Initial commit

.gitignore

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

INSTALL

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

LICENSE

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+COPYING

MANIFEST

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

MANIFEST.in

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

README

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+INSTALL

astra/ASTRAProjector.py

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

astra/PyAlgorithmFactory.pxd

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