[Insight-users] MetaImage Read Problem

[Dan Mueller]

Hi Kevin,

Thanks for letting us know you got it sorted.

Cheers, Dan

On 19 November 2010 16:30, Kevin Neff <kevin.l.neff at gmail.com> wrote:
> Dan,
>
> After looking at the header, I realized that it could be a byte-order
> issue.  Changing it to True did the trick.
>
> NDims = 3
> DimSize = 1388 560 48
> ElementSpacing = 1.29 1.29 5.44
> Position = 0 0 0
> ElementByteOrderMSB = False
> ElementType = MET_USHORT
> ElementDataFile = img8.raw
>
> Thanks,
>
> KLN
>
>
>
>
>
> On Thu, Nov 18, 2010 at 11:52 PM, Dan Mueller <dan.muel at gmail.com> wrote:
>>
>> 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
>
>