diff options
Diffstat (limited to 'python')
57 files changed, 1301 insertions, 876 deletions
diff --git a/python/astra/PyAlgorithmFactory.pxd b/python/astra/PyAlgorithmFactory.pxd index 256d7b2..5e335e4 100644 --- a/python/astra/PyAlgorithmFactory.pxd +++ b/python/astra/PyAlgorithmFactory.pxd @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + from libcpp.string cimport string from libcpp cimport bool from .PyIncludes cimport * diff --git a/python/astra/PyAlgorithmManager.pxd b/python/astra/PyAlgorithmManager.pxd index a99a807..dfc7961 100644 --- a/python/astra/PyAlgorithmManager.pxd +++ b/python/astra/PyAlgorithmManager.pxd @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# -------------------------------------------------------------------- + from libcpp.string cimport string from libcpp cimport bool from .PyIncludes cimport * diff --git a/python/astra/PyData2DManager.pxd b/python/astra/PyData2DManager.pxd index db8ec84..7cf60c7 100644 --- a/python/astra/PyData2DManager.pxd +++ b/python/astra/PyData2DManager.pxd @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + from libcpp.string cimport string from .PyIncludes cimport * diff --git a/python/astra/PyData3DManager.pxd b/python/astra/PyData3DManager.pxd index 9264a82..250147e 100644 --- a/python/astra/PyData3DManager.pxd +++ b/python/astra/PyData3DManager.pxd @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + from libcpp.string cimport string from .PyIncludes cimport * diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd index 61425c9..1c7973a 100644 --- a/python/astra/PyIncludes.pxd +++ b/python/astra/PyIncludes.pxd @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + from libcpp cimport bool from libcpp.string cimport string from .PyXMLDocument cimport XMLNode @@ -30,246 +30,266 @@ from .PyXMLDocument cimport XMLNode include "config.pxi" 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 + 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() - void initialize(string rootname) - XMLNode self + cdef cppclass Config: + Config() + void initialize(string rootname) + 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() - Config* getConfiguration() - bool isEqual(CVolumeGeometry2D*) + 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() + Config* getConfiguration() + bool isEqual(CVolumeGeometry2D*) cdef extern from "astra/Float32Data2D.h" namespace "astra": - cdef cppclass CFloat32CustomMemory: - pass + cdef cppclass CFloat32CustomMemory: + pass cdef extern from "astra/Float32VolumeData2D.h" namespace "astra": - cdef cppclass CFloat32VolumeData2D: - CFloat32VolumeData2D(CVolumeGeometry2D*) - CFloat32VolumeData2D(CVolumeGeometry2D*, CFloat32CustomMemory*) - CVolumeGeometry2D * getGeometry() - int getWidth() - int getHeight() - void changeGeometry(CVolumeGeometry2D*) - Config* getConfiguration() + cdef cppclass CFloat32VolumeData2D: + CFloat32VolumeData2D(CVolumeGeometry2D*) + CFloat32VolumeData2D(CVolumeGeometry2D*, CFloat32CustomMemory*) + CVolumeGeometry2D * getGeometry() + int getWidth() + int getHeight() + void changeGeometry(CVolumeGeometry2D*) + Config* getConfiguration() 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() - Config* getConfiguration() - bool isEqual(CProjectionGeometry2D*) + cdef cppclass CProjectionGeometry2D: + CProjectionGeometry2D() + bool initialize(Config) + int getDetectorCount() + int getProjectionAngleCount() + bool isOfType(string) + float32 getProjectionAngle(int) + float32 getDetectorWidth() + Config* getConfiguration() + bool isEqual(CProjectionGeometry2D*) cdef extern from "astra/Float32Data2D.h" namespace "astra::CFloat32Data2D": - cdef enum TWOEDataType "astra::CFloat32Data2D::EDataType": - TWOPROJECTION "astra::CFloat32Data2D::PROJECTION" - TWOVOLUME "astra::CFloat32Data2D::VOLUME" + cdef enum TWOEDataType "astra::CFloat32Data2D::EDataType": + TWOPROJECTION "astra::CFloat32Data2D::PROJECTION" + TWOVOLUME "astra::CFloat32Data2D::VOLUME" cdef extern from "astra/Float32Data3D.h" namespace "astra::CFloat32Data3D": - cdef enum THREEEDataType "astra::CFloat32Data3D::EDataType": - THREEPROJECTION "astra::CFloat32Data3D::PROJECTION" - THREEVOLUME "astra::CFloat32Data3D::VOLUME" + cdef enum THREEEDataType "astra::CFloat32Data3D::EDataType": + THREEPROJECTION "astra::CFloat32Data3D::PROJECTION" + THREEVOLUME "astra::CFloat32Data3D::VOLUME" cdef extern from "astra/Float32Data2D.h" namespace "astra": - cdef cppclass CFloat32Data2D: - bool isInitialized() - int getSize() - float32 *getData() - float32 **getData2D() - int getWidth() - int getHeight() - TWOEDataType getType() + cdef cppclass CFloat32Data2D: + bool isInitialized() + int getSize() + float32 *getData() + float32 **getData2D() + int getWidth() + int getHeight() + TWOEDataType getType() cdef extern from "astra/SparseMatrixProjectionGeometry2D.h" namespace "astra": - cdef cppclass CSparseMatrixProjectionGeometry2D: - CSparseMatrixProjectionGeometry2D() + cdef cppclass CSparseMatrixProjectionGeometry2D: + CSparseMatrixProjectionGeometry2D() cdef extern from "astra/FanFlatProjectionGeometry2D.h" namespace "astra": - cdef cppclass CFanFlatProjectionGeometry2D: - CFanFlatProjectionGeometry2D() + cdef cppclass CFanFlatProjectionGeometry2D: + CFanFlatProjectionGeometry2D() cdef extern from "astra/FanFlatVecProjectionGeometry2D.h" namespace "astra": - cdef cppclass CFanFlatVecProjectionGeometry2D: - CFanFlatVecProjectionGeometry2D() + cdef cppclass CFanFlatVecProjectionGeometry2D: + CFanFlatVecProjectionGeometry2D() cdef extern from "astra/ParallelVecProjectionGeometry2D.h" namespace "astra": cdef cppclass CParallelVecProjectionGeometry2D: CParallelVecProjectionGeometry2D() cdef extern from "astra/ParallelProjectionGeometry2D.h" namespace "astra": - cdef cppclass CParallelProjectionGeometry2D: - CParallelProjectionGeometry2D() + cdef cppclass CParallelProjectionGeometry2D: + CParallelProjectionGeometry2D() cdef extern from "astra/Float32ProjectionData2D.h" namespace "astra": - cdef cppclass CFloat32ProjectionData2D: - CFloat32ProjectionData2D(CProjectionGeometry2D*) - CFloat32ProjectionData2D(CProjectionGeometry2D*, CFloat32CustomMemory*) - CProjectionGeometry2D * getGeometry() - void changeGeometry(CProjectionGeometry2D*) - int getDetectorCount() - int getAngleCount() + cdef cppclass CFloat32ProjectionData2D: + CFloat32ProjectionData2D(CProjectionGeometry2D*) + CFloat32ProjectionData2D(CProjectionGeometry2D*, CFloat32CustomMemory*) + 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) nogil - bool isInitialized() + cdef cppclass CAlgorithm: + bool initialize(Config) + void run(int) nogil + bool isInitialized() cdef extern from "astra/ReconstructionAlgorithm2D.h" namespace "astra": - cdef cppclass CReconstructionAlgorithm2D: - bool getResidualNorm(float32&) + 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 cppclass CProjector2D: + bool isInitialized() + CProjectionGeometry2D* getProjectionGeometry() + CVolumeGeometry2D* getVolumeGeometry() + CSparseMatrix* getMatrix() cdef extern from "astra/Projector3D.h" namespace "astra": - cdef cppclass CProjector3D: - bool isInitialized() - CProjectionGeometry3D* getProjectionGeometry() - CVolumeGeometry3D* getVolumeGeometry() + cdef cppclass CProjector3D: + bool isInitialized() + CProjectionGeometry3D* getProjectionGeometry() + CVolumeGeometry3D* getVolumeGeometry() IF HAVE_CUDA==True: - cdef extern from "astra/CudaProjector3D.h" namespace "astra": - cdef cppclass CCudaProjector3D + cdef extern from "astra/CudaProjector3D.h" namespace "astra": + cdef cppclass CCudaProjector3D + + cdef extern from "astra/CudaProjector2D.h" namespace "astra": + cdef cppclass CCudaProjector2D + + cdef extern from "astra/Float32Data3DGPU.h" namespace "astraCUDA3d": + cdef cppclass MemHandle3D: + pass - cdef extern from "astra/CudaProjector2D.h" namespace "astra": - cdef cppclass CCudaProjector2D + cdef extern from "astra/Float32Data3DGPU.h" namespace "astraCUDA3d": + cdef MemHandle3D wrapHandle(float *D_ptr, unsigned int x, unsigned int y, unsigned int z, unsigned int pitch) 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 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/Float32Data3D.h" namespace "astra": + cdef cppclass CFloat32Data3D: + bool isInitialized() + int getSize() + int