DICOM Multiframe True Color Secondary Capture dataset generator for Node.js

dcmjs-sc-jpeg-gen.js

// dcmjs-sc-jpeg-gen
// This Node.js utility can generate DICOM Multiframe True Color Secondary Capture datasets
// with JPEG baseline frames, for testing purposes. Custom frame parameters could be defined,
// such as count, width and height.

// The following npm packages are required:
// canvas
// dcmjs
// faker
// moment
// parse-int
// e.g. npm install canvas dcmjs faker@5.5.3 moment parse-int

// Usage:
// [OPTIONS] node dcmjs-sc-jpeg-gen.js
// [OPTIONS]:
// FRAME_WIDTH: Frame width (default: 512).
// FRAME_HEIGHT: Frame height (default: 512).
// NUMBER_OF_FRAMES: Number of frames (default: 3).
// FRAMES_PER_SECOND: Frame increment rate (default: 10).
// OUTPUT_FILE: Output file path (default: sc.dcm).
// e.g. FRAME_WIDTH=256 FRAME_HEIGHT=256 NUMBER_OF_FRAMES=5 FRAMES_PER_SECOND=20 node dcmjs-sc-jpeg-gen.js

const fs = require('fs');

const parseInt = require('parse-int');
const faker = require('faker');
const moment = require('moment');

const { createCanvas } = require('canvas');

const dcmjs = require('dcmjs');
const { DicomMetaDictionary, DicomDict } = dcmjs.data;

//////////////////////////////////////////////////////////////////////////
// Constant UIDs
/**
 * 	Secondary Capture Image Storage SOP class UID.
 * @constant {string}
 */
const MultiframeTrueColorSecondaryCaptureSopClassUid = '1.2.840.10008.5.1.4.1.1.7.4';

/**
 * Baseline JPEG transfer syntax UID.
 * @constant {string}
 */
const JpegBaselineTransferSyntaxUid = '1.2.840.10008.1.2.4.50';

/**
 * Implementation UID (using fo-dicom's!).
 * @constant {string}
 */
const ImplementationUid = '1.3.6.1.4.1.30071.8';

//////////////////////////////////////////////////////////////////////////
// Functions
/**
 * Generates a DICOM Multiframe True Color Secondary Capture dataset.
 * @method
 * @param {number} frameWidth - The frame width.
 * @param {number} frameHeight - The frame height.
 * @param {number} numberOfFrames - Number of frames.
 * @param {number} framesPerSecond - The frame increment rate.
 * @returns {Buffer} The DICOM dataset buffer.
 */
function generateDataset(frameWidth, frameHeight, numberOfFrames, framesPerSecond) {
  // Create dataset dates and times
  const birthDate = `${moment(faker.date.between('1950-01-01', '2000-01-01')).format('YYYYMMDD')}`;
  const date = `${moment(faker.date.between('1950-01-01', '2010-01-01')).format('YYYYMMDD')}`;
  const time = '000000';

  // Create dataset UIDs
  const studyInstanceUid = DicomMetaDictionary.uid();
  const seriesInstanceUid = DicomMetaDictionary.uid();
  const sopInstanceUid = DicomMetaDictionary.uid();

  // Create JPEG frame buffers
  const frameBuffers = [];
  for (let i = 0; i < numberOfFrames; i++) {
    let frameBuffer = generateFrame(frameWidth, frameHeight, `${i}`);
    if (frameBuffer.length & 1) {
      frameBuffer = Buffer.concat([frameBuffer, Buffer.from([0x00])]);
    }
    frameBuffers.push(frameBuffer.buffer);
  }

  // Create dataset
  const dataset = {
    _vrMap: {
      PixelData: 'OB',
    },
    _meta: {
      _vrMap: {},
      FileMetaInformationVersion: new Uint8Array([0, 1]).buffer,
      MediaStorageSOPClassUID: MultiframeTrueColorSecondaryCaptureSopClassUid,
      MediaStorageSOPInstanceUID: sopInstanceUid,
      TransferSyntaxUID: JpegBaselineTransferSyntaxUid,
      ImplementationClassUID: ImplementationUid,
    },

    // Patient Module Attributes
    PatientID: `${faker.random.alphaNumeric(6).toUpperCase()}`,
    PatientName: `${faker.name.firstName().toUpperCase()}^${faker.name.lastName().toUpperCase()}`,
    PatientBirthDate: birthDate,
    PatientSex: 'O',

    // General Study Module Attributes
    StudyInstanceUID: studyInstanceUid,
    StudyDate: date,
    StudyTime: time,
    StudyID: `${faker.random.alphaNumeric(3).toUpperCase()}`,
    AccessionNumber: `${faker.random.alphaNumeric(6).toUpperCase()}`,
    ReferringPhysicianName: `${faker.name.firstName().toUpperCase()}^${faker.name
      .lastName()
      .toUpperCase()}`,

