[Insight-users] mrc data format
Bradley Lowekamp
blowekamp at mail.nih.gov
Thu Oct 14 17:20:40 EDT 2010
Hello,
This was a recent contribution from the insight journal:
http://www.midasjournal.org/browse/publication/729
You can also use the ImageIO factory mechanism so that you don't have to explicitly set the ImageIO. You can register it with the following line of code:
itk::MRCImageIOFactory::RegisterOneFactory();
Then you don't need to set the ImageIO, it should just be able to figure it out.
The orientation and the origin are not consistent across many common applications which use the MRC format. I opted not to utilize the orientation information in the file. There are some more details in the article.
Brad
On Oct 14, 2010, at 4:03 AM, Mauro Maiorca wrote:
> 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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>
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