getWidth() + int getHeight() + int getDepth() + 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() - THREEEDataType getType() + cdef cppclass CFloat32Data3DMemory(CFloat32Data3D): + CFloat32Data3DMemory() + void updateStatistics() + float32 *getData() + float32 ***getData3D() + THREEEDataType getType() cdef extern from "astra/VolumeGeometry3D.h" namespace "astra": - cdef cppclass CVolumeGeometry3D: - CVolumeGeometry3D() - bool initialize(Config) - Config * getConfiguration() - int getGridColCount() - int getGridRowCount() - int getGridSliceCount() + cdef cppclass CVolumeGeometry3D: + CVolumeGeometry3D() + bool initialize(Config) + Config * getConfiguration() + int getGridColCount() + int getGridRowCount() + int getGridSliceCount() cdef extern from "astra/ProjectionGeometry3D.h" namespace "astra": - cdef cppclass CProjectionGeometry3D: - CProjectionGeometry3D() - bool initialize(Config) - Config * getConfiguration() - int getProjectionCount() - int getDetectorColCount() - int getDetectorRowCount() + cdef cppclass CProjectionGeometry3D: + CProjectionGeometry3D() + bool initialize(Config) + Config * getConfiguration() + int getProjectionCount() + int getDetectorColCount() + int getDetectorRowCount() cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra": - cdef cppclass CFloat32VolumeData3DMemory: - CFloat32VolumeData3DMemory(CVolumeGeometry3D*) - CFloat32VolumeData3DMemory(CVolumeGeometry3D*, CFloat32CustomMemory*) - CVolumeGeometry3D* getGeometry() - void changeGeometry(CVolumeGeometry3D*) - int getRowCount() - int getColCount() - int getSliceCount() - bool isInitialized() - - + cdef cppclass CFloat32VolumeData3DMemory: + CFloat32VolumeData3DMemory(CVolumeGeometry3D*) + CFloat32VolumeData3DMemory(CVolumeGeometry3D*, CFloat32CustomMemory*) + CVolumeGeometry3D* getGeometry() + void changeGeometry(CVolumeGeometry3D*) + int getRowCount() + int getColCount() + int getSliceCount() + bool isInitialized() cdef extern from "astra/ParallelProjectionGeometry3D.h" namespace "astra": - cdef cppclass CParallelProjectionGeometry3D: - CParallelProjectionGeometry3D() + cdef cppclass CParallelProjectionGeometry3D: + CParallelProjectionGeometry3D() cdef extern from "astra/ParallelVecProjectionGeometry3D.h" namespace "astra": - cdef cppclass CParallelVecProjectionGeometry3D: - CParallelVecProjectionGeometry3D() + cdef cppclass CParallelVecProjectionGeometry3D: + CParallelVecProjectionGeometry3D() cdef extern from "astra/ConeProjectionGeometry3D.h" namespace "astra": - cdef cppclass CConeProjectionGeometry3D: - CConeProjectionGeometry3D() - bool initialize(Config) + cdef cppclass CConeProjectionGeometry3D: + CConeProjectionGeometry3D() + bool initialize(Config) cdef extern from "astra/ConeVecProjectionGeometry3D.h" namespace "astra": - cdef cppclass CConeVecProjectionGeometry3D: - CConeVecProjectionGeometry3D() + cdef cppclass CConeVecProjectionGeometry3D: + CConeVecProjectionGeometry3D() cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra": - cdef cppclass CFloat32ProjectionData3DMemory: - CFloat32ProjectionData3DMemory(CProjectionGeometry3D*) - CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*) - CFloat32ProjectionData3DMemory(CProjectionGeometry3D*, CFloat32CustomMemory*) - CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*, CFloat32CustomMemory*) - CProjectionGeometry3D* getGeometry() - void changeGeometry(CProjectionGeometry3D*) - int getDetectorColCount() - int getDetectorRowCount() - int getAngleCount() - bool isInitialized() + cdef cppclass CFloat32ProjectionData3DMemory: + CFloat32ProjectionData3DMemory(CProjectionGeometry3D*) + CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*) + CFloat32ProjectionData3DMemory(CProjectionGeometry3D*, CFloat32CustomMemory*) + CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*, CFloat32CustomMemory*) + CProjectionGeometry3D* getGeometry() + void changeGeometry(CProjectionGeometry3D*) + int getDetectorColCount() + int getDetectorRowCount() + int getAngleCount() + bool isInitialized() -cdef extern from "astra/Float32Data3D.h" namespace "astra": - cdef cppclass CFloat32Data3D: - CFloat32Data3D() - bool isInitialized() - int getSize() - int getWidth() - int getHeight() - int getDepth() - void updateStatistics() +IF HAVE_CUDA==True: + cdef extern from "astra/Float32VolumeData3DGPU.h" namespace "astra": + cdef cppclass CFloat32VolumeData3DGPU: + CFloat32VolumeData3DGPU(CVolumeGeometry3D*, MemHandle3D) + CVolumeGeometry3D* getGeometry() + void changeGeometry(CVolumeGeometry3D*) + int getRowCount() + int getColCount() + int getSliceCount() + bool isInitialized() + + cdef extern from "astra/Float32ProjectionData3DGPU.h" namespace "astra": + cdef cppclass CFloat32ProjectionData3DGPU: + CFloat32ProjectionData3DGPU(CProjectionGeometry3D*, MemHandle3D) + CProjectionGeometry3D* getGeometry() + void changeGeometry(CProjectionGeometry3D*) + int getRowCount() + int getColCount() + int getSliceCount() + bool isInitialized() diff --git a/python/astra/PyIndexManager.pxd b/python/astra/PyIndexManager.pxd index c1ad502..5eeff02 100644 --- a/python/astra/PyIndexManager.pxd +++ b/python/astra/PyIndexManager.pxd @@ -3,7 +3,7 @@ # 2013-2016, CWI, Amsterdam # # Contact: astra@uantwerpen.be -# Website: http://sf.net/projects/astra-toolbox +# Website: http://www.astra-toolbox.com/ # # This file is part of the ASTRA Toolbox. # diff --git a/python/astra/PyMatrixManager.pxd b/python/astra/PyMatrixManager.pxd index b2b84c4..38ad7f1 100644 --- a/python/astra/PyMatrixManager.pxd +++ b/python/astra/PyMatrixManager.pxd @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + from libcpp.string cimport string from .PyIncludes cimport * diff --git a/python/astra/PyProjector2DFactory.pxd b/python/astra/PyProjector2DFactory.pxd index 3314544..8c751fc 100644 --- a/python/astra/PyProjector2DFactory.pxd +++ b/python/astra/PyProjector2DFactory.pxd @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + from libcpp.string cimport string from libcpp cimport bool from .PyIncludes cimport * diff --git a/python/astra/PyProjector2DManager.pxd b/python/astra/PyProjector2DManager.pxd index 92176ba..86bd3cf 100644 --- a/python/astra/PyProjector2DManager.pxd +++ b/python/astra/PyProjector2DManager.pxd @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + from libcpp.string cimport string from .PyIncludes cimport * diff --git a/python/astra/PyProjector3DFactory.pxd b/python/astra/PyProjector3DFactory.pxd index bcbce94..345678b 100644 --- a/python/astra/PyProjector3DFactory.pxd +++ b/python/astra/PyProjector3DFactory.pxd @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + from libcpp.string cimport string from libcpp cimport bool from .PyIncludes cimport * diff --git a/python/astra/PyProjector3DManager.pxd b/python/astra/PyProjector3DManager.pxd index b1eac6b..cdd739a 100644 --- a/python/astra/PyProjector3DManager.pxd +++ b/python/astra/PyProjector3DManager.pxd @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + from libcpp.string cimport string from .PyIncludes cimport * diff --git a/python/astra/PyXMLDocument.pxd b/python/astra/PyXMLDocument.pxd index 033b8ef..dbd84d5 100644 --- a/python/astra/PyXMLDocument.pxd +++ b/python/astra/PyXMLDocument.pxd @@ -1,28 +1,27 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- # distutils: language = c++ # distutils: libraries = astra diff --git a/python/astra/__init__.py b/python/astra/__init__.py index 515d9a2..b73fff5 100644 --- a/python/astra/__init__.py +++ b/python/astra/__init__.py @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with 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 @@ -35,9 +35,12 @@ from . import projector from . import projector3d from . import matrix from . import plugin +from . import plugins from . import log from .optomo import OpTomo +__version__ = '1.8' + import os if 'ASTRA_GPU_INDEX' in os.environ: diff --git a/python/astra/algorithm.py b/python/astra/algorithm.py index 46cfccc..b6dfb95 100644 --- a/python/astra/algorithm.py +++ b/python/astra/algorithm.py @@ -1,28 +1,27 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- from . import algorithm_c as a diff --git a/python/astra/algorithm_c.pyx b/python/astra/algorithm_c.pyx index 4e96578..0a48de8 100644 --- a/python/astra/algorithm_c.pyx +++ b/python/astra/algorithm_c.pyx @@ -3,7 +3,7 @@ # 2013-2016, CWI, Amsterdam # # Contact: astra@uantwerpen.be -# Website: http://sf.net/projects/astra-toolbox +# Website: http://www.astra-toolbox.com/ # # This file is part of the ASTRA Toolbox. # @@ -44,7 +44,7 @@ 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 + CReconstructionAlgorithm2D * dynamic_cast_recAlg "dynamic_cast<astra::CReconstructionAlgorithm2D*>" (CAlgorithm * ) except NULL def create(config): diff --git a/python/astra/astra.py b/python/astra/astra.py index 61c26ee..3804d51 100644 --- a/python/astra/astra.py +++ b/python/astra/astra.py @@ -1,28 +1,27 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- from . import astra_c as a @@ -38,17 +37,6 @@ def use_cuda(): """ 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, memory=0): """Set default GPU index to use. diff --git a/python/astra/astra_c.pyx b/python/astra/astra_c.pyx index 8e30e69..6de10da 100644 --- a/python/astra/astra_c.pyx +++ b/python/astra/astra_c.pyx @@ -3,7 +3,7 @@ # 2013-2016, CWI, Amsterdam # # Contact: astra@uantwerpen.be -# Website: http://sf.net/projects/astra-toolbox +# Website: http://www.astra-toolbox.com/ # # This file is part of the ASTRA Toolbox. # @@ -37,8 +37,6 @@ cimport PyIndexManager from .PyIndexManager cimport CAstraObjectManagerBase cdef extern from "astra/Globals.h" namespace "astra": - int getVersion() - string getVersionString() bool cudaEnabled() IF HAVE_CUDA==True: @@ -74,13 +72,6 @@ def credits(): def use_cuda(): return cudaEnabled() - -def version(printToScreen=False): - if printToScreen: - six.print_(wrap_from_bytes(getVersionString())) - else: - return getVersion() - IF HAVE_CUDA==True: def set_gpu_index(idx, memory=0): import collections diff --git a/python/astra/creators.py b/python/astra/creators.py index 82fd9d1..4ddaf0c 100644 --- a/python/astra/creators.py +++ b/python/astra/creators.py @@ -1,28 +1,27 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- import six import numpy as np @@ -272,7 +271,7 @@ This method can be called in a number of ways: 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, origin_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]} + 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)') @@ -547,8 +546,8 @@ def create_reconstruction(rec_type, proj_id, sinogram, iterations=1, use_mask='n return recon_id -def create_projector(proj_type, proj_geom, vol_geom): - """Create a 2D projector. +def create_projector(proj_type, proj_geom, vol_geom, options=None): + """Create a 2D or 3D projector. :param proj_type: Projector type, such as ``'line'``, ``'linear'``, ... :type proj_type: :class:`string` @@ -556,6 +555,8 @@ def create_projector(proj_type, proj_geom, vol_geom): :type proj_geom: :class:`dict` :param vol_geom: Volume geometry. :type vol_geom: :class:`dict` +:param options: Projector options structure defining ``'VoxelSuperSampling'``, ``'DetectorSuperSampling'``. +:type options: :class:`dict` :returns: :class:`int` -- The ID of the projector. """ @@ -564,6 +565,8 @@ def create_projector(proj_type, proj_geom, vol_geom): cfg = astra_dict(proj_type) cfg['ProjectionGeometry'] = proj_geom cfg['VolumeGeometry'] = vol_geom + if options is not None: + cfg['options'] = options types3d = ['linear3d', 'linearcone', 'cuda3d'] if proj_type in types3d: return projector3d.create(cfg) diff --git a/python/astra/data2d.py b/python/astra/data2d.py index f119f05..674161d 100644 --- a/python/astra/data2d.py +++ b/python/astra/data2d.py @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + from . import data2d_c as d import numpy as np diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx index 2242d3b..1b1125d 100644 --- a/python/astra/data2d_c.pyx +++ b/python/astra/data2d_c.pyx @@ -3,7 +3,7 @@ # 2013-2016, CWI, Amsterdam # # Contact: astra@uantwerpen.be -# Website: http://sf.net/projects/astra-toolbox +# Website: http://www.astra-toolbox.com/ # # This file is part of the ASTRA Toolbox. # @@ -83,8 +83,10 @@ def create(datatype, geometry, data=None, link=False): cdef CFloat32Data2D * pDataObject2D cdef CFloat32CustomMemory * pCustom - if link and data.shape!=geom_size(geometry): - raise Exception("The dimensions of the data do not match those specified in the geometry.") + if link: + geom_shape = geom_size(geometry) + if data.shape != geom_shape: + raise ValueError("The dimensions of the data do not match those specified in the geometry: {} != {}".format(data.shape, geom_shape)) if datatype == '-vol': cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry) @@ -92,7 +94,7 @@ def create(datatype, geometry, data=None, link=False): if not pGeometry.initialize(cfg[0]): del cfg del pGeometry - raise Exception('Geometry class not initialized.') + raise RuntimeError('Geometry class not initialized.') if link: pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data) pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry, pCustom) @@ -116,7 +118,7 @@ def create(datatype, geometry, data=None, link=False): if not ppGeometry.initialize(cfg[0]): del cfg del ppGeometry - raise Exception('Geometry class not initialized.') + raise RuntimeError('Geometry class not initialized.') if link: pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data) pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry, pCustom) @@ -125,11 +127,11 @@ def create(datatype, geometry, data=None, link=False): del ppGeometry del cfg else: - raise Exception("Invalid datatype. Please specify '-vol' or '-sino'.") + raise ValueError("Invalid datatype. Please specify '-vol' or '-sino'.") if not pDataObject2D.isInitialized(): del pDataObject2D - raise Exception("Couldn't initialize data object.") + raise RuntimeError("Couldn't initialize data object.") if not link: fillDataObject(pDataObject2D, data) @@ -140,6 +142,10 @@ cdef fillDataObject(CFloat32Data2D * obj, data): fillDataObjectScalar(obj, 0) else: if isinstance(data, np.ndarray): + obj_shape = (obj.getHeight(), obj.getWidth()) + if data.shape != obj_shape: + raise ValueError( + "The dimensions of the data do not match those specified in the geometry: {} != {}".format(data.shape, obj_shape)) fillDataObjectArray(obj, np.ascontiguousarray(data,dtype=np.float32)) else: fillDataObjectScalar(obj, np.float32(data)) @@ -152,18 +158,15 @@ cdef fillDataObjectScalar(CFloat32Data2D * obj, float 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") + raise ValueError("Data object not found") if not pDataObject.isInitialized(): - raise Exception("Data object not initialized properly.") + raise RuntimeError("Data object not initialized properly.") return pDataObject @@ -182,15 +185,15 @@ def get_geometry(i): pDataObject3 = <CFloat32VolumeData2D * >pDataObject geom = utils.configToDict(pDataObject3.getGeometry().getConfiguration()) else: - raise Exception("Not a known data object") + raise RuntimeError("Not a known data object") return geom cdef CProjector2D * getProjector(i) except NULL: cdef CProjector2D * proj = manProj.get(i) if proj == NULL: - raise Exception("Projector not initialized.") + raise RuntimeError("Projector not initialized.") if not proj.isInitialized(): - raise Exception("Projector not initialized.") + raise RuntimeError("Projector not initialized.") return proj def check_compatible(i, proj_id): @@ -205,7 +208,7 @@ def check_compatible(i, proj_id): pDataObject3 = <CFloat32VolumeData2D * >pDataObject return pDataObject3.getGeometry().isEqual(proj.getVolumeGeometry()) else: - raise Exception("Not a known data object") + raise RuntimeError("Not a known data object") def change_geometry(i, geom): cdef Config *cfg @@ -231,12 +234,14 @@ def change_geometry(i, geom): if not ppGeometry.initialize(cfg[0]): del cfg del ppGeometry - raise Exception('Geometry class not initialized.') - if (ppGeometry.getDetectorCount() != pDataObject2.getDetectorCount() or ppGeometry.getProjectionAngleCount() != pDataObject2.getAngleCount()): + raise RuntimeError('Geometry class not initialized.') + geom_shape = (ppGeometry.getProjectionAngleCount(), ppGeometry.getDetectorCount()) + obj_shape = (pDataObject2.getAngleCount(), pDataObject2.getDetectorCount()) + if geom_shape != obj_shape: del ppGeometry del cfg - raise Exception( - "The dimensions of the data do not match those specified in the