]{@link http://dicom.nema.org/dicom/2013/output/chtml/part03/sect_C.12.html#sect_C.12.1.1.2}
* - [TextDecoder#Parameters]{@link https://developer.mozilla.org/en-US/docs/Web/API/TextDecoder/TextDecoder#Parameters}
*
* @param {string} charSetTerm The DICOM character set.
* @returns {string} The corresponding UTF label.
*/
function getUtfLabel(charSetTerm) {
let label = 'utf-8';
if (charSetTerm === 'ISO_IR 100') {
label = 'iso-8859-1';
} else if (charSetTerm === 'ISO_IR 101') {
label = 'iso-8859-2';
} else if (charSetTerm === 'ISO_IR 109') {
label = 'iso-8859-3';
} else if (charSetTerm === 'ISO_IR 110') {
label = 'iso-8859-4';
} else if (charSetTerm === 'ISO_IR 144') {
label = 'iso-8859-5';
} else if (charSetTerm === 'ISO_IR 127') {
label = 'iso-8859-6';
} else if (charSetTerm === 'ISO_IR 126') {
label = 'iso-8859-7';
} else if (charSetTerm === 'ISO_IR 138') {
label = 'iso-8859-8';
} else if (charSetTerm === 'ISO_IR 148') {
label = 'iso-8859-9';
} else if (charSetTerm === 'ISO_IR 13') {
label = 'shift-jis';
} else if (charSetTerm === 'ISO_IR 166') {
label = 'iso-8859-11';
} else if (charSetTerm === 'ISO 2022 IR 87') {
label = 'iso-2022-jp';
} else if (charSetTerm === 'ISO 2022 IR 149') {
// not supported by TextDecoder when it says it should...
//label = "iso-2022-kr";
} else if (charSetTerm === 'ISO 2022 IR 58') {
// not supported by TextDecoder...
//label = "iso-2022-cn";
} else if (charSetTerm === 'ISO_IR 192') {
label = 'utf-8';
} else if (charSetTerm === 'GB18030') {
label = 'gb18030';
} else if (charSetTerm === 'GB2312') {
label = 'gb2312';
} else if (charSetTerm === 'GBK') {
label = 'chinese';
}
return label;
}
/**
* Default text decoder
*/
class DefaultTextDecoder {
/**
* Decode an input string buffer.
*
* @param {Uint8Array} buffer The buffer to decode.
* @returns {string} The decoded string.
*/
decode(buffer) {
let result = '';
for (let i = 0, leni = buffer.length; i < leni; ++i) {
result += String.fromCharCode(buffer[i]);
}
return result;
}
}
/**
* Get patient orientation label in the reverse direction.
*
* @param {string} ori Patient Orientation value.
* @returns {string} Reverse Orientation Label.
*/
export function getReverseOrientation(ori) {
if (!ori) {
return null;
}
// reverse labels
const rlabels = {
L: 'R',
R: 'L',
A: 'P',
P: 'A',
H: 'F',
F: 'H'
};
let rori = '';
for (let n = 0; n < ori.length; n++) {
const o = ori.substring(n, n + 1);
const r = rlabels[o];
if (r) {
rori += r;
}
}
// return
return rori;
}
/**
* Get the name of an image orientation patient.
*
* @param {Array} orientation The image orientation patient.
* @returns {string} The orientation name: axial, coronal or sagittal.
*/
export function getOrientationName(orientation) {
const axialOrientation = [1, 0, 0, 0, 1, 0];
const coronalOrientation = [1, 0, 0, 0, 0, -1];
const sagittalOrientation = [0, 1, 0, 0, 0, -1];
let name;
if (arrayEquals(orientation, axialOrientation)) {
name = 'axial';
} else if (arrayEquals(orientation, coronalOrientation)) {
name = 'coronal';
} else if (arrayEquals(orientation, sagittalOrientation)) {
name = 'sagittal';
}
return name;
}
/**
* Tell if a given syntax is an implicit one (element with no VR).
*
* @param {string} syntax The transfer syntax to test.
* @returns {boolean} True if an implicit syntax.
*/
export function isImplicitTransferSyntax(syntax) {
return syntax === '1.2.840.10008.1.2';
}
/**
* Tell if a given syntax is a big endian syntax.
*
* @param {string} syntax The transfer syntax to test.
* @returns {boolean} True if a big endian syntax.
*/
export function isBigEndianTransferSyntax(syntax) {
return syntax === '1.2.840.10008.1.2.2';
}
/**
* Tell if a given syntax is a JPEG baseline one.
*
* @param {string} syntax The transfer syntax to test.
* @returns {boolean} True if a jpeg baseline syntax.
