// Declarations of utility functions/classes used by topup // // topupfns.h // // Jesper Andersson, FMRIB Image Analysis Group // // Copyright (C) 2012 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 topupfns_h #define topupfns_h #include #include #include "newmat.h" #include "newimage/newimage.h" #include "basisfield/basisfield.h" #include "basisfield/splinefield.h" #include "basisfield/dctfield.h" #include "utils/options.h" #include "miscmaths/nonlin.h" #include "topup_costfunctions.h" #include "topup_file_io.h" namespace TOPUP { std::string path(const std::string& fullname); std::string filename(const std::string& fullname); std::string extension(const std::string& fullname); enum PrecisionType {FloatPrecision, DoublePrecision}; /////////////////////////////////////////////////////////////////////////////////////////////// // // topup_clp is a glorified struct that holds the command line parameters of topup // /////////////////////////////////////////////////////////////////////////////////////////////// class topup_clp { public: topup_clp(const Utilities::Option& imain, const Utilities::Option& datain, const Utilities::Option& cout, const Utilities::Option& fout, const Utilities::Option& iout, const Utilities::Option& lout, const Utilities::Option >& warpres, const Utilities::Option >& subsamp, const Utilities::Option >& fwhm, const Utilities::Option >& miter, const Utilities::Option >& lambda, const Utilities::Option& ssqlambda, const Utilities::Option >& estmov, const Utilities::Option >& minmet, const Utilities::Option& regmod, const Utilities::Option& sporder, const Utilities::Option& numprec, const Utilities::Option& interp, const Utilities::Option& indscale, const Utilities::Option& regrid, const Utilities::Option& verbose, const Utilities::Option& debug, const Utilities::Option& trace); const std::string& ImaFname() const { return(_imain); } std::string CoefFname() const { if (!_out.length()) _out = TOPUP::path(_imain) + TOPUP::filename(_imain); return(_out + string("_fieldcoef")); } std::string MovParFname() const { if (!_out.length()) _out = TOPUP::path(_imain) + TOPUP::filename(_imain); return(_out + string("_movpar.txt")); } const std::string& LogFname() const { if (!_lout.length()) _lout = TOPUP::path(_imain) + TOPUP::filename(_imain) + string(".topup_log"); return(_lout); } const std::string& FieldFname() const { return(_fout); } const std::string& ImaOutFname() const { return(_iout); } const NEWMAT::Matrix PhaseEncodeVectors() const { return(_datafile.PhaseEncodeVectors()); } const NEWMAT::ColumnVector ReadoutTimes() const { return(_datafile.ReadOutTimes()); } unsigned int NoOfLevels() const { return(_nlev); } TopupInterpolationType InterpolationModel() const { return(_interp); } MISCMATHS::BFMatrixPrecisionType HessianPrecision() const { return(_numprec); } RegularisationType RegularisationModel() const { return(_regtype); } unsigned int SplineOrder() const { return(_sporder); } unsigned int DebugLevel() const { return(_debug); } bool Verbose() const { return(_verbose); } bool Trace() const { return(_trace); } bool SSQLambda() const { return(_ssqlambda); } bool IndividualScaling() const { return(_indscale); } std::vector Regridding(const NEWIMAGE::volume4D& invols) const; unsigned int SubSampling(unsigned int level) const { if (level < 1 || level > _nlev) throw TopupException("topup_clp::SubSampling: Out-of-range value of level"); return(static_cast(_subsamp[level-1])); } double WarpRes(unsigned int level) const { if (level < 1 || level > _nlev) throw TopupException("topup_clp::WarpRes: Out-of-range value of level"); return(_warpres[level-1]); } double FWHM(unsigned int level) const { if (level < 1 || level > _nlev) throw TopupException("topup_clp::FWHM: Out-of-range value of level"); return(_fwhm[level-1]); } double Lambda(unsigned int level) const { if (level < 1 || level > _nlev) throw TopupException("topup_clp::Lambda: Out-of-range value of level"); return(_lambda[level-1]); } unsigned int MaxIter(unsigned int level) const { if (level < 1 || level > _nlev) throw TopupException("topup_clp::MaxIter: Out-of-range value of level"); return(static_cast(_miter[level-1])); } bool EstimateMovements(unsigned int level) const { if (level < 1 || level > _nlev) throw TopupException("topup_clp::EstimateMovements: Out-of-range value of level"); return(static_cast(_estmov[level-1] != 0)); } MISCMATHS::NLMethod OptimisationMethod(unsigned int level) const { if (level < 1 || level > _nlev) throw TopupException("topup_clp::OptimisationMethod: Out-of-range value of level"); return(_optmet[level-1]); } private: unsigned int _nlev; std::string _imain; mutable std::string _out; std::string _fout; std::string _iout; mutable std::string _lout; TopupDatafileReader _datafile; std::vector _warpres; std::vector _subsamp; std::vector _fwhm; std::vector _miter; std::vector _lambda; bool _ssqlambda; bool _indscale; bool _regrid; RegularisationType _regtype; TopupInterpolationType _interp; MISCMATHS::BFMatrixPrecisionType _numprec; std::vector _optmet; std::vector _estmov; unsigned int _sporder; bool _verbose; bool _trace; unsigned int _debug; }; /////////////////////////////////////////////////////////////////////////////////////////////// // // Declarations of global functions used by topup // /////////////////////////////////////////////////////////////////////////////////////////////// boost::shared_ptr parse_topup_command_line(unsigned int narg, char *args[]); bool check_exist(const std::string& fname); std::string existing_conf_file(const std::string& cfname); } // End namespace TOPUP #endif // End #ifndef topupfns_h