[Insight-users] mrc data format
Shekhar Chandra
Shekhar.Chandra at monash.edu
Thu Oct 14 03:57:34 EDT 2010
Hi Mauro,
'undefined reference to' error means a linking problem. You need to link
to the ITKIOReview library, which should have been built when u turned
on the review option.
HTH
Cheers
Shekhar
On 14/10/2010 6:07 PM, Mauro Maiorca wrote:
> Hi all,
>
> thank you guys for the inputs and thanks Shekhar for pointing me the
> MRCImageIO (I wasn't aware of).
> I recompiled ITK with Use Review code ON, but when I compile my
> application the compiler doesn't like the:
>
> "stackReader->SetImageIO( itk::MRCImageIO::New() );"
> I've unsuccessfully tried few variation of it but I'm a bit clueless at
> the moment.
>
>
> this is the error message I got:
>
> CMakeFiles/mrc2dcm.dir/src/
> mrc2dcm.cxx.o: In function `main':
> mrc2dcm.cxx:(.text+0xd1): undefined reference to `typeinfo for
> itk::MRCImageIO'
> mrc2dcm.cxx:(.text+0xed): undefined reference to `typeinfo for
> itk::MRCImageIO'
> mrc2dcm.cxx:(.text+0x264): undefined reference to
> `itk::MRCImageIO::MRCImageIO()'
> collect2: ld returned 1 exit status
> make[2]: *** [bin/mrc2dcm] Error 1
> make[1]: *** [CMakeFiles/mrc2dcm.dir/all] Error 2
> make: *** [all] Error 2
>
> and this is the (simplified) code:
>
> #include "itkImage.h"
> #include "itkImageFileReader.h"
> #include "itkMRCImageIO.h"
> int main( int argc, char* argv[]){
> typedef signed int InputPixelType;
> const unsigned int Dimension = 3;
> typedef itk::Image< InputPixelType, Dimension > ImageType;
> typedef itk::ImageFileReader< ImageType > ReaderType;
>
> ReaderType::Pointer stackReader = ReaderType::New();
> stackReader->SetImageIO( itk::MRCImageIO::New() );
> stackReader->SetFileName( argv[1] );
> return 0;
> }
>
> thanks a lot,
> Mauro
>
>
> On Thu, Oct 14, 2010 at 9:45 AM, Shekhar Chandra
> <Shekhar.Chandra at monash.edu <mailto:Shekhar.Chandra at monash.edu>> wrote:
>
> Hi Guys,
>
> ITK has the MRCImageIO class in the Code Review area for MRC images.
> I have used it successfully.
>
> Compile ITK with Use Review code ON and use it something like
>
> ReaderType::Pointer stackReader = ReaderType::New();
> stackReader->SetImageIO( itk::MRCImageIO::New() );
> stackReader->SetFileName( argv[1] );
>
> HTH
> Cheers
> Shakes
>
>
> On 14/10/2010 3:23 AM, Jeff Donner wrote:
>
> I have code just about ready to go - I just need to rebase the
> patches
> for the current build. I've been holding off because I've been
> confused about the meaning of MRC's orientation, for non-orthogonal
> (and maybe for any rotation at all) cases. I'm not a dev;
> perhaps I'll
> post them to this list, for someone else to do the commits. If
> anyone's in a hurry I can just post what I have, but otherwise I
> estimate maybe 2 days.
>
> On Wed, Oct 13, 2010 at 1:44 AM, Sergio
> Vera<sergio.vera at alma3d.com <mailto:sergio.vera at alma3d.com>> wrote:
>
> Hi
> One of the improvements of the next version of ITK (v4) will
> be better
> support for microscopy images:
> http://www.itk.org/Wiki/ITK_Release_4/Microscopy
> however, I don't know the specific file formats that ITK
> will or will not
> support.
> It may be a good idea to get in touch with some of the
> developers to give a
> hand and/or publish your code
> regards
> On Wed, Oct 13, 2010 at 6:38 AM, Mauro
> Maiorca<mauromaiorca at gmail.com <mailto:mauromaiorca at gmail.com>>
> wrote:
>
>
> Hello all,
>
> I'm currently working with electron microscope images,
> and I found ITK
> and related applications (i.e. itk-snap) very useful.
> Unfortunately, it seems to me that ITK doesn't
> (natively) support the mrc
> file format. Am I right? There is any plan to include
> microscopy file
> formats into itk?
> (At the moment I'm using a mrc-MetaIO (and vice-versa)
> converter I wrote,
> I don't have any problem to publish the software
> somewhere if useful to
> other people).
>
> cheers,
> Mauro
>
>
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> Sergio Vera
>
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