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‎.gitignore

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build/
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dist/
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docSRC/_build/
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*.c
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*.cpp
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*.so
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*.pyc

‎COPYING

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‎INSTALL

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#-----------------------------------------------------------------------
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#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
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#
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#Author: Daniel M. Pelt
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#Contact: [email protected]
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#Website: http://dmpelt.github.io/pyastratoolbox/
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#
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#
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#This file is part of the Python interface to the
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#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
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#
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#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
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#it under the terms of the GNU General Public License as published by
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#the Free Software Foundation, either version 3 of the License, or
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#(at your option) any later version.
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#
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#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
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#but WITHOUT ANY WARRANTY; without even the implied warranty of
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#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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#GNU General Public License for more details.
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#
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#You should have received a copy of the GNU General Public License
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#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
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#
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#-----------------------------------------------------------------------
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To use the Python interface, you need the All Scale Tomographic Reconstruction Antwerp Toolbox:
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https://code.google.com/p/astra-toolbox/
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Please install the ASTRA toolbox first.
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Other requirements: Cython (version >= 0.13), NumPy
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Use install.sh to install the Python interface to the ASTRA toolbox.
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Only run install.sh as ./install.sh in the base directory of the interface code.
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You need write permission to the $PYTHON_PATH directory.
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We recommend using a Python virtualenv if root access is impossible.
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The Python interface to the ASTRA Toolbox uses Python version 2.
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Usage: ./install.sh [-i astra_include_path] [-l astra_library_path] [-p python_executable_path] [-c cuda_path]
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-i astra_include_path: specify path to astra header files (without trailing astra/) (Optional)
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-l astra_library_path: specify parent path of astra library file (Optional)
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-p python_executable_path: specify path to python executable (Optional)
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-c cuda_path: path to CUDA (Optional)
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-h: print this help (Optional)
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Note that the paths only have to be specified if they are not already in your $LD_LIBRARY_PATH, etcetera.
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When compiling with CUDA, the astra_include_path should be set to the 'include' directory of the ASTRA toolbox
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source.

