PantelisGeorgiadis/dcmjs-wsi-gen.js

## dcmjs-wsi-gen.js
// dcmjs-wsi-gen
// This Node.js utility can generate DICOM Whole Slide Imaging datasets
// with baseline images (higher resolution only) for testing purposes.
// Custom tile parameters could be defined (count in each row/column,
// width, height) as well as slice thickness, pixel spacing and slide offset.

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

// Usage:
// [OPTIONS] node dcmjs-wsi-gen.js
// [OPTIONS]:
// TILE_WIDTH: Tile width (default: 512).
// TILE_HEIGHT: Tile height (default: 512).
// TILES_X: Number of tiles in each row (default: 3).
// TILES_Y: Number of tiles in each columns (default: 3).
// SLICE_THICKNESS: Slice thickness (default: 1.0).
// PIXEL_SPACING_X: Pixel spacing in the horizontal axis (default: 1.0).
// PIXEL_SPACING_Y: Pixel spacing in the vertical axis (default: 1.0).
// SLIDE_OFFSET_X : Horizontal axis offset in the slide coordinate system (default: 0.0).
// SLIDE_OFFSET_Y : Vertical axis offset in the slide coordinate system (default: 0.0).
// OUTPUT_FILE: Output file path (default: wsi.dcm).
// e.g. TILE_WIDTH=256 TILE_HEIGHT=256 TILES_X=5 TILES_Y=5 node dcmjs-wsi-gen.js

const fs = require('fs');

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

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

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

//////////////////////////////////////////////////////////////////////////
// Constant UIDs
/**
 * Whole Slide Imaging SOP class UID.
 * @constant {string}
 */
const WsiSopClassUid = '1.2.840.10008.5.1.4.1.1.77.1.6';

/**
 * 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 WSI dataset.
 * @method
 * @param {number} tileWidth - The tile width.
 * @param {number} tileHeight - The tile height.
 * @param {number} tilesX - Number of tiles in each row.
 * @param {number} tilesY - Number of tiles in each column.
 * @param {number} sliceThickness -The slice thickness.
 * @param {number} pixelSpacingX - The pixel spacing in the horizontal axis.
 * @param {number} pixelSpacingY - The pixel spacing in the vertical axis.
 * @param {number} slideOffsetX - The horizontal axis offset in the slide coordinate system.
 * @param {number} slideOffsetY - The vertical axis offset in the slide coordinate system.
 * @returns {Buffer} The DICOM WSI dataset buffer.
 */
function generateWsiDataset(
  tileWidth,
  tileHeight,
  tilesX,
  tilesY,
  sliceThickness,
  pixelSpacingX,
  pixelSpacingY,
  slideOffsetX,
  slideOffsetY
) {
  // 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();
  const dimensionOrganizationUid = DicomMetaDictionary.uid();
  const frameOfReferenceUid = DicomMetaDictionary.uid();
  const specimenUid = DicomMetaDictionary.uid();
  const containerAndSpecimenIdentifier = `${faker.random.alphaNumeric(8).toUpperCase()}`;
  const opticalPathIdentifier = `${faker.datatype.number(100)}`;

  // Create JPEG tile buffers
  const tileBuffers = [];
  for (let i = 0; i < tilesY; i++) {
    for (let j = 0; j < tilesX; j++) {
      let tileBuffer = generateWsiTile(tileWidth, tileHeight, `${i}-${j}`);
      if (tileBuffer.length & 1) {
        tileBuffer = Buffer.concat([tileBuffer, Buffer.from([0x00])]);
      }
      tileBuffers.push(tileBuffer.buffer);
    }
  }

  // Create position sequence values
  let dimensionIndexValues = 1;
  let offsetX = slideOffsetX;
  let offsetY = slideOffsetY;

  const perFrameFunctionalGroupsSequenceItems = [];
  for (let x = 0; x < tilesX; x++) {
    offsetY = slideOffsetY;
    for (let y = 0; y < tilesY; y++) {
      const item = {
        FrameContentSequence: [
          {
            DimensionIndexValues: dimensionIndexValues,
          },
        ],
        PlanePositionSlideSequence: [
          {
            XOffsetInSlideCoordinateSystem: `${offsetX}`,
            YOffsetInSlideCoordinateSystem: `${offsetY}`,
            ZOffsetInSlideCoordinateSystem: '0',
            ColumnPositionInTotalImagePixelMatrix: `${x * tileWidth + 1}`,
            RowPositionInTotalImagePixelMatrix: `${y * tileHeight + 1}`,
          },
        ],
      };
      perFrameFunctionalGroupsSequenceItems.push(item);
      offsetY = offsetY - tileHeight * pixelSpacingY;
      dimensionIndexValues++;
    }
    offsetX -= tileWidth * pixelSpacingX;
  }

