Feat/parse raw dicom

.circleci/config.yml

@@ -3,7 +3,7 @@ version: 2
 defaults: &defaults
   working_directory: ~/repo
   docker:
-    - image: circleci/node:latest
+    - image: circleci/node:16.13
 
 jobs:
   test:

package.json

@@ -1,6 +1,6 @@
 {
   "name": "dicom-parser",
-  "version": "1.8.5",
+  "version": "1.8.6",
   "description": "Javascript parser for DICOM Part 10 data",
   "main": "dist/dicomParser.min.js",
   "module": "dist/dicomParser.min.js",
@@ -50,9 +50,9 @@
     "webpack:watch": "webpack --progress --watch  --config ./config/webpack"
   },
   "devDependencies": {
-    "@babel/core": "^7.15.5",
-    "@babel/eslint-parser": "^7.15.7",
-    "@babel/preset-env": "^7.15.6",
+    "@babel/core": "^7.17.0",
+    "@babel/eslint-parser": "^7.17.0",
+    "@babel/preset-env": "^7.16.11",
     "babel-eslint": "^10.1.0",
     "babel-loader": "^8.2.2",
     "chai": "^4.3.4",

src/byteArrayParser.js

@@ -5,7 +5,7 @@
 /**
  * Reads a string of 8-bit characters from an array of bytes and advances
  * the position by length bytes.  A null terminator will end the string
- * but will not effect advancement of the position.  Trailing and leading
+ * but will not affect advancement of the position.  Trailing and leading
  * spaces are preserved (not trimmed)
  * @param byteArray the byteArray to read from
  * @param position the position in the byte array to read from

src/byteStream.js

@@ -76,6 +76,10 @@ export default class ByteStream {
     return new ByteStream(this.byteArrayParser, byteArrayView);
   }
 
+  getSize() {
+    return this.byteArray.length;
+  }
+
   /**
      *
      * Parses an unsigned int 16 from a byte array and advances

src/findEndOfEncapsulatedPixelData.js

@@ -33,6 +33,8 @@ export default function findEndOfEncapsulatedElement (byteStream, element, warni
   const basicOffsetTableItemlength = byteStream.readUint32();
   const numFragments = basicOffsetTableItemlength / 4;
 
+  // Bad idea to not include the basic offset table, as it means writing the data out is inconsistent with reading it
+  // but leave this for now.  To fix later.
   for (let i = 0; i < numFragments; i++) {
     const offset = byteStream.readUint32();
 

src/parseDicom.js

@@ -32,7 +32,7 @@ export default function parseDicom (byteArray, options) {
 
     const transferSyntaxElement = metaHeaderDataSet.elements.x00020010;
 
-    return byteArrayParser.readFixedString(byteArray, transferSyntaxElement.dataOffset, transferSyntaxElement.length);
+    return transferSyntaxElement.Value || byteArrayParser.readFixedString(byteArray, transferSyntaxElement.dataOffset, transferSyntaxElement.length);
   }
 
   function isExplicit (transferSyntax) {
@@ -148,7 +148,7 @@ export default function parseDicom (byteArray, options) {
   function parseTheByteStream () {
     const metaHeaderDataSet = readPart10Header(byteArray, options);
     const dataSet = readDataSet(metaHeaderDataSet);
-
+    
     return mergeDataSets(metaHeaderDataSet, dataSet);
   }
 

src/readPart10Header.js

@@ -15,31 +15,51 @@ import readDicomElementExplicit from './readDicomElementExplicit.js';
  *         elements successfully parsed before the error.
  */
 
-export default function readPart10Header (byteArray, options) {
+export default function readPart10Header(byteArray, options) {
   if (byteArray === undefined) {
     throw 'dicomParser.readPart10Header: missing required parameter \'byteArray\'';
   }
 
   const littleEndianByteStream = new ByteStream(littleEndianByteArrayParser, byteArray);
 
