// // Declarations for displacement vector class DispVec // // displacement_vector.h // // Implements a displacement vector class that can be // used to obtain inverses, K-matrices etc. // // Jesper Andersson, FMRIB Image Analysis Group // // Copyright (C) 2010 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 displacement_vector_h #define displacement_vector_h #include #include #include #include "newmat.h" #include "newimage/newimage.h" #include "miscmaths/SpMat.h" namespace TOPUP { class DispVecException: public std::exception { private: std::string m_msg; public: DispVecException(const std::string& msg) throw(): m_msg(msg) {} virtual const char * what() const throw() { return string("DispVec::" + m_msg).c_str(); } ~DispVecException() throw() {} }; //@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ // // Class CircularArray: // Helper class that facilitates implementation of wrap-around. // Interface includes: // operator[i]: Allows you to access it as a circular array, so e.g. // ca[-1] will return the v[n-1] and ca[n] would return // v[0]. // IndexInRange(i): Translates the index i into the index of the // actual element that it would access. So e.g. // ca.IndexInRange(-1) would return n-1 and // ca.IndexInRange(n) returns 0. // //@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ class CircularArray { public: CircularArray() : _n(0), _v(0), _sf(1.0) {} CircularArray(unsigned int n) : _n(n), _v(new double[_n]), _sf(1.0) { for (unsigned int i=0; i<_n; i++) _v[i]=0.0; } CircularArray(const std::vector& v) : _n(v.size()), _v(new double[_n]), _sf(1.0) { for (unsigned int i=0; i<_n; i++) _v[i]=static_cast(v[i]); } CircularArray(const std::vector& v) : _n(v.size()), _v(new double[_n]), _sf(1.0) { for (unsigned int i=0; i<_n; i++) _v[i]=v[i]; } CircularArray(const NEWMAT::ColumnVector& v) : _n(v.Nrows()), _v(new double[_n]), _sf(1.0) { for (unsigned int i=0; i<_n; i++) _v[i]=static_cast(v(i+1)); } ~CircularArray() { delete [] _v; } void Set(const std::vector& v) { if (_n!=v.size()) { if (_v) delete [] _v; _n=v.size(); _v=new double[_n]; } for (unsigned int i=0; i<_n; i++) _v[i]=double(v[i]); } void Set(const std::vector& v) { if (_n!=v.size()) { if (_v) delete [] _v; _n=v.size(); _v=new double[_n]; } for (unsigned int i=0; i<_n; i++) _v[i]=v[i]; } void Set(const NEWMAT::ColumnVector& v) { if (int(_n)!=v.Nrows()) { if (_v) delete [] _v; _n=v.Nrows(); _v=new double[_n]; } for (unsigned int i=0; i<_n; i++) _v[i]=double(v(i+1)); } void SetFromRow(const NEWIMAGE::volume& ima, unsigned int k, unsigned int j) { set_from_row_or_col(ima,k,j,true); } void SetFromColumn(const NEWIMAGE::volume& ima, unsigned int k, unsigned int i) { set_from_row_or_col(ima,k,i,false); } void Print(const std::string& fname) const; unsigned int N() const { return(_n); } void SetScaleFactor(double sf) const { _sf=sf; } double GetScaleFactor() const { return(_sf); } int Find(double x) const; double operator[](int i) const { int j=i%_n; if (j<0) return(i+_sf*_v[_n+j]); else return(i+_sf*_v[j]); } double Inv(double x) const; unsigned int IndexInRange(int i) const { int j=i%static_cast(_n); if (j<0) return(static_cast(_n+j)); else return(static_cast(j)); } private: unsigned int _n; double *_v; mutable double _sf; void set_from_row_or_col(const NEWIMAGE::volume& ima, int k, int ij, bool row); }; //@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ // // Class DispVec: // Holds one row/column of a displacement field. The interface // includes: // SetFromRow: Picks values from a row in a volume. // SetFromColumn: Picks values from a column in a volume. // GetK_Matrix: Returns a corresponding K-matrix such that // y=K*x gives a distorted vector y from a "true" // vector x. For this to work the values in it // should be scaled to units of voxels. If this is // not the case (let's say it is in units of Hz) // one can use the form K=v.GetK_Matrix(scale_fac) // where in this case scale_fac would be readout // time in seconds. It can also be negative to // facilitate its use for top-down-bottom-up // calculations. // //@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ class DispVec { public: DispVec() {} DispVec(unsigned int n) : _ca(n) {} DispVec(const std::vector& v) : _ca(v) {} DispVec(const std::vector& v) : _ca(v) {} DispVec(const NEWMAT::ColumnVector& v) : _ca(v) {} ~DispVec() {} void Set(const std::vector& v) { _ca.Set(v); } void Set(const std::vector& v) { _ca.Set(v); } void Set(const NEWMAT::ColumnVector& v) { _ca.Set(v); } void SetScaleFactor(double sf) { _ca.SetScaleFactor(sf); } double GetScaleFactor() const { return(_ca.GetScaleFactor()); } void SetFromRow(const NEWIMAGE::volume& ima, int k, int j) { _ca.SetFromRow(ima,k,j); } void SetFromColumn(const NEWIMAGE::volume& ima, int k, int i) { _ca.SetFromColumn(ima,k,i); } bool RowIsAlright(const NEWIMAGE::volume& mask, int slice, int row) const; bool ColumnIsAlright(const NEWIMAGE::volume& mask, int slice, int col) const; void Print(const std::string fname=string("")) const { _ca.Print(fname); } double operator[](int i) const { return(_ca[i]); } double Inv(int i) const { return(_ca.Inv(static_cast(i))); } NEWMAT::ReturnMatrix GetDisplacements() const; NEWMAT::ReturnMatrix GetInverseDisplacements(double sf=1.0) const; NEWMAT::ReturnMatrix GetK_Matrix(double sf=1.0) const; NEWMAT::ReturnMatrix GetS_Matrix(bool wrap=true) const; MISCMATHS::SpMat GetSparseK_Matrix(double sf=1.0) const { NEWMAT::Matrix K=GetK_Matrix(sf); return(MISCMATHS::SpMat(K)); } // Should be re-written for efficiency private: CircularArray _ca; unsigned int get_non_zero_entries_of_row(unsigned int i, unsigned int *indx, double *val) const; }; } // End of namespace TOPUP #endif