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PRIMAL-DUAL TOOLBOX

C++/Cuda implementation of various Total Variation (TV) and second-order Total Generalized Variation (TGV) [1,2] problems using the primal-dual algorithm [3], including Python and Matlab wrappers. This toolbox is used for TGV-based MRI reconstruction presented in [4]. If you find this software useful for your academic work, please cite the related publications.

Currently supported operators

  • Denoising (real-valued and complex-valued)
  • Cartesian MRI reconstruction (2D)
  • Radial MRI reconstruction (2D, requires gpuNUFFT) [5,6]

The single operators can be used in the different optimizers (TV, TGV) or standalone.

Dependencies

These modules are added as submodules to this repository. You can either clone this repository with the flag --recursive or do a

$ git submodule update --init --recursive --remote

Note: The framework was tested using Ubuntu 16.04, gcc 5.4 and cuda 8.0. We support both python2 and python3. We highly recommend to use an Anaconda environment.

Installation

  • Set up environment variable COMPUTE_CAPABILITY with the CC of your CUDA-enabled GPU

  • Set up environment variable CUDA_SDK_ROOT_DIR to point to the NVidia CUDA examples (required to find <matlab_helper.h>)

  • Set up environment variable IMAGEUTILITIES_ROOT to point to the path of the ImageUtilities root directory

  • Set up environment variable MATLAB_ROOT to point to the matlab root directory

  • Optional: Set up environment variable GPUNUFFT_ROOT_DIR to point to the path of the gpuNUFFT root directory

  • Make sure that you have boost-python installed. We highly recommend to use an Anaconda environment. To install boost-python here, simply do

    $ conda install boost

    Note: Please make sure to use the same environment for building this software and running your code. If you update boost or numpy, you might have to re-build this software, because the versions have to match. If you wish to build this software for a specific Anaconda environment, activate this environment before the building process using source activate <your_python_environment>.

    If you want to use your system python, you can install boost-python using:

    $ sudo apt-get install libboost-python

To build the primal-dual toolbox including the dependencies, simply perform the following steps:

  • ImageUtilities (requires libboost-python, libopenexr-dev, libeigen3-dev)

    $ cd imageutilities/build
$ cmake .. -DWITH_PYTHON=ON -DWITH_MATLAB=ON
$ make
$ make install
$ cd ../../

    If you wish to exclude the Matlab wrapper, simply set -DWITH_MATLAB=OFF in above building steps.

  • gpuNUFFT (optional)

    $ cd gpuNUFFT/CUDA/build
$ cmake .. -DGEN_MEX_FILES=ON -DMATLAB_ROOT_DIR=$MATLAB_ROOT
$ make
$ cd ../../../

    If you wish to build gpuNUFFT without the mex files, replace above CMake command by:

    $ cmake .. -DGEN_MEX_FILES=OFF

  • Primal-Dual-Toolbox

    $ mkdir build
$ cd build
$ cmake .. -DWITH_GPUNUFFT=ON
$ make
$ cd ../

    To build without gpuNUFFT, use cmake .. -DWITH_GPUNUFFT=OFF instead of cmake .. -DWITH_GPUNUFFT=ON.

After building the C-code, you can build and install the Python package from the root directory of this repository as follows:

$ python setup.py bdist_wheel
$ pip install dist/<your-PrimalDualToolbox-wheel-package>.whl

Please make sure to use the same python environment that you built this software with.

Documentation

To build the documentation (requires doxygen), additionally execute following command in the build directory:

$ make apidoc

Test Python Module

To test the python module simply check if following works without error:

$ ipython
$ import primaldualtoolbox

Run tests

Go into the bin directory. To run the python samples, simply type

$ python denoising_test.py
$ python denoising_complex_test.py
$ python mri_cartesian_test.py
$ python mri_radial_test.py

To run the Matlab samples, open Matlab and run mri_cartesian_test.m or mri_radial_test.m. The data used for the radial tests is the same as provided in the gpuNUFFT. The examples show simple use of the implemented operators and how to run TGV reconstructions.

Common issues:

Invalid MEX-file '~/pd_toolbox/lib/gpuMriCartesianRemoveROOSAdj.mexa64': ~/MATLAB/R2014a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by
~/pd_toolbox/lib/gpuMriCartesianFwd.mexa64)

Start your Matlab with LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6 matlab.

References

  • [1] K Bredies, K Kunisch, T Pock. Total generalized variation. SIAM Journal on Imaging Sciences 3 (3), pp. 492-526, 2010.
  • [2] A Chambolle, T Pock. An introduction to continuous optimization for imaging. Acta Numerica, 25, pp. 161-319, 2016.
  • [3] A Chambolle, T Pock. A first-order primal-dual algorithm for convex problems with applications to imaging. Journal of Mathematical Imaging and Vision 40 (1), pp. 120-145, 2011.
  • [4] K Hammernik, T Klatzer, E Kobler, MP Recht, DK Sodickson, T Pock, F Knoll. Learning a Variational Network for Reconstruction of Accelerated MRI Data. Magnetic Resonance in Medicine, 2017 (early view).
  • [5] F Knoll, K Bredies, T Pock, R Stollberger. Second order total generalized variation (TGV) for MRI. Magnetic Resonance in Medicine 65 (2), pp. 480-491, 2011.
  • [6] F Knoll, A Schwarzl, C Diwoky, DK Sodickson. gpuNUFFT-an open source GPU library for 3D regridding with direct Matlab interface. Proceedings of the 22nd Annual Meeting of ISMRM, Milan, Italy, p. 4297, 2014.