// Declarations of class used to decode and // read files written by fnirt, and potentially // by other pieces of software as long as they // are valid displacement-field files. // // fnirt_file_reader.h // // Jesper Andersson, FMRIB Image Analysis Group // // Copyright (C) 2007-2012 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 fnirt_file_reader_h #define fnirt_file_reader_h #include #include #include #include "newmat.h" #include "basisfield/basisfield.h" #include "basisfield/splinefield.h" #include "basisfield/dctfield.h" namespace NEWIMAGE { class FnirtFileReaderException: public std::exception { private: std::string m_msg; public: FnirtFileReaderException(const std::string& msg) throw(): m_msg(msg) {} virtual const char * what() const throw() { return string("FnirtFileReader:: msg=" + m_msg).c_str(); } ~FnirtFileReaderException() throw() {} }; // // Non-standard nifti intent-codes used for FSL-derived // displacement/coefficient files. // #define FSL_FNIRT_DISPLACEMENT_FIELD 2006 #define FSL_CUBIC_SPLINE_COEFFICIENTS 2007 #define FSL_DCT_COEFFICIENTS 2008 #define FSL_QUADRATIC_SPLINE_COEFFICIENTS 2009 enum DisplacementFileType {FnirtSplineDispType, FnirtDCTDispType, FnirtFieldDispType, UnknownDispType, InvalidDispType}; enum AbsOrRelWarps {RelativeWarps, AbsoluteWarps, UnknownWarps}; // These are global routines that I have chosen to leave outside FnirtFileReader to // allow them to be called independently. They probably don't really belong here, but // I can't really come up with a better place for them. void deffield2jacobian(const BASISFIELD::basisfield& dx, const BASISFIELD::basisfield& dy, const BASISFIELD::basisfield& dz, NEWIMAGE::volume& jac); void deffield2jacobian(const BASISFIELD::basisfield& dx, const BASISFIELD::basisfield& dy, const BASISFIELD::basisfield& dz, const NEWMAT::Matrix& aff, volume& jac); void add_affine_part(const NEWMAT::Matrix& aff, unsigned int indx, NEWIMAGE::volume& warps); void remove_affine_part(const NEWMAT::Matrix& aff, unsigned int indx, NEWIMAGE::volume& warps); NEWMAT::Matrix estimate_affine_part(NEWIMAGE::volume4D& warps, unsigned int every=1); /////////////////////////////////////////////////////////////////////////////////////////////// // // The FnirtFileReader is a class that reads, checks and decodes a displacement-field file. // This can be a file created by fnirt, but it could also have been created for example // from a fieldmap. For files created by other applications than fnirt it only reads // "proper" displacement fields. For fnirt-files it also reads coefficient-files. // // The ultimate purpose of FnirtFileReader and FnirtFileWriter is to provide an // interface that makes it easy and transparent not only to read and write displacement // files, buat also to convert between the different representations. For example we // want it to be easy to take a file with a direct representation of the field // (no basis-set) and write that out as a spline-coefficient file. Therefore we // have internal space for all representations. When a file is read in it is stored // in its "native" representation. When/if asked for another representation that // representation is calculated and returned. // /////////////////////////////////////////////////////////////////////////////////////////////// class FnirtFileReader { public: // Default constructor FnirtFileReader() : _type(InvalidDispType), _aor(UnknownWarps), _aff(IdentityMatrix(4)), _coef_rep(3) {} // Copy constructor FnirtFileReader(const FnirtFileReader& src); // Construct from file FnirtFileReader(const std::string& fname, AbsOrRelWarps wt=UnknownWarps, bool verbose=false) : _fname(fname) { common_read(fname,wt,verbose); } // Destructor. No clean up thanks to boost. ~FnirtFileReader() {} void Read(const std::string& fname, AbsOrRelWarps wt=UnknownWarps, bool verbose=false) {common_read(fname,wt,verbose);} bool IsValid() const {if (_type==InvalidDispType) return(false); else return(true);} std::string FileName() const {return(_fname);} DisplacementFileType Type() const {return(_type);} AbsOrRelWarps AbsOrRel() const {return(_aor);} std::vector FieldSize() const; std::vector VoxelSize() const; std::vector KnotSpacing() const; unsigned int SplineOrder() const; std::vector DCTOrder() const; NEWMAT::Matrix AffineMat() const {return(_aff);} NEWMAT::ReturnMatrix FieldAsNewmatMatrix(int indx=-1, bool inc_aff=false) const; NEWIMAGE::volume4D FieldAsNewimageVolume4D(bool inc_aff=false) const; NEWIMAGE::volume FieldAsNewimageVolume(unsigned int indx, bool inc_aff=false) const; NEWIMAGE::volume Jacobian(bool inc_aff=false) const; BASISFIELD::splinefield FieldAsSplinefield(unsigned int indx, std::vector ksp=std::vector(0), unsigned int order=0) const; BASISFIELD::dctfield FieldAsDctfield(unsigned int indx, std::vector order=std::vector(0)) const; protected: void common_read(const std::string& fname, AbsOrRelWarps wt, bool verbose); std::vector > read_coef_file(const NEWIMAGE::volume4D& vcoef, bool verbose) const; // void add_affine_part(NEWMAT::Matrix aff, unsigned int indx, NEWIMAGE::volume& warps) const; private: std::string _fname; DisplacementFileType _type; AbsOrRelWarps _aor; NEWMAT::Matrix _aff; mutable std::vector > _coef_rep; mutable boost::shared_ptr > _vol_rep; }; } // End namespace NEWIMAGE #endif // end #ifndef fnirt_file_reader_h