[Insight-users] Need to correct this example

[Syrine Sahmim]

Hi,
I send again the same mail because i need help really.
i
try to apply a discrete gaussian filter on a serie of 3D dicom
images.so i try to do what Luis said to me to read the dicom serie
before and then add the discrete gaussian filter. the code that i wrote
is the follwing, please can you help me toi correct it. really i need
help.
#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif


#include "itkOrientedImage.h"
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkImageSeriesReader.h"
#include "itkImageFileWriter.h"


#include "itkRescaleIntensityImageFilter.h"
#include "itkDiscreteGaussianImageFilter.h"


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

 /* if( argc < 3 )
    {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << " DicomDirectory  outputFileName  [seriesName]" << std::endl;
    return EXIT_FAILURE;
    }

*/

    argc = 2;
    argv[1] = "dicom";
    argv[2] = "dicomMRA.hdr";
  typedef signed short    PixelType;
  const unsigned int      Dimension = 3;

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

  typedef itk::ImageSeriesReader< ImageType >        ReaderType;
  ReaderType::Pointer reader = ReaderType::New();

  typedef itk::GDCMImageIO       ImageIOType;
  ImageIOType::Pointer dicomIO = ImageIOType::New();
  
  reader->SetImageIO( dicomIO );

  typedef itk::GDCMSeriesFileNames NamesGeneratorType;
  NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();

  nameGenerator->SetUseSeriesDetails( true );
  nameGenerator->AddSeriesRestriction("0008|0021" );
  
  nameGenerator->SetDirectory( argv[1] );

  

  try
    {
    std::cout << std::endl << "The directory: " << std::endl;
    std::cout << std::endl << argv[1] << std::endl ;
    std::cout << "Contains the following DICOM Series: ";
    std::cout << std::endl << std::endl;



    typedef std::vector< std::string >    SeriesIdContainer;
    
    const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
    
    SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
    SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
    while( seriesItr != seriesEnd )
      {
      std::cout << seriesItr->c_str() << std::endl;
      seriesItr++;
      }


    std::string seriesIdentifier;

    if( argc > 3 ) // If no optional series identifier
      {
      seriesIdentifier = argv[3];
      }
    else
      {
      seriesIdentifier = seriesUID.begin()->c_str();
      }



    std::cout << std::endl << std::endl;
    std::cout << "Now reading series: " << std::endl << std::endl;
    std::cout << seriesIdentifier << std::endl;
    std::cout << std::endl << std::endl;





    typedef std::vector< std::string >   FileNamesContainer;
    FileNamesContainer fileNames;

    fileNames = nameGenerator->GetFileNames( seriesIdentifier );

    reader->SetFileNames( fileNames );



    try
      {
      reader->Update();
      }
    catch (itk::ExceptionObject &ex)
      {
      std::cout << ex << std::endl;
      return EXIT_FAILURE;
      }


}
  catch (itk::ExceptionObject &ex)
    {
    std::cout << ex << std::endl;
    return EXIT_FAILURE;
    }

typedef itk::DiscreteGaussianImageFilter<
                 InputImageType, OutputImageType >  FilterType;

  FilterType::Pointer filter = FilterType::New();
 filter->SetInput( reader->GetOutput() );

const double gaussianVariance = atof( argv[3] );
  const unsigned int maxKernelWidth = atoi( argv[4] );
 filter->SetVariance( gaussianVariance );
  filter->SetMaximumKernelWidth( maxKernelWidth );
  filter->Update();


  typedef unsigned char WritePixelType;
  typedef itk::Image< WritePixelType, 2 > WriteImageType;
  typedef itk::RescaleIntensityImageFilter< 
               OutputImageType, WriteImageType > RescaleFilterType;
  RescaleFilterType::Pointer rescaler = RescaleFilterType::New();

  rescaler->SetOutputMinimum(   0 );
  rescaler->SetOutputMaximum( 255 );

  typedef itk::ImageFileWriter< WriteImageType >  WriterType;
  WriterType::Pointer writer = WriterType::New();
  writer->SetFileName( argv[2] );
  rescaler->SetInput( filter->GetOutput() );
  writer->SetInput( rescaler->GetOutput() );
  writer->Update();
  return EXIT_SUCCESS;

}
    thanks to all




________________________________
De : John Drescher <drescherjm at gmail.com>
À : Syrine Sahmim <syrine.sahmim at yahoo.fr>; Insight Users <insight-users at itk.org>
Envoyé le : Lundi, 3 Août 2009, 12h03mn 30s
Objet : Re: [Insight-users] Re : Re : Re : Re : Re : trying examples

On Mon, Aug 3, 2009 at 6:51 AM, Syrine Sahmim<syrine.sahmim at yahoo.fr> wrote:
> Where exactly please?
>

Looks like the recommendation was DicomImageViewer

http://public.kitware.com/cgi-bin/viewcvs.cgi/DicomImageViewer/?root=InsightApplications

from InsightApplications.


This is a separate download from itk.


http://itk.org/ITK/resources/software.html



John



      
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