diff options
Diffstat (limited to 'include')
39 files changed, 736 insertions, 302 deletions
diff --git a/include/astra/Algorithm.h b/include/astra/Algorithm.h index 049417c..18c465f 100644 --- a/include/astra/Algorithm.h +++ b/include/astra/Algorithm.h @@ -81,7 +81,7 @@ public: * * @return initialized */ - bool isInitialized(); + bool isInitialized() const; /** get a description of the class * @@ -133,7 +133,7 @@ private: // inline functions inline std::string CAlgorithm::description() const { return "Algorithm"; }; -inline bool CAlgorithm::isInitialized() { return m_bIsInitialized; } +inline bool CAlgorithm::isInitialized() const { return m_bIsInitialized; } } // end namespace diff --git a/include/astra/ArtAlgorithm.h b/include/astra/ArtAlgorithm.h index d232b95..1ad9f3f 100644 --- a/include/astra/ArtAlgorithm.h +++ b/include/astra/ArtAlgorithm.h @@ -59,7 +59,7 @@ namespace astra { * \astra_xml_item_option{MinConstraintValue, float, 0, Minimum constraint value.} * \astra_xml_item_option{UseMaxConstraint, bool, false, Use maximum value constraint.} * \astra_xml_item_option{MaxConstraintValue, float, 255, Maximum constraint value.} - * \astra_xml_item_option{Lamda, float, 1, The relaxation factor.} + * \astra_xml_item_option{Relaxation, float, 1, The relaxation factor.} * \astra_xml_item_option{RayOrder, string, "sequential", the order in which the rays are updated. 'sequential' or 'custom'} * \astra_xml_item_option{RayOrderList, n by 2 vector of float, not used, if RayOrder='custom': use this ray order. Each row consist of a projection id and detector id.} * @@ -73,7 +73,7 @@ namespace astra { * cfg.option.UseMinConstraint = 'yes';\n * cfg.option.UseMaxConstraint = 'yes';\n * cfg.option.MaxConstraintValue = 1024;\n - * cfg.option.Lamda = 0.7;\n + * cfg.option.Relaxation = 0.7;\n * cfg.option.RayOrder = 'custom';\n * cfg.option.RayOrderList = [0\,0; 0\,2; 1\,0];\n * alg_id = astra_mex_algorithm('create'\, cfg);\n diff --git a/include/astra/AstraObjectFactory.h b/include/astra/AstraObjectFactory.h index 1ed4955..6af9cd8 100644 --- a/include/astra/AstraObjectFactory.h +++ b/include/astra/AstraObjectFactory.h @@ -40,6 +40,10 @@ $Id$ #include "AlgorithmTypelist.h" +#ifdef ASTRA_PYTHON +#include "PluginAlgorithm.h" +#endif + namespace astra { @@ -59,20 +63,27 @@ public: */ ~CAstraObjectFactory(); - /** Create, but don't initialize, a new projector object. + /** Create, but don't initialize, a new object. * - * @param _sType Type of the new projector. - * @return Pointer to a new, unitialized projector. + * @param _sType Type of the new object. + * @return Pointer to a new, uninitialized object. */ T* create(std::string _sType); - /** Create and initialize a new projector object. + /** Create and initialize a new object. * - * @param _cfg Configuration object to create and initialize a new projector. + * @param _cfg Configuration object to create and initialize a new object. * @return Pointer to a new, initialized projector. */ T* create(const Config& _cfg); + /** Find a plugin. + * + * @param _sType Name of plugin to find. + * @return Pointer to a new, uninitialized object, or NULL if not found. + */ + T* findPlugin(std::string _sType); + }; @@ -93,6 +104,15 @@ CAstraObjectFactory<T, TypeList>::~CAstraObjectFactory() } + +//---------------------------------------------------------------------------------------- +// Hook for finding plugin in registered plugins. +template <typename T, typename TypeList> +T* CAstraObjectFactory<T, TypeList>::findPlugin(std::string _sType) +{ + return NULL; +} + //---------------------------------------------------------------------------------------- // Create template <typename T, typename TypeList> @@ -101,6 +121,9 @@ T* CAstraObjectFactory<T, TypeList>::create(std::string _sType) functor_find<T> finder = functor_find<T>(); finder.tofind = _sType; CreateObject<TypeList>::find(finder); + if (finder.res == NULL) { + finder.res = findPlugin(_sType); + } return finder.res; } @@ -109,14 +132,11 @@ T* CAstraObjectFactory<T, TypeList>::create(std::string _sType) template <typename T, typename TypeList> T* CAstraObjectFactory<T, TypeList>::create(const Config& _cfg) { - functor_find<T> finder = functor_find<T>(); - finder.tofind = _cfg.self.getAttribute("type"); - CreateObject<TypeList>::find(finder); - if (finder.res == NULL) return NULL; - if (finder.res->initialize(_cfg)) - return finder.res; - - delete finder.res; + T* object = create(_cfg.self.getAttribute("type")); + if (object == NULL) return NULL; + if (object->initialize(_cfg)) + return object; + delete object; return NULL; } //---------------------------------------------------------------------------------------- @@ -131,6 +151,18 @@ T* CAstraObjectFactory<T, TypeList>::create(const Config& _cfg) */ class _AstraExport CAlgorithmFactory : public CAstraObjectFactory<CAlgorithm, AlgorithmTypeList> {}; +#ifdef ASTRA_PYTHON +template <> +inline CAlgorithm* CAstraObjectFactory<CAlgorithm, AlgorithmTypeList>::findPlugin(std::string _sType) + { + CPluginAlgorithmFactory *fac = CPluginAlgorithmFactory::getFactory(); + if (fac) + return fac->getPlugin(_sType); + else + return 0; + } +#endif + /** * Class used to create 2D projectors from a string or a config object */ diff --git a/include/astra/AstraObjectManager.h b/include/astra/AstraObjectManager.h index 895f955..9faecbe 100644 --- a/include/astra/AstraObjectManager.h +++ b/include/astra/AstraObjectManager.h @@ -52,17 +52,49 @@ namespace astra { * among all ObjectManagers. */ +class CAstraObjectManagerBase { +public: + virtual std::string getInfo(int index) const =0; + virtual void remove(int index) =0; + virtual std::string getType() const =0; +}; -class CAstraIndexManager { -protected: - /** The index of the previously stored data object. + +class _AstraExport CAstraIndexManager : public Singleton<CAstraIndexManager> { +public: + CAstraIndexManager() : m_iLastIndex(0) { } + + int store(CAstraObjectManagerBase* m) { + m_table[++m_iLastIndex] = m; + return m_iLastIndex; + } + + CAstraObjectManagerBase* get(int index) const { + std::map<int, CAstraObjectManagerBase*>::const_iterator i; + i = m_table.find(index); + if (i != m_table.end()) + return i->second; + else + return 0; + } + + void remove(int index) { + std::map<int, CAstraObjectManagerBase*>::iterator i; + i = m_table.find(index); + if (i != m_table.end()) + m_table.erase(i); + } + +private: + /** The index last handed out */ - static int m_iPreviousIndex; + int m_iLastIndex; + std::map<int, CAstraObjectManagerBase*> m_table; }; template <typename T> -class CAstraObjectManager : public Singleton<CAstraObjectManager<T> >, CAstraIndexManager { +class CAstraObjectManager : public CAstraObjectManagerBase { public: @@ -117,7 +149,11 @@ public: */ void clear(); - /** Get info. + /** Get info of object. + */ + std::string getInfo(int index) const; + + /** Get list with info of all managed objects. */ std::string info(); @@ -149,9 +185,9 @@ CAstraObjectManager<T>::~CAstraObjectManager() template <typename T> int CAstraObjectManager<T>::store(T* _pDataObject) { - m_iPreviousIndex++; - m_mIndexToObject[m_iPreviousIndex] = _pDataObject; - return m_iPreviousIndex; + int iIndex = CAstraIndexManager::getSingleton().store(this); + m_mIndexToObject[iIndex] = _pDataObject; + return iIndex; } //---------------------------------------------------------------------------------------- @@ -180,15 +216,16 @@ T* CAstraObjectManager<T>::get(int _iIndex) const template <typename T> void