  // Create dataset
  const dataset = {
    _vrMap: {
      PixelData: 'OB',
    },
    _meta: {
      _vrMap: {},
      FileMetaInformationVersion: new Uint8Array([0, 1]).buffer,
      MediaStorageSOPClassUID: WsiSopClassUid,
      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: 'SM',
    SeriesInstanceUID: seriesInstanceUid,
    SeriesNumber: `${faker.datatype.number(100)}`,

    // General 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()}`,

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

    // Image Pixel Module Attributes
    PixelData: tileBuffers,

    // Acquisition Context Module Attributes
    AcquisitionContextSequence: [],

    // VL Image Module Attributes
    ImageType: ['DERIVED', 'PRIMARY', 'VOLUME', 'NONE'],
    SamplesPerPixel: 3,
    PhotometricInterpretation: 'YBR_FULL_422',
    PlanarConfiguration: 0,
    NumberOfFrames: `${tilesX * tilesY}`,
    Rows: tileHeight,
    Columns: tileWidth,
    BitsAllocated: 8,
    BitsStored: 8,
    HighBit: 7,
    PixelRepresentation: 0,
    LossyImageCompression: '01',
    LossyImageCompressionRatio: ['1', '1'],
    LossyImageCompressionMethod: ['ISO_10918_1', 'ISO_10918_1'],
    VolumetricProperties: 'VOLUME',
    AcquisitionDuration: faker.datatype.number({ min: 100, max: 200 }),
    ImagedVolumeWidth: tilesX * tileWidth * pixelSpacingX,
    ImagedVolumeHeight: tilesY * tileHeight * pixelSpacingY,
    ImagedVolumeDepth: sliceThickness,
    TotalPixelMatrixColumns: tilesX * tileWidth,
    TotalPixelMatrixRows: tilesY * tileHeight,
    TotalPixelMatrixOriginSequence: [
      {
        XOffsetInSlideCoordinateSystem: `${slideOffsetX}`,
        YOffsetInSlideCoordinateSystem: `${slideOffsetY}`,
      },
    ],
    SpecimenLabelInImage: 'NO',
    FocusMethod: 'MANUAL',
    ExtendedDepthOfField: 'NO',
    ImageOrientationSlide: ['0', '1', '0', '1', '0', '0'],

    // SOP Common Module Attributes
    SOPClassUID: WsiSopClassUid,
    SOPInstanceUID: sopInstanceUid,
    SpecificCharacterSet: 'ISO_IR 100',

    // Specimen Module Attributes
    ContainerIdentifier: containerAndSpecimenIdentifier,
    IssuerOfTheContainerIdentifierSequence: [],
    SpecimenDescriptionSequence: [
      {
        SpecimenIdentifier: containerAndSpecimenIdentifier,
        SpecimenUID: specimenUid,
        SpecimenPreparationSequence: [],
        IssuerOfTheSpecimenIdentifierSequence: [],
      },
    ],
    ContainerTypeCodeSequence: [],

    // Optical Path Module Attributes
    OpticalPathSequence: [
      {
        IlluminationTypeCodeSequence: [
          {
            CodeValue: '111741',
            CodingSchemeDesignator: 'DCM',
            CodeMeaning: 'Transmission illumination',
          },
        ],
        ICCProfile: '',
        OpticalPathIdentifier: opticalPathIdentifier,
        OpticalPathDescription: '',
        IlluminationColorCodeSequence: [
          {
            CodeValue: '414298005',
            CodingSchemeDesignator: 'SCT',
            CodeMeaning: 'Full Spectrum',
          },
        ],
      },
    ],

    // Frame of Reference Module Attributes
    FrameOfReferenceUID: frameOfReferenceUid,
    PositionReferenceIndicator: 'SLIDE_CORNER',

    // Shared Functional Groups Sequence Attribute
    SharedFunctionalGroupsSequence: [
      {
        PixelMeasuresSequence: [
          {
            SliceThickness: `${sliceThickness}`,
            PixelSpacing: [`${pixelSpacingX}`, `${pixelSpacingY}`],
          },
        ],
        OpticalPathIdentificationSequence: [
          {
            OpticalPathIdentifier: opticalPathIdentifier,
          },
        ],
        WholeSlideMicroscopyImageFrameTypeSequence: [
          {
            FrameType: ['DERIVED', 'PRIMARY', 'VOLUME', 'NONE'],
          },
        ],
      },
    ],

