[Insight-developers] reading Image<Matrix> as Image<SymmetricSecondRankTensor>
Luke Bloy
luke.bloy at gmail.com
Mon Jun 14 11:38:20 EDT 2010
Matt and Karthik,
I believe that Nifti format does support general 2nd rank tensors, via
the NIFTI_INTENT_SYMMATRIX intent code or genreal matrices via
NIFTI_INTENT_GENMATRIX intent code.
see
http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/group__NIFTI1__INTENT__CODES.html#a29
for how the data is stored.
-Luke
On 06/14/2010 11:21 AM, Karthik Krishnan wrote:
> Matt:
>
> As you've mentioned, I don't think the NRRD and NifTi formats support
> anything but 3 dimensional, 2nd rank symmetric tensors. The meta-image
> does support it, simply by virtue of the fact that a N-D, rank 2
> Symmetric tensor derives from a fixed array and is serializable as a
> N*(N-1) component image.
>
> The patch logged in http://vtk.org/Bug/view.php?id=10732 looks fine to me.
>
> As you've mentioned the test to exercise your modification to
> itkImageIOBase (what I think is your real question) would need to use
> MetaImages. I would just add a separate test
> itkSymmetricSecondRankSecondDimensionTensorImageReadTest that uses
> MetaImage instead of Nrrd and then add the proposed patch in.
>
> Thanks
> --
> karthik
>
>
>
> On Mon, Jun 14, 2010 at 7:26 PM, Matthew McCormick (thewtex)
> <matt at mmmccormick.com <mailto:matt at mmmccormick.com>> wrote:
>
> Hi Luis,
>
> On Mon, Jun 14, 2010 at 6:47 AM, Luis Ibanez
> <luis.ibanez at kitware.com <mailto:luis.ibanez at kitware.com>> wrote:
>
>
> Hi Matt,
>
> Thanks for looking into this problem.
>
> I'm a bit confused about what you suggest in your email.
>
> Are you suggesting to change the test
> in order to also exercise a 2D case ?
>
>
> Yes.
>
>
> or is it the core of the change, to use an image of
> SymmetricSecondRankTensor instead of Matrix2x2
> as the source for the image ?
>
>
> Yes. In any case, I need to write an image of
> SymmetricSecondRankTensor to test the bug. For consistency, I
> should then change the 3D case too? But I do not know if reading
> an image of Matrix as SymmetricSecondRankTensor is behavior that
> is expected. If so, I do not want to remove the test for it.
> Also if so, readers will need to be fixed to behave this way.
> Personally, I would not necessarily expect this behavior.
>
> Also, have you identified the changes that we will
> have to introduce in the Writer/Reader in order to
> get this test to pass ?
>
>
> Changing the file name on the test shows that MetaImage, NRRD, and
> NIfTI all pass for the 3D case.
>
> As far as I can tell, NRRD and NIfTI do not support 3 component
> symmetric second rank tensor. MetaImage does support it, but its
> behavior would have to change. I am working on adding support to
> the VTKImageIO, but it can not support generic 2x2 or 3x3 matrices.
>
>
>
> Could you please clarify ?
>
>
> Hopefully this clarifies, but let me know if it is still unclear.
>
> Thanks,
> Matt
>
>
> Thanks
>
>
> Luis
>
>
> ----------------------------------------------------------
> On Sun, Jun 13, 2010 at 12:38 AM, Matthew McCormick (thewtex)
> <matt at mmmccormick.com <mailto:matt at mmmccormick.com>> wrote:
>
> Hi,
>
> I am working on adding 2D SymmetricSecondRankTensor image
> write support. The bug is here.
> http://vtk.org/Bug/view.php?id=10732
>
> In order to add a test for the bug, I was thinking of
> modifying
> Testing/Code/IO/itkSymmetricSecondRankTensorImageReadTest.cxx
>
> Currently, this test creates an Image of 3x3 itk::Matrix,
> writes it to file, reads it in as an Image of
> SymmetricSecondRankTensor's, and checks to ensure the
> content is the same.
>
> If I try to do the same with 2x2 itk::Matrix, the
> SymmetricSecondRankTensor reader does not read the correct
> components:
> 941: Test command: /mnt/datab/itkcvsb/bin/itkIOTests
> itkSymmetricSecondRankTensorImageReadTest
> /mnt/datab/itkcvsb/Testing/Temporary/testSymmetricTensor1.nrrd
> /mnt/datab/itkcvsb/Testing/Temporary/testSymmetricTensor2.nrrd
> 941: Test timeout computed to be: 1500
> 941: Tensor read does not match expected values
> 941: Index [0, 0]
> 941: Tensor value
> 941: 1 2 2
> 941: Matrix value
> 941: 1 2
> 941: 2 3
> 941:
>
> If the commented code, where an image of 2D
> SymmetricSecondRankTensor ( instead of itk::Matrix ) is
> written, is used with the MetaImage format the test can pass.
>
> Is it OK to change the test as in the commented code, or
> are other changes required?
>
> Thanks,
> Matt
>
>
>
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