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

Mon Jun 14 12:32:28 EDT 2010

NRRD should also be able to support 2D matrices in both symmetric and
non-symmetric forms.

http://teem.sourceforge.net/nrrd/format.html#kinds

Casey

On Mon, Jun 14, 2010 at 12:08 PM, Matthew McCormick (thewtex) <
matt at mmmccormick.com> wrote:

>
>
> On Mon, Jun 14, 2010 at 10:38 AM, Luke Bloy <luke.bloy at gmail.com> wrote:
>
>>  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#a29for how the data is stored.
>>
>> -Luke
>>
>
> Hi Luke,
>
> Thanks for the clarification and link.
>
> Matt
>
>
>>
>>
>> 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> 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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