*/
export function isJpegBaselineTransferSyntax(syntax) {
return syntax === '1.2.840.10008.1.2.4.50' ||
syntax === '1.2.840.10008.1.2.4.51';
}
/**
* Tell if a given syntax is a retired JPEG one.
*
* @param {string} syntax The transfer syntax to test.
* @returns {boolean} True if a retired jpeg syntax.
*/
function isJpegRetiredTransferSyntax(syntax) {
return (syntax.match(/1.2.840.10008.1.2.4.5/) !== null &&
!isJpegBaselineTransferSyntax(syntax) &&
!isJpegLosslessTransferSyntax(syntax)) ||
syntax.match(/1.2.840.10008.1.2.4.6/) !== null;
}
/**
* Tell if a given syntax is a JPEG Lossless one.
*
* @param {string} syntax The transfer syntax to test.
* @returns {boolean} True if a jpeg lossless syntax.
*/
export function isJpegLosslessTransferSyntax(syntax) {
return syntax === '1.2.840.10008.1.2.4.57' ||
syntax === '1.2.840.10008.1.2.4.70';
}
/**
* Tell if a given syntax is a JPEG-LS one.
*
* @param {string} syntax The transfer syntax to test.
* @returns {boolean} True if a jpeg-ls syntax.
*/
function isJpeglsTransferSyntax(syntax) {
return syntax.match(/1.2.840.10008.1.2.4.8/) !== null;
}
/**
* Tell if a given syntax is a JPEG 2000 one.
*
* @param {string} syntax The transfer syntax to test.
* @returns {boolean} True if a jpeg 2000 syntax.
*/
export function isJpeg2000TransferSyntax(syntax) {
return syntax.match(/1.2.840.10008.1.2.4.9/) !== null;
}
/**
* Tell if a given syntax is a RLE (Run-length encoding) one.
*
* @param {string} syntax The transfer syntax to test.
* @returns {boolean} True if a RLE syntax.
*/
function isRleTransferSyntax(syntax) {
return syntax.match(/1.2.840.10008.1.2.5/) !== null;
}
/**
* Tell if a given syntax needs decompression.
*
* @param {string} syntax The transfer syntax to test.
* @returns {string} The name of the decompression algorithm.
*/
export function getSyntaxDecompressionName(syntax) {
let algo = null;
if (isJpeg2000TransferSyntax(syntax)) {
algo = 'jpeg2000';
} else if (isJpegBaselineTransferSyntax(syntax)) {
algo = 'jpeg-baseline';
} else if (isJpegLosslessTransferSyntax(syntax)) {
algo = 'jpeg-lossless';
} else if (isRleTransferSyntax(syntax)) {
algo = 'rle';
}
return algo;
}
/**
* Tell if a given syntax is supported for reading.
*
* @param {string} syntax The transfer syntax to test.
* @returns {boolean} True if a supported syntax.
*/
function isReadSupportedTransferSyntax(syntax) {
// Unsupported:
// "1.2.840.10008.1.2.1.99": Deflated Explicit VR - Little Endian
// "1.2.840.10008.1.2.4.100": MPEG2 Image Compression
// isJpegRetiredTransferSyntax(syntax): non supported JPEG
// isJpeglsTransferSyntax(syntax): JPEG-LS
return (syntax === '1.2.840.10008.1.2' || // Implicit VR - Little Endian
syntax === '1.2.840.10008.1.2.1' || // Explicit VR - Little Endian
syntax === '1.2.840.10008.1.2.2' || // Explicit VR - Big Endian
isJpegBaselineTransferSyntax(syntax) || // JPEG baseline
isJpegLosslessTransferSyntax(syntax) || // JPEG Lossless
isJpeg2000TransferSyntax(syntax) || // JPEG 2000
isRleTransferSyntax(syntax)); // RLE
}
/**
* Get the transfer syntax name.
* Reference: [UID Values]{@link http://dicom.nema.org/dicom/2013/output/chtml/part06/chapter_A.html}.
*
* @param {string} syntax The transfer syntax.
* @returns {string} The name of the transfer syntax.