CAstraObjectManager<T>::remove(int _iIndex) { - if (!hasIndex(_iIndex)) { - return; - } // find data typename map<int,T*>::iterator it = m_mIndexToObject.find(_iIndex); + if (it == m_mIndexToObject.end()) + return; // delete data delete (*it).second; // delete from map - m_mIndexToObject.erase(it); + m_mIndexToObject.erase(it); + + CAstraIndexManager::getSingleton().remove(_iIndex); } //---------------------------------------------------------------------------------------- @@ -220,19 +257,29 @@ void CAstraObjectManager<T>::clear() //---------------------------------------------------------------------------------------- // Print info to string template <typename T> +std::string CAstraObjectManager<T>::getInfo(int index) const { + typename map<int,T*>::const_iterator it = m_mIndexToObject.find(index); + if (it == m_mIndexToObject.end()) + return ""; + const T* pObject = it->second; + std::stringstream res; + res << index << " \t"; + if (pObject->isInitialized()) { + res << "v "; + } else { + res << "x "; + } + res << pObject->description(); + return res.str(); +} + +template <typename T> std::string CAstraObjectManager<T>::info() { std::stringstream res; res << "id init description" << std::endl; res << "-----------------------------------------" << std::endl; - for (typename map<int,T*>::iterator it = m_mIndexToObject.begin(); it != m_mIndexToObject.end(); it++) { - res << (*it).first << " \t"; - T* pObject = m_mIndexToObject[(*it).first]; - if (pObject->isInitialized()) { - res << "v "; - } else { - res << "x "; - } - res << pObject->description() << endl; + for (typename map<int,T*>::const_iterator it = m_mIndexToObject.begin(); it != m_mIndexToObject.end(); it++) { + res << getInfo(it->first) << endl; } res << "-----------------------------------------" << std::endl; return res.str(); @@ -247,42 +294,60 @@ std::string CAstraObjectManager<T>::info() { * assigned to each data object by which it can be accessed in the future. * Indices are always >= 1. */ -class _AstraExport CProjector2DManager : public CAstraObjectManager<CProjector2D>{}; +class _AstraExport CProjector2DManager : public Singleton<CProjector2DManager>, public CAstraObjectManager<CProjector2D> +{ + virtual std::string getType() const { return "projector2d"; } +}; /** * This class contains functionality to store 3D projector objects. A unique index handle will be * assigned to each data object by which it can be accessed in the future. * Indices are always >= 1. */ -class _AstraExport CProjector3DManager : public CAstraObjectManager<CProjector3D>{}; +class _AstraExport CProjector3DManager : public Singleton<CProjector3DManager>, public CAstraObjectManager<CProjector3D> +{ + virtual std::string getType() const { return "projector3d"; } +}; /** * This class contains functionality to store 2D data objects. A unique index handle will be * assigned to each data object by which it can be accessed in the future. * Indices are always >= 1. */ -class _AstraExport CData2DManager : public CAstraObjectManager<CFloat32Data2D>{}; +class _AstraExport CData2DManager : public Singleton<CData2DManager>, public CAstraObjectManager<CFloat32Data2D> +{ + virtual std::string getType() const { return "data2d"; } +}; /** * This class contains functionality to store 3D data objects. A unique index handle will be * assigned to each data object by which it can be accessed in the future. * Indices are always >= 1. */ -class _AstraExport CData3DManager : public CAstraObjectManager<CFloat32Data3D>{}; +class _AstraExport CData3DManager : public Singleton<CData3DManager>, public CAstraObjectManager<CFloat32Data3D> +{ + virtual std::string getType() const { return "data3d"; } +}; /** * This class contains functionality to store algorithm objects. A unique index handle will be * assigned to each data object by which it can be accessed in the future. * Indices are always >= 1. */ -class _AstraExport CAlgorithmManager : public CAstraObjectManager<CAlgorithm>{}; +class _AstraExport CAlgorithmManager : public Singleton<CAlgorithmManager>, public CAstraObjectManager<CAlgorithm> +{ + virtual std::string getType() const { return "algorithm"; } +}; /** * This class contains functionality to store matrix objects. A unique index handle will be * assigned to each data object by which it can be accessed in the future. * Indices are always >= 1. */ -class _AstraExport CMatrixManager : public CAstraObjectManager<CSparseMatrix>{}; +class _AstraExport CMatrixManager : public Singleton<CMatrixManager>, public CAstraObjectManager<CSparseMatrix> +{ + virtual std::string getType() const { return "matrix"; } +}; } // end namespace diff --git a/include/astra/CompositeGeometryManager.h b/include/astra/CompositeGeometryManager.h new file mode 100644 index 0000000..18dd72f --- /dev/null +++ b/include/astra/CompositeGeometryManager.h @@ -0,0 +1,181 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +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/>. + +----------------------------------------------------------------------- +*/ + +#ifndef _INC_ASTRA_COMPOSITEGEOMETRYMANAGER +#define _INC_ASTRA_COMPOSITEGEOMETRYMANAGER + +#include "Globals.h" + +#ifdef ASTRA_CUDA + +#include <list> +#include <map> +#include <vector> +#include <boost/shared_ptr.hpp> + + +namespace astra { + +class CCompositeVolume; +class CCompositeProjections; +class CFloat32Data3DMemory; +class CFloat32ProjectionData3DMemory; +class CFloat32VolumeData3DMemory; +class CVolumeGeometry3D; +class CProjectionGeometry3D; +class CProjector3D; + + +struct SGPUParams { + std::vector<int> GPUIndices; + size_t memory; +}; + + +class _AstraExport CCompositeGeometryManager { +public: + CCompositeGeometryManager(); + + class CPart; + typedef std::list<boost::shared_ptr<CPart> > TPartList; + class CPart { + public: + CPart() { } + CPart(const CPart& other); + virtual ~CPart() { } + + enum { + PART_VOL, PART_PROJ + } eType; + + CFloat32Data3DMemory* pData; + unsigned int subX; + unsigned int subY; + unsigned int subZ; + + bool uploadToGPU(); + bool downloadFromGPU(/*mode?*/); + virtual void splitX(TPartList& out, size_t maxSize, size_t maxDim, int div) = 0; + virtual void splitY(TPartList& out, size_t maxSize, size_t maxDim, int div) = 0; + virtual void splitZ(TPartList& out, size_t maxSize, size_t maxDim, int div) = 0; + virtual CPart* reduce(const CPart *other) = 0; + virtual void getDims(size_t &x, size_t &y, size_t &z) = 0; + size_t getSize(); + }; + + class CVolumePart : public CPart { + public: + CVolumePart() { eType = PART_VOL; } + CVolumePart(const CVolumePart& other); + virtual ~CVolumePart(); + + CVolumeGeometry3D* pGeom; + + virtual void splitX(TPartList& out, size_t maxSize, size_t maxDim, int div); + virtual void splitY(TPartList& out, size_t maxSize, size_t maxDim, int div); + virtual void splitZ(TPartList& out, size_t maxSize, size_t maxDim, int div); + virtual CPart* reduce(const CPart *other); + virtual void getDims(size_t &x, size_t &y, size_t &z); + + CVolumePart* clone() const; + }; + class CProjectionPart : public CPart { + public: + CProjectionPart() { eType = PART_PROJ; } + CProjectionPart(const CProjectionPart& other); + virtual ~CProjectionPart(); + + CProjectionGeometry3D* pGeom; + + virtual void splitX(TPartList& out, size_t maxSize, size_t maxDim, int div); + virtual void splitY(TPartList& out, size_t maxSize, size_t maxDim, int div); + virtual void splitZ(TPartList& out, size_t maxSize, size_t maxDim, int div); + virtual CPart* reduce(const CPart *other); + virtual void getDims(size_t &x, size_t &y, size_t &z); + + CProjectionPart* clone() const; + }; + + struct SJob { + public: + boost::shared_ptr<CPart> pInput; + boost::shared_ptr<CPart> pOutput; + CProjector3D *pProjector; // For a `global' geometry. It will not match + // the geometries of the input and output. + + + enum { + JOB_FP, JOB_BP, JOB_NOP + } eType; + enum { + MODE_ADD, MODE_SET + } eMode; + + }; + + typedef std::list<SJob> TJobList; + // output part -> list of jobs for that output + typedef std::map<CPart*, TJobList > TJobSet; + + bool doJobs(TJobList &jobs); + + SJob createJobFP(CProjector3D *pProjector, + CFloat32VolumeData3DMemory *pVolData, + CFloat32ProjectionData3DMemory *pProjData); + SJob createJobBP(CProjector3D *pProjector, + CFloat32VolumeData3DMemory *pVolData, + CFloat32ProjectionData3DMemory *pProjData); + + // Convenience functions for creating and running a single FP or BP job + bool doFP(CProjector3D *pProjector, CFloat32VolumeData3DMemory *pVolData, + CFloat32ProjectionData3DMemory *pProjData); + bool doBP(CProjector3D *pProjector, CFloat32VolumeData3DMemory *pVolData, + CFloat32ProjectionData3DMemory *pProjData); + + bool doFP(CProjector3D *pProjector, const std::vector<CFloat32VolumeData3DMemory *>& volData, const std::vector<CFloat32ProjectionData3DMemory *>& projData); + bool doBP(CProjector3D *pProjector, const std::vector<CFloat32VolumeData3DMemory *>& volData, const std::vector<CFloat32ProjectionData3DMemory *>& projData); + + void setGPUIndices(const std::vector<int>& GPUIndices); + + static void setGlobalGPUParams(const SGPUParams& params); + +protected: + + bool splitJobs(TJobSet &jobs, size_t maxSize, int div, TJobSet &split); + + std::vector<int> m_GPUIndices; + size_t m_iMaxSize; + + + static SGPUParams* s_params; +}; + +} + +#endif + +#endif diff --git a/include/astra/ConeProjectionGeometry3D.h b/include/astra/ConeProjectionGeometry3D.h index 00e72ce..dede6e1 100644 --- a/include/astra/ConeProjectionGeometry3D.h +++ b/include/astra/ConeProjectionGeometry3D.h @@ -186,9 +186,15 @@ public: */ virtual CVector3D getProjectionDirection(int _iProjectionIndex, int _iDetectorIndex) const; - virtual void projectPoint(float32 fX, float32 fY, float32 fZ, + virtual void projectPoint(double fX, double fY, double fZ, int iAngleIndex, - float32 &fU, float32 &fV) const; + double &fU, double &fV) const; + virtual void backprojectPointX(int iAngleIndex, double fU, double fV, + double fX, double &fY, double &fZ) const; + virtual void backprojectPointY(int iAngleIndex, double fU, double fV, + double fY, double &fX, double &fZ) const; + virtual void backprojectPointZ(int iAngleIndex, double fU, double fV, + double fZ, double &fX, double &fY) const; }; diff --git a/include/astra/ConeVecProjectionGeometry3D.h b/include/astra/ConeVecProjectionGeometry3D.h index 71e8010..f76f9dd 100644 --- a/include/astra/ConeVecProjectionGeometry3D.h +++ b/include/astra/ConeVecProjectionGeometry3D.h @@ -148,9 +148,16 @@ public: const SConeProjection* getProjectionVectors() const { return m_pProjectionAngles; } - virtual void projectPoint(float32 fX, float32 fY, float32 fZ, + virtual void projectPoint(double fX, double fY, double fZ, int iAngleIndex, - float32 &fU, float32 &fV) const; + double &fU, double &fV) const; + virtual void backprojectPointX(int iAngleIndex, double fU, double fV, + double fX, double &fY, double &fZ) const; + virtual void backprojectPointY(int iAngleIndex, double fU, double fV, + double fY, double &fX, double &fZ) const; + virtual void backprojectPointZ(int iAngleIndex, double fU, double fV, + double fZ, double &fX, double &fY) const; + }; } // namespace astra diff --git a/include/astra/CudaBackProjectionAlgorithm.h b/include/astra/CudaBackProjectionAlgorithm.h index 84899b0..2450376 100644 --- a/include/astra/CudaBackProjectionAlgorithm.h +++ b/include/astra/CudaBackProjectionAlgorithm.h @@ -85,13 +85,10 @@ public: * @param _pProjector Projector Object. (Ignored) * @param _pSinogram ProjectionData2D object containing the sinogram data. * @param _pReconstruction VolumeData2D object for storing the reconstructed volume. - * @param _iGPUindex GPU to use. - * @param _iPixelSuperSampling Square root of number of samples per voxel, used to compute the backprojection */ bool initialize(CProjector2D* _pProjector, CFloat32ProjectionData2D* _pSinogram, - CFloat32VolumeData2D* _pReconstruction, - int _iGPUindex = -1, int _iPixelSuperSampling = 1); + CFloat32VolumeData2D* _pReconstruction); /** Get a description of the class. * diff --git a/include/astra/CudaBackProjectionAlgorithm3D.h b/include/astra/CudaBackProjectionAlgorithm3D.h index 2d98218..74aeec8 100644 --- a/include/astra/CudaBackProjectionAlgorithm3D.h +++ b/include/astra/CudaBackProjectionAlgorithm3D.h @@ -147,6 +147,8 @@ protected: */ bool m_bSIRTWeighting; + + void initializeFromProjector(); }; // inline functions diff --git a/include/astra/CudaCglsAlgorithm.h b/include/astra/CudaCglsAlgorithm.h index c51093c..6aa0343 100644 --- a/include/astra/CudaCglsAlgorithm.h +++ b/include/astra/CudaCglsAlgorithm.h @@ -91,18 +91,13 @@ public: /** Initialize class, use sequential order. * - * @param _pProjector Projector Object. (Ignored) + * @param _pProjector Projector Object. (Optional) * @param _pSinogram ProjectionData2D object containing the sinogram * @param _pReconstruction VolumeData2D for storing the reconstruction - * @param _iGPUindex Index of GPU to use. (Starting at 0.) - * @param _iDetectorSuperSampling Supersampling factor for the FP. - * @param _iPixelSuperSampling Square root of number of samples per voxel, used to compute the backprojection */ bool initialize(CProjector2D* _pProjector, CFloat32ProjectionData2D* _pSinogram, - CFloat32VolumeData2D* _pReconstruction, - int _iGPUindex = -1, int _iDetectorSuperSampling = 1, - int _iPixelSuperSampling = 1); + CFloat32VolumeData2D* _pReconstruction); /** Get a description of the class. * diff --git a/include/astra/CudaCglsAlgorithm3D.h b/include/astra/CudaCglsAlgorithm3D.h index 77c41c1..3e4084b 100644 --- a/include/astra/CudaCglsAlgorithm3D.h +++ b/include/astra/CudaCglsAlgorithm3D.h @@ -161,6 +161,8 @@ protected: bool m_bAstraCGLSInit; int m_iDetectorSuperSampling; int m_iVoxelSuperSampling; + + void initializeFromProjector(); }; // inline functions diff --git a/include/astra/CudaEMAlgorithm.h b/include/astra/CudaEMAlgorithm.h index 97eb7ca..a9d2711 100644 --- a/include/astra/CudaEMAlgorithm.h +++ b/include/astra/CudaEMAlgorithm.h @@ -63,17 +63,13 @@ public: /** Initialize class. * - * @param _pProjector Projector Object. (Ignored) + * @param _pProjector Projector Object. (Optional) * @param _pSinogram ProjectionData2D object containing the sinogram data. * @param _pReconstruction VolumeData2D object for storing the reconstructed volume. - * @param _iGPUindex GPU to use. - * @param _iDetectorSuperSampling Supersampling factor for the FP. */ bool initialize(CProjector2D* _pProjector, - CFloat32ProjectionData2D* _pSinogram, - CFloat32VolumeData2D* _pReconstruction, - int _iGPUindex = -1, int _iDetectorSuperSampling = 1, - int _iPixelSuperSampling = 1); + CFloat32ProjectionData2D* _pSinogram, + CFloat32VolumeData2D* _pReconstruction); /** Get a description of the class. * diff --git a/include/astra/CudaFDKAlgorithm3D.h b/include/astra/CudaFDKAlgorithm3D.h index 1b025f1..63f07fd 100644 --- a/include/astra/CudaFDKAlgorithm3D.h +++ b/include/astra/CudaFDKAlgorithm3D.h @@ -152,6 +152,8 @@ protected: int m_iGPUIndex; int