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diff --git a/python/COPYING b/python/COPYING new file mode 100644 index 0000000..94a9ed0 --- /dev/null +++ b/python/COPYING @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. 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Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +<http://www.gnu.org/licenses/>. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +<http://www.gnu.org/philosophy/why-not-lgpl.html>. diff --git a/python/LICENSE b/python/LICENSE new file mode 120000 index 0000000..d24842f --- /dev/null +++ b/python/LICENSE @@ -0,0 +1 @@ +COPYING
\ No newline at end of file diff --git a/python/astra/ASTRAProjector.py b/python/astra/ASTRAProjector.py new file mode 100644 index 0000000..96acb10 --- /dev/null +++ b/python/astra/ASTRAProjector.py @@ -0,0 +1,138 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 math +from . import creators as ac +from . 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, useCUDA=self.useCUDA, returnData=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, useCUDA=self.useCUDA, returnData=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) diff --git a/python/astra/PyAlgorithmFactory.pxd b/python/astra/PyAlgorithmFactory.pxd new file mode 100644 index 0000000..256d7b2 --- /dev/null +++ b/python/astra/PyAlgorithmFactory.pxd @@ -0,0 +1,36 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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() diff --git a/python/astra/PyAlgorithmManager.pxd b/python/astra/PyAlgorithmManager.pxd new file mode 100644 index 0000000..a99a807 --- /dev/null +++ b/python/astra/PyAlgorithmManager.pxd @@ -0,0 +1,40 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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/AstraObjectManager.h" namespace "astra": + cdef cppclass CAlgorithmManager: + int store(CAlgorithm *) + CAlgorithm * get(int) + void remove(int) + void clear() + string info() + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CAlgorithmManager": + cdef CAlgorithmManager* getSingletonPtr() + diff --git a/python/astra/PyData2DManager.pxd b/python/astra/PyData2DManager.pxd new file mode 100644 index 0000000..db8ec84 --- /dev/null +++ b/python/astra/PyData2DManager.pxd @@ -0,0 +1,39 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CData2DManager: + string info() + void clear() + void remove(int i) + int store(CFloat32Data2D *) + CFloat32Data2D * get(int i) + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CData2DManager": + cdef CData2DManager* getSingletonPtr() diff --git a/python/astra/PyData3DManager.pxd b/python/astra/PyData3DManager.pxd new file mode 100644 index 0000000..9264a82 --- /dev/null +++ b/python/astra/PyData3DManager.pxd @@ -0,0 +1,39 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CData3DManager: + string info() + void clear() + void remove(int i) + int store(CFloat32Data3D *) + CFloat32Data3D * get(int i) + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CData3DManager": + cdef CData3DManager* getSingletonPtr() diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd new file mode 100644 index 0000000..fc5980f --- /dev/null +++ b/python/astra/PyIncludes.pxd @@ -0,0 +1,215 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 cimport bool +from libcpp.string cimport string +from .PyXMLDocument cimport XMLNode + +cdef extern from "astra/Globals.h" namespace "astra": + ctypedef float float32 + ctypedef double float64 + ctypedef unsigned short int uint16 + ctypedef signed short int sint16 + ctypedef unsigned char uchar8 + ctypedef signed char schar8 + ctypedef int int32 + ctypedef short int int16 + +cdef extern from "astra/Config.h" namespace "astra": + cdef cppclass Config: + Config() + XMLNode *self + +cdef extern from "astra/VolumeGeometry2D.h" namespace "astra": + cdef cppclass CVolumeGeometry2D: + bool initialize(Config) + int getGridColCount() + int getGridRowCount() + int getGridTotCount() + float32 getWindowLengthX() + float32 getWindowLengthY() + float32 getWindowArea() + float32 getPixelLengthX() + float32 getPixelLengthY() + float32 getPixelArea() + float32 getWindowMinX() + float32 getWindowMinY() + float32 getWindowMaxX() + float32 getWindowMaxY() + + +cdef extern from "astra/Float32VolumeData2D.h" namespace "astra": + cdef cppclass CFloat32VolumeData2D: + CFloat32VolumeData2D(CVolumeGeometry2D*) + CVolumeGeometry2D * getGeometry() + int getWidth() + int getHeight() + void changeGeometry(CVolumeGeometry2D*) + + + +cdef extern from "astra/ProjectionGeometry2D.h" namespace "astra": + cdef cppclass CProjectionGeometry2D: + CProjectionGeometry2D() + bool initialize(Config) + int getDetectorCount() + int getProjectionAngleCount() + bool isOfType(string) + float32 getProjectionAngle(int) + float32 getDetectorWidth() + +cdef extern from "astra/Float32Data2D.h" namespace "astra::CFloat32Data2D": + cdef enum EDataType: + BASE,PROJECTION,VOLUME + +cdef extern from "astra/Float32Data2D.h" namespace "astra": + cdef cppclass CFloat32Data2D: + bool isInitialized() + int getSize() + float32 *getData() + float32 **getData2D() + int getWidth() + int getHeight() + EDataType getType() + + + + +cdef extern from "astra/SparseMatrixProjectionGeometry2D.h" namespace "astra": + cdef cppclass CSparseMatrixProjectionGeometry2D: + CSparseMatrixProjectionGeometry2D() + +cdef extern from "astra/FanFlatProjectionGeometry2D.h" namespace "astra": + cdef cppclass CFanFlatProjectionGeometry2D: + CFanFlatProjectionGeometry2D() + +cdef extern from "astra/FanFlatVecProjectionGeometry2D.h" namespace "astra": + cdef cppclass CFanFlatVecProjectionGeometry2D: + CFanFlatVecProjectionGeometry2D() + +cdef extern from "astra/ParallelProjectionGeometry2D.h" namespace "astra": + cdef cppclass CParallelProjectionGeometry2D: + CParallelProjectionGeometry2D() + + +cdef extern from "astra/Float32ProjectionData2D.h" namespace "astra": + cdef cppclass CFloat32ProjectionData2D: + CFloat32ProjectionData2D(CProjectionGeometry2D*) + CProjectionGeometry2D * getGeometry() + void changeGeometry(CProjectionGeometry2D*) + int getDetectorCount() + int getAngleCount() + +cdef extern from "astra/Algorithm.h" namespace "astra": + cdef cppclass CAlgorithm: + bool initialize(Config) + void run(int) + bool isInitialized() + +cdef extern from "astra/ReconstructionAlgorithm2D.h" namespace "astra": + cdef cppclass CReconstructionAlgorithm2D: + bool getResidualNorm(float32&) + +cdef extern from "astra/Projector2D.h" namespace "astra": + cdef cppclass CProjector2D: + bool isInitialized() + CProjectionGeometry2D* getProjectionGeometry() + CVolumeGeometry2D* getVolumeGeometry() + CSparseMatrix* getMatrix() + +cdef extern from "astra/SparseMatrix.h" namespace "astra": + cdef cppclass CSparseMatrix: + CSparseMatrix(unsigned int,unsigned int,unsigned long) + unsigned int m_iWidth + unsigned int m_iHeight + unsigned long m_lSize + bool isInitialized() + float32* m_pfValues + unsigned int* m_piColIndices + unsigned long* m_plRowStarts + +cdef extern from "astra/Float32Data3DMemory.h" namespace "astra": + cdef cppclass CFloat32Data3DMemory: + CFloat32Data3DMemory() + bool isInitialized() + int getSize() + int getWidth() + int getHeight() + int getDepth() + void updateStatistics() + float32 *getData() + float32 ***getData3D() + + +cdef extern from "astra/VolumeGeometry3D.h" namespace "astra": + cdef cppclass CVolumeGeometry3D: + CVolumeGeometry3D() + bool initialize(Config) + +cdef extern from "astra/ProjectionGeometry3D.h" namespace "astra": + cdef cppclass CProjectionGeometry3D: + CProjectionGeometry3D() + bool initialize(Config) + + +cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra": + cdef cppclass CFloat32VolumeData3DMemory: + CFloat32VolumeData3DMemory(CVolumeGeometry3D*) + + +cdef extern from "astra/ParallelProjectionGeometry3D.h" namespace "astra": + cdef cppclass CParallelProjectionGeometry3D: + CParallelProjectionGeometry3D() + +cdef extern from "astra/ParallelVecProjectionGeometry3D.h" namespace "astra": + cdef cppclass CParallelVecProjectionGeometry3D: + CParallelVecProjectionGeometry3D() + +cdef extern from "astra/ConeProjectionGeometry3D.h" namespace "astra": + cdef cppclass CConeProjectionGeometry3D: + CConeProjectionGeometry3D() + bool initialize(Config) + +cdef extern from "astra/ConeVecProjectionGeometry3D.h" namespace "astra": + cdef cppclass CConeVecProjectionGeometry3D: + CConeVecProjectionGeometry3D() + +cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra": + cdef cppclass CFloat32ProjectionData3DMemory: + CFloat32ProjectionData3DMemory(CProjectionGeometry3D*) + CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*) + +cdef extern from "astra/Float32Data3D.h" namespace "astra": + cdef cppclass CFloat32Data3D: + CFloat32Data3D() + bool isInitialized() + int getSize() + int getWidth() + int getHeight() + int getDepth() + void updateStatistics() + + + diff --git a/python/astra/PyMatrixManager.pxd b/python/astra/PyMatrixManager.pxd new file mode 100644 index 0000000..b2b84c4 --- /dev/null +++ b/python/astra/PyMatrixManager.pxd @@ -0,0 +1,39 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CMatrixManager: + string info() + void clear() + void remove(int i) + int store(CSparseMatrix *) + CSparseMatrix * get(int i) + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CMatrixManager": + cdef CMatrixManager* getSingletonPtr() diff --git a/python/astra/PyProjector2DFactory.pxd b/python/astra/PyProjector2DFactory.pxd new file mode 100644 index 0000000..3314544 --- /dev/null +++ b/python/astra/PyProjector2DFactory.pxd @@ -0,0 +1,35 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 CProjector2DFactory: + CProjector2D *create(Config) + +cdef extern from "astra/AstraObjectFactory.h" namespace "astra::CProjector2DFactory": + cdef CProjector2DFactory* getSingletonPtr() diff --git a/python/astra/PyProjector2DManager.pxd b/python/astra/PyProjector2DManager.pxd new file mode 100644 index 0000000..92176ba --- /dev/null +++ b/python/astra/PyProjector2DManager.pxd @@ -0,0 +1,39 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CProjector2DManager: + string info() + void clear() + void remove(int i) + int store(CProjector2D *) + CProjector2D * get(int i) + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CProjector2DManager": + cdef CProjector2DManager* getSingletonPtr() diff --git a/python/astra/PyXMLDocument.pxd b/python/astra/PyXMLDocument.pxd new file mode 100644 index 0000000..69781f1 --- /dev/null +++ b/python/astra/PyXMLDocument.pxd @@ -0,0 +1,65 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +from libcpp.string cimport string +from libcpp cimport bool +from libcpp.list cimport list +from libcpp.vector cimport vector + +cdef extern from "astra/Globals.h" namespace "astra": + ctypedef float float32 + ctypedef double float64 + ctypedef unsigned short int uint16 + ctypedef signed short int sint16 + ctypedef unsigned char uchar8 + ctypedef signed char schar8 + ctypedef int int32 + ctypedef short int int16 + +cdef extern from "astra/XMLNode.h" namespace "astra": + cdef cppclass XMLNode: + string getName() + XMLNode *addChildNode(string name) + XMLNode *addChildNode(string, string) + void addAttribute(string, string) + void addAttribute(string, float32) + void addOption(string, string) + bool hasOption(string) + string getAttribute(string) + list[XMLNode *] getNodes() + vector[float32] getContentNumericalArray() + string getContent() + bool hasAttribute(string) + +cdef extern from "astra/XMLDocument.h" namespace "astra": + cdef cppclass XMLDocument: + void saveToFile(string sFilename) + XMLNode *getRootNode() + +cdef extern from "astra/XMLDocument.h" namespace "astra::XMLDocument": + cdef XMLDocument *createDocument(string rootname) diff --git a/python/astra/__init__.py b/python/astra/__init__.py new file mode 100644 index 0000000..a61aafc --- /dev/null +++ b/python/astra/__init__.py @@ -0,0 +1,42 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 . import matlab as m +from .creators import astra_dict,create_vol_geom, create_proj_geom, create_backprojection, create_sino, create_reconstruction, create_projector,create_sino3d_gpu, create_backprojection3d_gpu +from .functions import data_op, add_noise_to_sino, clear, move_vol_geom +from .extrautils import clipCircle +from .ASTRAProjector import ASTRAProjector2D +from . import data2d +from . import astra +from . import data3d +from . import algorithm +from . import projector +from . import matrix + +import os +try: + astra.set_gpu_index(int(os.environ['ASTRA_GPU_INDEX'])) +except KeyError: + pass diff --git a/python/astra/algorithm.py b/python/astra/algorithm.py new file mode 100644 index 0000000..46cfccc --- /dev/null +++ b/python/astra/algorithm.py @@ -0,0 +1,76 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 . import algorithm_c as a + +def create(config): + """Create algorithm object. + + :param config: Algorithm options. + :type config: :class:`dict` + :returns: :class:`int` -- the ID of the constructed object. + + """ + return a.create(config) + +def run(i, iterations=1): + """Run an algorithm. + + :param i: ID of object. + :type i: :class:`int` + :param iterations: Number of iterations to run. + :type iterations: :class:`int` + + """ + return a.run(i,iterations) + +def get_res_norm(i): + """Get residual norm of algorithm. + + :param i: ID of object. + :type i: :class:`int` + :returns: :class:`float` -- The residual norm. + + """ + + return a.get_res_norm(i) + +def delete(ids): + """Delete a matrix object. + + :param ids: ID or list of ID's to delete. + :type ids: :class:`int` or :class:`list` + + """ + return a.delete(ids) + +def clear(): + """Clear all matrix objects.""" + return a.clear() + +def info(): + """Print info on matrix objects in memory.""" + return a.info() diff --git a/python/astra/algorithm_c.pyx b/python/astra/algorithm_c.pyx new file mode 100644 index 0000000..0c2999c --- /dev/null +++ b/python/astra/algorithm_c.pyx @@ -0,0 +1,106 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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/>. +# +#----------------------------------------------------------------------- + +# distutils: language = c++ +# distutils: libraries = astra + +import six +from .PyIncludes cimport * + +cimport PyAlgorithmManager +from .PyAlgorithmManager cimport CAlgorithmManager + +cimport PyAlgorithmFactory +from .PyAlgorithmFactory cimport CAlgorithmFactory + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument + +cimport utils +from .utils import wrap_from_bytes + +cdef CAlgorithmManager * manAlg = <CAlgorithmManager * >PyAlgorithmManager.getSingletonPtr() + +cdef extern from *: + CReconstructionAlgorithm2D * dynamic_cast_recAlg "dynamic_cast<CReconstructionAlgorithm2D*>" (CAlgorithm * ) except NULL + + +def create(config): + cdef XMLDocument * xml = utils.dict2XML(six.b('Algorithm'), config) + cdef Config cfg + cdef CAlgorithm * alg + cfg.self = xml.getRootNode() + alg = PyAlgorithmFactory.getSingletonPtr().create(cfg.self.getAttribute(six.b('type'))) + if alg == NULL: + del xml + raise Exception("Unknown algorithm.") + if not alg.initialize(cfg): + del xml + del alg + raise Exception("Algorithm not initialized.") + del xml + return manAlg.store(alg) + +cdef CAlgorithm * getAlg(i) except NULL: + cdef CAlgorithm * alg = manAlg.get(i) + if alg == NULL: + raise Exception("Unknown algorithm.") + if not alg.isInitialized(): + raise Exception("Algorithm not initialized.") + return alg + + +def run(i, iterations=0): + cdef CAlgorithm * alg = getAlg(i) + alg.run(iterations) + + +def get_res_norm(i): + cdef CReconstructionAlgorithm2D * pAlg2D + cdef CAlgorithm * alg = getAlg(i) + cdef float32 res = 0.0 + pAlg2D = dynamic_cast_recAlg(alg) + if pAlg2D == NULL: + raise Exception("Operation not supported.") + if not pAlg2D.getResidualNorm(res): + raise Exception("Operation not supported.") + return res + + +def delete(ids): + try: + for i in ids: + manAlg.remove(i) + except TypeError: + manAlg.remove(ids) + + +def clear(): + manAlg.clear() + + +def info(): + six.print_(wrap_from_bytes(manAlg.info())) diff --git a/python/astra/astra.py b/python/astra/astra.py new file mode 100644 index 0000000..26b1ff0 --- /dev/null +++ b/python/astra/astra.py @@ -0,0 +1,58 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 . import astra_c as a + +def credits(): + """Print credits of the ASTRA Toolbox.""" + return a.credits() + + +def use_cuda(): + """Test if CUDA is enabled. + + :returns: :class:`bool` -- ``True`` if CUDA is enabled. + """ + return a.use_cuda() + + +def version(printToScreen=False): + """Check version of the ASTRA Toolbox. + + :param printToScreen: If ``True``, print version string. If ``False``, return version integer. + :type printToScreen: :class:`bool` + :returns: :class:`string` or :class:`int` -- The version string or integer. + + """ + return a.version(printToScreen) + +def set_gpu_index(idx): + """Set default GPU index to use. + + :param idx: GPU index + :type idx: :class:`int` + """ + a.set_gpu_index(idx) diff --git a/python/astra/astra_c.pyx b/python/astra/astra_c.pyx new file mode 100644 index 0000000..342a214 --- /dev/null +++ b/python/astra/astra_c.pyx @@ -0,0 +1,79 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +include "config.pxi" +import six +from .utils import wrap_from_bytes + +from libcpp.string cimport string +from libcpp cimport bool +cdef extern from "astra/Globals.h" namespace "astra": + int getVersion() + string getVersionString() + bool cudaEnabled() + +IF HAVE_CUDA==True: + cdef extern from "../cuda/2d/darthelper.h" namespace "astraCUDA": + bool setGPUIndex(int) +ELSE: + def setGPUIndex(): + pass + +def credits(): + six.print_(""" +All Scale Tomographic Reconstruction Antwerp Toolbox (ASTRA-Toolbox) +was developed at the University of Antwerp by + * Prof. dr. Joost Batenburg + * Andrei Dabravolski + * Gert Merckx + * Willem Jan Palenstijn + * Tom Roelandts + * Prof. dr. Jan Sijbers + * dr. Wim van Aarle + * Sander van der Maar + * dr. Gert Van Gompel + +Python interface written by + * Daniel M. Pelt (CWI, Amsterdam)""") + + +def use_cuda(): + return cudaEnabled() + + +def version(printToScreen=False): + if printToScreen: + six.print_(wrap_from_bytes(getVersionString())) + else: + return getVersion() + +def set_gpu_index(idx): + if use_cuda()==True: + ret = setGPUIndex(idx) + if not ret: + six.print_("Failed to set GPU " + str(idx)) diff --git a/python/astra/creators.py b/python/astra/creators.py new file mode 100644 index 0000000..9aba464 --- /dev/null +++ b/python/astra/creators.py @@ -0,0 +1,563 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 six +import numpy as np +import math +from . import data2d +from . import data3d +from . import projector +from . import algorithm + +def astra_dict(intype): + """Creates a dict to use with the ASTRA Toolbox. + + :param intype: Type of the ASTRA object. + :type intype: :class:`string` + :returns: :class:`dict` -- An ASTRA dict of type ``intype``. + + """ + if intype == 'SIRT_CUDA2': + intype = 'SIRT_CUDA' + six.print_('SIRT_CUDA2 has been deprecated. Use SIRT_CUDA instead.') + elif intype == 'FP_CUDA2': + intype = 'FP_CUDA' + six.print_('FP_CUDA2 has been deprecated. Use FP_CUDA instead.') + return {'type': intype} + +def create_vol_geom(*varargin): + """Create a volume geometry structure. + +This method can be called in a number of ways: + +``create_vol_geom(N)``: + :returns: A 2D volume geometry of size :math:`N \\times N`. + +``create_vol_geom((M, N))``: + :returns: A 2D volume geometry of size :math:`M \\times N`. + +``create_vol_geom(M, N)``: + :returns: A 2D volume geometry of size :math:`M \\times N`. + +``create_vol_geom(M, N, minx, maxx, miny, maxy)``: + :returns: A 2D volume geometry of size :math:`M \\times N`, windowed as :math:`minx \\leq x \\leq maxx` and :math:`miny \\leq y \\leq maxy`. + +``create_vol_geom((M, N, Z))``: + :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`. + +``create_vol_geom(M, N, Z)``: + :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`. + +""" + vol_geom = {'option': {}} + # astra_create_vol_geom(row_count) + if len(varargin) == 1 and isinstance(varargin[0], int) == 1: + vol_geom['GridRowCount'] = varargin[0] + vol_geom['GridColCount'] = varargin[0] + vol_geom['option']['WindowMinX'] = -varargin[0] / 2. + vol_geom['option']['WindowMaxX'] = varargin[0] / 2. + vol_geom['option']['WindowMinY'] = -varargin[0] / 2. + vol_geom['option']['WindowMaxY'] = varargin[0] / 2. + # astra_create_vol_geom([row_count col_count]) + elif len(varargin) == 1 and len(varargin[0]) == 2: + vol_geom['GridRowCount'] = varargin[0][0] + vol_geom['GridColCount'] = varargin[0][1] + vol_geom['option']['WindowMinX'] = -varargin[0][1] / 2. + vol_geom['option']['WindowMaxX'] = varargin[0][1] / 2. + vol_geom['option']['WindowMinY'] = -varargin[0][0] / 2. + vol_geom['option']['WindowMaxY'] = varargin[0][0] / 2. + # astra_create_vol_geom([row_count col_count slice_count]) + elif len(varargin) == 1 and len(varargin[0]) == 3: + vol_geom['GridRowCount'] = varargin[0][0] + vol_geom['GridColCount'] = varargin[0][1] + vol_geom['GridSliceCount'] = varargin[0][2] + vol_geom['option']['WindowMinX'] = -varargin[0][1] / 2. + vol_geom['option']['WindowMaxX'] = varargin[0][1] / 2. + vol_geom['option']['WindowMinY'] = -varargin[0][0] / 2. + vol_geom['option']['WindowMaxY'] = varargin[0][0] / 2. + vol_geom['option']['WindowMinZ'] = -varargin[0][2] / 2. + vol_geom['option']['WindowMaxZ'] = varargin[0][2] / 2. + # astra_create_vol_geom(row_count, col_count) + elif len(varargin) == 2: + vol_geom['GridRowCount'] = varargin[0] + vol_geom['GridColCount'] = varargin[1] + vol_geom['option']['WindowMinX'] = -varargin[1] / 2. + vol_geom['option']['WindowMaxX'] = varargin[1] / 2. + vol_geom['option']['WindowMinY'] = -varargin[0] / 2. + vol_geom['option']['WindowMaxY'] = varargin[0] / 2. + # astra_create_vol_geom(row_count, col_count, min_x, max_x, min_y, max_y) + elif len(varargin) == 6: + vol_geom['GridRowCount'] = varargin[0] + vol_geom['GridColCount'] = varargin[1] + vol_geom['option']['WindowMinX'] = varargin[2] + vol_geom['option']['WindowMaxX'] = varargin[3] + vol_geom['option']['WindowMinY'] = varargin[4] + vol_geom['option']['WindowMaxY'] = varargin[5] + # astra_create_vol_geom(row_count, col_count, slice_count) + elif len(varargin) == 3: + vol_geom['GridRowCount'] = varargin[0] + vol_geom['GridColCount'] = varargin[1] + vol_geom['GridSliceCount'] = varargin[2] + return vol_geom + + +def create_proj_geom(intype, *args): + """Create a projection geometry. + +This method can be called in a number of ways: + +``create_proj_geom('parallel', detector_spacing, det_count, angles)``: + +:param detector_spacing: Distance between two adjacent detector pixels. +:type detector_spacing: :class:`float` +:param det_count: Number of detector pixels. +:type det_count: :class:`int` +:param angles: Array of angles in radians. +:type angles: :class:`numpy.ndarray` +:returns: A parallel projection geometry. + + +``create_proj_geom('fanflat', det_width, det_count, angles, source_origin, source_det)``: + +:param det_width: Size of a detector pixel. +:type det_width: :class:`float` +:param det_count: Number of detector pixels. +:type det_count: :class:`int` +:param angles: Array of angles in radians. +:type angles: :class:`numpy.ndarray` +:param source_origin: Position of the source. +:param source_det: Position of the detector +:returns: A fan-beam projection geometry. + +``create_proj_geom('fanflat_vec', det_count, V)``: + +:param det_count: Number of detector pixels. +:type det_count: :class:`int` +:param V: Vector array. +:type V: :class:`numpy.ndarray` +:returns: A fan-beam projection geometry. + +``create_proj_geom('parallel3d', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles)``: + +:param detector_spacing_*: Distance between two adjacent detector pixels. +:type detector_spacing_*: :class:`float` +:param det_row_count: Number of detector pixel rows. +:type det_row_count: :class:`int` +:param det_col_count: Number of detector pixel columns. +:type det_col_count: :class:`int` +:param angles: Array of angles in radians. +:type angles: :class:`numpy.ndarray` +:returns: A parallel projection geometry. + +``create_proj_geom('cone', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det)``: + +:param detector_spacing_*: Distance between two adjacent detector pixels. +:type detector_spacing_*: :class:`float` +:param det_row_count: Number of detector pixel rows. +:type det_row_count: :class:`int` +:param det_col_count: Number of detector pixel columns. +:type det_col_count: :class:`int` +:param angles: Array of angles in radians. +:type angles: :class:`numpy.ndarray` +:param source_origin: Distance between point source and origin. +:type source_origin: :class:`float` +:param source_det: Distance between the detector and origin. +:type source_det: :class:`float` +:returns: A cone-beam projection geometry. + +``create_proj_geom('cone_vec', det_row_count, det_col_count, V)``: + +:param det_row_count: Number of detector pixel rows. +:type det_row_count: :class:`int` +:param det_col_count: Number of detector pixel columns. +:type det_col_count: :class:`int` +:param V: Vector array. +:type V: :class:`numpy.ndarray` +:returns: A cone-beam projection geometry. + +``create_proj_geom('parallel3d_vec', det_row_count, det_col_count, V)``: + +:param det_row_count: Number of detector pixel rows. +:type det_row_count: :class:`int` +:param det_col_count: Number of detector pixel columns. +:type det_col_count: :class:`int` +:param V: Vector array. +:type V: :class:`numpy.ndarray` +:returns: A parallel projection geometry. + +``create_proj_geom('sparse_matrix', det_width, det_count, angles, matrix_id)``: + +:param det_width: Size of a detector pixel. +:type det_width: :class:`float` +:param det_count: Number of detector pixels. +:type det_count: :class:`int` +:param angles: Array of angles in radians. +:type angles: :class:`numpy.ndarray` +:param matrix_id: ID of the sparse matrix. +:type matrix_id: :class:`int` +:returns: A projection geometry based on a sparse matrix. + +""" + if intype == 'parallel': + if len(args) < 3: + raise Exception( + 'not enough variables: astra_create_proj_geom(parallel, detector_spacing, det_count, angles)') + return {'type': 'parallel', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2]} + elif intype == 'fanflat': + if len(args) < 5: + raise Exception('not enough variables: astra_create_proj_geom(fanflat, det_width, det_count, angles, source_origin, source_det)') + return {'type': 'fanflat', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2], 'DistanceOriginSource': args[3], 'DistanceOriginDetector': args[4]} + elif intype == 'fanflat_vec': + if len(args) < 2: + raise Exception('not enough variables: astra_create_proj_geom(fanflat_vec, det_count, V)') + if not args[1].shape[1] == 6: + raise Exception('V should be a Nx6 matrix, with N the number of projections') + return {'type':'fanflat_vec', 'DetectorCount':args[0], 'Vectors':args[1]} + elif intype == 'parallel3d': + if len(args) < 5: + raise Exception('not enough variables: astra_create_proj_geom(parallel3d, detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles)') + return {'type':'parallel3d', 'DetectorSpacingX':args[0], 'DetectorSpacingY':args[1], 'DetectorRowCount':args[2], 'DetectorColCount':args[3],'ProjectionAngles':args[4]} + elif intype == 'cone': + if len(args) < 7: + raise Exception('not enough variables: astra_create_proj_geom(cone, detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det)') + return {'type': 'cone','DetectorSpacingX':args[0], 'DetectorSpacingY':args[1], 'DetectorRowCount':args[2],'DetectorColCount':args[3],'ProjectionAngles':args[4],'DistanceOriginSource': args[5],'DistanceOriginDetector':args[6]} + elif intype == 'cone_vec': + if len(args) < 3: + raise Exception('not enough variables: astra_create_proj_geom(cone_vec, det_row_count, det_col_count, V)') + if not args[2].shape[1] == 12: + raise Exception('V should be a Nx12 matrix, with N the number of projections') + return {'type': 'cone_vec','DetectorRowCount':args[0],'DetectorColCount':args[1],'Vectors':args[2]} + elif intype == 'parallel3d_vec': + if len(args) < 3: + raise Exception('not enough variables: astra_create_proj_geom(parallel3d_vec, det_row_count, det_col_count, V)') + if not args[2].shape[1] == 12: + raise Exception('V should be a Nx12 matrix, with N the number of projections') + return {'type': 'parallel3d_vec','DetectorRowCount':args[0],'DetectorColCount':args[1],'Vectors':args[2]} + elif intype == 'sparse_matrix': + if len(args) < 4: + raise Exception( + 'not enough variables: astra_create_proj_geom(sparse_matrix, det_width, det_count, angles, matrix_id)') + return {'type': 'sparse_matrix', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2], 'MatrixID': args[3]} + else: + raise Exception('Error: unknown type ' + intype) + + +def create_backprojection(data, proj_id, useCUDA=False, returnData=True): + """Create a backprojection of a sinogram (2D). + +:param data: Sinogram data or ID. +:type data: :class:`numpy.ndarray` or :class:`int` +:param proj_id: ID of the projector to use. +:type proj_id: :class:`int` +:param useCUDA: If ``True``, use CUDA for the calculation. +:type useCUDA: :class:`bool` +:param returnData: If False, only return the ID of the backprojection. +:type returnData: :class:`bool` +:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order. + +""" + proj_geom = projector.projection_geometry(proj_id) + vol_geom = projector.volume_geometry(proj_id) + if isinstance(data, np.ndarray): + sino_id = data2d.create('-sino', proj_geom, data) + else: + sino_id = data + vol_id = data2d.create('-vol', vol_geom, 0) + + algString = 'BP' + if useCUDA: + algString = algString + '_CUDA' + + cfg = astra_dict(algString) + if not useCUDA: + cfg['ProjectorId'] = proj_id + cfg['ProjectionDataId'] = sino_id + cfg['ReconstructionDataId'] = vol_id + alg_id = algorithm.create(cfg) + algorithm.run(alg_id) + algorithm.delete(alg_id) + + if isinstance(data, np.ndarray): + data2d.delete(sino_id) + + if returnData: + return vol_id, data2d.get(vol_id) + else: + return vol_id + +def create_backprojection3d_gpu(data, proj_geom, vol_geom, returnData=True): + """Create a backprojection of a sinogram (3D) using CUDA. + +:param data: Sinogram data or ID. +:type data: :class:`numpy.ndarray` or :class:`int` +:param proj_geom: Projection geometry. +:type proj_geom: :class:`dict` +:param vol_geom: Volume geometry. +:type vol_geom: :class:`dict` +:param returnData: If False, only return the ID of the backprojection. +:type returnData: :class:`bool` +:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order. + +""" + if isinstance(data, np.ndarray): + sino_id = data3d.create('-sino', proj_geom, data) + else: + sino_id = data + + vol_id = data3d.create('-vol', vol_geom, 0) + + cfg = astra_dict('BP3D_CUDA') + cfg['ProjectionDataId'] = sino_id + cfg['ReconstructionDataId'] = vol_id + alg_id = algorithm.create(cfg) + algorithm.run(alg_id) + algorithm.delete(alg_id) + + if isinstance(data, np.ndarray): + data3d.delete(sino_id) + + if returnData: + return vol_id, data3d.get(vol_id) + else: + return vol_id + + +def create_sino(data, proj_id=None, proj_geom=None, vol_geom=None, + useCUDA=False, returnData=True, gpuIndex=None): + """Create a forward projection of an image (2D). + + :param data: Image data or ID. + :type data: :class:`numpy.ndarray` or :class:`int` + :param proj_id: ID of the projector to use. + :type proj_id: :class:`int` + :param proj_geom: Projection geometry. + :type proj_geom: :class:`dict` + :param vol_geom: Volume geometry. + :type vol_geom: :class:`dict` + :param useCUDA: If ``True``, use CUDA for the calculation. + :type useCUDA: :class:`bool` + :param returnData: If False, only return the ID of the forward projection. + :type returnData: :class:`bool` + :param gpuIndex: Optional GPU index. + :type gpuIndex: :class:`int` + :returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) + + If ``returnData=False``, returns the ID of the forward + projection. Otherwise, returns a tuple containing the ID of the + forward projection and the forward projection itself, in that + order. + + The geometry of setup is defined by ``proj_id`` or with + ``proj_geom`` and ``vol_geom``. If ``proj_id`` is given, then + ``proj_geom`` and ``vol_geom`` must be None and vice versa. +""" + if proj_id is not None: + proj_geom = projector.projection_geometry(proj_id) + vol_geom = projector.volume_geometry(proj_id) + elif proj_geom is not None and vol_geom is not None: + if not useCUDA: + # We need more parameters to create projector. + raise ValueError( + """A ``proj_id`` is needed when CUDA is not used.""") + else: + raise Exception("""The geometry setup is not defined. + The geometry of setup is defined by ``proj_id`` or with + ``proj_geom`` and ``vol_geom``. If ``proj_id`` is given, then + ``proj_geom`` and ``vol_geom`` must be None and vice versa.""") + + if isinstance(data, np.ndarray): + volume_id = data2d.create('-vol', vol_geom, data) + else: + volume_id = data + sino_id = data2d.create('-sino', proj_geom, 0) + algString = 'FP' + if useCUDA: + algString = algString + '_CUDA' + cfg = astra_dict(algString) + if not useCUDA: + cfg['ProjectorId'] = proj_id + if gpuIndex is not None: + cfg['option'] = {'GPUindex': gpuIndex} + cfg['ProjectionDataId'] = sino_id + cfg['VolumeDataId'] = volume_id + alg_id = algorithm.create(cfg) + algorithm.run(alg_id) + algorithm.delete(alg_id) + + if isinstance(data, np.ndarray): + data2d.delete(volume_id) + if returnData: + return sino_id, data2d.get(sino_id) + else: + return sino_id + + + +def create_sino3d_gpu(data, proj_geom, vol_geom, returnData=True, gpuIndex=None): + """Create a forward projection of an image (3D). + +:param data: Image data or ID. +:type data: :class:`numpy.ndarray` or :class:`int` +:param proj_geom: Projection geometry. +:type proj_geom: :class:`dict` +:param vol_geom: Volume geometry. +:type vol_geom: :class:`dict` +:param returnData: If False, only return the ID of the forward projection. +:type returnData: :class:`bool` +:param gpuIndex: Optional GPU index. +:type gpuIndex: :class:`int` +:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the forward projection. Otherwise, returns a tuple containing the ID of the forward projection and the forward projection itself, in that order. + +""" + + if isinstance(data, np.ndarray): + volume_id = data3d.create('-vol', vol_geom, data) + else: + volume_id = data + sino_id = data3d.create('-sino', proj_geom, 0) + algString = 'FP3D_CUDA' + cfg = astra_dict(algString) + if not gpuIndex==None: + cfg['option']={'GPUindex':gpuIndex} + cfg['ProjectionDataId'] = sino_id + cfg['VolumeDataId'] = volume_id + alg_id = algorithm.create(cfg) + algorithm.run(alg_id) + algorithm.delete(alg_id) + + if isinstance(data, np.ndarray): + data3d.delete(volume_id) + if returnData: + return sino_id, data3d.get(sino_id) + else: + return sino_id + + +def create_reconstruction(rec_type, proj_id, sinogram, iterations=1, use_mask='no', mask=np.array([]), use_minc='no', minc=0, use_maxc='no', maxc=255, returnData=True, filterType=None, filterData=None): + """Create a reconstruction of a sinogram (2D). + +:param rec_type: Name of the reconstruction algorithm. +:type rec_type: :class:`string` +:param proj_id: ID of the projector to use. +:type proj_id: :class:`int` +:param sinogram: Sinogram data or ID. +:type sinogram: :class:`numpy.ndarray` or :class:`int` +:param iterations: Number of iterations to run. +:type iterations: :class:`int` +:param use_mask: Whether to use a mask. +:type use_mask: ``'yes'`` or ``'no'`` +:param mask: Mask data or ID +:type mask: :class:`numpy.ndarray` or :class:`int` +:param use_minc: Whether to force a minimum value on the reconstruction pixels. +:type use_minc: ``'yes'`` or ``'no'`` +:param minc: Minimum value to use. +:type minc: :class:`float` +:param use_maxc: Whether to force a maximum value on the reconstruction pixels. +:type use_maxc: ``'yes'`` or ``'no'`` +:param maxc: Maximum value to use. +:type maxc: :class:`float` +:param returnData: If False, only return the ID of the reconstruction. +:type returnData: :class:`bool` +:param filterType: Which type of filter to use for filter-based methods. +:type filterType: :class:`string` +:param filterData: Optional filter data for filter-based methods. +:type filterData: :class:`numpy.ndarray` +:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the reconstruction. Otherwise, returns a tuple containing the ID of the reconstruction and reconstruction itself, in that order. + +""" + proj_geom = projector.projection_geometry(proj_id) + if isinstance(sinogram, np.ndarray): + sino_id = data2d.create('-sino', proj_geom, sinogram) + else: + sino_id = sinogram + vol_geom = projector.volume_geometry(proj_id) + recon_id = data2d.create('-vol', vol_geom, 0) + cfg = astra_dict(rec_type) + if not 'CUDA' in rec_type: + cfg['ProjectorId'] = proj_id + cfg['ProjectionDataId'] = sino_id + cfg['ReconstructionDataId'] = recon_id + cfg['options'] = {} + if use_mask == 'yes': + if isinstance(mask, np.ndarray): + mask_id = data2d.create('-vol', vol_geom, mask) + else: + mask_id = mask + cfg['options']['ReconstructionMaskId'] = mask_id + if not filterType == None: + cfg['FilterType'] = filterType + if not filterData == None: + if isinstance(filterData, np.ndarray): + nexpow = int( + pow(2, math.ceil(math.log(2 * proj_geom['DetectorCount'], 2)))) + filtSize = nexpow / 2 + 1 + filt_proj_geom = create_proj_geom( + 'parallel', 1.0, filtSize, proj_geom['ProjectionAngles']) + filt_id = data2d.create('-sino', filt_proj_geom, filterData) + else: + filt_id = filterData + cfg['FilterSinogramId'] = filt_id + cfg['options']['UseMinConstraint'] = use_minc + cfg['options']['MinConstraintValue'] = minc + cfg['options']['UseMaxConstraint'] = use_maxc + cfg['options']['MaxConstraintValue'] = maxc + cfg['options']['ProjectionOrder'] = 'random' + alg_id = algorithm.create(cfg) + algorithm.run(alg_id, iterations) + + algorithm.delete(alg_id) + + if isinstance(sinogram, np.ndarray): + data2d.delete(sino_id) + if use_mask == 'yes' and isinstance(mask, np.ndarray): + data2d.delete(mask_id) + if not filterData == None: + if isinstance(filterData, np.ndarray): + data2d.delete(filt_id) + if returnData: + return recon_id, data2d.get(recon_id) + else: + return recon_id + + +def create_projector(proj_type, proj_geom, vol_geom): + """Create a 2D projector. + +:param proj_type: Projector type, such as ``'line'``, ``'linear'``, ... +:type proj_type: :class:`string` +:param proj_geom: Projection geometry. +:type proj_geom: :class:`dict` +:param vol_geom: Volume geometry. +:type vol_geom: :class:`dict` +:returns: :class:`int` -- The ID of the projector. + +""" + if proj_type == 'blob': + raise Exception('Blob type not yet implemented') + cfg = astra_dict(proj_type) + cfg['ProjectionGeometry'] = proj_geom + cfg['VolumeGeometry'] = vol_geom + return projector.create(cfg) diff --git a/python/astra/data2d.py b/python/astra/data2d.py new file mode 100644 index 0000000..8c4be03 --- /dev/null +++ b/python/astra/data2d.py @@ -0,0 +1,120 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 . import data2d_c as d + +def clear(): + """Clear all 2D data objects.""" + return d.clear() + +def delete(ids): + """Delete a 2D object. + + :param ids: ID or list of ID's to delete. + :type ids: :class:`int` or :class:`list` + + """ + return d.delete(ids) + +def create(datatype, geometry, data=None): + """Create a 2D object. + + :param datatype: Data object type, '-vol' or '-sino'. + :type datatype: :class:`string` + :param geometry: Volume or projection geometry. + :type geometry: :class:`dict` + :param data: Data to fill the constructed object with, either a scalar or array. + :type data: :class:`float` or :class:`numpy.ndarray` + :returns: :class:`int` -- the ID of the constructed object. + + """ + return d.create(datatype,geometry,data) + +def store(i, data): + """Fill existing 2D object with data. + + :param i: ID of object to fill. + :type i: :class:`int` + :param data: Data to fill the object with, either a scalar or array. + :type data: :class:`float` or :class:`numpy.ndarray` + + """ + return d.store(i, data) + +def get_geometry(i): + """Get the geometry of a 2D object. + + :param i: ID of object. + :type i: :class:`int` + :returns: :class:`dict` -- The geometry of object with ID ``i``. + + """ + return d.get_geometry(i) + +def change_geometry(i, geom): + """Change the geometry of a 2D object. + + :param i: ID of object. + :type i: :class:`int` + :param geom: new geometry. + :type geom: :class:`dict` + + """ + return d.change_geometry(i, geom) + +def get(i): + """Get a 2D object. + + :param i: ID of object to get. + :type i: :class:`int` + :returns: :class:`numpy.ndarray` -- The object data. + + """ + return d.get(i) + +def get_shared(i): + """Get a 2D object with memory shared between the ASTRA toolbox and numpy array. + + :param i: ID of object to get. + :type i: :class:`int` + :returns: :class:`numpy.ndarray` -- The object data. + + """ + return d.get_shared(i) + + +def get_single(i): + """Get a 2D object in single precision. + + :param i: ID of object to get. + :type i: :class:`int` + :returns: :class:`numpy.ndarray` -- The object data. + + """ + return d.get_single(i) + +def info(): + """Print info on 2D objects in memory.""" + return d.info() diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx new file mode 100644 index 0000000..ec1b478 --- /dev/null +++ b/python/astra/data2d_c.pyx @@ -0,0 +1,241 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +import six + +cimport cython +from cython cimport view + +cimport PyData2DManager +from .PyData2DManager cimport CData2DManager + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument + +import numpy as np + +cimport numpy as np +np.import_array() + + +from .PyIncludes cimport * +cimport utils +from .utils import wrap_from_bytes + + +cdef CData2DManager * man2d = <CData2DManager * >PyData2DManager.getSingletonPtr() + + +def clear(): + man2d.clear() + + +def delete(ids): + try: + for i in ids: + man2d.remove(i) + except TypeError: + man2d.remove(ids) + + +def create(datatype, geometry, data=None): + cdef XMLDocument * xml + cdef Config cfg + cdef CVolumeGeometry2D * pGeometry + cdef CProjectionGeometry2D * ppGeometry + cdef CFloat32Data2D * pDataObject2D + if datatype == '-vol': + xml = utils.dict2XML(six.b('VolumeGeometry'), geometry) + cfg.self = xml.getRootNode() + pGeometry = new CVolumeGeometry2D() + if not pGeometry.initialize(cfg): + del xml + del pGeometry + raise Exception('Geometry class not initialized.') + pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry) + del xml + del pGeometry + elif datatype == '-sino': + xml = utils.dict2XML(six.b('ProjectionGeometry'), geometry) + cfg.self = xml.getRootNode() + tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type'))) + if (tpe == 'sparse_matrix'): + ppGeometry = <CProjectionGeometry2D * >new CSparseMatrixProjectionGeometry2D() + elif (tpe == 'fanflat'): + ppGeometry = <CProjectionGeometry2D * >new CFanFlatProjectionGeometry2D() + elif (tpe == 'fanflat_vec'): + ppGeometry = <CProjectionGeometry2D * >new CFanFlatVecProjectionGeometry2D() + else: + ppGeometry = <CProjectionGeometry2D * >new CParallelProjectionGeometry2D() + if not ppGeometry.initialize(cfg): + del xml + del ppGeometry + raise Exception('Geometry class not initialized.') + pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry) + del ppGeometry + del xml + else: + raise Exception("Invalid datatype. Please specify '-vol' or '-sino'.") + + if not pDataObject2D.isInitialized(): + del pDataObject2D + raise Exception("Couldn't initialize data object.") + + fillDataObject(pDataObject2D, data) + + return man2d.store(pDataObject2D) + +cdef fillDataObject(CFloat32Data2D * obj, data): + if data is None: + fillDataObjectScalar(obj, 0) + else: + if isinstance(data, np.ndarray): + fillDataObjectArray(obj, np.ascontiguousarray(data,dtype=np.float32)) + else: + fillDataObjectScalar(obj, np.float32(data)) + +cdef fillDataObjectScalar(CFloat32Data2D * obj, float s): + cdef int i + for i in range(obj.getSize()): + obj.getData()[i] = s + +@cython.boundscheck(False) +@cython.wraparound(False) +cdef fillDataObjectArray(CFloat32Data2D * obj, float [:,::1] data): + if (not data.shape[0] == obj.getHeight()) or (not data.shape[1] == obj.getWidth()): + raise Exception( + "The dimensions of the data do not match those specified in the geometry.") + cdef float [:,::1] cView = <float[:data.shape[0],:data.shape[1]]> obj.getData2D()[0] + cView[:] = data + +cdef CFloat32Data2D * getObject(i) except NULL: + cdef CFloat32Data2D * pDataObject = man2d.get(i) + if pDataObject == NULL: + raise Exception("Data object not found") + if not pDataObject.isInitialized(): + raise Exception("Data object not initialized properly.") + return pDataObject + + +def store(i, data): + cdef CFloat32Data2D * pDataObject = getObject(i) + fillDataObject(pDataObject, data) + + +def get_geometry(i): + cdef CFloat32Data2D * pDataObject = getObject(i) + cdef CFloat32ProjectionData2D * pDataObject2 + cdef CFloat32VolumeData2D * pDataObject3 + if pDataObject.getType() == PROJECTION: + pDataObject2 = <CFloat32ProjectionData2D * >pDataObject + geom = utils.createProjectionGeometryStruct(pDataObject2.getGeometry()) + elif pDataObject.getType() == VOLUME: + pDataObject3 = <CFloat32VolumeData2D * >pDataObject + geom = utils.createVolumeGeometryStruct(pDataObject3.getGeometry()) + else: + raise Exception("Not a known data object") + return geom + + +def change_geometry(i, geom): + cdef XMLDocument * xml + cdef Config cfg + cdef CVolumeGeometry2D * pGeometry + cdef CProjectionGeometry2D * ppGeometry + cdef CFloat32Data2D * pDataObject = getObject(i) + cdef CFloat32ProjectionData2D * pDataObject2 + cdef CFloat32VolumeData2D * pDataObject3 + if pDataObject.getType() == PROJECTION: + pDataObject2 = <CFloat32ProjectionData2D * >pDataObject + xml = utils.dict2XML(six.b('ProjectionGeometry'), geom) + cfg.self = xml.getRootNode() + tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type'))) + if (tpe == 'sparse_matrix'): + ppGeometry = <CProjectionGeometry2D * >new CSparseMatrixProjectionGeometry2D() + elif (tpe == 'fanflat'): + ppGeometry = <CProjectionGeometry2D * >new CFanFlatProjectionGeometry2D() + elif (tpe == 'fanflat_vec'): + ppGeometry = <CProjectionGeometry2D * >new CFanFlatVecProjectionGeometry2D() + else: + ppGeometry = <CProjectionGeometry2D * >new CParallelProjectionGeometry2D() + if not ppGeometry.initialize(cfg): + del xml + del ppGeometry + raise Exception('Geometry class not initialized.') + if (ppGeometry.getDetectorCount() != pDataObject2.getDetectorCount() or ppGeometry.getProjectionAngleCount() != pDataObject2.getAngleCount()): + del ppGeometry + del xml + raise Exception( + "The dimensions of the data do not match those specified in the geometry.") + pDataObject2.changeGeometry(ppGeometry) + del ppGeometry + del xml + elif pDataObject.getType() == VOLUME: + pDataObject3 = <CFloat32VolumeData2D * >pDataObject + xml = utils.dict2XML(six.b('VolumeGeometry'), geom) + cfg.self = xml.getRootNode() + pGeometry = new CVolumeGeometry2D() + if not pGeometry.initialize(cfg): + del xml + del pGeometry + raise Exception('Geometry class not initialized.') + if (pGeometry.getGridColCount() != pDataObject3.getWidth() or pGeometry.getGridRowCount() != pDataObject3.getHeight()): + del xml + del pGeometry + raise Exception( + 'The dimensions of the data do not match those specified in the geometry.') + pDataObject3.changeGeometry(pGeometry) + del xml + del pGeometry + else: + raise Exception("Not a known data object") + +@cython.boundscheck(False) +@cython.wraparound(False) +def get(i): + cdef CFloat32Data2D * pDataObject = getObject(i) + outArr = np.empty((pDataObject.getHeight(), pDataObject.getWidth()),dtype=np.float32,order='C') + cdef float [:,::1] mView = outArr + cdef float [:,::1] cView = <float[:outArr.shape[0],:outArr.shape[1]]> pDataObject.getData2D()[0] + mView[:] = cView + return outArr + +def get_shared(i): + cdef CFloat32Data2D * pDataObject = getObject(i) + cdef np.npy_intp shape[2] + shape[0] = <np.npy_intp> pDataObject.getHeight() + shape[1] = <np.npy_intp> pDataObject.getWidth() + return np.PyArray_SimpleNewFromData(2,shape,np.NPY_FLOAT32,<void *>pDataObject.getData2D()[0]) + + +def get_single(i): + raise Exception("Not yet implemented") + + +def info(): + six.print_(wrap_from_bytes(man2d.info())) diff --git a/python/astra/data3d.py b/python/astra/data3d.py new file mode 100644 index 0000000..33bde51 --- /dev/null +++ b/python/astra/data3d.py @@ -0,0 +1,108 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 . import data3d_c as d + +def create(datatype,geometry,data=None): + """Create a 3D object. + + :param datatype: Data object type, '-vol' or '-sino'. + :type datatype: :class:`string` + :param geometry: Volume or projection geometry. + :type geometry: :class:`dict` + :param data: Data to fill the constructed object with, either a scalar or array. + :type data: :class:`float` or :class:`numpy.ndarray` + :returns: :class:`int` -- the ID of the constructed object. + + """ + return d.create(datatype,geometry,data) + +def get(i): + """Get a 3D object. + + :param i: ID of object to get. + :type i: :class:`int` + :returns: :class:`numpy.ndarray` -- The object data. + + """ + return d.get(i) + +def get_shared(i): + """Get a 3D object with memory shared between the ASTRA toolbox and numpy array. + + :param i: ID of object to get. + :type i: :class:`int` + :returns: :class:`numpy.ndarray` -- The object data. + + """ + return d.get_shared(i) + +def get_single(i): + """Get a 3D object in single precision. + + :param i: ID of object to get. + :type i: :class:`int` + :returns: :class:`numpy.ndarray` -- The object data. + + """ + return g.get_single(i) + +def store(i,data): + """Fill existing 3D object with data. + + :param i: ID of object to fill. + :type i: :class:`int` + :param data: Data to fill the object with, either a scalar or array. + :type data: :class:`float` or :class:`numpy.ndarray` + + """ + return d.store(i,data) + +def dimensions(i): + """Get dimensions of a 3D object. + + :param i: ID of object. + :type i: :class:`int` + :returns: :class:`tuple` -- dimensions of object with ID ``i``. + + """ + return d.dimensions(i) + +def delete(ids): + """Delete a 2D object. + + :param ids: ID or list of ID's to delete. + :type ids: :class:`int` or :class:`list` + + """ + return d.delete(ids) + +def clear(): + """Clear all 3D data objects.""" + return d.clear() + +def info(): + """Print info on 3D objects in memory.""" + return d.info() diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx new file mode 100644 index 0000000..f821aaf --- /dev/null +++ b/python/astra/data3d_c.pyx @@ -0,0 +1,188 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +import six + +cimport cython + +cimport PyData3DManager +from .PyData3DManager cimport CData3DManager + +from .PyIncludes cimport * +import numpy as np + +cimport numpy as np +np.import_array() + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument + +cimport utils +from .utils import wrap_from_bytes + +cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr() + +cdef extern from *: + CFloat32Data3DMemory * dynamic_cast_mem "dynamic_cast<astra::CFloat32Data3DMemory*>" (CFloat32Data3D * ) except NULL + +def create(datatype,geometry,data=None): + cdef XMLDocument * xml + cdef Config cfg + cdef CVolumeGeometry3D * pGeometry + cdef CProjectionGeometry3D * ppGeometry + cdef CFloat32Data3DMemory * pDataObject3D + cdef CConeProjectionGeometry3D* pppGeometry + if datatype == '-vol': + xml = utils.dict2XML(six.b('VolumeGeometry'), geometry) + cfg.self = xml.getRootNode() + pGeometry = new CVolumeGeometry3D() + if not pGeometry.initialize(cfg): + del xml + del pGeometry + raise Exception('Geometry class not initialized.') + pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry) + del xml + del pGeometry + elif datatype == '-sino' or datatype == '-proj3d': + xml = utils.dict2XML(six.b('ProjectionGeometry'), geometry) + cfg.self = xml.getRootNode() + tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type'))) + if (tpe == "parallel3d"): + ppGeometry = <CProjectionGeometry3D*> new CParallelProjectionGeometry3D(); + elif (tpe == "parallel3d_vec"): + ppGeometry = <CProjectionGeometry3D*> new CParallelVecProjectionGeometry3D(); + elif (tpe == "cone"): + ppGeometry = <CProjectionGeometry3D*> new CConeProjectionGeometry3D(); + elif (tpe == "cone_vec"): + ppGeometry = <CProjectionGeometry3D*> new CConeVecProjectionGeometry3D(); + else: + raise Exception("Invalid geometry type.") + + if not ppGeometry.initialize(cfg): + del xml + del ppGeometry + raise Exception('Geometry class not initialized.') + pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry) + del ppGeometry + del xml + elif datatype == "-sinocone": + xml = utils.dict2XML(six.b('ProjectionGeometry'), geometry) + cfg.self = xml.getRootNode() + pppGeometry = new CConeProjectionGeometry3D() + if not pppGeometry.initialize(cfg): + del xml + del pppGeometry + raise Exception('Geometry class not initialized.') + pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry) + else: + raise Exception("Invalid datatype. Please specify '-vol' or '-proj3d'.") + + if not pDataObject3D.isInitialized(): + del pDataObject3D + raise Exception("Couldn't initialize data object.") + + fillDataObject(pDataObject3D, data) + + pDataObject3D.updateStatistics() + + return man3d.store(<CFloat32Data3D*>pDataObject3D) + + +cdef fillDataObject(CFloat32Data3DMemory * obj, data): + if data is None: + fillDataObjectScalar(obj, 0) + else: + if isinstance(data, np.ndarray): + fillDataObjectArray(obj, np.ascontiguousarray(data,dtype=np.float32)) + else: + fillDataObjectScalar(obj, np.float32(data)) + +cdef fillDataObjectScalar(CFloat32Data3DMemory * obj, float s): + cdef int i + for i in range(obj.getSize()): + obj.getData()[i] = s + +@cython.boundscheck(False) +@cython.wraparound(False) +cdef fillDataObjectArray(CFloat32Data3DMemory * obj, float [:,:,::1] data): + if (not data.shape[0] == obj.getDepth()) or (not data.shape[1] == obj.getHeight()) or (not data.shape[2] == obj.getWidth()): + raise Exception( + "The dimensions of the data do not match those specified in the geometry.") + cdef float [:,:,::1] cView = <float[:data.shape[0],:data.shape[1],:data.shape[2]]> obj.getData3D()[0][0] + cView[:] = data + +cdef CFloat32Data3D * getObject(i) except NULL: + cdef CFloat32Data3D * pDataObject = man3d.get(i) + if pDataObject == NULL: + raise Exception("Data object not found") + if not pDataObject.isInitialized(): + raise Exception("Data object not initialized properly.") + return pDataObject + +@cython.boundscheck(False) +@cython.wraparound(False) +def get(i): + cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i)) + outArr = np.empty((pDataObject.getDepth(),pDataObject.getHeight(), pDataObject.getWidth()),dtype=np.float32,order='C') + cdef float [:,:,::1] mView = outArr + cdef float [:,:,::1] cView = <float[:outArr.shape[0],:outArr.shape[1],:outArr.shape[2]]> pDataObject.getData3D()[0][0] + mView[:] = cView + return outArr + +def get_shared(i): + cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i)) + outArr = np.empty((pDataObject.getDepth(),pDataObject.getHeight(), pDataObject.getWidth()),dtype=np.float32,order='C') + cdef np.npy_intp shape[3] + shape[0] = <np.npy_intp> pDataObject.getDepth() + shape[1] = <np.npy_intp> pDataObject.getHeight() + shape[2] = <np.npy_intp> pDataObject.getWidth() + return np.PyArray_SimpleNewFromData(3,shape,np.NPY_FLOAT32,<void *>pDataObject.getData3D()[0][0]) + +def get_single(i): + raise Exception("Not yet implemented") + +def store(i,data): + cdef CFloat32Data3D * pDataObject = getObject(i) + fillDataObject(dynamic_cast_mem(pDataObject), data) + +def dimensions(i): + cdef CFloat32Data3D * pDataObject = getObject(i) + return (pDataObject.getWidth(),pDataObject.getHeight(),pDataObject.getDepth()) + +def delete(ids): + try: + for i in ids: + man3d.remove(i) + except TypeError: + man3d.remove(ids) + +def clear(): + man3d.clear() + +def info(): + six.print_(wrap_from_bytes(man3d.info())) diff --git a/python/astra/extrautils.pyx b/python/astra/extrautils.pyx new file mode 100644 index 0000000..998f5cb --- /dev/null +++ b/python/astra/extrautils.pyx @@ -0,0 +1,43 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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/>. +# +#----------------------------------------------------------------------- + +def clipCircle(img): + cdef int i,j + cdef double x2,y2,mid,bnd + cdef long sz,sz2 + sz = img.shape[0] + sz2 = sz*sz + bnd = sz2/4. + mid = (sz-1.)/2. + nDel=0 + for i in range(sz): + for j in range(sz): + x2 = (i-mid)*(i-mid) + y2 = (j-mid)*(j-mid) + if x2+y2>bnd: + img[i,j]=0 + nDel=nDel+1 + return nDel diff --git a/python/astra/functions.py b/python/astra/functions.py new file mode 100644 index 0000000..4025468 --- /dev/null +++ b/python/astra/functions.py @@ -0,0 +1,270 @@ +#----------------------------------------------------------------------- +# Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +# Author: Daniel M. Pelt +# Contact: D.M.Pelt@cwi.nl +# 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/>. +# +#----------------------------------------------------------------------- +"""Additional functions for PyAstraToolbox. + +.. moduleauthor:: Daniel M. Pelt <D.M.Pelt@cwi.nl> + + +""" + +from . import creators as ac +import numpy as np +from six.moves import range + +from . import data2d +from . import data3d +from . import projector +from . import algorithm + + + +def clear(): + """Clears all used memory of the ASTRA Toolbox. + + .. note:: + This is irreversible. + + """ + data2d.clear() + data3d.clear() + projector.clear() + algorithm.clear() + + +def data_op(op, data, scalar, gpu_core, mask=None): + """Perform data operation on data. + + :param op: Operation to perform. + :param data: Data to perform operation on. + :param scalar: Scalar argument to data operation. + :param gpu_core: GPU core to perform operation on. + :param mask: Optional mask. + + """ + + cfg = ac.astra_dict('DataOperation_CUDA') + cfg['Operation'] = op + cfg['Scalar'] = scalar + cfg['DataId'] = data + if not mask == None: + cfg['MaskId'] = mask + cfg['option']['GPUindex'] = gpu_core + alg_id = algorithm.create(cfg) + algorithm.run(alg_id) + algorithm.delete(alg_id) + + +def add_noise_to_sino(sinogram_in, I0, seed=None): + """Adds Poisson noise to a sinogram. + + :param sinogram_in: Sinogram to add noise to. + :type sinogram_in: :class:`numpy.ndarray` + :param I0: Background intensity. Lower values lead to higher noise. + :type I0: :class:`float` + :returns: :class:`numpy.ndarray` -- the sinogram with added noise. + + """ + + if not seed==None: + curstate = np.random.get_state() + np.random.seed(seed) + + if isinstance(sinogram_in, np.ndarray): + sinogramRaw = sinogram_in + else: + sinogramRaw = data2d.get(sinogram_in) + max_sinogramRaw = sinogramRaw.max() + sinogramRawScaled = sinogramRaw / max_sinogramRaw + # to detector count + sinogramCT = I0 * np.exp(-sinogramRawScaled) + # add poison noise + sinogramCT_C = np.zeros_like(sinogramCT) + for i in range(sinogramCT_C.shape[0]): + for j in range(sinogramCT_C.shape[1]): + sinogramCT_C[i, j] = np.random.poisson(sinogramCT[i, j]) + # to density + sinogramCT_D = sinogramCT_C / I0 + sinogram_out = -max_sinogramRaw * np.log(sinogramCT_D) + + if not isinstance(sinogram_in, np.ndarray): + at.data2d.store(sinogram_in, sinogram_out) + + if not seed==None: + np.random.set_state(curstate) + + return sinogram_out + +def move_vol_geom(geom, pos, is_relative=False): + """Moves center of volume geometry to new position. + + :param geom: Input volume geometry + :type geom: :class:`dict` + :param pos: Tuple (x,y[,z]) for new position, with the center of the image at (0,0[,0]) + :type pos: :class:`tuple` + :param is_relative: Whether new position is relative to the old position + :type is_relative: :class:`bool` + :returns: :class:`dict` -- Volume geometry with the new center + """ + + ret_geom = geom.copy() + ret_geom['option'] = geom['option'].copy() + + if not is_relative: + ret_geom['option']['WindowMinX'] = -geom['GridColCount']/2. + ret_geom['option']['WindowMaxX'] = geom['GridColCount']/2. + ret_geom['option']['WindowMinY'] = -geom['GridRowCount']/2. + ret_geom['option']['WindowMaxY'] = geom['GridRowCount']/2. + if len(pos)>2: + ret_geom['option']['WindowMinZ'] = -geom['GridSliceCount']/2. + ret_geom['option']['WindowMaxZ'] = geom['GridSliceCount']/2. + ret_geom['option']['WindowMinX'] += pos[0] + ret_geom['option']['WindowMaxX'] += pos[0] + ret_geom['option']['WindowMinY'] += pos[1] + ret_geom['option']['WindowMaxY'] += pos[1] + if len(pos)>2: + ret_geom['option']['WindowMinZ'] += pos[2] + ret_geom['option']['WindowMaxZ'] += pos[2] + return ret_geom + + +def geom_size(geom, dim=None): + """Returns the size of a volume or sinogram, based on the projection or volume geometry. + + :param geom: Geometry to calculate size from + :type geometry: :class:`dict` + :param dim: Optional axis index to return + :type dim: :class:`int` + """ + + if 'GridSliceCount' in geom: + # 3D Volume geometry? + s = (geom['GridSliceCount'], geom[ + 'GridRowCount'], geom['GridColCount']) + elif 'GridColCount' in geom: + # 2D Volume geometry? + s = (geom['GridRowCount'], geom['GridColCount']) + elif geom['type'] == 'parallel' or geom['type'] == 'fanflat': + s = (len(geom['ProjectionAngles']), geom['DetectorCount']) + elif geom['type'] == 'parallel3d' or geom['type'] == 'cone': + s = (geom['DetectorRowCount'], len( + geom['ProjectionAngles']), geom['DetectorColCount']) + elif geom['type'] == 'fanflat_vec': + s = (geom['Vectors'].shape[0], geom['DetectorCount']) + elif geom['type'] == 'parallel3d_vec' or geom['type'] == 'cone_vec': + s = (geom['DetectorRowCount'], geom[ + 'Vectors'].shape[0], geom['DetectorColCount']) + + if dim != None: + s = s[dim] + + return s + + +def geom_2vec(proj_geom): + """Returns a vector-based projection geometry from a basic projection geometry. + + :param proj_geom: Projection geometry to convert + :type proj_geom: :class:`dict` + """ + if proj_geom['type'] == 'fanflat': + angles = proj_geom['ProjectionAngles'] + vectors = np.zeros((len(angles), 6)) + for i in range(len(angles)): + + # source + vectors[i, 0] = np.sin(angles[i]) * proj_geom['DistanceOriginSource'] + vectors[i, 1] = -np.cos(angles[i]) * proj_geom['DistanceOriginSource'] + + # center of detector + vectors[i, 2] = -np.sin(angles[i]) * proj_geom['DistanceOriginDetector'] + vectors[i, 3] = np.cos(angles[i]) * proj_geom['DistanceOriginDetector'] + + # vector from detector pixel 0 to 1 + vectors[i, 4] = np.cos(angles[i]) * proj_geom['DetectorWidth'] + vectors[i, 5] = np.sin(angles[i]) * proj_geom['DetectorWidth'] + proj_geom_out = ac.create_proj_geom( + 'fanflat_vec', proj_geom['DetectorCount'], vectors) + + elif proj_geom['type'] == 'cone': + angles = proj_geom['ProjectionAngles'] + vectors = np.zeros((len(angles), 12)) + for i in range(len(angles)): + # source + vectors[i, 0] = np.sin(angles[i]) * proj_geom['DistanceOriginSource'] + vectors[i, 1] = -np.cos(angles[i]) * proj_geom['DistanceOriginSource'] + vectors[i, 2] = 0 + + # center of detector + vectors[i, 3] = -np.sin(angles[i]) * proj_geom['DistanceOriginDetector'] + vectors[i, 4] = np.cos(angles[i]) * proj_geom['DistanceOriginDetector'] + vectors[i, 5] = 0 + + # vector from detector pixel (0,0) to (0,1) + vectors[i, 6] = np.cos(angles[i]) * proj_geom['DetectorSpacingX'] + vectors[i, 7] = np.sin(angles[i]) * proj_geom['DetectorSpacingX'] + vectors[i, 8] = 0 + + # vector from detector pixel (0,0) to (1,0) + vectors[i, 9] = 0 + vectors[i, 10] = 0 + vectors[i, 11] = proj_geom['DetectorSpacingY'] + + proj_geom_out = ac.create_proj_geom( + 'cone_vec', proj_geom['DetectorRowCount'], proj_geom['DetectorColCount'], vectors) + + # PARALLEL + elif proj_geom['type'] == 'parallel3d': + angles = proj_geom['ProjectionAngles'] + vectors = np.zeros((len(angles), 12)) + for i in range(len(angles)): + + # ray direction + vectors[i, 0] = np.sin(angles[i]) + vectors[i, 1] = -np.cos(angles[i]) + vectors[i, 2] = 0 + + # center of detector + vectors[i, 3] = 0 + vectors[i, 4] = 0 + vectors[i, 5] = 0 + + # vector from detector pixel (0,0) to (0,1) + vectors[i, 6] = np.cos(angles[i]) * proj_geom['DetectorSpacingX'] + vectors[i, 7] = np.sin(angles[i]) * proj_geom['DetectorSpacingX'] + vectors[i, 8] = 0 + + # vector from detector pixel (0,0) to (1,0) + vectors[i, 9] = 0 + vectors[i, 10] = 0 + vectors[i, 11] = proj_geom['DetectorSpacingY'] + + proj_geom_out = ac.create_proj_geom( + 'parallel3d_vec', proj_geom['DetectorRowCount'], proj_geom['DetectorColCount'], vectors) + + else: + raise ValueError( + 'No suitable vector geometry found for type: ' + proj_geom['type']) + return proj_geom_out diff --git a/python/astra/matlab.py b/python/astra/matlab.py new file mode 100644 index 0000000..83b345d --- /dev/null +++ b/python/astra/matlab.py @@ -0,0 +1,112 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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/>. +# +#----------------------------------------------------------------------- +"""This module implements a MATLAB-like interface to the ASTRA Toolbox. + +Note that all functions are called with a :class:`string` as the first +argument, specifying the operation to perform. This un-pythonic way +is used to make transitioning from MATLAB code to Python code easier, as +the MATLAB interface uses the same type of method calling. + +After an initial ``import astra``, these functions can be accessed in the +``astra.m`` module. + +""" + +from . import astra_c +from . import data2d_c +from . import data3d_c +from . import projector_c +from . import algorithm_c +from . import matrix_c +import numpy as np + + +def astra(command, *args): + """MATLAB-like interface to the :mod:`astra.astra` module + + For example: + + ``astra.m.astra('use_cuda')`` -- Check if CUDA is enabled. + + """ + return getattr(astra_c, command)(*args) + + +def data2d(command, *args): + """MATLAB-like interface to the :mod:`astra.data2d` module + + For example: + + ``astra.m.data2d('create',type,geometry,data)`` -- Create a 2D object. + + """ + return getattr(data2d_c, command)(*args) + + +def data3d(command, *args): + """MATLAB-like interface to the :mod:`astra.data3d` module + + For example: + + ``astra.m.data3d('get',i)`` -- Get 3D object data. + + """ + return getattr(data3d_c, command)(*args) + + +def projector(command, *args): + """MATLAB-like interface to the :mod:`astra.projector` module + + For example: + + ``astra.m.projector('volume_geometry',i)`` -- Get volume geometry. + + """ + return getattr(projector_c, command)(*args) + + +def matrix(command, *args): + """MATLAB-like interface to the :mod:`astra.matrix` module + + For example: + + ``astra.m.matrix('delete',i)`` -- Delete a matrix. + + """ + return getattr(matrix_c, command)(*args) + + +def algorithm(command, *args): + """MATLAB-like interface to the :mod:`astra.algorithm` module + + For example: + + ``astra.m.algorithm('run',i,1000)`` -- Run an algorithm with 1000 iterations. + + """ + if command == 'iterate': + command = 'run' + return getattr(algorithm_c, command)(*args) diff --git a/python/astra/matrix.py b/python/astra/matrix.py new file mode 100644 index 0000000..27e4823 --- /dev/null +++ b/python/astra/matrix.py @@ -0,0 +1,86 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 . import matrix_c as m + +def delete(ids): + """Delete a matrix object. + + :param ids: ID or list of ID's to delete. + :type ids: :class:`int` or :class:`list` + + """ + return m.delete(ids) + +def clear(): + """Clear all matrix objects.""" + return m.clear() + +def create(data): + """Create matrix object with data. + + :param data: Data to fill the created object with. + :type data: :class:`scipy.sparse.csr_matrix` + :returns: :class:`int` -- the ID of the constructed object. + + """ + return m.create(data) + + +def store(i,data): + """Fill existing matrix object with data. + + :param i: ID of object to fill. + :type i: :class:`int` + :param data: Data to fill the object with. + :type data: :class:`scipy.sparse.csr_matrix` + + """ + return m.store(i,data) + +def get_size(i): + """Get matrix dimensions. + + :param i: ID of object. + :type i: :class:`int` + :returns: :class:`tuple` -- matrix dimensions. + """ + return m.get_size(i) + +def get(i): + """Get a matrix object. + + :param i: ID of object to get. + :type i: :class:`int` + :returns: :class:`scipy.sparse.csr_matrix` -- The object data. + + """ + return m.get(i) + +def info(): + """Print info on matrix objects in memory.""" + return m.info() + + diff --git a/python/astra/matrix_c.pyx b/python/astra/matrix_c.pyx new file mode 100644 index 0000000..b0d8bc4 --- /dev/null +++ b/python/astra/matrix_c.pyx @@ -0,0 +1,116 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +import six +from six.moves import range +import numpy as np +import scipy.sparse as ss + +from libcpp cimport bool + +cimport PyMatrixManager +from .PyMatrixManager cimport CMatrixManager +from .PyIncludes cimport * +from .utils import wrap_from_bytes + +cdef CMatrixManager * manM = <CMatrixManager * >PyMatrixManager.getSingletonPtr() + + +def delete(ids): + try: + for i in ids: + manM.remove(i) + except TypeError: + manM.remove(ids) + +def clear(): + manM.clear() + +cdef int csr_matrix_to_astra(data,CSparseMatrix *mat) except -1: + if isinstance(data,ss.csr_matrix): + csrD = data + else: + csrD = data.tocsr() + if not mat.isInitialized(): + raise Exception("Couldn't initialize data object.") + if csrD.nnz > mat.m_lSize or csrD.shape[0] > mat.m_iHeight: + raise Exception("Matrix too large to store in this object.") + for i in range(len(csrD.indptr)): + mat.m_plRowStarts[i] = csrD.indptr[i] + for i in range(csrD.nnz): + mat.m_piColIndices[i] = csrD.indices[i] + mat.m_pfValues[i] = csrD.data[i] + +cdef astra_to_csr_matrix(CSparseMatrix *mat): + indptr = np.zeros(mat.m_iHeight+1,dtype=np.int) + indices = np.zeros(mat.m_plRowStarts[mat.m_iHeight],dtype=np.int) + data = np.zeros(mat.m_plRowStarts[mat.m_iHeight]) + for i in range(mat.m_iHeight+1): + indptr[i] = mat.m_plRowStarts[i] + for i in range(mat.m_plRowStarts[mat.m_iHeight]): + indices[i] = mat.m_piColIndices[i] + data[i] = mat.m_pfValues[i] + return ss.csr_matrix((data,indices,indptr),shape=(mat.m_iHeight,mat.m_iWidth)) + +def create(data): + cdef CSparseMatrix* pMatrix + pMatrix = new CSparseMatrix(data.shape[0], data.shape[1], data.nnz) + if not pMatrix.isInitialized(): + del pMatrix + raise Exception("Couldn't initialize data object.") + try: + csr_matrix_to_astra(data,pMatrix) + except: + del pMatrix + raise Exception("Failed to create data object.") + + return manM.store(pMatrix) + +cdef CSparseMatrix * getObject(i) except NULL: + cdef CSparseMatrix * pDataObject = manM.get(i) + if pDataObject == NULL: + raise Exception("Data object not found") + if not pDataObject.isInitialized(): + raise Exception("Data object not initialized properly.") + return pDataObject + + +def store(i,data): + cdef CSparseMatrix * pDataObject = getObject(i) + csr_matrix_to_astra(data,pDataObject) + +def get_size(i): + cdef CSparseMatrix * pDataObject = getObject(i) + return (pDataObject.m_iHeight,pDataObject.m_iWidth) + +def get(i): + cdef CSparseMatrix * pDataObject = getObject(i) + return astra_to_csr_matrix(pDataObject) + +def info(): + six.print_(wrap_from_bytes(manM.info())) diff --git a/python/astra/projector.py b/python/astra/projector.py new file mode 100644 index 0000000..c916c52 --- /dev/null +++ b/python/astra/projector.py @@ -0,0 +1,100 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 . import projector_c as p + +def create(config): + """Create projector object. + + :param config: Projector options. + :type config: :class:`dict` + :returns: :class:`int` -- the ID of the constructed object. + + """ + return p.create(config) + + +def delete(ids): + """Delete a projector object. + + :param ids: ID or list of ID's to delete. + :type ids: :class:`int` or :class:`list` + + """ + return p.delete(ids) + + +def clear(): + """Clear all projector objects.""" + return p.clear() + + +def info(): + """Print info on projector objects in memory.""" + return p.info() + +def projection_geometry(i): + """Get projection geometry of a projector. + + :param i: ID of projector. + :type i: :class:`int` + :returns: :class:`dict` -- projection geometry + + """ + return p.projection_geometry(i) + + +def volume_geometry(i): + """Get volume geometry of a projector. + + :param i: ID of projector. + :type i: :class:`int` + :returns: :class:`dict` -- volume geometry + + """ + return p.volume_geometry(i) + + +def weights_single_ray(i, projection_index, detector_index): + return p.weights_single_ray(i, projection_index, detector_index) + + +def weights_projection(i, projection_index): + return p.weights_projection(i, projection_index) + + +def splat(i, row, col): + return p.splat(i, row, col) + + +def matrix(i): + """Get sparse matrix of a projector. + + :param i: ID of projector. + :type i: :class:`int` + :returns: :class:`int` -- ID of sparse matrix. + + """ + return p.matrix(i) diff --git a/python/astra/projector_c.pyx b/python/astra/projector_c.pyx new file mode 100644 index 0000000..978ca09 --- /dev/null +++ b/python/astra/projector_c.pyx @@ -0,0 +1,119 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +import six +from .PyIncludes cimport * + +cimport utils +from .utils import wrap_from_bytes + +cimport PyProjector2DFactory +from .PyProjector2DFactory cimport CProjector2DFactory + +cimport PyProjector2DManager +from .PyProjector2DManager cimport CProjector2DManager + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument + +cimport PyMatrixManager +from .PyMatrixManager cimport CMatrixManager + +cdef CProjector2DManager * manProj = <CProjector2DManager * >PyProjector2DManager.getSingletonPtr() +cdef CMatrixManager * manM = <CMatrixManager * >PyMatrixManager.getSingletonPtr() + + +def create(config): + cdef XMLDocument * xml = utils.dict2XML(six.b('Projector2D'), config) + cdef Config cfg + cdef CProjector2D * proj + cfg.self = xml.getRootNode() + proj = PyProjector2DFactory.getSingletonPtr().create(cfg) + if proj == NULL: + del xml + raise Exception("Error creating projector.") + del xml + return manProj.store(proj) + + +def delete(ids): + try: + for i in ids: + manProj.remove(i) + except TypeError: + manProj.remove(ids) + + +def clear(): + manProj.clear() + + +def info(): + six.print_(wrap_from_bytes(manProj.info())) + +cdef CProjector2D * getObject(i) except NULL: + cdef CProjector2D * proj = manProj.get(i) + if proj == NULL: + raise Exception("Projector not initialized.") + if not proj.isInitialized(): + raise Exception("Projector not initialized.") + return proj + + +def projection_geometry(i): + cdef CProjector2D * proj = getObject(i) + return utils.createProjectionGeometryStruct(proj.getProjectionGeometry()) + + +def volume_geometry(i): + cdef CProjector2D * proj = getObject(i) + return utils.createVolumeGeometryStruct(proj.getVolumeGeometry()) + + +def weights_single_ray(i, projection_index, detector_index): + raise Exception("Not yet implemented") + + +def weights_projection(i, projection_index): + raise Exception("Not yet implemented") + + +def splat(i, row, col): + raise Exception("Not yet implemented") + + +def matrix(i): + cdef CProjector2D * proj = getObject(i) + cdef CSparseMatrix * mat = proj.getMatrix() + if mat == NULL: + del mat + raise Exception("Data object not found") + if not mat.isInitialized(): + del mat + raise Exception("Data object not initialized properly.") + return manM.store(mat) diff --git a/python/astra/utils.pxd b/python/astra/utils.pxd new file mode 100644 index 0000000..55db9d3 --- /dev/null +++ b/python/astra/utils.pxd @@ -0,0 +1,37 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument +from .PyXMLDocument cimport XMLNode + +from .PyIncludes cimport * + +cdef XMLDocument *dict2XML(string rootname, dc) +cdef XML2dict(XMLDocument *) +cdef createVolumeGeometryStruct(CVolumeGeometry2D* geom) +cdef createProjectionGeometryStruct(CProjectionGeometry2D* geom) diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx new file mode 100644 index 0000000..53e84a9 --- /dev/null +++ b/python/astra/utils.pyx @@ -0,0 +1,260 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +import numpy as np +import six +from libcpp.string cimport string +from libcpp.list cimport list +from libcpp.vector cimport vector +from cython.operator cimport dereference as deref +from cpython.version cimport PY_MAJOR_VERSION + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument +from .PyXMLDocument cimport XMLNode +from .PyIncludes cimport * + + +cdef XMLDocument * dict2XML(string rootname, dc): + cdef XMLDocument * doc = PyXMLDocument.createDocument(rootname) + cdef XMLNode * node = doc.getRootNode() + try: + readDict(node, dc) + except: + six.print_('Error reading XML') + del doc + doc = NULL + finally: + del node + return doc + +def convert_item(item): + if isinstance(item, six.string_types): + return item.encode('ascii') + + if type(item) is not dict: + return item + + out_dict = {} + for k in item: + out_dict[convert_item(k)] = convert_item(item[k]) + return out_dict + + +def wrap_to_bytes(value): + if isinstance(value, six.binary_type): + return value + s = str(value) + if PY_MAJOR_VERSION == 3: + s = s.encode('ascii') + return s + + +def wrap_from_bytes(value): + s = value + if PY_MAJOR_VERSION == 3: + s = s.decode('ascii') + return s + + +cdef void readDict(XMLNode * root, _dc): + cdef XMLNode * listbase + cdef XMLNode * itm + cdef int i + cdef int j + + dc = convert_item(_dc) + for item in dc: + val = dc[item] + if isinstance(val, np.ndarray): + if val.size == 0: + break + listbase = root.addChildNode(item) + listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size) + index = 0 + if val.ndim == 2: + for i in range(val.shape[0]): + for j in range(val.shape[1]): + itm = listbase.addChildNode(six.b('ListItem')) + itm.addAttribute(< string > six.b('index'), < float32 > index) + itm.addAttribute( < string > six.b('value'), < float32 > val[i, j]) + index += 1 + del itm + elif val.ndim == 1: + for i in range(val.shape[0]): + itm = listbase.addChildNode(six.b('ListItem')) + itm.addAttribute(< string > six.b('index'), < float32 > index) + itm.addAttribute(< string > six.b('value'), < float32 > val[i]) + index += 1 + del itm + else: + raise Exception("Only 1 or 2 dimensions are allowed") + del listbase + elif isinstance(val, dict): + if item == six.b('option') or item == six.b('options') or item == six.b('Option') or item == six.b('Options'): + readOptions(root, val) + else: + itm = root.addChildNode(item) + readDict(itm, val) + del itm + else: + if item == six.b('type'): + root.addAttribute(< string > six.b('type'), <string> wrap_to_bytes(val)) + else: + itm = root.addChildNode(item, wrap_to_bytes(val)) + del itm + +cdef void readOptions(XMLNode * node, dc): + cdef XMLNode * listbase + cdef XMLNode * itm + cdef int i + cdef int j + for item in dc: + val = dc[item] + if node.hasOption(item): + raise Exception('Duplicate Option: %s' % item) + if isinstance(val, np.ndarray): + if val.size == 0: + break + listbase = node.addChildNode(six.b('Option')) + listbase.addAttribute(< string > six.b('key'), < string > item) + listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size) + index = 0 + if val.ndim == 2: + for i in range(val.shape[0]): + for j in range(val.shape[1]): + itm = listbase.addChildNode(six.b('ListItem')) + itm.addAttribute(< string > six.b('index'), < float32 > index) + itm.addAttribute( < string > six.b('value'), < float32 > val[i, j]) + index += 1 + del itm + elif val.ndim == 1: + for i in range(val.shape[0]): + itm = listbase.addChildNode(six.b('ListItem')) + itm.addAttribute(< string > six.b('index'), < float32 > index) + itm.addAttribute(< string > six.b('value'), < float32 > val[i]) + index += 1 + del itm + else: + raise Exception("Only 1 or 2 dimensions are allowed") + del listbase + else: + node.addOption(item, wrap_to_bytes(val)) + +cdef vectorToNumpy(vector[float32] inp): + cdef int i + cdef int sz = inp.size() + ret = np.empty(sz) + for i in range(sz): + ret[i] = inp[i] + return ret + +cdef XMLNode2dict(XMLNode * node): + cdef XMLNode * subnode + cdef list[XMLNode * ] nodes + cdef list[XMLNode * ].iterator it + dct = {} + if node.hasAttribute(six.b('type')): + dct['type'] = node.getAttribute(six.b('type')) + nodes = node.getNodes() + it = nodes.begin() + while it != nodes.end(): + subnode = deref(it) + if subnode.hasAttribute(six.b('listsize')): + dct[subnode.getName( + )] = vectorToNumpy(subnode.getContentNumericalArray()) + else: + dct[subnode.getName()] = subnode.getContent() + del subnode + return dct + +cdef XML2dict(XMLDocument * xml): + cdef XMLNode * node = xml.getRootNode() + dct = XMLNode2dict(node) + del node; + return dct; + +cdef createProjectionGeometryStruct(CProjectionGeometry2D * geom): + cdef int i + cdef CFanFlatVecProjectionGeometry2D * fanvecGeom + # cdef SFanProjection* p + dct = {} + dct['DetectorCount'] = geom.getDetectorCount() + if not geom.isOfType(< string > six.b('fanflat_vec')): + dct['DetectorWidth'] = geom.getDetectorWidth() + angles = np.empty(geom.getProjectionAngleCount()) + for i in range(geom.getProjectionAngleCount()): + angles[i] = geom.getProjectionAngle(i) + dct['ProjectionAngles'] = angles + else: + raise Exception("Not yet implemented") + # fanvecGeom = <CFanFlatVecProjectionGeometry2D*> geom + # vecs = np.empty(fanvecGeom.getProjectionAngleCount()*6) + # iDetCount = pVecGeom.getDetectorCount() + # for i in range(fanvecGeom.getProjectionAngleCount()): + # p = &fanvecGeom.getProjectionVectors()[i]; + # out[6*i + 0] = p.fSrcX + # out[6*i + 1] = p.fSrcY + # out[6*i + 2] = p.fDetSX + 0.5f*iDetCount*p.fDetUX + # out[6*i + 3] = p.fDetSY + 0.5f*iDetCount*p.fDetUY + # out[6*i + 4] = p.fDetUX + # out[6*i + 5] = p.fDetUY + # dct['Vectors'] = vecs + if (geom.isOfType(< string > six.b('parallel'))): + dct["type"] = "parallel" + elif (geom.isOfType(< string > six.b('fanflat'))): + raise Exception("Not yet implemented") + # astra::CFanFlatProjectionGeometry2D* pFanFlatGeom = dynamic_cast<astra::CFanFlatProjectionGeometry2D*>(_pProjGeom) + # mGeometryInfo["DistanceOriginSource"] = mxCreateDoubleScalar(pFanFlatGeom->getOriginSourceDistance()) + # mGeometryInfo["DistanceOriginDetector"] = + # mxCreateDoubleScalar(pFanFlatGeom->getOriginDetectorDistance()) + dct["type"] = "fanflat" + elif (geom.isOfType(< string > six.b('sparse_matrix'))): + raise Exception("Not yet implemented") + # astra::CSparseMatrixProjectionGeometry2D* pSparseMatrixGeom = + # dynamic_cast<astra::CSparseMatrixProjectionGeometry2D*>(_pProjGeom); + dct["type"] = "sparse_matrix" + # dct["MatrixID"] = + # mxCreateDoubleScalar(CMatrixManager::getSingleton().getIndex(pSparseMatrixGeom->getMatrix())) + elif(geom.isOfType(< string > six.b('fanflat_vec'))): + dct["type"] = "fanflat_vec" + return dct + +cdef createVolumeGeometryStruct(CVolumeGeometry2D * geom): + mGeometryInfo = {} + mGeometryInfo["GridColCount"] = geom.getGridColCount() + mGeometryInfo["GridRowCount"] = geom.getGridRowCount() + + mGeometryOptions = {} + mGeometryOptions["WindowMinX"] = geom.getWindowMinX() + mGeometryOptions["WindowMaxX"] = geom.getWindowMaxX() + mGeometryOptions["WindowMinY"] = geom.getWindowMinY() + mGeometryOptions["WindowMaxY"] = geom.getWindowMaxY() + + mGeometryInfo["option"] = mGeometryOptions + return mGeometryInfo diff --git a/python/builder.py b/python/builder.py new file mode 100644 index 0000000..bdfd092 --- /dev/null +++ b/python/builder.py @@ -0,0 +1,70 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#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 sys +import os +import numpy as np + +from distutils.version import LooseVersion +from distutils.core import setup +from distutils.extension import Extension + +from Cython.Distutils import build_ext +from Cython.Build import cythonize +import Cython +if LooseVersion(Cython.__version__)<LooseVersion('0.13'): raise ImportError("Cython version should be at least 0.13") +usecuda=False +try: + if os.environ['CPPFLAGS'].find('-DASTRA_CUDA')!=-1: + usecuda=True +except KeyError: + pass +cfg = open('astra/config.pxi','w') +cfg.write('DEF HAVE_CUDA=' + str(usecuda) + "\n") +cfg.close() + +cmdclass = { } +ext_modules = [ ] + +language_level = 3 if int(sys.version[0]) > 2 else 2 +ext_modules = cythonize("astra/*.pyx", language_level=language_level) +cmdclass = { 'build_ext': build_ext } + +setup (name = 'PyASTRAToolbox', + version = '1.6', + description = 'Python interface to the ASTRA-Toolbox', + author='D.M. Pelt', + author_email='D.M.Pelt@cwi.nl', + url='http://dmpelt.github.io/pyastratoolbox/', + #ext_package='astra', + #ext_modules = cythonize(Extension("astra/*.pyx",extra_compile_args=extra_compile_args,extra_linker_args=extra_compile_args)), + license='GPLv3', + ext_modules = ext_modules, + include_dirs=[np.get_include()], + cmdclass = cmdclass, + #ext_modules = [Extension("astra","astra/astra.pyx")], + packages=['astra'], + requires=["numpy"], + ) diff --git a/python/doc b/python/doc new file mode 120000 index 0000000..3705b55 --- /dev/null +++ b/python/doc @@ -0,0 +1 @@ +docSRC/_build/html