*/
export function getTransferSyntaxName(syntax) {
let name = 'Unknown';
if (syntax === '1.2.840.10008.1.2') {
// Implicit VR - Little Endian
name = 'Little Endian Implicit';
} else if (syntax === '1.2.840.10008.1.2.1') {
// Explicit VR - Little Endian
name = 'Little Endian Explicit';
} else if (syntax === '1.2.840.10008.1.2.1.99') {
// Deflated Explicit VR - Little Endian
name = 'Little Endian Deflated Explicit';
} else if (syntax === '1.2.840.10008.1.2.2') {
// Explicit VR - Big Endian
name = 'Big Endian Explicit';
} else if (isJpegBaselineTransferSyntax(syntax)) {
// JPEG baseline
if (syntax === '1.2.840.10008.1.2.4.50') {
name = 'JPEG Baseline';
} else { // *.51
name = 'JPEG Extended, Process 2+4';
}
} else if (isJpegLosslessTransferSyntax(syntax)) {
// JPEG Lossless
if (syntax === '1.2.840.10008.1.2.4.57') {
name = 'JPEG Lossless, Nonhierarchical (Processes 14)';
} else { // *.70
name = 'JPEG Lossless, Non-hierarchical, 1st Order Prediction';
}
} else if (isJpegRetiredTransferSyntax(syntax)) {
// Retired JPEG
name = 'Retired JPEG';
} else if (isJpeglsTransferSyntax(syntax)) {
// JPEG-LS
name = 'JPEG-LS';
} else if (isJpeg2000TransferSyntax(syntax)) {
// JPEG 2000
if (syntax === '1.2.840.10008.1.2.4.91') {
name = 'JPEG 2000 (Lossless or Lossy)';
} else { // *.90
name = 'JPEG 2000 (Lossless only)';
}
} else if (syntax === '1.2.840.10008.1.2.4.100') {
// MPEG2 Image Compression
name = 'MPEG2';
} else if (isRleTransferSyntax(syntax)) {
// RLE (lossless)
name = 'RLE';
}
// return
return name;
}
/**
* Guess the transfer syntax from the first data element.
* See https://github.com/ivmartel/dwv/issues/188
* (Allow to load DICOM with no DICM preamble) for more details.
*
* @param {DataElement} firstDataElement The first data element
* of the DICOM header.
* @returns {DataElement} The transfer syntax data element.
*/
function guessTransferSyntax(firstDataElement) {
const oEightGroupBigEndian = '0800';
const oEightGroupLittleEndian = '0008';
// check that group is 0008
const group = firstDataElement.tag.getGroup();
if (group !== oEightGroupBigEndian &&
group !== oEightGroupLittleEndian) {
throw new Error(
'Not a valid DICOM file (no magic DICM word found' +
' and first element not in 0008 group)'
);
}
// reasonable assumption: 2 uppercase characters => explicit vr
const vr = firstDataElement.vr;
const vr0 = vr.charCodeAt(0);
const vr1 = vr.charCodeAt(1);
const implicit = (vr0 >= 65 && vr0 <= 90 && vr1 >= 65 && vr1 <= 90)
? false : true;
// guess transfer syntax
let syntax = null;
if (group === oEightGroupLittleEndian) {
if (implicit) {
// ImplicitVRLittleEndian
syntax = '1.2.840.10008.1.2';
} else {
// ExplicitVRLittleEndian
syntax = '1.2.840.10008.1.2.1';
}
} else {
if (implicit) {
// ImplicitVRBigEndian: impossible
throw new Error(
'Not a valid DICOM file (no magic DICM word found' +
'and implicit VR big endian detected)'
);
} else {
// ExplicitVRBigEndian
syntax = '1.2.840.10008.1.2.2';
}
}
// set transfer syntax data element
const dataElement = new DataElement('UI');
dataElement.tag = new Tag('0002', '0010');
dataElement.value = [syntax + ' ']; // even length
dataElement.vl = dataElement.value[0].length;
dataElement.startOffset = firstDataElement.startOffset;
dataElement.endOffset = dataElement.startOffset + dataElement.vl;
return dataElement;
}
/**
* Get the appropriate TypedArray in function of arguments.
*
* @param {number} bitsAllocated The number of bites used to store
* the data: [8, 16, 32].
* @param {number} pixelRepresentation The pixel representation,
* 0:unsigned;1:signed.
* @param {number} size The size of the new array.
* @returns {Uint8Array|Int8Array|Uint16Array|Int16Array|Uint32Array|Int32Array}
* The good typed array.
*/
export function getTypedArray(bitsAllocated, pixelRepresentation, size) {
let res = null;
try {
if (bitsAllocated === 8) {
if (pixelRepresentation === 0) {
res = new Uint8Array(size);
} else {
res = new Int8Array(size);
}
} else if (bitsAllocated === 16) {
if (pixelRepresentation === 0) {
res = new Uint16Array(size);
} else {
res = new Int16Array(size);
}
} else if (bitsAllocated === 32) {
if (pixelRepresentation === 0) {
res = new Uint32Array(size);
} else {
res = new Int32Array(size);
}
}
} catch (error) {
if (error instanceof RangeError) {
const powerOf2 = Math.floor(Math.log(size) / Math.log(2));
logger.error('Cannot allocate array of size: ' +
size + ' (>2^' + powerOf2 + ').');
}
}
return res;
}
/**
* Get the number of bytes occupied by a data element prefix,
* i.e. without its value.
