[Insight-users] mrc data format

[Mauro Maiorca]

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
> 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>
>>  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>
>>> 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
>>>
>>> _____________________________________
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>
> _____________________________________
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>
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>
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> http://www.kitware.com/products/protraining.html
>
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