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@@ -1,12 +1,12 @@ ----------------------------------------------------------------------- This file is part of the ASTRA Toolbox -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/ License: Open Source under GPLv3 Contact: astra@uantwerpen.be -Website: http://sf.net/projects/astra-toolbox +Website: http://www.astra-toolbox.com/ ----------------------------------------------------------------------- @@ -29,7 +29,7 @@ Documentation / samples: ------------------------- See the MATLAB and Python code samples in samples/ and on -http://sf.net/projects/astra-toolbox . +http://www.astra-toolbox.com/ . @@ -42,61 +42,123 @@ 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 $HOME/astra/octave . NB: Each matlab version only supports a specific range of g++ versions. Despite this, if you have a newer g++ and if you get errors related to missing GLIBCXX_3.4.xx symbols, it is often possible to work around this requirement by deleting the version of libstdc++ supplied by matlab in -MATLAB_PATH/bin/glnx86 or MATLAB_PATH/bin/glnxa64 (at your own risk). +MATLAB_PATH/bin/glnx86 or MATLAB_PATH/bin/glnxa64 (at your own risk), +or setting LD_PRELOAD=/usr/lib64/libstdc++.so.6 (or similar) when starting +matlab. + + +For Python: + +Requirements: g++, boost, CUDA (5.5 or higher), Python (2.7 or 3.x) + +cd build/linux +./autogen.sh # when building a git version +./configure --with-cuda=/usr/local/cuda \ + --with-python \ + --with-install-type=module +make +make install +This will install Astra into your current Python environment. -Windows, from source using Visual Studio 2008: + +macOS, from source: +-------------------- + +Use the Homebrew package manager to install boost, libtool, autoconf, automake. + +cd build/linux +./autogen.sh +CPPFLAGS="-I/usr/local/include" NVCCFLAGS="-I/usr/local/include" ./configure \ + --with-cuda=/usr/local/cuda \ + --with-matlab=/Applications/MATLAB_R2016b.app \ + --prefix=$HOME/astra \ + --with-install-type=module +make +make install + + +Windows, from source using Visual Studio 2015: ----------------------------------------------- -Requirements: Visual Studio 2008, boost, CUDA (driver+toolkit), matlab. -Note that a .zip with all required (and precompiled) boost files is - available from our website. +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, vol. 24, no. 22, pp. 25129-25147, 2016 -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 +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, vol. 157, pp. 35–47, 2015 Additionally, if you use parallel beam GPU code, we would appreciate it if you would refer to the following paper: |