[ITK Community] RawImageIO volume writing

[Emiliano Pastorelli]

Hi Matt,

is the way I use the RawImageIO together with the image writer correct?
I'm still trying to change directions, swapping them, playing around 
with some other values, and it just keeps on producing the same wrong 
output (i'm sure the raw image is newly generated though and i'm loading 
that one in paraview to visualize the results or in my software to 
analze it).
I start wondering because nothing i do seems to cause real changes, so i 
think i might be misusing the whole thing, but i don't get how.

Thanks and Best,
Emiliano

Il 18/03/14 15:24, Matt McCormick ha scritto:
> Hi Emiliano,
>
> I am not sure I see the issue.  Is the image missing the correct 
> spacing information?
>
> Matt
>
>
> On Tue, Mar 18, 2014 at 8:32 AM, Emiliano Pastorelli 
> <emiliano.pastorelli at gmail.com <mailto:emiliano.pastorelli at gmail.com>> 
> wrote:
>
>     Hi all,
>
>     I am trying to write to file a processed volume on which i'm
>     working. Due to the fact that another software of mine that
>     performs another analysis on the filtered dataset reads in
>     nhdr+raw files (i write manually the nhdr, and from there i only
>     take size and endianness of the raw data).
>
>     the look of a nhdr header that i was loading in my software is this  :
>     #################################
>     NRRD0004
>     # Complete NRRD file format specification at:
>     # http://teem.sourceforge.net/nrrd/format.html
>     type: short
>     dimension: 3
>     space: left-posterior-superior
>     sizes: 795 788 576
>     space directions: (1,0,0) (0,1,0) (0,0,1)
>     kinds: domain domain domain
>     endian: little
>     encoding: raw
>     space origin: (-397,-393.5,-287.5)
>     data file: 4a.raw
>     #################################
>
>     what i am trying to do in the code to write a file in a similar
>     format that my software can understand and read. it's my first
>     attempt at using the RawImageIO, but doesn't matter what i change,
>     the saved volume it's always wrongly reconstructed.
>
>     A topdown view of the volume as it should look like
>     http://www.kyb3.org/images/MhdRaw.png
>     A topdown of how it looks like
>     http://www.kyb3.org/images/NhdrRaw.png
>
>     #################################
>     typedef RawImageIO<short, 3> rawWriter;
>         rawWriter::Pointer newRawWriter = rawWriter::New();
>         newRawWriter->SetFileTypeToBinary();
>
>         newRawWriter->SetDimensions(0,150);
>         newRawWriter->SetDimensions(1,150);
>         newRawWriter->SetDimensions(2,150);
>
>         vector<double> dirX(3);
>         dirX[0]=1.0;dirX[1]=0.0;dirX[2]=0.0;
>         vector<double> dirZ(3);
>         dirZ[0]=0.0;dirZ[1]=0.0;dirZ[2]=1.0;
>         vector<double> dirY(3);
>         dirY[0]=0.0;dirY[1]=1.0;dirY[2]=0.0;
>
>         newRawWriter->SetDirection(0,dirX);
>         newRawWriter->SetDirection(1,dirZ);
>         newRawWriter->SetDirection(2,dirY);
>         newRawWriter->SetSpacing(0,1);
>         newRawWriter->SetSpacing(1,1);
>         newRawWriter->SetSpacing(2,1);
>
>         newRawWriter->SetHeaderSize(0);
>         newRawWriter->SetByteOrderToLittleEndian();
>         newRawWriter->SetNumberOfComponents(1);
>
>         /*
>          * SAVE TO FILE
>          */
>         typedef itk::ImageFileWriter< OutputImageType > WriterType;
>         WriterType::Pointer writer = WriterType::New();
>         writer->SetInput( LabelToBinary->GetOutput() );
>         writer->SetImageIO(newRawWriter);
>         writer->SetFileName( "../VolumeAnalysis/Frangi.raw" );
>
>         try{
>             writer->Update();
>         }
>         catch( itk::ExceptionObject & error ){
>             std::cerr << "Error: " << error << std::endl;
>             return EXIT_FAILURE;
>         }
>
>         cout << "Volume Saved" << endl;
>     #################################
>
>     Best,
>     Emiliano
>
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