gdcm_conv 0.2.0

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

  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.

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

/*
 * Simple C# example
 *
 * Shows multiple steps:
 * Steps 1.
 * Create a fake (dummy) DICOM file, with size 512 x 512 x 2 We use a small
 * image to be able to create the volume in memory Of course you can use any
 * existing DICOM instead
 *
 * Step 2.
 * Hack the DICOM file to pretend the number of frames is 1000 (instead of 2)
 * At this point in time this makes the DICOM file invalid (truncated). But the
 * next step will fix this.
 *
 * Step 3.
 * Use C# to create a binary data which will represent our source object for
 * image.
 *
 * Step 4.
 * We use gdcm.FileStreamer to merge the template DICOM file from Step 2, with
 * the binary data from Step 3. We decide to read a scanline at a time, but
 * this can be read with any number of bytes. AppendToDataElement() will always
 * do the proper computation.
 *
 * Step 5.
 * We compress this gigantic file, into [JPEG Lossless, Non-Hierarchical,
 * First-Order Prediction (Process 14 [Selection Value 1])]
 *
 * Usage:
 * $ mono bin/FileChangeTS.exe small.dcm big.dcm raw.data merge.dcm jpeg.dcm
 */
using System;
using System.IO;
using gdcm;

public class FileChangeTS
{
  public static byte[] StrToByteArray(string str)
    {
    System.Text.ASCIIEncoding  encoding=new System.Text.ASCIIEncoding();
    return encoding.GetBytes(str);
    }
  // Create a 256 x 256 Secondary Capture Image Storage
  static private void CreateSmallDICOM(string fileName)
    {
    using( var writer = new gdcm.PixmapWriter() )
      {
      gdcm.Pixmap img = writer.GetImage();
      img.SetNumberOfDimensions( 3 );
      img.SetDimension(0, 512 );
      img.SetDimension(1, 512 );
      img.SetDimension(2, 2 ); // fake a 3d volume
      PhotometricInterpretation pi = new PhotometricInterpretation( PhotometricInterpretation.PIType.MONOCHROME2 );
      img.SetPhotometricInterpretation( pi );
      gdcm.DataElement pixeldata = new gdcm.DataElement( new gdcm.Tag(0x7fe0,0x0010) );
      byte[] buffer = new byte[ 512 * 512 * 2 ];
      pixeldata.SetByteValue( buffer, new gdcm.VL((uint)buffer.Length) );
      img.SetDataElement( pixeldata );

      gdcm.File file = writer.GetFile();
      gdcm.DataSet ds = file.GetDataSet();
      gdcm.DataElement ms = new gdcm.DataElement(new gdcm.Tag(0x0008,0x0016));
      string mediastorage = "1.2.840.10008.5.1.4.1.1.7.2"; // Multi-frame Grayscale Byte Secondary Capture Image Storage
      byte[] val = StrToByteArray(mediastorage);
      ms.SetByteValue( val, new gdcm.VL( (uint)val.Length) );
      ds.Insert( ms );

      writer.SetFileName( fileName );
      writer.Write();
      }
    }
  static private void CreateBigDICOM(string fileName, string outfilename)
    {
    using( var ano = new gdcm.FileAnonymizer() )
      {
      // The following is somewhat dangerous, do not try at home:
      string nframes = "1000";
      ano.Replace( new gdcm.Tag(0x0028,0x0008), nframes );
      ano.SetInputFileName(fileName);
      ano.SetOutputFileName(outfilename);
      ano.Write(); // at this point the DICOM is invalid !
      }
    }
  static private void CreateDummyFile(string fileName, long length)
    {
    using (var fileStream = new FileStream(fileName, FileMode.Create, FileAccess.Write, FileShare.None))
      {
      // Looks like C# always init to 0 (fallocate ?)
      // For the purpose of the test we could add some random noise
      fileStream.SetLength(length);
      }
    }
  static private void ReadBytesIntoArray( byte[] array, FileStream source )
    {
    int numBytesToRead = array.Length;
    int numBytesRead = 0;
    while (numBytesToRead > 0)
      {
      // According to spec: Read() may return anything from 0 to numBytesToRead.
      int n = source.Read(array, numBytesRead, numBytesToRead);

      // Break when the end of the file is reached.
      if (n == 0)
        break;

      numBytesRead += n;
      numBytesToRead -= n;
      }
    }
  static private void AssembleDICOMAndRaw(string dicomfn, string rawdata, string outfn)
    {
    using ( var fs = new gdcm.FileStreamer() )
      {
      fs.SetTemplateFileName(dicomfn);
      fs.SetOutputFileName(outfn);
      gdcm.Tag pixeldata = new gdcm.Tag(0x7fe0, 0x0010);
      // FileStreamer support automatic checking of pixel data length
      // based on DICOM attributes, only if we say so:
      fs.CheckDataElement( pixeldata );
      // Declare we are working on Pixel Data attribute:
      fs.StartDataElement( pixeldata );
      using (FileStream rawSource = new FileStream(rawdata,
          FileMode.Open, FileAccess.Read))
        {
        byte[] bytes = new byte[512];
        // Only read one scanline at a time
        // We could have been reading more at once, if this is more efficient,
        // AppendToDataElement will do the logic in all cases.
        for( int i = 0; i < 512 * 1000; ++i )
          {
          // Read the source file into a byte array.
          ReadBytesIntoArray( bytes, rawSource );
          fs.AppendToDataElement( pixeldata, bytes, (uint)bytes.Length );
          }
        }
      if( !fs.StopDataElement( pixeldata ) )
        {
        // Most likely an issue with Pixel Data Length computation:
        throw new Exception("StopDataElement failed");
        }
      }
    }
  static private void CompressIntoJPEG(string rawdicom, string jpegdicom)
    {
    using( var sfcts = FileChangeTransferSyntax.New() )
      {
      // Need to retrieve the actual C++ reference, to pass to
      // SimpleSubjectWatcher:
      FileChangeTransferSyntax fcts = sfcts.__ref__();
      SimpleSubjectWatcher watcher = new SimpleSubjectWatcher(fcts, "FileChangeTransferSyntax");
      gdcm.TransferSyntax ts = new TransferSyntax( TransferSyntax.TSType.JPEGLosslessProcess14_1 );
      fcts.SetTransferSyntax( ts );
      fcts.SetInputFileName( rawdicom );
      fcts.SetOutputFileName( jpegdicom );
      fcts.Change();
      }
    }
  public static int Main(string[] args)
    {
    string filename = args[0];
    string outfilename = args[1];
    string rawfilename = args[2];
    string mergefn = args[3];
    string jpegfn = args[4];

    CreateSmallDICOM(filename);
    CreateBigDICOM(filename, outfilename);
    CreateDummyFile(rawfilename, 512 * 512 * 1000 );
    AssembleDICOMAndRaw(outfilename, rawfilename, mergefn);
    CompressIntoJPEG(mergefn, jpegfn);

    return 0;
    }
}