/*=========================================================================

  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.
 *
 * Usage:
 * $ LD_LIBRARY_PATH=. CLASSPATH=gdcm.jar:. java ExtractImageRegion input.dcm
 */
import gdcm.*;
import java.io.FileOutputStream;

public class ExtractImageRegion
{
  public static void main(String[] args) throws Exception
    {
    String filename = args[0];

    // instantiate the reader:
    ImageRegionReader reader = new ImageRegionReader();
    reader.SetFileName( filename );

    // pull DICOM info:
    if (!reader.ReadInformation()) return;
    // Get file infos
    File f = reader.GetFile();

    // get some info about image
    UIntArrayType dims = ImageHelper.GetDimensionsValue(f);
    PixelFormat pf = ImageHelper.GetPixelFormatValue (f);
    int pixelsize = pf.GetPixelSize();

    // buffer to get the pixels
    long buffer_length = dims.get(0) * dims.get(1) * pixelsize;
    byte[] buffer = new byte[ (int)buffer_length ];

    // define a simple box region.
    BoxRegion box = new BoxRegion();
    for (int z = 0; z < dims.get(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.get(0) - 1, 0, dims.get(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:
      // long buf_len = reader.ComputeBufferLength(); // take into account pixel size
      // to get the exact size of minimum buffer
      if (reader.ReadIntoBuffer(buffer, buffer_length))
        {
        FileOutputStream fos = new FileOutputStream("/tmp/frame.raw");
        fos.write(buffer);
        fos.close();
        }
      else
        {
        throw new Exception("can't read pixels error");
        }
      }

    }
}