[Insight-users] Help with ImageSeriesReadWrite

[Jonathan Wong]

I'm new to ITK and I'm currently having problems assemble my series of Tiff
files into a vtkImage. I've simply edited the PNGSeriesWriter example. A vtk
image does get generated, and I've managed to load it in VolView and
MicroView by using ITK 2.4.1. However, when I look at the volume, the whole
volume is composed of only the first Tiff file , and is repeated along the z
axis.

Anyone know how to fix this? Help is greatly appreciated. I've pasted my
code below.

Jon

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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: ImageSeriesReadWrite.cxx,v $
  Language:  C++
  Date:      $Date: 2005/11/20 13:27:53 $
  Version:   $Revision: 1.10 $

  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

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif

//  Software Guide : BeginLatex
//
//  This example illustrates how to read a series of 2D slices from
independent
//  files in order to compose a volume. The class
\doxygen{ImageSeriesReader}
//  is used for this purpose. This class works in combination with a
generator
//  of filenames that will provide a list of files to be read. In this
//  particular example we use the \doxygen{NumericSeriesFileNames} class as
//  filename generator. This generator uses a \code{printf} style of string
format
//  with a ``\code{\%d}'' field that will be successively replaced by a
number specified
//  by the user. Here we will use a format like ``\code{file\%03d.png}'' for
reading
//  PNG files named file001.png, file002.png, file003.png... and so on.
//
//  This requires the following headers as shown.
//
//  \index{itk::ImageSeriesReader!header}
//  \index{itk::NumericSeriesFileNames!header}
//
//  Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkImage.h"
#include "itkImageSeriesReader.h"
#include "itkImageFileWriter.h"
#include "itkNumericSeriesFileNames.h"
#include "itkTIFFImageIO.h"
// Software Guide : EndCodeSnippet


int main( int argc, char ** argv )
{
  // Verify the number of parameters in the command line
  if( argc < 4 )
    {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << " firstSliceValue lastSliceValue
outputImageFile " << std::endl;
    return EXIT_FAILURE;
    }


// Software Guide : BeginLatex
//
// We start by defining the \code{PixelType} and \code{ImageType}.
//
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
  typedef unsigned char                       PixelType;
  const unsigned int Dimension = 3;

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

  typedef itk::ImageSeriesReader< ImageType >  ReaderType;
  typedef itk::ImageFileWriter<   ImageType >  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 * outputFilename = argv[3];


  typedef itk::NumericSeriesFileNames    NameGeneratorType;

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

  nameGenerator->SetSeriesFormat( "vol%03d.tiff" ); //set file name
imageformat here

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

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

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

  writer->SetFileName( outputFilename );

  try
     {
         reader->Update();
     }
     catch( itk::ExceptionObject & err )
     {
    std::cerr << "ExceptionObject caught !" << std::endl;
    std::cerr << err << std::endl;
    return EXIT_FAILURE;
     }
/*
  // JW: Get Image set spacing
  ImageType::Pointer image = reader->GetOutput();

  ImageType::SpacingType spacing;

  // Note: measurement units (in this application it's in mm)
  spacing[0] = 0.021; // spacing along X
  spacing[1] = 0.021; // spacing along Y
  spacing[2] = 0.022; // spacing along Z


  image->SetSpacing( spacing );

  ImageType::PointType origin;

  origin[0] = 0.0;  // coordinates of the
  origin[1] = 0.0;  // first pixel in N-D
  origin[2] = 0.0;

  image->SetOrigin( origin );

  const ImageType::SpacingType& sp = image->GetSpacing();

  std::cout << "Spacing = ";
  std::cout << sp[0] << ", " << sp[1] << ", " << sp[2] << std::endl;

  writer->SetInput( image );
// Software Guide : EndCodeSnippet
  */
    writer->SetInput(reader->GetOutput());

  try
    {
    writer->Update();

    }
  catch( itk::ExceptionObject & err )
    {
    std::cerr << "ExceptionObject caught !" << std::endl;
    std::cerr << err << std::endl;
    return EXIT_FAILURE;
    }
// Software Guide : EndCodeSnippet


  return EXIT_SUCCESS;
}
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