ExtractImageRegionWithLUT.cs

/*=========================================================================
 
  Program: GDCM (Grassroots DICOM). A DICOM library
 
  Copyright (c) 2006-2011 Mathieu Malaterre
  All rights reserved.
  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
 
     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notice for more information.
 
=========================================================================*/
 
/*
 * This small code shows how to use the gdcm.ImageRegionReader API
 * In this example we are taking each frame by frame and dump them to
 * /tmp/frame.raw.
 * Furthermore we are applying the LUT on this image.
 * Special care should be taken in case the image is not PALETTE COLOR
 *
 * Usage:
 * $ bin/ExtractImageRegionWithLUT.exe input.dcm
 *
 * Example:
 * $ bin/ExtractImageRegionWithLUT.exe gdcmData/rle16loo.dcm
 * $ md5sum /tmp/frame_rgb.raw
 * 73bf61325fdb6e2830244a2b7b0c4ae2  /tmp/frame_rgb.raw
 * $ gdcmimg --depth 16 --spp 3 --size 600,430 /tmp/frame_rgb.raw rgb.dcm 
 * $ gdcmviewer rgb.dcm
 */
using System;
using gdcm;
 
public class ExtractImageRegion
{
  public static int Main(string[] args)
    {
    string filename = args[0];
 
    // instantiate the reader:
    gdcm.ImageRegionReader reader = new gdcm.ImageRegionReader();
    reader.SetFileName( filename );
 
    // pull DICOM info:
    if (!reader.ReadInformation()) return 1;
    // Get file infos
    gdcm.File f = reader.GetFile();
 
    gdcm.LookupTable lut = reader.GetImage().GetLUT();
 
    // get some info about image
    UIntArrayType dims = ImageHelper.GetDimensionsValue(f);
    PixelFormat pf = ImageHelper.GetPixelFormatValue (f);
    int pixelsize = pf.GetPixelSize();
 
    // buffer to get the pixels
    byte[] buffer = new byte[ dims[0] * dims[1] * pixelsize ];
 
    // output buffer for the RGB decoded image:
    byte[] buffer2 = new byte[ dims[0] * dims[1] * pixelsize * 3 ];
 
    // define a simple box region.
    BoxRegion box = new BoxRegion();
    for (uint z = 0; z < dims[2]; z++)
      {
      // Define that I want the image 0, full size (dimx x dimy pixels)
      // and do that for each z:
      box.SetDomain(0, dims[0] - 1, 0, dims[1] - 1, z, z);
      //System.Console.WriteLine( box.toString() );
      reader.SetRegion( box );
 
      // reader will try to load the uncompressed image region into buffer.
      // the call returns an error when buffer.Length is too small. For instance
      // one can call:
      // uint buf_len = reader.ComputeBufferLength(); // take into account pixel size
      // to get the exact size of minimum buffer
      if (reader.ReadIntoBuffer(buffer, (uint)buffer.Length))
        {
        if( !lut.Decode( buffer2, (uint)buffer2.Length, buffer, (uint)buffer.Length ) )
          {
          throw new Exception("can't decode");
          }
 
        using (System.IO.Stream stream =
          System.IO.File.Open(@"/tmp/frame_rgb.raw",
            System.IO.FileMode.Create))
          {
          System.IO.BinaryWriter writer = new System.IO.BinaryWriter(stream);
          writer.Write(buffer2);
          }
        }
      else
        {
        throw new Exception("can't read pixels error");
        }
      }
 
    return 0;
    }
}