m_iVoxelSuperSampling; bool m_bShortScan; + + void initializeFromProjector(); }; // inline functions diff --git a/include/astra/CudaFilteredBackProjectionAlgorithm.h b/include/astra/CudaFilteredBackProjectionAlgorithm.h index 33445b6..cf1f19f 100644 --- a/include/astra/CudaFilteredBackProjectionAlgorithm.h +++ b/include/astra/CudaFilteredBackProjectionAlgorithm.h @@ -85,6 +85,9 @@ protected: AstraFBP* m_pFBP; bool m_bAstraFBPInit; + + void initializeFromProjector(); + virtual bool requiresProjector() const { return false; } }; // inline functions diff --git a/include/astra/CudaForwardProjectionAlgorithm.h b/include/astra/CudaForwardProjectionAlgorithm.h index d172a7a..449a610 100644 --- a/include/astra/CudaForwardProjectionAlgorithm.h +++ b/include/astra/CudaForwardProjectionAlgorithm.h @@ -33,16 +33,15 @@ $Id$ #include "Algorithm.h" -#include "ParallelProjectionGeometry2D.h" -#include "VolumeGeometry2D.h" - -#include "Float32ProjectionData2D.h" -#include "Float32VolumeData2D.h" - #ifdef ASTRA_CUDA namespace astra { +class CProjector2D; +class CProjectionGeometry2D; +class CFloat32ProjectionData2D; +class CFloat32VolumeData2D; + /** * \brief * This class contains a GPU implementation of an algorithm that creates a forward projection @@ -91,19 +90,15 @@ public: /** Initialize class. * - * @param _pVolumeGeometry Geometry of the volume. - * @param _pProjectionGeometry Geometry of the projection. + * @param _pProjector Projector2D object. (Optional) * @param _pVolume VolumeData2D object containing the phantom to compute sinogram from * @param _pSinogram ProjectionData2D object to store sinogram data in. - * @param _iGPUindex Index of GPU to use. (Starting at 0.) - * @param _iDetectorSuperSampling Number of samples per detector element, used to compute the forward projection * @return success */ - bool initialize(CProjectionGeometry2D* _pProjectionGeometry, - CVolumeGeometry2D* _pVolumeGeometry, - CFloat32VolumeData2D* _pVolume, - CFloat32ProjectionData2D* _pSinogram, - int _iGPUindex = -1, int _iDetectorSuperSampling = 1); + bool initialize(CProjector2D* _pProjector, + CFloat32VolumeData2D* _pVolume, + CFloat32ProjectionData2D* _pSinogram); + /** Get all information parameters * @@ -147,6 +142,9 @@ public: void setGPUIndex(int _iGPUIndex); protected: + //< Optional Projector2D object + CProjector2D* m_pProjector; + //< ProjectionData2D object containing the sinogram. CFloat32ProjectionData2D* m_pSinogram; //< VolumeData2D object containing the phantom. @@ -157,6 +155,7 @@ protected: //< Number of rays per detector element int m_iDetectorSuperSampling; + void initializeFromProjector(); }; // inline functions diff --git a/include/astra/CudaForwardProjectionAlgorithm3D.h b/include/astra/CudaForwardProjectionAlgorithm3D.h index bdd1356..4198d56 100644 --- a/include/astra/CudaForwardProjectionAlgorithm3D.h +++ b/include/astra/CudaForwardProjectionAlgorithm3D.h @@ -122,6 +122,7 @@ protected: int m_iGPUIndex; int m_iDetectorSuperSampling; + void initializeFromProjector(); }; // inline functions diff --git a/include/astra/CudaProjector2D.h b/include/astra/CudaProjector2D.h index a571851..2b4bacb 100644 --- a/include/astra/CudaProjector2D.h +++ b/include/astra/CudaProjector2D.h @@ -121,9 +121,17 @@ public: virtual std::string description() const; + Cuda2DProjectionKernel getProjectionKernel() const { return m_projectionKernel; } + int getVoxelSuperSampling() const { return m_iVoxelSuperSampling; } + int getDetectorSuperSampling() const { return m_iDetectorSuperSampling; } + int getGPUIndex() const { return m_iGPUIndex; } + protected: Cuda2DProjectionKernel m_projectionKernel; + int m_iVoxelSuperSampling; + int m_iDetectorSuperSampling; + int m_iGPUIndex; }; //---------------------------------------------------------------------------------------- diff --git a/include/astra/CudaProjector3D.h b/include/astra/CudaProjector3D.h index a181531..da88d6d 100644 --- a/include/astra/CudaProjector3D.h +++ b/include/astra/CudaProjector3D.h @@ -115,11 +115,16 @@ public: Cuda3DProjectionKernel getProjectionKernel() const { return m_projectionKernel; } + int getVoxelSuperSampling() const { return m_iVoxelSuperSampling; } + int getDetectorSuperSampling() const { return m_iDetectorSuperSampling; } + int getGPUIndex() const { return m_iGPUIndex; } protected: Cuda3DProjectionKernel m_projectionKernel; - + int m_iVoxelSuperSampling; + int m_iDetectorSuperSampling; + int m_iGPUIndex; }; diff --git a/include/astra/CudaReconstructionAlgorithm2D.h b/include/astra/CudaReconstructionAlgorithm2D.h index e19bb8f..bb5f2a7 100644 --- a/include/astra/CudaReconstructionAlgorithm2D.h +++ b/include/astra/CudaReconstructionAlgorithm2D.h @@ -70,28 +70,13 @@ public: /** Initialize class. * - * @param _pProjector Projector Object. (Ignored) + * @param _pProjector Projector Object. (Optional) * @param _pSinogram ProjectionData2D object containing the sinogram data. * @param _pReconstruction VolumeData2D object for storing the reconstructed volume. */ - bool initialize(CProjector2D* _pProjector, - CFloat32ProjectionData2D* _pSinogram, - CFloat32VolumeData2D* _pReconstruction); - - /** Initialize class. - * - * @param _pProjector Projector Object. (Ignored) - * @param _pSinogram ProjectionData2D object containing the sinogram data. - * @param _pReconstruction VolumeData2D object for storing the reconstructed volume. - * @param _iGPUindex GPU to use. - * @param _iDetectorSuperSampling Supersampling factor for the FP. - * @param _iPixelSuperSampling Square root of number of samples per voxel, used to compute the backprojection - */ virtual bool initialize(CProjector2D* _pProjector, CFloat32ProjectionData2D* _pSinogram, - CFloat32VolumeData2D* _pReconstruction, - int _iGPUindex = -1, int _iDetectorSuperSampling = 1, - int _iPixelSuperSampling = 1); + CFloat32VolumeData2D* _pReconstruction); /** Clear this class. @@ -156,6 +141,9 @@ protected: */ bool setupGeometry(); + /** Initialize CUDA algorithm. For internal use only. + */ + virtual void initCUDAAlgorithm(); /** The internally used CUDA algorithm object */ @@ -166,6 +154,9 @@ protected: int m_iGPUIndex; bool m_bAlgoInit; + + void initializeFromProjector(); + virtual bool requiresProjector() const { return false; } }; // inline functions diff --git a/include/astra/CudaSartAlgorithm.h b/include/astra/CudaSartAlgorithm.h index b370bd0..e5e18f0 100644 --- a/include/astra/CudaSartAlgorithm.h +++ b/include/astra/CudaSartAlgorithm.h @@ -46,6 +46,7 @@ namespace astra { * \astra_xml_item{ProjectionDataId, integer, Identifier of a projection data object as it is stored in the DataManager.} * \astra_xml_item{ReconstructionDataId, integer, Identifier of a volume data object as it is stored in the DataManager.} * \astra_xml_item_option{ReconstructionMaskId, integer, not used, Identifier of a volume data object that acts as a reconstruction mask. 0 = reconstruct on this pixel. 1 = don't reconstruct on this pixel.} + * \astra_xml_item_option{Relaxation, float, 1, The relaxation factor.