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

  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.

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

/*
$ gdcminfo ~/Desktop/angiogram-06.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.12.1 [X-Ray Angiographic Image Storage]
TransferSyntax is 1.2.840.10008.1.2.4.50 [JPEG Baseline (Process 1): Default Transfer Syntax for Lossy JPEG 8 Bit Image Compression]
NumberOfDimensions: 3
Dimensions: (512,512,355)
Origin: (0,0,0)
Spacing: (1,1,40)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
SamplesPerPixel    :1
BitsAllocated      :8
BitsStored         :8
HighBit            :7
PixelRepresentation:0
ScalarType found   :UINT8
PhotometricInterpretation: MONOCHROME2
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.4.50
Orientation Label: AXIAL
*/

/*
 * Description:
 *
 * Assume we have a file angiogram-06.dcm as described above.
 * the following program will decompress directly from the extracted jpeg stream.
 *
 * First step extract the jpeg stream (but not the Basic Offset Table):
 *
 * $ gdcmraw -i angiogram-06.dcm -o /tmp/output/chris --split-frags --pattern %d.jpg
 *
 * Check that indeed there are 355 files, while there are 356 fragments in the original DICOM file, since
 * gdcmraw always skip the first fragment (Basic Offset Table).
 *
 * Now from those individual jpeg stream, recreate a fake gdcm.DataElement...
 *
 * Usage:
 *
 * $ export LD_LIBRARY_PATH=$HOME/Projects/gdcm/debug-gcc/bin
 * $ mono ./bin/DecompressImageMultiframe.exe /tmp/output
 */
using System;
using gdcm;

public class DecompressImageMultiframe
{
  public static int Main(string[] args)
    {
    string directory = args[0];
    gdcm.Directory dir = new gdcm.Directory();
    uint nfiles = dir.Load(directory);
    //System.Console.WriteLine(dir.toString());
    gdcm.FilenamesType filenames = dir.GetFilenames();

    Image image = new Image();
    image.SetNumberOfDimensions( 3 ); // important for now
    DataElement pixeldata = new DataElement( new gdcm.Tag(0x7fe0,0x0010) );

    // Create a new SequenceOfFragments C++ object, store it as a SmartPointer :
    SmartPtrFrag sq = SequenceOfFragments.New();

    // Yeah, the file are not garantee to be in order, please adapt...
    for(uint i = 0; i < nfiles; ++i)
      {
      System.Console.WriteLine( filenames[(int)i] );
      string file = filenames[(int)i];
      System.IO.FileStream infile =
        new System.IO.FileStream(file, System.IO.FileMode.Open, System.IO.FileAccess.Read);
      uint fsize = gdcm.PosixEmulation.FileSize(file);

      byte[] jstream  = new byte[fsize];
      infile.Read(jstream, 0 , jstream.Length);

      Fragment frag = new Fragment();
      frag.SetByteValue( jstream, new gdcm.VL( (uint)jstream.Length) );
      sq.AddFragment( frag );
      }

    // Pass by reference:
    pixeldata.SetValue( sq.__ref__() );

    // insert:
    image.SetDataElement( pixeldata );

    // JPEG use YBR to achieve better compression ratio by default (not RGB)
    // FIXME hardcoded:
    PhotometricInterpretation pi = new PhotometricInterpretation( PhotometricInterpretation.PIType.MONOCHROME2 );
    image.SetPhotometricInterpretation( pi );
    // FIXME hardcoded:
    PixelFormat pixeltype = new PixelFormat(1,8,8,7);
    image.SetPixelFormat( pixeltype );

    // FIXME hardcoded:
    image.SetTransferSyntax( new TransferSyntax( TransferSyntax.TSType.JPEGLosslessProcess14_1 ) );
    image.SetDimension(0, 512);
    image.SetDimension(1, 512);
    image.SetDimension(2, 355);

    // Decompress !
    byte[] decompressedData = new byte[(int)image.GetBufferLength()];
    image.GetBuffer(decompressedData);

    // Write out the decompressed bytes
    System.Console.WriteLine(image.toString());
    using (System.IO.Stream stream =
      System.IO.File.Open(@"/tmp/dd.raw",
        System.IO.FileMode.Create))
      {
      System.IO.BinaryWriter writer = new System.IO.BinaryWriter(stream);
      writer.Write(decompressedData);
      }


    return 0;
    }
}