*
* @param {string} vr The Value Representation of the element.
* @param {boolean} isImplicit Does the data use implicit VR?
* @returns {number} The size of the element prefix.
* WARNING: this is valid for tags with a VR, if not sure use
* the 'isTagWithVR' function first.
* Reference:
* - [Data Element explicit]{@link http://dicom.nema.org/dicom/2013/output/chtml/part05/chapter_7.html#table_7.1-1},
* - [Data Element implicit]{@link http://dicom.nema.org/dicom/2013/output/chtml/part05/sect_7.5.html#table_7.5-1}.
*
* | Tag | VR | VL | Value |
* | 4 | 2 | 2 | X | -> regular explicit: 8 + X
* | 4 | 2+2 | 4 | X | -> 32bit VL: 12 + X
*
* | Tag | VL | Value |
* | 4 | 4 | X | -> implicit (32bit VL): 8 + X
*
* | Tag | Len | Value |
* | 4 | 4 | X | -> item: 8 + X
*/
export function getDataElementPrefixByteSize(vr, isImplicit) {
return isImplicit ? 8 : is32bitVLVR(vr) ? 12 : 8;
}
/**
* DicomParser class.
*
* @example
* // XMLHttpRequest onload callback
* const onload = function (event) {
* // setup the dicom parser
* const dicomParser = new dwv.DicomParser();
* // parse the buffer
* dicomParser.parse(event.target.response);
* // get the dicom tags
* const tags = dicomParser.getDicomElements();
* // display the modality
* const div = document.getElementById('dwv');
* div.appendChild(document.createTextNode(
* 'Modality: ' + tags['00080060'].value[0]
* ));
* };
* // DICOM file request
* const request = new XMLHttpRequest();
* const url = 'https://raw.githubusercontent.com/ivmartel/dwv/master/tests/data/bbmri-53323851.dcm';
* request.open('GET', url);
* request.responseType = 'arraybuffer';
* request.onload = onload;
* request.send();
*/
export class DicomParser {
/**
* The list of DICOM elements.
*
* @type {DataElements}
*/
#dataElements = {};
/**
* Default character set (optional).
*
* @type {string}
*/
#defaultCharacterSet;
/**
* Default text decoder.
*
* @type {DefaultTextDecoder}
*/
#defaultTextDecoder = new DefaultTextDecoder();
/**
* Special text decoder.
*
* @type {DefaultTextDecoder|TextDecoder}
*/
#textDecoder = this.#defaultTextDecoder;
/**
* Decode an input string buffer using the default text decoder.
*
* @param {Uint8Array} buffer The buffer to decode.
* @returns {string} The decoded string.
*/
#decodeString(buffer) {
return this.#defaultTextDecoder.decode(buffer);
}
/**
* Decode an input string buffer using the 'special' text decoder.
*
* @param {Uint8Array} buffer The buffer to decode.
* @returns {string} The decoded string.
*/
#decodeSpecialString(buffer) {
return this.#textDecoder.decode(buffer);
}
/**
* Get the default character set.
*
* @returns {string} The default character set.
*/
getDefaultCharacterSet() {
return this.#defaultCharacterSet;
}
/**
* Set the default character set.
*
* @param {string} characterSet The input character set.
*/
setDefaultCharacterSet(characterSet) {
this.#defaultCharacterSet = characterSet;
}
/**
* Set the text decoder character set.
*
* @param {string} characterSet The input character set.
*/
setDecoderCharacterSet(characterSet) {
/**
* The text decoder.
*
* @external TextDecoder
* @see https://developer.mozilla.org/en-US/docs/Web/API/TextDecoder
*/
this.#textDecoder = new TextDecoder(characterSet);
}
// not using type DataElements since the typedef is not exported with the API
/**
* Get the DICOM data elements.
*
* @returns {Object<string, DataElement>} The data elements.
*/
getDicomElements() {
return this.#dataElements;
}
/**
* Read a DICOM tag.
*
* @param {DataReader} reader The raw data reader.
* @param {number} offset The offset where to start to read.
* @returns {object} An object containing the tag and the end offset.
*/
#readTag(reader, offset) {
// group
const group = reader.readHex(offset);
offset += Uint16Array.BYTES_PER_ELEMENT;
// element
const element = reader.readHex(offset);
offset += Uint16Array.BYTES_PER_ELEMENT;
// return
return {
tag: new Tag(group, element),
endOffset: offset
};
}
/**
* Read an item data element.