} * * \par MATLAB example * \astra_code{ @@ -53,6 +54,7 @@ namespace astra { * cfg.ProjectionDataId = sino_id;\n * cfg.ReconstructionDataId = recon_id;\n * cfg.option.ReconstructionMaskId = mask_id;\n + * cfg.option.Relaxation = 1.0;\n * alg_id = astra_mex_algorithm('create'\, cfg);\n * astra_mex_algorithm('iterate'\, alg_id\, 10);\n * astra_mex_algorithm('delete'\, alg_id);\n @@ -84,22 +86,27 @@ public: /** Initialize class. * - * @param _pProjector Projector Object. (Ignored) + * @param _pProjector Projector Object. (Optional) * @param _pSinogram ProjectionData2D object containing the sinogram data. * @param _pReconstruction VolumeData2D object for storing the reconstructed volume. - * @param _iGPUindex GPU to use. - * @param _iDetectorSuperSampling Supersampling factor for the FP. */ bool initialize(CProjector2D* _pProjector, - CFloat32ProjectionData2D* _pSinogram, - CFloat32VolumeData2D* _pReconstruction, - int _iGPUindex = -1, int _iDetectorSuperSampling = 1); + CFloat32ProjectionData2D* _pSinogram, + CFloat32VolumeData2D* _pReconstruction); /** Get a description of the class. * * @return description string */ virtual std::string description() const; + +protected: + + /** Relaxation factor + */ + float m_fLambda; + + virtual void initCUDAAlgorithm(); }; // inline functions diff --git a/include/astra/CudaSirtAlgorithm.h b/include/astra/CudaSirtAlgorithm.h index 607889a..3cd8acc 100644 --- a/include/astra/CudaSirtAlgorithm.h +++ b/include/astra/CudaSirtAlgorithm.h @@ -53,6 +53,7 @@ namespace astra { * \astra_xml_item{ProjectionDataId, integer, Identifier of a projection data object as it is stored in the DataManager.} * \astra_xml_item{ReconstructionDataId, integer, Identifier of a volume data object as it is stored in the DataManager.} * \astra_xml_item_option{ReconstructionMaskId, integer, not used, Identifier of a volume data object that acts as a reconstruction mask. 0 = reconstruct on this pixel. 1 = don't reconstruct on this pixel.} + * \astra_xml_item_option{Relaxation, float, 1, Relaxation parameter.} * * \par MATLAB example * \astra_code{ @@ -62,6 +63,7 @@ namespace astra { * cfg.ProjectionDataId = sino_id;\n * cfg.ReconstructionDataId = recon_id;\n * cfg.option.ReconstructionMaskId = mask_id;\n + * cfg.option.Relaxation = 1.0;\n * alg_id = astra_mex_algorithm('create'\, cfg);\n * astra_mex_algorithm('iterate'\, alg_id\, 10);\n * astra_mex_algorithm('delete'\, alg_id);\n @@ -93,22 +95,15 @@ public: */ virtual bool initialize(const Config& _cfg); - virtual void run(int _iNrIterations); - /** Initialize class. * - * @param _pProjector Projector Object. (Ignored) + * @param _pProjector Projector Object. (Optional) * @param _pSinogram ProjectionData2D object containing the sinogram data. * @param _pReconstruction VolumeData2D object for storing the reconstructed volume. - * @param _iGPUindex GPU to use. - * @param _iDetectorSuperSampling Supersampling factor for the FP. - * @param _iPixelSuperSampling Square root of number of samples per voxel, used to compute the backprojection */ bool initialize(CProjector2D* _pProjector, - CFloat32ProjectionData2D* _pSinogram, - CFloat32VolumeData2D* _pReconstruction, - int _iGPUindex = -1, int _iDetectorSuperSampling = 1, - int _iPixelSuperSampling = 1); + CFloat32ProjectionData2D* _pSinogram, + CFloat32VolumeData2D* _pReconstruction); /** Get a description of the class. * @@ -119,6 +114,12 @@ public: protected: CFloat32VolumeData2D* m_pMinMask; CFloat32VolumeData2D* m_pMaxMask; + + /** Relaxation factor + */ + float m_fLambda; + + virtual void initCUDAAlgorithm(); }; // inline functions diff --git a/include/astra/CudaSirtAlgorithm3D.h b/include/astra/CudaSirtAlgorithm3D.h index fda4635..60191cd 100644 --- a/include/astra/CudaSirtAlgorithm3D.h +++ b/include/astra/CudaSirtAlgorithm3D.h @@ -50,7 +50,7 @@ class AstraSIRT3d; * * The update step of pixel \f$v_j\f$ for iteration \f$k\f$ is given by: * \f[ - * v_j^{(k+1)} = v_j^{(k)} + \alpha \sum_{i=1}^{M} \left( \frac{w_{ij}\left( p_i - \sum_{r=1}^{N} w_{ir}v_r^{(k)}\right)}{\sum_{k=1}^{N} w_{ik}} \right) \frac{1}{\sum_{l=1}^{M}w_{lj}} + * v_j^{(k+1)} = v_j^{(k)} + \lambda \sum_{i=1}^{M} \left( \frac{w_{ij}\left( p_i - \sum_{r=1}^{N} w_{ir}v_r^{(k)}\right)}{\sum_{k=1}^{N} w_{ik}} \right) \frac{1}{\sum_{l=1}^{M}w_{lj}} * \f] * * \par XML Configuration @@ -175,6 +175,9 @@ protected: bool m_bAstraSIRTInit; int m_iDetectorSuperSampling; int m_iVoxelSuperSampling; + float m_fLambda; + + void initializeFromProjector(); }; // inline functions diff --git a/include/astra/DataProjectorPolicies.h b/include/astra/DataProjectorPolicies.h index c258f5c..acfb36f 100644 --- a/include/astra/DataProjectorPolicies.h +++ b/include/astra/DataProjectorPolicies.h @@ -319,10 +319,12 @@ class SIRTBPPolicy { CFloat32ProjectionData2D* m_pTotalRayLength; CFloat32VolumeData2D* m_pTotalPixelWeight; + float m_fRelaxation; + public: FORCEINLINE SIRTBPPolicy(); - FORCEINLINE SIRTBPPolicy(CFloat32VolumeData2D* _pReconstruction, CFloat32ProjectionData2D* _pSinogram, CFloat32VolumeData2D* _pTotalPixelWeight, CFloat32ProjectionData2D* _pTotalRayLength); + FORCEINLINE SIRTBPPolicy(CFloat32VolumeData2D* _pReconstruction, CFloat32ProjectionData2D* _pSinogram, CFloat32VolumeData2D* _pTotalPixelWeight, CFloat32ProjectionData2D* _pTotalRayLength, float _fRelaxation); FORCEINLINE ~SIRTBPPolicy(); FORCEINLINE bool rayPrior(int _iRayIndex); diff --git a/include/astra/DataProjectorPolicies.inl b/include/astra/DataProjectorPolicies.inl index 0c0eddd..f300761 100644 --- a/include/astra/DataProjectorPolicies.inl +++ b/include/astra/DataProjectorPolicies.inl @@ -712,12 +712,14 @@ SIRTBPPolicy::SIRTBPPolicy() SIRTBPPolicy::SIRTBPPolicy(CFloat32VolumeData2D* _pReconstruction, CFloat32ProjectionData2D* _pSinogram, CFloat32VolumeData2D* _pTotalPixelWeight, - CFloat32ProjectionData2D* _pTotalRayLength) + CFloat32ProjectionData2D* _pTotalRayLength, + float _fRelaxation) { m_pReconstruction = _pReconstruction; m_pSinogram = _pSinogram; m_pTotalPixelWeight = _pTotalPixelWeight; m_pTotalRayLength = _pTotalRayLength; + m_fRelaxation = _fRelaxation; } //---------------------------------------------------------------------------------------- SIRTBPPolicy::~SIRTBPPolicy() @@ -739,7 +741,7 @@ void SIRTBPPolicy::addWeight(int _iRayIndex, int _iVolumeIndex, float32 _fWeight { float32 fGammaBeta = m_pTotalPixelWeight->getData()[_iVolumeIndex] * m_pTotalRayLength->getData()[_iRayIndex]; if ((fGammaBeta > 0.001f) || (fGammaBeta < -0.001f)) { - m_pReconstruction->getData()[_iVolumeIndex] += _fWeight * m_pSinogram->getData()[_iRayIndex] / fGammaBeta; + m_pReconstruction->getData()[_iVolumeIndex] += _fWeight * m_fRelaxation * m_pSinogram->getData()[_iRayIndex] / fGammaBeta; } } //---------------------------------------------------------------------------------------- diff --git a/include/astra/Fourier.h b/include/astra/Fourier.h index b515dc6..68f9f38 100644 --- a/include/astra/Fourier.h +++ b/include/astra/Fourier.h @@ -33,94 +33,50 @@ $Id$ namespace astra { - -/** - * Perform a 1D DFT or inverse DFT. - * - * @param iLength number of elements - * @param pfRealIn real part of input - * @param pfImaginaryIn imaginary part of input - * @param pfRealOut real part of output - * @param pfImaginaryOut imaginary part of output - * @param iStrideIn distance between elements in pf*In - * @param iStrideOut distance between elements in pf*Out - * @param bInverse if true, perform an inverse DFT - */ - -void _AstraExport discreteFourierTransform1D(unsigned int iLength, - const float32* pfRealIn, - const float32* pfImaginaryIn, - float32* pfRealOut, - float32* pfImaginaryOut, - unsigned int iStrideIn, - unsigned int iStrideOut, - bool bInverse); - -/** - * Perform a 2D DFT or inverse DFT. - * - * @param iHeight number of rows - * @param iWidth number of columns - * @param pfRealIn real part of input - * @param pfImaginaryIn imaginary part of input - * @param pfRealOut real part of output - * @param pfImaginaryOut