[Insight-users] MetaImage Read Problem

[Dan Mueller]

Hi Kevin,

Please post the Meta Header (*.mhd) file corresponding to the raw
file. The header can skip leading bytes by specifying HeaderSize. See
here:
    http://www.itk.org/Wiki/MetaIO/Documentation
    http://www.itk.org/Wiki/images/2/27/MetaIO-Introduction.pdf

Cheers, Dan

On 18 November 2010 22:25, Kevin Neff <kevin.l.neff at gmail.com> wrote:
>
> I am trying to read in a raw data file (via MetaImage reader).  It's
> skipping the first byte of my file.
>
> The file, according to xxd -b <file> | less
>
> 0000000: 00000000 00001001 00000000 00000110 00000000 00001010  ......
> 0000006: 00000000 00000101 00000000 00000101 00000000 00000110  ......
> 000000c: 00000000 00000000 00000000 00000100 00000000 00000100  ......
> 0000012: 00000000 00001001 00000000 00000011 00000000 00000100  ......
>
> The code:
>
> #include <iostream>
> #include "itkImage.h"
> #include "itkImageFileReader.h"
> #include "itkImageFileWriter.h"
> //#include "itkRawImageIO.h"
> #include "itkMetaImageIO.h"
>
> #define print std::cout
> #define nl    std::endl
>
> int main( int argc, char** argv )
> {
>   typedef itk::Image< unsigned short, 3 > ImageType;
>
>   ImageType::Pointer image = ImageType::New();
>
>   ImageType::IndexType start;
>   start[0] =   0;  // first index on X
>   start[1] =   0;  // first index on Y
>   start[2] =   0;  // first index on Z
>
>   ImageType::SizeType  size;
>   size[0]  = 1388;  // size along X
>   size[1]  =  560;  // size along Y
>   size[2]  =   48;  // size along Z
>
>   ImageType::RegionType region;
>   region.SetSize( size );
>   region.SetIndex( start );
>   image->SetRegions( region );
>
>   image->Allocate();
>
>   typedef itk::ImageFileReader< ImageType > ReaderType;
>   typedef itk::ImageFileWriter< ImageType > WriterType;
>   typedef itk::MetaImageIO                  ImageIOType;
>
>   ImageIOType::Pointer MIIO = ImageIOType::New();
>
>   ReaderType::Pointer reader = ReaderType::New();
>   const char * infile = argv[1];
>   reader->SetFileName( infile );
>   image = reader->GetOutput();
>
>   print << "Reading from file (" << argv[0] << ")" << nl;
>   try{ reader->Update(); }
>   catch( itk::ExceptionObject & err )    {
>     std::cerr << "ExceptionObject caught!  Check filename" << std::endl;
>     std::cerr << err << std::endl;
>     return EXIT_FAILURE;
>   }
>
>   const ImageType::SpacingType& sp = image->GetSpacing();
>   print << "Spacing = ";
>   print << sp[0] << ", " << sp[1] << ", " << sp[2] << std::endl;
>
>   const ImageType::PointType& orgn = image->GetOrigin();
>   std::cout << "Origin = ";
>   std::cout << orgn[0] << ", " << orgn[1] << ", " << orgn[2] << std::endl;
>
>   typedef itk::Point< double, ImageType::ImageDimension > PointType;
>
>   PointType p;
>   ImageType::IndexType i;
>   ImageType::PixelType v;
>   for(  int x = 0;  x < 10;  x += 1  )   {
>     p[0] = x; p[1] = 0; p[2] = 0;
>     image->TransformPhysicalPointToIndex(p,i);
>     v = image->GetPixel( i );
>     print << "Value of (" << p[0] << "," << p[1] << "," << p[2] << ") is "
> << v << " and has index " << i << nl;
>   }
>
>   return 0;
> }
>
> The output:
>
>
> tukey # make && ./register img8.mhd
> Scanning dependencies of target register
> [100%] Building CXX object CMakeFiles/register.dir/main.cxx.o
> Linking CXX executable register
> [100%] Built target register
> Reading from file (./register)
> Spacing = 1.29, 1.29, 5.44
> Origin = 0, 0, 0
> Value of (0,0,0) is 2304 and has index [0, 0, 0]
> Value of (1,0,0) is 1536 and has index [1, 0, 0]
> Value of (2,0,0) is 2560 and has index [2, 0, 0]
> Value of (3,0,0) is 2560 and has index [2, 0, 0]
> Value of (4,0,0) is 1280 and has index [3, 0, 0]
> Value of (5,0,0) is 1280 and has index [4, 0, 0]
> Value of (6,0,0) is 1536 and has index [5, 0, 0]
> Value of (7,0,0) is 1536 and has index [5, 0, 0]
> Value of (8,0,0) is 0 and has index [6, 0, 0]
> Value of (9,0,0) is 1024 and has index [7, 0, 0]
>
> Looks like the first byte of the file is being skipped.  Is this an error or
> a feature?
>
> KLN
>
>
> ---------
> Kevin Neff, Ph.D.
> Mayo Clinic College of Medicine
> Rochester, MN