*
* @param {DataReader} reader The raw data reader.
* @param {number} offset The offset where to start to read.
* @param {boolean} implicit Is the DICOM VR implicit?
* @returns {object} The item data as a list of data elements.
*/
#readItemDataElement(reader, offset, implicit) {
const itemData = {};
// read the first item
let item = this.#readDataElement(reader, offset, implicit);
offset = item.endOffset;
// exit if it is a sequence delimitation item
if (isSequenceDelimitationItemTag(item.tag)) {
return {
data: itemData,
endOffset: item.endOffset,
isSeqDelim: true
};
}
// store item (mainly to keep vl)
itemData[item.tag.getKey()] = {
tag: item.tag,
vr: 'NONE',
vl: item.vl,
undefinedLength: item.undefinedLength
};
if (!item.undefinedLength) {
// explicit VR item: read until the end offset
const endOffset = offset;
offset -= item.vl;
while (offset < endOffset) {
item = this.#readDataElement(reader, offset, implicit);
offset = item.endOffset;
itemData[item.tag.getKey()] = item;
}
} else {
// implicit VR item: read until the item delimitation item
let isItemDelim = false;
while (!isItemDelim) {
item = this.#readDataElement(reader, offset, implicit);
offset = item.endOffset;
isItemDelim = isItemDelimitationItemTag(item.tag);
if (!isItemDelim) {
itemData[item.tag.getKey()] = item;
}
}
}
return {
data: itemData,
endOffset: offset,
isSeqDelim: false
};
}
/**
* Read the pixel item data element.
* Ref: [Single frame fragments]{@link http://dicom.nema.org/dicom/2013/output/chtml/part05/sect_A.4.html#table_A.4-1}.
*
* @param {DataReader} reader The raw data reader.
* @param {number} offset The offset where to start to read.
* @param {boolean} implicit Is the DICOM VR implicit?
* @returns {object} The item data as an array of data elements.
*/
#readPixelItemDataElement(
reader, offset, implicit) {
const itemData = [];
// first item: basic offset table
let item = this.#readDataElement(reader, offset, implicit);
const offsetTableVl = item.vl;
offset = item.endOffset;
// read until the sequence delimitation item
let isSeqDelim = false;
while (!isSeqDelim) {
item = this.#readDataElement(reader, offset, implicit);
offset = item.endOffset;
isSeqDelim = isSequenceDelimitationItemTag(item.tag);
if (!isSeqDelim) {
// force pixel item vr to OB
item.vr = 'OB';
itemData.push(item);
}
}
return {
data: itemData,
endOffset: offset,
offsetTableVl: offsetTableVl
};
}
/**
* Read a DICOM data element.
* Reference: [DICOM VRs]{@link http://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html#table_6.2-1}.
*
* @param {DataReader} reader The raw data reader.
* @param {number} offset The offset where to start to read.
* @param {boolean} implicit Is the DICOM VR implicit?
* @returns {DataElement} The data element.
*/
#readDataElement(reader, offset, implicit) {
// Tag: group, element
const readTagRes = this.#readTag(reader, offset);
const tag = readTagRes.tag;
offset = readTagRes.endOffset;
// Value Representation (VR)
let vr = null;
let is32bitVL = false;
if (tag.isWithVR()) {
// implicit VR
if (implicit) {
vr = tag.getVrFromDictionary();
if (typeof vr === 'undefined') {
vr = 'UN';
}
is32bitVL = true;
} else {
vr = this.#decodeString(reader.readUint8Array(offset, 2));
offset += 2 * Uint8Array.BYTES_PER_ELEMENT;
is32bitVL = is32bitVLVR(vr);
// reserved 2 bytes
if (is32bitVL) {
offset += 2 * Uint8Array.BYTES_PER_ELEMENT;
}
}
} else {
vr = 'NONE';
is32bitVL = true;
}
// Value Length (VL)
let vl = 0;
if (is32bitVL) {
vl = reader.readUint32(offset);
offset += Uint32Array.BYTES_PER_ELEMENT;
} else {
vl = reader.readUint16(offset);
offset += Uint16Array.BYTES_PER_ELEMENT;
}
// check the value of VL
let undefinedLength = false;
if (vl === 0xffffffff) {
undefinedLength = true;
vl = 0;
}
// treat private tag with unknown VR and zero VL as a sequence (see #799)
if (tag.isPrivate() && vr === 'UN' && vl === 0) {
vr = 'SQ';
}
let startOffset = offset;
let endOffset = startOffset + vl;
// read sequence elements
let data;
if (isPixelDataTag(tag) && undefinedLength) {
