[Insight-users] mrc data format

Mauro Maiorca mauromaiorca at gmail.com
Thu Oct 14 04:03:03 EDT 2010 

indeed, thanks Shekhar, it's working now!

cheers,
Mauro

On Thu, Oct 14, 2010 at 6:57 PM, Shekhar Chandra <Shekhar.Chandra at monash.edu
> wrote:

> 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
>>
>>              Alma IT Systems
>>              C/ Vilana, 4B, 4º 1ª
>>              08022 Barcelona
>>              T. (+34) 932 380 592
>>            www.alma3d.com <http://www.alma3d.com>
>>
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