dicom-microscopy-viewer/src/webWorker/decodeAndTransformTask.js

Interactive web-based viewer for DICOM Microscopy Images

import JPEG2000Decoder from './decoders/decoderJPEG2000.js'
import JPEGLSDecoder from './decoders/decoderJPEGLS.js'
import JPEGDecoder from './decoders/decoderJPEGBaseline8Bit.js'
import ColorTransformer from './transformers/transformerICC.js'
import imageType from 'image-type'

const decoderJPEG2000 = new JPEG2000Decoder()
const decoderJPEGLS = new JPEGLSDecoder()
const decoderJPEG = new JPEGDecoder()
let transformerColor

/**
 * Task handler function
 *
 * @param {object} - handler data
 * @param {function} - handler done call back
 *
 * @private
 */
function _handler (data, doneCallback) {
  const {
    bitsAllocated,
    columns,
    rows,
    samplesPerPixel,
    pixelRepresentation,
    frame,
    sopInstanceUID,
    metadata,
    iccProfiles
  } = data.data

  _checkImageTypeAndDecode(
    {
      bitsAllocated,
      columns,
      rows,
      samplesPerPixel,
      pixelRepresentation,
      frame
    }
  ).then((decodedFrame) => {
    if (iccProfiles != null && iccProfiles.length > 0) {
      // Only instantiate the transformer once and cache it for reuse.
      if (transformerColor === undefined) {
        transformerColor = new ColorTransformer(metadata, iccProfiles)
      }
      // Apply ICC color transform
      transformerColor.transform(
        sopInstanceUID,
        decodedFrame
      ).then((transformedFrame) => {
        /*
         * Invoke the callback with our result and pass the frameData in the
         * transferList to move it to UI thread without making a copy.
         */
        doneCallback(
          { frameData: transformedFrame.buffer },
          [transformedFrame.buffer]
        )
      }).catch(
        (error) => {
          throw new Error(`Failed to transform frame: ${error}`)
        }
      )
    } else {
      doneCallback(
        { frameData: decodedFrame.buffer },
        [decodedFrame.buffer]
      )
    }
  }).catch(
    (error) => {
      throw new Error(`Failed to decode frame: ${error}`)
    }
  )
}

/** Check image type of a compressed array and returns a decoded image.
 * @param {number} - bits per sample
 * @param {number} - columns
 * @param {number} - rows
 * @param {number} - samples per pixel
 * @param {number} - pixel representation
 * @param {Uint8Array} byteArray - Image array
 *
 * @returns {Uint8Array} decoded array
 * @private
 */
async function _checkImageTypeAndDecode ({
  bitsAllocated,
  columns,
  rows,
  samplesPerPixel,
  pixelRepresentation,
  frame
}) {
  let byteArray = new Uint8Array(frame)
  const imageTypeObject = imageType(byteArray)

  const toHex = function (value) {
    return value.toString(16).padStart(2, '0').toUpperCase()
  }

  let mediaType
  if (imageTypeObject == null) {
    /**
     * This hack is required to recognize JPEG 2000 bit streams that are zero
     * padded, i.e., that have a "00" byte after the JPEG 2000 End of Image
     * (EOI) marker "FFD9".
     */
    if (
      toHex(byteArray[byteArray.length - 3]) === 'FF' &&
      toHex(byteArray[byteArray.length - 2]) === 'D9' &&
      toHex(byteArray[byteArray.length - 1]) === '00'
    ) {
      mediaType = 'image/jp2'
      byteArray = new Uint8Array(byteArray.buffer, 0, byteArray.length - 1)
    } else {
      if (
        toHex(byteArray[byteArray.length - 2]) === 'FF' &&
        toHex(byteArray[byteArray.length - 1]) === 'D9'
      ) {
        mediaType = 'image/jp2'
      } else {
        mediaType = 'application/octet-stream'
      }
    }
  } else {
    /**
     * This hack is required to distinguish JPEG-LS from baseline JPEG, which
     * both contain the JPEG Start of Image (SOI) marker and share the first
     * three bytes.
     */
    if ((toHex(byteArray[3]) === 'F7') || (toHex(byteArray[3]) === 'E8')) {
      mediaType = 'image/jls'
    } else {
      const supportedImageMediaTypes = new Set([
        'image/jpeg',
        'image/jls',
        'image/jp2',
        'image/jpx'
      ])
      if (supportedImageMediaTypes.has(imageTypeObject.mime)) {
        mediaType = imageTypeObject.mime
      } else {
        mediaType = 'application/octet-stream'
      }
    }
  }

  if (mediaType === 'application/octet-stream') {
    console.debug(`decode uncompressed frame with media type "${mediaType}"`)
    return byteArray
  }

  console.debug(`decode compressed frame with media type "${mediaType}"`)

  const { frameBuffer, frameInfo } = await _decode(mediaType, byteArray)
  if (frameInfo.bitsPerSample !== bitsAllocated) {
    throw new Error(
      'Frame does not have expected Bits Allocated: ' +
      `${frameInfo.bitsPerSample} instead of ${bitsAllocated}.`
    )
  }

  if (frameInfo.height !== rows) {
    throw new Error(
      'Frame does not have expected Rows: ' +
      `${frameInfo.height} instead of ${rows}.`
    )
  }

  if (frameInfo.width !== columns) {
    throw new Error(
      'Frame does not have expected Columns: ' +
      `${frameInfo.width} instead of ${columns}.`
    )
  }

  if (frameInfo.componentCount !== samplesPerPixel) {
    throw new Error(
      'Frame does not have expected Samples Per Pixel: ' +
      `${frameInfo.componentCount} instead of ${samplesPerPixel}.`
    )
  }

  if (frameInfo.isSigned != null) {
    const isSigned = pixelRepresentation === 1
    if (frameInfo.isSigned !== isSigned) {
      throw new Error(
        'Frame does not have expected Pixel Representation: ' +
        `"${frameInfo.isSigned}" instead of "${isSigned}".`
      )
    }
  }

  const length = columns * rows * samplesPerPixel * (bitsAllocated / 8)
  if (length !== frameBuffer.length) {
    throw new Error(
      'Frame value does not have expected length: ' +
      `${frameBuffer.length} instead of ${length}.`
    )
  }

  return frameBuffer
}

/** Decode image.
 *
 * @param {string} mediaType - Media Type
 * @param {Uint8Array} byteArray - Image array
 *
 * @returns {object} decoded array and frameInfo
 * @private
 */
async function _decode (mediaType, byteArray) {
  if (mediaType === 'image/jpeg') {
    return await decoderJPEG.decode(byteArray)
  } else if (mediaType === 'image/jp2' || mediaType === 'image/jpx') {
    return await decoderJPEG2000.decode(byteArray)
  } else if (mediaType === 'image/jls') {
    return await decoderJPEGLS.decode(byteArray)
  }
}

export default {
  taskType: 'decodeAndTransformTask',
  _handler
}