\ No newline at end of file diff --git a/python/docSRC/ASTRAProjector.rst b/python/docSRC/ASTRAProjector.rst new file mode 100644 index 0000000..1c267e3 --- /dev/null +++ b/python/docSRC/ASTRAProjector.rst @@ -0,0 +1,8 @@ +Helper class: the :mod:`ASTRAProjector` module +============================================== + +.. automodule:: astra.ASTRAProjector + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/Makefile b/python/docSRC/Makefile new file mode 100644 index 0000000..a005bab --- /dev/null +++ b/python/docSRC/Makefile @@ -0,0 +1,153 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make <target>' where <target> is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + -rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. 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If you use many repeated operations, directly +using the PyAstraToolbox methods directly is faster.</p> +<p>You can use this class as an abstracted weight matrix <span class="math">\(W\)</span>: multiplying an instance +<tt class="docutils literal"><span class="pre">proj</span></tt> of this class by an image results in a forward projection of the image, and multiplying +<tt class="docutils literal"><span class="pre">proj.T</span></tt> by a sinogram results in a backprojection of the sinogram:</p> +<div class="highlight-python"><div class="highlight"><pre><span class="n">proj</span> <span class="o">=</span> <span class="n">ASTRAProjector2D</span><span class="p">(</span><span class="o">...</span><span class="p">)</span> +<span class="n">fp</span> <span class="o">=</span> <span class="n">proj</span><span class="o">*</span><span class="n">image</span> +<span class="n">bp</span> <span class="o">=</span> <span class="n">proj</span><span class="o">.</span><span class="n">T</span><span class="o">*</span><span class="n">sinogram</span> +</pre></div> +</div> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>proj_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – The projection geometry.</li> +<li><strong>vol_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – The volume geometry.</li> +<li><strong>proj_type</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Projector type, such as <tt class="docutils literal"><span class="pre">'line'</span></tt>, <tt class="docutils literal"><span class="pre">'linear'</span></tt>, ...</li> +<li><strong>useCUDA</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If <tt class="docutils literal"><span class="pre">True</span></tt>, use CUDA for calculations, when possible.</li> +</ul> +</td> +</tr> +</tbody> +</table> +<dl class="method"> +<dt id="astra.ASTRAProjector.ASTRAProjector2D.backProject"> +<tt class="descname">backProject</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="_modules/astra/ASTRAProjector.html#ASTRAProjector2D.backProject"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.ASTRAProjector.ASTRAProjector2D.backProject" title="Permalink to this definition">¶</a></dt> +<dd><p>Backproject a sinogram.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – The sinogram data or ID.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The backprojection.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="method"> +<dt id="astra.ASTRAProjector.ASTRAProjector2D.forwardProject"> +<tt class="descname">forwardProject</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="_modules/astra/ASTRAProjector.html#ASTRAProjector2D.forwardProject"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.ASTRAProjector.ASTRAProjector2D.forwardProject" title="Permalink to this definition">¶</a></dt> +<dd><p>Forward project an image.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – The image data or ID.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The forward projection.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="method"> +<dt id="astra.ASTRAProjector.ASTRAProjector2D.reconstruct"> +<tt class="descname">reconstruct</tt><big>(</big><em>data</em>, <em>method</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="_modules/astra/ASTRAProjector.html#ASTRAProjector2D.reconstruct"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.ASTRAProjector.ASTRAProjector2D.reconstruct" title="Permalink to this definition">¶</a></dt> +<dd><p>Reconstruct an image from a sinogram.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – The sinogram data or ID.</li> +<li><strong>method</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Name of the reconstruction algorithm.</li> +<li><strong>kwargs</strong> – Additional named parameters to pass to <a class="reference internal" href="creators.html#astra.creators.create_reconstruction" title="astra.creators.create_reconstruction"><tt class="xref py py-func docutils literal"><span class="pre">astra.creators.create_reconstruction()</span></tt></a>.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The reconstruction.</p> +</td> +</tr> +</tbody> +</table> +<p>Example of a SIRT reconstruction using CUDA:</p> +<div class="highlight-python"><div class="highlight"><pre><span class="n">proj</span> <span class="o">=</span> <span class="n">ASTRAProjector2D</span><span class="p">(</span><span class="o">...</span><span class="p">)</span> +<span class="n">rec</span> <span class="o">=</span> <span class="n">proj</span><span class="o">.</span><span class="n">reconstruct</span><span class="p">(</span><span class="n">sinogram</span><span class="p">,</span><span class="s">'SIRT_CUDA'</span><span class="p">,</span><span class="n">iterations</span><span class="o">=</span><span class="mi">1000</span><span class="p">)</span> +</pre></div> +</div> +</dd></dl> + +</dd></dl> + +<dl class="class"> +<dt id="astra.ASTRAProjector.ASTRAProjector2DTranspose"> +<em class="property">class </em><tt class="descclassname">astra.ASTRAProjector.</tt><tt class="descname">ASTRAProjector2DTranspose</tt><big>(</big><em>parentProj</em><big>)</big><a class="reference internal" href="_modules/astra/ASTRAProjector.html#ASTRAProjector2DTranspose"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.ASTRAProjector.ASTRAProjector2DTranspose" title="Permalink to this definition">¶</a></dt> +<dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">builtins.object</span></tt></p> +<p>Implements the <tt class="docutils literal"><span class="pre">proj.T</span></tt> functionality.</p> +<p>Do not use directly, since it can be accessed as member <tt class="docutils literal"><span class="pre">.T</span></tt> of +an <a class="reference internal" href="#astra.ASTRAProjector.ASTRAProjector2D" title="astra.ASTRAProjector.ASTRAProjector2D"><tt class="xref py py-class docutils literal"><span class="pre">ASTRAProjector2D</span></tt></a> object.</p> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div 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\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/ASTRAProjector.html b/python/docSRC/_build/html/_modules/astra/ASTRAProjector.html new file mode 100644 index 0000000..08789f2 --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/ASTRAProjector.html @@ -0,0 +1,243 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.ASTRAProjector — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.ASTRAProjector</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> + +<span class="kn">import</span> <span class="nn">math</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">creators</span> <span class="k">as</span> <span class="n">ac</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data2d</span> + + +<div class="viewcode-block" id="ASTRAProjector2DTranspose"><a class="viewcode-back" href="../../ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2DTranspose">[docs]</a><span class="k">class</span> <span class="nc">ASTRAProjector2DTranspose</span><span class="p">():</span> + <span class="sd">"""Implements the ``proj.T`` functionality.</span> + +<span class="sd"> Do not use directly, since it can be accessed as member ``.T`` of</span> +<span class="sd"> an :class:`ASTRAProjector2D` object.</span> + +<span class="sd"> """</span> + <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parentProj</span><span class="p">):</span> + <span class="bp">self</span><span class="o">.</span><span class="n">parentProj</span> <span class="o">=</span> <span class="n">parentProj</span> + + <span class="k">def</span> <span class="nf">__mul__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span> + <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">parentProj</span><span class="o">.</span><span class="n">backProject</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="ASTRAProjector2D"><a class="viewcode-back" href="../../ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D">[docs]</a><span class="k">class</span> <span class="nc">ASTRAProjector2D</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> + <span class="sd">"""Helps with various common ASTRA Toolbox 2D operations.</span> + +<span class="sd"> This class can perform several often used toolbox operations, such as:</span> + +<span class="sd"> * Forward projecting</span> +<span class="sd"> * Back projecting</span> +<span class="sd"> * Reconstructing</span> + +<span class="sd"> Note that this class has a some computational overhead, because it</span> +<span class="sd"> copies a lot of data. If you use many repeated operations, directly</span> +<span class="sd"> using the PyAstraToolbox methods directly is faster.</span> + +<span class="sd"> You can use this class as an abstracted weight matrix :math:`W`: multiplying an instance</span> +<span class="sd"> ``proj`` of this class by an image results in a forward projection of the image, and multiplying</span> +<span class="sd"> ``proj.T`` by a sinogram results in a backprojection of the sinogram::</span> + +<span class="sd"> proj = ASTRAProjector2D(...)</span> +<span class="sd"> fp = proj*image</span> +<span class="sd"> bp = proj.T*sinogram</span> + +<span class="sd"> :param proj_geom: The projection geometry.</span> +<span class="sd"> :type proj_geom: :class:`dict`</span> +<span class="sd"> :param vol_geom: The volume geometry.</span> +<span class="sd"> :type vol_geom: :class:`dict`</span> +<span class="sd"> :param proj_type: Projector type, such as ``'line'``, ``'linear'``, ...</span> +<span class="sd"> :type proj_type: :class:`string`</span> +<span class="sd"> :param useCUDA: If ``True``, use CUDA for calculations, when possible.</span> +<span class="sd"> :type useCUDA: :class:`bool`</span> +<span class="sd"> """</span> + + <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="n">proj_type</span><span class="p">,</span> <span class="n">useCUDA</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span> + <span class="bp">self</span><span class="o">.</span><span class="n">vol_geom</span> <span class="o">=</span> <span class="n">vol_geom</span> + <span class="bp">self</span><span class="o">.</span><span class="n">recSize</span> <span class="o">=</span> <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span> + <span class="bp">self</span><span class="o">.</span><span class="n">angles</span> <span class="o">=</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'ProjectionAngles'</span><span class="p">]</span> + <span class="bp">self</span><span class="o">.</span><span class="n">nDet</span> <span class="o">=</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorCount'</span><span class="p">]</span> + <span class="n">nexpow</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">pow</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="n">math</span><span class="o">.</span><span class="n">ceil</span><span class="p">(</span><span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">nDet</span><span class="p">,</span> <span class="mi">2</span><span class="p">))))</span> + <span class="bp">self</span><span class="o">.</span><span class="n">filterSize</span> <span class="o">=</span> <span class="n">nexpow</span> <span class="o">/</span> <span class="mi">2</span> <span class="o">+</span> <span class="mi">1</span> + <span class="bp">self</span><span class="o">.</span><span class="n">nProj</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">angles</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="bp">self</span><span class="o">.</span><span class="n">proj_geom</span> <span class="o">=</span> <span class="n">proj_geom</span> + <span class="bp">self</span><span class="o">.</span><span class="n">proj_id</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">create_projector</span><span class="p">(</span><span class="n">proj_type</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">)</span> + <span class="bp">self</span><span class="o">.</span><span class="n">useCUDA</span> <span class="o">=</span> <span class="n">useCUDA</span> + <span class="bp">self</span><span class="o">.</span><span class="n">T</span> <span class="o">=</span> <span class="n">ASTRAProjector2DTranspose</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> + +<div class="viewcode-block" id="ASTRAProjector2D.backProject"><a class="viewcode-back" href="../../ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D.backProject">[docs]</a> <span class="k">def</span> <span class="nf">backProject</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span> + <span class="sd">"""Backproject a sinogram.</span> + +<span class="sd"> :param data: The sinogram data or ID.</span> +<span class="sd"> :type data: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The backprojection.</span> + +<span class="sd"> """</span> + <span class="n">vol_id</span><span class="p">,</span> <span class="n">vol</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">create_backprojection</span><span class="p">(</span> + <span class="n">data</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">proj_id</span><span class="p">,</span> <span class="n">useCUDA</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">useCUDA</span><span class="p">,</span> <span class="n">returnData</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">vol_id</span><span class="p">)</span> + <span class="k">return</span> <span class="n">vol</span> +</div> +<div class="viewcode-block" id="ASTRAProjector2D.forwardProject"><a class="viewcode-back" href="../../ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D.forwardProject">[docs]</a> <span class="k">def</span> <span class="nf">forwardProject</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span> + <span class="sd">"""Forward project an image.</span> + +<span class="sd"> :param data: The image data or ID.</span> +<span class="sd"> :type data: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The forward projection.</span> + +<span class="sd"> """</span> + <span class="n">sin_id</span><span class="p">,</span> <span class="n">sino</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">create_sino</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">proj_id</span><span class="p">,</span> <span class="n">useCUDA</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">useCUDA</span><span class="p">,</span> <span class="n">returnData</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">sin_id</span><span class="p">)</span> + <span class="k">return</span> <span class="n">sino</span> +</div> +<div class="viewcode-block" id="ASTRAProjector2D.reconstruct"><a class="viewcode-back" href="../../ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D.reconstruct">[docs]</a> <span class="k">def</span> <span class="nf">reconstruct</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">method</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> + <span class="sd">"""Reconstruct an image from a sinogram.</span> + +<span class="sd"> :param data: The sinogram data or ID.</span> +<span class="sd"> :type data: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd"> :param method: Name of the reconstruction algorithm.</span> +<span class="sd"> :type method: :class:`string`</span> +<span class="sd"> :param kwargs: Additional named parameters to pass to :func:`astra.creators.create_reconstruction`.</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The reconstruction.</span> + +<span class="sd"> Example of a SIRT reconstruction using CUDA::</span> + +<span class="sd"> proj = ASTRAProjector2D(...)</span> +<span class="sd"> rec = proj.reconstruct(sinogram,'SIRT_CUDA',iterations=1000)</span> + +<span class="sd"> """</span> + <span class="n">kwargs</span><span class="p">[</span><span class="s">'returnData'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">True</span> + <span class="n">rec_id</span><span class="p">,</span> <span class="n">rec</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">create_reconstruction</span><span class="p">(</span> + <span class="n">method</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">proj_id</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">rec_id</span><span class="p">)</span> + <span class="k">return</span> <span class="n">rec</span> +</div> + <span class="k">def</span> <span class="nf">__mul__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span> + <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">forwardProject</span><span class="p">(</span><span class="n">data</span><span class="p">)</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" >Module code</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + 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\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/algorithm.html b/python/docSRC/_build/html/_modules/astra/algorithm.html new file mode 100644 index 0000000..39816fd --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/algorithm.html @@ -0,0 +1,181 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.algorithm — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.algorithm</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> + +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">algorithm_c</span> <span class="k">as</span> <span class="n">a</span> + +<div class="viewcode-block" id="create"><a class="viewcode-back" href="../../algorithm.html#astra.algorithm.create">[docs]</a><span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="n">config</span><span class="p">):</span> + <span class="sd">"""Create algorithm object.</span> +<span class="sd"> </span> +<span class="sd"> :param config: Algorithm options.</span> +<span class="sd"> :type config: :class:`dict`</span> +<span class="sd"> :returns: :class:`int` -- the ID of the constructed object.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">config</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="run"><a class="viewcode-back" href="../../algorithm.html#astra.algorithm.run">[docs]</a><span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">iterations</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span> + <span class="sd">"""Run an algorithm.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :param iterations: Number of iterations to run.</span> +<span class="sd"> :type iterations: :class:`int`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">iterations</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="get_res_norm"><a class="viewcode-back" href="../../algorithm.html#astra.algorithm.get_res_norm">[docs]</a><span class="k">def</span> <span class="nf">get_res_norm</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get residual norm of algorithm.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`float` -- The residual norm.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">get_res_norm</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> + </div> +<div class="viewcode-block" id="delete"><a class="viewcode-back" href="../../algorithm.html#astra.algorithm.delete">[docs]</a><span class="k">def</span> <span class="nf">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">):</span> + <span class="sd">"""Delete a matrix object.</span> +<span class="sd"> </span> +<span class="sd"> :param ids: ID or list of ID's to delete.</span> +<span class="sd"> :type ids: :class:`int` or :class:`list`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="clear"><a class="viewcode-back" href="../../algorithm.html#astra.algorithm.clear">[docs]</a><span class="k">def</span> <span class="nf">clear</span><span class="p">():</span> + <span class="sd">"""Clear all matrix objects."""</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> +</div> +<div class="viewcode-block" id="info"><a class="viewcode-back" href="../../algorithm.html#astra.algorithm.info">[docs]</a><span class="k">def</span> <span class="nf">info</span><span class="p">():</span> + <span class="sd">"""Print info on matrix objects in memory."""</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">info</span><span class="p">()</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" >Module code</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/astra.html b/python/docSRC/_build/html/_modules/astra/astra.html new file mode 100644 index 0000000..53fac8e --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/astra.html @@ -0,0 +1,163 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.astra — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.astra</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> + +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">astra_c</span> <span class="k">as</span> <span class="n">a</span> + +<div class="viewcode-block" id="credits"><a class="viewcode-back" href="../../astra.html#astra.astra.credits">[docs]</a><span class="k">def</span> <span class="nf">credits</span><span class="p">():</span> + <span class="sd">"""Print credits of the ASTRA Toolbox."""</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">credits</span><span class="p">()</span> + +</div> +<div class="viewcode-block" id="use_cuda"><a class="viewcode-back" href="../../astra.html#astra.astra.use_cuda">[docs]</a><span class="k">def</span> <span class="nf">use_cuda</span><span class="p">():</span> + <span class="sd">"""Test if CUDA is enabled.</span> +<span class="sd"> </span> +<span class="sd"> :returns: :class:`bool` -- ``True`` if CUDA is enabled.</span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">use_cuda</span><span class="p">()</span> + +</div> +<div class="viewcode-block" id="version"><a class="viewcode-back" href="../../astra.html#astra.astra.version">[docs]</a><span class="k">def</span> <span class="nf">version</span><span class="p">(</span><span class="n">printToScreen</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span> + <span class="sd">"""Check version of the ASTRA Toolbox.</span> +<span class="sd"> </span> +<span class="sd"> :param printToScreen: If ``True``, print version string. If ``False``, return version integer.</span> +<span class="sd"> :type printToScreen: :class:`bool`</span> +<span class="sd"> :returns: :class:`string` or :class:`int` -- The version string or integer.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">version</span><span class="p">(</span><span class="n">printToScreen</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="set_gpu_index"><a class="viewcode-back" href="../../astra.html#astra.astra.set_gpu_index">[docs]</a><span class="k">def</span> <span class="nf">set_gpu_index</span><span class="p">(</span><span class="n">idx</span><span class="p">):</span> + <span class="sd">"""Set default GPU index to use.</span> +<span class="sd"> </span> +<span class="sd"> :param idx: GPU index</span> +<span class="sd"> :type idx: :class:`int`</span> +<span class="sd"> """</span> + <span class="n">a</span><span class="o">.</span><span class="n">set_gpu_index</span><span class="p">(</span><span class="n">idx</span><span class="p">)</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" >Module code</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/creators.html b/python/docSRC/_build/html/_modules/astra/creators.html new file mode 100644 index 0000000..c43978a --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/creators.html @@ -0,0 +1,668 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.creators — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.creators</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> + +<span class="kn">import</span> <span class="nn">six</span> +<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span> +<span class="kn">import</span> <span class="nn">math</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data2d</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data3d</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">projector</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">algorithm</span> + +<div class="viewcode-block" id="astra_dict"><a class="viewcode-back" href="../../creators.html#astra.creators.astra_dict">[docs]</a><span class="k">def</span> <span class="nf">astra_dict</span><span class="p">(</span><span class="n">intype</span><span class="p">):</span> + <span class="sd">"""Creates a dict to use with the ASTRA Toolbox.</span> +<span class="sd"> </span> +<span class="sd"> :param intype: Type of the ASTRA object.</span> +<span class="sd"> :type intype: :class:`string`</span> +<span class="sd"> :returns: :class:`dict` -- An ASTRA dict of type ``intype``.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">if</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'SIRT_CUDA2'</span><span class="p">:</span> + <span class="n">intype</span> <span class="o">=</span> <span class="s">'SIRT_CUDA'</span> + <span class="n">six</span><span class="o">.</span><span class="n">print_</span><span class="p">(</span><span class="s">'SIRT_CUDA2 has been deprecated. Use SIRT_CUDA instead.'</span><span class="p">)</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'FP_CUDA2'</span><span class="p">:</span> + <span class="n">intype</span> <span class="o">=</span> <span class="s">'FP_CUDA'</span> + <span class="n">six</span><span class="o">.</span><span class="n">print_</span><span class="p">(</span><span class="s">'FP_CUDA2 has been deprecated. Use FP_CUDA instead.'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span> <span class="n">intype</span><span class="p">}</span> +</div> +<div class="viewcode-block" id="create_vol_geom"><a class="viewcode-back" href="../../creators.html#astra.creators.create_vol_geom">[docs]</a><span class="k">def</span> <span class="nf">create_vol_geom</span><span class="p">(</span><span class="o">*</span><span class="n">varargin</span><span class="p">):</span> + <span class="sd">"""Create a volume geometry structure.</span> + +<span class="sd">This method can be called in a number of ways:</span> + +<span class="sd">``create_vol_geom(N)``:</span> +<span class="sd"> :returns: A 2D volume geometry of size :math:`N \\times N`.</span> + +<span class="sd">``create_vol_geom((M, N))``:</span> +<span class="sd"> :returns: A 2D volume geometry of size :math:`M \\times N`.</span> + +<span class="sd">``create_vol_geom(M, N)``:</span> +<span class="sd"> :returns: A 2D volume geometry of size :math:`M \\times N`.</span> + +<span class="sd">``create_vol_geom(M, N, minx, maxx, miny, maxy)``:</span> +<span class="sd"> :returns: A 2D volume geometry of size :math:`M \\times N`, windowed as :math:`minx \\leq x \\leq maxx` and :math:`miny \\leq y \\leq maxy`.</span> + +<span class="sd">``create_vol_geom((M, N, Z))``:</span> +<span class="sd"> :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`.</span> + +<span class="sd">``create_vol_geom(M, N, Z)``:</span> +<span class="sd"> :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`.</span> + +<span class="sd">"""</span> + <span class="n">vol_geom</span> <span class="o">=</span> <span class="p">{</span><span class="s">'option'</span><span class="p">:</span> <span class="p">{}}</span> + <span class="c"># astra_create_vol_geom(row_count)</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="nb">int</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinX'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxX'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinY'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxY'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="c"># astra_create_vol_geom([row_count col_count])</span> + <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinX'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxX'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinY'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxY'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="c"># astra_create_vol_geom([row_count col_count slice_count])</span> + <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridSliceCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinX'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxX'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinY'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxY'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinZ'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxZ'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="c"># astra_create_vol_geom(row_count, col_count)</span> + <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinX'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxX'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinY'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxY'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="c"># astra_create_vol_geom(row_count, col_count, min_x, max_x, min_y, max_y)</span> + <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">)</span> <span class="o">==</span> <span class="mi">6</span><span class="p">:</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinX'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxX'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinY'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxY'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> + <span class="c"># astra_create_vol_geom(row_count, col_count, slice_count)</span> + <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridSliceCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> + <span class="k">return</span> <span class="n">vol_geom</span> + +</div> +<div class="viewcode-block" id="create_proj_geom"><a class="viewcode-back" href="../../creators.html#astra.creators.create_proj_geom">[docs]</a><span class="k">def</span> <span class="nf">create_proj_geom</span><span class="p">(</span><span class="n">intype</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span> + <span class="sd">"""Create a projection geometry.</span> + +<span class="sd">This method can be called in a number of ways:</span> + +<span class="sd">``create_proj_geom('parallel', detector_spacing, det_count, angles)``:</span> + +<span class="sd">:param detector_spacing: Distance between two adjacent detector pixels.</span> +<span class="sd">:type detector_spacing: :class:`float`</span> +<span class="sd">:param det_count: Number of detector pixels.</span> +<span class="sd">:type det_count: :class:`int`</span> +<span class="sd">:param angles: Array of angles in radians.</span> +<span class="sd">:type angles: :class:`numpy.ndarray`</span> +<span class="sd">:returns: A parallel projection geometry.</span> + + +<span class="sd">``create_proj_geom('fanflat', det_width, det_count, angles, source_origin, source_det)``:</span> + +<span class="sd">:param det_width: Size of a detector pixel.</span> +<span class="sd">:type det_width: :class:`float`</span> +<span class="sd">:param det_count: Number of detector pixels.</span> +<span class="sd">:type det_count: :class:`int`</span> +<span class="sd">:param angles: Array of angles in radians.</span> +<span class="sd">:type angles: :class:`numpy.ndarray`</span> +<span class="sd">:param source_origin: Position of the source.</span> +<span class="sd">:param source_det: Position of the detector</span> +<span class="sd">:returns: A fan-beam projection geometry.</span> + +<span class="sd">``create_proj_geom('fanflat_vec', det_count, V)``:</span> + +<span class="sd">:param det_count: Number of detector pixels.</span> +<span class="sd">:type det_count: :class:`int`</span> +<span class="sd">:param V: Vector array.</span> +<span class="sd">:type V: :class:`numpy.ndarray`</span> +<span class="sd">:returns: A fan-beam projection geometry.</span> + +<span class="sd">``create_proj_geom('parallel3d', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles)``:</span> + +<span class="sd">:param detector_spacing_*: Distance between two adjacent detector pixels.</span> +<span class="sd">:type detector_spacing_*: :class:`float`</span> +<span class="sd">:param det_row_count: Number of detector pixel rows.</span> +<span class="sd">:type det_row_count: :class:`int`</span> +<span class="sd">:param det_col_count: Number of detector pixel columns.</span> +<span class="sd">:type det_col_count: :class:`int`</span> +<span class="sd">:param angles: Array of angles in radians.</span> +<span class="sd">:type angles: :class:`numpy.ndarray`</span> +<span class="sd">:returns: A parallel projection geometry.</span> + +<span class="sd">``create_proj_geom('cone', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det)``:</span> + +<span class="sd">:param detector_spacing_*: Distance between two adjacent detector pixels.</span> +<span class="sd">:type detector_spacing_*: :class:`float`</span> +<span class="sd">:param det_row_count: Number of detector pixel rows.</span> +<span class="sd">:type det_row_count: :class:`int`</span> +<span class="sd">:param det_col_count: Number of detector pixel columns.</span> +<span class="sd">:type det_col_count: :class:`int`</span> +<span class="sd">:param angles: Array of angles in radians.</span> +<span class="sd">:type angles: :class:`numpy.ndarray`</span> +<span class="sd">:param source_origin: Distance between point source and origin.</span> +<span class="sd">:type source_origin: :class:`float`</span> +<span class="sd">:param source_det: Distance between the detector and origin.</span> +<span class="sd">:type source_det: :class:`float`</span> +<span class="sd">:returns: A cone-beam projection geometry.</span> + +<span class="sd">``create_proj_geom('cone_vec', det_row_count, det_col_count, V)``:</span> + +<span class="sd">:param det_row_count: Number of detector pixel rows.</span> +<span class="sd">:type det_row_count: :class:`int`</span> +<span class="sd">:param det_col_count: Number of detector pixel columns.</span> +<span class="sd">:type det_col_count: :class:`int`</span> +<span class="sd">:param V: Vector array.</span> +<span class="sd">:type V: :class:`numpy.ndarray`</span> +<span class="sd">:returns: A cone-beam projection geometry.</span> + +<span class="sd">``create_proj_geom('parallel3d_vec', det_row_count, det_col_count, V)``:</span> + +<span class="sd">:param det_row_count: Number of detector pixel rows.</span> +<span class="sd">:type det_row_count: :class:`int`</span> +<span class="sd">:param det_col_count: Number of detector pixel columns.</span> +<span class="sd">:type det_col_count: :class:`int`</span> +<span class="sd">:param V: Vector array.</span> +<span class="sd">:type V: :class:`numpy.ndarray`</span> +<span class="sd">:returns: A parallel projection geometry.</span> + +<span class="sd">``create_proj_geom('sparse_matrix', det_width, det_count, angles, matrix_id)``:</span> + +<span class="sd">:param det_width: Size of a detector pixel.</span> +<span class="sd">:type det_width: :class:`float`</span> +<span class="sd">:param det_count: Number of detector pixels.</span> +<span class="sd">:type det_count: :class:`int`</span> +<span class="sd">:param angles: Array of angles in radians.</span> +<span class="sd">:type angles: :class:`numpy.ndarray`</span> +<span class="sd">:param matrix_id: ID of the sparse matrix.</span> +<span class="sd">:type matrix_id: :class:`int`</span> +<span class="sd">:returns: A projection geometry based on a sparse matrix.</span> + +<span class="sd">"""</span> + <span class="k">if</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'parallel'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">3</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span> + <span class="s">'not enough variables: astra_create_proj_geom(parallel, detector_spacing, det_count, angles)'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span> <span class="s">'parallel'</span><span class="p">,</span> <span class="s">'DetectorWidth'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">'DetectorCount'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">'ProjectionAngles'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">]}</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'fanflat'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">5</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'not enough variables: astra_create_proj_geom(fanflat, det_width, det_count, angles, source_origin, source_det)'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span> <span class="s">'fanflat'</span><span class="p">,</span> <span class="s">'DetectorWidth'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">'DetectorCount'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">'ProjectionAngles'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="s">'DistanceOriginSource'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="s">'DistanceOriginDetector'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">4</span><span class="p">]}</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'fanflat_vec'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">2</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'not enough variables: astra_create_proj_geom(fanflat_vec, det_count, V)'</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="mi">6</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'V should be a Nx6 matrix, with N the number of projections'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span><span class="s">'fanflat_vec'</span><span class="p">,</span> <span class="s">'DetectorCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">'Vectors'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">]}</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'parallel3d'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">5</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'not enough variables: astra_create_proj_geom(parallel3d, detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles)'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span><span class="s">'parallel3d'</span><span class="p">,</span> <span class="s">'DetectorSpacingX'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">'DetectorSpacingY'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">'DetectorRowCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="s">'DetectorColCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span><span class="s">'ProjectionAngles'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">4</span><span class="p">]}</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'cone'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">7</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'not enough variables: astra_create_proj_geom(cone, detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det)'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span> <span class="s">'cone'</span><span class="p">,</span><span class="s">'DetectorSpacingX'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">'DetectorSpacingY'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">'DetectorRowCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span><span class="s">'DetectorColCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span><span class="s">'ProjectionAngles'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span><span class="s">'DistanceOriginSource'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">5</span><span class="p">],</span><span class="s">'DistanceOriginDetector'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">6</span><span class="p">]}</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'cone_vec'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">3</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'not enough variables: astra_create_proj_geom(cone_vec, det_row_count, det_col_count, V)'</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="mi">12</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'V should be a Nx12 matrix, with N the number of projections'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span> <span class="s">'cone_vec'</span><span class="p">,</span><span class="s">'DetectorRowCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="s">'DetectorColCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span><span class="s">'Vectors'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">]}</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'parallel3d_vec'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">3</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'not enough variables: astra_create_proj_geom(parallel3d_vec, det_row_count, det_col_count, V)'</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="mi">12</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'V should be a Nx12 matrix, with N the number of projections'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span> <span class="s">'parallel3d_vec'</span><span class="p">,</span><span class="s">'DetectorRowCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="s">'DetectorColCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span><span class="s">'Vectors'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">]}</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'sparse_matrix'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">4</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span> + <span class="s">'not enough variables: astra_create_proj_geom(sparse_matrix, det_width, det_count, angles, matrix_id)'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span> <span class="s">'sparse_matrix'</span><span class="p">,</span> <span class="s">'DetectorWidth'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">'DetectorCount'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">'ProjectionAngles'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="s">'MatrixID'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">3</span><span class="p">]}</span> + <span class="k">else</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'Error: unknown type '</span> <span class="o">+</span> <span class="n">intype</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="create_backprojection"><a class="viewcode-back" href="../../creators.html#astra.creators.create_backprojection">[docs]</a><span class="k">def</span> <span class="nf">create_backprojection</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">proj_id</span><span class="p">,</span> <span class="n">useCUDA</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span> <span class="n">returnData</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span> + <span class="sd">"""Create a backprojection of a sinogram (2D).