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

[Karthik Krishnan]

Thanks for reporting the bug.

Andinet found a bug in the filter. The Output image direction was not 
correctly updated when the extracted output image had dimensions less 
than the input image.

Please update
Code/BasicFilters/itkExtractImageFilter.txx

Regards
karthik


Didier Rajon wrote:

> 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.
>
>------------------------------------------------------------------------
>
>// 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;
>  }
>
>  
>
>------------------------------------------------------------------------
>
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