Module: DICOM::ImageProcessor::DcmRMagick

Defined in:
lib/dicom/image_processor_r_magick.rb

Overview

This module contains methods for interacting with pixel data using the RMagick gem.

Class Method Summary collapse

Class Method Details

.decompress(blobs) ⇒ Array<Magick::Image>, FalseClass

Creates image objects from an array of compressed, binary string blobs.

Note

The method tries to use RMagick for unpacking, but unortunately, it seems that ImageMagick is not able to handle most of the compressed image variants used in the DICOM standard. To get a more robust implementation which is able to handle most types of compressed DICOM files, something else is needed.

Probably a good candidate to use is the PVRG-JPEG library, which seems to be able to handle everything that is jpeg. It exists in the Ubuntu repositories, where it can be installed and run through terminal. For source code, and some additional information, check out this link: www.panix.com/~eli/jpeg/

Another idea would be to study how other open source libraries, like GDCM handle these files.

Parameters:

  • blobs (Array<String>) —

    an array of binary string blobs containing compressed pixel data

Returns:

  • (Array<Magick::Image>, FalseClass) —

    • an array of images, or false (if decompression failed)



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# File 'lib/dicom/image_processor_r_magick.rb', line 29

def decompress(blobs)
  # FIXME:
  # The following transfer syntaxes have been verified as failing with ImageMagick:
  # TXS_JPEG_LOSSLESS_NH is not supported by (my) ImageMagick version: "Unsupported JPEG process: SOF type 0xc3"
  # TXS_JPEG_LOSSLESS_NH_FOP is not supported by (my) ImageMagick version: "Unsupported JPEG process: SOF type 0xc3"
  # TXS_JPEG_2000_PART1_LOSSLESS is not supported by (my) ImageMagick version: "jpc_dec_decodepkts failed"
  #
  images = Array.new
  # We attempt to decompress the pixels using ImageMagick:
    blobs.each do |string|
      images << Magick::Image.from_blob(string).first
    end
  return images
end

.export_pixels(image, photometry) ⇒ Array<Integer>

Extracts an array of pixels (integers) from an image object.

Parameters:

  • image (Magick::Image) —

    an RMagick image object

  • photometry (String) —

    a code describing the photometry of the pixel data (e.g. ‘MONOCHROME1’ or ‘COLOR’)

Returns:

  • (Array<Integer>) —

    an array of pixel values

Raises:

  • (ArgumentError) 


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# File 'lib/dicom/image_processor_r_magick.rb', line 50

def export_pixels(image, photometry)
  raise ArgumentError, "Expected Magick::Image, got #{image.class}." unless image.is_a?(Magick::Image)
  pixels = image.export_pixels(0, 0, image.columns, image.rows, rm_map(photometry))
  return pixels
end

.import_pixels(blob, columns, rows, depth, photometry, format = 'png') ⇒ Magick::Image

Creates an image object from a binary string blob.

Parameters:

  • blob (String) —

    binary string blob containing pixel data

  • columns (Integer) —

    the number of columns

  • rows (Integer) —

    the number of rows

  • depth (Integer) —

    the bit depth of the encoded pixel data

  • photometry (String) —

    a code describing the photometry of the pixel data (e.g. ‘MONOCHROME1’ or ‘COLOR’)

  • format (String) (defaults to: 'png') —

    the image format to use

Returns:

  • (Magick::Image) —

    an RMagick image object



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# File 'lib/dicom/image_processor_r_magick.rb', line 66

def import_pixels(blob, columns, rows, depth, photometry, format='png')
  image = Magick::Image.new(columns,rows).import_pixels(0, 0, columns, rows, rm_map(photometry), blob, rm_data_type(depth))
end

.rm_data_type(bit_depth) ⇒ Magick::CharPixel, Magick::ShortPixel

Converts a given bit depth to an RMagick StorageType.

Parameters:

  • bit_depth (Integer) —

    the bit depth of the pixel data

Returns:

  • (Magick::CharPixel, Magick::ShortPixel) —

    the proper storage type

Raises:

  • (ArgumentError) —

    if given an unsupported bit depth



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# File 'lib/dicom/image_processor_r_magick.rb', line 76

def rm_data_type(bit_depth)
  return case bit_depth
  when 8
    Magick::CharPixel
  when 16
    Magick::ShortPixel
  else
    raise ArgumentError, "Unsupported bit depth: #{bit_depth}."
  end
end

.rm_map(photometry) ⇒ String

Converts a given DICOM photometry string to an RMagick pixel map string.

Parameters:

  • photometry (String) —

    a code describing the photometry of the pixel data (e.g. ‘MONOCHROME1’ or ‘COLOR’)

Returns:

  • (String) —

    an RMagick pixel map string

Raises:

  • (ArgumentError) 


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# File 'lib/dicom/image_processor_r_magick.rb', line 92

def rm_map(photometry)
  raise ArgumentError, "Expected String, got #{photometry.class}." unless photometry.is_a?(String)
  if photometry.include?('COLOR') or photometry.include?('RGB')
    return 'RGB'
  elsif photometry.include?('YBR')
    return 'YBR'
  else
    return 'I' # (Assuming monochromeX - greyscale)
  end
end