</span> + +<span class="sd">:param data: Sinogram data or ID.</span> +<span class="sd">:type data: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd">:param proj_id: ID of the projector to use.</span> +<span class="sd">:type proj_id: :class:`int`</span> +<span class="sd">:param useCUDA: If ``True``, use CUDA for the calculation.</span> +<span class="sd">:type useCUDA: :class:`bool`</span> +<span class="sd">:param returnData: If False, only return the ID of the backprojection.</span> +<span class="sd">:type returnData: :class:`bool`</span> +<span class="sd">:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.</span> + +<span class="sd">"""</span> + <span class="n">proj_geom</span> <span class="o">=</span> <span class="n">projector</span><span class="o">.</span><span class="n">projection_geometry</span><span class="p">(</span><span class="n">proj_id</span><span class="p">)</span> + <span class="n">vol_geom</span> <span class="o">=</span> <span class="n">projector</span><span class="o">.</span><span class="n">volume_geometry</span><span class="p">(</span><span class="n">proj_id</span><span class="p">)</span> + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-sino'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">data</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">data</span> + <span class="n">vol_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-vol'</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> + + <span class="n">algString</span> <span class="o">=</span> <span class="s">'BP'</span> + <span class="k">if</span> <span class="n">useCUDA</span><span class="p">:</span> + <span class="n">algString</span> <span class="o">=</span> <span class="n">algString</span> <span class="o">+</span> <span class="s">'_CUDA'</span> + + <span class="n">cfg</span> <span class="o">=</span> <span class="n">astra_dict</span><span class="p">(</span><span class="n">algString</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">useCUDA</span><span class="p">:</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectorId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">proj_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">sino_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ReconstructionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">vol_id</span> + <span class="n">alg_id</span> <span class="o">=</span> <span class="n">algorithm</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">sino_id</span><span class="p">)</span> + + <span class="k">if</span> <span class="n">returnData</span><span class="p">:</span> + <span class="k">return</span> <span class="n">vol_id</span><span class="p">,</span> <span class="n">data2d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">vol_id</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="k">return</span> <span class="n">vol_id</span> +</div> +<div class="viewcode-block" id="create_backprojection3d_gpu"><a class="viewcode-back" href="../../creators.html#astra.creators.create_backprojection3d_gpu">[docs]</a><span class="k">def</span> <span class="nf">create_backprojection3d_gpu</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="n">returnData</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span> + <span class="sd">"""Create a backprojection of a sinogram (3D) using CUDA.</span> + +<span class="sd">:param data: Sinogram data or ID.</span> +<span class="sd">:type data: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd">:param proj_geom: Projection geometry.</span> +<span class="sd">:type proj_geom: :class:`dict`</span> +<span class="sd">:param vol_geom: Volume geometry.</span> +<span class="sd">:type vol_geom: :class:`dict`</span> +<span class="sd">:param returnData: If False, only return the ID of the backprojection.</span> +<span class="sd">:type returnData: :class:`bool`</span> +<span class="sd">:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.</span> + +<span class="sd">"""</span> + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">data3d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-sino'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">data</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">data</span> + + <span class="n">vol_id</span> <span class="o">=</span> <span class="n">data3d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-vol'</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> + + <span class="n">cfg</span> <span class="o">=</span> <span class="n">astra_dict</span><span class="p">(</span><span class="s">'BP3D_CUDA'</span><span class="p">)</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">sino_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ReconstructionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">vol_id</span> + <span class="n">alg_id</span> <span class="o">=</span> <span class="n">algorithm</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">data3d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">sino_id</span><span class="p">)</span> + + <span class="k">if</span> <span class="n">returnData</span><span class="p">:</span> + <span class="k">return</span> <span class="n">vol_id</span><span class="p">,</span> <span class="n">data3d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">vol_id</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="k">return</span> <span class="n">vol_id</span> + +</div> +<div class="viewcode-block" id="create_sino"><a class="viewcode-back" href="../../creators.html#astra.creators.create_sino">[docs]</a><span class="k">def</span> <span class="nf">create_sino</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">proj_id</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">proj_geom</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">vol_geom</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> + <span class="n">useCUDA</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span> <span class="n">returnData</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span> <span class="n">gpuIndex</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Create a forward projection of an image (2D).</span> + +<span class="sd"> :param data: Image data or ID.</span> +<span class="sd"> :type data: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd"> :param proj_id: ID of the projector to use.</span> +<span class="sd"> :type proj_id: :class:`int`</span> +<span class="sd"> :param proj_geom: Projection geometry.</span> +<span class="sd"> :type proj_geom: :class:`dict`</span> +<span class="sd"> :param vol_geom: Volume geometry.</span> +<span class="sd"> :type vol_geom: :class:`dict`</span> +<span class="sd"> :param useCUDA: If ``True``, use CUDA for the calculation.</span> +<span class="sd"> :type useCUDA: :class:`bool`</span> +<span class="sd"> :param returnData: If False, only return the ID of the forward projection.</span> +<span class="sd"> :type returnData: :class:`bool`</span> +<span class="sd"> :param gpuIndex: Optional GPU index.</span> +<span class="sd"> :type gpuIndex: :class:`int`</span> +<span class="sd"> :returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`)</span> + +<span class="sd"> If ``returnData=False``, returns the ID of the forward</span> +<span class="sd"> projection. Otherwise, returns a tuple containing the ID of the</span> +<span class="sd"> forward projection and the forward projection itself, in that</span> +<span class="sd"> order.</span> + +<span class="sd"> The geometry of setup is defined by ``proj_id`` or with</span> +<span class="sd"> ``proj_geom`` and ``vol_geom``. If ``proj_id`` is given, then</span> +<span class="sd"> ``proj_geom`` and ``vol_geom`` must be None and vice versa.</span> +<span class="sd">"""</span> + <span class="k">if</span> <span class="n">proj_id</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> + <span class="n">proj_geom</span> <span class="o">=</span> <span class="n">projector</span><span class="o">.</span><span class="n">projection_geometry</span><span class="p">(</span><span class="n">proj_id</span><span class="p">)</span> + <span class="n">vol_geom</span> <span class="o">=</span> <span class="n">projector</span><span class="o">.</span><span class="n">volume_geometry</span><span class="p">(</span><span class="n">proj_id</span><span class="p">)</span> + <span class="k">elif</span> <span class="n">proj_geom</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">vol_geom</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">useCUDA</span><span class="p">:</span> + <span class="c"># We need more parameters to create projector.</span> + <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span> + <span class="sd">"""A ``proj_id`` is needed when CUDA is not used."""</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"""The geometry setup is not defined.</span> +<span class="s"> The geometry of setup is defined by ``proj_id`` or with</span> +<span class="s"> ``proj_geom`` and ``vol_geom``. If ``proj_id`` is given, then</span> +<span class="s"> ``proj_geom`` and ``vol_geom`` must be None and vice versa."""</span><span class="p">)</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">volume_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-vol'</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="n">data</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">volume_id</span> <span class="o">=</span> <span class="n">data</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-sino'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> + <span class="n">algString</span> <span class="o">=</span> <span class="s">'FP'</span> + <span class="k">if</span> <span class="n">useCUDA</span><span class="p">:</span> + <span class="n">algString</span> <span class="o">=</span> <span class="n">algString</span> <span class="o">+</span> <span class="s">'_CUDA'</span> + <span class="n">cfg</span> <span class="o">=</span> <span class="n">astra_dict</span><span class="p">(</span><span class="n">algString</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">useCUDA</span><span class="p">:</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectorId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">proj_id</span> + <span class="k">if</span> <span class="n">gpuIndex</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'option'</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">'GPUindex'</span><span class="p">:</span> <span class="n">gpuIndex</span><span class="p">}</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">sino_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'VolumeDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">volume_id</span> + <span class="n">alg_id</span> <span class="o">=</span> <span class="n">algorithm</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">volume_id</span><span class="p">)</span> + <span class="k">if</span> <span class="n">returnData</span><span class="p">:</span> + <span class="k">return</span> <span class="n">sino_id</span><span class="p">,</span> <span class="n">data2d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">sino_id</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="k">return</span> <span class="n">sino_id</span> + + +</div> +<div class="viewcode-block" id="create_sino3d_gpu"><a class="viewcode-back" href="../../creators.html#astra.creators.create_sino3d_gpu">[docs]</a><span class="k">def</span> <span class="nf">create_sino3d_gpu</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="n">returnData</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span> <span class="n">gpuIndex</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Create a forward projection of an image (3D).</span> + +<span class="sd">:param data: Image data or ID.</span> +<span class="sd">:type data: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd">:param proj_geom: Projection geometry.</span> +<span class="sd">:type proj_geom: :class:`dict`</span> +<span class="sd">:param vol_geom: Volume geometry.</span> +<span class="sd">:type vol_geom: :class:`dict`</span> +<span class="sd">:param returnData: If False, only return the ID of the forward projection.</span> +<span class="sd">:type returnData: :class:`bool`</span> +<span class="sd">:param gpuIndex: Optional GPU index.</span> +<span class="sd">:type gpuIndex: :class:`int`</span> +<span class="sd">:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the forward projection. Otherwise, returns a tuple containing the ID of the forward projection and the forward projection itself, in that order.</span> + +<span class="sd">"""</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">volume_id</span> <span class="o">=</span> <span class="n">data3d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-vol'</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="n">data</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">volume_id</span> <span class="o">=</span> <span class="n">data</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">data3d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-sino'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> + <span class="n">algString</span> <span class="o">=</span> <span class="s">'FP3D_CUDA'</span> + <span class="n">cfg</span> <span class="o">=</span> <span class="n">astra_dict</span><span class="p">(</span><span class="n">algString</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">gpuIndex</span><span class="o">==</span><span class="bp">None</span><span class="p">:</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'option'</span><span class="p">]</span><span class="o">=</span><span class="p">{</span><span class="s">'GPUindex'</span><span class="p">:</span><span class="n">gpuIndex</span><span class="p">}</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">sino_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'VolumeDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">volume_id</span> + <span class="n">alg_id</span> <span class="o">=</span> <span class="n">algorithm</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">data3d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">volume_id</span><span class="p">)</span> + <span class="k">if</span> <span class="n">returnData</span><span class="p">:</span> + <span class="k">return</span> <span class="n">sino_id</span><span class="p">,</span> <span class="n">data3d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">sino_id</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="k">return</span> <span class="n">sino_id</span> + +</div> +<div class="viewcode-block" id="create_reconstruction"><a class="viewcode-back" href="../../creators.html#astra.creators.create_reconstruction">[docs]</a><span class="k">def</span> <span class="nf">create_reconstruction</span><span class="p">(</span><span class="n">rec_type</span><span class="p">,</span> <span class="n">proj_id</span><span class="p">,</span> <span class="n">sinogram</span><span class="p">,</span> <span class="n">iterations</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">use_mask</span><span class="o">=</span><span class="s">'no'</span><span class="p">,</span> <span class="n">mask</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([]),</span> <span class="n">use_minc</span><span class="o">=</span><span class="s">'no'</span><span class="p">,</span> <span class="n">minc</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">use_maxc</span><span class="o">=</span><span class="s">'no'</span><span class="p">,</span> <span class="n">maxc</span><span class="o">=</span><span class="mi">255</span><span class="p">,</span> <span class="n">returnData</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span> <span class="n">filterType</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">filterData</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Create a reconstruction of a sinogram (2D).</span> + +<span class="sd">:param rec_type: Name of the reconstruction algorithm.</span> +<span class="sd">:type rec_type: :class:`string`</span> +<span class="sd">:param proj_id: ID of the projector to use.</span> +<span class="sd">:type proj_id: :class:`int`</span> +<span class="sd">:param sinogram: Sinogram data or ID.</span> +<span class="sd">:type sinogram: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd">:param iterations: Number of iterations to run.</span> +<span class="sd">:type iterations: :class:`int`</span> +<span class="sd">:param use_mask: Whether to use a mask.</span> +<span class="sd">:type use_mask: ``'yes'`` or ``'no'``</span> +<span class="sd">:param mask: Mask data or ID</span> +<span class="sd">:type mask: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd">:param use_minc: Whether to force a minimum value on the reconstruction pixels.</span> +<span class="sd">:type use_minc: ``'yes'`` or ``'no'``</span> +<span class="sd">:param minc: Minimum value to use.</span> +<span class="sd">:type minc: :class:`float`</span> +<span class="sd">:param use_maxc: Whether to force a maximum value on the reconstruction pixels.</span> +<span class="sd">:type use_maxc: ``'yes'`` or ``'no'``</span> +<span class="sd">:param maxc: Maximum value to use.</span> +<span class="sd">:type maxc: :class:`float`</span> +<span class="sd">:param returnData: If False, only return the ID of the reconstruction.</span> +<span class="sd">:type returnData: :class:`bool`</span> +<span class="sd">:param filterType: Which type of filter to use for filter-based methods.</span> +<span class="sd">:type filterType: :class:`string`</span> +<span class="sd">:param filterData: Optional filter data for filter-based methods.</span> +<span class="sd">:type filterData: :class:`numpy.ndarray`</span> +<span class="sd">:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the reconstruction. Otherwise, returns a tuple containing the ID of the reconstruction and reconstruction itself, in that order.</span> + +<span class="sd">"""</span> + <span class="n">proj_geom</span> <span class="o">=</span> <span class="n">projector</span><span class="o">.</span><span class="n">projection_geometry</span><span class="p">(</span><span class="n">proj_id</span><span class="p">)</span> + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">sinogram</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-sino'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">sinogram</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">sinogram</span> + <span class="n">vol_geom</span> <span class="o">=</span> <span class="n">projector</span><span class="o">.</span><span class="n">volume_geometry</span><span class="p">(</span><span class="n">proj_id</span><span class="p">)</span> + <span class="n">recon_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-vol'</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> + <span class="n">cfg</span> <span class="o">=</span> <span class="n">astra_dict</span><span class="p">(</span><span class="n">rec_type</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="s">'CUDA'</span> <span class="ow">in</span> <span class="n">rec_type</span><span class="p">:</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectorId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">proj_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">sino_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ReconstructionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">recon_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'options'</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span> + <span class="k">if</span> <span class="n">use_mask</span> <span class="o">==</span> <span class="s">'yes'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">mask</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">mask_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-vol'</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="n">mask</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">mask_id</span> <span class="o">=</span> <span class="n">mask</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'options'</span><span class="p">][</span><span class="s">'ReconstructionMaskId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">mask_id</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">filterType</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'FilterType'</span><span class="p">]</span> <span class="o">=</span> <span class="n">filterType</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">filterData</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">filterData</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">nexpow</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span> + <span class="nb">pow</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="n">math</span><span class="o">.</span><span class="n">ceil</span><span class="p">(</span><span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorCount'</span><span class="p">],</span> <span class="mi">2</span><span class="p">))))</span> + <span class="n">filtSize</span> <span class="o">=</span> <span class="n">nexpow</span> <span class="o">/</span> <span class="mi">2</span> <span class="o">+</span> <span class="mi">1</span> + <span class="n">filt_proj_geom</span> <span class="o">=</span> <span class="n">create_proj_geom</span><span class="p">(</span> + <span class="s">'parallel'</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="n">filtSize</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'ProjectionAngles'</span><span class="p">])</span> + <span class="n">filt_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-sino'</span><span class="p">,</span> <span class="n">filt_proj_geom</span><span class="p">,</span> <span class="n">filterData</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">filt_id</span> <span class="o">=</span> <span class="n">filterData</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'FilterSinogramId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">filt_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'options'</span><span class="p">][</span><span class="s">'UseMinConstraint'</span><span class="p">]</span> <span class="o">=</span> <span class="n">use_minc</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'options'</span><span class="p">][</span><span class="s">'MinConstraintValue'</span><span class="p">]</span> <span class="o">=</span> <span class="n">minc</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'options'</span><span class="p">][</span><span class="s">'UseMaxConstraint'</span><span class="p">]</span> <span class="o">=</span> <span class="n">use_maxc</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'options'</span><span class="p">][</span><span class="s">'MaxConstraintValue'</span><span class="p">]</span> <span class="o">=</span> <span class="n">maxc</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'options'</span><span class="p">][</span><span class="s">'ProjectionOrder'</span><span class="p">]</span> <span class="o">=</span> <span class="s">'random'</span> + <span class="n">alg_id</span> <span class="o">=</span> <span class="n">algorithm</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">alg_id</span><span class="p">,</span> <span class="n">iterations</span><span class="p">)</span> + + <span class="n">algorithm</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">sinogram</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">sino_id</span><span class="p">)</span> + <span class="k">if</span> <span class="n">use_mask</span> <span class="o">==</span> <span class="s">'yes'</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">mask</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">mask_id</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">filterData</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">filterData</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">filt_id</span><span class="p">)</span> + <span class="k">if</span> <span class="n">returnData</span><span class="p">:</span> + <span class="k">return</span> <span class="n">recon_id</span><span class="p">,</span> <span class="n">data2d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">recon_id</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="k">return</span> <span class="n">recon_id</span> + +</div> +<div class="viewcode-block" id="create_projector"><a class="viewcode-back" href="../../creators.html#astra.creators.create_projector">[docs]</a><span class="k">def</span> <span class="nf">create_projector</span><span class="p">(</span><span class="n">proj_type</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">):</span> + <span class="sd">"""Create a 2D projector.</span> + +<span class="sd">:param proj_type: Projector type, such as ``'line'``, ``'linear'``, ...</span> +<span class="sd">:type proj_type: :class:`string`</span> +<span class="sd">:param proj_geom: Projection geometry.</span> +<span class="sd">:type proj_geom: :class:`dict`</span> +<span class="sd">:param vol_geom: Volume geometry.</span> +<span class="sd">:type vol_geom: :class:`dict`</span> +<span class="sd">:returns: :class:`int` -- The ID of the projector.</span> + +<span class="sd">"""</span> + <span class="k">if</span> <span class="n">proj_type</span> <span class="o">==</span> <span class="s">'blob'</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'Blob type not yet implemented'</span><span class="p">)</span> + <span class="n">cfg</span> <span class="o">=</span> <span class="n">astra_dict</span><span class="p">(</span><span class="n">proj_type</span><span class="p">)</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectionGeometry'</span><span class="p">]</span> <span class="o">=</span> <span class="n">proj_geom</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'VolumeGeometry'</span><span class="p">]</span> <span class="o">=</span> <span class="n">vol_geom</span> + <span class="k">return</span> <span class="n">projector</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + 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\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/data2d.html b/python/docSRC/_build/html/_modules/astra/data2d.html new file mode 100644 index 0000000..d77cddd --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/data2d.html @@ -0,0 +1,225 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.data2d — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.data2d</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data2d_c</span> <span class="k">as</span> <span class="n">d</span> + +<div class="viewcode-block" id="clear"><a class="viewcode-back" href="../../data2d.html#astra.data2d.clear">[docs]</a><span class="k">def</span> <span class="nf">clear</span><span class="p">():</span> + <span class="sd">"""Clear all 2D data objects."""</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> +</div> +<div class="viewcode-block" id="delete"><a class="viewcode-back" href="../../data2d.html#astra.data2d.delete">[docs]</a><span class="k">def</span> <span class="nf">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">):</span> + <span class="sd">"""Delete a 2D object.</span> +<span class="sd"> </span> +<span class="sd"> :param ids: ID or list of ID's to delete.</span> +<span class="sd"> :type ids: :class:`int` or :class:`list`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="create"><a class="viewcode-back" href="../../data2d.html#astra.data2d.create">[docs]</a><span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="n">datatype</span><span class="p">,</span> <span class="n">geometry</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Create a 2D object.</span> +<span class="sd"> </span> +<span class="sd"> :param datatype: Data object type, '-vol' or '-sino'.</span> +<span class="sd"> :type datatype: :class:`string`</span> +<span class="sd"> :param geometry: Volume or projection geometry.</span> +<span class="sd"> :type geometry: :class:`dict`</span> +<span class="sd"> :param data: Data to fill the constructed object with, either a scalar or array.</span> +<span class="sd"> :type data: :class:`float` or :class:`numpy.ndarray`</span> +<span class="sd"> :returns: :class:`int` -- the ID of the constructed object.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">datatype</span><span class="p">,</span><span class="n">geometry</span><span class="p">,</span><span class="n">data</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="store"><a class="viewcode-back" href="../../data2d.html#astra.data2d.store">[docs]</a><span class="k">def</span> <span class="nf">store</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span> + <span class="sd">"""Fill existing 2D object with data.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to fill.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :param data: Data to fill the object with, either a scalar or array.</span> +<span class="sd"> :type data: :class:`float` or :class:`numpy.ndarray`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">store</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">data</span><span class="p">)</span> + </div> +<div class="viewcode-block" id="get_geometry"><a class="viewcode-back" href="../../data2d.html#astra.data2d.get_geometry">[docs]</a><span class="k">def</span> <span class="nf">get_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get the geometry of a 2D object.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`dict` -- The geometry of object with ID ``i``.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">get_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="change_geometry"><a class="viewcode-back" href="../../data2d.html#astra.data2d.change_geometry">[docs]</a><span class="k">def</span> <span class="nf">change_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">geom</span><span class="p">):</span> + <span class="sd">"""Change the geometry of a 2D object.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :param geom: new geometry.</span> +<span class="sd"> :type geom: :class:`dict`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">change_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">geom</span><span class="p">)</span> + </div> +<div class="viewcode-block" id="get"><a class="viewcode-back" href="../../data2d.html#astra.data2d.get">[docs]</a><span class="k">def</span> <span class="nf">get</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get a 2D object.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to get.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="get_shared"><a class="viewcode-back" href="../../data2d.html#astra.data2d.get_shared">[docs]</a><span class="k">def</span> <span class="nf">get_shared</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get a 2D object with memory shared between the ASTRA toolbox and numpy array.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to get.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">get_shared</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="get_single"><a class="viewcode-back" href="../../data2d.html#astra.data2d.get_single">[docs]</a><span class="k">def</span> <span class="nf">get_single</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get a 2D object in single precision.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to get.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">get_single</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="info"><a class="viewcode-back" href="../../data2d.html#astra.data2d.info">[docs]</a><span class="k">def</span> <span class="nf">info</span><span class="p">():</span> + <span class="sd">"""Print info on 2D objects in memory."""</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">info</span><span class="p">()</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" >Module code</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + 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\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/data3d.html b/python/docSRC/_build/html/_modules/astra/data3d.html new file mode 100644 index 0000000..674d6d1 --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/data3d.html @@ -0,0 +1,213 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.data3d — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.data3d</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data3d_c</span> <span class="k">as</span> <span class="n">d</span> + +<div class="viewcode-block" id="create"><a class="viewcode-back" href="../../data3d.html#astra.data3d.create">[docs]</a><span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="n">datatype</span><span class="p">,</span><span class="n">geometry</span><span class="p">,</span><span class="n">data</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Create a 3D object.</span> +<span class="sd"> </span> +<span class="sd"> :param datatype: Data object type, '-vol' or '-sino'.</span> +<span class="sd"> :type datatype: :class:`string`</span> +<span class="sd"> :param geometry: Volume or projection geometry.</span> +<span class="sd"> :type geometry: :class:`dict`</span> +<span class="sd"> :param data: Data to fill the constructed object with, either a scalar or array.</span> +<span class="sd"> :type data: :class:`float` or :class:`numpy.ndarray`</span> +<span class="sd"> :returns: :class:`int` -- the ID of the constructed object.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">datatype</span><span class="p">,</span><span class="n">geometry</span><span class="p">,</span><span class="n">data</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="get"><a class="viewcode-back" href="../../data3d.html#astra.data3d.get">[docs]</a><span class="k">def</span> <span class="nf">get</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get a 3D object.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to get.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="get_shared"><a class="viewcode-back" href="../../data3d.html#astra.data3d.get_shared">[docs]</a><span class="k">def</span> <span class="nf">get_shared</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get a 3D object with memory shared between the ASTRA toolbox and numpy array.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to get.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">get_shared</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="get_single"><a class="viewcode-back" href="../../data3d.html#astra.data3d.get_single">[docs]</a><span class="k">def</span> <span class="nf">get_single</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get a 3D object in single precision.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to get.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">g</span><span class="o">.</span><span class="n">get_single</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="store"><a class="viewcode-back" href="../../data3d.html#astra.data3d.store">[docs]</a><span class="k">def</span> <span class="nf">store</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">data</span><span class="p">):</span> + <span class="sd">"""Fill existing 3D object with data.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to fill.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :param data: Data to fill the object with, either a scalar or array.</span> +<span class="sd"> :type data: :class:`float` or :class:`numpy.ndarray`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">store</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">data</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="dimensions"><a class="viewcode-back" href="../../data3d.html#astra.data3d.dimensions">[docs]</a><span class="k">def</span> <span class="nf">dimensions</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get dimensions of a 3D object.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`tuple` -- dimensions of object with ID ``i``.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">dimensions</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="delete"><a class="viewcode-back" href="../../data3d.html#astra.data3d.delete">[docs]</a><span class="k">def</span> <span class="nf">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">):</span> + <span class="sd">"""Delete a 2D object.</span> +<span class="sd"> </span> +<span class="sd"> :param ids: ID or list of ID's to delete.</span> +<span class="sd"> :type ids: :class:`int` or :class:`list`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="clear"><a class="viewcode-back" href="../../data3d.html#astra.data3d.clear">[docs]</a><span class="k">def</span> <span class="nf">clear</span><span class="p">():</span> + <span class="sd">"""Clear all 3D data objects."""</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> +</div> +<div class="viewcode-block" id="info"><a class="viewcode-back" href="../../data3d.html#astra.data3d.info">[docs]</a><span class="k">def</span> <span class="nf">info</span><span class="p">():</span> + <span class="sd">"""Print info on 3D objects in memory."""</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">info</span><span class="p">()</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function 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\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/functions.html b/python/docSRC/_build/html/_modules/astra/functions.html new file mode 100644 index 0000000..336431f --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/functions.html @@ -0,0 +1,375 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.functions — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.functions</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c"># Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c"># Author: Daniel M. Pelt</span> +<span class="c"># Contact: D.M.Pelt@cwi.nl</span> +<span class="c"># Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c"># This file is part of the Python interface to the</span> +<span class="c"># All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c"># The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c"># it under the terms of the GNU General Public License as published by</span> +<span class="c"># the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c"># The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c"># but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c"># GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c"># You should have received a copy of the GNU General Public License</span> +<span class="c"># along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="sd">"""Additional functions for PyAstraToolbox.