Merge pull request #16 from dmpelt/python-interface

Add Python interface

1 files changed, 215 insertions, 0 deletions

diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd
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+#-----------------------------------------------------------------------
+#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
+#
+#Author: Daniel M. Pelt
+#Contact: D.M.Pelt@cwi.nl
+#Website: http://dmpelt.github.io/pyastratoolbox/
+#
+#
+#This file is part of the Python interface to the
+#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
+#
+#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
+#it under the terms of the GNU General Public License as published by
+#the Free Software Foundation, either version 3 of the License, or
+#(at your option) any later version.
+#
+#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+#GNU General Public License for more details.
+#
+#You should have received a copy of the GNU General Public License
+#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+#-----------------------------------------------------------------------
+from libcpp cimport bool
+from libcpp.string cimport string
+from .PyXMLDocument cimport XMLNode
+
+cdef extern from "astra/Globals.h" namespace "astra":
+	ctypedef float float32
+	ctypedef double float64
+	ctypedef unsigned short int uint16
+	ctypedef signed short int sint16
+	ctypedef unsigned char uchar8
+	ctypedef signed char schar8
+	ctypedef int int32
+	ctypedef short int int16
+
+cdef extern from "astra/Config.h" namespace "astra":
+	cdef cppclass Config:
+		Config()
+		XMLNode *self
+
+cdef extern from "astra/VolumeGeometry2D.h" namespace "astra":
+	cdef cppclass CVolumeGeometry2D:
+		bool initialize(Config)
+		int getGridColCount()
+		int getGridRowCount()
+		int getGridTotCount()
+		float32 getWindowLengthX()
+		float32 getWindowLengthY()
+		float32 getWindowArea()
+		float32 getPixelLengthX()
+		float32 getPixelLengthY()
+		float32 getPixelArea()
+		float32 getWindowMinX()
+		float32 getWindowMinY()
+		float32 getWindowMaxX()
+		float32 getWindowMaxY()
+
+
+cdef extern from "astra/Float32VolumeData2D.h" namespace "astra":
+	cdef cppclass CFloat32VolumeData2D:
+		CFloat32VolumeData2D(CVolumeGeometry2D*)
+		CVolumeGeometry2D * getGeometry()
+		int getWidth()
+		int getHeight()
+		void changeGeometry(CVolumeGeometry2D*)
+
+
+
+cdef extern from "astra/ProjectionGeometry2D.h" namespace "astra":
+	cdef cppclass CProjectionGeometry2D:
+		CProjectionGeometry2D()
+		bool initialize(Config)
+		int getDetectorCount()
+		int getProjectionAngleCount()
+		bool isOfType(string)
+		float32 getProjectionAngle(int)
+		float32 getDetectorWidth()
+
+cdef extern from "astra/Float32Data2D.h" namespace "astra::CFloat32Data2D":
+	cdef enum EDataType:
+		BASE,PROJECTION,VOLUME
+
+cdef extern from "astra/Float32Data2D.h" namespace "astra":
+	cdef cppclass CFloat32Data2D:
+		bool isInitialized()
+		int getSize()
+		float32 *getData()
+		float32 **getData2D()
+		int getWidth()
+		int getHeight()
+		EDataType getType()
+
+
+
+
+cdef extern from "astra/SparseMatrixProjectionGeometry2D.h" namespace "astra":
+	cdef cppclass CSparseMatrixProjectionGeometry2D:
+		CSparseMatrixProjectionGeometry2D()
+
+cdef extern from "astra/FanFlatProjectionGeometry2D.h" namespace "astra":
+	cdef cppclass CFanFlatProjectionGeometry2D:
+		CFanFlatProjectionGeometry2D()
+		