-  function readPrefix () {
+  function readPrefix() {
+    const { TransferSyntaxUID } = options || {};
+    if( littleEndianByteStream.getSize() <=132 && TransferSyntaxUID ) {
+      return false;
+    }
     littleEndianByteStream.seek(128);
     const prefix = littleEndianByteStream.readFixedString(4);
 
     if (prefix !== 'DICM') {
-      throw 'dicomParser.readPart10Header: DICM prefix not found at location 132 - this is not a valid DICOM P10 file.';
+      const { TransferSyntaxUID } = options || {};
+      if (!TransferSyntaxUID) {
+        throw 'dicomParser.readPart10Header: DICM prefix not found at location 132 - this is not a valid DICOM P10 file.';
+      }
+      littleEndianByteStream.seek(0);
+      return false;
     }
+    return true;
   }
 
   // main function here
-  function readTheHeader () {
+  function readTheHeader() {
     // Per the DICOM standard, the header is always encoded in Explicit VR Little Endian (see PS3.10, section 7.1)
     // so use littleEndianByteStream throughout this method regardless of the transfer syntax
-    readPrefix();
+    const isPart10 = readPrefix();
 
     const warnings = [];
     const elements = {};
 
+    if (!isPart10) {
+      littleEndianByteStream.position = 0;
+      const metaHeaderDataSet = {
+        elements: {x00020010: { tag: 'x00020010', vr: 'UI', Value: options.TransferSyntaxUID }},
+        warnings, 
+      };
+      // console.log('Returning metaHeaderDataSet', metaHeaderDataSet);
+      return metaHeaderDataSet;
+    }
+
     while (littleEndianByteStream.position < littleEndianByteStream.byteArray.length) {
       const position = littleEndianByteStream.position;
       const element = readDicomElementExplicit(littleEndianByteStream, warnings);

src/version.js

@@ -1 +1 @@
-export default '1.8.5';
+export default '1.8.6';

test/parseDicom_test.js

@@ -139,7 +139,26 @@ describe('parseDicom', () => {
 
     return convertToByteArray(rawData);
   }
-
+
+  /**
+   * 
+   * @returns a DICOM file consisting of just the raw data
+   */
+  function makeRawData() {
+    const rawData = [
+      // Transfer Syntax UID
+      // x00020010          UI         20         1.2.840.10008.1.2.1 (Explicit VR Little Endian)
+      // Slice Location
+      // x00201041          DS               4      '-43'
+      0x20,0x00,0x41,0x10, 0x44,0x53, 0x04,0x00, 0x2D,0x34,0x33,0x00,
+      // Rows
+      // x00280010          US         2          512
+      0x28,0x00,0x10,0x00, 0x55,0x53, 0x02,0x00, 0x00,0x02
+    ];
+
+    return convertToByteArray(rawData);
+  }
+
   function assertMetaHeaderElements(dataSet, transferSyntax, groupLength) {
     expect(dataSet.uint32('x00020000')).to.equal(groupLength); // '(0002,0000) was not read correctly');
     expect(dataSet.uint16('x00020001')).to.equal(256); //'(0002,0001) was not read correctly');
@@ -174,7 +193,20 @@ describe('parseDicom', () => {
     expect(dataSet.uint16('x00280010')).to.equal(512);
     expect(dataSet.string('x00201041')).to.equal('-43');
   });
-
+
+  it('should parse the dataset correctly (raw LEE)', () => {
+    // Arrange
+    const byteArray = makeRawData();
+
+    // Act
+    const dataSet = parseDicom(byteArray, {TransferSyntaxUID: '1.2.840.10008.1.2.1'});
+
+    // Assert
+    // assertMetaHeaderElements(dataSet, '1.2.840.10008.1.2.1', 159);
+    expect(dataSet.uint16('x00280010')).to.equal(512);
+    expect(dataSet.string('x00201041')).to.equal('-43');
+  });
+
   it('should parse the dataset correctly (implicitLittleEndian)', () => {
     // Arrange
     const byteArray = makeImplicitLittleEndianTestData();