[Insight-users] I am really desperate... ImageReadRegionOfInterestWrite

[Sohaib Majzoub]

Dear all,
I am new to itk, and i am using the example provided with the toolkit:
ImageReadRegionOfInterestWrite
I need to extract a 3D ROI from a 3D image,
they said that the class RegionOfInterestImageFilter works for any dimension,
the example code of ImageReadRegionOfInterestWrite works only for 2D,
I am trying to modify the code so that i can do the 3D but it doesn't
want to work,
something is missing, i don't know where,
please any help, I am really desperate...
Thanks you very much for any hint or any kind of help,
Best Regards,

sorry again but the code for the ImageReadRegionOfInterestWrite is below

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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: ImageReadRegionOfInterestWrite.cxx,v $
  Language:  C++
  Date:      $Date: 2004/12/22 21:10:15 $
  Version:   $Revision: 1.7 $

  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.

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

//  Software Guide : BeginLatex
//
//  This example should arguably be placed in the previous filtering
//  chapter. However its usefulness for typical IO operations makes it
//  interesting to mention here. The purpose of this example is to read and
//  image, extract a subregion and write this subregion to a file. This is a
//  common task when we want to apply a computationally intensive method to
//  the region of interest of an image.
//
// As usual with ITK IO, we begin by including the appropriate header files.
//
//  Software Guide : EndLatex 

// Software Guide : BeginCodeSnippet
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
// Software Guide : EndCodeSnippet


//  Software Guide : BeginLatex
//  
//  The filter used to extract a region from an image is the
//  \doxygen{RegionOfInterestImageFilter}. Its header is included below.
//
//  \index{itk::RegionOfInterestImageFilter!header}
//
//  Software Guide : EndLatex 

// Software Guide : BeginCodeSnippet
#include "itkRegionOfInterestImageFilter.h"
// Software Guide : EndCodeSnippet

#include "itkImage.h"

int main( int argc, char *argv[] )
{
  // Verify the number of parameters in the command line
  if( argc < 7 )
    {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << " inputImageFile  outputImageFile " << std::endl;
    std::cerr << " startX startY startZ sizeX sizeY sizeZ" << std::endl;
    return -1;
    }


  //  Software Guide : BeginLatex
  //
  //  Image types are defined below.
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  typedef float        InputPixelType;
  typedef float        OutputPixelType;
  const   unsigned int        Dimension = 3;

  typedef itk::Image< InputPixelType,  Dimension >    InputImageType;
  typedef itk::Image< OutputPixelType, Dimension >    OutputImageType;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //  
  //  The types for the \doxygen{ImageFileReader} and \doxygen{ImageFileWriter}
  //  are instantiated using the image types.
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  typedef itk::ImageFileReader< InputImageType  >  ReaderType;
  typedef itk::ImageFileWriter< OutputImageType >  WriterType;
  // Software Guide : EndCodeSnippet

// Software Guide : BeginCodeSnippet
  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();



  // Software Guide : EndCodeSnippet
//FixedImageType::Pointer fixedImage = fixedSetFileNameImageReader->GetOutput();
  //  Software Guide : BeginLatex
  //  
  //  The RegionOfInterestImageFilter type is instantiated using
  //  the input and output image types. A filter object is created with the
  //  New() method and assigned to a \doxygen{SmartPointer}.
  //
  //  Software Guide : EndLatex 

  // Software Guindexide : BeginCodeSnippet
  typedef itk::RegionOfInterestImageFilter< InputImageType,
OutputImageType > FilterType;
  FilterType::Pointer filter = FilterType::New();
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //  
  //  The RegionOfInterestImageFilter requires a region to be
  //  defined by the user. The region is specified by an \doxygen{Index}
  //  indicating the pixel where the region starts and an \doxygen{Size}
  //  indication how many pixels the region has along each dimension. In this
  //  example, the specification of the region is taken from the command line
  //  arguments (this example assumes a 2D image is being processed).
  //
  //  Software Guide : EndLatex 

  
  // Software Guide : BeginCodeSnippet
  OutputImageType::IndexType start;
  start[0] = atoi( argv[3] );
  start[1] = atoi( argv[4] );
  start[2] = atoi( argv[5] );
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginCodeSnippet
  OutputImageType::SizeType size;
  size[0] = atoi( argv[6] );
  size[1] = atoi( argv[7] );
  size[2] = atoi( argv[8] );
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //  
  //  An \doxygen{ImageRegion} object is created and initialized with start
  //  and size obtained from the command line.
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  OutputImageType::RegionType desiredRegion;
  desiredRegion.SetSize(  size  );
  desiredRegion.SetIndex( start );
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //  
  //  Then the region is passed to the filter using the
  //  SetRegionOfInterest() method.
  //
  //  \index{itk::RegionOfInterestImageFilter!SetRegionOfInterest()}
  //
  //  Software Guide : EndLatex 


  // Software Guide : BeginCodeSnippet
  filter->SetRegionOfInterest( desiredRegion );
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Below, we create the reader and writer using the New() method and
  //  assigning the result to a SmartPointer.
  //
  //  \index{itk::ImageFileReader!New()}
  //  \index{itk::ImageFileWriter!New()}
  //  \index{itk::ImageFileReader!SmartPointer}
  //  \index{itk::ImageFileWriter!SmartPointer}
  //
  //  Software Guide : EndLatex 

  


  //
  // Here we recover the file names from the command line arguments
  //
  const char * inputFilename  = argv[1];
  const char * outputFilename = argv[2];


  //  Software Guide : BeginLatex
  //
  //  The name of the file to be read or written is passed with the
  //  SetFileName() method. 
  //
  //  \index{itk::ImageFileReader!SetFileName()}
  //  \index{itk::ImageFileWriter!SetFileName()}
  //  \index{SetFileName()!itk::ImageFileReader}
  //  \index{SetFileName()!itk::ImageFileWriter}
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  reader->SetFileName( inputFilename  );
  writer->SetFileName( outputFilename );
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Below we connect the reader, filter and writer to form the data
  //  processing pipeline.
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  filter->SetInput( reader->GetOutput() );
  writer->SetInput( filter->GetOutput() );
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //  
  //  Finally we execute the pipeline by invoking Update() on the writer. The
  //  call is placed in a \code{try/catch} block in case exceptions are
  //  thrown.
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  try 
    { 
    writer->Update(); 
    } 
  catch( itk::ExceptionObject & err ) 
    { 
    std::cout << "ExceptionObject caught !" << std::endl; 
    std::cout << err << std::endl; 
    return -1;
    } 
  // Software Guide : EndCodeSnippet


  return 0;
}