imaginary part of output - * @param bInverse if true, perform an inverse DFT - */ - -void _AstraExport discreteFourierTransform2D(unsigned int iHeight, unsigned int iWidth, - const float32* pfRealIn, - const float32* pfImaginaryIn, - float32* pfRealOut, - float32* pfImaginaryOut, - bool bInverse); - -/** - * Perform a 1D FFT or inverse FFT. The size must be a power of two. - * This transform can be done in-place, so the input and output pointers - * may point to the same data. - * - * @param iLength number of elements, must be a power of two - * @param pfRealIn real part of input - * @param pfImaginaryIn imaginary part of input - * @param pfRealOut real part of output - * @param pfImaginaryOut imaginary part of output - * @param iStrideIn distance between elements in pf*In - * @param iStrideOut distance between elements in pf*Out - * @param bInverse if true, perform an inverse DFT - */ - -void _AstraExport fastTwoPowerFourierTransform1D(unsigned int iLength, - const float32* pfRealIn, - const float32* pfImaginaryIn, - float32* pfRealOut, - float32* pfImaginaryOut, - unsigned int iStrideIn, - unsigned int iStrideOut, - bool bInverse); - -/** - * Perform a 2D FFT or inverse FFT. The size must be a power of two. - * This transform can be done in-place, so the input and output pointers - * may point to the same data. - * - * @param iHeight number of rows, must be a power of two - * @param iWidth number of columns, must be a power of two - * @param pfRealIn real part of input - * @param pfImaginaryIn imaginary part of input - * @param pfRealOut real part of output - * @param pfImaginaryOut imaginary part of output - * @param bInverse if true, perform an inverse DFT - */ - -void _AstraExport fastTwoPowerFourierTransform2D(unsigned int iHeight, - unsigned int iWidth, - const float32* pfRealIn, - const float32* pfImaginaryIn, - float32* pfRealOut, - float32* pfImaginaryOut, - bool bInverse); - +/* +-------- Complex DFT (Discrete Fourier Transform) -------- + [definition] + <case1> + X[k] = sum_j=0^n-1 x[j]*exp(2*pi*i*j*k/n), 0<=k<n + <case2> + X[k] = sum_j=0^n-1 x[j]*exp(-2*pi*i*j*k/n), 0<=k<n + (notes: sum_j=0^n-1 is a summation from j=0 to n-1) + [usage] + <case1> + ip[0] = 0; // first time only + cdft(2*n, 1, a, ip, w); + <case2> + ip[0] = 0; // first time only + cdft(2*n, -1, a, ip, w); + [parameters] + 2*n :data length (int) + n >= 1, n = power of 2 + a[0...2*n-1] :input/output data (float32 *) + input data + a[2*j] = Re(x[j]), + a[2*j+1] = Im(x[j]), 0<=j<n + output data + a[2*k] = Re(X[k]), + a[2*k+1] = Im(X[k]), 0<=k<n + ip[0...*] :work area for bit reversal (int *) + length of ip >= 2+sqrt(n) + strictly, + length of ip >= + 2+(1<<(int)(log(n+0.5)/log(2))/2). + ip[0],ip[1] are pointers of the cos/sin table. + w[0...n/2-1] :cos/sin table (float32 *) + w[],ip[] are initialized if ip[0] == 0. + [remark] + Inverse of + cdft(2*n, -1, a, ip, w); + is + cdft(2*n, 1, a, ip, w); + for (j = 0; j <= 2 * n - 1; j++) { + a[j] *= 1.0 / n; + } + . +*/ +_AstraExport void cdft(int n, int isgn, float32 *a, int *ip, float32 *w); } diff --git a/include/astra/GeometryUtil3D.h b/include/astra/GeometryUtil3D.h index 698372e..e4d73e4 100644 --- a/include/astra/GeometryUtil3D.h +++ b/include/astra/GeometryUtil3D.h @@ -43,6 +43,33 @@ struct SConeProjection { // the V-edge of a detector pixel double fDetVX, fDetVY, fDetVZ; + + + + + void translate(double dx, double dy, double dz) { + fSrcX += dx; + fSrcY += dy; + fSrcZ += dz; + fDetSX += dx; + fDetSY += dy; + fDetSZ += dz; + + } + void scale(double factor) { + fSrcX *= factor; + fSrcY *= factor; + fSrcZ *= factor; + fDetSX *= factor; + fDetSY *= factor; + fDetSZ *= factor; + fDetUX *= factor; + fDetUY *= factor; + fDetUZ *= factor; + fDetVX *= factor; + fDetVY *= factor; + fDetVZ *= factor; + } }; struct SPar3DProjection { @@ -57,6 +84,29 @@ struct SPar3DProjection { // the V-edge of a detector pixel double fDetVX, fDetVY, fDetVZ; + + + + + void translate(double dx, double dy, double dz) { + fDetSX += dx; + fDetSY += dy; + fDetSZ += dz; + } + void scale(double factor) { + fRayX *= factor; + fRayY *= factor; + fRayZ *= factor; + fDetSX *= factor; + fDetSY *= factor; + fDetSZ *= factor; + fDetUX *= factor; + fDetUY *= factor; + fDetUZ *= factor; + fDetVX *= factor; + fDetVY *= factor; + fDetVZ *= factor; + } }; void computeBP_UV_Coeffs(const SPar3DProjection& proj, @@ -68,6 +118,26 @@ void computeBP_UV_Coeffs(const SConeProjection& proj, double &fVX, double &fVY, double &fVZ, double &fVC, double &fDX, double &fDY, double &fDZ, double &fDC); + +SConeProjection* genConeProjections(unsigned int iProjAngles, + unsigned int iProjU, + unsigned int iProjV, + double fOriginSourceDistance, + double fOriginDetectorDistance, + double fDetUSize, + double fDetVSize, + const float *pfAngles); + +SPar3DProjection* genPar3DProjections(unsigned int iProjAngles, + unsigned int iProjU, + unsigned int iProjV, + double fDetUSize, + double fDetVSize, + const float *pfAngles); + + + + } #endif diff --git a/include/astra/Globals.h b/include/astra/Globals.h index 9c8ddfb..5dbac83 100644 --- a/include/astra/Globals.h +++ b/include/astra/Globals.h @@ -61,9 +61,9 @@ $Id$ // macro's #define ASTRA_TOOLBOXVERSION_MAJOR 1 -#define ASTRA_TOOLBOXVERSION_MINOR 5 +#define ASTRA_TOOLBOXVERSION_MINOR 7 #define ASTRA_TOOLBOXVERSION ((ASTRA_TOOLBOXVERSION_MAJOR)*100 + (ASTRA_TOOLBOXVERSION_MINOR)) -#define ASTRA_TOOLBOXVERSION_STRING "1.5" +#define ASTRA_TOOLBOXVERSION_STRING "1.7.1" #define ASTRA_ASSERT(a) assert(a) @@ -146,6 +146,8 @@ namespace astra { const float32 PIdiv2 = PI / 2; const float32 PIdiv4 = PI / 4; const float32 eps = 1e-7f; + + extern _AstraExport bool running_in_matlab; } //---------------------------------------------------------------------------------------- diff --git a/include/astra/ParallelProjectionGeometry3D.h b/include/astra/ParallelProjectionGeometry3D.h index 72401e5..d95c050 100644 --- a/include/astra/ParallelProjectionGeometry3D.h +++ b/include/astra/ParallelProjectionGeometry3D.h @@ -147,9 +147,16 @@ public: */ virtual CVector3D getProjectionDirection(int _iProjectionIndex, int _iDetectorIndex) const; - virtual void projectPoint(float32 fX, float32 fY, float32 fZ, + virtual void projectPoint(double fX, double fY, double fZ, int iAngleIndex, - float32 &fU, float32 &fV) const; + double &fU, double &fV) const; + virtual void backprojectPointX(int iAngleIndex, double fU, double fV, + double fX, double &fY, double &fZ) const; + virtual void backprojectPointY(int iAngleIndex, double fU, double fV, + double fY, double &fX, double &fZ) const; + virtual void backprojectPointZ(int iAngleIndex, double fU, double fV, + double fZ, double &fX, double &fY) const; + /** * Creates (= allocates) a 2D projection geometry used when projecting one slice using a 2D projector diff --git a/include/astra/ParallelVecProjectionGeometry3D.h b/include/astra/ParallelVecProjectionGeometry3D.h index 59238c8..ec91086 100644 --- a/include/astra/ParallelVecProjectionGeometry3D.h +++ b/include/astra/ParallelVecProjectionGeometry3D.h @@ -149,9 +149,15 @@ public: const SPar3DProjection* getProjectionVectors() const { return m_pProjectionAngles; } - virtual void projectPoint(float32 fX, float32 fY, float32 fZ, + virtual void projectPoint(double fX, double fY, double fZ, int iAngleIndex, - float32 &fU, float32 &fV) const; + double &fU, double &fV) const; + virtual void backprojectPointX(int iAngleIndex, double fU, double fV, + double fX, double &fY, double &fZ) const; + virtual