UTL HelperFunctions¶
UTL Module¶
This module contains some helper functions, logging macros, debug macros, and an N-dimensional array class implemented using expression template with support for MKL, OpenBlas, Lapack and OpenMP.
Although OOP is good, sometimes functional style of programming is more attractive, and classes are too heavy for some specific tasks, e.g. reading text lines from a file, converting a container object to another container object. Thus we prefer using some small functions for those tasks.
Build¶
UTL module has only header files and can be used separately based on the different dependencies. See file dependency.
To build codes using utl::NDArray, you need to have MKL or OpenBlas + Lapack, and your compile needs to support C++11.
MKL is free for students, educators, academic researchers and open source contributors. See the free download link. OpenBlas and Lapack are always free and easy to use.
If you choose OpenBlas + Lapack, you can use them from system repositories. In this case, you need to set environment variables correctly. See FAQ of OpenBlas.
git clone https://github.com/xianyi/OpenBLAS.git cd OpenBlas git checkout v0.2.13 make BINARY=64 USE_THREAD=0 USE_OPENMP=1 cc=gcc FC=gfortran make install
utl::NDArray¶
utl::NDArray<T,N>is an N-dimensional array based on expression template.utl::NDArray<T,1>andutl::NDArray<T,2>are more efficient thanvnl_vector<T>andvnl_matrix<T>because
utl::NDArray<T,N>is implemented based on openblas, lapack or mkl.utl::NDArray<T,N>uses expression template to avoid temporary copies.utl::NDArray<T,N>uses rvalue references and move constructors, move assignment from C++11.
- You can run
utlVNLBlasGTestandutlVNLLapackGTestto compare efficiency ofutl::NDArrayandvnl_vector,vnl_matrix.
File structure and dependency¶
| Files | Dependency | Description |
|---|---|---|
| utlSmartAssert.h | std | macros for smart assert, modified based on the SMART_ASSERT library by John Torjo. |
| utlCoreMacro.h | std | macros for print and debug |
| utlCore.h | std | useful functions for general purpose |
| utlCore11.h | std, c++11 specific | useful functions for general purpose |
| utlCoreMKL.h | std, (mkl optional) | useful functions for mkl. If mkl is not found, a manual implementation is used. |
| utlCommandLineParser.h | std | small but powerful command line parser, borrowed from CImg |
| utlMath.h | std | math related functions |
| utlRotationMatrixFromVectors.h | std | functions to find rotation 3x3 matrix from two 3D vectors |
| utlSTDHeaders.h | std | macros to avoid include confliction issues for different versions of std |
| utlTypeinfo.h | std, c++11 specific | type alias for c++11 |
| utlGTest.h | google gtest | useful macros for gtest |
| utl_cblas.h | cblas | header file from cblas.h. Add some macro conditions to avoid multiple definition issues from other versions of cblas. |
| utlBlas.h | cblas, (mkl optional) | templated version of interface for cblas |
| utlLapack.h | lapack | templated version of interface for lapacke |
| utlMKL.h | mkl | templated version of interface for mkl |
| utlExpression.h | std | Implementation of Expression Template to avoid temporary copies in expression. |
| utlFunctors.h | std | Some functor classes, and functions for utl::NDArray<T,N>. |
| utlNDArray.h | std, blas, lapack, (mkl optional) | utl::NDArray<T,N> class (N-dimensional array) based on expression template, blas and mkl. |
| utlVector.h | std, blas, lapack, (mkl optional) | utl::NDArray<T,1> class (vector). |
| utlMatrix.h | std, blas, lapack, (mkl optional) | utl::NDArray<T,2> class (matrix). |
| utl4thOrderTensor.h | std, blas, lapack, (mkl optional) | utl::NDArray<T,4> class (4th order tensor). |
| utlNDArrayFunctions.h | std, blas, lapack, (mkl optional) | utl::NDArray<T,N> related functions. |
| utlDMRI.h | std, utl::NDArray |
Useful functions for dMRI |
| utlDMRIStoredTables.h | std, utl::NDArray |
Precomputed tables for dmritool |
| utlOpenMP.h | openmp | openmp related functions |
| utlVNL.h | vnl | vnl related functions |
| utlVNLBlas.h | vnl, blas | useful functions for vnl vector and matrix using blas implementation |
| utlVNLLapack.h | vnl, blas, lapack | useful functions for vnl vector and matrix using blas and lapack implementation |
| utlVNLIO.h | std, vnl, blas, lapack, (mkl optional) | conversion between utl::NDArray and vnl_vector, vnl_matrix |
| utlITKMacro.h | itk | macros for itk |
| utlITK.h | itk | functions for itk |
| utlVTKMacro.h | vtk | macros for vtk |
| utl.h | std, itk, blas, lapack, gsl, (mkl optional) | useful functions for dmritool |
