/*
 * #%L
 * Bio-Formats plugin for the Insight Toolkit.
 * %%
 * Copyright (C) 2010 - 2012 Insight Software Consortium, and Open Microscopy
 * Environment:
 *   - Board of Regents of the University of Wisconsin-Madison
 *   - Glencoe Software, Inc.
 *   - University of Dundee
 * %%
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 *
 * The views and conclusions contained in the software and documentation are
 * those of the authors and should not be interpreted as representing official
 * policies, either expressed or implied, of any organization.
 *
 * ----------------------------------------------------------------
 * Adapted from the Slicer3 project: http://www.slicer.org/
 * http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/MGHImageIO/
 *
 * See slicer-license.txt for Slicer3's licensing information.
 *
 * For more information about the ITK Plugin IO mechanism, see:
 * http://www.itk.org/Wiki/Plugin_IO_mechanisms
 * #L%
 */

#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif

#include <iostream>
#include "itkBioFormatsImageIO.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImage.h"
#include "itkRGBPixel.h"
#include "itkMetaDataObject.h"
#include "itkStreamingImageFilter.h"
#include <itkImageIORegion.h>

#if defined(ITK_USE_MODULAR_BUILD)
  #define SPECIFIC_IMAGEIO_MODULE_TEST
#endif

int main( int argc, char * argv [] )
{
  if( argc < 2)
    {
    std::cerr << "Usage: " << argv[0] << " input";
    return EXIT_FAILURE;
    }

  typedef unsigned char       PixelType;
  const unsigned int                         Dimension = 3;

  typedef itk::Image< PixelType, Dimension >   ImageType;

  typedef itk::ImageFileReader<ImageType> ReaderType;
  typedef itk::ImageIORegion ImageIORegionType;
  typedef itk::StreamingImageFilter<ImageType, ImageType> StreamingFilter;
  typedef itk::ImageFileWriter<ImageType> WriterType;

  itk::BioFormatsImageIO::Pointer io = itk::BioFormatsImageIO::New();
  //io->DebugOn();

  std::string inputFilename = argv[1];
  io->SetFileName(argv[1]);
  io->ReadImageInformation();
  unsigned int numberOfDim = io->GetNumberOfDimensions();

  ImageIORegionType region(5);
  for( unsigned long i = 0; i < numberOfDim; i++ )
  {
    std::cout << "Setting index: " << i << " to: " << io->GetDimensions(i) << std::endl;
    region.SetIndex( i, 0 );
    region.SetSize( i, io->GetDimensions(i) );
  }
  //region.SetSize( numberOfDim-2, 1 );

  for( unsigned int i = 0; i < io->GetDimensions( numberOfDim-2 ); i++ )
  {
    std::cout << i << std::endl;

    std::cout << region << std::endl;
    region.SetIndex( numberOfDim-2, i );
    region.SetSize(numberOfDim-2, i+1);
    io->SetIORegion( region );

    std::cout << region << std::endl;

    ReaderType::Pointer reader = ReaderType::New();
    reader->SetFileName(argv[1]);
    reader->SetImageIO(io);
    reader->Update();

    std::ostringstream istream;
    istream << i << ".ome.tiff";
    std::string fname = istream.str();

    WriterType::Pointer writer = WriterType::New();
    writer->SetInput(reader->GetOutput());
    writer->SetFileName( fname.c_str() );
    std::cout << i << " writer region:\n" << writer->GetIORegion() << std::endl;

  try
    {
    writer->Update();
    }
  catch (itk::ExceptionObject &e)
    {
    std::cerr << e << std::endl;
    return EXIT_FAILURE;
    }
  }

  return EXIT_SUCCESS;
}