geometry.") + raise ValueError( + "The dimensions of the data do not match those specified in the geometry: {} != {}", obj_shape, geom_shape) pDataObject2.changeGeometry(ppGeometry) del ppGeometry del cfg @@ -247,17 +252,19 @@ def change_geometry(i, geom): if not pGeometry.initialize(cfg[0]): del cfg del pGeometry - raise Exception('Geometry class not initialized.') - if (pGeometry.getGridColCount() != pDataObject3.getWidth() or pGeometry.getGridRowCount() != pDataObject3.getHeight()): + raise RuntimeError('Geometry class not initialized.') + geom_shape = (pGeometry.getGridRowCount(), pGeometry.getGridColCount()) + obj_shape = (pDataObject3.getHeight(), pDataObject3.getWidth()) + if geom_shape != obj_shape: del cfg del pGeometry - raise Exception( - 'The dimensions of the data do not match those specified in the geometry.') + raise ValueError( + "The dimensions of the data do not match those specified in the geometry: {} != {}", obj_shape, geom_shape) pDataObject3.changeGeometry(pGeometry) del cfg del pGeometry else: - raise Exception("Not a known data object") + raise RuntimeError("Not a known data object") @cython.boundscheck(False) @cython.wraparound(False) @@ -278,7 +285,7 @@ def get_shared(i): def get_single(i): - raise Exception("Not yet implemented") + raise NotImplementedError("Not yet implemented") def info(): diff --git a/python/astra/data3d.py b/python/astra/data3d.py index f143659..ecb99d0 100644 --- a/python/astra/data3d.py +++ b/python/astra/data3d.py @@ -1,31 +1,33 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + from . import data3d_c as d import numpy as np +from .pythonutils import GPULink + def create(datatype,geometry,data=None): """Create a 3D object. @@ -52,12 +54,13 @@ def link(datatype, geometry, data): :returns: :class:`int` -- the ID of the constructed object. """ - if not isinstance(data,np.ndarray): - raise ValueError("Input should be a numpy array") - if not data.dtype==np.float32: - raise ValueError("Numpy array should be float32") - if not (data.flags['C_CONTIGUOUS'] and data.flags['ALIGNED']): - raise ValueError("Numpy array should be C_CONTIGUOUS and ALIGNED") + if not isinstance(data,np.ndarray) and not isinstance(data,GPULink): + raise TypeError("Input should be a numpy ndarray or GPULink object") + if isinstance(data, np.ndarray): + if data.dtype != np.float32: + raise ValueError("Numpy array should be float32") + if not (data.flags['C_CONTIGUOUS'] and data.flags['ALIGNED']): + raise ValueError("Numpy array should be C_CONTIGUOUS and ALIGNED") return d.create(datatype,geometry,data,True) diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx index 811d1e4..78ed620 100644 --- a/python/astra/data3d_c.pyx +++ b/python/astra/data3d_c.pyx @@ -3,7 +3,7 @@ # 2013-2016, CWI, Amsterdam # # Contact: astra@uantwerpen.be -# Website: http://sf.net/projects/astra-toolbox +# Website: http://www.astra-toolbox.com/ # # This file is part of the ASTRA Toolbox. # @@ -45,12 +45,17 @@ from .PyXMLDocument cimport XMLDocument cimport utils from .utils import wrap_from_bytes -from .pythonutils import geom_size +from .pythonutils import geom_size, GPULink import operator from six.moves import reduce +include "config.pxi" + +cdef extern from "Python.h": + void* PyLong_AsVoidPtr(object) + cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr() @@ -65,12 +70,22 @@ def create(datatype,geometry,data=None, link=False): cdef Config *cfg cdef CVolumeGeometry3D * pGeometry cdef CProjectionGeometry3D * ppGeometry - cdef CFloat32Data3DMemory * pDataObject3D + cdef CFloat32Data3D * pDataObject3D cdef CConeProjectionGeometry3D* pppGeometry - cdef CFloat32CustomMemory * pCustom + cdef CFloat32CustomMemory * pCustom = NULL + IF HAVE_CUDA==True: + cdef MemHandle3D hnd - if link and data.shape!=geom_size(geometry): - raise Exception("The dimensions of the data do not match those specified in the geometry.") + if link: + geom_shape = geom_size(geometry) + if isinstance(data, np.ndarray): + data_shape = data.shape + elif isinstance(data, GPULink): + data_shape = ( data.z, data.y, data.x ) + else: + raise TypeError("data should be a numpy.ndarray or a GPULink object") + if geom_shape != data_shape: + raise ValueError("The dimensions of the data do not match those specified in the geometry: {} != {}".format(data_shape, geom_shape)) if datatype == '-vol': cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry) @@ -78,15 +93,25 @@ def create(datatype,geometry,data=None, link=False): if not pGeometry.initialize(cfg[0]): del cfg del pGeometry - raise Exception('Geometry class not initialized.') + raise RuntimeError('Geometry class not initialized.') if link: - pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data) - pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry, pCustom) + if isinstance(data, np.ndarray): + pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data) + pDataObject3D = <CFloat32Data3D * > new CFloat32VolumeData3DMemory(pGeometry, pCustom) + elif isinstance(data, GPULink): + IF HAVE_CUDA==True: + s = geom_size(geometry) + hnd = wrapHandle(<float*>PyLong_AsVoidPtr(data.ptr), data.x, data.y, data.z, data.pitch/4) + pDataObject3D = <CFloat32Data3D * > new CFloat32VolumeData3DGPU(pGeometry, hnd) + ELSE: + raise NotImplementedError("CUDA support is not enabled in ASTRA") + else: + raise TypeError("data should be a numpy.ndarray or a GPULink object") else: - pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry) + pDataObject3D = <CFloat32Data3D * > new CFloat32VolumeData3DMemory(pGeometry) del cfg del pGeometry - elif datatype == '-sino' or datatype == '-proj3d': + elif datatype == '-sino' or datatype == '-proj3d' or datatype == '-sinocone': cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geometry) tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type'))) if (tpe == "parallel3d"): @@ -98,41 +123,38 @@ def create(datatype,geometry,data=None, link=False): elif (tpe == "cone_vec"): ppGeometry = <CProjectionGeometry3D*> new CConeVecProjectionGeometry3D(); else: - raise Exception("Invalid geometry type.") + raise ValueError("Invalid geometry type.") if not ppGeometry.initialize(cfg[0]): del cfg del ppGeometry - raise Exception('Geometry class not initialized.') + raise RuntimeError('Geometry class not initialized.') if link: - pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data) - pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry, pCustom) + if isinstance(data, np.ndarray): + pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data) + pDataObject3D = <CFloat32Data3D * > new CFloat32ProjectionData3DMemory(ppGeometry, pCustom) + elif isinstance(data, GPULink): + IF HAVE_CUDA==True: + s = geom_size(geometry) + hnd = wrapHandle(<float*>PyLong_AsVoidPtr(data.ptr), data.x, data.y, data.z, data.pitch/4) + pDataObject3D = <CFloat32Data3D * > new CFloat32ProjectionData3DGPU(ppGeometry, hnd) + ELSE: + raise NotImplementedError("CUDA support is not enabled in ASTRA") + else: + raise TypeError("data should be a numpy.ndarray or a GPULink object") else: pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry) del ppGeometry del cfg - elif datatype == "-sinocone": - cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geometry) - pppGeometry = new CConeProjectionGeometry3D() - if not pppGeometry.initialize(cfg[0]): - del cfg - del pppGeometry - raise Exception('Geometry class not initialized.') - if link: - pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data) - pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry, pCustom) - else: - pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry) else: - raise Exception("Invalid datatype. Please specify '-vol' or '-proj3d'.") + raise ValueError("Invalid datatype. Please specify '-vol' or '-proj3d'.") if not pDataObject3D.isInitialized(): del pDataObject3D - raise Exception("Couldn't initialize data object.") - - if not link: fillDataObject(pDataObject3D, data) + raise RuntimeError("Couldn't initialize data object.") - pDataObject3D.updateStatistics() + if not link: + fillDataObject(dynamic_cast_mem(pDataObject3D), data) return man3d.store(<CFloat32Data3D*>pDataObject3D) @@ -147,7 +169,7 @@ def get_geometry(i): pDataObject3 = <CFloat32VolumeData3DMemory * >pDataObject geom = utils.configToDict(pDataObject3.getGeometry().getConfiguration()) else: - raise Exception("Not a known data object") + raise RuntimeError("Not a known data object") return geom def change_geometry(i, geom): @@ -168,18 +190,18 @@ def change_geometry(i, geom): elif (tpe == "cone_vec"): ppGeometry = <CProjectionGeometry3D*> new CConeVecProjectionGeometry3D(); else: - raise Exception("Invalid geometry type.") + raise ValueError("Invalid geometry type.") if not ppGeometry.initialize(cfg[0]): del cfg del ppGeometry - raise Exception('Geometry class not initialized.') + raise RuntimeError('Geometry class not initialized.') del cfg - if (ppGeometry.getDetectorColCount() != pDataObject2.getDetectorColCount() or \ - ppGeometry.getProjectionCount() != pDataObject2.getAngleCount() or \ - ppGeometry.getDetectorRowCount() != pDataObject2.getDetectorRowCount()): + geom_shape = (ppGeometry.getDetectorRowCount(), ppGeometry.getProjectionCount(), ppGeometry.getDetectorColCount()) + obj_shape = (pDataObject2.getDetectorRowCount(), pDataObject2.getAngleCount(), pDataObject2.getDetectorColCount()) + if geom_shape != obj_shape: del ppGeometry - raise Exception( - "The dimensions of the data do not match those specified in the geometry.") + raise ValueError( + "The dimensions of the data do not match those specified in the geometry: {} != {}".format(obj_shape, geom_shape)) pDataObject2.changeGeometry(ppGeometry) del ppGeometry @@ -190,19 +212,19 @@ def change_geometry(i, geom): if not pGeometry.initialize(cfg[0]): del cfg del pGeometry - raise Exception('Geometry class not initialized.') + raise RuntimeError('Geometry class not initialized.') del cfg - if (pGeometry.getGridColCount() != pDataObject3.getColCount() or \ - pGeometry.getGridRowCount() != pDataObject3.getRowCount() or \ - pGeometry.getGridSliceCount() != pDataObject3.getSliceCount()): + geom_shape = (pGeometry.getGridSliceCount(), pGeometry.getGridRowCount(), pGeometry.getGridColCount()) + obj_shape = (pDataObject3.getSliceCount(), pDataObject3.getRowCount(), pDataObject3.getColCount()) + if geom_shape != obj_shape: del pGeometry - raise Exception( - "The dimensions of the data do not match those specified in the geometry.") + raise ValueError( + "The dimensions of the data do not match those specified in the geometry.".format(obj_shape, geom_shape)) pDataObject3.changeGeometry(pGeometry) del pGeometry else: - raise Exception("Not a known data object") + raise RuntimeError("Not a known data object") cdef fillDataObject(CFloat32Data3DMemory * obj, data): @@ -210,6 +232,10 @@ cdef fillDataObject(CFloat32Data3DMemory * obj, data): fillDataObjectScalar(obj, 0) else: if isinstance(data, np.ndarray): + obj_shape = (obj.getDepth(), obj.getHeight(), obj.getWidth()) + if data.shape != obj_shape: + raise ValueError( + "The dimensions of the data do not match those specified in the geometry: {} != {}".format(data.shape, obj_shape)) fillDataObjectArray(obj, np.ascontiguousarray(data,dtype=np.float32)) else: fillDataObjectScalar(obj, np.float32(data)) @@ -222,18 +248,15 @@ cdef fillDataObjectScalar(CFloat32Data3DMemory * obj, float 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") + raise ValueError("Data object not found") if not pDataObject.isInitialized(): - raise Exception("Data object not initialized properly.") + raise RuntimeError("Data object not initialized properly.") return pDataObject @cython.boundscheck(False) @@ -256,7 +279,7 @@ def get_shared(i): return np.PyArray_SimpleNewFromData(3,shape,np.NPY_FLOAT32,<void *>pDataObject.getData3D()[0][0]) def get_single(i): - raise Exception("Not yet implemented") + raise NotImplementedError("Not yet implemented") def store(i,data): cdef CFloat32Data3D * pDataObject = getObject(i) diff --git a/python/astra/experimental.pyx b/python/astra/experimental.pyx index 9bb73a2..0af3118 100644 --- a/python/astra/experimental.pyx +++ b/python/astra/experimental.pyx @@ -3,7 +3,7 @@ # 2013-2016, CWI, Amsterdam # # Contact: astra@uantwerpen.be -# Website: http://sf.net/projects/astra-toolbox +# Website: http://www.astra-toolbox.com/ # # This file is part of the ASTRA Toolbox. # @@ -36,12 +36,20 @@ IF HAVE_CUDA==True: cdef extern from "astra/CompositeGeometryManager.h" namespace "astra": cdef cppclass CCompositeGeometryManager: - bool doFP(CProjector3D *, vector[CFloat32VolumeData3DMemory *], vector[CFloat32ProjectionData3DMemory *]) - bool doBP(CProjector3D *, vector[CFloat32VolumeData3DMemory *], vector[CFloat32ProjectionData3DMemory *]) + bool doFP(CProjector3D *, vector[CFloat32VolumeData3D *], vector[CFloat32ProjectionData3D *]) + bool doBP(CProjector3D *, vector[CFloat32VolumeData3D *], vector[CFloat32ProjectionData3D *]) cdef extern from *: - CFloat32VolumeData3DMemory * dynamic_cast_vol_mem "dynamic_cast<astra::CFloat32VolumeData3DMemory*>" (CFloat32Data3D * ) except NULL - CFloat32ProjectionData3DMemory * dynamic_cast_proj_mem "dynamic_cast<astra::CFloat32ProjectionData3DMemory*>" (CFloat32Data3D * ) except NULL + CFloat32VolumeData3D * dynamic_cast_vol_mem "dynamic_cast<astra::CFloat32VolumeData3D*>" (CFloat32Data3D * ) except NULL + CFloat32ProjectionData3D * dynamic_cast_proj_mem "dynamic_cast<astra::CFloat32ProjectionData3D*>" (CFloat32Data3D * ) except NULL + + cdef extern from "astra/Float32ProjectionData3D.h" namespace "astra": + cdef cppclass CFloat32ProjectionData3D: + bool isInitialized() + cdef extern from "astra/Float32VolumeData3D.h" namespace "astra": + cdef cppclass CFloat32VolumeData3D: + bool isInitialized() + cimport PyProjector3DManager from .PyProjector3DManager cimport CProjector3DManager @@ -52,9 +60,9 @@ IF HAVE_CUDA==True: cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr() def do_composite(projector_id, vol_ids, proj_ids, t): - cdef vector[CFloat32VolumeData3DMemory *] vol - cdef CFloat32VolumeData3DMemory * pVolObject - cdef CFloat32ProjectionData3DMemory * pProjObject + cdef vector[CFloat32VolumeData3D *] vol + cdef CFloat32VolumeData3D * pVolObject + cdef CFloat32ProjectionData3D * pProjObject for v in vol_ids: pVolObject = dynamic_cast_vol_mem(man3d.get(v)) if pVolObject == NULL: @@ -62,7 +70,7 @@ IF HAVE_CUDA==True: if not pVolObject.isInitialized(): raise Exception("Data object not initialized properly") vol.push_back(pVolObject) - cdef vector[CFloat32ProjectionData3DMemory *] proj + cdef vector[CFloat32ProjectionData3D *] proj for v in proj_ids: pProjObject = dynamic_cast_proj_mem(man3d.get(v)) if pProjObject == NULL: diff --git a/python/astra/extrautils.pyx b/python/astra/extrautils.pyx index 2c7771e..248c6ee 100644 --- a/python/astra/extrautils.pyx +++ b/python/astra/extrautils.pyx @@ -3,7 +3,7 @@ # 2013-2016, CWI, Amsterdam # # Contact: astra@uantwerpen.be -# Website: http://sf.net/projects/astra-toolbox +# Website: http://www.astra-toolbox.com/ # # This file is part of the ASTRA Toolbox. # @@ -26,19 +26,19 @@ 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 + 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 index 9927eee..b3a470d 100644 --- a/python/astra/functions.py +++ b/python/astra/functions.py @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -# Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -# Author: Daniel M. Pelt -# Contact: D.M.Pelt@cwi.nl -# Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -# 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 +# 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. +# (at your option) any later version. # -# The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +# 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/>. +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + """Additional functions for PyAstraToolbox. .. moduleauthor:: Daniel M. Pelt <D.M.Pelt@cwi.nl> diff --git a/python/astra/log.py b/python/astra/log.py index 3ec0df5..a54ed08 100644 --- a/python/astra/log.py +++ b/python/astra/log.py @@ -1,28 +1,27 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- from . import log_c as l @@ -150,4 +149,4 @@ def setOutputFile(filename, level): :param level: Logging level to use (DEBUG, INFO, WARN, or ERROR). :type level: :class:`int` """ - l.log_setOutputFile(filename, level)
