[Insight-users] Problem when using seriesreader together with series writer

[Wen Shi]

Hi John,

Thanks for your reply.
But your opinion is not correct since inputimage is an instance of class image, it's not a filter, so you can't use setinput to initialize it.

Actually What I am doing is using VED(Vesselness Enhancement Diffusion) filter to process data.
But VED can only deal with 3D data. So I use seriesreader to read a serie of 2D slice images to form a 3D data set, Then use VED to process the data set.
Finally I want to write these 3D data back to 2D slices for visualization. 
That's why I mentioned I use seriesreader together with serieswriter. (I don't have the 3D image which is in just one file such as RAW image data).

The whole code is here:

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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: itkMultiScaleHessianSmoothed3DToVesselnessMeasureImageFilterTest.cxx,v $
  Language:  C++
  Date:      $Date: 2007/04/01 21:19:46 $
  Version:   $Revision: 1.5 $

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm 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 notices for more information.

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


#include "itkMultiScaleHessianSmoothed3DToVesselnessMeasureImageFilter.h"
//#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImageSeriesWriter.h"
#include "itkImageSeriesReader.h"
#include "itkNumericSeriesFileNames.h"
#include "itkBMPImageIO.h"


#include "itkRescaleIntensityImageFilter.h"

int main(int argc, char* argv [] )
{
  argc=4;
	if ( argc < 3 )
    {
    std::cerr << "Missing Parameters: " 
              << argv[0]
              << " Input_Image"
              << " Vessel_Enhanced_Output_Image [SigmaMin SigmaMax NumberOfScales]" << std::endl; 
    return EXIT_FAILURE;
    }
 
 
  // Define the dimension of the images
  const unsigned int Dimension = 3;
  typedef short      InputPixelType;
  typedef double     OutputVesselnessPixelType;

  // Declare the types of the images
 

  typedef itk::Image< InputPixelType, Dimension>            InputImageType;
  typedef itk::Image<unsigned char, 3>              OutputImageType;
  typedef itk::Image<unsigned char, 2>                ImageType;
  typedef itk::Image< OutputVesselnessPixelType, Dimension> VesselnessOutputImageType;

  typedef itk::ImageSeriesReader< InputImageType >  ReaderType;
  //typedef itk::ImageFileWriter<  OutputImageType >  WriterType;
  ReaderType::Pointer   reader = ReaderType::New();
 // WriterType::Pointer   writer = WriterType::New(); 
  const unsigned int first =001;
  const unsigned int last  =005;

  typedef itk::NumericSeriesFileNames    NameGeneratorType;
  NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
  nameGenerator->SetSeriesFormat( "vessel-%03d.bmp" );
  nameGenerator->SetStartIndex( first );
  nameGenerator->SetEndIndex( last );
  nameGenerator->SetIncrementIndex( 1 );

  reader->SetImageIO( itk::BMPImageIO::New() );
  reader->SetFileNames(nameGenerator->GetFileNames() );

  //reader->SetFileName ( "CT-Head.pvm" ); 

/*typedef itk::ImageFileReader< InputImageType  >      ImageReaderType;
  ImageReaderType::Pointer reader = ImageReaderType::New();
  reader->SetFileName( "vessel-001.bmp" );*/

  std::cout << "Reading input image : " << "vessel-.bmp" << std::endl;
  try
    {
    reader->Update();
    }
  catch ( itk::ExceptionObject &err )
    {
    std::cerr << "Exception thrown: " << err << std::endl;
    return EXIT_FAILURE;
    }


  // Declare the type of multiscale vesselness filter
  typedef itk::MultiScaleHessianSmoothed3DToVesselnessMeasureImageFilter<
                                            InputImageType,
                                            VesselnessOutputImageType>  
                                            MultiScaleVesselnessFilterType;

  // Create a vesselness Filter
  MultiScaleVesselnessFilterType::Pointer MultiScaleVesselnessFilter = 
                                      MultiScaleVesselnessFilterType::New();

  MultiScaleVesselnessFilter->SetInput( reader->GetOutput() );

 // if ( argc >= 4 ) 
   // { 
    MultiScaleVesselnessFilter->SetSigmaMin( 0.5  ); 
   // }
 
  //if ( argc >= 5 )
  //  {
    MultiScaleVesselnessFilter->SetSigmaMax( 1.0 ); 
  //  }

 // if ( argc >= 6 )
  //  {
    MultiScaleVesselnessFilter->SetNumberOfSigmaSteps( 5 ); 
 //   }

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

  std::cout << "Writing out the enhanced image to " <<  "vessel(enhanced).png"  << std::endl;

  //Rescale the output of the vesslness image
   
  typedef itk::RescaleIntensityImageFilter< VesselnessOutputImageType,
                                            OutputImageType> 
                                            RescaleFilterType;

  RescaleFilterType::Pointer rescale = RescaleFilterType::New();
  rescale->SetInput( MultiScaleVesselnessFilter->GetOutput() );
  rescale->SetOutputMinimum(   0 );
  rescale->SetOutputMaximum( 255 );

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



  typedef itk::ImageSeriesWriter< OutputImageType, OutputImageType  >      ImageWriterType;
  ImageWriterType::Pointer writer = ImageWriterType::New();


  typedef itk::NumericSeriesFileNames    NameGeneratorType;
  NameGeneratorType::Pointer nameGenerator1 = NameGeneratorType::New();
 
  std::string format = "output";
  format += "%03d.";
  format += "png";   // filename extension
  nameGenerator1->SetSeriesFormat( format.c_str() );

 // writer->SetFileName( "vessel(enhanced).png"  );
 // writer->SetInput ( rescale->GetOutput() );

  InputImageType::ConstPointer inputImage = rescale->GetOutput();
/*  InputImageType::Pointer inputImage = InputImageType::New();//modified based on John's opinion
  inputImage->SetInput(rescale->GetOutput());*/
  InputImageType::RegionType   region     = inputImage->GetLargestPossibleRegion();
  InputImageType::IndexType    start      = region.GetIndex(); 
  InputImageType::SizeType     size       = region.GetSize(); 
 
  const unsigned int firstSlice = start[2];
  const unsigned int lastSlice  = start[2] + size[2] - 1;

  nameGenerator1->SetStartIndex( firstSlice );
  nameGenerator1->SetEndIndex( lastSlice );
  nameGenerator1->SetIncrementIndex( 1 );

  writer->SetFileNames( nameGenerator1->GetFileNames() );

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

  return EXIT_SUCCESS;

}

Thank you very much John!!!

Wen Shi