// pixel data sequence (implicit)
const pixItemData =
this.#readPixelItemDataElement(reader, offset, implicit);
offset = pixItemData.endOffset;
startOffset += pixItemData.offsetTableVl;
data = pixItemData.data;
endOffset = offset;
vl = offset - startOffset;
} else if (vr === 'SQ') {
// sequence
data = [];
let itemData;
if (!undefinedLength) {
if (vl !== 0) {
// explicit VR sequence: read until the end offset
const sqEndOffset = offset + vl;
while (offset < sqEndOffset) {
itemData = this.#readItemDataElement(reader, offset, implicit);
data.push(itemData.data);
offset = itemData.endOffset;
}
endOffset = offset;
vl = offset - startOffset;
}
} else {
// implicit VR sequence: read until the sequence delimitation item
let isSeqDelim = false;
while (!isSeqDelim) {
itemData = this.#readItemDataElement(reader, offset, implicit);
isSeqDelim = itemData.isSeqDelim;
offset = itemData.endOffset;
// do not store the delimitation item
if (!isSeqDelim) {
data.push(itemData.data);
}
}
endOffset = offset;
vl = offset - startOffset;
}
}
// return
const element = new DataElement(vr);
element.tag = tag;
element.vl = vl;
element.startOffset = startOffset;
element.endOffset = endOffset;
// only set if true (only for sequences and items)
if (undefinedLength) {
element.undefinedLength = undefinedLength;
}
if (data) {
element.items = data;
}
return element;
}
/**
* Interpret the data of an element.
*
* @param {DataElement} element The data element.
* @param {DataReader} reader The raw data reader.
* @param {number} [pixelRepresentation] PixelRepresentation 0->unsigned,
* 1->signed (needed for pixel data or VR=xs).
* @param {number} [bitsAllocated] Bits allocated (needed for pixel data).
* @returns {object} The interpreted data.
*/
#interpretElement(
element, reader, pixelRepresentation, bitsAllocated) {
const tag = element.tag;
const vl = element.vl;
const vr = element.vr;
const offset = element.startOffset;
// data
let data = null;
const vrType = vrTypes[vr];
if (isPixelDataTag(tag)) {
if (element.undefinedLength) {
// implicit pixel data sequence
data = [];
for (let j = 0; j < element.items.length; ++j) {
data.push(this.#interpretElement(
element.items[j], reader,
pixelRepresentation, bitsAllocated));
}
// remove non parsed items
delete element.items;
} else {
// check bits allocated and VR
// https://dicom.nema.org/medical/dicom/2022a/output/chtml/part05/sect_A.2.html
if (bitsAllocated > 8 && vr === 'OB') {
logger.warn(
'Reading DICOM pixel data with bitsAllocated>8 and OB VR.'
);
}
// read
data = [];
if (bitsAllocated === 1) {
data.push(reader.readBinaryArray(offset, vl));
} else if (bitsAllocated === 8) {
if (pixelRepresentation === 0) {
data.push(reader.readUint8Array(offset, vl));
} else {
data.push(reader.readInt8Array(offset, vl));
}
} else if (bitsAllocated === 16) {
if (pixelRepresentation === 0) {
data.push(reader.readUint16Array(offset, vl));
} else {
data.push(reader.readInt16Array(offset, vl));
}
} else {
throw new Error('Unsupported bits allocated: ' + bitsAllocated);
}
}
} else if (typeof vrType !== 'undefined') {
if (vrType === 'Uint8') {
data = reader.readUint8Array(offset, vl);
} else if (vrType === 'Uint16') {
data = reader.readUint16Array(offset, vl);
// keep as binary for 'O*' VR
if (vr[0] !== 'O') {
data = Array.from(data);
}
} else if (vrType === 'Uint32') {
data = reader.readUint32Array(offset, vl);
// keep as binary for 'O*' VR
if (vr[0] !== 'O') {
data = Array.from(data);
}
} else if (vrType === 'Uint64') {
data = reader.readUint64Array(offset, vl);
} else if (vrType === 'Int16') {
data = Array.from(reader.readInt16Array(offset, vl));
} else if (vrType === 'Int32') {
data = Array.from(reader.readInt32Array(offset, vl));
} else if (vrType === 'Int64') {
data = reader.readInt64Array(offset, vl);
} else if (vrType === 'Float32') {
data = Array.from(reader.readFloat32Array(offset, vl));
} else if (vrType === 'Float64') {
data = Array.from(reader.readFloat64Array(offset, vl));
