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authorWillem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>2017-09-15 16:38:08 +0200
committerWillem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>2017-09-15 16:38:08 +0200
commitaa31a06235496c0d808e57c8ce914cb4b640bc6e (patch)
tree33385e828ddca0b2857bac9e3dac4dd3723a3eee /python/astra
parentf6aa2db83dfea89f9d2cfc6fcbd3da141ee77e02 (diff)
parent00a1c6118b2d64b867c8e640c295462bcccfc7c9 (diff)
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Merge branch 'master' into parallel_vec
Diffstat (limited to 'python/astra')
-rw-r--r--python/astra/PyAlgorithmFactory.pxd36
-rw-r--r--python/astra/PyAlgorithmManager.pxd36
-rw-r--r--python/astra/PyData2DManager.pxd36
-rw-r--r--python/astra/PyData3DManager.pxd36
-rw-r--r--python/astra/PyIncludes.pxd398
-rw-r--r--python/astra/PyIndexManager.pxd2
-rw-r--r--python/astra/PyMatrixManager.pxd36
-rw-r--r--python/astra/PyProjector2DFactory.pxd36
-rw-r--r--python/astra/PyProjector2DManager.pxd36
-rw-r--r--python/astra/PyProjector3DFactory.pxd36
-rw-r--r--python/astra/PyProjector3DManager.pxd36
-rw-r--r--python/astra/PyXMLDocument.pxd35
-rw-r--r--python/astra/__init__.py39
-rw-r--r--python/astra/algorithm.py35
-rw-r--r--python/astra/algorithm_c.pyx4
-rw-r--r--python/astra/astra.py46
-rw-r--r--python/astra/astra_c.pyx11
-rw-r--r--python/astra/creators.py45
-rw-r--r--python/astra/data2d.py36
-rw-r--r--python/astra/data2d_c.pyx59
-rw-r--r--python/astra/data3d.py51
-rw-r--r--python/astra/data3d_c.pyx129
-rw-r--r--python/astra/experimental.pyx26
-rw-r--r--python/astra/extrautils.pyx34
-rw-r--r--python/astra/functions.py24
-rw-r--r--python/astra/log.py37
-rw-r--r--python/astra/log_c.pyx2
-rw-r--r--python/astra/matlab.py36
-rw-r--r--python/astra/matrix.py36
-rw-r--r--python/astra/matrix_c.pyx2
-rw-r--r--python/astra/optomo.py35
-rw-r--r--python/astra/plugin.py37
-rw-r--r--python/astra/plugin_c.pyx2
-rw-r--r--python/astra/plugins/__init__.py29
-rw-r--r--python/astra/plugins/cgls.py99
-rw-r--r--python/astra/plugins/sirt.py90
-rw-r--r--python/astra/projector.py36
-rw-r--r--python/astra/projector3d.py36
-rw-r--r--python/astra/projector3d_c.pyx2
-rw-r--r--python/astra/projector_c.pyx2
-rw-r--r--python/astra/pythonutils.py42
-rw-r--r--python/astra/src/PythonPluginAlgorithm.cpp2
-rw-r--r--python/astra/src/PythonPluginAlgorithm.h2
-rw-r--r--python/astra/utils.pxd36
-rw-r--r--python/astra/utils.pyx2
45 files changed, 1070 insertions, 793 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.
#