[ITK-users] Convert 2D itkImage to vnl_matrix

[Matt McCormick]

Hi Marco,

Make sure to call

  extractor->UpdateLargestPossibleRegion();

before trying to examine its output.

HTH,
Matt

On Wed, Apr 29, 2015 at 8:46 AM, Marco Ulgelmo <marco.ulge at gmail.com> wrote:
> Hello,
>
> I was trying to get a matrix out of a 2D image as i need to perform
> particular calculations. At first i open a 3D image and using
> ExtractImageFilter i extract the 2D image collapsing the 3rd dimension.
> There must be something wrong in the code as every time i try to perform any
> kind of operation on the newly created matrix i get a segfault. It might be
> really stupid but i haven't been able to spot it.
>
> Code:
>
>     typedef float OutputPixelType;
>
>     typedef itk::Image< OutputPixelType, 4 > InputImageType;
>     typedef itk::Image< OutputPixelType, 3 > OutputImageType;
>     typedef itk::Image< OutputPixelType, 2 > BidimensionalImageType;
>
>     typedef itk::ImageFileReader< InputImageType > ReaderType;
>     typedef itk::ImageFileReader< OutputImageType > OutputReaderType;
>     typedef itk::ImageFileWriter< OutputImageType > WriterType;
>
>     //mediaFilePath is the path to a 3D image (mha extension)
>
>     char* MediaFileName = (char*)mediaFilePath.c_str();
>
>     OutputReaderType::Pointer reader = OutputReaderType::New();
>     reader->SetFileName(MediaFileName);
>     reader->Update();
>
>     typedef itk::ExtractImageFilter< OutputImageType, BidimensionalImageType
>> BidimensionalExtractorType;
>
>     BidimensionalExtractorType::Pointer extractor =
> BidimensionalExtractorType::New();
>
>     extractor->InPlaceOn();
>     extractor->SetDirectionCollapseToSubmatrix();
>     try{
>         reader->UpdateOutputInformation();
>         }
>     catch ( itk::ExceptionObject & exp ){
>         return 0;// "Couldn't read selected Subject, format not supported.";
>     }
>
>     OutputImageType::RegionType inputRegion3 =
> reader->GetOutput()->GetLargestPossibleRegion();
>     OutputImageType::SizeType size3 = inputRegion3.GetSize();
>     size3[2] = 0;
>
>     OutputImageType::IndexType start3 = inputRegion3.GetIndex();
>     start3[2] = 0;
>     OutputImageType::RegionType desiredRegion3;
>     desiredRegion3.SetSize( size3 );
>     desiredRegion3.SetIndex( start3 );
>
>     extractor->SetExtractionRegion( desiredRegion3 );
>
>     extractor->SetInput( reader->GetOutput() );
>     //writer->SetInput( extractor->GetOutput() );
>
>     int width =
> reader->GetOutput()->GetLargestPossibleRegion().GetSize()[0];
>     int height =
> reader->GetOutput()->GetLargestPossibleRegion().GetSize()[1];
>
>     const unsigned int rows = height;
>     const unsigned int cols = width;
>
>     typedef vnl_matrix_ref< OutputPixelType > MatrixType;
>
>     BidimensionalImageType::Pointer image = extractor->GetOutput();
>
>     MatrixType matrix( rows, cols, image->GetBufferPointer());
>
>     matrix.data_array();
>
>     std::cout << matrix[1][1] << std::endl;
>
> Thanks,
> Marco
>
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