void backprojectPointY(int iAngleIndex, double fU, double fV, + double fY, double &fX, double &fZ) const; + virtual void backprojectPointZ(int iAngleIndex, double fU, double fV, + double fZ, double &fX, double &fY) const; }; } // namespace astra diff --git a/include/astra/PluginAlgorithm.h b/include/astra/PluginAlgorithm.h new file mode 100644 index 0000000..cbd80fc --- /dev/null +++ b/include/astra/PluginAlgorithm.h @@ -0,0 +1,65 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +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/>. + +----------------------------------------------------------------------- +$Id$ +*/ + +#ifndef _INC_ASTRA_PLUGINALGORITHM +#define _INC_ASTRA_PLUGINALGORITHM + +#include "astra/Globals.h" + +#include <map> +#include <string> + +namespace astra { + +class CAlgorithm; + +class _AstraExport CPluginAlgorithmFactory { + +public: + CPluginAlgorithmFactory() { } + virtual ~CPluginAlgorithmFactory() { } + + virtual CAlgorithm * getPlugin(const std::string &name) = 0; + + virtual bool registerPlugin(std::string name, std::string className) = 0; + virtual bool registerPlugin(std::string className) = 0; + + virtual std::map<std::string, std::string> getRegisteredMap() = 0; + + virtual std::string getHelp(const std::string &name) = 0; + + static void registerFactory(CPluginAlgorithmFactory *factory) { m_factory = factory; } + static CPluginAlgorithmFactory* getFactory() { return m_factory; } + +private: + static CPluginAlgorithmFactory *m_factory; +}; + +} + +#endif diff --git a/include/astra/ProjectionGeometry3D.h b/include/astra/ProjectionGeometry3D.h index 19ac3ab..0b60287 100644 --- a/include/astra/ProjectionGeometry3D.h +++ b/include/astra/ProjectionGeometry3D.h @@ -317,9 +317,24 @@ public: * @param iAngleIndex the index of the angle to use * @param fU,fV the projected point. */ - virtual void projectPoint(float32 fX, float32 fY, float32 fZ, + virtual void projectPoint(double fX, double fY, double fZ, int iAngleIndex, - float32 &fU, float32 &fV) const = 0; + double &fU, double &fV) const = 0; + + /* Backproject a point onto a plane parallel to a coordinate plane. + * The 2D point coordinates are the (unrounded) indices of the detector + * column and row. The output is in 3D coordinates in units. + * are in units. The output fU,fV are the (unrounded) indices of the + * detector column and row. + * This may fall outside of the actual detector. + */ + virtual void backprojectPointX(int iAngleIndex, double fU, double fV, + double fX, double &fY, double &fZ) const = 0; + virtual void backprojectPointY(int iAngleIndex, double fU, double fV, + double fY, double &fX, double &fZ) const = 0; + virtual void backprojectPointZ(int iAngleIndex, double fU, double fV, + double fZ, double &fX, double &fY) const = 0; + /** Returns true if the type of geometry defined in this class is the one specified in _sType. * diff --git a/include/astra/Projector2D.h b/include/astra/Projector2D.h index a1ea0ce..c7a899d 100644 --- a/include/astra/Projector2D.h +++ b/include/astra/Projector2D.h @@ -174,7 +174,7 @@ public: * * @return initialized successfully */ - bool isInitialized(); + bool isInitialized() const; /** get a description of the class * @@ -191,7 +191,7 @@ private: }; // inline functions -inline bool CProjector2D::isInitialized() { return m_bIsInitialized; } +inline bool CProjector2D::isInitialized() const { return m_bIsInitialized; } inline CProjectionGeometry2D* CProjector2D::getProjectionGeometry() { return m_pProjectionGeometry; } inline CVolumeGeometry2D* CProjector2D::getVolumeGeometry() { return m_pVolumeGeometry; } diff --git a/include/astra/Projector3D.h b/include/astra/Projector3D.h index 1ef1ba7..88ca2be 100644 --- a/include/astra/Projector3D.h +++ b/include/astra/Projector3D.h @@ -153,7 +153,7 @@ public: * * @return initialized successfully */ - bool isInitialized(); + bool isInitialized() const; /** get a description of the class * @@ -174,7 +174,7 @@ private: }; // inline functions -inline bool CProjector3D::isInitialized() { return m_bIsInitialized; } +inline bool CProjector3D::isInitialized() const { return m_bIsInitialized; } inline CProjectionGeometry3D* CProjector3D::getProjectionGeometry() { return m_pProjectionGeometry; } inline CVolumeGeometry3D* CProjector3D::getVolumeGeometry() { return m_pVolumeGeometry; } diff --git a/include/astra/ReconstructionAlgorithm2D.h b/include/astra/ReconstructionAlgorithm2D.h index 60584e0..ac87c4f 100644 --- a/include/astra/ReconstructionAlgorithm2D.h +++ b/include/astra/ReconstructionAlgorithm2D.h @@ -208,6 +208,9 @@ protected: //< Use the fixed reconstruction mask? bool m_bUseSinogramMask; + + //< Specify if initialize/check should check for a valid Projector + virtual bool requiresProjector() const { return true; } }; // inline functions diff --git a/include/astra/SartAlgorithm.h b/include/astra/SartAlgorithm.h index eb4c61e..cdae029 100644 --- a/include/astra/SartAlgorithm.h +++ b/include/astra/SartAlgorithm.h @@ -49,7 +49,7 @@ namespace astra { * * The update step of pixel \f$v_j\f$ for projection \f$phi\f$ and iteration \f$k\f$ is given by: * \f[ - * v_j^{(k+1)} = v_j^{(k)} + \frac{\sum_{p_i \in P_\phi} \left( \lambda \frac{p_i - \sum_{r=1}^{N} w_{ir}v_r^{(k)}} {\sum_{r=1}^{N}w_{ir} } \right)} {\sum_{p_i \in P_\phi}w_{ij}} + * v_j^{(k+1)} = v_j^{(k)} + \lambda \frac{\sum_{p_i \in P_\phi} \left( \frac{p_i - \sum_{r=1}^{N} w_{ir}v_r^{(k)}} {\sum_{r=1}^{N}w_{ir} } \right)} {\sum_{p_i \in P_\phi}w_{ij}} * \f] * * \par XML Configuration @@ -64,6 +64,7 @@ namespace astra { * \astra_xml_item_option{MaxConstraintValue, float, 255, Maximum constraint value.} * \astra_xml_item_option{ProjectionOrder, string, "sequential", the order in which the projections are updated. 'sequential', 'random' or 'custom'} * \astra_xml_item_option{ProjectionOrderList, vector of float, not used, if ProjectionOrder='custom': use this order.} + * \astra_xml_item_option{Relaxation, float, 1, The relaxation parameter.} * * \par MATLAB example * \astra_code{ @@ -76,7 +77,8 @@ namespace astra { * cfg.option.UseMaxConstraint = 'yes';\n * cfg.option.MaxConstraintValue = 1024;\n * cfg.option.ProjectionOrder = 'custom';\n -* cfg.option.ProjectionOrderList = randperm(100);\n + * cfg.option.ProjectionOrderList = randperm(100);\n + * cfg.option.Relaxation = 1.0;\n * alg_id = astra_mex_algorithm('create'\, cfg);\n * astra_mex_algorithm('iterate'\, alg_id\, 10);\n * astra_mex_algorithm('delete'\, alg_id);\n @@ -215,6 +217,8 @@ protected: //< Current index in the projection order array. int m_iCurrentProjection; + //< Relaxation parameter + float m_fLambda; }; // inline functions diff --git a/include/astra/Singleton.h b/include/astra/Singleton.h index a256187..9d3c088 100644 --- a/include/astra/Singleton.h +++ b/include/astra/Singleton.h @@ -45,11 +45,7 @@ class Singleton { public: // constructor - Singleton() { - assert(!m_singleton); - int offset = (uintptr_t)(T*)1 - (uintptr_t)(Singleton<T>*)(T*)1; - m_singleton = (T*)((uintptr_t)this + offset); - }; + Singleton() { } // destructor virtual ~Singleton() { @@ -57,15 +53,17 @@ class Singleton { m_singleton = 0; } + static void construct(); + // get singleton static T& getSingleton() { if (!m_singleton) - m_singleton = new T(); + construct(); return *m_singleton; } static T* getSingletonPtr() { if (!m_singleton) - m_singleton = new T(); + construct(); return m_singleton; } @@ -76,11 +74,23 @@ class Singleton { }; -#define DEFINE_SINGLETON(T) template<> T* Singleton<T >::m_singleton = 0 +// We specifically avoid defining construct() in the header. +// That way, the call to new is always executed by code inside libastra. +// This avoids the situation where a singleton gets created by a copy +// of the constructor linked into an object file outside of libastra, such +// as a .mex file, which would then also cause the vtable to be outside of +// libastra. This situation would cause issues when .mex files are unloaded. + +#define DEFINE_SINGLETON(T) \ +template<> void Singleton<T >::construct() { assert(!m_singleton); m_singleton = new T(); } \ +template<> T* Singleton<T >::m_singleton = 0 + // This is a hack to support statements like // DEFINE_SINGLETON2(CTemplatedClass<C1, C2>); -#define DEFINE_SINGLETON2(A,B) template<> A,B* Singleton<A,B >::m_singleton = 0 +#define DEFINE_SINGLETON2(A,B) \ +template<> void Singleton<A,B >::construct() { assert(!m_singleton); m_singleton = new A,B(); } \ +template<> A,B* Singleton<A,B >::m_singleton = 0 } // end namespace diff --git a/include/astra/SirtAlgorithm.h b/include/astra/SirtAlgorithm.h index 05b3fa9..8044d09 100644 --- a/include/astra/SirtAlgorithm.h +++ b/include/astra/SirtAlgorithm.h @@ -49,7 +49,7 @@ namespace astra { * * The update step of pixel \f$v_j\f$ for iteration \f$k\f$ is given by: * \f[ - * v_j^{(k+1)} = v_j^{(k)} + \alpha \sum_{i=1}^{M} \left( \frac{w_{ij}\left( p_i - \sum_{r=1}^{N} w_{ir}v_r^{(k)}\right)}{\sum_{k=1}^{N} w_{ik}} \right) \frac{1}{\sum_{l=1}^{M}w_{lj}} + * v_j^{(k+1)} = v_j^{(k)} + \lambda \sum_{i=1}^{M} \left( \frac{w_{ij}\left( p_i - \sum_{r=1}^{N} w_{ir}v_r^{(k)}\right)}{\sum_{k=1}^{N} w_{ik}} \right) \frac{1}{\sum_{l=1}^{M}w_{lj}} * \f] * * \par XML Configuration @@ -62,6 +62,7 @@ namespace astra { * \astra_xml_item_option{MinConstraintValue, float, 0, Minimum constraint value.} * \astra_xml_item_option{UseMaxConstraint, bool, false, Use maximum value constraint.} * \astra_xml_item_option{MaxConstraintValue, float, 255, Maximum constraint value.} + * \astra_xml_item_option{Relaxation, float, 1, The relaxation factor.} * * \par XML Example * \astra_code{ @@ -74,6 +75,7 @@ namespace astra { * <Option key="UseMinConstraint" value="yes"/>\n * <Option key="UseMaxConstraint" value="yes"/>\n * <Option key="MaxConstraintValue" value="1024"/>\n + * <Option key="Relaxation" value="1"/>\n * </Algorithm> * } * @@ -88,6 +90,7 @@ namespace astra { * cfg.option.UseMinConstraint = 'yes';\n * cfg.option.UseMaxConstraint = 'yes';\n * cfg.option.MaxConstraintValue = 1024;\n + * cfg.option.Relaxation = 1.0;\n * alg_id = astra_mex_algorithm('create'\, cfg);\n * astra_mex_algorithm('iterate'\, alg_id\, 10);\n * astra_mex_algorithm('delete'\, alg_id);\n @@ -136,6 +139,10 @@ protected: */ int m_iIterationCount; + /** Relaxation parameter + */ + float m_fLambda; + public: // type of the algorithm, needed to register with CAlgorithmFactory diff --git a/include/astra/Utilities.h b/include/astra/Utilities.h index 68471d0..8d7c44d 100644 --- a/include/astra/Utilities.h +++ b/include/astra/Utilities.h @@ -31,89 +31,63 @@ $Id$ #include <string> #include <vector> -#include <algorithm> -#include <sstream> #include <map> #include "Globals.h" namespace astra { -/** - * This class contains some usefull static utility functions for std strings. - */ -class StringUtil { + +namespace StringUtil { + +// Exception thrown by functions below +class bad_cast : public std::exception { public: - /** - * Removes whitespace characters such as spaces and tabs at the extremas. - * Optionally you can specify which extrema to trim (default=both) - * - * @param _sString The string to trim. - * @param _bLeft Trim the left extrema? Default = true. - * @param _bRight Trim the right extrema? Default = true. - */ - static void trim(std::string& _sString, bool _bLeft = true, bool _bRight = true); - - /** - * Returns a vector of strings that contains all the substrings delimited by - * the characters in _sDelims. - * - * @param _sString The string to split. - * @param _sDelims The delimiter string. - * @return Vector of strings. - */ - static std::vector<std::string> split(const std::string& _sString, const std::string& _sDelims); - - /** - * Cast a string to an integer. - * - * @param _sString The string to cast. - * @param _iValue Output integer parameter. - * @return success? - */ - static bool toInt(const std::string& _sString, int& _iValue); - - /** - * Cast a string to a float32. - * - * @param _sString The string to cast. - * @param _fValue Output float32 parameter. - * @return success? - */ - static bool toFloat32(const std::string& _sString, float32& _fValue); - - /** - * Convert a string to lower case. - * - * @param _sString The string to convert. - */ - static void toLowerCase(std::string& _sString); - - /** - * Convert a string to upper case. - * - * @param _sString The string to convert. - */ - static void toUpperCase(std::string& _sString); + bad_cast() { } }; -/** - * This class contains some usefull static utility functions for std strings. - */ -class FileSystemUtil { -public: - /** - * Get the extensions of a filename. Always in lower case. - * - * @param _sFilename file to get extensions from. - * @return Extension (lower case). Empty string if filename is a directory or not a valid file format. - */ - static std::string getExtension(std::string& _sFilename); +//< Parse string as int. +//< Throw exception on failure. +_AstraExport int stringToInt(const std::string& s); + +//< Parse string as float. +//< Throw exception on failure. +_AstraExport float stringToFloat(const std::string& s); + +//< Parse string as double. +//< Throw exception on failure. +_AstraExport double stringToDouble(const std::string& s); + +template<typename T> +_AstraExport T stringTo(const std::string& s); + +//< Parse comma/semicolon-separated string as float vector. +//< Throw exception on failure. +_AstraExport std::vector<float> stringToFloatVector(const std::string& s); + +//< Parse comma/semicolon-separated string as double vector. +//< Throw exception on failure. +_AstraExport std::vector<double> stringToDoubleVector(const std::string& s); + +template<typename T> +_AstraExport std::vector<T> stringToVector(const std::string& s); + + + +//< Generate string from float. +_AstraExport std::string floatToString(float f); + +//< Generate string from double. +_AstraExport std::string doubleToString(double f); + +template<typename T> +_AstraExport std::string toString(T f); + +} -}; template<typename T, typename S> diff --git a/include/astra/XMLNode.h b/include/astra/XMLNode.h index 4d29d5c..7d1edf5 100644 --- a/include/astra/XMLNode.h +++ b/include/astra/XMLNode.h @@ -101,6 +101,12 @@ public: */ string getContent() const; + /** Get the content of the XML node as an integer + * + * @return node content + */ + int getContentInt() const; + /** Get the content of the XML node as a numerical. * * @return node content @@ -152,6 +158,7 @@ public: */ float32 getAttributeNumerical(string _sName, float32 _fDefaultValue = 0) const; double getAttributeNumericalDouble(string _sName, double _fDefaultValue = 0) const; + int getAttributeInt(string _sName, int _fDefaultValue = 0) const; /** Get the value of a boolean attribute. * @@ -186,6 +193,7 @@ public: * @return option value, _fDefaultValue if the option doesn't exist */ float32 getOptionNumerical(string _sKey, float32 _fDefaultValue = 0) const; + int getOptionInt(string _sKey, int _fDefaultValue = 0) const; /** Get the value of an option within this XML Node * |