+cdef extern from "astra/FanFlatVecProjectionGeometry2D.h" namespace "astra":
+	cdef cppclass CFanFlatVecProjectionGeometry2D:
+		CFanFlatVecProjectionGeometry2D()
+
+cdef extern from "astra/ParallelProjectionGeometry2D.h" namespace "astra":
+	cdef cppclass CParallelProjectionGeometry2D:
+		CParallelProjectionGeometry2D()
+
+
+cdef extern from "astra/Float32ProjectionData2D.h" namespace "astra":
+	cdef cppclass CFloat32ProjectionData2D:
+		CFloat32ProjectionData2D(CProjectionGeometry2D*)
+		CProjectionGeometry2D * getGeometry()
+		void changeGeometry(CProjectionGeometry2D*)
+		int getDetectorCount()
+		int getAngleCount()
+
+cdef extern from "astra/Algorithm.h" namespace "astra":
+	cdef cppclass CAlgorithm:
+		bool initialize(Config)
+		void run(int)
+		bool isInitialized()
+
+cdef extern from "astra/ReconstructionAlgorithm2D.h" namespace "astra":
+	cdef cppclass CReconstructionAlgorithm2D:
+		bool getResidualNorm(float32&)
+
+cdef extern from "astra/Projector2D.h" namespace "astra":
+	cdef cppclass CProjector2D:
+		bool isInitialized()
+		CProjectionGeometry2D* getProjectionGeometry()
+		CVolumeGeometry2D* getVolumeGeometry()
+		CSparseMatrix* getMatrix()
+
+cdef extern from "astra/SparseMatrix.h" namespace "astra":
+	cdef cppclass CSparseMatrix:
+		CSparseMatrix(unsigned int,unsigned int,unsigned long)
+		unsigned int m_iWidth
+		unsigned int m_iHeight
+		unsigned long m_lSize
+		bool isInitialized()
+		float32* m_pfValues
+		unsigned int* m_piColIndices
+		unsigned long* m_plRowStarts
+		
+cdef extern from "astra/Float32Data3DMemory.h" namespace "astra":		
+	cdef cppclass CFloat32Data3DMemory:
+		CFloat32Data3DMemory()
+		bool isInitialized()
+		int getSize()
+		int getWidth()
+		int getHeight()
+		int getDepth()
+		void updateStatistics()
+		float32 *getData()
+		float32 ***getData3D()
+
+
+cdef extern from "astra/VolumeGeometry3D.h" namespace "astra":
+	cdef cppclass CVolumeGeometry3D:
+		CVolumeGeometry3D()
+		bool initialize(Config)
+
+cdef extern from "astra/ProjectionGeometry3D.h" namespace "astra":
+	cdef cppclass CProjectionGeometry3D:
+		CProjectionGeometry3D()
+		bool initialize(Config)
+		
+		
+cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra":
+	cdef cppclass CFloat32VolumeData3DMemory:
+		CFloat32VolumeData3DMemory(CVolumeGeometry3D*)
+
+
+cdef extern from "astra/ParallelProjectionGeometry3D.h" namespace "astra":
+	cdef cppclass CParallelProjectionGeometry3D:
+		CParallelProjectionGeometry3D()
+
+cdef extern from "astra/ParallelVecProjectionGeometry3D.h" namespace "astra":
+	cdef cppclass CParallelVecProjectionGeometry3D:
+		CParallelVecProjectionGeometry3D()
+
+cdef extern from "astra/ConeProjectionGeometry3D.h" namespace "astra":
+	cdef cppclass CConeProjectionGeometry3D:
+		CConeProjectionGeometry3D()
+		bool initialize(Config)
+		
+cdef extern from "astra/ConeVecProjectionGeometry3D.h" namespace "astra":
+	cdef cppclass CConeVecProjectionGeometry3D:
+		CConeVecProjectionGeometry3D()
+
+cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra":
+	cdef cppclass CFloat32ProjectionData3DMemory:
+		CFloat32ProjectionData3DMemory(CProjectionGeometry3D*)
+		CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*)		
+
+cdef extern from "astra/Float32Data3D.h" namespace "astra":		
+	cdef cppclass CFloat32Data3D:
+		CFloat32Data3D()
+		bool isInitialized()
+		int getSize()
+		int getWidth()
+		int getHeight()
+		int getDepth()
+		void updateStatistics()
+
+
+