// Declarations of class basisfield. // // This class cannot be used as it stands. Its purpose is // to serve as a base-class for e.g. splinefield and DCTfield. // // basisfield.h // // Jesper Andersson, FMRIB Image Analysis Group // // Copyright (C) 2007 University of Oxford // /* Part of FSL - FMRIB's Software Library http://www.fmrib.ox.ac.uk/fsl fsl@fmrib.ox.ac.uk Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance Imaging of the Brain), Department of Clinical Neurology, Oxford University, Oxford, UK LICENCE FMRIB Software Library, Release 5.0 (c) 2012, The University of Oxford (the "Software") The Software remains the property of the University of Oxford ("the University"). 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Contact details are: innovation@isis.ox.ac.uk quoting reference DE/9564. */ // #ifndef basisfield_h #define basisfield_h #include #include #include #include "newmat.h" #include "newimage/newimage.h" #include "miscmaths/bfmatrix.h" namespace BASISFIELD { const unsigned int MAX_SIZE = 2048; // Largest field I ever hope to see // enum BasisFieldPrecision {FloatPrec, DoublePrec}; class BasisfieldException: public std::exception { private: std::string m_msg; public: BasisfieldException(const std::string& msg) throw(): m_msg(msg) {} virtual const char * what() const throw() { return string("Basisfield:: msg=" + m_msg).c_str(); } ~BasisfieldException() throw() {} }; typedef enum _FieldIndex {FIELD=0, DFDX=1, DFDY=2, DFDZ=3} FieldIndex; class basisfield { private: unsigned int ndim; // Dimensionality of field (1,2 or 3) std::vector sz; // Size of field in x-, y- and z-direction std::vector vxs; // Voxel-size in x-, y- and z-direction boost::shared_ptr coef; // Basis coefficients std::vector futd; // If true, field accurately reflects coef std::vector > field; // Field, dfdx, dfdy, dfdz protected: // Functions for use in this and derived classes virtual void set_update_flag(bool state, FieldIndex fi=FIELD) {futd[fi] = state;} virtual void set_coef_ptr(boost::shared_ptr& cptr) {coef = cptr;} // Get smart read/write pointer to updated field virtual boost::shared_ptr get(FieldIndex fi=FIELD); // Get smart read/write pointer to (possibly) not updated field virtual boost::shared_ptr get_ptr(FieldIndex fi=FIELD); virtual boost::shared_ptr get_coef() const; double get_coef(unsigned int i, unsigned int j, unsigned int k) const; double get_coef(unsigned int i) const; virtual void assign(const basisfield& inf); virtual double peek_outside_fov(int i, int j, int k, FieldIndex fi) const {return(0.0);} // Should be replaced by proper method in derived classes public: // Constructors and destructor, including assignment basisfield(const std::vector& psz, const std::vector& pvxz); basisfield(const basisfield& inf); basisfield& operator=(const basisfield& inf); virtual ~basisfield(); // General utility functions virtual unsigned int NDim() const {return(ndim);} virtual bool UpToDate(FieldIndex fi=FIELD) const {return(futd[fi]);} virtual unsigned int CoefSz() const {return(CoefSz_x()*CoefSz_y()*CoefSz_z());} virtual unsigned int FieldSz() const {return(FieldSz_x()*FieldSz_y()*FieldSz_z());} virtual unsigned int FieldSz_x() const {return(sz[0]);} virtual unsigned int FieldSz_y() const {return(sz[1]);} virtual unsigned int FieldSz_z() const {return(sz[2]);} virtual double Vxs_x() const {return(vxs[0]);} virtual double Vxs_y() const {return(vxs[1]);} virtual double Vxs_z() const {return(vxs[2]);} virtual NEWMAT::ReturnMatrix mm2vox(unsigned int sz=4) const; virtual NEWMAT::ReturnMatrix vox2mm(unsigned int sz=4) const; // Looking at individual voxels of the field virtual double Peek(unsigned int x, unsigned int y, unsigned int z, FieldIndex fi=FIELD); virtual double Peek(unsigned int vi, FieldIndex fi=FIELD); virtual double UnsafePeek(unsigned int x, unsigned int y, unsigned int z, FieldIndex fi=FIELD) const { return(field[fi]->element(z*FieldSz_x()*FieldSz_y()+y*FieldSz_x()+x)); } virtual double UnsafePeek(unsigned int vi, FieldIndex fi=FIELD) const {return(field[fi]->element(vi));} // Get values at individual voxels of the field, where the voxel // may be outside the actual defined FOV. I.e. x, y or z may be // negative or greater than FieldSz. For DCT the field will just // "continue" and for splines it will slowly taper off to zero // over the range of a few knot-spacings. virtual double PeekWide(int i, int j, int k, FieldIndex fi=FIELD); // Getting values of the field at non-integer voxel locations. // N.B. that the top one of these is pure virtual. virtual double Peek(double x, double y, double