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

  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.

=========================================================================*/
// We are required to call the package 'vtk' eventhough I (MM) would have prefered
// an import statement along the line of:
// import vtkgdcm.*;
import vtk.*;

/*
 * Compilation:
 * CLASSPATH=vtkgdcm.jar:/usr/share/java/vtk.jar javac HelloVTKWorld.java
 *
 * Usage:
 * LD_LIBRARY_PATH=/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/xawt:/usr/lib/jni:. CLASSPATH=/usr/share/java/vtk.jar:vtkgdcm.jar:gdcm.jar:. java HelloVTKWorld gdcmData/012345.002.050.dcm bla.dcm
 *
 */
public class HelloVTKWorld
{
  static {
    System.loadLibrary("vtkCommonJava");
    System.loadLibrary("vtkFilteringJava");
    System.loadLibrary("vtkIOJava");
    System.loadLibrary("vtkImagingJava");
    System.loadLibrary("vtkGraphicsJava");
    System.loadLibrary("vtkgdcmJava");
    try {
      System.loadLibrary("vtkRenderingJava");
    } catch (Throwable e) {
      System.out.println("cannot load vtkHybrid, skipping...");
    }
    try {
      System.loadLibrary("vtkHybridJava");
    } catch (Throwable e) {
      System.out.println("cannot load vtkHybrid, skipping...");
    }
    try {
      System.loadLibrary("vtkVolumeRenderingJava");
    } catch (Throwable e) {
      System.out.println("cannot load vtkVolumeRendering, skipping...");
    }
  }

  public static void main(String[] args)
    {
    String filename = args[0];
    vtkGDCMImageReader reader = new vtkGDCMImageReader();
    reader.SetFileName( filename );
    reader.Update();

    vtkMedicalImageProperties prop = reader.GetMedicalImageProperties();
    System.out.println( prop.GetPatientName() ); //

//    if( reader.GetImageFormat() == vtkgdcm.vtkgdcm.VTK_LUMINANCE ) // MONOCHROME2
//      {
//      System.out.println( "Image is MONOCHROME2" ); //
//      }

    // Just for fun, invert the direction cosines, output should reflect that:
    vtkMatrix4x4 dircos = reader.GetDirectionCosines();
    dircos.Invert();

    // We need to maintain in sync information stored in vtkMedicalImageProperties:
    double[] cosines = new double[6];
    cosines[0] = dircos.GetElement(0,0);
    cosines[1] = dircos.GetElement(1,0);
    cosines[2] = dircos.GetElement(2,0);
    cosines[3] = dircos.GetElement(0,1);
    cosines[4] = dircos.GetElement(1,1);
    cosines[5] = dircos.GetElement(2,1);
    reader.GetMedicalImageProperties().SetDirectionCosine( cosines );

    String outfilename = args[1];
    vtkGDCMImageWriter writer = new vtkGDCMImageWriter();
    writer.SetMedicalImageProperties( reader.GetMedicalImageProperties() );
    writer.SetDirectionCosines( dircos );
    writer.SetShift( reader.GetShift() );
    writer.SetScale( reader.GetScale() );
    writer.SetImageFormat( reader.GetImageFormat() );
    writer.SetFileName( outfilename );
    writer.SetInputConnection( reader.GetOutputPort() ); // new
    //writer.SetInput( reader.GetOutput() ); // old
    writer.Write();

    System.out.println("Success reading: " + filename );
    }
}