bf-itk-pipe time splitting example

BFITKTest.cxxitkLSMBioFormatsImageIOTest.cxx

/*
* #%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 <fstream>
#include "itkBioFormatsImageIO.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImage.h"
#include "itkRGBPixel.h"
#include "itkMetaDataObject.h"
#include "itkExtractImageFilter.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 = 5;

  typedef itk::Image< PixelType, Dimension > ImageType;
  typedef itk::ImageFileReader<ImageType> ReaderType;
  typedef itk::ImageIORegion ImageIORegionType;
  typedef itk::ImageFileWriter<ImageType> WriterType;
  typedef itk::ExtractImageFilter<ImageType, ImageType> ExtractImageFilter;

  // This ImageIO won't actually be used, it's just a reference to remember how many
  // T-slices there are, as the extracted ImageIO will be truncated.
  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();

  // Similarly this region will be reused to ensure when we know how big the image is when
  // we try to extract a single T-slice
  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) );
  }
  ReaderType::Pointer reader = ReaderType::New();
  reader->SetFileName(argv[1]);
  reader->UseStreamingOn();
  WriterType::Pointer writer = WriterType::New();

  for( unsigned int i = 0; i < region.GetSize( numberOfDim-2 ); i++ )
  {
    std::cout << i << std::endl;

    // When I was persisting these objects between iterations I ran into
    // I ran into errors based on remembering the wrong region sizes
    itk::BioFormatsImageIO::Pointer imageIO = itk::BioFormatsImageIO::New();
    ExtractImageFilter::Pointer extractor = ExtractImageFilter::New();

    imageIO->DebugOn();
    imageIO->SetFileName(argv[1]);
    imageIO->SetUseStreamedReading(true);
    imageIO->SetUseStreamedWriting(true);
    // reset to the largest possible region, so that the extraction region is contained
    imageIO->SetIORegion( region );

    imageIO->ReadImageInformation();

    reader->SetImageIO(imageIO);

    std::cout << "ImageIO Region: " << imageIO << std::endl;

    ImageType::IndexType start;
    ImageType::SizeType size;

    for( unsigned int j = 0; j < 5; j++ )
    {
      start[j] = 0;
      size[j] = io->GetDimensions(j);
    }

    start[ numberOfDim-2 ] = i;
    size[ numberOfDim-2 ] = 1;

    ImageType::RegionType desiredRegion;
    desiredRegion.SetSize(size);
    desiredRegion.SetIndex(start);

    extractor->SetExtractionRegion(desiredRegion);

    std::cout << "Region of extraction: " << extractor->GetExtractionRegion() << std::endl;

    std::cout << "Largest possible reader region, pre-update: " << reader->GetImageIO()->GetIORegion() << std::endl;

    extractor->SetInput(reader->GetOutput());
    extractor->Update();

    std::cout << "Largest possible reader region, post-update: " << reader->GetImageIO()->GetIORegion() << std::endl;

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

    writer->SetFileName( fname.c_str() );
    writer->SetImageIO(imageIO);
    writer->SetInput(extractor->GetOutput());

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

  return EXIT_SUCCESS;
}