[Insight-users] Re: ITK LSM READER

[Gaëtan Lehmann]

Hi Daniel,

The code I'm using is available at  
http://voxel.jouy.inra.fr/darcs/contrib-itk/WrapITK-unstable/ExternalProjects/ItkVtkGlue/Wrapping/Python/itkExtras/itkvtkExtras.py  
and is in python.

You can't convert a color image directly, but you can pass the images one  
by one, and recreate a colored image if you want in ITK.

Kalle and Dan are working on the BioImageXD project where this code come  
from. They should be able to say better than me what their reader is able  
to do :-)

Gaetan

Le Sat, 09 Dec 2006 02:26:03 +0100, Daniel Mace <dlm19 at duke.edu> a écrit:

> 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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>



-- 
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
http://voxel.jouy.inra.fr