    // Multi-frame Functional Groups Module
    PerFrameFunctionalGroupsSequence: perFrameFunctionalGroupsSequenceItems,

    // Multi-frame Dimension Module
    DimensionOrganizationSequence: [{ DimensionOrganizationUID: dimensionOrganizationUid }],
    DimensionIndexSequence: [
      {
        DimensionOrganizationUID: dimensionOrganizationUid,
        DimensionIndexPointer: 0x0048021a,
        DimensionDescriptionLabel: 'Plane Position (Slide)',
      },
    ],
  };

  // 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 WSI tile.
 * @method
 * @param {number} tileWidth - The tile width.
 * @param {number} tileHeight - The tile height.
 * @param {string} text - Text to write on tile.
 * @returns {Buffer} The tile buffer.
 */
function generateWsiTile(tileWidth, tileHeight, text) {
  const canvas = createCanvas(tileWidth, tileHeight);
  const context = canvas.getContext('2d');

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

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

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

//////////////////////////////////////////////////////////////////////////
// Gather params
const tileWidth = parseInt(process.env.TILE_WIDTH) || 512;
const tileHeight = parseInt(process.env.TILE_HEIGHT) || 512;

const tilesX = parseInt(process.env.TILES_X) || 3;
const tilesY = parseInt(process.env.TILES_Y) || 3;

const sliceThickness = parseFloat(process.env.SLICE_THICKNESS) || 1.0;
const pixelSpacingX = parseFloat(process.env.PIXEL_SPACING_X) || 1.0;
const pixelSpacingY = parseFloat(process.env.PIXEL_SPACING_Y) || 1.0;

const slideOffsetX = parseFloat(process.env.SLIDE_OFFSET_X) || 0.0;
const slideOffsetY = parseFloat(process.env.SLIDE_OFFSET_Y) || 0.0;

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

//////////////////////////////////////////////////////////////////////////
// Generate WSI dataset and persist it to file
const wsiDatasetBuffer = generateWsiDataset(
  tileWidth,
  tileHeight,
  tilesX,
  tilesY,
  sliceThickness,
  pixelSpacingX,
  pixelSpacingY,
  slideOffsetX,
  slideOffsetY
);
fs.writeFileSync(outFile, wsiDatasetBuffer);
	// dcmjs-wsi-gen
	// This Node.js utility can generate DICOM Whole Slide Imaging datasets
	// with baseline images (higher resolution only) for testing purposes.
	// Custom tile parameters could be defined (count in each row/column,
	// width, height) as well as slice thickness, pixel spacing and slide offset.

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

	// Usage:
	// [OPTIONS] node dcmjs-wsi-gen.js
	// [OPTIONS]:
	// TILE_WIDTH: Tile width (default: 512).
	// TILE_HEIGHT: Tile height (default: 512).
	// TILES_X: Number of tiles in each row (default: 3).
	// TILES_Y: Number of tiles in each columns (default: 3).
	// SLICE_THICKNESS: Slice thickness (default: 1.0).
	// PIXEL_SPACING_X: Pixel spacing in the horizontal axis (default: 1.0).
	// PIXEL_SPACING_Y: Pixel spacing in the vertical axis (default: 1.0).
	// SLIDE_OFFSET_X : Horizontal axis offset in the slide coordinate system (default: 0.0).
	// SLIDE_OFFSET_Y : Vertical axis offset in the slide coordinate system (default: 0.0).
	// OUTPUT_FILE: Output file path (default: wsi.dcm).
	// e.g. TILE_WIDTH=256 TILE_HEIGHT=256 TILES_X=5 TILES_Y=5 node dcmjs-wsi-gen.js

	const fs = require('fs');

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

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

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

	//////////////////////////////////////////////////////////////////////////
	// Constant UIDs
	/**
	* Whole Slide Imaging SOP class UID.
	* @constant {string}
	*/
	const WsiSopClassUid = '1.2.840.10008.5.1.4.1.1.77.1.6';

