[ITK] [ITK-dev] efficiency of vnl_matrix

[M.Staring at lumc.nl]

Hi,

I think the eigen library is a mature and very fast library for these kind of things:
http://eigen.tuxfamily.org/index.php?title=Main_Page

You may want to check it out, to see if it offers what you need.

It would be great to be able to use these within the itk.

2c
Marius

-----Original Message-----
From: Insight-developers [mailto:insight-developers-bounces at itk.org] On Behalf Of Jian Cheng
Sent: Wednesday, March 11, 2015 23:17
To: Matt McCormick
Cc: Chuck Atkins; ITK
Subject: Re: [ITK-dev] efficiency of vnl_matrix

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/CommunitySo
> ftwareProcess/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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