</span> + +<span class="sd">.. moduleauthor:: Daniel M. Pelt <D.M.Pelt@cwi.nl></span> + + +<span class="sd">"""</span> + +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">creators</span> <span class="k">as</span> <span class="n">ac</span> +<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span> +<span class="kn">from</span> <span class="nn">six.moves</span> <span class="kn">import</span> <span class="nb">range</span> + +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data2d</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data3d</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">projector</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">algorithm</span> + + + +<div class="viewcode-block" id="clear"><a class="viewcode-back" href="../../functions.html#astra.functions.clear">[docs]</a><span class="k">def</span> <span class="nf">clear</span><span class="p">():</span> + <span class="sd">"""Clears all used memory of the ASTRA Toolbox.</span> + +<span class="sd"> .. note::</span> +<span class="sd"> This is irreversible.</span> + +<span class="sd"> """</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> + <span class="n">data3d</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> + <span class="n">projector</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> + +</div> +<div class="viewcode-block" id="data_op"><a class="viewcode-back" href="../../functions.html#astra.functions.data_op">[docs]</a><span class="k">def</span> <span class="nf">data_op</span><span class="p">(</span><span class="n">op</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">scalar</span><span class="p">,</span> <span class="n">gpu_core</span><span class="p">,</span> <span class="n">mask</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Perform data operation on data.</span> + +<span class="sd"> :param op: Operation to perform.</span> +<span class="sd"> :param data: Data to perform operation on.</span> +<span class="sd"> :param scalar: Scalar argument to data operation.</span> +<span class="sd"> :param gpu_core: GPU core to perform operation on.</span> +<span class="sd"> :param mask: Optional mask.</span> + +<span class="sd"> """</span> + + <span class="n">cfg</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">astra_dict</span><span class="p">(</span><span class="s">'DataOperation_CUDA'</span><span class="p">)</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'Operation'</span><span class="p">]</span> <span class="o">=</span> <span class="n">op</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'Scalar'</span><span class="p">]</span> <span class="o">=</span> <span class="n">scalar</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'DataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">mask</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'MaskId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">mask</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'GPUindex'</span><span class="p">]</span> <span class="o">=</span> <span class="n">gpu_core</span> + <span class="n">alg_id</span> <span class="o">=</span> <span class="n">algorithm</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="add_noise_to_sino"><a class="viewcode-back" href="../../functions.html#astra.functions.add_noise_to_sino">[docs]</a><span class="k">def</span> <span class="nf">add_noise_to_sino</span><span class="p">(</span><span class="n">sinogram_in</span><span class="p">,</span> <span class="n">I0</span><span class="p">,</span> <span class="n">seed</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Adds Poisson noise to a sinogram.</span> + +<span class="sd"> :param sinogram_in: Sinogram to add noise to.</span> +<span class="sd"> :type sinogram_in: :class:`numpy.ndarray`</span> +<span class="sd"> :param I0: Background intensity. Lower values lead to higher noise.</span> +<span class="sd"> :type I0: :class:`float`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- the sinogram with added noise.</span> + +<span class="sd"> """</span> + + <span class="k">if</span> <span class="ow">not</span> <span class="n">seed</span><span class="o">==</span><span class="bp">None</span><span class="p">:</span> + <span class="n">curstate</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">get_state</span><span class="p">()</span> + <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">seed</span><span class="p">(</span><span class="n">seed</span><span class="p">)</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">sinogram_in</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">sinogramRaw</span> <span class="o">=</span> <span class="n">sinogram_in</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">sinogramRaw</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">sinogram_in</span><span class="p">)</span> + <span class="n">max_sinogramRaw</span> <span class="o">=</span> <span class="n">sinogramRaw</span><span class="o">.</span><span class="n">max</span><span class="p">()</span> + <span class="n">sinogramRawScaled</span> <span class="o">=</span> <span class="n">sinogramRaw</span> <span class="o">/</span> <span class="n">max_sinogramRaw</span> + <span class="c"># to detector count</span> + <span class="n">sinogramCT</span> <span class="o">=</span> <span class="n">I0</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">sinogramRawScaled</span><span class="p">)</span> + <span class="c"># add poison noise</span> + <span class="n">sinogramCT_C</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros_like</span><span class="p">(</span><span class="n">sinogramCT</span><span class="p">)</span> + <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">sinogramCT_C</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span> + <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">sinogramCT_C</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]):</span> + <span class="n">sinogramCT_C</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">poisson</span><span class="p">(</span><span class="n">sinogramCT</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">])</span> + <span class="c"># to density</span> + <span class="n">sinogramCT_D</span> <span class="o">=</span> <span class="n">sinogramCT_C</span> <span class="o">/</span> <span class="n">I0</span> + <span class="n">sinogram_out</span> <span class="o">=</span> <span class="o">-</span><span class="n">max_sinogramRaw</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">sinogramCT_D</span><span class="p">)</span> + + <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">sinogram_in</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">at</span><span class="o">.</span><span class="n">data2d</span><span class="o">.</span><span class="n">store</span><span class="p">(</span><span class="n">sinogram_in</span><span class="p">,</span> <span class="n">sinogram_out</span><span class="p">)</span> + + <span class="k">if</span> <span class="ow">not</span> <span class="n">seed</span><span class="o">==</span><span class="bp">None</span><span class="p">:</span> + <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">set_state</span><span class="p">(</span><span class="n">curstate</span><span class="p">)</span> + + <span class="k">return</span> <span class="n">sinogram_out</span> +</div> +<div class="viewcode-block" id="move_vol_geom"><a class="viewcode-back" href="../../functions.html#astra.functions.move_vol_geom">[docs]</a><span class="k">def</span> <span class="nf">move_vol_geom</span><span class="p">(</span><span class="n">geom</span><span class="p">,</span> <span class="n">pos</span><span class="p">,</span> <span class="n">is_relative</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span> + <span class="sd">"""Moves center of volume geometry to new position.</span> + +<span class="sd"> :param geom: Input volume geometry</span> +<span class="sd"> :type geom: :class:`dict`</span> +<span class="sd"> :param pos: Tuple (x,y[,z]) for new position, with the center of the image at (0,0[,0])</span> +<span class="sd"> :type pos: :class:`tuple`</span> +<span class="sd"> :param is_relative: Whether new position is relative to the old position</span> +<span class="sd"> :type is_relative: :class:`bool`</span> +<span class="sd"> :returns: :class:`dict` -- Volume geometry with the new center</span> +<span class="sd"> """</span> + + <span class="n">ret_geom</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">]</span> <span class="o">=</span> <span class="n">geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">]</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span> + + <span class="k">if</span> <span class="ow">not</span> <span class="n">is_relative</span><span class="p">:</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinX'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxX'</span><span class="p">]</span> <span class="o">=</span> <span class="n">geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinY'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxY'</span><span class="p">]</span> <span class="o">=</span> <span class="n">geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">pos</span><span class="p">)</span><span class="o">></span><span class="mi">2</span><span class="p">:</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinZ'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">geom</span><span class="p">[</span><span class="s">'GridSliceCount'</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxZ'</span><span class="p">]</span> <span class="o">=</span> <span class="n">geom</span><span class="p">[</span><span class="s">'GridSliceCount'</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinX'</span><span class="p">]</span> <span class="o">+=</span> <span class="n">pos</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxX'</span><span class="p">]</span> <span class="o">+=</span> <span class="n">pos</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinY'</span><span class="p">]</span> <span class="o">+=</span> <span class="n">pos</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxY'</span><span class="p">]</span> <span class="o">+=</span> <span class="n">pos</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">pos</span><span class="p">)</span><span class="o">></span><span class="mi">2</span><span class="p">:</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinZ'</span><span class="p">]</span> <span class="o">+=</span> <span class="n">pos</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxZ'</span><span class="p">]</span> <span class="o">+=</span> <span class="n">pos</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> + <span class="k">return</span> <span class="n">ret_geom</span> + +</div> +<div class="viewcode-block" id="geom_size"><a class="viewcode-back" href="../../functions.html#astra.functions.geom_size">[docs]</a><span class="k">def</span> <span class="nf">geom_size</span><span class="p">(</span><span class="n">geom</span><span class="p">,</span> <span class="n">dim</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Returns the size of a volume or sinogram, based on the projection or volume geometry.</span> + +<span class="sd"> :param geom: Geometry to calculate size from</span> +<span class="sd"> :type geometry: :class:`dict`</span> +<span class="sd"> :param dim: Optional axis index to return</span> +<span class="sd"> :type dim: :class:`int`</span> +<span class="sd"> """</span> + + <span class="k">if</span> <span class="s">'GridSliceCount'</span> <span class="ow">in</span> <span class="n">geom</span><span class="p">:</span> + <span class="c"># 3D Volume geometry?</span> + <span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="n">geom</span><span class="p">[</span><span class="s">'GridSliceCount'</span><span class="p">],</span> <span class="n">geom</span><span class="p">[</span> + <span class="s">'GridRowCount'</span><span class="p">],</span> <span class="n">geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">])</span> + <span class="k">elif</span> <span class="s">'GridColCount'</span> <span class="ow">in</span> <span class="n">geom</span><span class="p">:</span> + <span class="c"># 2D Volume geometry?</span> + <span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="n">geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">],</span> <span class="n">geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">])</span> + <span class="k">elif</span> <span class="n">geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'parallel'</span> <span class="ow">or</span> <span class="n">geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'fanflat'</span><span class="p">:</span> + <span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">geom</span><span class="p">[</span><span class="s">'ProjectionAngles'</span><span class="p">]),</span> <span class="n">geom</span><span class="p">[</span><span class="s">'DetectorCount'</span><span class="p">])</span> + <span class="k">elif</span> <span class="n">geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'parallel3d'</span> <span class="ow">or</span> <span class="n">geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'cone'</span><span class="p">:</span> + <span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="n">geom</span><span class="p">[</span><span class="s">'DetectorRowCount'</span><span class="p">],</span> <span class="nb">len</span><span class="p">(</span> + <span class="n">geom</span><span class="p">[</span><span class="s">'ProjectionAngles'</span><span class="p">]),</span> <span class="n">geom</span><span class="p">[</span><span class="s">'DetectorColCount'</span><span class="p">])</span> + <span class="k">elif</span> <span class="n">geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'fanflat_vec'</span><span class="p">:</span> + <span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="n">geom</span><span class="p">[</span><span class="s">'Vectors'</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">geom</span><span class="p">[</span><span class="s">'DetectorCount'</span><span class="p">])</span> + <span class="k">elif</span> <span class="n">geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'parallel3d_vec'</span> <span class="ow">or</span> <span class="n">geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'cone_vec'</span><span class="p">:</span> + <span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="n">geom</span><span class="p">[</span><span class="s">'DetectorRowCount'</span><span class="p">],</span> <span class="n">geom</span><span class="p">[</span> + <span class="s">'Vectors'</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">geom</span><span class="p">[</span><span class="s">'DetectorColCount'</span><span class="p">])</span> + + <span class="k">if</span> <span class="n">dim</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span> + <span class="n">s</span> <span class="o">=</span> <span class="n">s</span><span class="p">[</span><span class="n">dim</span><span class="p">]</span> + + <span class="k">return</span> <span class="n">s</span> + +</div> +<div class="viewcode-block" id="geom_2vec"><a class="viewcode-back" href="../../functions.html#astra.functions.geom_2vec">[docs]</a><span class="k">def</span> <span class="nf">geom_2vec</span><span class="p">(</span><span class="n">proj_geom</span><span class="p">):</span> + <span class="sd">"""Returns a vector-based projection geometry from a basic projection geometry.</span> + +<span class="sd"> :param proj_geom: Projection geometry to convert</span> +<span class="sd"> :type proj_geom: :class:`dict`</span> +<span class="sd"> """</span> + <span class="k">if</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'fanflat'</span><span class="p">:</span> + <span class="n">angles</span> <span class="o">=</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'ProjectionAngles'</span><span class="p">]</span> + <span class="n">vectors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="nb">len</span><span class="p">(</span><span class="n">angles</span><span class="p">),</span> <span class="mi">6</span><span class="p">))</span> + <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">angles</span><span class="p">)):</span> + + <span class="c"># source</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginSource'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginSource'</span><span class="p">]</span> + + <span class="c"># center of detector</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginDetector'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginDetector'</span><span class="p">]</span> + + <span class="c"># vector from detector pixel 0 to 1</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">4</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorWidth'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">5</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorWidth'</span><span class="p">]</span> + <span class="n">proj_geom_out</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">create_proj_geom</span><span class="p">(</span> + <span class="s">'fanflat_vec'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorCount'</span><span class="p">],</span> <span class="n">vectors</span><span class="p">)</span> + + <span class="k">elif</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'cone'</span><span class="p">:</span> + <span class="n">angles</span> <span class="o">=</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'ProjectionAngles'</span><span class="p">]</span> + <span class="n">vectors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="nb">len</span><span class="p">(</span><span class="n">angles</span><span class="p">),</span> <span class="mi">12</span><span class="p">))</span> + <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">angles</span><span class="p">)):</span> + <span class="c"># source</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginSource'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginSource'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + + <span class="c"># center of detector</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginDetector'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">4</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginDetector'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">5</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + + <span class="c"># vector from detector pixel (0,0) to (0,1)</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">6</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorSpacingX'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">7</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorSpacingX'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">8</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + + <span class="c"># vector from detector pixel (0,0) to (1,0)</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">9</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">10</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">11</span><span class="p">]</span> <span class="o">=</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorSpacingY'</span><span class="p">]</span> + + <span class="n">proj_geom_out</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">create_proj_geom</span><span class="p">(</span> + <span class="s">'cone_vec'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorRowCount'</span><span class="p">],</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorColCount'</span><span class="p">],</span> <span class="n">vectors</span><span class="p">)</span> + + <span class="c"># PARALLEL</span> + <span class="k">elif</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'parallel3d'</span><span class="p">:</span> + <span class="n">angles</span> <span class="o">=</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'ProjectionAngles'</span><span class="p">]</span> + <span class="n">vectors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="nb">len</span><span class="p">(</span><span class="n">angles</span><span class="p">),</span> <span class="mi">12</span><span class="p">))</span> + <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">angles</span><span class="p">)):</span> + + <span class="c"># ray direction</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + + <span class="c"># center of detector</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">4</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">5</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + + <span class="c"># vector from detector pixel (0,0) to (0,1)</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">6</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorSpacingX'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">7</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorSpacingX'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">8</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + + <span class="c"># vector from detector pixel (0,0) to (1,0)</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">9</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">10</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">11</span><span class="p">]</span> <span class="o">=</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorSpacingY'</span><span class="p">]</span> + + <span class="n">proj_geom_out</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">create_proj_geom</span><span class="p">(</span> + <span class="s">'parallel3d_vec'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorRowCount'</span><span class="p">],</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorColCount'</span><span class="p">],</span> <span class="n">vectors</span><span class="p">)</span> + + <span class="k">else</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span> + <span class="s">'No suitable vector geometry found for type: '</span> <span class="o">+</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">])</span> + <span class="k">return</span> <span class="n">proj_geom_out</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p 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\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/matlab.html b/python/docSRC/_build/html/_modules/astra/matlab.html new file mode 100644 index 0000000..b58ff06 --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/matlab.html @@ -0,0 +1,217 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.matlab — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.matlab</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="sd">"""This module implements a MATLAB-like interface to the ASTRA Toolbox.</span> + +<span class="sd">Note that all functions are called with a :class:`string` as the first</span> +<span class="sd">argument, specifying the operation to perform. This un-pythonic way</span> +<span class="sd">is used to make transitioning from MATLAB code to Python code easier, as</span> +<span class="sd">the MATLAB interface uses the same type of method calling.</span> + +<span class="sd">After an initial ``import astra``, these functions can be accessed in the</span> +<span class="sd">``astra.m`` module.</span> + +<span class="sd">"""</span> + +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">astra_c</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data2d_c</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data3d_c</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">projector_c</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">algorithm_c</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">matrix_c</span> +<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span> + + +<div class="viewcode-block" id="astra"><a class="viewcode-back" href="../../matlab.html#astra.matlab.astra">[docs]</a><span class="k">def</span> <span class="nf">astra</span><span class="p">(</span><span class="n">command</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span> + <span class="sd">"""MATLAB-like interface to the :mod:`astra.astra` module</span> +<span class="sd"> </span> +<span class="sd"> For example:</span> +<span class="sd"> </span> +<span class="sd"> ``astra.m.astra('use_cuda')`` -- Check if CUDA is enabled.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">astra_c</span><span class="p">,</span> <span class="n">command</span><span class="p">)(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="data2d"><a class="viewcode-back" href="../../matlab.html#astra.matlab.data2d">[docs]</a><span class="k">def</span> <span class="nf">data2d</span><span class="p">(</span><span class="n">command</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span> + <span class="sd">"""MATLAB-like interface to the :mod:`astra.data2d` module</span> +<span class="sd"> </span> +<span class="sd"> For example:</span> +<span class="sd"> </span> +<span class="sd"> ``astra.m.data2d('create',type,geometry,data)`` -- Create a 2D object.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">data2d_c</span><span class="p">,</span> <span class="n">command</span><span class="p">)(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="data3d"><a class="viewcode-back" href="../../matlab.html#astra.matlab.data3d">[docs]</a><span class="k">def</span> <span class="nf">data3d</span><span class="p">(</span><span class="n">command</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span> + <span class="sd">"""MATLAB-like interface to the :mod:`astra.data3d` module</span> +<span class="sd"> </span> +<span class="sd"> For example:</span> +<span class="sd"> </span> +<span class="sd"> ``astra.m.data3d('get',i)`` -- Get 3D object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">data3d_c</span><span class="p">,</span> <span class="n">command</span><span class="p">)(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="projector"><a class="viewcode-back" href="../../matlab.html#astra.matlab.projector">[docs]</a><span class="k">def</span> <span class="nf">projector</span><span class="p">(</span><span class="n">command</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span> + <span class="sd">"""MATLAB-like interface to the :mod:`astra.projector` module</span> +<span class="sd"> </span> +<span class="sd"> For example:</span> +<span class="sd"> </span> +<span class="sd"> ``astra.m.projector('volume_geometry',i)`` -- Get volume geometry.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">projector_c</span><span class="p">,</span> <span class="n">command</span><span class="p">)(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="matrix"><a class="viewcode-back" href="../../matlab.html#astra.matlab.matrix">[docs]</a><span class="k">def</span> <span class="nf">matrix</span><span class="p">(</span><span class="n">command</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span> + <span class="sd">"""MATLAB-like interface to the :mod:`astra.matrix` module</span> +<span class="sd"> </span> +<span class="sd"> For example:</span> +<span class="sd"> </span> +<span class="sd"> ``astra.m.matrix('delete',i)`` -- Delete a matrix.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">matrix_c</span><span class="p">,</span> <span class="n">command</span><span class="p">)(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="algorithm"><a class="viewcode-back" href="../../matlab.html#astra.matlab.algorithm">[docs]</a><span class="k">def</span> <span class="nf">algorithm</span><span class="p">(</span><span class="n">command</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span> + <span class="sd">"""MATLAB-like interface to the :mod:`astra.algorithm` module</span> +<span class="sd"> </span> +<span class="sd"> For example:</span> +<span class="sd"> </span> +<span class="sd"> ``astra.m.algorithm('run',i,1000)`` -- Run an algorithm with 1000 iterations.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">if</span> <span class="n">command</span> <span class="o">==</span> <span class="s">'iterate'</span><span class="p">:</span> + <span class="n">command</span> <span class="o">=</span> <span class="s">'run'</span> + <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">algorithm_c</span><span class="p">,</span> <span class="n">command</span><span class="p">)(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" >Module code</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/matrix.html b/python/docSRC/_build/html/_modules/astra/matrix.html new file mode 100644 index 0000000..5f75455 --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/matrix.html @@ -0,0 +1,191 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.matrix — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.matrix</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">matrix_c</span> <span class="k">as</span> <span class="n">m</span> + +<div class="viewcode-block" id="delete"><a class="viewcode-back" href="../../matrix.html#astra.matrix.delete">[docs]</a><span class="k">def</span> <span class="nf">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">):</span> + <span class="sd">"""Delete a matrix object.</span> +<span class="sd"> </span> +<span class="sd"> :param ids: ID or list of ID's to delete.</span> +<span class="sd"> :type ids: :class:`int` or :class:`list`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="clear"><a class="viewcode-back" href="../../matrix.html#astra.matrix.clear">[docs]</a><span class="k">def</span> <span class="nf">clear</span><span class="p">():</span> + <span class="sd">"""Clear all matrix objects."""</span> + <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> +</div> +<div class="viewcode-block" id="create"><a class="viewcode-back" href="../../matrix.html#astra.matrix.create">[docs]</a><span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="n">data</span><span class="p">):</span> + <span class="sd">"""Create matrix object with data.</span> +<span class="sd"> </span> +<span class="sd"> :param data: Data to fill the created object with.</span> +<span class="sd"> :type data: :class:`scipy.sparse.csr_matrix`</span> +<span class="sd"> :returns: :class:`int` -- the ID of the constructed object.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> + + </div> +<div class="viewcode-block" id="store"><a class="viewcode-back" href="../../matrix.html#astra.matrix.store">[docs]</a><span class="k">def</span> <span class="nf">store</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">data</span><span class="p">):</span> + <span class="sd">"""Fill existing matrix object with data.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to fill.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :param data: Data to fill the object with.</span> +<span class="sd"> :type data: :class:`scipy.sparse.csr_matrix`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">store</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">data</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="get_size"><a class="viewcode-back" href="../../matrix.html#astra.matrix.get_size">[docs]</a><span class="k">def</span> <span class="nf">get_size</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get matrix dimensions.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`tuple` -- matrix dimensions.</span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">get_size</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> + </div> +<div class="viewcode-block" id="get"><a class="viewcode-back" href="../../matrix.html#astra.matrix.get">[docs]</a><span class="k">def</span> <span class="nf">get</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get a matrix object.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to get.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`scipy.sparse.csr_matrix` -- The object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="info"><a class="viewcode-back" href="../../matrix.html#astra.matrix.info">[docs]</a><span class="k">def</span> <span class="nf">info</span><span class="p">():</span> + <span class="sd">"""Print info on matrix objects in memory."""</span> + <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">info</span><span class="p">()</span> + + </div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" >Module code</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/projector.html b/python/docSRC/_build/html/_modules/astra/projector.html new file mode 100644 index 0000000..5982b54 --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/projector.html @@ -0,0 +1,205 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.projector — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.projector</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">projector_c</span> <span class="k">as</span> <span class="n">p</span> + +<div class="viewcode-block" id="create"><a class="viewcode-back" href="../../projector.html#astra.projector.create">[docs]</a><span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="n">config</span><span class="p">):</span> + <span class="sd">"""Create projector object.</span> +<span class="sd"> </span> +<span class="sd"> :param config: Projector options.</span> +<span class="sd"> :type config: :class:`dict`</span> +<span class="sd"> :returns: :class:`int` -- the ID of the constructed object.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">config</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="delete"><a class="viewcode-back" href="../../projector.html#astra.projector.delete">[docs]</a><span class="k">def</span> <span class="nf">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">):</span> + <span class="sd">"""Delete a projector object.</span> +<span class="sd"> </span> +<span class="sd"> :param ids: ID or list of ID's to delete.</span> +<span class="sd"> :type ids: :class:`int` or :class:`list`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="clear"><a class="viewcode-back" href="../../projector.html#astra.projector.clear">[docs]</a><span class="k">def</span> <span class="nf">clear</span><span class="p">():</span> + <span class="sd">"""Clear all projector objects."""</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> + +</div> +<div class="viewcode-block" id="info"><a class="viewcode-back" href="../../projector.html#astra.projector.info">[docs]</a><span class="k">def</span> <span class="nf">info</span><span class="p">():</span> + <span class="sd">"""Print info on projector objects in memory."""</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">info</span><span class="p">()</span> +</div> +<div class="viewcode-block" id="projection_geometry"><a class="viewcode-back" href="../../projector.html#astra.projector.projection_geometry">[docs]</a><span class="k">def</span> <span class="nf">projection_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get projection geometry of a projector.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of projector.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`dict` -- projection geometry</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">projection_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="volume_geometry"><a class="viewcode-back" href="../../projector.html#astra.projector.volume_geometry">[docs]</a><span class="k">def</span> <span class="nf">volume_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get volume geometry of a projector.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of projector.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`dict` -- volume geometry</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">volume_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="weights_single_ray"><a class="viewcode-back" href="../../projector.html#astra.projector.weights_single_ray">[docs]</a><span class="k">def</span> <span class="nf">weights_single_ray</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">projection_index</span><span class="p">,</span> <span class="n">detector_index</span><span class="p">):</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">weights_single_ray</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">projection_index</span><span class="p">,</span> <span class="n">detector_index</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="weights_projection"><a class="viewcode-back" href="../../projector.html#astra.projector.weights_projection">[docs]</a><span class="k">def</span> <span class="nf">weights_projection</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">projection_index</span><span class="p">):</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">weights_projection</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">projection_index</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="splat"><a class="viewcode-back" href="../../projector.html#astra.projector.splat">[docs]</a><span class="k">def</span> <span class="nf">splat</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">row</span><span class="p">,</span> <span class="n">col</span><span class="p">):</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">splat</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">row</span><span class="p">,</span> <span class="n">col</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="matrix"><a class="viewcode-back" href="../../projector.html#astra.projector.matrix">[docs]</a><span class="k">def</span> <span class="nf">matrix</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get sparse matrix of a projector.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of projector.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`int` -- ID of sparse matrix.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">matrix</span><span class="p">(</span><span class="n">i</span><span class="p">)</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" 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\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/index.html b/python/docSRC/_build/html/_modules/index.html new file mode 100644 index 0000000..a844d93 --- /dev/null +++ b/python/docSRC/_build/html/_modules/index.html @@ -0,0 +1,112 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Overview: module code — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../_static/jquery.js"></script> + <script type="text/javascript" src="../_static/underscore.js"></script> + <script type="text/javascript" src="../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>All modules for which code is available</h1> +<ul><li><a href="astra/ASTRAProjector.html">astra.ASTRAProjector</a></li> +<li><a href="astra/algorithm.html">astra.algorithm</a></li> +<li><a href="astra/astra.html">astra.astra</a></li> +<li><a href="astra/creators.html">astra.creators</a></li> +<li><a href="astra/data2d.html">astra.data2d</a></li> +<li><a href="astra/data3d.html">astra.data3d</a></li> +<li><a href="astra/functions.html">astra.functions</a></li> +<li><a href="astra/matlab.html">astra.matlab</a></li> +<li><a href="astra/matrix.html">astra.matrix</a></li> +<li><a href="astra/projector.html">astra.projector</a></li> +</ul> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/_sources/ASTRAProjector.txt b/python/docSRC/_build/html/_sources/ASTRAProjector.txt new file mode 100644 index 0000000..1c267e3 --- /dev/null +++ b/python/docSRC/_build/html/_sources/ASTRAProjector.txt @@ -0,0 +1,8 @@ +Helper class: the :mod:`ASTRAProjector` module +============================================== + +.. automodule:: astra.ASTRAProjector + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/algorithm.txt b/python/docSRC/_build/html/_sources/algorithm.txt new file mode 100644 index 0000000..83752bd --- /dev/null +++ b/python/docSRC/_build/html/_sources/algorithm.txt @@ -0,0 +1,8 @@ +Algorithms: the :mod:`algorithm` module +======================================= + +.. automodule:: astra.algorithm + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/astra.txt b/python/docSRC/_build/html/_sources/astra.txt new file mode 100644 index 0000000..5d5fdf0 --- /dev/null +++ b/python/docSRC/_build/html/_sources/astra.txt @@ -0,0 +1,8 @@ +Additional ASTRA methods: the :mod:`astra` module +======================================================== + +.. automodule:: astra.astra + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/creators.txt b/python/docSRC/_build/html/_sources/creators.txt new file mode 100644 index 0000000..d6249c3 --- /dev/null +++ b/python/docSRC/_build/html/_sources/creators.txt @@ -0,0 +1,8 @@ +Creation of objects: the :mod:`creators` module +=============================================== + +.. automodule:: astra.creators + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/data2d.txt b/python/docSRC/_build/html/_sources/data2d.txt new file mode 100644 index 0000000..342cbec --- /dev/null +++ b/python/docSRC/_build/html/_sources/data2d.txt @@ -0,0 +1,8 @@ +2D data objects: the :mod:`data2d` module +========================================= + +.. automodule:: astra.data2d + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/data3d.txt b/python/docSRC/_build/html/_sources/data3d.txt new file mode 100644 index 0000000..5b7de23 --- /dev/null +++ b/python/docSRC/_build/html/_sources/data3d.txt @@ -0,0 +1,8 @@ +3D data objects: the :mod:`data3d` module +========================================= + +.. automodule:: astra.data3d + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/functions.txt b/python/docSRC/_build/html/_sources/functions.txt new file mode 100644 index 0000000..749eb27 --- /dev/null +++ b/python/docSRC/_build/html/_sources/functions.txt @@ -0,0 +1,8 @@ +Additional functions: the :mod:`functions` module +================================================= + +.. automodule:: astra.functions + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/index.txt b/python/docSRC/_build/html/_sources/index.txt new file mode 100644 index 0000000..8d17a4a --- /dev/null +++ b/python/docSRC/_build/html/_sources/index.txt @@ -0,0 +1,34 @@ +.. .. documentation master file, created by + sphinx-quickstart on Wed Mar 13 16:36:32 2013. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to PyASTRAToolbox's documentation! +========================================== + +Contents: + +.. toctree:: + :maxdepth: 4 + + data2d + data3d + projector + algorithm + matrix + creators + functions + ASTRAProjector + matlab + astra +.. astra +.. builder + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/python/docSRC/_build/html/_sources/matlab.txt b/python/docSRC/_build/html/_sources/matlab.txt new file mode 100644 index 0000000..fb7033e --- /dev/null +++ b/python/docSRC/_build/html/_sources/matlab.txt @@ -0,0 +1,8 @@ +MATLAB compatibility interface: the :mod:`matlab` module +======================================================== + +.. automodule:: astra.matlab + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/matrix.txt b/python/docSRC/_build/html/_sources/matrix.txt new file mode 100644 index 0000000..6f11d8a --- /dev/null +++ b/python/docSRC/_build/html/_sources/matrix.txt @@ -0,0 +1,8 @@ +Sparse matrices: the :mod:`matrix` module +========================================= + +.. automodule:: astra.matrix + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/projector.txt b/python/docSRC/_build/html/_sources/projector.txt new file mode 100644 index 0000000..b0854e8 --- /dev/null +++ b/python/docSRC/_build/html/_sources/projector.txt @@ -0,0 +1,8 @@ +Projector object: the :mod:`projector` module +============================================= + +.. automodule:: astra.projector + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_static/ajax-loader.gif b/python/docSRC/_build/html/_static/ajax-loader.gif Binary files differnew file mode 100644 index 0000000..61faf8c --- /dev/null +++ b/python/docSRC/_build/html/_static/ajax-loader.gif diff --git a/python/docSRC/_build/html/_static/basic.css b/python/docSRC/_build/html/_static/basic.css new file mode 100644 index 0000000..967e36c --- /dev/null +++ b/python/docSRC/_build/html/_static/basic.css @@ -0,0 +1,537 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox input[type="text"] { + width: 170px; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + width: 30px; +} + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li div.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable dl, table.indextable dd { + margin-top: 0; + margin-bottom: 0; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- general body styles --------------------------------------------------- */ + +a.headerlink { + visibility: hidden; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.field-list ul { + padding-left: 1em; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px 7px 0 7px; + background-color: #ffe; + width: 40%; + float: right; +} + +p.sidebar-title { + font-weight: bold; +} + +/* -- topics ---------------------------------------------------------------- */ + +div.topic { + border: 1px solid #ccc; + padding: 7px 7px 0 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +div.admonition dl { + margin-bottom: 0; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + border: 0; + border-collapse: collapse; +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + 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+ + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + + + +/** + * Simple result scoring code. + */ +var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [filename, title, anchor, descr, score] + // and returns the new score. + /* + score: function(result) { + return result[4]; + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: {0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5}, // used to be unimportantResults + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + // query found in terms + term: 5 +}; + + +/** + * Search Module + */ +var Search = { + + _index : null, + _queued_query : null, + _pulse_status : -1, + + init : function() { + var params = $.getQueryParameters(); + if (params.q) { + var query = params.q[0]; + $('input[name="q"]')[0].value = query; + this.performSearch(query); + } + }, + + loadIndex : function(url) { + $.ajax({type: "GET", url: url, data: null, + dataType: "script", cache: true, + complete: function(jqxhr, textstatus) { + if (textstatus != "success") { + document.getElementById("searchindexloader").src = url; + } + }}); + }, + + setIndex : function(index) { + var q; + this._index = index; + if ((q = this._queued_query) !== null) { + this._queued_query = null; + Search.query(q); + } + }, + + hasIndex : function() { + return this._index !== null; + }, + + deferQuery : function(query) { + this._queued_query = query; + }, + + stopPulse : function() { + this._pulse_status = 0; + }, + + startPulse : function() { + if (this._pulse_status >= 0) + return; + function pulse() { + var i; + Search._pulse_status = (Search._pulse_status + 1) % 4; + var dotString = ''; + for (i = 0; i < Search._pulse_status; i++) + dotString += '.'; + Search.dots.text(dotString); + if (Search._pulse_status > -1) + window.setTimeout(pulse, 500); + } + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch : function(query) { + // create the required interface elements + this.out = $('#search-results'); + this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out); + this.dots = $('<span></span>').appendTo(this.title); + this.status = $('<p style="display: none"></p>').appendTo(this.out); + this.output = $('<ul class="search"/>').appendTo(this.out); + + $('#search-progress').text(_('Preparing search...')); + this.startPulse(); + + // index already loaded, the browser was quick! + if (this.hasIndex()) + this.query(query); + else + this.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query : function(query) { + var i; + var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"]; + + // stem the searchterms and add them to the correct list + var stemmer = new Stemmer(); + var searchterms = []; + var excluded = []; + var hlterms = []; + var tmp = query.split(/\s+/); + var objectterms = []; + for (i = 0; i < tmp.length; i++) { + if (tmp[i] !== "") { + objectterms.push(tmp[i].toLowerCase()); + } + + if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) || + tmp[i] === "") { + // skip this "word" + continue; + } + // stem the word + var word = stemmer.stemWord(tmp[i].toLowerCase()); + var toAppend; + // select the correct list + if (word[0] == '-') { + toAppend = excluded; + word = word.substr(1); + } + else { + toAppend = searchterms; + hlterms.push(tmp[i].toLowerCase()); + } + // only add if not already in the list + if (!$u.contains(toAppend, word)) + toAppend.push(word); + } + var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" ")); + + // console.debug('SEARCH: searching for:'); + // console.info('required: ', searchterms); + // console.info('excluded: ', excluded); + + // prepare search + var terms = this._index.terms; + var titleterms = this._index.titleterms; + + // array of [filename, title, anchor, descr, score] + var results = []; + $('#search-progress').empty(); + + // lookup as object + for (i = 0; i < objectterms.length; i++) { + var others = [].concat(objectterms.slice(0, i), + objectterms.slice(i+1, objectterms.length)); + results = results.concat(this.performObjectSearch(objectterms[i], others)); + } + + // lookup as search terms in fulltext + results = results.concat(this.performTermsSearch(searchterms, excluded, terms, Scorer.term)) + .concat(this.performTermsSearch(searchterms, excluded, titleterms, Scorer.title)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + for (i = 0; i < results.length; i++) + results[i][4] = Scorer.score(results[i]); + } + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort(function(a, b) { + var left = a[4]; + var right = b[4]; + if (left > right) { + return 1; + } else if (left < right) { + return -1; + } else { + // same score: sort alphabetically + left = a[1].toLowerCase(); + right = b[1].toLowerCase(); + return (left > right) ? -1 : ((left < right) ? 1 : 0); + } + }); + + // for debugging + //Search.lastresults = results.slice(); // a copy + //console.info('search results:', Search.lastresults); + + // print the results + var resultCount = results.length; + function displayNextItem() { + // results left, load the summary and display it + if (results.length) { + var item = results.pop(); + var listItem = $('<li style="display:none"></li>'); + if (DOCUMENTATION_OPTIONS.FILE_SUFFIX === '') { + // dirhtml builder + var dirname = item[0] + '/'; + if (dirname.match(/\/index\/$/)) { + dirname = dirname.substring(0, dirname.length-6); + } else if (dirname == 'index/') { + dirname = ''; + } + listItem.append($('<a/>').attr('href', + DOCUMENTATION_OPTIONS.URL_ROOT + dirname + + highlightstring + item[2]).html(item[1])); + } else { + // normal html builders + listItem.append($('<a/>').attr('href', + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX + + highlightstring + item[2]).html(item[1])); + } + if (item[3]) { + listItem.append($('<span> (' + item[3] + ')</span>')); + Search.output.append(listItem); + listItem.slideDown(5, function() { + displayNextItem(); + }); + } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) { + $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[0] + '.txt', + dataType: "text", + complete: function(jqxhr, textstatus) { + var data = jqxhr.responseText; + if (data !== '') { + listItem.append(Search.makeSearchSummary(data, searchterms, hlterms)); + } + Search.output.append(listItem); + listItem.slideDown(5, function() { + displayNextItem(); + }); + }}); + } else { + // no source available, just display title + Search.output.append(listItem); + listItem.slideDown(5, function() { + displayNextItem(); + }); + } + } + // search finished, update title and status message + else { + Search.stopPulse(); + Search.title.text(_('Search Results')); + if (!resultCount) + Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.')); + else + Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount)); + Search.status.fadeIn(500); + } + } + displayNextItem(); + }, + + /** + * search for object names + */ + performObjectSearch : function(object, otherterms) { + var filenames = this._index.filenames; + var objects = this._index.objects; + var objnames = this._index.objnames; + var titles = this._index.titles; + + var i; + var results = []; + + for (var prefix in objects) { + for (var name in objects[prefix]) { + var fullname = (prefix ? prefix + '.' : '') + name; + if (fullname.toLowerCase().indexOf(object) > -1) { + var score = 0; + var parts = fullname.split('.'); + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullname == object || parts[parts.length - 1] == object) { + score += Scorer.objNameMatch; + // matches in last name + } else if (parts[parts.length - 1].indexOf(object) > -1) { + score += Scorer.objPartialMatch; + } + var match = objects[prefix][name]; + var objname = objnames[match[1]][2]; + var title = titles[match[0]]; + // If more than one term searched for, we require other words to be + // found in the name/title/description + if (otherterms.length > 0) { + var haystack = (prefix + ' ' + name + ' ' + + objname + ' ' + title).toLowerCase(); + var allfound = true; + for (i = 0; i < otherterms.length; i++) { + if (haystack.indexOf(otherterms[i]) == -1) { + allfound = false; + break; + } + } + if (!allfound) { + continue; + } + } + var descr = objname + _(', in ') + title; + + var anchor = match[3]; + if (anchor === '') + anchor = fullname; + else if (anchor == '-') + anchor = objnames[match[1]][1] + '-' + fullname; + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) { + score += Scorer.objPrio[match[2]]; + } else { + score += Scorer.objPrioDefault; + } + results.push([filenames[match[0]], fullname, '#'+anchor, descr, score]); + } + } + } + + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch : function(searchterms, excluded, terms, score) { + var filenames = this._index.filenames; + var titles = this._index.titles; + + var i, j, file, files; + var fileMap = {}; + var results = []; + + // perform the search on the required terms + for (i = 0; i < searchterms.length; i++) { + var word = searchterms[i]; + // no match but word was a required one + if ((files = terms[word]) === undefined) + break; + if (files.length === undefined) { + files = [files]; + } + // create the mapping + for (j = 0; j < files.length; j++) { + file = files[j]; + if (file in fileMap) + fileMap[file].push(word); + else + fileMap[file] = [word]; + } + } + + // now check if the files don't contain excluded terms + for (file in fileMap) { + var valid = true; + + // check if all requirements are matched + if (fileMap[file].length != searchterms.length) + continue; + + // ensure that none of the excluded terms is in the search result + for (i = 0; i < excluded.length; i++) { + if (terms[excluded[i]] == file || + $u.contains(terms[excluded[i]] || [], file)) { + valid = false; + break; + } + } + + // if we have still a valid result we can add it to the result list + if (valid) { + results.push([filenames[file], titles[file], '', null, score]); + } + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words, hlwords is the list of normal, unstemmed + * words. the first one is used to find the occurance, the + * latter for highlighting it. + */ + makeSearchSummary : function(text, keywords, hlwords) { + var textLower = text.toLowerCase(); + var start = 0; + $.each(keywords, function() { + var i = textLower.indexOf(this.toLowerCase()); + if (i > -1) + start = i; + }); + start = Math.max(start - 120, 0); + var excerpt = ((start > 0) ? 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diff --git a/python/docSRC/_build/html/_static/up-pressed.png b/python/docSRC/_build/html/_static/up-pressed.png Binary files differnew file mode 100644 index 0000000..8bd587a --- /dev/null +++ b/python/docSRC/_build/html/_static/up-pressed.png diff --git a/python/docSRC/_build/html/_static/up.png b/python/docSRC/_build/html/_static/up.png Binary files differnew file mode 100644 index 0000000..b946256 --- /dev/null +++ b/python/docSRC/_build/html/_static/up.png diff --git a/python/docSRC/_build/html/_static/websupport.js b/python/docSRC/_build/html/_static/websupport.js new file mode 100644 index 0000000..71c0a13 --- /dev/null +++ b/python/docSRC/_build/html/_static/websupport.js @@ -0,0 +1,808 @@ +/* + * websupport.js + * ~~~~~~~~~~~~~ + * + * sphinx.websupport utilties for all documentation. + * + * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +(function($) { + $.fn.autogrow = function() { + return this.each(function() { + var textarea = this; + + $.fn.autogrow.resize(textarea); + + $(textarea) + .focus(function() { + textarea.interval = setInterval(function() { + $.fn.autogrow.resize(textarea); + }, 500); + }) + .blur(function() { + clearInterval(textarea.interval); + }); + }); + }; + + $.fn.autogrow.resize = function(textarea) { + var lineHeight = parseInt($(textarea).css('line-height'), 10); + var lines = textarea.value.split('\n'); + var columns = textarea.cols; + var lineCount = 0; + $.each(lines, function() { + lineCount += Math.ceil(this.length / columns) || 1; + }); + var height = lineHeight * (lineCount + 1); + $(textarea).css('height', height); + }; +})(jQuery); + +(function($) { + var comp, by; + + function init() { + initEvents(); + initComparator(); + } + + function initEvents() { + $('a.comment-close').live("click", function(event) { + event.preventDefault(); + hide($(this).attr('id').substring(2)); + }); + $('a.vote').live("click", function(event) { + event.preventDefault(); + handleVote($(this)); + }); + $('a.reply').live("click", function(event) { + event.preventDefault(); + openReply($(this).attr('id').substring(2)); + }); + $('a.close-reply').live("click", function(event) { + event.preventDefault(); + closeReply($(this).attr('id').substring(2)); + }); + $('a.sort-option').live("click", function(event) { + event.preventDefault(); + handleReSort($(this)); + }); + $('a.show-proposal').live("click", function(event) { + event.preventDefault(); + showProposal($(this).attr('id').substring(2)); + }); + $('a.hide-proposal').live("click", function(event) { + event.preventDefault(); + hideProposal($(this).attr('id').substring(2)); + }); + $('a.show-propose-change').live("click", function(event) { + event.preventDefault(); + showProposeChange($(this).attr('id').substring(2)); + }); + $('a.hide-propose-change').live("click", function(event) { + event.preventDefault(); + hideProposeChange($(this).attr('id').substring(2)); + }); + $('a.accept-comment').live("click", function(event) { + event.preventDefault(); + acceptComment($(this).attr('id').substring(2)); + }); + $('a.delete-comment').live("click", function(event) { + event.preventDefault(); + deleteComment($(this).attr('id').substring(2)); + }); + $('a.comment-markup').live("click", function(event) { + event.preventDefault(); + toggleCommentMarkupBox($(this).attr('id').substring(2)); + }); + } + + /** + * Set comp, which is a comparator function used for sorting and + * inserting comments into the list. + */ + function setComparator() { + // If the first three letters are "asc", sort in ascending order + // and remove the prefix. + if (by.substring(0,3) == 'asc') { + var i = by.substring(3); + comp = function(a, b) { return a[i] - b[i]; }; + } else { + // Otherwise sort in descending order. + comp = function(a, b) { return b[by] - a[by]; }; + } + + // Reset link styles and format the selected sort option. + $('a.sel').attr('href', '#').removeClass('sel'); + $('a.by' + by).removeAttr('href').addClass('sel'); + } + + /** + * Create a comp function. If the user has preferences stored in + * the sortBy cookie, use those, otherwise use the default. + */ + function initComparator() { + by = 'rating'; // Default to sort by rating. + // If the sortBy cookie is set, use that instead. + if (document.cookie.length > 0) { + var start = document.cookie.indexOf('sortBy='); + if (start != -1) { + start = start + 7; + var end = document.cookie.indexOf(";", start); + if (end == -1) { + end = document.cookie.length; + by = unescape(document.cookie.substring(start, end)); + } + } + } + setComparator(); + } + + /** + * Show a comment div. + */ + function show(id) { + $('#ao' + id).hide(); + $('#ah' + id).show(); + var context = $.extend({id: id}, opts); + var popup = $(renderTemplate(popupTemplate, context)).hide(); + popup.find('textarea[name="proposal"]').hide(); + popup.find('a.by' + by).addClass('sel'); + var form = popup.find('#cf' + id); + form.submit(function(event) { + event.preventDefault(); + addComment(form); + }); + $('#s' + id).after(popup); + popup.slideDown('fast', function() { + getComments(id); + }); + } + + /** + * Hide a comment div. + */ + function hide(id) { + $('#ah' + id).hide(); + $('#ao' + id).show(); + var div = $('#sc' + id); + div.slideUp('fast', function() { + div.remove(); + }); + } + + /** + * Perform an ajax request to get comments for a node + * and insert the comments into the comments tree. + */ + function getComments(id) { + $.ajax({ + type: 'GET', + url: opts.getCommentsURL, + data: {node: id}, + success: function(data, textStatus, request) { + var ul = $('#cl' + id); + var speed = 100; + $('#cf' + id) + .find('textarea[name="proposal"]') + .data('source', data.source); + + if (data.comments.length === 0) { + ul.html('<li>No comments yet.</li>'); + ul.data('empty', true); + } else { + // If there are comments, sort them and put them in the list. + var comments = sortComments(data.comments); + speed = data.comments.length * 100; + appendComments(comments, ul); + ul.data('empty', false); + } + $('#cn' + id).slideUp(speed + 200); + ul.slideDown(speed); + }, + error: function(request, textStatus, error) { + showError('Oops, there was a problem retrieving the comments.'); + }, + dataType: 'json' + }); + } + + /** + * Add a comment via ajax and insert the comment into the comment tree. + */ + function addComment(form) { + var node_id = form.find('input[name="node"]').val(); + var parent_id = form.find('input[name="parent"]').val(); + var text = form.find('textarea[name="comment"]').val(); + var proposal = form.find('textarea[name="proposal"]').val(); + + if (text == '') { + showError('Please enter a comment.'); + return; + } + + // Disable the form that is being submitted. + form.find('textarea,input').attr('disabled', 'disabled'); + + // Send the comment to the server. + $.ajax({ + type: "POST", + url: opts.addCommentURL, + dataType: 'json', + data: { + node: node_id, + parent: parent_id, + text: text, + proposal: proposal + }, + success: function(data, textStatus, error) { + // Reset the form. + if (node_id) { + hideProposeChange(node_id); + } + form.find('textarea') + .val('') + .add(form.find('input')) + .removeAttr('disabled'); + var ul = $('#cl' + (node_id || parent_id)); + if (ul.data('empty')) { + $(ul).empty(); + ul.data('empty', false); + } + insertComment(data.comment); + var ao = $('#ao' + node_id); + ao.find('img').attr({'src': opts.commentBrightImage}); + if (node_id) { + // if this was a "root" comment, remove the commenting box + // (the user can get it back by reopening the comment popup) + $('#ca' + node_id).slideUp(); + } + }, + error: function(request, textStatus, error) { + form.find('textarea,input').removeAttr('disabled'); + showError('Oops, there was a problem adding the comment.'); + } + }); + } + + /** + * Recursively append comments to the main comment list and children + * lists, creating the comment tree. + */ + function appendComments(comments, ul) { + $.each(comments, function() { + var div = createCommentDiv(this); + ul.append($(document.createElement('li')).html(div)); + appendComments(this.children, div.find('ul.comment-children')); + // To avoid stagnating data, don't store the comments children in data. + this.children = null; + div.data('comment', this); + }); + } + + /** + * After adding a new comment, it must be inserted in the correct + * location in the comment tree. + */ + function insertComment(comment) { + var div = createCommentDiv(comment); + + // To avoid stagnating data, don't store the comments children in data. + comment.children = null; + div.data('comment', comment); + + var ul = $('#cl' + (comment.node || comment.parent)); + var siblings = getChildren(ul); + + var li = $(document.createElement('li')); + li.hide(); + + // Determine where in the parents children list to insert this comment. + for(i=0; i < siblings.length; i++) { + if (comp(comment, siblings[i]) <= 0) { + $('#cd' + siblings[i].id) + .parent() + .before(li.html(div)); + li.slideDown('fast'); + return; + } + } + + // If we get here, this comment rates lower than all the others, + // or it is the only comment in the list. + ul.append(li.html(div)); + li.slideDown('fast'); + } + + function acceptComment(id) { + $.ajax({ + type: 'POST', + url: opts.acceptCommentURL, + data: {id: id}, + success: function(data, textStatus, request) { + $('#cm' + id).fadeOut('fast'); + $('#cd' + id).removeClass('moderate'); + }, + error: function(request, textStatus, error) { + showError('Oops, there was a problem accepting the comment.'); + } + }); + } + + function deleteComment(id) { + $.ajax({ + type: 'POST', + url: opts.deleteCommentURL, + data: {id: id}, + success: function(data, textStatus, request) { + var div = $('#cd' + id); + if (data == 'delete') { + // Moderator mode: remove the comment and all children immediately + div.slideUp('fast', function() { + div.remove(); + }); + return; + } + // User mode: only mark the comment as deleted + div + .find('span.user-id:first') + .text('[deleted]').end() + .find('div.comment-text:first') + .text('[deleted]').end() + .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id + + ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id) + .remove(); + var comment = div.data('comment'); + comment.username = '[deleted]'; + comment.text = '[deleted]'; + div.data('comment', comment); + }, + error: function(request, textStatus, error) { + showError('Oops, there was a problem deleting the comment.'); + } + }); + } + + function showProposal(id) { + $('#sp' + id).hide(); + $('#hp' + id).show(); + $('#pr' + id).slideDown('fast'); + } + + function hideProposal(id) { + $('#hp' + id).hide(); + $('#sp' + id).show(); + $('#pr' + id).slideUp('fast'); + } + + function showProposeChange(id) { + $('#pc' + id).hide(); + $('#hc' + id).show(); + var textarea = $('#pt' + id); + textarea.val(textarea.data('source')); + $.fn.autogrow.resize(textarea[0]); + textarea.slideDown('fast'); + } + + function hideProposeChange(id) { + $('#hc' + id).hide(); + $('#pc' + id).show(); + var textarea = $('#pt' + id); + textarea.val('').removeAttr('disabled'); + textarea.slideUp('fast'); + } + + function toggleCommentMarkupBox(id) { + $('#mb' + id).toggle(); + } + + /** Handle when the user clicks on a sort by link. */ + function handleReSort(link) { + var classes = link.attr('class').split(/\s+/); + for (var i=0; i<classes.length; i++) { + if (classes[i] != 'sort-option') { + by = classes[i].substring(2); + } + } + setComparator(); + // Save/update the sortBy cookie. + var expiration = new Date(); + expiration.setDate(expiration.getDate() + 365); + document.cookie= 'sortBy=' + escape(by) + + ';expires=' + expiration.toUTCString(); + $('ul.comment-ul').each(function(index, ul) { + var comments = getChildren($(ul), true); + comments = sortComments(comments); + appendComments(comments, $(ul).empty()); + }); + } + + /** + * Function to process a vote when a user clicks an arrow. + */ + function handleVote(link) { + if (!opts.voting) { + showError("You'll need to login to vote."); + return; + } + + var id = link.attr('id'); + if (!id) { + // Didn't click on one of the voting arrows. + return; + } + // If it is an unvote, the new vote value is 0, + // Otherwise it's 1 for an upvote, or -1 for a downvote. + var value = 0; + if (id.charAt(1) != 'u') { + value = id.charAt(0) == 'u' ? 1 : -1; + } + // The data to be sent to the server. + var d = { + comment_id: id.substring(2), + value: value + }; + + // Swap the vote and unvote links. + link.hide(); + $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id) + .show(); + + // The div the comment is displayed in. + var div = $('div#cd' + d.comment_id); + var data = div.data('comment'); + + // If this is not an unvote, and the other vote arrow has + // already been pressed, unpress it. + if ((d.value !== 0) && (data.vote === d.value * -1)) { + $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide(); + $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show(); + } + + // Update the comments rating in the local data. + data.rating += (data.vote === 0) ? d.value : (d.value - data.vote); + data.vote = d.value; + div.data('comment', data); + + // Change the rating text. + div.find('.rating:first') + .text(data.rating + ' point' + (data.rating == 1 ? '' : 's')); + + // Send the vote information to the server. + $.ajax({ + type: "POST", + url: opts.processVoteURL, + data: d, + error: function(request, textStatus, error) { + showError('Oops, there was a problem casting that vote.'); + } + }); + } + + /** + * Open a reply form used to reply to an existing comment. + */ + function openReply(id) { + // Swap out the reply link for the hide link + $('#rl' + id).hide(); + $('#cr' + id).show(); + + // Add the reply li to the children ul. + var div = $(renderTemplate(replyTemplate, {id: id})).hide(); + $('#cl' + id) + .prepend(div) + // Setup the submit handler for the reply form. + .find('#rf' + id) + .submit(function(event) { + event.preventDefault(); + addComment($('#rf' + id)); + closeReply(id); + }) + .find('input[type=button]') + .click(function() { + closeReply(id); + }); + div.slideDown('fast', function() { + $('#rf' + id).find('textarea').focus(); + }); + } + + /** + * Close the reply form opened with openReply. + */ + function closeReply(id) { + // Remove the reply div from the DOM. + $('#rd' + id).slideUp('fast', function() { + $(this).remove(); + }); + + // Swap out the hide link for the reply link + $('#cr' + id).hide(); + $('#rl' + id).show(); + } + + /** + * Recursively sort a tree of comments using the comp comparator. + */ + function sortComments(comments) { + comments.sort(comp); + $.each(comments, function() { + this.children = sortComments(this.children); + }); + return comments; + } + + /** + * Get the children comments from a ul. If recursive is true, + * recursively include childrens' children. + */ + function getChildren(ul, recursive) { + var children = []; + ul.children().children("[id^='cd']") + .each(function() { + var comment = $(this).data('comment'); + if (recursive) + comment.children = getChildren($(this).find('#cl' + comment.id), true); + children.push(comment); + }); + return children; + } + + /** Create a div to display a comment in. */ + function createCommentDiv(comment) { + if (!comment.displayed && !opts.moderator) { + return $('<div class="moderate">Thank you! Your comment will show up ' + + 'once it is has been approved by a moderator.</div>'); + } + // Prettify the comment rating. + comment.pretty_rating = comment.rating + ' point' + + (comment.rating == 1 ? '' : 's'); + // Make a class (for displaying not yet moderated comments differently) + comment.css_class = comment.displayed ? '' : ' moderate'; + // Create a div for this comment. + var context = $.extend({}, opts, comment); + var div = $(renderTemplate(commentTemplate, context)); + + // If the user has voted on this comment, highlight the correct arrow. + if (comment.vote) { + var direction = (comment.vote == 1) ? 'u' : 'd'; + div.find('#' + direction + 'v' + comment.id).hide(); + div.find('#' + direction + 'u' + comment.id).show(); + } + + if (opts.moderator || comment.text != '[deleted]') { + div.find('a.reply').show(); + if (comment.proposal_diff) + div.find('#sp' + comment.id).show(); + if (opts.moderator && !comment.displayed) + div.find('#cm' + comment.id).show(); + if (opts.moderator || (opts.username == comment.username)) + div.find('#dc' + comment.id).show(); + } + return div; + } + + /** + * A simple template renderer. Placeholders such as <%id%> are replaced + * by context['id'] with items being escaped. Placeholders such as <#id#> + * are not escaped. + */ + function renderTemplate(template, context) { + var esc = $(document.createElement('div')); + + function handle(ph, escape) { + var cur = context; + $.each(ph.split('.'), function() { + cur = cur[this]; + }); + return escape ? esc.text(cur || "").html() : cur; + } + + return template.replace(/<([%#])([\w\.]*)\1>/g, function() { + return handle(arguments[2], arguments[1] == '%' ? true : false); + }); + } + + /** Flash an error message briefly. */ + function showError(message) { + $(document.createElement('div')).attr({'class': 'popup-error'}) + .append($(document.createElement('div')) + .attr({'class': 'error-message'}).text(message)) + .appendTo('body') + .fadeIn("slow") + .delay(2000) + .fadeOut("slow"); + } + + /** Add a link the user uses to open the comments popup. */ + $.fn.comment = function() { + return this.each(function() { + var id = $(this).attr('id').substring(1); + var count = COMMENT_METADATA[id]; + var title = count + ' comment' + (count == 1 ? '' : 's'); + var image = count > 0 ? opts.commentBrightImage : opts.commentImage; + var addcls = count == 0 ? ' nocomment' : ''; + $(this) + .append( + $(document.createElement('a')).attr({ + href: '#', + 'class': 'sphinx-comment-open' + addcls, + id: 'ao' + id + }) + .append($(document.createElement('img')).attr({ + src: image, + alt: 'comment', + title: title + })) + .click(function(event) { + event.preventDefault(); + show($(this).attr('id').substring(2)); + }) + ) + .append( + $(document.createElement('a')).attr({ + href: '#', + 'class': 'sphinx-comment-close hidden', + id: 'ah' + id + }) + .append($(document.createElement('img')).attr({ + src: opts.closeCommentImage, + alt: 'close', + title: 'close' + })) + .click(function(event) { + event.preventDefault(); + hide($(this).attr('id').substring(2)); + }) + ); + }); + }; + + var opts = { + processVoteURL: '/_process_vote', + addCommentURL: '/_add_comment', + getCommentsURL: '/_get_comments', + acceptCommentURL: '/_accept_comment', + deleteCommentURL: '/_delete_comment', + commentImage: '/static/_static/comment.png', + closeCommentImage: 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xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Algorithms: the algorithm module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="index.html" /> + <link rel="next" title="Sparse matrices: the matrix module" href="matrix.html" /> + <link rel="prev" title="Projector object: the projector module" href="projector.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="matrix.html" title="Sparse matrices: the matrix module" + accesskey="N">next</a> |</li> + <li class="right" > + <a href="projector.html" title="Projector object: the projector module" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.algorithm"> +<span id="algorithms-the-algorithm-module"></span><h1>Algorithms: the <tt class="xref py py-mod docutils literal"><span class="pre">algorithm</span></tt> module<a class="headerlink" href="#module-astra.algorithm" title="Permalink to this headline">¶</a></h1> +<dl class="function"> +<dt id="astra.algorithm.clear"> +<tt class="descclassname">astra.algorithm.</tt><tt class="descname">clear</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/algorithm.html#clear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.algorithm.clear" title="Permalink to this definition">¶</a></dt> +<dd><p>Clear all matrix objects.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.algorithm.create"> +<tt class="descclassname">astra.algorithm.</tt><tt class="descname">create</tt><big>(</big><em>config</em><big>)</big><a class="reference internal" href="_modules/astra/algorithm.html#create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.algorithm.create" title="Permalink to this definition">¶</a></dt> +<dd><p>Create algorithm object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>config</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Algorithm options.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – the ID of the constructed object.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.algorithm.delete"> +<tt class="descclassname">astra.algorithm.</tt><tt class="descname">delete</tt><big>(</big><em>ids</em><big>)</big><a class="reference internal" href="_modules/astra/algorithm.html#delete"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.algorithm.delete" title="Permalink to this definition">¶</a></dt> +<dd><p>Delete a matrix object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ids</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a>) – ID or list of ID’s to delete.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.algorithm.get_res_norm"> +<tt class="descclassname">astra.algorithm.</tt><tt class="descname">get_res_norm</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/algorithm.html#get_res_norm"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.algorithm.get_res_norm" title="Permalink to this definition">¶</a></dt> +<dd><p>Get residual norm of algorithm.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a> – The residual norm.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.algorithm.info"> +<tt class="descclassname">astra.algorithm.</tt><tt class="descname">info</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/algorithm.html#info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.algorithm.info" title="Permalink to this definition">¶</a></dt> +<dd><p>Print info on matrix objects in memory.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.algorithm.run"> +<tt class="descclassname">astra.algorithm.</tt><tt class="descname">run</tt><big>(</big><em>i</em>, <em>iterations=1</em><big>)</big><a class="reference internal" href="_modules/astra/algorithm.html#run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.algorithm.run" title="Permalink to this definition">¶</a></dt> +<dd><p>Run an algorithm.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object.</li> +<li><strong>iterations</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of iterations to run.</li> +</ul> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="projector.html" + title="previous chapter">Projector object: the <tt class="docutils literal"><span class="pre">projector</span></tt> module</a></p> + <h4>Next topic</h4> + <p class="topless"><a href="matrix.html" + title="next chapter">Sparse matrices: the <tt class="docutils literal"><span class="pre">matrix</span></tt> module</a></p> + <h3>This Page</h3> + <ul class="this-page-menu"> + <li><a href="_sources/algorithm.txt" + rel="nofollow">Show Source</a></li> + </ul> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" 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\ No newline at end of file diff --git a/python/docSRC/_build/html/astra.html b/python/docSRC/_build/html/astra.html new file mode 100644 index 0000000..42d68b8 --- /dev/null +++ b/python/docSRC/_build/html/astra.html @@ -0,0 +1,169 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Additional ASTRA methods: the astra module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script 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class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.astra"> +<span id="additional-astra-methods-the-astra-module"></span><h1>Additional ASTRA methods: the <tt class="xref py py-mod docutils literal"><span class="pre">astra</span></tt> module<a class="headerlink" href="#module-astra.astra" title="Permalink to this headline">¶</a></h1> +<dl class="function"> +<dt id="astra.astra.credits"> +<tt class="descclassname">astra.astra.</tt><tt class="descname">credits</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/astra.html#credits"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.astra.credits" title="Permalink to this definition">¶</a></dt> +<dd><p>Print credits of the ASTRA Toolbox.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.astra.set_gpu_index"> +<tt class="descclassname">astra.astra.</tt><tt class="descname">set_gpu_index</tt><big>(</big><em>idx</em><big>)</big><a class="reference internal" href="_modules/astra/astra.html#set_gpu_index"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.astra.set_gpu_index" title="Permalink to this definition">¶</a></dt> +<dd><p>Set default GPU index to use.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>idx</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – GPU index</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.astra.use_cuda"> +<tt class="descclassname">astra.astra.</tt><tt class="descname">use_cuda</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/astra.html#use_cuda"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.astra.use_cuda" title="Permalink to this definition">¶</a></dt> +<dd><p>Test if CUDA is enabled.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a> – <tt class="docutils literal"><span class="pre">True</span></tt> if CUDA is enabled.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.astra.version"> +<tt class="descclassname">astra.astra.</tt><tt class="descname">version</tt><big>(</big><em>printToScreen=False</em><big>)</big><a class="reference internal" href="_modules/astra/astra.html#version"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.astra.version" title="Permalink to this definition">¶</a></dt> +<dd><p>Check version of the ASTRA Toolbox.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>printToScreen</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If <tt class="docutils literal"><span class="pre">True</span></tt>, print version string. If <tt class="docutils literal"><span class="pre">False</span></tt>, return version integer.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><tt class="xref py py-class docutils literal"><span class="pre">string</span></tt> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – The version string or integer.</td> +</tr> +</tbody> +</table> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="matlab.html" + title="previous chapter">MATLAB compatibility interface: the <tt class="docutils literal"><span class="pre">matlab</span></tt> module</a></p> + <h3>This Page</h3> + <ul class="this-page-menu"> + <li><a href="_sources/astra.txt" + rel="nofollow">Show Source</a></li> + </ul> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="matlab.html" title="MATLAB compatibility interface: the matlab module" + >previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/creators.html b/python/docSRC/_build/html/creators.html new file mode 100644 index 0000000..2f29232 --- /dev/null +++ b/python/docSRC/_build/html/creators.html @@ -0,0 +1,520 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Creation of objects: the creators module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + 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href="matrix.html" title="Sparse matrices: the matrix module" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.creators"> +<span id="creation-of-objects-the-creators-module"></span><h1>Creation of objects: the <tt class="xref py py-mod docutils literal"><span class="pre">creators</span></tt> module<a class="headerlink" href="#module-astra.creators" title="Permalink to this headline">¶</a></h1> +<dl class="function"> +<dt id="astra.creators.astra_dict"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">astra_dict</tt><big>(</big><em>intype</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#astra_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.astra_dict" title="Permalink to this definition">¶</a></dt> +<dd><p>Creates a dict to use with the ASTRA Toolbox.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>intype</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Type of the ASTRA object.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a> – An ASTRA dict of type <tt class="docutils literal"><span class="pre">intype</span></tt>.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_backprojection"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_backprojection</tt><big>(</big><em>data</em>, <em>proj_id</em>, <em>useCUDA=False</em>, <em>returnData=True</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_backprojection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_backprojection" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a backprojection of a sinogram (2D).