[Insight-users] Reading complex image file

[Martin Kavec]

Hi Luis,

many thanks for fantastic support! The changes in IOBase were really minor, 
but implications big. Lots of algorithms in MRI are done in complex data 
space (k-space), so it will be comfortable to start implementing these and 
that's exactly what I'm working on. I'm updating my ITK right now.

Thanks again.

Martin

On Thursday 19 May 2005 17:35, Luis Ibanez wrote:
> Hi Martin,
>
>
> Thanks for pointing this out.
>
>
> There is actually a very simple way to extend the factories for managing
> std::complex<> pixel types.  This is done in the file:
>
>
>             Insight/Code/IO/
>                      itkImageIOBase.h
>                      itkImageIOBase.cxx
>
>
> In this files we list all the "known" pixel types, meaning that we
> specify how they should be managed (number of compoentes, component
> type etc.).
>
>
> Responding to your request, We just commited a change to this files
> in order to make possible for you to read and write images whose pixel
> type is std::complex<>
>
> http://www.itk.org/cgi-bin/viewcvs.cgi/Code/IO/itkImageIOBase.cxx?root=Insi
>ght&sortby=date&r2=1.54&r1=1.53
> http://www.itk.org/cgi-bin/viewcvs.cgi/Code/IO/itkImageIOBase.h?root=Insigh
>t&sortby=date&r2=1.37&r1=1.36
>
>
> You can now use *ANY* fileformat that support multiple component
> datasets. For example:
>
>
>         - MetaImage
>         - VTK
>         - GIPL
>
>
>
> For an example on how your code will look like,
> please check the file:
>
>
>
>        Insight/Examples/Filtering/
>                            FFTImageFilter.cxx
>
>
> It will be something like:
>
>
>    typedef std::complex<float> ComplexPixelType;
>
>    typedef itk::Image< ComplexPixelType, 2 > ComplexImageType;
>
>    typedef itk::ImageFileWriter< ComplexImageType > ComplexWriterType;
>
>    ComplexWriterType::Pointer complexWriter = ComplexWriterType::New();
>
>    complexWriter->SetFileName("complexImage.mhd");
>
>    complexWriter->SetInput( filter->GetOutput() );
>    complexWriter->Update();
>
>
>
> Note that you will have to use an updated CVS version of ITK
> in order to take advantage of this feature.
>
>
>
> Regards,
>
>
>
>      Luis
>
>
>
> --------------------
>
> Martin Kavec wrote:
> > After further reading of the ITK docs, replying myself :).
> >
> > It seems that I can use VECTOR pixel type to read complex data points
> > from a file, since complex number is indeed a vector. However, still have
> > a problem. In ITK, FFT needs as an input std::complex< Type >.
> >
> > So it seems that I will have to do manual conversion from
> > itk::Vector<double, 2> to std::complex<double>. Am a right or is there
> > any other - easier - way?
> >
> > Regards.
> >
> > Martin
> >
> > On Wednesday 18 May 2005 15:09, Martin Kavec wrote:
> >>Hi,
> >>
> >>I am writing a class (by inheriting from ImageIOBase) to read  from an
> >>unknown file a complex image data, which I want to FFT afterwards (using
> >>VnlFFTComplex To* filter). So, I want to have somewhere:
> >>
> >>typedef std::complex< double> ComplexPixelType;
> >>typedef itk::Image< ComplexPixelType, Dimension > ComplexImageType;
> >>typedef itk::MyComplexImageReader< ComplexImageType >;
> >>
> >>to easy perform FFT.
> >>
> >>I am running into problem in writing MyComplexImageReader. This class
> >> uses virtual void Read(void* buffer) to read from file and store the
> >> image data in the provided buffer. My question is, how to store the data
> >> in the buffer? I tried to figure out this from existing TIFF, JPEG, ...,
> >> readers, but got lost. Also, these file formats don't store complex
> >> data, I suppose. If I read the data sequentially (as they are stored in
> >> a file), complex double pairs, how would
> >> MyComplexImageReader::GetOutput() know how to format the data into
> >> ComplexPixelType? I guess that in RGB pixel type images, GetOutput()
> >> method knows the order from from
> >>ImageIOBase::SetPixelType( PixelType ) method, where PixelType can be one
> >>of SCALAR, VECTOR, RGB and so on.
> >>
> >>Am I concerned with something, which is solved upstream of the
> >> ImageIOBase inheritance tree and don't need to be bothered with. Or, am
> >> I missing anything else?
> >>
> >>Thanks for help.
> >>
> >>Martin
> >>_______________________________________________
> >>Insight-users mailing list
> >>Insight-users at itk.org
> >>http://www.itk.org/mailman/listinfo/insight-users

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