[Insight-users] Problem when collapsing a dimension in itkExtractImageFilter

[Didier Rajon]

Hi
I'm having a problem with itkExtractImageFilter. When I try to extract a 
2D slice from a 3D image dataset, the slice seems to be extracted 
correctly, but the spacing of the first dimension of the slice is always 0.
I just switched from ITK 2.0 to ITK 2.2 and the problem only happens 
with ITK 2.2, never with ITK 2.0.
I'm using ITK on redhat linux 9.0.
I attached a little C++ program to show the problem.  The program reads 
a 3D image from a file, display the spacing of the image, extract a 
slice perpendicular to the 3rd dimension, and display the spacing of the 
slice.
If I compile the program with ITK 2.0 and execute the program, I get the 
following result:

Executing program ExtractSlice.
Input file name:   My3DImage.vtk.
Slice no:          15.
Reading input image.
Execution terminated successfully.
Input spacing: [2, 2, 2]
Extracting slice no 15.
Execution terminated successfully.
Slice spacing: [2, 2]

If I compile the program with ITK 2.2 and execute the program I get the 
following result:

Executing program ExtractSlice.
Input file name:   My3DImage.vtk.
Slice no:          15.
Reading input image.
Execution terminated successfully.
Input spacing: [2, 2, 2]
Extracting slice no 15.
Execution terminated successfully.
Slice spacing: [0, 2]

The first dimension of the slice has been set to 0 by the filter.

Note that if I don't collapse the dimension (by setting the size of the 
extraction region to [Nx, Ny, 1]  instead of [Nx, Ny, 0] and setting the 
filter output type to a 3D image), I get the correct spacing: [2, 2, 
2].  This problem seems to occur only if I try to collapse a dimension.

Is there anything that has changed with ITK 2.2 and that I should 
incorporate to my program in order to get the correct spacing?
Thanks for helping me solving this problem.

Didier.

-- 
Didier Rajon
Department of Neurological Surgery
University of Florida
MBI, L2100 PO Box 100265
Gainesville, FL, 32610-0265
Tel: (352) 294 0144
Fax: (352) 392 8413

-------------- next part --------------
// system include files
#include <string>

// itk include files
#include "itkImageFileReader.h"
#include "itkExtractImageFilter.h"

// local include files.

main (int argc, char **argv)
  {
  // 0) To get and check the program arguments.
  /////////////////////////////////////////////
  std::string inputFileName;
  int sliceNo;
    {
    // To check the command line
    if ( argc != 3 )
      {
      std::cerr << "Error: bad command-line. Try again with command-line:" << std::endl;
      std::cerr << "ExtractSlice InputFileName SliceNo" << std::endl;
      std::cerr << " - InputFileName: The full path name of the file that contains the input image." << std::endl;
      std::cerr << " - SliceNo: The slice to be extracted." << std::endl;
      std::cerr << "ex: ExtractSlice ./LowResolution.vtk 12" << std::endl;
      exit(0);
      }
    // To get the arguments.
    inputFileName = argv[1];
    sliceNo = atoi(argv[2]);
    std::cout << std::endl << "Executing program ExtractSlice." << std::endl;
    std::cout << "Input file name:   " << inputFileName << "." << std::endl;
    std::cout << "Slice no:          " << sliceNo << "." << std::endl;
    std::cout << std::endl;
    }

  // 1) To define the image type.
  ///////////////////////////////
  const unsigned int ImageDimension = 3;
  const unsigned int SliceDimension = 2;
  typedef unsigned short VoxelType;
  typedef itk::Image<VoxelType, ImageDimension> ImageType;
  typedef itk::Image<VoxelType, SliceDimension> SliceType;

  // 2) To read the input image.
  //////////////////////////////
  ImageType::Pointer inputImage;
    {
    std::cout << "Reading input image." << std::endl;
    typedef itk::ImageFileReader<ImageType> ReaderType;
    ReaderType::Pointer imageReader = ReaderType::New();
    imageReader->SetFileName(inputFileName.c_str());
    try {
      imageReader->Update();
      std::cout << "Execution terminated successfully." << std::endl;
      }
    catch(itk::ExceptionObject & err) {
      std::cerr << err << std::endl;
      exit(0);
      }
    inputImage = imageReader->GetOutput();
    }
  std::cout << "Input spacing: " << inputImage->GetSpacing() << std::endl;

  // 3) To extract the slice.
  ///////////////////////////
  SliceType::Pointer extractedSlice;
    {
    std::cout << "Extracting slice no " << sliceNo << "." << std::endl;
    typedef itk::ExtractImageFilter<ImageType, SliceType> FilterType;
    FilterType::Pointer sliceExtractor = FilterType::New();
    sliceExtractor->SetInput(inputImage);
    ImageType::RegionType extractionRegion = inputImage->GetLargestPossibleRegion();
    ImageType::SizeType extractionSize = extractionRegion.GetSize();
    ImageType::IndexType extractionIndex = extractionRegion.GetIndex();
    extractionSize[2] = 0;
    extractionIndex[2] = sliceNo;
    extractionRegion.SetSize(extractionSize);
    extractionRegion.SetIndex(extractionIndex);
    sliceExtractor->SetExtractionRegion(extractionRegion);
    try {
      sliceExtractor->Update();
      std::cout << "Execution terminated successfully."
                << std::endl;
      }
    catch(itk::ExceptionObject & err) {
      std::cerr << err << std::endl;
      exit(0);
      }
    extractedSlice = sliceExtractor->GetOutput();
    }
  std::cout << "Slice spacing: " << extractedSlice->GetSpacing() << std::endl;
  }