[Insight-users] Origin in shrink image filter wrong?

[Lodron, Gerald]

Hi

I already managed it an i found out that the error was not the shrink image filter, the error was the visualization. The vtkCheckerboard filter cannot handle images with differnet size or different origin so my visualization showed me two unregistered images (where one image was the shrinked version of the other one). I now put the resample image filter between the shrink and checkerboard filter to upscale the image again for visualization purposes. Not the best way but now it works.

But thanks for your reply,
Best regards 

-----Ursprüngliche Nachricht-----
Von: Luis Ibanez [mailto:luis.ibanez at kitware.com] 
Gesendet: Dienstag, 22. Dezember 2009 01:30
An: Lodron, Gerald
Cc: insight-users at itk.org
Betreff: Re: [Insight-users] Origin in shrink image filter wrong?

Hi Lodron,

The computation of the origin for the ShrinkImageFilter is not as trivial as one may expect at first sight.

We spent three or four Tcons discussing this issue, See, for example:

           http://www.itk.org/Wiki/Minutes_032709


To summarize:

    NO, the origin of the Shrunk image is not the
    same as the origin of the input image.


They are related by the following code:

  typename TOutputImage::PointType outputOrigin = outputPtr->GetOrigin();
  outputOrigin = outputOrigin + (inputCenterPoint - outputCenterPoint);
  outputPtr->SetOrigin(outputOrigin);


that you can find in lines 355-357 of the file

     Insight/Code/BasicFilters
             itkShrinkImageFilter.txx


In order to make sense of these computation you should consider that:

    1) ITK origin is given in physical coordinates

    2) Pixel coordinates in ITK are associated with
        the center of the pixel
        (not its corner, as it is done in VTK).


    Regards,


           Luis


-------------------------------------------------------------
On Tue, Dec 15, 2009 at 4:42 AM, Lodron, Gerald <Gerald.Lodron at joanneum.at> wrote:
> Hi
>
> I try to downsample a DICOM image with shrink image filter and i come to no sollution. The problem is that the origin of the result is wrong:
>
> When i load the same DICOM 3D image with the same code and downsample one of them by factor two the images should be aligned, am i right? So when i use the checkerboard the only difference should be the ressolution, am i right? But the images are not aligned so what went wrong? I am really at the end of my vodoo.
>
> I use ITK 3.16.0 with following settings on:
> ITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE
> ITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY
> ITK_USE_CONSOLATED_MORPHOLOGY
> ITK_USE_OPTIMIZED_REGISTRATION_METHODS
> ITK_USE_ORIENTED_IMAGE_DIRECTION
> ITK_USE_PATENTED
> ITK_USE_REGION_VALIDATION_IN_ITERATORS
> ITK_USE_REVIEW
> ITK_USE_SYSTEM_GDCM     (i installed and use gdcm 2.0.14) 
> ITK_USE_TEMPLATE_META_PROGRAMMING_LOOP_UNROLLING
>
> The rest is off.
>
> Here my pseudocode
>
> vtkImageData    image1; //3D image of short vtkImageData    image2; 
> //the same
>
> //Image1 is exactly the same as image 2, i use vtkCheckerboard to 
> compare them and they are the same
>
> //first i convert both to ITK
> Itk::VTKImageToImageFilter<...>::Pointer connector1 = ...::New(); 
> Itk::VTKImageToImageFilter<...>::Pointer connector2 = ...::New();
>
> Connector1->SetInput(...)
> ...
> Itk::OrientedImage<...>::pointer image1ITK; 
> Itk::OrientedImage<...>::pointer image2ITK;
>
> //now i use shrink image filter to downsample one of them
>
> itk::ShrinkImageFilter<>::Pointer filter = 
> itk::ShrinkImageFilter<>::New();
> filter->SetInput(image2ITK);
> filter->SetShrinkFactor(2);
>
>
> Itk::OrientedImage<...>::pointer image2ITKSmall = filter->getOutput();
>
>
> //and back to vtk
> Itk::ImageToVTKImageFilter::Pointer c1 = ...::New(); 
> Itk::ImageToVTKImageFilter::Pointer c2 = ...::New();
>
> C1->setInput(image1ITK);
> //C2->setInput(image2ITK);              //with that the images are 
> aligned
> C2->setInput(image2ITKSmall);           //with that not aligned
>
> //back to vtk and visualize with checkerboard
>
> vtkImageCheckerboard*   Checkerboard= vtkImageCheckerboard::New();
>
> Checkerboard->SetInput(0, C1->getOutput()); SetInput(1, 
> Checkerboard->C2->getOutput()); SetNumberOfDivisions(2, 2, 2);
>
> //visualize Checkerboard->getOutput()
> ...
>
>
>
>
>
>
>
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