	/**
	* 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 WSI dataset.
	* @method
	* @param {number} tileWidth - The tile width.
	* @param {number} tileHeight - The tile height.
	* @param {number} tilesX - Number of tiles in each row.
	* @param {number} tilesY - Number of tiles in each column.
	* @param {number} sliceThickness -The slice thickness.
	* @param {number} pixelSpacingX - The pixel spacing in the horizontal axis.
	* @param {number} pixelSpacingY - The pixel spacing in the vertical axis.
	* @param {number} slideOffsetX - The horizontal axis offset in the slide coordinate system.
	* @param {number} slideOffsetY - The vertical axis offset in the slide coordinate system.
	* @returns {Buffer} The DICOM WSI dataset buffer.
	*/
	function generateWsiDataset(
	tileWidth,
	tileHeight,
	tilesX,
	tilesY,
	sliceThickness,
	pixelSpacingX,
	pixelSpacingY,
	slideOffsetX,
	slideOffsetY
	) {
	// 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();
	const dimensionOrganizationUid = DicomMetaDictionary.uid();
	const frameOfReferenceUid = DicomMetaDictionary.uid();
	const specimenUid = DicomMetaDictionary.uid();
	const containerAndSpecimenIdentifier = `${faker.random.alphaNumeric(8).toUpperCase()}`;
	const opticalPathIdentifier = `${faker.datatype.number(100)}`;

	// Create JPEG tile buffers
	const tileBuffers = [];
	for (let i = 0; i < tilesY; i++) {
	for (let j = 0; j < tilesX; j++) {
	let tileBuffer = generateWsiTile(tileWidth, tileHeight, `${i}-${j}`);
	if (tileBuffer.length & 1) {
	tileBuffer = Buffer.concat([tileBuffer, Buffer.from([0x00])]);
	}
	tileBuffers.push(tileBuffer.buffer);
	}
	}

	// Create position sequence values
	let dimensionIndexValues = 1;
	let offsetX = slideOffsetX;
	let offsetY = slideOffsetY;

	const perFrameFunctionalGroupsSequenceItems = [];
	for (let x = 0; x < tilesX; x++) {
	offsetY = slideOffsetY;
	for (let y = 0; y < tilesY; y++) {
	const item = {
	FrameContentSequence: [
	{
	DimensionIndexValues: dimensionIndexValues,
	},
	],
	PlanePositionSlideSequence: [
	{
	XOffsetInSlideCoordinateSystem: `${offsetX}`,
	YOffsetInSlideCoordinateSystem: `${offsetY}`,
	ZOffsetInSlideCoordinateSystem: '0',
	ColumnPositionInTotalImagePixelMatrix: `${x * tileWidth + 1}`,
	RowPositionInTotalImagePixelMatrix: `${y * tileHeight + 1}`,
	},
	],
	};
	perFrameFunctionalGroupsSequenceItems.push(item);
	offsetY = offsetY - tileHeight * pixelSpacingY;
	dimensionIndexValues++;
	}
	offsetX -= tileWidth * pixelSpacingX;
	}

	// Create dataset
	const dataset = {
	_vrMap: {
	PixelData: 'OB',
	},
	_meta: {
	_vrMap: {},
	FileMetaInformationVersion: new Uint8Array([0, 1]).buffer,
	MediaStorageSOPClassUID: WsiSopClassUid,
	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: 'SM',
	SeriesInstanceUID: seriesInstanceUid,
	SeriesNumber: `${faker.datatype.number(100)}`,

	// General 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()}`,

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

	// Image Pixel Module Attributes
	PixelData: tileBuffers,

	// Acquisition Context Module Attributes
	AcquisitionContextSequence: [],

	// VL Image Module Attributes
	ImageType: ['DERIVED', 'PRIMARY', 'VOLUME', 'NONE'],
	SamplesPerPixel: 3,
	PhotometricInterpretation: 'YBR_FULL_422',
	PlanarConfiguration: 0,
	NumberOfFrames: `${tilesX * tilesY}`,
	Rows: tileHeight,
	Columns: tileWidth,
	BitsAllocated: 8,
	BitsStored: 8,
	HighBit: 7,
	PixelRepresentation: 0,
	LossyImageCompression: '01',
	LossyImageCompressionRatio: ['1', '1'],
	LossyImageCompressionMethod: ['ISO_10918_1', 'ISO_10918_1'],
	VolumetricProperties: 'VOLUME',
	AcquisitionDuration: faker.datatype.number({ min: 100, max: 200 }),
	ImagedVolumeWidth: tilesX * tileWidth * pixelSpacingX,
	ImagedVolumeHeight: tilesY * tileHeight * pixelSpacingY,
	ImagedVolumeDepth: sliceThickness,
	TotalPixelMatrixColumns: tilesX * tileWidth,
	TotalPixelMatrixRows: tilesY * tileHeight,
	TotalPixelMatrixOriginSequence: [
	{
	XOffsetInSlideCoordinateSystem: `${slideOffsetX}`,
	YOffsetInSlideCoordinateSystem: `${slideOffsetY}`,
	},
	],
	SpecimenLabelInImage: 'NO',
	FocusMethod: 'MANUAL',
	ExtendedDepthOfField: 'NO',
	ImageOrientationSlide: ['0', '1', '0', '1', '0', '0'],