‎LICENSE

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COPYING

‎MANIFEST

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# file GENERATED by distutils, do NOT edit
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COPYING
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INSTALL
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README
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builder.py
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install.sh
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astra/ASTRAProjector.py
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astra/PyAlgorithmFactory.pxd
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astra/PyAlgorithmManager.pxd
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astra/PyData2DManager.pxd
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astra/PyData3DManager.pxd
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astra/PyIncludes.pxd
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astra/PyMatrixManager.pxd
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astra/PyProjector2DFactory.pxd
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astra/PyProjector2DManager.pxd
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astra/PyXMLDocument.pxd
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astra/__init__.py
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astra/algorithm.py
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astra/algorithm_c.cpp
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astra/algorithm_c.pyx
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astra/astra.py
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astra/astra_c.cpp
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astra/astra_c.pyx
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astra/creators.py
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astra/data2d.py
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astra/data2d_c.cpp
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astra/data2d_c.pyx
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astra/data3d.py
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astra/data3d_c.cpp
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astra/data3d_c.pyx
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astra/extrautils.c
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astra/extrautils.pyx
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astra/functions.py
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astra/matlab.py
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astra/matrix.py
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astra/matrix_c.cpp
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astra/matrix_c.pyx
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astra/projector.py
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astra/projector_c.cpp
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astra/projector_c.pyx
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astra/utils.cpp
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astra/utils.pxd
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astra/utils.pyx
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doc/.buildinfo
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doc/ASTRAProjector.html
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doc/algorithm.html
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doc/creators.html
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doc/data2d.html
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doc/data3d.html
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doc/functions.html
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doc/genindex.html
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doc/index.html
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doc/matlab.html
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doc/matrix.html
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doc/objects.inv
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doc/projector.html
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doc/py-modindex.html
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doc/search.html
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doc/searchindex.js
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doc/_modules/index.html
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doc/_modules/astra/ASTRAProjector.html
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doc/_modules/astra/algorithm.html
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doc/_modules/astra/creators.html
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doc/_modules/astra/data2d.html
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doc/_modules/astra/data3d.html
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doc/_modules/astra/functions.html
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doc/_modules/astra/matlab.html
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doc/_modules/astra/matrix.html
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doc/_modules/astra/projector.html
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doc/_sources/ASTRAProjector.txt
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doc/_sources/algorithm.txt
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doc/_sources/creators.txt
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doc/_sources/data2d.txt
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doc/_sources/data3d.txt
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doc/_sources/functions.txt
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doc/_sources/index.txt
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doc/_sources/matlab.txt
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doc/_sources/matrix.txt
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doc/_sources/projector.txt
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doc/_static/ajax-loader.gif
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doc/_static/basic.css
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doc/_static/comment-bright.png
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doc/_static/comment-close.png
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doc/_static/comment.png
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doc/_static/default.css
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doc/_static/doctools.js
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doc/_static/down-pressed.png
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doc/_static/down.png
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doc/_static/file.png
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doc/_static/jquery.js
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doc/_static/minus.png
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doc/_static/plus.png
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doc/_static/pygments.css
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doc/_static/searchtools.js
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doc/_static/sidebar.js
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doc/_static/underscore.js
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doc/_static/up-pressed.png
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doc/_static/up.png
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doc/_static/websupport.js
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examples/phantom.mat
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examples/s001_sinogram_par2d.py
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examples/s002_data2d.py
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examples/s003_gpu_reconstruction.py
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examples/s004_cpu_reconstruction.py
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examples/s005_3d_geometry.py
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examples/s006_3d_data.py
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examples/s007_3d_reconstruction.py
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examples/s008_gpu_selection.py
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examples/s009_projection_matrix.py
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examples/s010_supersampling.py
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examples/s011_object_info.py
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examples/s012_masks.py
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examples/s013_constraints.py
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examples/s014_FBP.py
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examples/s015_fp_bp.py
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examples/s016_plots.py

‎MANIFEST.in

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include INSTALL
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include COPYING
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include install.sh
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recursive-include examples *.py *.mat
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recursive-include astra *.pyx *.pxd
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recursive-include doc *
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‎README

