Class: RImageAnalysisTools::ImageWriter

Inherits:
Object
  • Object
show all
Defined in:
lib/rimageanalysistools/image/io/image_writer.rb

Instance Method Summary collapse

Constructor Details

#initialize ⇒ ImageWriter

Returns a new instance of ImageWriter.



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# File 'lib/rimageanalysistools/image/io/image_writer.rb', line 38

def initialize
  
end

Instance Method Details

#write(filename, image_to_write) ⇒ Object 



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# File 'lib/rimageanalysistools/image/io/image_writer.rb', line 42

def write(filename, image_to_write)

  wr = ImageWriter.new

  m = image_to_write.getMetadata

  pixels = image_to_write.getPixelData

  pixel_array = pixels.toImagePlus.getProcessor.getPixels

  m.setPixelsDimensionOrder(DimensionOrder.fromString(pixels.getDimensionOrder.upcase), 0)

  m.setPixelsType(PixelType.fromString(FormatTools.getPixelTypeString(pixels.getDataType)), 0)

  wr.setMetadataRetrieve(m)

  File.unlink(filename) if File.exist?(filename)

  wr.setId(filename)

  pixels.getNumPlanes.times do |i|

    c = i % pixels::size_c
    z = ((i - c)/pixels::size_c) % pixels::size_z
    t = (i - c - pixels::size_c * z)/(pixels::size_z * pixels::size_c)

    conv_index = pixels.toImagePlus.getStackIndex(c+1, z+1, t+1)

    pixels.toImagePlus.setSliceWithoutUpdate(conv_index)
    pixelData = pixels.toImagePlus.getProcessor.getPixels

    size_to_allocate = pixels::size_x * pixels::size_y * FormatTools.getBytesPerPixel(pixels::dataType)

    out = ByteBuffer.allocate(size_to_allocate)

    out.asFloatBuffer.put(pixelData)

    wr.savePlane(i, out.array)
  
  end

  wr.close

end