[Insight-users] Re: ITK LSM READER

[Daniel Mace]

Well, it seems that there really is no way to convert anything more than 
a 3D image back into ITK.  I started to rewrite the itkVTKImageImport 
class to extend to more than 3 dimensions when I realized that the 3D 
limitation is hard coded all the way through the vtk code as well.  Ohh 
well, good motivation to fix the itkLSMImageIO channel issue I guess.

Cheers,
Dan

Daniel Mace wrote:
> Gaeten,
>
> Could you post your code for using the vtkLSMReader and converting it 
> into the ITK framework?  My problem seems to be with the ImageType 
> parameters that the vtkLSMReader is outputing.  The LSM image I am 
> trying to read is a 4 Dimensional image with two channels (x * y * 
> x_tiling * y_tiling).  I've tried setting my itkVTKImageToImageFilter 
> to a 4D Image with pixel type of Vector (2 and 3 dimensional vectors, 
> neither worked), and also as a 5D image, and as a VectorImage to no 
> avail (it seems that the itkVTKImageToImageFilter does not like 
> VectorImages).  BioImageXD correctly reads the LSM file and sets it to 
> it's correct settings for viewing, so I'm guessing my issue is with my 
> templating of the itkVTKImageToImageFilter.
>
> I can send you the LSM file I am trying to read if that would help.
>
> Cheers,
> Dan
>
> Gaetan Lehmann <gaetan.lehmann at ...> writes:
>
> >
> >
> > Hi,
> >
> > LSM reader doesn't seem to be fully functional in ITK. The last time 
> I  > tried it, I was able to read an lsm file only if it contains a 
> single  > channel.
> >
> > You should prefer the very good vtkLSMReader developed for 
> BioImageXD. I'm  > using it daily, and it works perfectly.
> >
> > http://svn.sourceforge.net/viewvc/bioimagexd/bioimagexd/trunk/C%2B%2B/
> > http://modeling.bio.jyu.fi:8080/bioimagexd
> >
> > Gaetan
> >
> > On Thu, 19 Oct 2006 15:08:29 +0200, Manuss <mac.manuss at ...> wrote:
> >
> > >   Hello,
> > > I  try to convert the LSM files (Zeiss) to VTK file format.
> > >
> > > I had a look on the different Library of VTK/ITK
> > > and i saw that on ITK->Code->IO, there is a file call itkLSMImageIO
> > > (.h and .cxx) which read a LSM file.
> > > But i have a problem when i read the LSM file and save it in a VTK
> > > format, it saves only the first image of the stack.
> > > It create all the different images in z and make a VTK matrix with
> > > all this stack, but only the first image on this stack is written,
> > > the other are all black ...
> > > Have you got an Idea, i think it's a problem of the reader.
> > >
> > >
> > >
> > > I use the file itkLSMImageIOTest.cxx
> > >
> > >
> > >    typedef itk::RGBPixel< unsigned char >   InputPixelType;
> > >    typedef itk::Image< InputPixelType, 3 > InputImageType;
> > >    typedef itk::ImageFileReader< InputImageType > ReaderType;
> > >    typedef itk::LSMImageIO ImageIOType;
> > >
> > >    ReaderType::Pointer reader = ReaderType::New();
> > >    reader->SetFileName( filename );
> > >
> > >    ImageIOType::Pointer lsmImageIO = ImageIOType::New();
> > >    reader->SetImageIO( lsmImageIO );
> > >
> > >    reader->Update();
> > >
> > >
> > >    typedef itk::ImageFileWriter< InputImageType >  WriterType;
> > >    WriterType::Pointer writer = WriterType::New();
> > >    writer->SetFileName( outfilename );
> > >    writer->SetInput( reader->GetOutput() );
> > >
> > >    writer->Update();
> > >
> > > lsmImageIO->Print(std::cout);
> > >
> >
>
>
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