[Insight-developers] reading Image<Matrix> as Image<SymmetricSecondRankTensor>

[Karthik Krishnan]

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> wrote:

> Hi Luis,
>
> On Mon, Jun 14, 2010 at 6:47 AM, Luis Ibanez <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> 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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>
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