\ No newline at end of file + l.log_setOutputFile(filename, level) diff --git a/python/astra/log_c.pyx b/python/astra/log_c.pyx index 0d187e9..0757d0c 100644 --- a/python/astra/log_c.pyx +++ b/python/astra/log_c.pyx @@ -3,7 +3,7 @@ # 2013-2016, CWI, Amsterdam # # Contact: astra@uantwerpen.be -# Website: http://sf.net/projects/astra-toolbox +# Website: http://www.astra-toolbox.com/ # # This file is part of the ASTRA Toolbox. # diff --git a/python/astra/matlab.py b/python/astra/matlab.py index 83b345d..c96931e 100644 --- a/python/astra/matlab.py +++ b/python/astra/matlab.py @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with 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 diff --git a/python/astra/matrix.py b/python/astra/matrix.py index 27e4823..eeb873c 100644 --- a/python/astra/matrix.py +++ b/python/astra/matrix.py @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + from . import matrix_c as m def delete(ids): diff --git a/python/astra/matrix_c.pyx b/python/astra/matrix_c.pyx index f5c0938..ba20b10 100644 --- a/python/astra/matrix_c.pyx +++ b/python/astra/matrix_c.pyx @@ -3,7 +3,7 @@ # 2013-2016, CWI, Amsterdam # # Contact: astra@uantwerpen.be -# Website: http://sf.net/projects/astra-toolbox +# Website: http://www.astra-toolbox.com/ # # This file is part of the ASTRA Toolbox. # diff --git a/python/astra/optomo.py b/python/astra/optomo.py index dde719e..74f34e5 100644 --- a/python/astra/optomo.py +++ b/python/astra/optomo.py @@ -1,28 +1,27 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- from . import data2d from . import data3d diff --git a/python/astra/plugin.py b/python/astra/plugin.py index 3e3528d..56c2761 100644 --- a/python/astra/plugin.py +++ b/python/astra/plugin.py @@ -1,28 +1,27 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- from . import plugin_c as p from . import log @@ -118,4 +117,4 @@ def get_help(name): :returns: :class:`str` -- Help string (docstring). """ - return p.get_help(name)
\ No newline at end of file + return p.get_help(name) diff --git a/python/astra/plugin_c.pyx b/python/astra/plugin_c.pyx index ee04853..3853cec 100644 --- a/python/astra/plugin_c.pyx +++ b/python/astra/plugin_c.pyx @@ -3,7 +3,7 @@ # 2013-2016, CWI, Amsterdam # # Contact: astra@uantwerpen.be -# Website: http://sf.net/projects/astra-toolbox +# Website: http://www.astra-toolbox.com/ # # This file is part of the ASTRA Toolbox. # diff --git a/python/astra/plugins/__init__.py b/python/astra/plugins/__init__.py new file mode 100644 index 0000000..88a68cb --- /dev/null +++ b/python/astra/plugins/__init__.py @@ -0,0 +1,29 @@ +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam +# +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ +# +# This file is part of the ASTRA Toolbox. +# +# +# 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 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 ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +# ----------------------------------------------------------------------- + + +from .sirt import SIRTPlugin +from .cgls import CGLSPlugin + diff --git a/python/astra/plugins/cgls.py b/python/astra/plugins/cgls.py new file mode 100644 index 0000000..5268f51 --- /dev/null +++ b/python/astra/plugins/cgls.py @@ -0,0 +1,99 @@ +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam +# +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ +# +# This file is part of the ASTRA Toolbox. +# +# +# 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 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 ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +# ----------------------------------------------------------------------- + + +import astra +import numpy as np +import six + +class CGLSPlugin(astra.plugin.base): + """CGLS.""" + + astra_name = "CGLS-PLUGIN" + + def initialize(self,cfg): + self.W = astra.OpTomo(cfg['ProjectorId']) + self.vid = cfg['ReconstructionDataId'] + self.sid = cfg['ProjectionDataId'] + + try: + v = astra.data2d.get_shared(self.vid) + s = astra.data2d.get_shared(self.sid) + self.data_mod = astra.data2d + except Exception: + v = astra.data3d.get_shared(self.vid) + s = astra.data3d.get_shared(self.sid) + self.data_mod = astra.data3d + + def run(self, its): + v = self.data_mod.get_shared(self.vid) + s = self.data_mod.get_shared(self.sid) + z = np.zeros(v.shape, dtype=np.float32) + p = np.zeros(v.shape, dtype=np.float32) + r = np.zeros(s.shape, dtype=np.float32) + w = np.zeros(s.shape, dtype=np.float32) + W = self.W + + # r = s - W*v + W.FP(v, out=w) + r[:] = s + r -= w + + # p = W'*r + W.BP(r, out=p) + + # gamma = <p,p> + gamma = np.dot(p.ravel(), p.ravel()) + + for i in range(its): + # w = W * p + W.FP(p, out=w) + + # alpha = gamma / <w,w> + alpha = gamma / np.dot(w.ravel(), w.ravel()) + + # v += alpha * p + z[:] = p + z *= alpha + v += z + + # r -= alpha * w + w *= -alpha; + r += w + + # z = W' * r + W.BP(r, out=z) + + # beta = <z,z> / gamma + newgamma = np.dot(z.ravel(), z.ravel()) + beta = newgamma / gamma + + # gamma = <z,z> + gamma = newgamma + + # p = z + beta * p + p *= beta + p += z + diff --git a/python/astra/plugins/sirt.py b/python/astra/plugins/sirt.py new file mode 100644 index 0000000..5238399 --- /dev/null +++ b/python/astra/plugins/sirt.py @@ -0,0 +1,90 @@ +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam +# +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ +# +# This file is part of the ASTRA Toolbox. +# +# +# 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 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 ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +# ----------------------------------------------------------------------- + + +import astra +import numpy as np +import six + +class SIRTPlugin(astra.plugin.base): + """SIRT. + + Options: + + 'Relaxation': relaxation factor (optional) + 'MinConstraint': constrain values to at least this (optional) + 'MaxConstraint': constrain values to at most this (optional) + """ + + astra_name = "SIRT-PLUGIN" + + def initialize(self,cfg, Relaxation = 1, MinConstraint = None, MaxConstraint = None): + self.W = astra.OpTomo(cfg['ProjectorId']) + self.vid = cfg['ReconstructionDataId'] + self.sid = cfg['ProjectionDataId'] + self.min_constraint = MinConstraint + self.max_constraint = MaxConstraint + + try: + v = astra.data2d.get_shared(self.vid) + s = astra.data2d.get_shared(self.sid) + self.data_mod = astra.data2d + except Exception: + v = astra.data3d.get_shared(self.vid) + s = astra.data3d.get_shared(self.sid) + self.data_mod = astra.data3d + + self.R = self.W * np.ones(v.shape,dtype=np.float32).ravel(); + self.R[self.R < 0.000001] = np.Inf + self.R = 1 / self.R + self.R = self.R.reshape(s.shape) + + self.mrC = self.W.T * np.ones(s.shape,dtype=np.float32).ravel(); + self.mrC[self.mrC < 0.000001] = np.Inf + self.mrC = -Relaxation / self.mrC + self.mrC = self.mrC.reshape(v.shape) + + + def run(self, its): + v = self.data_mod.get_shared(self.vid) + s = self.data_mod.get_shared(self.sid) + tv = np.zeros(v.shape, dtype=np.float32) + ts = np.zeros(s.shape, dtype=np.float32) + W = self.W + mrC = self.mrC + R = self.R + for i in range(its): + W.FP(v,out=ts) + ts -= s + ts *= R # ts = R * (W*v - s) + + W.BP(ts,out=tv) + tv *= mrC + + v += tv # v = v - rel * C * W' * ts + + if self.min_constraint is not None or self.max_constraint is not None: + v.clip(min=self.min_constraint, max=self.max_constraint, out=v) + diff --git a/python/astra/projector.py b/python/astra/projector.py index e370e5a..878e011 100644 --- a/python/astra/projector.py +++ b/python/astra/projector.py @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + from . import projector_c as p def create(config): diff --git a/python/astra/projector3d.py b/python/astra/projector3d.py index d1086b9..9befa3f 100644 --- a/python/astra/projector3d.py +++ b/python/astra/projector3d.py @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + from . import projector3d_c as p def create(config): diff --git a/python/astra/projector3d_c.pyx b/python/astra/projector3d_c.pyx index e355e38..98eccc1 100644 --- a/python/astra/projector3d_c.pyx +++ b/python/astra/projector3d_c.pyx @@ -3,7 +3,7 @@ # 2013-2016, CWI, Amsterdam # # Contact: astra@uantwerpen.be -# Website: http://sf.net/projects/astra-toolbox +# Website: http://www.astra-toolbox.com/ # # This file is part of the ASTRA Toolbox. # diff --git a/python/astra/projector_c.pyx