z, FieldIndex fi=FIELD) const = 0; virtual double Peek(float x, float y, float z, FieldIndex fi=FIELD) const {return(Peek(static_cast(x),static_cast(y),static_cast(z)));} virtual double operator()(double x, double y, double z) const {return(Peek(x,y,z));} virtual double operator()(float x, float y, float z) const{return(Peek(x,y,z));} // Setting or getting coefficients, or getting whole field virtual void SetCoef(const NEWMAT::ColumnVector& pcoef); virtual void SetToConstant(double fv) = 0; virtual const boost::shared_ptr GetCoef() const {return(get_coef());} virtual double GetCoef(unsigned int i, unsigned int j, unsigned int k) const {return(get_coef(i,j,k));} virtual double GetCoef(unsigned int i) const {return(get_coef(i));} virtual const boost::shared_ptr Get(FieldIndex fi=FIELD) const { return(const_cast(this)->get(fi)); } virtual void Set(const NEWMAT::ColumnVector& pfield); virtual void Set(const NEWIMAGE::volume& pfield); virtual void AsVolume(NEWIMAGE::volume& vol, FieldIndex fi=FIELD); virtual void ScaleField(double sf) { NEWMAT::ColumnVector coef(*GetCoef()); SetCoef(sf*coef); } // Pure virtual functions that must be defined in derived classes virtual unsigned int CoefSz_x() const = 0; virtual unsigned int CoefSz_y() const = 0; virtual unsigned int CoefSz_z() const = 0; virtual bool HasGlobalSupport() const = 0; // Get the range of basis-functions with support at point xyz virtual void RangeOfBasesWithSupportAtXyz(const NEWMAT::ColumnVector& xyz, std::vector& first, std::vector& last) const = 0; // Get the value of basis lmn at point xyz virtual double ValueOfBasisLmnAtXyz(const std::vector& lmn, const NEWMAT::ColumnVector& xyz) const = 0; virtual std::vector SubsampledVoxelSize(unsigned int ss, std::vector vxs = std::vector(), std::vector ms = std::vector()) const = 0; virtual std::vector SubsampledVoxelSize(const std::vector& ss, std::vector vxs = std::vector(), std::vector ms = std::vector()) const = 0; virtual std::vector SubsampledMatrixSize(unsigned int ss, std::vector ms = std::vector()) const = 0; virtual std::vector SubsampledMatrixSize(const std::vector& ss, std::vector ms = std::vector()) const = 0; virtual void Update(FieldIndex fi=FIELD) = 0; virtual NEWMAT::ReturnMatrix Jte(const NEWIMAGE::volume& ima1, const NEWIMAGE::volume& ima2, const NEWIMAGE::volume *mask) const = 0; virtual NEWMAT::ReturnMatrix Jte(const std::vector& deriv, const NEWIMAGE::volume& ima1, const NEWIMAGE::volume& ima2, const NEWIMAGE::volume *mask) const = 0; virtual NEWMAT::ReturnMatrix Jte(const NEWIMAGE::volume& ima, const NEWIMAGE::volume *mask) const = 0; virtual NEWMAT::ReturnMatrix Jte(const std::vector& deriv, const NEWIMAGE::volume& ima, const NEWIMAGE::volume *mask) const = 0; virtual boost::shared_ptr JtJ(const NEWIMAGE::volume& ima, const NEWIMAGE::volume *mask=0, MISCMATHS::BFMatrixPrecisionType prec=BFMatrixDoublePrecision) const = 0; virtual boost::shared_ptr JtJ(const NEWIMAGE::volume& ima1, const NEWIMAGE::volume& ima2, const NEWIMAGE::volume *mask=0, MISCMATHS::BFMatrixPrecisionType prec=BFMatrixDoublePrecision) const = 0; virtual boost::shared_ptr JtJ(const std::vector& deriv, const NEWIMAGE::volume& ima, const NEWIMAGE::volume *mask=0, MISCMATHS::BFMatrixPrecisionType prec=BFMatrixDoublePrecision) const = 0; virtual boost::shared_ptr JtJ(const std::vector& deriv, const NEWIMAGE::volume& ima1, const NEWIMAGE::volume& ima2, const NEWIMAGE::volume *mask=0, MISCMATHS::BFMatrixPrecisionType prec=BFMatrixDoublePrecision) const = 0; virtual boost::shared_ptr JtJ(const std::vector& deriv1, const NEWIMAGE::volume& ima1, const std::vector& deriv2, const NEWIMAGE::volume& ima2, const NEWIMAGE::volume *mask=0, MISCMATHS::BFMatrixPrecisionType prec=BFMatrixDoublePrecision) const = 0; virtual boost::shared_ptr JtJ(const NEWIMAGE::volume& ima1, const basisfield& bf2, const NEWIMAGE::volume& ima2, const NEWIMAGE::volume *mask=0, MISCMATHS::BFMatrixPrecisionType prec=BFMatrixDoublePrecision) const = 0; virtual double MemEnergy() const = 0; virtual double BendEnergy() const = 0; virtual NEWMAT::ReturnMatrix MemEnergyGrad() const = 0; virtual NEWMAT::ReturnMatrix BendEnergyGrad() const = 0; virtual boost::shared_ptr MemEnergyHess(MISCMATHS::BFMatrixPrecisionType prec=BFMatrixDoublePrecision) const = 0; virtual boost::shared_ptr BendEnergyHess(MISCMATHS::BFMatrixPrecisionType prec=BFMatrixDoublePrecision) const = 0; virtual boost::shared_ptr ZoomField(const std::vector& psz, const std::vector& pvxs, std::vector well=std::vector()) const = 0; }; } // End namespace BASISFIELD #endif // end #ifndef basisfield_h