} else if (vrType === 'string') {
const stream = reader.readUint8Array(offset, vl);
if (isCharSetStringVR(vr)) {
data = this.#decodeSpecialString(stream);
} else {
data = this.#decodeString(stream);
}
data = cleanString(data).split('\\');
} else {
throw Error('Unknown VR type: ' + vrType);
}
} else if (vr === 'xx') {
// US or OW
data = Array.from(reader.readUint16Array(offset, vl));
} else if (vr === 'ox') {
// OB or OW
if (bitsAllocated === 8) {
data = Array.from(reader.readUint8Array(offset, vl));
} else {
data = Array.from(reader.readUint16Array(offset, vl));
}
} else if (vr === 'xs') {
// (US or SS) or (US or SS or OW)
if (pixelRepresentation === 0) {
data = Array.from(reader.readUint16Array(offset, vl));
} else {
data = Array.from(reader.readInt16Array(offset, vl));
}
} else if (vr === 'AT') {
// attribute
const raw = reader.readUint16Array(offset, vl);
data = [];
for (let i = 0, leni = raw.length; i < leni; i += 2) {
const stri = raw[i].toString(16);
const stri1 = raw[i + 1].toString(16);
let str = '(';
str += '0000'.substring(0, 4 - stri.length) + stri.toUpperCase();
str += ',';
str += '0000'.substring(0, 4 - stri1.length) + stri1.toUpperCase();
str += ')';
data.push(str);
}
} else if (vr === 'SQ') {
// sequence
data = [];
for (let k = 0; k < element.items.length; ++k) {
const item = element.items[k];
const itemData = {};
const keys = Object.keys(item);
for (let l = 0; l < keys.length; ++l) {
const subElement = item[keys[l]];
subElement.value = this.#interpretElement(
subElement, reader,
pixelRepresentation, bitsAllocated);
delete subElement.tag;
delete subElement.vl;
delete subElement.startOffset;
delete subElement.endOffset;
itemData[keys[l]] = subElement;
}
data.push(itemData);
}
// remove non parsed elements
delete element.items;
} else if (vr === 'NONE') {
// no VR -> no data
data = [];
} else {
logger.warn('Unknown VR: ' + vr +
' (for tag ' + element.tag.getKey() + ')');
// empty data...
data = [];
}
return data;
}
/**
* Interpret the data of a list of elements.
*
* @param {DataElements} elements A list of data elements.
* @param {DataReader} reader The raw data reader.
* @param {number} pixelRepresentation PixelRepresentation 0->unsigned,
* 1->signed.
* @param {number} bitsAllocated Bits allocated.
*/
#interpret(
elements, reader,
pixelRepresentation, bitsAllocated) {
const keys = Object.keys(elements);
for (let i = 0; i < keys.length; ++i) {
const element = elements[keys[i]];
if (typeof element.value === 'undefined') {
element.value = this.#interpretElement(
element, reader, pixelRepresentation, bitsAllocated);
}
// delete interpretation specific properties
delete element.tag;
delete element.vl;
delete element.startOffset;
delete element.endOffset;
}
}
/**
* Parse the complete DICOM file (given as input to the class).
* Fills in the member object 'dataElements'.
*
* @param {ArrayBuffer} buffer The input array buffer.
*/
parse(buffer) {
let offset = 0;
let syntax = '';
let dataElement = null;
// default readers
const metaReader = new DataReader(buffer);
let dataReader = new DataReader(buffer);
// 128 -> 132: magic word
offset = 128;
const magicword = this.#decodeString(metaReader.readUint8Array(offset, 4));
offset += 4 * Uint8Array.BYTES_PER_ELEMENT;
if (magicword === 'DICM') {
// 0002, 0000: FileMetaInformationGroupLength (vr='UL')
dataElement = this.#readDataElement(metaReader, offset, false);
dataElement.value = this.#interpretElement(dataElement, metaReader);
// increment offset
offset = dataElement.endOffset;
// store the data element
this.#dataElements[dataElement.tag.getKey()] = dataElement;
// get meta length
const metaLength = dataElement.value[0];
// meta elements
const metaEnd = offset + metaLength;
while (offset < metaEnd) {
// get the data element
dataElement = this.#readDataElement(metaReader, offset, false);
offset = dataElement.endOffset;
// store the data element
this.#dataElements[dataElement.tag.getKey()] = dataElement;
}
// check the TransferSyntaxUID (has to be there!)