b/python/astra/projector_c.pyx index 53d38c3..be529da 100644 --- a/python/astra/projector_c.pyx +++ b/python/astra/projector_c.pyx @@ -3,7 +3,7 @@ # 2013-2016, CWI, Amsterdam # # Contact: astra@uantwerpen.be -# Website: http://sf.net/projects/astra-toolbox +# Website: http://www.astra-toolbox.com/ # # This file is part of the ASTRA Toolbox. # diff --git a/python/astra/pythonutils.py b/python/astra/pythonutils.py index 8ea4af5..27fa8fd 100644 --- a/python/astra/pythonutils.py +++ b/python/astra/pythonutils.py @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -# Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -# Author: Daniel M. Pelt -# Contact: D.M.Pelt@cwi.nl -# Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -# 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 +# 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. +# (at your option) any later version. # -# The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +# 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/>. +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + """Additional purely Python functions for PyAstraToolbox. .. moduleauthor:: Daniel M. Pelt <D.M.Pelt@cwi.nl> @@ -61,3 +61,21 @@ def geom_size(geom, dim=None): s = s[dim] return s + +class GPULink(object): + """Utility class for astra.data3d.link with a CUDA pointer + + The CUDA pointer ptr must point to an array of floats. + + x is the fastest-changing coordinate, z the slowest-changing. + + pitch is the width in bytes of the memory block. For a contiguous + memory block, pitch is equal to sizeof(float) * x. For a memory block + allocated by cudaMalloc3D, pitch is the pitch as returned by cudaMalloc3D. + """ + def __init__(self, ptr, x, y, z, pitch): + self.ptr = ptr + self.x = x + self.y = y + self.z = z + self.pitch = pitch diff --git a/python/astra/src/PythonPluginAlgorithm.cpp b/python/astra/src/PythonPluginAlgorithm.cpp index 893db94..69b3d06 100644 --- a/python/astra/src/PythonPluginAlgorithm.cpp +++ b/python/astra/src/PythonPluginAlgorithm.cpp @@ -4,7 +4,7 @@ Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp 2014-2016, CWI, Amsterdam Contact: astra@uantwerpen.be -Website: http://sf.net/projects/astra-toolbox +Website: http://www.astra-toolbox.com/ This file is part of the ASTRA Toolbox. diff --git a/python/astra/src/PythonPluginAlgorithm.h b/python/astra/src/PythonPluginAlgorithm.h index ea4c6fb..dacd0e4 100644 --- a/python/astra/src/PythonPluginAlgorithm.h +++ b/python/astra/src/PythonPluginAlgorithm.h @@ -4,7 +4,7 @@ Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp 2014-2016, CWI, Amsterdam Contact: astra@uantwerpen.be -Website: http://sf.net/projects/astra-toolbox +Website: http://www.astra-toolbox.com/ This file is part of the ASTRA Toolbox. diff --git a/python/astra/utils.pxd b/python/astra/utils.pxd index ca84836..695081f 100644 --- a/python/astra/utils.pxd +++ b/python/astra/utils.pxd @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://www.astra-toolbox.com/ # +# This file is part of the ASTRA Toolbox. # -#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 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. +# 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/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- + from libcpp.string cimport string cimport PyXMLDocument diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx index 34d1902..a40916b 100644 --- a/python/astra/utils.pyx +++ b/python/astra/utils.pyx @@ -3,7 +3,7 @@ # 2013-2016, CWI, Amsterdam # # Contact: astra@uantwerpen.be -# Website: http://sf.net/projects/astra-toolbox +# Website: http://www.astra-toolbox.com/ # # This file is part of the ASTRA Toolbox. # diff --git a/python/builder.py b/python/builder.py index dcd62d8..ec0bd23 100644 --- a/python/builder.py +++ b/python/builder.py @@ -3,7 +3,7 @@ # 2013-2016, CWI, Amsterdam # # Contact: astra@uantwerpen.be -# Website: http://sf.net/projects/astra-toolbox +# Website: http://www.astra-toolbox.com/ # # This file is part of the ASTRA Toolbox. # @@ -21,72 +21,72 @@ # You should have received a copy of the GNU General Public License # along with 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 pkg_resources import parse_version 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 -try: - if os.environ['CL'].find('/DASTRA_CUDA')!=-1: - usecuda=True -except KeyError: - pass +if parse_version(Cython.__version__) < parse_version('0.13'): + raise ImportError('Cython version should be at least 0.13') + +use_cuda = ('-DASTRA_CUDA' in os.environ.get('CPPFLAGS', '') or + '/DASTRA_CUDA' in os.environ.get('CL', '')) +self_path = os.path.dirname(os.path.abspath(__file__)) -cfgToWrite = 'DEF HAVE_CUDA=' + str(usecuda) + "\n" -cfgHasToBeUpdated = True +cfg_string = 'DEF HAVE_CUDA=' + str(use_cuda) + '\n' +update_cfg = True try: - cfg = open('astra/config.pxi','r') - cfgIn = cfg.read() - cfg.close() - if cfgIn==cfgToWrite: - cfgHasToBeUpdated = False + with open(os.path.join(self_path, 'astra', 'config.pxi'), 'r') as cfg: + cfg_fromfile = cfg.read() + if cfg_fromfile == cfg_string: + update_cfg = False except IOError: pass -if cfgHasToBeUpdated: - cfg = open('astra/config.pxi','w') - cfg.write(cfgToWrite) - cfg.close() +if update_cfg: + with open(os.path.join(self_path, 'astra', 'config.pxi'), 'w') as cfg: + cfg.write(cfg_string) + +pkgdata = {} +if os.environ.get('ASTRA_INSTALL_LIBRARY_AS_DATA', ''): + pkgdata['astra'] = [os.environ['ASTRA_INSTALL_LIBRARY_AS_DATA']] -cmdclass = { } -ext_modules = [ ] +cmdclass = {} +ext_modules = [] -ext_modules = cythonize("astra/*.pyx", language_level=2) -cmdclass = { 'build_ext': build_ext } +ext_modules = cythonize(os.path.join(self_path, 'astra', '*.pyx'), + language_level=2) +cmdclass = {'build_ext': build_ext} for m in ext_modules: - if m.name == 'astra.plugin_c': - m.sources.append('astra/src/PythonPluginAlgorithm.cpp') + if m.name == 'astra.plugin_c': + m.sources.append(os.path.join(self_path, 'astra', 'src', + 'PythonPluginAlgorithm.cpp')) -setup (name = 'PyASTRAToolbox', - version = '1.7.1', - description = 'Python interface to the ASTRA-Toolbox', - author='D.M. Pelt', - author_email='D.M.Pelt@cwi.nl', - url='http://sf.net/projects/astra-toolbox', - #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"], - ) +setup(name='astra-toolbox', + version='1.8', + description='Python interface to the ASTRA Toolbox', + author='D.M. Pelt', + author_email='D.M.Pelt@cwi.nl', + url='https://github.com/astra-toolbox/astra-toolbox', + # 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', 'astra.plugins'], + package_data=pkgdata, + requires=['numpy', 'scipy', 'six'], + ) diff --git a/python/conda/astra-toolbox/bld.bat b/python/conda/astra-toolbox/bld.bat new file mode 100644 index 0000000..15777ce --- /dev/null +++ b/python/conda/astra-toolbox/bld.bat @@ -0,0 +1,33 @@ +@echo off + +set R=%SRC_DIR% + +set B_VC=C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\bin\amd64 +call "%B_VC%\vcvars64.bat" + +set B_BV=1_62 +set B_BOOST=D:\wjp\boost_%B_BV%_0 + +cd /D "%B_BOOST%\lib64-msvc-14.0" + +mkdir "%R%\lib\x64" +mkdir "%R%\bin\x64\Release_CUDA" + +copy boost_unit_test_framework-vc140-mt-%B_BV%.lib %R%\lib\x64 +copy libboost_chrono-vc140-mt-%B_BV%.lib %R%\lib\x64 +copy libboost_date_time-vc140-mt-%B_BV%.lib %R%\lib\x64 +copy libboost_system-vc140-mt-%B_BV%.lib %R%\lib\x64 +copy libboost_thread-vc140-mt-%B_BV%.lib %R%\lib\x64 + +cd %B_BOOST% + +xcopy /i /e /q boost "%R%\lib\include\boost" + +cd /D %R% + +cd python + +set VS90COMNTOOLS=%VS140COMNTOOLS% +set CL=/DASTRA_CUDA /DASTRA_PYTHON "/I%R%\include" "/I%R%\lib\include" "/I%CUDA_PATH%\include" +copy "%CONDA_PREFIX%\Library\lib\AstraCuda64.lib" astra.lib +python builder.py build_ext --compiler=msvc install diff --git a/python/conda/astra-toolbox/build.sh b/python/conda/astra-toolbox/build.sh new file mode 100644 index 0000000..951fd88 --- /dev/null +++ b/python/conda/astra-toolbox/build.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +cd $SRC_DIR/python/ +CPPFLAGS="-DASTRA_CUDA -DASTRA_PYTHON $CPPFLAGS -I$SRC_DIR/ -I$SRC_DIR/include -I$CUDA_ROOT/include" CC=$CC python ./builder.py build install diff --git a/python/conda/meta.yaml b/python/conda/astra-toolbox/meta.yaml index e6a7f52..942397e 100644 --- a/python/conda/meta.yaml +++ b/python/conda/astra-toolbox/meta.yaml @@ -1,35 +1,41 @@ package: name: astra-toolbox - version: '1.8b' + version: '1.8' source: git_url: https://github.com/astra-toolbox/astra-toolbox.git - #git_tag: v1.7.1 # Change to 1.8 after release + git_tag: v1.8 build: number: 0 script_env: - - CUDA_ROOT - - MAKEOPTS + - CC # [not win] + - CUDA_ROOT # [not win] test: imports: - astra + requires: + # To avoid large downloads just for testing after build phase + - nomkl # [not win] + requirements: build: - python - cython >=0.13 + - nomkl # [not win] - numpy - scipy - six + - libastra ==1.8 run: - python - - numpy + - numpy x.x - scipy - six - - libastra ==1.8b + - libastra ==1.8 about: diff --git a/python/conda/build.sh b/python/conda/build.sh deleted file mode 100644 index 13ae3f8..0000000 --- a/python/conda/build.sh +++ /dev/null @@ -1,8 +0,0 @@ -cd build/linux -./autogen.sh -./configure --with-python --with-cuda=$CUDA_ROOT --prefix=$PREFIX -if [ $MAKEOPTS == '<UNDEFINED>' ] - then - MAKEOPTS="" -fi -make $MAKEOPTS python-root-install
