[ITK Community] RawImageIO volume writing

[Bradley Lowekamp]

Emiliano,

In your initial description you didn't indicate that you were trying to change the order of the axis.

The RawImageIO does not write out the Spacing,Orientation,byte order,size, etc, it just rights out the image buffer as raw. When writing those have not effect, they are however required when writing.

Why not just write it out as an nhdr file directly?

In SimpleITK I can just do:

In [9]: sitk.WriteImage(sitk.Image(120,120,120,sitk.sitkUInt16), "img.nhdr")

In [10]: cat img.nhdr
NRRD0004
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format.html
type: unsigned short
dimension: 3
space: left-posterior-superior
sizes: 120 120 120
space directions: (1,0,0) (0,1,0) (0,0,1)
kinds: domain domain domain
endian: little
encoding: raw
space origin: (0,0,0)
data file: img.raw

And the img.raw file is right there.

Hope that helps.
Brad

On Mar 18, 2014, at 9:49 AM, Emiliano Pastorelli <emiliano.pastorelli at gmail.com> wrote:

> 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> 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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>> 
>> 
> 
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