[ITK Community] RawImageIO volume writing

[Luis Ibanez]

Hi Emiliano,

Please note that the RawImageIO class will throw away all the Image
Metadata.

RawImageIO only stores the byte data corresponding to pixel intensity
values.

The rest:  direction, spacing, origin...etc..  is dismissed.

In practice, there is no real advantage in using the RawImageIO.

You may want to rather use the MetaImageIO format,
and get two files:

.mhd with a text header
.raw with the raw byte data for the pixel intensities.


Hope this helps,

    Luis



On Tue, 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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>> Community at itk.org
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>>
>>
>
>
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