</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Sinogram data or ID.</li> +<li><strong>proj_id</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of the projector to use.</li> +<li><strong>useCUDA</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If <tt class="docutils literal"><span class="pre">True</span></tt>, use CUDA for the calculation.</li> +<li><strong>returnData</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If False, only return the ID of the backprojection.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>, <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – If <tt class="docutils literal"><span class="pre">returnData=False</span></tt>, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_backprojection3d_gpu"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_backprojection3d_gpu</tt><big>(</big><em>data</em>, <em>proj_geom</em>, <em>vol_geom</em>, <em>returnData=True</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_backprojection3d_gpu"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_backprojection3d_gpu" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a backprojection of a sinogram (3D) using CUDA.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Sinogram data or ID.</li> +<li><strong>proj_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Projection geometry.</li> +<li><strong>vol_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Volume geometry.</li> +<li><strong>returnData</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If False, only return the ID of the backprojection.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>, <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – If <tt class="docutils literal"><span class="pre">returnData=False</span></tt>, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_proj_geom"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_proj_geom</tt><big>(</big><em>intype</em>, <em>*args</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_proj_geom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_proj_geom" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a projection geometry.</p> +<p>This method can be called in a number of ways:</p> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('parallel',</span> <span class="pre">detector_spacing,</span> <span class="pre">det_count,</span> <span class="pre">angles)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>detector_spacing</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Distance between two adjacent detector pixels.</li> +<li><strong>det_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixels.</li> +<li><strong>angles</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Array of angles in radians.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A parallel projection geometry.</p> +</td> +</tr> +</tbody> +</table> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('fanflat',</span> <span class="pre">det_width,</span> <span class="pre">det_count,</span> <span class="pre">angles,</span> <span class="pre">source_origin,</span> <span class="pre">source_det)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>det_width</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Size of a detector pixel.</li> +<li><strong>det_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixels.</li> +<li><strong>angles</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Array of angles in radians.</li> +<li><strong>source_origin</strong> – Position of the source.</li> +<li><strong>source_det</strong> – Position of the detector</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A fan-beam projection geometry.</p> +</td> +</tr> +</tbody> +</table> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('fanflat_vec',</span> <span class="pre">det_count,</span> <span class="pre">V)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>det_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixels.</li> +<li><strong>V</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Vector array.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A fan-beam projection geometry.</p> +</td> +</tr> +</tbody> +</table> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('parallel3d',</span> <span class="pre">detector_spacing_x,</span> <span class="pre">detector_spacing_y,</span> <span class="pre">det_row_count,</span> <span class="pre">det_col_count,</span> <span class="pre">angles)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>detector_spacing_*</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Distance between two adjacent detector pixels.</li> +<li><strong>det_row_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel rows.</li> +<li><strong>det_col_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel columns.</li> +<li><strong>angles</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Array of angles in radians.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A parallel projection geometry.</p> +</td> +</tr> +</tbody> +</table> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('cone',</span> <span class="pre">detector_spacing_x,</span> <span class="pre">detector_spacing_y,</span> <span class="pre">det_row_count,</span> <span class="pre">det_col_count,</span> <span class="pre">angles,</span> <span class="pre">source_origin,</span> <span class="pre">source_det)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>detector_spacing_*</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Distance between two adjacent detector pixels.</li> +<li><strong>det_row_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel rows.</li> +<li><strong>det_col_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel columns.</li> +<li><strong>angles</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Array of angles in radians.</li> +<li><strong>source_origin</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Distance between point source and origin.</li> +<li><strong>source_det</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Distance between the detector and origin.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A cone-beam projection geometry.</p> +</td> +</tr> +</tbody> +</table> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('cone_vec',</span> <span class="pre">det_row_count,</span> <span class="pre">det_col_count,</span> <span class="pre">V)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>det_row_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel rows.</li> +<li><strong>det_col_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel columns.</li> +<li><strong>V</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Vector array.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A cone-beam projection geometry.</p> +</td> +</tr> +</tbody> +</table> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('parallel3d_vec',</span> <span class="pre">det_row_count,</span> <span class="pre">det_col_count,</span> <span class="pre">V)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>det_row_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel rows.</li> +<li><strong>det_col_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel columns.</li> +<li><strong>V</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Vector array.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A parallel projection geometry.</p> +</td> +</tr> +</tbody> +</table> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('sparse_matrix',</span> <span class="pre">det_width,</span> <span class="pre">det_count,</span> <span class="pre">angles,</span> <span class="pre">matrix_id)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>det_width</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Size of a detector pixel.</li> +<li><strong>det_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixels.</li> +<li><strong>angles</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Array of angles in radians.</li> +<li><strong>matrix_id</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of the sparse matrix.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A projection geometry based on a sparse matrix.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_projector"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_projector</tt><big>(</big><em>proj_type</em>, <em>proj_geom</em>, <em>vol_geom</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_projector"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_projector" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a 2D projector.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>proj_type</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Projector type, such as <tt class="docutils literal"><span class="pre">'line'</span></tt>, <tt class="docutils literal"><span class="pre">'linear'</span></tt>, ...</li> +<li><strong>proj_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Projection geometry.</li> +<li><strong>vol_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Volume geometry.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – The ID of the projector.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_reconstruction"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_reconstruction</tt><big>(</big><em>rec_type</em>, <em>proj_id</em>, <em>sinogram</em>, <em>iterations=1</em>, <em>use_mask='no'</em>, <em>mask=array([]</em>, <em>dtype=float64)</em>, <em>use_minc='no'</em>, <em>minc=0</em>, <em>use_maxc='no'</em>, <em>maxc=255</em>, <em>returnData=True</em>, <em>filterType=None</em>, <em>filterData=None</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_reconstruction"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_reconstruction" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a reconstruction of a sinogram (2D).</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>rec_type</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Name of the reconstruction algorithm.</li> +<li><strong>proj_id</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of the projector to use.</li> +<li><strong>sinogram</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Sinogram data or ID.</li> +<li><strong>iterations</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of iterations to run.</li> +<li><strong>use_mask</strong> (<tt class="docutils literal"><span class="pre">'yes'</span></tt> or <tt class="docutils literal"><span class="pre">'no'</span></tt>) – Whether to use a mask.</li> +<li><strong>mask</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Mask data or ID</li> +<li><strong>use_minc</strong> (<tt class="docutils literal"><span class="pre">'yes'</span></tt> or <tt class="docutils literal"><span class="pre">'no'</span></tt>) – Whether to force a minimum value on the reconstruction pixels.</li> +<li><strong>minc</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Minimum value to use.</li> +<li><strong>use_maxc</strong> (<tt class="docutils literal"><span class="pre">'yes'</span></tt> or <tt class="docutils literal"><span class="pre">'no'</span></tt>) – Whether to force a maximum value on the reconstruction pixels.</li> +<li><strong>maxc</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Maximum value to use.</li> +<li><strong>returnData</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If False, only return the ID of the reconstruction.</li> +<li><strong>filterType</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Which type of filter to use for filter-based methods.</li> +<li><strong>filterData</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Optional filter data for filter-based methods.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>, <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – If <tt class="docutils literal"><span class="pre">returnData=False</span></tt>, returns the ID of the reconstruction. Otherwise, returns a tuple containing the ID of the reconstruction and reconstruction itself, in that order.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_sino"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_sino</tt><big>(</big><em>data</em>, <em>proj_id=None</em>, <em>proj_geom=None</em>, <em>vol_geom=None</em>, <em>useCUDA=False</em>, <em>returnData=True</em>, <em>gpuIndex=None</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_sino"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_sino" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a forward projection of an image (2D).</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Image data or ID.</li> +<li><strong>proj_id</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of the projector to use.</li> +<li><strong>proj_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Projection geometry.</li> +<li><strong>vol_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Volume geometry.</li> +<li><strong>useCUDA</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If <tt class="docutils literal"><span class="pre">True</span></tt>, use CUDA for the calculation.</li> +<li><strong>returnData</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If False, only return the ID of the forward projection.</li> +<li><strong>gpuIndex</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Optional GPU index.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>, <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>)</p> +</td> +</tr> +</tbody> +</table> +<p>If <tt class="docutils literal"><span class="pre">returnData=False</span></tt>, returns the ID of the forward +projection. Otherwise, returns a tuple containing the ID of the +forward projection and the forward projection itself, in that +order.</p> +<p>The geometry of setup is defined by <tt class="docutils literal"><span class="pre">proj_id</span></tt> or with +<tt class="docutils literal"><span class="pre">proj_geom</span></tt> and <tt class="docutils literal"><span class="pre">vol_geom</span></tt>. If <tt class="docutils literal"><span class="pre">proj_id</span></tt> is given, then +<tt class="docutils literal"><span class="pre">proj_geom</span></tt> and <tt class="docutils literal"><span class="pre">vol_geom</span></tt> must be None and vice versa.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_sino3d_gpu"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_sino3d_gpu</tt><big>(</big><em>data</em>, <em>proj_geom</em>, <em>vol_geom</em>, <em>returnData=True</em>, <em>gpuIndex=None</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_sino3d_gpu"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_sino3d_gpu" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a forward projection of an image (3D).</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Image data or ID.</li> +<li><strong>proj_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Projection geometry.</li> +<li><strong>vol_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Volume geometry.</li> +<li><strong>returnData</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If False, only return the ID of the forward projection.</li> +<li><strong>gpuIndex</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Optional GPU index.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>, <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – If <tt class="docutils literal"><span class="pre">returnData=False</span></tt>, returns the ID of the forward projection. Otherwise, returns a tuple containing the ID of the forward projection and the forward projection itself, in that order.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_vol_geom"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_vol_geom</tt><big>(</big><em>*varargin</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_vol_geom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_vol_geom" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a volume geometry structure.</p> +<p>This method can be called in a number of ways:</p> +<dl class="docutils"> +<dt><tt class="docutils literal"><span class="pre">create_vol_geom(N)</span></tt>:</dt> +<dd><table class="first last docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">returns:</th><td class="field-body">A 2D volume geometry of size <span class="math">\(N \times N\)</span>.</td> +</tr> +</tbody> +</table> +</dd> +<dt><tt class="docutils literal"><span class="pre">create_vol_geom((M,</span> <span class="pre">N))</span></tt>:</dt> +<dd><table class="first last docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">returns:</th><td class="field-body">A 2D volume geometry of size <span class="math">\(M \times N\)</span>.</td> +</tr> +</tbody> +</table> +</dd> +<dt><tt class="docutils literal"><span class="pre">create_vol_geom(M,</span> <span class="pre">N)</span></tt>:</dt> +<dd><table class="first last docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">returns:</th><td class="field-body">A 2D volume geometry of size <span class="math">\(M \times N\)</span>.</td> +</tr> +</tbody> +</table> +</dd> +<dt><tt class="docutils literal"><span class="pre">create_vol_geom(M,</span> <span class="pre">N,</span> <span class="pre">minx,</span> <span class="pre">maxx,</span> <span class="pre">miny,</span> <span class="pre">maxy)</span></tt>:</dt> +<dd><table class="first last docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">returns:</th><td class="field-body">A 2D volume geometry of size <span class="math">\(M \times N\)</span>, windowed as <span class="math">\(minx \leq x \leq maxx\)</span> and <span class="math">\(miny \leq y \leq maxy\)</span>.</td> +</tr> +</tbody> +</table> +</dd> +<dt><tt class="docutils literal"><span class="pre">create_vol_geom((M,</span> <span class="pre">N,</span> <span class="pre">Z))</span></tt>:</dt> +<dd><table class="first last docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">returns:</th><td class="field-body">A 3D volume geometry of size <span class="math">\(M \times N \times Z\)</span>.</td> +</tr> +</tbody> +</table> +</dd> +<dt><tt class="docutils literal"><span class="pre">create_vol_geom(M,</span> <span class="pre">N,</span> <span class="pre">Z)</span></tt>:</dt> +<dd><table class="first last docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">returns:</th><td class="field-body">A 3D volume geometry of size <span class="math">\(M \times N \times Z\)</span>.</td> +</tr> +</tbody> +</table> +</dd> +</dl> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + 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\ No newline at end of file diff --git a/python/docSRC/_build/html/data2d.html b/python/docSRC/_build/html/data2d.html new file mode 100644 index 0000000..6b01d41 --- /dev/null +++ b/python/docSRC/_build/html/data2d.html @@ -0,0 +1,277 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>2D data objects: the data2d module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script 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PyASTRAToolbox’s documentation!" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.data2d"> +<span id="d-data-objects-the-data2d-module"></span><h1>2D data objects: the <tt class="xref py py-mod docutils literal"><span class="pre">data2d</span></tt> module<a class="headerlink" href="#module-astra.data2d" title="Permalink to this headline">¶</a></h1> +<dl class="function"> +<dt id="astra.data2d.change_geometry"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">change_geometry</tt><big>(</big><em>i</em>, <em>geom</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#change_geometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.change_geometry" title="Permalink to this definition">¶</a></dt> +<dd><p>Change the geometry of a 2D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object.</li> +<li><strong>geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – new geometry.</li> +</ul> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.clear"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">clear</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#clear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.clear" title="Permalink to this definition">¶</a></dt> +<dd><p>Clear all 2D data objects.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.create"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">create</tt><big>(</big><em>datatype</em>, <em>geometry</em>, <em>data=None</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.create" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a 2D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>datatype</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Data object type, ‘-vol’ or ‘-sino’.</li> +<li><strong>geometry</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Volume or projection geometry.</li> +<li><strong>data</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a> or <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Data to fill the constructed object with, either a scalar or array.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – the ID of the constructed object.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.delete"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">delete</tt><big>(</big><em>ids</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#delete"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.delete" title="Permalink to this definition">¶</a></dt> +<dd><p>Delete a 2D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ids</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a>) – ID or list of ID’s to delete.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.get"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">get</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#get"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.get" title="Permalink to this definition">¶</a></dt> +<dd><p>Get a 2D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to get.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The object data.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.get_geometry"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">get_geometry</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#get_geometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.get_geometry" title="Permalink to this definition">¶</a></dt> +<dd><p>Get the geometry of a 2D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a> – The geometry of object with ID <tt class="docutils literal"><span class="pre">i</span></tt>.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.get_shared"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">get_shared</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#get_shared"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.get_shared" title="Permalink to this definition">¶</a></dt> +<dd><p>Get a 2D object with memory shared between the ASTRA toolbox and numpy array.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to get.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The object data.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.get_single"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">get_single</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#get_single"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.get_single" title="Permalink to this definition">¶</a></dt> +<dd><p>Get a 2D object in single precision.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to get.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The object data.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.info"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">info</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.info" title="Permalink to this definition">¶</a></dt> +<dd><p>Print info on 2D objects in memory.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.store"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">store</tt><big>(</big><em>i</em>, <em>data</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#store"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.store" title="Permalink to this definition">¶</a></dt> +<dd><p>Fill existing 2D object with data.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to fill.</li> +<li><strong>data</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a> or <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Data to fill the object with, either a scalar or array.</li> +</ul> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="index.html" + title="previous chapter">Welcome to PyASTRAToolbox’s documentation!</a></p> + <h4>Next topic</h4> + <p class="topless"><a href="data3d.html" + title="next chapter">3D data objects: the <tt class="docutils literal"><span class="pre">data3d</span></tt> module</a></p> + <h3>This Page</h3> + <ul class="this-page-menu"> + <li><a href="_sources/data2d.txt" + rel="nofollow">Show Source</a></li> + </ul> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p 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\ No newline at end of file diff --git a/python/docSRC/_build/html/data3d.html b/python/docSRC/_build/html/data3d.html new file mode 100644 index 0000000..926bd6e --- /dev/null +++ b/python/docSRC/_build/html/data3d.html @@ -0,0 +1,259 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>3D data objects: the data3d module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script 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objects: the data2d module" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.data3d"> +<span id="d-data-objects-the-data3d-module"></span><h1>3D data objects: the <tt class="xref py py-mod docutils literal"><span class="pre">data3d</span></tt> module<a class="headerlink" href="#module-astra.data3d" title="Permalink to this headline">¶</a></h1> +<dl class="function"> +<dt id="astra.data3d.clear"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">clear</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#clear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.clear" title="Permalink to this definition">¶</a></dt> +<dd><p>Clear all 3D data objects.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.create"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">create</tt><big>(</big><em>datatype</em>, <em>geometry</em>, <em>data=None</em><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.create" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a 3D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>datatype</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Data object type, ‘-vol’ or ‘-sino’.</li> +<li><strong>geometry</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Volume or projection geometry.</li> +<li><strong>data</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a> or <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Data to fill the constructed object with, either a scalar or array.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – the ID of the constructed object.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.delete"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">delete</tt><big>(</big><em>ids</em><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#delete"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.delete" title="Permalink to this definition">¶</a></dt> +<dd><p>Delete a 2D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ids</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a>) – ID or list of ID’s to delete.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.dimensions"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">dimensions</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#dimensions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.dimensions" title="Permalink to this definition">¶</a></dt> +<dd><p>Get dimensions of a 3D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><tt class="xref py py-class docutils literal"><span class="pre">tuple</span></tt> – dimensions of object with ID <tt class="docutils literal"><span class="pre">i</span></tt>.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.get"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">get</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#get"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.get" title="Permalink to this definition">¶</a></dt> +<dd><p>Get a 3D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to get.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The object data.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.get_shared"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">get_shared</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#get_shared"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.get_shared" title="Permalink to this definition">¶</a></dt> +<dd><p>Get a 3D object with memory shared between the ASTRA toolbox and numpy array.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to get.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The object data.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.get_single"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">get_single</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#get_single"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.get_single" title="Permalink to this definition">¶</a></dt> +<dd><p>Get a 3D object in single precision.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to get.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The object data.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.info"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">info</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.info" title="Permalink to this definition">¶</a></dt> +<dd><p>Print info on 3D objects in memory.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.store"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">store</tt><big>(</big><em>i</em>, <em>data</em><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#store"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.store" title="Permalink to this definition">¶</a></dt> +<dd><p>Fill existing 3D object with data.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to fill.</li> +<li><strong>data</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a> or <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Data to fill the object with, either a scalar or array.</li> +</ul> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="data2d.html" + title="previous chapter">2D data objects: the <tt class="docutils literal"><span class="pre">data2d</span></tt> module</a></p> + <h4>Next topic</h4> + <p class="topless"><a href="projector.html" + title="next chapter">Projector object: the <tt class="docutils literal"><span 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\ No newline at end of file diff --git a/python/docSRC/_build/html/functions.html b/python/docSRC/_build/html/functions.html new file mode 100644 index 0000000..7ec397e --- /dev/null +++ b/python/docSRC/_build/html/functions.html @@ -0,0 +1,236 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Additional functions: the functions module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="index.html" /> + <link rel="next" title="Helper class: the ASTRAProjector module" href="ASTRAProjector.html" /> + <link rel="prev" title="Creation of objects: the creators module" href="creators.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="ASTRAProjector.html" title="Helper class: the ASTRAProjector module" + accesskey="N">next</a> |</li> + <li class="right" > + <a href="creators.html" title="Creation of objects: the creators module" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.functions"> +<span id="additional-functions-the-functions-module"></span><h1>Additional functions: the <tt class="xref py py-mod docutils literal"><span class="pre">functions</span></tt> module<a class="headerlink" href="#module-astra.functions" title="Permalink to this headline">¶</a></h1> +<p>Additional functions for PyAstraToolbox.</p> +<dl class="function"> +<dt id="astra.functions.add_noise_to_sino"> +<tt class="descclassname">astra.functions.</tt><tt class="descname">add_noise_to_sino</tt><big>(</big><em>sinogram_in</em>, <em>I0</em>, <em>seed=None</em><big>)</big><a class="reference internal" href="_modules/astra/functions.html#add_noise_to_sino"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.functions.add_noise_to_sino" title="Permalink to this definition">¶</a></dt> +<dd><p>Adds Poisson noise to a sinogram.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>sinogram_in</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Sinogram to add noise to.</li> +<li><strong>I0</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Background intensity. Lower values lead to higher noise.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – the sinogram with added noise.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.functions.clear"> +<tt class="descclassname">astra.functions.</tt><tt class="descname">clear</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/functions.html#clear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.functions.clear" title="Permalink to this definition">¶</a></dt> +<dd><p>Clears all used memory of the ASTRA Toolbox.</p> +<div class="admonition note"> +<p class="first admonition-title">Note</p> +<p class="last">This is irreversible.</p> +</div> +</dd></dl> + +<dl class="function"> +<dt id="astra.functions.data_op"> +<tt class="descclassname">astra.functions.</tt><tt class="descname">data_op</tt><big>(</big><em>op</em>, <em>data</em>, <em>scalar</em>, <em>gpu_core</em>, <em>mask=None</em><big>)</big><a class="reference internal" href="_modules/astra/functions.html#data_op"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.functions.data_op" title="Permalink to this definition">¶</a></dt> +<dd><p>Perform data operation on data.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>op</strong> – Operation to perform.</li> +<li><strong>data</strong> – Data to perform operation on.</li> +<li><strong>scalar</strong> – Scalar argument to data operation.</li> +<li><strong>gpu_core</strong> – GPU core to perform operation on.</li> +<li><strong>mask</strong> – Optional mask.</li> +</ul> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.functions.geom_2vec"> +<tt class="descclassname">astra.functions.</tt><tt class="descname">geom_2vec</tt><big>(</big><em>proj_geom</em><big>)</big><a class="reference internal" href="_modules/astra/functions.html#geom_2vec"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.functions.geom_2vec" title="Permalink to this definition">¶</a></dt> +<dd><p>Returns a vector-based projection geometry from a basic projection geometry.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>proj_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Projection geometry to convert</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.functions.geom_size"> +<tt class="descclassname">astra.functions.</tt><tt class="descname">geom_size</tt><big>(</big><em>geom</em>, <em>dim=None</em><big>)</big><a class="reference internal" href="_modules/astra/functions.html#geom_size"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.functions.geom_size" title="Permalink to this definition">¶</a></dt> +<dd><p>Returns the size of a volume or sinogram, based on the projection or volume geometry.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>geom</strong> – Geometry to calculate size from</li> +<li><strong>dim</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Optional axis index to return</li> +</ul> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.functions.move_vol_geom"> +<tt class="descclassname">astra.functions.</tt><tt class="descname">move_vol_geom</tt><big>(</big><em>geom</em>, <em>pos</em>, <em>is_relative=False</em><big>)</big><a class="reference internal" href="_modules/astra/functions.html#move_vol_geom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.functions.move_vol_geom" title="Permalink to this definition">¶</a></dt> +<dd><p>Moves center of volume geometry to new position.