Hi Heike (and Daniel),
I have improved the support the handling of non-scalar images (as e.g.
RGB images) in MITK with svn rev 14885. This fixes the problem that
AccessByItk/AccessTwoImagesFixedDimensionByItk did not recognize the
image as RGB. Unfortunately, they will not do anything (except issuing a
warning) for RGB images. This is because many algorithms do not support
RGB images, including many itk registration methods.
The images that you used are 8 bit, but have a color palette (which is
of course nonesense for grayvalue images). The itk-image-io for png
(which is used by MITK) has the following code:
itk::PNGImageIO::Read:
// convert palettes to RGB
if (colorType == PNG_COLOR_TYPE_PALETTE)
{
png_set_palette_to_rgb(png_ptr);
}
Thus, all png images with a palette are converted to RGB images.
So the solution still stays the same: change the image file, e.g. by
removing the palette. Maybe ask the ITK people to put the changed file
in their repository.
Best regards,
Ivo
Stein Daniel wrote:
> Hi Heike,
>
> this is because of a bug within the casts from MITK images to ITK images. The
> caster cannot handle RGB *.png images, which is the fact for some of the ITK
> example images. We already have a bug for this in our internal bug tracker. A
> solution in your case is to change the color depth from RGB to gray values
> and save and use the "new" images.
>
>
> Regards,
> Daniel
>
> ---
>
> Dipl.-Inform. Med. Daniel Stein
> German Cancer Research Center
> Div. Medical and Biological Informatics
> Im Neuenheimer Feld 280
> D-69120 Heidelberg, Germany
> Phone: (+49) 6221/42-3547
> Fax: (+49) 6221/42-2345
> http://www.dkfz-heidelberg.de/de/mbi/
> Homepage: http://www.dkfz-heidelberg.de/de/mbi/people/Daniel_Stein.html
>
>
>
> -----Ursprüngliche Nachricht-----
> Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im Auftrag von Heike Moll
> Gesendet: Donnerstag, 24. Juli 2008 12:57
> An: [email protected]
> Betreff: [mitk-users] Problem with the adapter class
>
> Hi all,
>
> I have a problem with the adapter classes.
>
> I import two images with the mitk application and I register them with ITK
> (like in Insight/Examples/Registration/ImageRegistration14.cxx).
>
> It works as long as the registration process only has to shift the picture
> but if a rotation is involved it gave bad results. To check my code I
> imported the same images with the itk imagereader and register them. This
> works without problems.
>
> I convert the mitk images with the adapter AccessTwoImagesFixedDimensionByItk.
>
> Can anyone help me to solve my problem ?
>
> ///////////////////////// Code //////////////////////////////////////
>
> const mitk::DataTreeNode* FixedImageNode =
> m_fixedDataTreeFilter->GetSelectedItem()->GetNode();
> //get the data
> if (!FixedImageNode->GetData())
> {
> // Nothing selected. Inform the user and return
> WARNING_EmptyImageNode();
> return false;
> }
>
> //now check the moving image
> const mitk::DataTreeNode* MovingImageNode =
> m_movingDataTreeFilter->GetSelectedItem()->GetNode();
> if (!MovingImageNode->GetData())
> {
> // Nothing selected. Inform the user and return
> WARNING_EmptyImageNode();
> return false;
> }
>
> // here we have everything valid
> mitk::BaseData* imageData_f = FixedImageNode->GetData();
> mitk::BaseData* imageData_m = MovingImageNode->GetData();
>
> //test if this data item is really an image
> mitk::Image* image_f = dynamic_cast<mitk::Image*>( imageData_f );
> mitk::Image* image_m = dynamic_cast<mitk::Image*>( imageData_m );
>
> if(image_f->GetDimension() != image_m->GetDimension()) return false;
> const int dim = image_f->GetDimension();
>
> if (image_f && image_m && (dim == 2)){
> AccessTwoImagesFixedDimensionByItk( image_f, image_m,
> itkNormalizedMutualInformation2D, 2 );
> }
> else{
> AccessTwoImagesFixedDimensionByItk( image_f, image_m,
> itkNormalizedMutualInformation3D, 3 );
> }
>
> template <typename TPixel_f, typename TPixel_m, unsigned int
> VImageDimension_f, unsigned int VImageDimension_m>
> void
> NormalizedMutualInformationRegistration::itkNormalizedMutualInformation2D(
> itk::Image< TPixel_f, VImageDimension_f >* itkImage_f, itk::Image< TPixel_m,
> VImageDimension_m >* itkImage_m)
> {
> typedef itk::Image< TPixel_f, VImageDimension_f > mitkFixedImageType;
> typedef itk::Image< TPixel_m, VImageDimension_m > mitkMovingImageType;
>
> typedef double PixelType;
> typedef unsigned char OutputPixelType;
> const unsigned int Dimension = 2;
>
> typedef itk::Image< PixelType, VImageDimension_f > ImageType;
> typedef itk::Image< PixelType, Dimension > FixedImageType;
> typedef itk::Image< PixelType, Dimension > MovingImageType;
>
> typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType;
> typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;
>
> typename FixedImageReaderType::Pointer fixedImageReader =
> FixedImageReaderType::New();
> typename MovingImageReaderType::Pointer movingImageReader =
> MovingImageReaderType::New();
>
> fixedImageReader->SetFileName( "....png" );
> movingImageReader->SetFileName( "....png" );
>
> fixedImageReader->Update();
> movingImageReader->Update();
>
>
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