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

Mon Jun 14 13:17:37 EDT 2010

Hi Casey,

Thanks for the pointer.  Good to know the format can support it.  A little
work on the itkNrrdImageIO should be all that's needed.

Matt

On Mon, Jun 14, 2010 at 11:32 AM, Casey Goodlett <casey.goodlett at kitware.com
> wrote:

> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>>  _______________________________________________
>>>>>> Powered by www.kitware.com
>>>>>>
>>>>>> Visit other Kitware open-source projects at
>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>>
>>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>>> http://kitware.com/products/protraining.html
>>>>>>
>>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>>
>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>> http://www.itk.org/mailman/listinfo/insight-developers
>>>>>>
>>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://kitware.com/products/protraining.html
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://www.itk.org/mailman/listinfo/insight-developers
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects athttp://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:http://kitware.com/products/protraining.html
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:http://www.itk.org/mailman/listinfo/insight-developers
>>>
>>>
>>
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://kitware.com/products/protraining.html
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.itk.org/mailman/listinfo/insight-developers
>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/mailman/private/insight-developers/attachments/20100614/1bf99571/attachment.htm>