[Insight-users] ImageSeriesReadWrite error - help?

[Tim Bhatnagar]

well, the individual files are displacement fields that were output from
the ImageRegistration5 routine.

The deformation vector magnitudes will most assuredly be different than
other sets, but the type of information and file are the same..

Here's the source code:

#include "itkImage.h"
#include "itkImageSeriesReader.h"
#include "itkImageFileWriter.h"
#include "itkNumericSeriesFileNames.h"
#include "itkPNGImageIO.h"
#include "itkVTKImageIO.h"
#include "itkChangeInformationImageFilter.h"



int main( int argc, char ** argv )
{

  if( argc < 4 )
    {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << " firstSliceValue lastSliceValue
filenamePrefix  outputImageSuffix " << std::endl;
    return EXIT_FAILURE;
    }


  typedef unsigned short                       PixelType;
  const unsigned int Dimension = 3;
  typedef itk::Vector< float,       3 >  Vector3DType;
  typedef itk::Image< Vector3DType, 2 >  VectorImage2DType;

  typedef itk::Image< Vector3DType, Dimension >  VectorImage3DType;

  typedef itk::ImageSeriesReader< VectorImage3DType >  ReaderType;
  typedef itk::ImageFileWriter<   VectorImage3DType >  WriterType;

  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();


  const unsigned int first = atoi( argv[1] );
  const unsigned int last  = atoi( argv[2] );

  const char * outputFilesuffix = argv[4];

  std::string format = argv[3];
  format += "%02d.vtk";
  std::string format2 = argv[3];
  format2 += argv[4];

  std::cerr << (format2.c_str() );


  typedef itk::NumericSeriesFileNames    NameGeneratorType;

  NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();

  nameGenerator->SetSeriesFormat( format.c_str() );

  nameGenerator->SetStartIndex( first );
  nameGenerator->SetEndIndex( last );
  nameGenerator->SetIncrementIndex( 1 );


  reader->SetImageIO( itk::VTKImageIO::New() );

  reader->SetFileNames( nameGenerator->GetFileNames()  );

  writer->SetFileName( format2.c_str() );


  typedef itk::ImageFileReader< VectorImage3DType  > RefImageReaderType;

  RefImageReaderType::Pointer reference = RefImageReaderType::New();

  reference->SetFileName( "48Slice-refField.vtk" ); // this is a reference
file I have designed

  typedef itk::ChangeInformationImageFilter<
                            VectorImage3DType >
ChangeInformationImageFilterType;

  ChangeInformationImageFilterType::Pointer changer =
ChangeInformationImageFilterType::New();

  changer->UseReferenceImageOn();
  changer->SetReferenceImage( reference->GetOutput() );
  changer->SetInput( reader->GetOutput() );
  changer->ChangeSpacingOn();

  writer->SetInput( changer->GetOutput() );

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


  return EXIT_SUCCESS;
}



On Wed, Sep 4, 2013 at 9:28 AM, Xiaoxiao Liu <xiaoxiao.liu at kitware.com>wrote:

> Hi,
> There  seem to be something different in this this last dataset than your
> other datasets?
> It's better to post the source code with the question so that others could
> help the diagnosis.
> Thanks.
>
> -Xiaoxiao
>
>
>
> On Wed, Sep 4, 2013 at 12:16 PM, Tim Bhatnagar <tim.bhatnagar at gmail.com>wrote:
>
>> Hello,
>>
>> I am combining a number of vector-component 2D images into a 3D volume,
>> using ImageSeriesReadWrite.
>>
>> The work has been going fine, but with my last sample set, I am receiving
>> an error:
>>
>> requested region is outside largest possible region itk
>>
>> Reading some old nabble ITK, I thought this type of error had been
>> addressed by having an automatic implementation of
>> UpdateLargestPossibleRegion(), but I'm seeing it here.
>>
>> Because this is only occurring on my last dataset (the others functioned
>> just fine), could someone help me in terms of what to look for/change?
>>
>> thanks,
>>
>> --
>> Tim Bhatnagar
>> PhD Candidate
>> Orthopaedic Injury Biomechanics Group
>> Department of Mechanical Engineering
>> University of British Columbia
>>
>> Rm 5000 - 818 West 10th Ave.
>> Vancouver, BC
>> Canada
>> V5Z 1M9
>>
>> Ph: (604) 675-8845
>> Fax: (604) 675-8820
>> Web: oibg.mech.ubc.ca
>>
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>
>
> --
>
>
> ---------------------------------------------
> *Xiaoxiao Liu*, Ph.D.
> R & D Engineer
> Kitware Inc <http://www.kitware.com/>.
> Clifton Park, NY
> Phone: (518) 881-4924  or  (518) 371-3971 x124
>
>


-- 
Tim Bhatnagar
PhD Candidate
Orthopaedic Injury Biomechanics Group
Department of Mechanical Engineering
University of British Columbia

Rm 5000 - 818 West 10th Ave.
Vancouver, BC
Canada
V5Z 1M9

Ph: (604) 675-8845
Fax: (604) 675-8820
Web: oibg.mech.ubc.ca
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