\ No newline at end of file diff --git a/python/conda/libastra/bld.bat b/python/conda/libastra/bld.bat new file mode 100644 index 0000000..29b894a --- /dev/null +++ b/python/conda/libastra/bld.bat @@ -0,0 +1,33 @@ +@echo off + +set R=%SRC_DIR% + +set B_VC=C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\bin\amd64 +call "%B_VC%\vcvars64.bat" + +set B_BV=1_62 +set B_BOOST=D:\wjp\boost_%B_BV%_0 + +cd /D "%B_BOOST%\lib64-msvc-14.0" + +mkdir "%R%\lib\x64" +mkdir "%R%\bin\x64\Release_CUDA" + +copy boost_unit_test_framework-vc140-mt-%B_BV%.lib %R%\lib\x64 +copy libboost_chrono-vc140-mt-%B_BV%.lib %R%\lib\x64 +copy libboost_date_time-vc140-mt-%B_BV%.lib %R%\lib\x64 +copy libboost_system-vc140-mt-%B_BV%.lib %R%\lib\x64 +copy libboost_thread-vc140-mt-%B_BV%.lib %R%\lib\x64 + +cd %B_BOOST% + +xcopy /i /e /q boost "%R%\lib\include\boost" + +cd /D %R% + +msbuild astra_vc14.sln /p:Configuration=Release_CUDA /p:Platform=x64 /t:astra_vc14 + +copy bin\x64\Release_CUDA\AstraCuda64.dll "%CONDA_PREFIX%\Library\bin" +copy bin\x64\Release_CUDA\AstraCuda64.lib "%CONDA_PREFIX%\Library\lib" +copy "%CUDA_PATH%\bin\cudart64_80.dll" "%CONDA_PREFIX%\Library\bin" +copy "%CUDA_PATH%\bin\cufft64_80.dll" "%CONDA_PREFIX%\Library\bin" diff --git a/python/conda/libastra/build.sh b/python/conda/libastra/build.sh index e1d9700..304c053 100644 --- a/python/conda/libastra/build.sh +++ b/python/conda/libastra/build.sh @@ -1,15 +1,29 @@ -cd build/linux -./autogen.sh -./configure --with-cuda=$CUDA_ROOT --prefix=$PREFIX -if [ $MAKEOPTS == '<UNDEFINED>' ] - then - MAKEOPTS="" -fi -make $MAKEOPTS install-libraries -LIBPATH=lib -if [ $ARCH == 64 ] - then - LIBPATH+=64 -fi -cp -P $CUDA_ROOT/$LIBPATH/libcudart.so.* $PREFIX/lib -cp -P $CUDA_ROOT/$LIBPATH/libcufft.so.* $PREFIX/lib +#!/bin/sh + +cd $SRC_DIR/build/linux + +$SRC_DIR/build/linux/autogen.sh + +# Add C++11 to compiler flags if nvcc supports it, mostly to work around a boost bug +NVCC=$CUDA_ROOT/bin/nvcc +echo "int main(){return 0;}" > $CONDA_PREFIX/test.cu +$NVCC $CONDA_PREFIX/test.cu -ccbin $CC --std=c++11 -o $CONDA_PREFIX/test.out > /dev/null 2>&1 && EXTRA_NVCCFLAGS="--std=c++11" || true +rm -f $CONDA_PREFIX/test.out + +$SRC_DIR/build/linux/configure --with-install-type=prefix --with-cuda=$CUDA_ROOT --prefix=$CONDA_PREFIX NVCCFLAGS="-ccbin $CC -I$CONDA_PREFIX/include $EXTRA_NVCCFLAGS" CC=$CC CXX=$CXX CPPFLAGS="-I$CONDA_PREFIX/include" + +make install-libraries + + +test -d $CUDA_ROOT/lib64 && LIBPATH="$CUDA_ROOT/lib64" || LIBPATH="$CUDA_ROOT/lib" + +case `uname` in + Darwin*) + cp -P $LIBPATH/libcudart.*.dylib $CONDA_PREFIX/lib + cp -P $LIBPATH/libcufft.*.dylib $CONDA_PREFIX/lib + ;; + *) + cp -P $LIBPATH/libcudart.so.* $CONDA_PREFIX/lib + cp -P $LIBPATH/libcufft.so.* $CONDA_PREFIX/lib + ;; +esac diff --git a/python/conda/libastra/meta.yaml b/python/conda/libastra/meta.yaml index 73fa0d7..68cf47a 100644 --- a/python/conda/libastra/meta.yaml +++ b/python/conda/libastra/meta.yaml @@ -1,16 +1,28 @@ package: name: libastra - version: '1.8b' + version: '1.8' source: git_url: https://github.com/astra-toolbox/astra-toolbox.git - #git_tag: v1.7.1 # Change to 1.8 after release + git_tag: v1.8 build: number: 0 script_env: - - CUDA_ROOT - - MAKEOPTS + - CC # [not win] + - CXX # [not win] + - CUDA_ROOT # [not win] + +requirements: + build: + - vs2015_runtime # [win] + - boost # [osx] + - automake # [osx] + - autoconf # [osx] + - libtool # [osx] + + run: + - vs2015_runtime # [win] about: home: http://www.astra-toolbox.com diff --git a/python/conda/linux_release/README.txt b/python/conda/linux_release/README.txt new file mode 100644 index 0000000..12cfcbb --- /dev/null +++ b/python/conda/linux_release/README.txt @@ -0,0 +1,2 @@ +This directory contains a Docker container based environment for building linux release packages for conda. + diff --git a/python/conda/linux_release/buildenv/Dockerfile b/python/conda/linux_release/buildenv/Dockerfile new file mode 100644 index 0000000..c73e4b9 --- /dev/null +++ b/python/conda/linux_release/buildenv/Dockerfile @@ -0,0 +1,15 @@ +FROM debian:7 +ENV PATH /root/miniconda3/bin:$PATH +ENV DEBIAN_FRONTEND noninteractive +# http://developer.download.nvidia.com/compute/cuda/5_5/rel/installers/cuda_5.5.22_linux_64.run +ADD cuda_5.5.22_linux_64.run /root/ +# https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh +ADD Miniconda3-4.2.12-Linux-x86_64.sh /root/ +RUN apt-get update +RUN apt-get install -y perl-modules build-essential autoconf libtool automake libboost-dev git +RUN /bin/bash /root/Miniconda3-4.2.12-Linux-x86_64.sh -b +RUN /bin/bash /root/cuda_5.5.22_linux_64.run -toolkit -silent +RUN conda install -y conda-build +ENV CUDA_ROOT /usr/local/cuda +ENV CC gcc +ENV CXX g++ diff --git a/python/conda/linux_release/builder/Dockerfile b/python/conda/linux_release/builder/Dockerfile new file mode 100644 index 0000000..2404609 --- /dev/null +++ b/python/conda/linux_release/builder/Dockerfile @@ -0,0 +1,17 @@ +FROM astra-build-env +ARG BUILD_NUMBER= +WORKDIR /root +RUN git clone --depth 1 https://github.com/astra-toolbox/astra-toolbox +RUN [ -z $BUILD_NUMBER ] || perl -pi -e "s/^(\s*number:\s*)[0-9]+$/\${1}$BUILD_NUMBER/" astra-toolbox/python/conda/libastra/meta.yaml astra-toolbox/python/conda/astra-toolbox/meta.yaml +RUN conda-build --python=3.5 astra-toolbox/python/conda/libastra +RUN conda-build --python 2.7 --numpy 1.8 astra-toolbox/python/conda/astra-toolbox +RUN conda-build --python 2.7 --numpy 1.9 astra-toolbox/python/conda/astra-toolbox +RUN conda-build --python 2.7 --numpy 1.10 astra-toolbox/python/conda/astra-toolbox +RUN conda-build --python 2.7 --numpy 1.11 astra-toolbox/python/conda/astra-toolbox +RUN conda-build --python 2.7 --numpy 1.12 astra-toolbox/python/conda/astra-toolbox +RUN conda-build --python 3.5 --numpy 1.9 astra-toolbox/python/conda/astra-toolbox +RUN conda-build --python 3.5 --numpy 1.10 astra-toolbox/python/conda/astra-toolbox +RUN conda-build --python 3.5 --numpy 1.11 astra-toolbox/python/conda/astra-toolbox +RUN conda-build --python 3.5 --numpy 1.12 astra-toolbox/python/conda/astra-toolbox +RUN conda-build --python 3.6 --numpy 1.11 astra-toolbox/python/conda/astra-toolbox +RUN conda-build --python 3.6 --numpy 1.12 astra-toolbox/python/conda/astra-toolbox diff --git a/python/conda/linux_release/release.sh b/python/conda/linux_release/release.sh new file mode 100644 index 0000000..cf62bd5 --- /dev/null +++ b/python/conda/linux_release/release.sh @@ -0,0 +1,20 @@ +#!/bin/bash + +D=`mktemp -d` + +[ -f buildenv/cuda_5.5.22_linux_64.run ] || (cd buildenv; wget http://developer.download.nvidia.com/compute/cuda/5_5/rel/installers/cuda_5.5.22_linux_64.run ) +[ -f buildenv/Miniconda3-4.2.12-Linux-x86_64.sh ] || (cd buildenv; wget https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh ) + +docker build -t astra-build-env buildenv +#docker build --no-cache --build-arg=BUILD_NUMBER=0 -t astra-builder builder +docker build --no-cache -t astra-builder builder + +docker run --name astra-build-cnt -v $D:/out:z astra-builder /bin/bash -c "cp /root/miniconda3/conda-bld/linux-64/*astra* /out" + +mkdir -p pkgs +mv $D/* pkgs +rmdir $D + +docker rm astra-build-cnt +docker rmi astra-builder + |