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@@ -12,64 +12,127 @@ The basic forward and backward projection operations are GPU-accelerated, and di ## Documentation / samples -See the MATLAB and Python code samples in samples/ and on http://sf.net/projects/astra-toolbox . +See the MATLAB and Python code samples in samples/ and on http://www.astra-toolbox.com/ . ## Installation instructions ### Windows, binary -Add the mex and tools subdirectories to your MATLAB path and the Python module to your Python path.. +Add the mex and tools subdirectories to your MATLAB path, or copy the Python +astra module to your Python site-packages directory. We require the Microsoft +Visual Studio 2015 redistributable package. If this is not already installed on +your system, it is included as vc_redist.x64.exe in the ASTRA zip file. + +### Linux/Windows, using conda for python + +Requirements: [conda](http://conda.pydata.org/) python environment, with 64 bit Python 2.7, 3.5 or 3.6. + +There are packages available for the ASTRA Toolbox in the astra-toolbox +channel for the conda package manager. To use these, run the following +inside a conda environment. + +``` +conda install -c astra-toolbox astra-toolbox +``` ### Linux, from source -Requirements: g++, boost, CUDA (driver+toolkit), Matlab and/or Python (2.7 or 3.x) +#### For Matlab + +Requirements: g++, boost, CUDA (5.5 or higher), Matlab (R2012a or higher) ``` 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 + --prefix=$HOME/astra \ + --with-install-type=module 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. +Add $HOME/astra/matlab and its subdirectories (tools, mex) to your matlab path. + +If you want to build the Octave interface instead of the Matlab interface, +specify --enable-octave instead of --with-matlab=... . The Octave files +will be installed into $HOME/astra/octave . NB: Each matlab version only supports a specific range of g++ versions. Despite this, if you have a newer g++ and if you get errors related to missing GLIBCXX_3.4.xx symbols, it is often possible to work around this requirement by deleting the version of libstdc++ supplied by matlab in -MATLAB_PATH/bin/glnx86 or MATLAB_PATH/bin/glnxa64 (at your own risk). +MATLAB_PATH/bin/glnx86 or MATLAB_PATH/bin/glnxa64 (at your own risk), +or setting LD_PRELOAD=/usr/lib64/libstdc++.so.6 (or similar) when starting +matlab. +#### For Python -### Windows, from source using Visual Studio 2008 +Requirements: g++, boost, CUDA (5.5 or higher), Python (2.7 or 3.x) + +``` +cd build/linux +./autogen.sh # when building a git version +./configure --with-cuda=/usr/local/cuda \ + --with-python \ + --with-install-type=module +make +make install +``` -Requirements: Visual Studio 2008, boost, CUDA (driver+toolkit), matlab. -Note that a .zip with all required (and precompiled) boost files is - available from our website. +This will install Astra into your current Python environment. + +### macOS, from source + +Use the Homebrew package manager to install boost, libtool, autoconf, automake. + +``` +cd build/linux +./autogen.sh +CPPFLAGS="-I/usr/local/include" NVCCFLAGS="-I/usr/local/include" ./configure \ + --with-cuda=/usr/local/cuda \ + --with-matlab=/Applications/MATLAB_R2016b.app \ + --prefix=$HOME/astra \ + --with-install-type=module +make +make install +``` + +### Windows, from source using Visual Studio 2015 + +Requirements: Visual Studio 2015 (full or community), boost (recent), CUDA 8.0, + Matlab (R2012a or higher) and/or WinPython 2.7/3.x. + +Using the Visual Studio IDE: 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) +Copy boost headers to lib\include\boost, and boost libraries to bin\x64. +Open astra_vc14.sln in Visual Studio. +Select the appropriate solution configuration (typically 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. +Install by copying AstraCuda64.dll and all .mexw64 files from + bin\x64\Release_CUDA and the entire matlab/tools directory to a directory + to be added to your matlab path. + + +Using .bat scripts in build\msvc: + +Edit build_env.bat and set up the correct directories. +Run build_setup.bat to automatically copy the boost headers and libraries. +For matlab: Run build_matlab.bat. The .dll and .mexw64 files will be in bin\x64\Release_Cuda. +For python 2.7/3.5: Run build_python27.bat or build_python35.bat. Astra will be directly installed into site-packages. + ## References -If you use the ASTRA Toolbox for your research, we would appreciate it if you would refer to the following paper: +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 -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 (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: @@ -83,8 +146,8 @@ The ASTRA Toolbox is open source under the GPLv3 license. ## Contact email: astra@uantwerpen.be -website: http://sf.net/projects/astra-toolbox +website: http://www.astra-toolbox.com/ -Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp - 2014-2015, CWI, Amsterdam +Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp + 2014-2016, CWI, Amsterdam http://visielab.uantwerpen.be/ and http://www.cwi.nl/ |