# The ASTRA Toolbox

The ASTRA Toolbox is a MATLAB and Python toolbox of high-performance GPU primitives for 2D and 3D tomography.

We support 2D parallel and fan beam geometries, and 3D parallel and cone beam.  All of them have highly flexible source/detector positioning.

A large number of 2D and 3D algorithms are available, including FBP, SIRT, SART, CGLS.

The basic forward and backward projection operations are GPU-accelerated, and directly callable from MATLAB and Python to enable building new algorithms.



## Documentation / samples

See the MATLAB and Python code samples in samples/ and on http://sf.net/projects/astra-toolbox .


## Installation instructions

### Windows, binary

Add the mex and tools subdirectories to your MATLAB path and the Python module to your Python path..

### Linux, from source

Requirements: g++, boost, CUDA (driver+toolkit), Matlab and/or Python (2.7 or 3.x)

```
cd build/linux
./autogen.sh   # when building a git version
./configure --with-cuda=/usr/local/cuda \
            --with-matlab=/usr/local/MATLAB/R2012a \
            --with-python \
            --prefix=/usr/local/astra
make
make install
```
Add /usr/local/astra/lib to your LD_LIBRARY_PATH.
Add /usr/local/astra/matlab and its subdirectories (tools, mex)
  to your matlab path.
Add /usr/local/astra/python to your PYTHONPATH.


NB: Each matlab version only supports a specific range of g++ versions.
Despite this, if you have a newer g++ and if you get errors related to missing
GLIBCXX_3.4.xx symbols, it is often possible to work around this requirement
by deleting the version of libstdc++ supplied by matlab in
MATLAB_PATH/bin/glnx86 or MATLAB_PATH/bin/glnxa64 (at your own risk).


### Windows, from source using Visual Studio 2008

Requirements: Visual Studio 2008, boost, CUDA (driver+toolkit), matlab.
Note that a .zip with all required (and precompiled) boost files is
  available from our website.

Set the environment variable MATLAB_ROOT to your matlab install location.
Open astra_vc08.sln in Visual Studio.
Select the appropriate solution configuration.
  (typically Release_CUDA|win32 or Release_CUDA|x64)
Build the solution.
Install by copying AstraCuda32.dll or AstraCuda64.dll from bin/ and
  all .mexw32 or .mexw64 files from bin/Release_CUDA or bin/Debug_CUDA
  and the entire matlab/tools directory to a directory to be added to
  your matlab path.


## References

If you use the ASTRA Toolbox for your research, we would appreciate it if you would refer to the following papers:

W. van Aarle, W. J. Palenstijn, J. Cant, E. Janssens, F. Bleichrodt, A. Dabravolski, J. De Beenhouwer, K. J. Batenburg, and J. Sijbers, “Fast and Flexible X-ray Tomography Using the ASTRA Toolbox”, Optics Express, 24(22), 25129-25147, (2016), http://dx.doi.org/10.1364/OE.24.025129

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography”, Ultramicroscopy, 157, 35–47, (2015), http://dx.doi.org/10.1016/j.ultramic.2015.05.002


Additionally, if you use parallel beam GPU code, we would appreciate it if you would refer to the following paper:

W. J. Palenstijn, K J. Batenburg, and J. Sijbers, "Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)", Journal of Structural Biology, vol. 176, issue 2, pp. 250-253, 2011, http://dx.doi.org/10.1016/j.jsb.2011.07.017


## License

The ASTRA Toolbox is open source under the GPLv3 license.

## Contact

email: astra@uantwerpen.be
website: http://sf.net/projects/astra-toolbox

Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp
           2014-2015, CWI, Amsterdam
           http://visielab.uantwerpen.be/ and http://www.cwi.nl/