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Input volume geometry</li> +<li><strong>pos</strong> (<tt class="xref py py-class docutils literal"><span class="pre">tuple</span></tt>) – Tuple (x,y[,z]) for new position, with the center of the image at (0,0[,0])</li> +<li><strong>is_relative</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – Whether new position is relative to the old position</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a> – Volume geometry with the new center</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="creators.html" + title="previous chapter">Creation of objects: the <tt class="docutils literal"><span class="pre">creators</span></tt> module</a></p> + <h4>Next topic</h4> + <p class="topless"><a href="ASTRAProjector.html" + title="next chapter">Helper class: the <tt class="docutils literal"><span class="pre">ASTRAProjector</span></tt> module</a></p> + <h3>This Page</h3> + 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\ No newline at end of file diff --git a/python/docSRC/_build/html/genindex.html b/python/docSRC/_build/html/genindex.html new file mode 100644 index 0000000..3099bfa --- /dev/null +++ b/python/docSRC/_build/html/genindex.html @@ -0,0 +1,575 @@ + +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Index — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="#" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + +<h1 id="index">Index</h1> + +<div class="genindex-jumpbox"> + <a href="#A"><strong>A</strong></a> + | <a href="#B"><strong>B</strong></a> + | <a href="#C"><strong>C</strong></a> + | <a href="#D"><strong>D</strong></a> + | <a href="#F"><strong>F</strong></a> + | <a href="#G"><strong>G</strong></a> + | <a href="#I"><strong>I</strong></a> + | <a href="#M"><strong>M</strong></a> + | <a href="#P"><strong>P</strong></a> + | <a href="#R"><strong>R</strong></a> + | <a href="#S"><strong>S</strong></a> + | <a href="#U"><strong>U</strong></a> + | <a href="#V"><strong>V</strong></a> + | <a href="#W"><strong>W</strong></a> + +</div> +<h2 id="A">A</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="functions.html#astra.functions.add_noise_to_sino">add_noise_to_sino() (in module astra.functions)</a> + </dt> + + + <dt><a href="matlab.html#astra.matlab.algorithm">algorithm() (in module astra.matlab)</a> + </dt> + + + <dt><a href="matlab.html#astra.matlab.astra">astra() (in module astra.matlab)</a> + </dt> + + + <dt><a href="algorithm.html#module-astra.algorithm">astra.algorithm (module)</a> + </dt> + + + <dt><a href="astra.html#module-astra.astra">astra.astra (module)</a> + </dt> + + + <dt><a href="ASTRAProjector.html#module-astra.ASTRAProjector">astra.ASTRAProjector (module)</a> + </dt> + + + <dt><a href="creators.html#module-astra.creators">astra.creators (module)</a> + </dt> + + + <dt><a href="data2d.html#module-astra.data2d">astra.data2d (module)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="data3d.html#module-astra.data3d">astra.data3d (module)</a> + </dt> + + + <dt><a href="functions.html#module-astra.functions">astra.functions (module)</a> + </dt> + + + <dt><a href="matlab.html#module-astra.matlab">astra.matlab (module)</a> + </dt> + + + <dt><a href="matrix.html#module-astra.matrix">astra.matrix (module)</a> + </dt> + + + <dt><a href="projector.html#module-astra.projector">astra.projector (module)</a> + </dt> + + + <dt><a href="creators.html#astra.creators.astra_dict">astra_dict() (in module astra.creators)</a> + </dt> + + + <dt><a href="ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D">ASTRAProjector2D (class in astra.ASTRAProjector)</a> + </dt> + + + <dt><a href="ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2DTranspose">ASTRAProjector2DTranspose (class in astra.ASTRAProjector)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="B">B</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D.backProject">backProject() (astra.ASTRAProjector.ASTRAProjector2D method)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="C">C</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="data2d.html#astra.data2d.change_geometry">change_geometry() (in module astra.data2d)</a> + </dt> + + + <dt><a href="algorithm.html#astra.algorithm.clear">clear() (in module astra.algorithm)</a> + </dt> + + <dd><dl> + + <dt><a href="data2d.html#astra.data2d.clear">(in module astra.data2d)</a> + </dt> + + + <dt><a href="data3d.html#astra.data3d.clear">(in module astra.data3d)</a> + </dt> + + + <dt><a href="functions.html#astra.functions.clear">(in module astra.functions)</a> + </dt> + + + <dt><a href="matrix.html#astra.matrix.clear">(in module astra.matrix)</a> + </dt> + + + <dt><a href="projector.html#astra.projector.clear">(in module astra.projector)</a> + </dt> + + </dl></dd> + + <dt><a href="algorithm.html#astra.algorithm.create">create() (in module astra.algorithm)</a> + </dt> + + <dd><dl> + + <dt><a href="data2d.html#astra.data2d.create">(in module astra.data2d)</a> + </dt> + + + <dt><a href="data3d.html#astra.data3d.create">(in module astra.data3d)</a> + </dt> + + + <dt><a href="matrix.html#astra.matrix.create">(in module astra.matrix)</a> + </dt> + + + <dt><a href="projector.html#astra.projector.create">(in module astra.projector)</a> + </dt> + + </dl></dd> + + <dt><a href="creators.html#astra.creators.create_backprojection">create_backprojection() (in module astra.creators)</a> + </dt> + + + <dt><a href="creators.html#astra.creators.create_backprojection3d_gpu">create_backprojection3d_gpu() (in module astra.creators)</a> + </dt> + + + <dt><a href="creators.html#astra.creators.create_proj_geom">create_proj_geom() (in module astra.creators)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="creators.html#astra.creators.create_projector">create_projector() (in module astra.creators)</a> + </dt> + + + <dt><a href="creators.html#astra.creators.create_reconstruction">create_reconstruction() (in module astra.creators)</a> + </dt> + + + <dt><a href="creators.html#astra.creators.create_sino">create_sino() (in module astra.creators)</a> + </dt> + + + <dt><a href="creators.html#astra.creators.create_sino3d_gpu">create_sino3d_gpu() (in module astra.creators)</a> + </dt> + + + <dt><a href="creators.html#astra.creators.create_vol_geom">create_vol_geom() (in module astra.creators)</a> + </dt> + + + <dt><a href="astra.html#astra.astra.credits">credits() (in module astra.astra)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="D">D</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="matlab.html#astra.matlab.data2d">data2d() (in module astra.matlab)</a> + </dt> + + + <dt><a href="matlab.html#astra.matlab.data3d">data3d() (in module astra.matlab)</a> + </dt> + + + <dt><a href="functions.html#astra.functions.data_op">data_op() (in module astra.functions)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="algorithm.html#astra.algorithm.delete">delete() (in module astra.algorithm)</a> + </dt> + + <dd><dl> + + <dt><a href="data2d.html#astra.data2d.delete">(in module astra.data2d)</a> + </dt> + + + <dt><a href="data3d.html#astra.data3d.delete">(in module astra.data3d)</a> + </dt> + + + <dt><a href="matrix.html#astra.matrix.delete">(in module astra.matrix)</a> + </dt> + + + <dt><a href="projector.html#astra.projector.delete">(in module astra.projector)</a> + </dt> + + </dl></dd> + + <dt><a href="data3d.html#astra.data3d.dimensions">dimensions() (in module astra.data3d)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="F">F</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D.forwardProject">forwardProject() (astra.ASTRAProjector.ASTRAProjector2D method)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="G">G</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="functions.html#astra.functions.geom_2vec">geom_2vec() (in module astra.functions)</a> + </dt> + + + <dt><a href="functions.html#astra.functions.geom_size">geom_size() (in module astra.functions)</a> + </dt> + + + <dt><a href="data2d.html#astra.data2d.get">get() (in module astra.data2d)</a> + </dt> + + <dd><dl> + + <dt><a href="data3d.html#astra.data3d.get">(in module astra.data3d)</a> + </dt> + + + <dt><a href="matrix.html#astra.matrix.get">(in module astra.matrix)</a> + </dt> + + </dl></dd> + + <dt><a href="data2d.html#astra.data2d.get_geometry">get_geometry() (in module astra.data2d)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="algorithm.html#astra.algorithm.get_res_norm">get_res_norm() (in module astra.algorithm)</a> + </dt> + + + <dt><a href="data2d.html#astra.data2d.get_shared">get_shared() (in module astra.data2d)</a> + </dt> + + <dd><dl> + + <dt><a href="data3d.html#astra.data3d.get_shared">(in module astra.data3d)</a> + </dt> + + </dl></dd> + + <dt><a href="data2d.html#astra.data2d.get_single">get_single() (in module astra.data2d)</a> + </dt> + + <dd><dl> + + <dt><a href="data3d.html#astra.data3d.get_single">(in module astra.data3d)</a> + </dt> + + </dl></dd> + + <dt><a href="matrix.html#astra.matrix.get_size">get_size() (in module astra.matrix)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="I">I</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="algorithm.html#astra.algorithm.info">info() (in module astra.algorithm)</a> + </dt> + + <dd><dl> + + <dt><a href="data2d.html#astra.data2d.info">(in module astra.data2d)</a> + </dt> + + + <dt><a href="data3d.html#astra.data3d.info">(in module astra.data3d)</a> + </dt> + + + <dt><a href="matrix.html#astra.matrix.info">(in module astra.matrix)</a> + </dt> + + + <dt><a href="projector.html#astra.projector.info">(in module astra.projector)</a> + </dt> + + </dl></dd> + </dl></td> +</tr></table> + +<h2 id="M">M</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="matlab.html#astra.matlab.matrix">matrix() (in module astra.matlab)</a> + </dt> + + <dd><dl> + + <dt><a href="projector.html#astra.projector.matrix">(in module astra.projector)</a> + </dt> + + </dl></dd> + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="functions.html#astra.functions.move_vol_geom">move_vol_geom() (in module astra.functions)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="P">P</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="projector.html#astra.projector.projection_geometry">projection_geometry() (in module astra.projector)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="matlab.html#astra.matlab.projector">projector() (in module astra.matlab)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="R">R</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D.reconstruct">reconstruct() (astra.ASTRAProjector.ASTRAProjector2D method)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="algorithm.html#astra.algorithm.run">run() (in module astra.algorithm)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="S">S</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="astra.html#astra.astra.set_gpu_index">set_gpu_index() (in module astra.astra)</a> + </dt> + + + <dt><a href="projector.html#astra.projector.splat">splat() (in module astra.projector)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="data2d.html#astra.data2d.store">store() (in module astra.data2d)</a> + </dt> + + <dd><dl> + + <dt><a href="data3d.html#astra.data3d.store">(in module astra.data3d)</a> + </dt> + + + <dt><a href="matrix.html#astra.matrix.store">(in module astra.matrix)</a> + </dt> + + </dl></dd> + </dl></td> +</tr></table> + +<h2 id="U">U</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="astra.html#astra.astra.use_cuda">use_cuda() (in module astra.astra)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="V">V</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="astra.html#astra.astra.version">version() (in module astra.astra)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="projector.html#astra.projector.volume_geometry">volume_geometry() (in module astra.projector)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="W">W</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="projector.html#astra.projector.weights_projection">weights_projection() (in module astra.projector)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="projector.html#astra.projector.weights_single_ray">weights_single_ray() (in module astra.projector)</a> + </dt> + + </dl></td> +</tr></table> + + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + + + +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + 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\ No newline at end of file diff --git a/python/docSRC/_build/html/index.html b/python/docSRC/_build/html/index.html new file mode 100644 index 0000000..817e07f --- /dev/null +++ b/python/docSRC/_build/html/index.html @@ -0,0 +1,148 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Welcome to PyASTRAToolbox’s documentation! — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script 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<div class="body"> + + <div class="section" id="welcome-to-pyastratoolbox-s-documentation"> +<h1>Welcome to PyASTRAToolbox’s documentation!<a class="headerlink" href="#welcome-to-pyastratoolbox-s-documentation" title="Permalink to this headline">¶</a></h1> +<p>Contents:</p> +<div class="toctree-wrapper compound"> +<ul> +<li class="toctree-l1"><a class="reference internal" href="data2d.html">2D data objects: the <tt class="docutils literal"><span class="pre">data2d</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="data3d.html">3D data objects: the <tt class="docutils literal"><span class="pre">data3d</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="projector.html">Projector object: the <tt class="docutils literal"><span class="pre">projector</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="algorithm.html">Algorithms: the <tt class="docutils literal"><span class="pre">algorithm</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="matrix.html">Sparse matrices: the <tt class="docutils literal"><span class="pre">matrix</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="creators.html">Creation of objects: the <tt class="docutils literal"><span class="pre">creators</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="functions.html">Additional functions: the <tt class="docutils literal"><span class="pre">functions</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="ASTRAProjector.html">Helper class: the <tt class="docutils literal"><span class="pre">ASTRAProjector</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="matlab.html">MATLAB compatibility interface: the <tt class="docutils literal"><span class="pre">matlab</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="astra.html">Additional ASTRA methods: the <tt class="docutils literal"><span class="pre">astra</span></tt> module</a></li> +</ul> +</div> +</div> +<div class="section" id="indices-and-tables"> +<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1> +<ul class="simple"> +<li><a class="reference internal" href="genindex.html"><em>Index</em></a></li> +<li><a class="reference internal" href="py-modindex.html"><em>Module Index</em></a></li> +<li><a class="reference internal" href="search.html"><em>Search Page</em></a></li> +</ul> +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h3><a href="#">Table Of Contents</a></h3> + <ul> +<li><a class="reference internal" href="#">Welcome to PyASTRAToolbox’s documentation!</a></li> +<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li> +</ul> + 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\ No newline at end of file diff --git a/python/docSRC/_build/html/matlab.html b/python/docSRC/_build/html/matlab.html new file mode 100644 index 0000000..8b4bf31 --- /dev/null +++ b/python/docSRC/_build/html/matlab.html @@ -0,0 +1,184 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>MATLAB compatibility interface: the matlab module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="index.html" /> + <link rel="next" title="Additional ASTRA methods: the astra module" href="astra.html" /> + <link rel="prev" title="Helper class: the ASTRAProjector module" href="ASTRAProjector.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="astra.html" title="Additional ASTRA methods: the astra module" + accesskey="N">next</a> |</li> + <li class="right" > + <a href="ASTRAProjector.html" title="Helper class: the ASTRAProjector module" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.matlab"> +<span id="matlab-compatibility-interface-the-matlab-module"></span><h1>MATLAB compatibility interface: the <tt class="xref py py-mod docutils literal"><span class="pre">matlab</span></tt> module<a class="headerlink" href="#module-astra.matlab" title="Permalink to this headline">¶</a></h1> +<p>This module implements a MATLAB-like interface to the ASTRA Toolbox.</p> +<p>Note that all functions are called with a <tt class="xref py py-class docutils literal"><span class="pre">string</span></tt> as the first +argument, specifying the operation to perform. This un-pythonic way +is used to make transitioning from MATLAB code to Python code easier, as +the MATLAB interface uses the same type of method calling.</p> +<p>After an initial <tt class="docutils literal"><span class="pre">import</span> <span class="pre">astra</span></tt>, these functions can be accessed in the +<tt class="docutils literal"><span class="pre">astra.m</span></tt> module.</p> +<dl class="function"> +<dt id="astra.matlab.algorithm"> +<tt class="descclassname">astra.matlab.</tt><tt class="descname">algorithm</tt><big>(</big><em>command</em>, <em>*args</em><big>)</big><a class="reference internal" href="_modules/astra/matlab.html#algorithm"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matlab.algorithm" title="Permalink to this definition">¶</a></dt> +<dd><p>MATLAB-like interface to the <a class="reference internal" href="algorithm.html#module-astra.algorithm" title="astra.algorithm"><tt class="xref py py-mod docutils literal"><span class="pre">astra.algorithm</span></tt></a> module</p> +<p>For example:</p> +<p><tt class="docutils literal"><span class="pre">astra.m.algorithm('run',i,1000)</span></tt> – Run an algorithm with 1000 iterations.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.matlab.astra"> +<tt class="descclassname">astra.matlab.</tt><tt class="descname">astra</tt><big>(</big><em>command</em>, <em>*args</em><big>)</big><a class="reference internal" href="_modules/astra/matlab.html#astra"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matlab.astra" title="Permalink to this definition">¶</a></dt> +<dd><p>MATLAB-like interface to the <a class="reference internal" href="astra.html#module-astra.astra" title="astra.astra"><tt class="xref py py-mod docutils literal"><span class="pre">astra.astra</span></tt></a> module</p> +<p>For example:</p> +<p><tt class="docutils literal"><span class="pre">astra.m.astra('use_cuda')</span></tt> – Check if CUDA is enabled.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.matlab.data2d"> +<tt class="descclassname">astra.matlab.</tt><tt class="descname">data2d</tt><big>(</big><em>command</em>, <em>*args</em><big>)</big><a class="reference internal" href="_modules/astra/matlab.html#data2d"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matlab.data2d" title="Permalink to this definition">¶</a></dt> +<dd><p>MATLAB-like interface to the <a class="reference internal" href="data2d.html#module-astra.data2d" title="astra.data2d"><tt class="xref py py-mod docutils literal"><span class="pre">astra.data2d</span></tt></a> module</p> +<p>For example:</p> +<p><tt class="docutils literal"><span class="pre">astra.m.data2d('create',type,geometry,data)</span></tt> – Create a 2D object.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.matlab.data3d"> +<tt class="descclassname">astra.matlab.</tt><tt class="descname">data3d</tt><big>(</big><em>command</em>, <em>*args</em><big>)</big><a class="reference internal" href="_modules/astra/matlab.html#data3d"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matlab.data3d" title="Permalink to this definition">¶</a></dt> +<dd><p>MATLAB-like interface to the <a class="reference internal" href="data3d.html#module-astra.data3d" title="astra.data3d"><tt class="xref py py-mod docutils literal"><span class="pre">astra.data3d</span></tt></a> module</p> +<p>For example:</p> +<p><tt class="docutils literal"><span class="pre">astra.m.data3d('get',i)</span></tt> – Get 3D object data.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.matlab.matrix"> +<tt class="descclassname">astra.matlab.</tt><tt class="descname">matrix</tt><big>(</big><em>command</em>, <em>*args</em><big>)</big><a class="reference internal" href="_modules/astra/matlab.html#matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matlab.matrix" title="Permalink to this definition">¶</a></dt> +<dd><p>MATLAB-like interface to the <a class="reference internal" href="matrix.html#module-astra.matrix" title="astra.matrix"><tt class="xref py py-mod docutils literal"><span class="pre">astra.matrix</span></tt></a> module</p> +<p>For example:</p> +<p><tt class="docutils literal"><span class="pre">astra.m.matrix('delete',i)</span></tt> – Delete a matrix.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.matlab.projector"> +<tt class="descclassname">astra.matlab.</tt><tt class="descname">projector</tt><big>(</big><em>command</em>, <em>*args</em><big>)</big><a class="reference internal" href="_modules/astra/matlab.html#projector"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matlab.projector" title="Permalink to this definition">¶</a></dt> +<dd><p>MATLAB-like interface to the <a class="reference internal" href="projector.html#module-astra.projector" title="astra.projector"><tt class="xref py py-mod docutils literal"><span class="pre">astra.projector</span></tt></a> module</p> +<p>For example:</p> +<p><tt class="docutils literal"><span class="pre">astra.m.projector('volume_geometry',i)</span></tt> – Get volume geometry.</p> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="ASTRAProjector.html" + title="previous chapter">Helper class: the <tt class="docutils literal"><span class="pre">ASTRAProjector</span></tt> module</a></p> + <h4>Next topic</h4> + <p class="topless"><a href="astra.html" + title="next chapter">Additional ASTRA methods: the <tt class="docutils literal"><span class="pre">astra</span></tt> module</a></p> + <h3>This Page</h3> + <ul class="this-page-menu"> + <li><a href="_sources/matlab.txt" + rel="nofollow">Show Source</a></li> + </ul> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="astra.html" title="Additional ASTRA methods: the astra module" + >next</a> |</li> + <li class="right" > + <a href="ASTRAProjector.html" title="Helper class: the ASTRAProjector module" + >previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/matrix.html b/python/docSRC/_build/html/matrix.html new file mode 100644 index 0000000..1df4c30 --- /dev/null +++ b/python/docSRC/_build/html/matrix.html @@ -0,0 +1,221 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Sparse matrices: the matrix module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="index.html" /> + <link rel="next" title="Creation of objects: the creators module" href="creators.html" /> + <link rel="prev" title="Algorithms: the algorithm module" href="algorithm.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="creators.html" title="Creation of objects: the creators module" + accesskey="N">next</a> |</li> + <li class="right" > + <a href="algorithm.html" title="Algorithms: the algorithm module" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.matrix"> +<span id="sparse-matrices-the-matrix-module"></span><h1>Sparse matrices: the <tt class="xref py py-mod docutils literal"><span class="pre">matrix</span></tt> module<a class="headerlink" href="#module-astra.matrix" title="Permalink to this headline">¶</a></h1> +<dl class="function"> +<dt id="astra.matrix.clear"> +<tt class="descclassname">astra.matrix.</tt><tt class="descname">clear</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/matrix.html#clear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matrix.clear" title="Permalink to this definition">¶</a></dt> +<dd><p>Clear all matrix objects.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.matrix.create"> +<tt class="descclassname">astra.matrix.</tt><tt class="descname">create</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="_modules/astra/matrix.html#create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matrix.create" title="Permalink to this definition">¶</a></dt> +<dd><p>Create matrix object with data.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data</strong> (<tt class="xref py py-class docutils literal"><span class="pre">scipy.sparse.csr_matrix</span></tt>) – Data to fill the created object with.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – the ID of the constructed object.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.matrix.delete"> +<tt class="descclassname">astra.matrix.</tt><tt class="descname">delete</tt><big>(</big><em>ids</em><big>)</big><a class="reference internal" href="_modules/astra/matrix.html#delete"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matrix.delete" title="Permalink to this definition">¶</a></dt> +<dd><p>Delete a matrix object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ids</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a>) – ID or list of ID’s to delete.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.matrix.get"> +<tt class="descclassname">astra.matrix.</tt><tt class="descname">get</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/matrix.html#get"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matrix.get" title="Permalink to this definition">¶</a></dt> +<dd><p>Get a matrix object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to get.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><tt class="xref py py-class docutils literal"><span class="pre">scipy.sparse.csr_matrix</span></tt> – The object data.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.matrix.get_size"> +<tt class="descclassname">astra.matrix.</tt><tt class="descname">get_size</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/matrix.html#get_size"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matrix.get_size" title="Permalink to this definition">¶</a></dt> +<dd><p>Get matrix dimensions.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><tt class="xref py py-class docutils literal"><span class="pre">tuple</span></tt> – matrix dimensions.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.matrix.info"> +<tt class="descclassname">astra.matrix.</tt><tt class="descname">info</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/matrix.html#info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matrix.info" title="Permalink to this definition">¶</a></dt> +<dd><p>Print info on matrix objects in memory.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.matrix.store"> +<tt class="descclassname">astra.matrix.</tt><tt class="descname">store</tt><big>(</big><em>i</em>, <em>data</em><big>)</big><a class="reference internal" href="_modules/astra/matrix.html#store"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matrix.store" title="Permalink to this definition">¶</a></dt> +<dd><p>Fill existing matrix object with data.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to fill.</li> +<li><strong>data</strong> (<tt class="xref py py-class docutils literal"><span class="pre">scipy.sparse.csr_matrix</span></tt>) – Data to fill the object with.</li> +</ul> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="algorithm.html" + title="previous chapter">Algorithms: the <tt class="docutils literal"><span class="pre">algorithm</span></tt> module</a></p> + <h4>Next topic</h4> + <p class="topless"><a href="creators.html" + title="next chapter">Creation of objects: the <tt class="docutils literal"><span class="pre">creators</span></tt> module</a></p> + <h3>This Page</h3> + <ul class="this-page-menu"> + <li><a 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\ No newline at end of file diff --git a/python/docSRC/_build/html/objects.inv b/python/docSRC/_build/html/objects.inv Binary files differnew file mode 100644 index 0000000..54bab0b --- /dev/null +++ b/python/docSRC/_build/html/objects.inv diff --git a/python/docSRC/_build/html/projector.html b/python/docSRC/_build/html/projector.html new file mode 100644 index 0000000..9df5d0b --- /dev/null +++ b/python/docSRC/_build/html/projector.html @@ -0,0 +1,234 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Projector object: the projector module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="index.html" /> + <link rel="next" title="Algorithms: the algorithm module" href="algorithm.html" /> + <link rel="prev" title="3D data objects: the data3d module" href="data3d.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="algorithm.html" title="Algorithms: the algorithm module" + accesskey="N">next</a> |</li> + <li class="right" > + <a href="data3d.html" title="3D data objects: the data3d module" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.projector"> +<span id="projector-object-the-projector-module"></span><h1>Projector object: the <tt class="xref py py-mod docutils literal"><span class="pre">projector</span></tt> module<a class="headerlink" href="#module-astra.projector" title="Permalink to this headline">¶</a></h1> +<dl class="function"> +<dt id="astra.projector.clear"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">clear</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/projector.html#clear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.clear" title="Permalink to this definition">¶</a></dt> +<dd><p>Clear all projector objects.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.projector.create"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">create</tt><big>(</big><em>config</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.create" title="Permalink to this definition">¶</a></dt> +<dd><p>Create projector object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>config</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Projector options.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – the ID of the constructed object.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.projector.delete"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">delete</tt><big>(</big><em>ids</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#delete"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.delete" title="Permalink to this definition">¶</a></dt> +<dd><p>Delete a projector object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ids</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a>) – ID or list of ID’s to delete.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.projector.info"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">info</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/projector.html#info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.info" title="Permalink to this definition">¶</a></dt> +<dd><p>Print info on projector objects in memory.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.projector.matrix"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">matrix</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.matrix" title="Permalink to this definition">¶</a></dt> +<dd><p>Get sparse matrix of a projector.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of projector.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – ID of sparse matrix.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.projector.projection_geometry"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">projection_geometry</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#projection_geometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.projection_geometry" title="Permalink to this definition">¶</a></dt> +<dd><p>Get projection geometry of a projector.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of projector.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a> – projection geometry</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.projector.splat"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">splat</tt><big>(</big><em>i</em>, <em>row</em>, <em>col</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#splat"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.splat" title="Permalink to this definition">¶</a></dt> +<dd></dd></dl> + +<dl class="function"> +<dt id="astra.projector.volume_geometry"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">volume_geometry</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#volume_geometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.volume_geometry" title="Permalink to this definition">¶</a></dt> +<dd><p>Get volume geometry of a projector.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of projector.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a> – volume geometry</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.projector.weights_projection"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">weights_projection</tt><big>(</big><em>i</em>, <em>projection_index</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#weights_projection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.weights_projection" title="Permalink to this definition">¶</a></dt> +<dd></dd></dl> + +<dl class="function"> +<dt id="astra.projector.weights_single_ray"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">weights_single_ray</tt><big>(</big><em>i</em>, <em>projection_index</em>, <em>detector_index</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#weights_single_ray"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.weights_single_ray" title="Permalink to this definition">¶</a></dt> +<dd></dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="data3d.html" + title="previous chapter">3D data objects: the <tt class="docutils literal"><span class="pre">data3d</span></tt> module</a></p> + <h4>Next topic</h4> + <p class="topless"><a 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\ No newline at end of file diff --git a/python/docSRC/_build/html/searchindex.js b/python/docSRC/_build/html/searchindex.js new file mode 100644 index 0000000..cc69a68 --- /dev/null +++ b/python/docSRC/_build/html/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({objtypes:{"0":"py:module","1":"py:function","2":"py:method","3":"py:class"},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"],"2":["py","method","Python method"],"3":["py","class","Python 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\ No newline at end of file diff --git a/python/docSRC/_templates/layout.html b/python/docSRC/_templates/layout.html new file mode 100644 index 0000000..f30df11 --- /dev/null +++ b/python/docSRC/_templates/layout.html @@ -0,0 +1,15 @@ +{% extends "!layout.html" %} + +{% block footer %} +{{ super() }} +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> +{% endblock %} diff --git a/python/docSRC/algorithm.rst b/python/docSRC/algorithm.rst new file mode 100644 index 0000000..83752bd --- /dev/null +++ b/python/docSRC/algorithm.rst @@ -0,0 +1,8 @@ +Algorithms: the :mod:`algorithm` module +======================================= + +.. automodule:: astra.algorithm + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/astra.rst b/python/docSRC/astra.rst new file mode 100644 index 0000000..5d5fdf0 --- /dev/null +++ b/python/docSRC/astra.rst @@ -0,0 +1,8 @@ +Additional ASTRA methods: the :mod:`astra` module +======================================================== + +.. automodule:: astra.astra + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/conf.py b/python/docSRC/conf.py new file mode 100644 index 0000000..e54bbb8 --- /dev/null +++ b/python/docSRC/conf.py @@ -0,0 +1,287 @@ +# -*- coding: utf-8 -*- +# +# .. documentation build configuration file, created by +# sphinx-quickstart on Wed Mar 13 16:36:32 2013. +# +# This file is execfile()d with the current directory set to its containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys, os + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +#sys.path.insert(0, os.path.abspath('.')) + +# -- General configuration ----------------------------------------------------- + +# If your documentation needs a minimal Sphinx version, state it here. +#needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be extensions +# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. +extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode','sphinx.ext.mathjax','sphinx.ext.intersphinx'] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'PyASTRAToolbox' +copyright = u'2013, Centrum Wiskunde & Informatica, Amsterdam' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = '1.6' +# The full version, including alpha/beta/rc tags. +release = '1.6' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ['_build'] + +# The reST default role (used for this markup: `text`) to use for all documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +#add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +#add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + + +# -- Options for HTML output --------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'default' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +#html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# "<project> v<release> documentation". +#html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +#html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_domain_indices = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a <link> tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +# Output file base name for HTML help builder. +htmlhelp_basename = 'doc' + + +# -- Options for LaTeX output -------------------------------------------------- + +latex_elements = { +# The paper size ('letterpaper' or 'a4paper'). +#'papersize': 'letterpaper', + +# The font size ('10pt', '11pt' or '12pt'). +#'pointsize': '10pt', + +# Additional stuff for the LaTeX preamble. +#'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, author, documentclass [howto/manual]). +latex_documents = [ + ('index', '.tex', u'.. Documentation', + u'Author', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +#latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +#latex_use_parts = False + +# If true, show page references after internal links. +#latex_show_pagerefs = False + +# If true, show URL addresses after external links. +#latex_show_urls = False + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +#latex_domain_indices = True + + +# -- Options for manual page output -------------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', '', u'.. Documentation', + [u'Author'], 1) +] + +# If true, show URL addresses after external links. +#man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------------ + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ('index', '', u'.. Documentation', + u'Author', '', 'One line description of project.', + 'Miscellaneous'), +] + +# Documents to append as an appendix to all manuals. +#texinfo_appendices = [] + +# If false, no module index is generated. +#texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +#texinfo_show_urls = 'footnote' + + +# -- Options for Epub output --------------------------------------------------- + +# Bibliographic Dublin Core info. +epub_title = u'..' +epub_author = u'Author' +epub_publisher = u'Author' +epub_copyright = u'2013, Author' + +# The language of the text. It defaults to the language option +# or en if the language is not set. +#epub_language = '' + +# The scheme of the identifier. Typical schemes are ISBN or URL. +#epub_scheme = '' + +# The unique identifier of the text. This can be a ISBN number +# or the project homepage. +#epub_identifier = '' + +# A unique identification for the text. +#epub_uid = '' + +# A tuple containing the cover image and cover page html template filenames. +#epub_cover = () + +# HTML files that should be inserted before the pages created by sphinx. +# The format is a list of tuples containing the path and title. +#epub_pre_files = [] + +# HTML files shat should be inserted after the pages created by sphinx. +# The format is a list of tuples containing the path and title. +#epub_post_files = [] + +# A list of files that should not be packed into the epub file. +#epub_exclude_files = [] + +# The depth of the table of contents in toc.ncx. +#epub_tocdepth = 3 + +# Allow duplicate toc entries. +#epub_tocdup = True + +intersphinx_mapping = {'python': ('http://docs.python.org/2.7', None), 'numpy':('http://docs.scipy.org/doc/numpy/',None)} diff --git a/python/docSRC/creators.rst b/python/docSRC/creators.rst new file mode 100644 index 0000000..d6249c3 --- /dev/null +++ b/python/docSRC/creators.rst @@ -0,0 +1,8 @@ +Creation of objects: the :mod:`creators` module +=============================================== + +.. automodule:: astra.creators + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/data2d.rst b/python/docSRC/data2d.rst new file mode 100644 index 0000000..342cbec --- /dev/null +++ b/python/docSRC/data2d.rst @@ -0,0 +1,8 @@ +2D data objects: the :mod:`data2d` module +========================================= + +.. automodule:: astra.data2d + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/data3d.rst b/python/docSRC/data3d.rst new file mode 100644 index 0000000..5b7de23 --- /dev/null +++ b/python/docSRC/data3d.rst @@ -0,0 +1,8 @@ +3D data objects: the :mod:`data3d` module +========================================= + +.. automodule:: astra.data3d + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/functions.rst b/python/docSRC/functions.rst new file mode 100644 index 0000000..749eb27 --- /dev/null +++ b/python/docSRC/functions.rst @@ -0,0 +1,8 @@ +Additional functions: the :mod:`functions` module +================================================= + +.. automodule:: astra.functions + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/index.rst b/python/docSRC/index.rst new file mode 100644 index 0000000..8d17a4a --- /dev/null +++ b/python/docSRC/index.rst @@ -0,0 +1,34 @@ +.. .. documentation master file, created by + sphinx-quickstart on Wed Mar 13 16:36:32 2013. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to PyASTRAToolbox's documentation! +========================================== + +Contents: + +.. toctree:: + :maxdepth: 4 + + data2d + data3d + projector + algorithm + matrix + creators + functions + ASTRAProjector + matlab + astra +.. astra +.. builder + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/python/docSRC/make.bat b/python/docSRC/make.bat new file mode 100644 index 0000000..d70c604 --- /dev/null +++ b/python/docSRC/make.bat @@ -0,0 +1,190 @@ +@ECHO OFF + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set BUILDDIR=_build +set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . +set I18NSPHINXOPTS=%SPHINXOPTS% . +if NOT "%PAPER%" == "" ( + set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% + set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% +) + +if "%1" == "" goto help + +if "%1" == "help" ( + :help + echo.Please use `make ^<target^>` where ^<target^> is one of + echo. html to make standalone HTML files + echo. dirhtml to make HTML files named index.html in directories + echo. singlehtml to make a single large HTML file + echo. pickle to make pickle files + echo. json to make JSON files + echo. htmlhelp to make HTML files and a HTML help project + echo. qthelp to make HTML files and a qthelp project + echo. devhelp to make HTML files and a Devhelp project + echo. epub to make an epub + echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter + echo. text to make text files + echo. man to make manual pages + echo. texinfo to make Texinfo files + echo. gettext to make PO message catalogs + echo. changes to make an overview over all changed/added/deprecated items + echo. linkcheck to check all external links for integrity + echo. doctest to run all doctests embedded in the documentation if enabled + goto end +) + +if "%1" == "clean" ( + for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i + del /q /s %BUILDDIR%\* + goto end +) + +if "%1" == "html" ( + %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/html. + goto end +) + +if "%1" == "dirhtml" ( + %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. + goto end +) + +if "%1" == "singlehtml" ( + %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. + goto end +) + +if "%1" == "pickle" ( + %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the pickle files. + goto end +) + +if "%1" == "json" ( + %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the JSON files. + goto end +) + +if "%1" == "htmlhelp" ( + %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run HTML Help Workshop with the ^ +.hhp project file in %BUILDDIR%/htmlhelp. + goto end +) + +if "%1" == "qthelp" ( + %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run "qcollectiongenerator" with the ^ +.qhcp project file in %BUILDDIR%/qthelp, like this: + echo.^> qcollectiongenerator %BUILDDIR%\qthelp\.qhcp + echo.To view the help file: + echo.^> assistant -collectionFile %BUILDDIR%\qthelp\.ghc + goto end +) + +if "%1" == "devhelp" ( + %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. + goto end +) + +if "%1" == "epub" ( + %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The epub file is in %BUILDDIR%/epub. + goto end +) + +if "%1" == "latex" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "text" ( + %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The text files are in %BUILDDIR%/text. + goto end +) + +if "%1" == "man" ( + %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The manual pages are in %BUILDDIR%/man. + goto end +) + +if "%1" == "texinfo" ( + %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. + goto end +) + +if "%1" == "gettext" ( + %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The message catalogs are in %BUILDDIR%/locale. + goto end +) + +if "%1" == "changes" ( + %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes + if errorlevel 1 exit /b 1 + echo. + echo.The overview file is in %BUILDDIR%/changes. + goto end +) + +if "%1" == "linkcheck" ( + %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck + if errorlevel 1 exit /b 1 + echo. + echo.Link check complete; look for any errors in the above output ^ +or in %BUILDDIR%/linkcheck/output.txt. + goto end +) + +if "%1" == "doctest" ( + %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest + if errorlevel 1 exit /b 1 + echo. + echo.Testing of doctests in the sources finished, look at the ^ +results in %BUILDDIR%/doctest/output.txt. + goto end +) + +:end diff --git a/python/docSRC/matlab.rst b/python/docSRC/matlab.rst new file mode 100644 index 0000000..fb7033e --- /dev/null +++ b/python/docSRC/matlab.rst @@ -0,0 +1,8 @@ +MATLAB compatibility interface: the :mod:`matlab` module +======================================================== + +.. automodule:: astra.matlab + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/matrix.rst b/python/docSRC/matrix.rst new file mode 100644 index 0000000..6f11d8a --- /dev/null +++ b/python/docSRC/matrix.rst @@ -0,0 +1,8 @@ +Sparse matrices: the :mod:`matrix` module +========================================= + +.. automodule:: astra.matrix + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/projector.rst b/python/docSRC/projector.rst new file mode 100644 index 0000000..b0854e8 --- /dev/null +++ b/python/docSRC/projector.rst @@ -0,0 +1,8 @@ +Projector object: the :mod:`projector` module +============================================= + +.. automodule:: astra.projector + :members: + :undoc-members: + :show-inheritance: + |