dataElement = this.#dataElements['00020010'];
if (typeof dataElement === 'undefined') {
throw new Error('Not a valid DICOM file (no TransferSyntaxUID found)');
}
dataElement.value = this.#interpretElement(dataElement, metaReader);
syntax = dataElement.value[0];
} else {
logger.warn('No DICM prefix, trying to guess tansfer syntax.');
// read first element
dataElement = this.#readDataElement(dataReader, 0, false);
// guess transfer syntax
const tsElement = guessTransferSyntax(dataElement);
// store
this.#dataElements[tsElement.tag.getKey()] = tsElement;
syntax = tsElement.value[0];
// reset offset
offset = 0;
}
// check transfer syntax support
if (!isReadSupportedTransferSyntax(syntax)) {
throw new Error('Unsupported DICOM transfer syntax: \'' + syntax +
'\' (' + getTransferSyntaxName(syntax) + ')');
}
// set implicit flag
let implicit = false;
if (isImplicitTransferSyntax(syntax)) {
implicit = true;
}
// Big Endian
if (isBigEndianTransferSyntax(syntax)) {
dataReader = new DataReader(buffer, false);
}
// DICOM data elements
while (offset < buffer.byteLength) {
// get the data element
dataElement = this.#readDataElement(dataReader, offset, implicit);
// increment offset
offset = dataElement.endOffset;
// store the data element
const key = dataElement.tag.getKey();
if (typeof this.#dataElements[key] === 'undefined') {
this.#dataElements[key] = dataElement;
} else {
logger.warn('Not saving duplicate tag: ' + key);
}
}
// safety checks...
if (isNaN(offset)) {
throw new Error('Problem while parsing, bad offset');
}
if (buffer.byteLength !== offset) {
logger.warn('Did not reach the end of the buffer: ' +
offset + ' != ' + buffer.byteLength);
}
//-------------------------------------------------
// values needed for data interpretation
// pixel specific
let pixelRepresentation = 0;
let bitsAllocated = 16;
if (typeof this.#dataElements['7FE00010'] !== 'undefined') {
// PixelRepresentation 0->unsigned, 1->signed
dataElement = this.#dataElements['00280103'];
if (typeof dataElement !== 'undefined') {
dataElement.value = this.#interpretElement(dataElement, dataReader);
pixelRepresentation = dataElement.value[0];
} else {
logger.warn(
'Reading DICOM pixel data with default pixelRepresentation.');
}
// BitsAllocated
dataElement = this.#dataElements['00280100'];
if (typeof dataElement !== 'undefined') {
dataElement.value = this.#interpretElement(dataElement, dataReader);
bitsAllocated = dataElement.value[0];
} else {
logger.warn('Reading DICOM pixel data with default bitsAllocated.');
}
}
// default character set
if (typeof this.#defaultCharacterSet !== 'undefined') {
this.setDecoderCharacterSet(this.#defaultCharacterSet);
}
// SpecificCharacterSet
dataElement = this.#dataElements['00080005'];
if (typeof dataElement !== 'undefined') {
dataElement.value = this.#interpretElement(dataElement, dataReader);
let charSetTerm;
if (dataElement.value.length === 1) {
charSetTerm = dataElement.value[0];
} else {
charSetTerm = dataElement.value[1];
logger.warn('Unsupported character set with code extensions: \'' +
charSetTerm + '\'.');
}
this.setDecoderCharacterSet(getUtfLabel(charSetTerm));
}
// interpret the dicom elements
this.#interpret(
this.#dataElements, dataReader,
pixelRepresentation, bitsAllocated
);
// handle fragmented pixel buffer
// Reference: http://dicom.nema.org/dicom/2013/output/chtml/part05/sect_8.2.html
// (third note, "Depending on the transfer syntax...")
dataElement = this.#dataElements['7FE00010'];
if (typeof dataElement !== 'undefined') {
if (dataElement.undefinedLength) {
let numberOfFrames = 1;
if (typeof this.#dataElements['00280008'] !== 'undefined') {
numberOfFrames = Number(this.#dataElements['00280008'].value[0]);
}
const pixItems = dataElement.value;
if (pixItems.length > 1 && pixItems.length > numberOfFrames) {
// concatenate pixel data items
// concat does not work on typed arrays
//this.pixelBuffer = this.pixelBuffer.concat( dataElement.data );
// manual concat...
const nItemPerFrame = pixItems.length / numberOfFrames;
const newPixItems = [];
let index = 0;
for (let f = 0; f < numberOfFrames; ++f) {
index = f * nItemPerFrame;
// calculate the size of a frame
let size = 0;
for (let i = 0; i < nItemPerFrame; ++i) {
size += pixItems[index + i].length;
}
// create new buffer
const newBuffer = new pixItems[0].constructor(size);
// fill new buffer
let fragOffset = 0;
for (let j = 0; j < nItemPerFrame; ++j) {
newBuffer.set(pixItems[index + j], fragOffset);
fragOffset += pixItems[index + j].length;
}
newPixItems[f] = newBuffer;
}
// store as pixel data
dataElement.value = newPixItems;
}
}
}
}
} // class DicomParser