Hi, I did test some mature matrix libs. Compared to eigen, I prefer armadillo http://arma.sourceforge.net/, because armadillo is more efficient for my task based on my experiments. Someone wrote did a numerical comparison on pseudo-inverse. http://nghiaho.com/?p=1726 Thus for picking a mature library, I vote for armadillo.
I decided to write my own matrix class for the codes, because it does not need to add additional dependency and it just contains 2-3 header files for a light-wright matrix lib to support blas, lapack, mkl, and expression template. best, Jian Cheng On 03/12/2015 05:15 AM, m.star...@lumc.nl wrote: > 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-boun...@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.1...@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 >>> _______________________________________________ >>> 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.php >>> >>> 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://public.kitware.com/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.php > > 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://public.kitware.com/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.php 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://public.kitware.com/mailman/listinfo/insight-developers