	// SOP Common Module Attributes
	SOPClassUID: WsiSopClassUid,
	SOPInstanceUID: sopInstanceUid,
	SpecificCharacterSet: 'ISO_IR 100',

	// Specimen Module Attributes
	ContainerIdentifier: containerAndSpecimenIdentifier,
	IssuerOfTheContainerIdentifierSequence: [],
	SpecimenDescriptionSequence: [
	{
	SpecimenIdentifier: containerAndSpecimenIdentifier,
	SpecimenUID: specimenUid,
	SpecimenPreparationSequence: [],
	IssuerOfTheSpecimenIdentifierSequence: [],
	},
	],
	ContainerTypeCodeSequence: [],

	// Optical Path Module Attributes
	OpticalPathSequence: [
	{
	IlluminationTypeCodeSequence: [
	{
	CodeValue: '111741',
	CodingSchemeDesignator: 'DCM',
	CodeMeaning: 'Transmission illumination',
	},
	],
	ICCProfile: '',
	OpticalPathIdentifier: opticalPathIdentifier,
	OpticalPathDescription: '',
	IlluminationColorCodeSequence: [
	{
	CodeValue: '414298005',
	CodingSchemeDesignator: 'SCT',
	CodeMeaning: 'Full Spectrum',
	},
	],
	},
	],

	// Frame of Reference Module Attributes
	FrameOfReferenceUID: frameOfReferenceUid,
	PositionReferenceIndicator: 'SLIDE_CORNER',

	// Shared Functional Groups Sequence Attribute
	SharedFunctionalGroupsSequence: [
	{
	PixelMeasuresSequence: [
	{
	SliceThickness: `${sliceThickness}`,
	PixelSpacing: [`${pixelSpacingX}`, `${pixelSpacingY}`],
	},
	],
	OpticalPathIdentificationSequence: [
	{
	OpticalPathIdentifier: opticalPathIdentifier,
	},
	],
	WholeSlideMicroscopyImageFrameTypeSequence: [
	{
	FrameType: ['DERIVED', 'PRIMARY', 'VOLUME', 'NONE'],
	},
	],
	},
	],

	// Multi-frame Functional Groups Module
	PerFrameFunctionalGroupsSequence: perFrameFunctionalGroupsSequenceItems,

	// Multi-frame Dimension Module
	DimensionOrganizationSequence: [{ DimensionOrganizationUID: dimensionOrganizationUid }],
	DimensionIndexSequence: [
	{
	DimensionOrganizationUID: dimensionOrganizationUid,
	DimensionIndexPointer: 0x0048021a,
	DimensionDescriptionLabel: 'Plane Position (Slide)',
	},
	],
	};

	// 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 WSI tile.
	* @method
	* @param {number} tileWidth - The tile width.
	* @param {number} tileHeight - The tile height.
	* @param {string} text - Text to write on tile.
	* @returns {Buffer} The tile buffer.
	*/
	function generateWsiTile(tileWidth, tileHeight, text) {
	const canvas = createCanvas(tileWidth, tileHeight);
	const context = canvas.getContext('2d');

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

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

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

	//////////////////////////////////////////////////////////////////////////
	// Gather params
	const tileWidth = parseInt(process.env.TILE_WIDTH) \|\| 512;
	const tileHeight = parseInt(process.env.TILE_HEIGHT) \|\| 512;

	const tilesX = parseInt(process.env.TILES_X) \|\| 3;
	const tilesY = parseInt(process.env.TILES_Y) \|\| 3;

	const sliceThickness = parseFloat(process.env.SLICE_THICKNESS) \|\| 1.0;
	const pixelSpacingX = parseFloat(process.env.PIXEL_SPACING_X) \|\| 1.0;
	const pixelSpacingY = parseFloat(process.env.PIXEL_SPACING_Y) \|\| 1.0;

	const slideOffsetX = parseFloat(process.env.SLIDE_OFFSET_X) \|\| 0.0;
	const slideOffsetY = parseFloat(process.env.SLIDE_OFFSET_Y) \|\| 0.0;

	const outFile = process.env.OUTPUT_FILE \|\| 'wsi.dcm';

	//////////////////////////////////////////////////////////////////////////
	// Generate WSI dataset and persist it to file
	const wsiDatasetBuffer = generateWsiDataset(
	tileWidth,
	tileHeight,
	tilesX,
	tilesY,
	sliceThickness,
	pixelSpacingX,
	pixelSpacingY,
	slideOffsetX,
	slideOffsetY
	);
	fs.writeFileSync(outFile, wsiDatasetBuffer);