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INSTALL

‎astra/ASTRAProjector.py

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#-----------------------------------------------------------------------
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#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
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#
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#Author: Daniel M. Pelt
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#Contact: [email protected]
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#Website: http://dmpelt.github.io/pyastratoolbox/
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#
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#
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#This file is part of the Python interface to the
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#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
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#
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#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
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#it under the terms of the GNU General Public License as published by
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#the Free Software Foundation, either version 3 of the License, or
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#(at your option) any later version.
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#
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#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
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#but WITHOUT ANY WARRANTY; without even the implied warranty of
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#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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#GNU General Public License for more details.
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#
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#You should have received a copy of the GNU General Public License
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#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
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#
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#-----------------------------------------------------------------------
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import creators as ac
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import math
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import data2d
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class ASTRAProjector2DTranspose():
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"""Implements the ``proj.T`` functionality.
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Do not use directly, since it can be accessed as member ``.T`` of
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an :class:`ASTRAProjector2D` object.
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"""
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def __init__(self, parentProj):
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self.parentProj = parentProj
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def __mul__(self, data):
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return self.parentProj.backProject(data)
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class ASTRAProjector2D(object):
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"""Helps with various common ASTRA Toolbox 2D operations.
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This class can perform several often used toolbox operations, such as:
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* Forward projecting
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* Back projecting
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* Reconstructing
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Note that this class has a some computational overhead, because it
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copies a lot of data. If you use many repeated operations, directly
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using the PyAstraToolbox methods directly is faster.
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You can use this class as an abstracted weight matrix :math:`W`: multiplying an instance
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``proj`` of this class by an image results in a forward projection of the image, and multiplying
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``proj.T`` by a sinogram results in a backprojection of the sinogram::
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proj = ASTRAProjector2D(...)
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fp = proj*image
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bp = proj.T*sinogram
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:param proj_geom: The projection geometry.
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:type proj_geom: :class:`dict`
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:param vol_geom: The volume geometry.
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:type vol_geom: :class:`dict`
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:param proj_type: Projector type, such as ``'line'``, ``'linear'``, ...
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:type proj_type: :class:`string`
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:param useCUDA: If ``True``, use CUDA for calculations, when possible.
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:type useCUDA: :class:`bool`
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"""
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def __init__(self, proj_geom, vol_geom, proj_type, useCUDA=False):
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self.vol_geom = vol_geom
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self.recSize = vol_geom['GridColCount']
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self.angles = proj_geom['ProjectionAngles']
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self.nDet = proj_geom['DetectorCount']
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nexpow = int(pow(2, math.ceil(math.log(2 * self.nDet, 2))))
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self.filterSize = nexpow / 2 + 1
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self.nProj = self.angles.shape[0]
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self.proj_geom = proj_geom
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self.proj_id = ac.create_projector(proj_type, proj_geom, vol_geom)
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self.useCUDA = useCUDA
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self.T = ASTRAProjector2DTranspose(self)
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def backProject(self, data):
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"""Backproject a sinogram.
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:param data: The sinogram data or ID.
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:type data: :class:`numpy.ndarray` or :class:`int`
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:returns: :class:`numpy.ndarray` -- The backprojection.
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"""
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vol_id, vol = ac.create_backprojection(
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data, self.proj_id, self.useCUDA, True)
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data2d.delete(vol_id)
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return vol
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def forwardProject(self, data):
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"""Forward project an image.
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:param data: The image data or ID.
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:type data: :class:`numpy.ndarray` or :class:`int`
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:returns: :class:`numpy.ndarray` -- The forward projection.
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"""
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sin_id, sino = ac.create_sino(data, self.proj_id, self.useCUDA, True)
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data2d.delete(sin_id)
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return sino
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def reconstruct(self, data, method, **kwargs):
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"""Reconstruct an image from a sinogram.
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:param data: The sinogram data or ID.
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:type data: :class:`numpy.ndarray` or :class:`int`
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:param method: Name of the reconstruction algorithm.
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:type method: :class:`string`
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:param kwargs: Additional named parameters to pass to :func:`astra.creators.create_reconstruction`.
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:returns: :class:`numpy.ndarray` -- The reconstruction.
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Example of a SIRT reconstruction using CUDA::
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proj = ASTRAProjector2D(...)
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rec = proj.reconstruct(sinogram,'SIRT_CUDA',iterations=1000)
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"""
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kwargs['returnData'] = True
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rec_id, rec = ac.create_reconstruction(
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method, self.proj_id, data, **kwargs)
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data2d.delete(rec_id)
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return rec
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def __mul__(self, data):
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return self.forwardProject(data)

‎astra/PyAlgorithmFactory.pxd

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#-----------------------------------------------------------------------
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#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
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#
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#Author: Daniel M. Pelt
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#Contact: [email protected]
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#Website: http://dmpelt.github.io/pyastratoolbox/
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#
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#
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#This file is part of the Python interface to the
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#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
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#
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#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
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#it under the terms of the GNU General Public License as published by
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#the Free Software Foundation, either version 3 of the License, or
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#(at your option) any later version.
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#
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#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
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#but WITHOUT ANY WARRANTY; without even the implied warranty of
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#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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#GNU General Public License for more details.
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#
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#You should have received a copy of the GNU General Public License
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#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
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#
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#-----------------------------------------------------------------------
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from libcpp.string cimport string
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from libcpp cimport bool
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from PyIncludes cimport *
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cdef extern from "astra/AstraObjectFactory.h" namespace "astra":
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cdef cppclass CAlgorithmFactory:
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CAlgorithmFactory()
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CAlgorithm *create(string)
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cdef extern from "astra/AstraObjectFactory.h" namespace "astra::CAlgorithmFactory":
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cdef CAlgorithmFactory* getSingletonPtr()

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