    // General Series Module Attributes
    Modality: 'OT',
    SeriesInstanceUID: seriesInstanceUid,
    SeriesNumber: `${faker.datatype.number(100)}`,
    Laterality: '',

    // General/SC Equipment Module Attributes
    Manufacturer: `${faker.company.companyName().toUpperCase()}`,
    ManufacturerModelName: `${faker.commerce.productName().toUpperCase()}`,
    DeviceSerialNumber: `${faker.random.alphaNumeric(6).toUpperCase()}`,
    SoftwareVersions: `${faker.random.alphaNumeric(1).toUpperCase()}.${faker.random
      .alphaNumeric(2)
      .toUpperCase()}`,
    ConversionType: 'SYN',

    // General/SC Image Module Attributes
    InstanceNumber: '1',
    AcquisitionDateTime: `${date}${time}`,
    ContentDate: date,
    ContentTime: time,
    BurnedInAnnotation: 'NO',
    PatientOrientation: '',

    // Image Pixel Module Attributes
    SamplesPerPixel: 3,
    PhotometricInterpretation: 'YBR_FULL_422',
    PlanarConfiguration: 0,
    NumberOfFrames: `${numberOfFrames}`,
    Rows: frameHeight,
    Columns: frameWidth,
    BitsAllocated: 8,
    BitsStored: 8,
    HighBit: 7,
    PixelRepresentation: 0,
    PixelData: frameBuffers,

    // Multi-frame Module Attributes
    FrameIncrementPointer: attributeNameToIdentifier('FrameTime'),

    // Cine Module Attributes
    FrameTime: `${numberOfFrames === 1 ? '0' : 1000 / framesPerSecond}`,
    FrameDelay: '0.0',

    // SOP Common Module Attributes
    SOPClassUID: MultiframeTrueColorSecondaryCaptureSopClassUid,
    SOPInstanceUID: sopInstanceUid,
    SpecificCharacterSet: 'ISO_IR 100',
  };

  // Convert the JSON dataset into a DICOM part10 file
  const denaturalizedMetaHeader = DicomMetaDictionary.denaturalizeDataset(dataset._meta);
  const dicomDict = new DicomDict(denaturalizedMetaHeader);
  dicomDict.dict = DicomMetaDictionary.denaturalizeDataset(dataset);

  return Buffer.from(dicomDict.write({ fragmentMultiframe: false }));
}

/**
 * Generates a DICOM frame.
 * @method
 * @param {number} width - The frame width.
 * @param {number} height - The frame height.
 * @param {string} text - Text to write on frame.
 * @returns {Buffer} The frame buffer.
 */
function generateFrame(width, height, text) {
  const canvas = createCanvas(width, height);
  const context = canvas.getContext('2d');

  context.font = 'bold 50pt Arial';
  context.textAlign = 'center';
  context.textBaseline = 'middle';
  context.fillStyle = '#fff';
  context.fillText(text, width / 2, height / 2);

  context.strokeStyle = '#fff';
  context.setLineDash([3, 3]);
  context.strokeRect(0, 0, width, height);

  return canvas.toBuffer('image/jpeg', 1);
}

/**
 * Get the attribute identifier from name.
 * @method
 * @param {string} text - Attribute name.
 * @returns {number} Attribute identifier.
 */
function attributeNameToIdentifier(attributeName) {
  let identifier = undefined;
  Object.keys(DicomMetaDictionary.dictionary).forEach((tag) => {
    const dictionaryEntry = DicomMetaDictionary.dictionary[tag];
    if (dictionaryEntry.version === 'DICOM' && attributeName === dictionaryEntry.name) {
      const group = Number(`0x${dictionaryEntry.tag.substring(1, 5)}`);
      const element = Number(`0x${dictionaryEntry.tag.substring(6, 10)}`);
      identifier = (group << 16) | (element & 0xffff);
    }
  });

  return identifier;
}

//////////////////////////////////////////////////////////////////////////
// Gather params
const frameWidth = parseInt(process.env.FRAME_WIDTH) || 512;
const frameHeight = parseInt(process.env.FRAME_HEIGHT) || 512;

const numberOfFrames = parseInt(process.env.NUMBER_OF_FRAMES) || 3;
const framesPerSecond = parseInt(process.env.FRAMES_PER_SECOND) || 10;

const outFile = process.env.OUTPUT_FILE || 'sc.dcm';

//////////////////////////////////////////////////////////////////////////
// Generate dataset and persist it to file
const datasetBuffer = generateDataset(frameWidth, frameHeight, numberOfFrames, framesPerSecond);
fs.writeFileSync(outFile, datasetBuffer);