[ITK] [ITK-dev] efficiency of vnl_matrix

[Johnson, Hans J]

Jian,

FYI:  I have used Eigen for similar tasks to your dmritool.  I have been very happy with it’s performance and feature set.

Hans

> On Mar 11, 2015, at 5:17 PM, Jian Cheng <jian.cheng.1983 at gmail.com> wrote:
>
> Hi Matt,
>
> Thanks for your help, and also for the ITK workshop in UNC last time.
>
> It is very unfortunate. The efficiency of these numerical math operators
> are very important for many applications.
>
> I recently released an ITK based toolbox, called dmritool, for diffusion
> MRI data processing.
> It has some files to add some supports of blas, lapack, mkl to
> vnl_matrix and vnl_vector.
> http://diffusionmritool.github.io/dmritool_doxygen/utlBlas_8h_source.html
> http://diffusionmritool.github.io/dmritool_doxygen/utlVNLBlas_8h_source.html
>
> Those functions are not internally for vnl_matrix class. They are
> operators for the data pointer stored in vnl_matrix object.
> Thus, later I made a N-dimensional array library which internally
> includes those functions, and also supports expression template to avoid
> temporary copies.
> http://diffusionmritool.github.io/dmritool_doxygen/utlMatrix_8h_source.html
> http://diffusionmritool.github.io/dmritool_doxygen/utlVector_8h_source.html
>
> The efficiency comparison between vnl_vector/vnl_matrix and the
> vector/matrix using openblas, lapack, or mkl can be found by running
> those two tests
> https://github.com/DiffusionMRITool/dmritool/blob/master/Modules/HelperFunctions/test/utlVNLBlasGTest.cxx
> https://github.com/DiffusionMRITool/dmritool/blob/master/Modules/HelperFunctions/test/utlVNLLapackGTest.cxx
>
> Maybe some codes can be used as patches in somewhere in ITK. I am not
> sure. Maybe we need more discussion on it.
> With your help and discussion, I will be very glad to make my first
> patch to ITK.
> Thanks.
>
> best,
> Jian Cheng
>
>
> On 03/11/2015 04:39 PM, Matt McCormick wrote:
>> Hi Jian,
>>
>> Yes, it would be wonderful to improve the efficiency of these basic
>> numerical operations.
>>
>> Funding for the Refactor Numerical Libraries has currently ended, and
>> the effort is currently frozen.  However, you are more than welcome to
>> pick it up and we can help you get it into ITK.  More information on
>> the patch submission process can be found here [1] and in the ITK
>> Software Guide.
>>
>> Thanks,
>> Matt
>>
>> [1] https://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/SubmitAPatchToGerrit/index.html
>>
>> On Wed, Mar 11, 2015 at 4:07 PM, Jian Cheng <jian.cheng.1983 at gmail.com> wrote:
>>> Hi,
>>>
>>> My task using ITK has intensive matrix-matrix product, pseudo-inverse, etc.
>>> Thus the performance is actually mainly determined by the matrix library
>>> I used.
>>> Firstly I use vnl_matrix and vnl_vector in ITK. Then I found it is very
>>> inefficient because vnl matrix lib does not use blas and lapack.
>>> After I wrote my own matrix class which uses openblas and lapack, I got
>>> a hug gain of performance.
>>>
>>> I found there is a proposal to improve the efficiency of numerical
>>> libraries in ITK.
>>> http://www.itk.org/Wiki/ITK/Release_4/Refactor_Numerical_Libraries
>>> I am not sure how is the progress of the proposal.
>>> I wonder when the vnl matrix lib can internally support blas and lapack,
>>> or mkl, so that we can just use it without lose of the efficiency.
>>> Thanks.
>>>
>>> best,
>>> Jian Cheng
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