// Declarations of intensity-mapper classes used by FNIRT // // intensity_mappers.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 intensity_mappers_h #define intensity_mappers_h #include #include #include "newmat.h" #include "miscmaths/bfmatrix.h" #include "basisfield/basisfield.h" #include "basisfield/splinefield.h" #include "basisfield/dctfield.h" namespace FNIRT { class IntensityMapperException: public std::exception { private: std::string m_msg; public: IntensityMapperException(const std::string& msg) throw(): m_msg(msg) {} virtual const char * what() const throw() { return string("IntensityMapper:: msg=" + m_msg).c_str(); } ~IntensityMapperException() throw() {} }; /////////////////////////////////////////////////////////////////////////////////////////////// // // The IntensityMapper is a class that takes care of the intensity-mapping between a // reference-volume and an object-colume within a firt_CF class. The IntensityMapper // may map the intensity in the following ways depending on the respective sizes of // _sfac and _sfld. // // 1. _sfac.size() == 1 && _sfld.size() == 0 : // In this case there is no intensity scaling and it is assumed that // obj(x,y,z) = ref(x,y,z) + err // Probably never useful. // // 2. _sfac.size() == 1 && _sfld.size() == 0 : // This is the "normal" case where we have a single scale-factor between the ref and // obj images such that // obj(x,y,z) = _sfac[0] * ref(x,y,z) + err // // 3. _sfac.size() > 1 && _sfld.size() == 0 : // This is used to accomplish a "global" non-linear mapping between the intensities // in the ref and obj such that // obj(x,y,z) = _sfac[0] + _sfac[1]*ref(x,y,z) + _sfac[2]*ref(x,y,z).^2 + ... + err // This gives a "correlation-ratio like" cost-function // // 4. _sfac.size() == 0 && _sfld.size() == 1 : // This is used to accomplish a "local" intensity modulation to account for e.g. // different bias-fields between the ref and end the obj volume such that // obj(x,y,z) = _sfld[0].Peek(x,y,z) * ref(x,y,z) + err // // 5. _sfac.size() > 1 && _sfld.size() == 1 : // This combines a global non-linear intensity mapping between ref and obj with a // a local bias-field modulation such that // obj(x,y,z) = _sfld[0].Peek(x,y,z) * (_sfac[0] + _sfac[1]*ref(x,y,z) + ...) + err // // 6. _sfac.size() == 0 && _sfld.size() > 1 // This is the most general case and and allows for a local non-linear intensity // mapping between ref and obj such that // obj(x,y,z) = _sfld[0].Peek(x,y,z) + _sfld[1].Peek(x,y,z)*ref(x,y,z) + ... + err // /////////////////////////////////////////////////////////////////////////////////////////////// class IntensityMapper { public: // Constructors and destructors // Constructor for no scaling IntensityMapper() : _sfac(), _presc(), _sfld(), _lambda(0.0), _mt(NO_SCALING), _fixed(false) {} // Constructor for global linear mapping IntensityMapper(double sfac) : _sfac(1,sfac), _presc(1,1.0), _sfld(), _lambda(0.0), _mt(GLOBAL_LINEAR), _fixed(false) {} // Constructor for global non-linear mapping IntensityMapper(const std::vector& sfac) : _sfac(sfac), _presc(_sfac.size(),1.0), _sfld(), _lambda(0.0), _mt((_sfac.size() > 1) ? GLOBAL_NON_LINEAR : GLOBAL_LINEAR), _fixed(false) { if (!_sfac.size()) throw IntensityMapperException("IntensityMapper::IntensityMapper: Cannot pass zero length vector"); } // Constructor for local linear mapping IntensityMapper(const boost::shared_ptr& sfld, double lambda=10000.0) : _sfac(), _presc(), _sfld(1,sfld), _lambda(lambda), _mt(LOCAL_LINEAR), _fixed(false) {} // Constructor for global non-linear mapping with local bias-field IntensityMapper(const std::vector& sfac, const boost::shared_ptr& sfld, double lambda=10000.0) : _sfac(sfac), _presc(_sfac.size(),1.0), _sfld(1,sfld), _lambda(lambda), _mt(LOCAL_BIAS_WITH_GLOBAL_NON_LINEAR), _fixed(false) { if (_sfac.size() < 2) throw IntensityMapperException("IntensityMapper::IntensityMapper: Global polynomial must have order > 1 when combined with bias field"); } // Constructor for local non-linear mapping IntensityMapper(const std::vector >& sfld, double lambda=10000.0) : _sfac(), _presc(), _sfld(sfld), _lambda(lambda), _mt(LOCAL_NON_LINEAR), _fixed(false) {} virtual ~IntensityMapper() {} // Thanks to boost // General utility functions // Number of "components" the the mapping consists of unsigned int NComp() const {return(_sfac.size() + _sfld.size());} // Number of parameters needed to completely determine the mapping unsigned int NPar() const { if (_fixed) return(0); // No parameters, just constants else return(_sfac.size() + ((_sfld.size()) ? _sfld.size() * _sfld[0]->CoefSz() : 0)); } // Returns the parameters of the mapping NEWMAT::ReturnMatrix GetPar() const; // Returns status of fixed-flag bool Fixed() const {return(_fixed);} // Sets the status of the fixed-flag void SetFixed(bool status=true) {_fixed = status;} // Returns the bending-energy weighting double Lambda() const {return(_lambda);} // Sets the bending-energy weighting void SetLambda(double lambda) {_lambda = lambda;} // Displays debug info void DebugPrint() const; // Sets new parameters for the mapping void SetPar(const NEWMAT::ColumnVector& par); // SCales the input volume void ScaleMe(const NEWIMAGE::volume& ivol, NEWIMAGE::volume& ovol) const; // Returns the scaled membrane energy of any local mapping double CFContribution() const; // Saves the global intensity mapping vector // in NEWMAT ColumnVector style. void SaveGlobalMapping(const std::string& fname) const; // Saves the local intensity mapping in // image format. void SaveLocalMapping(const std::string& fname) const; // Updates the fields (if any) in accordance with // the new parameters. void NewSubSampling(const std::vector& ms, // New matrix size const std::vector& vxs, // New voxel-size const std::vector& new_ss, // New level of sub-sampling const std::vector& old_ss); // Old level of sub-sampling // Calculates the gradient of the cost-function with // respect to the parameters determining the scaling. virtual NEWMAT::ReturnMatrix Gradient(const NEWIMAGE::volume& ref, const NEWIMAGE::volume& diff, const NEWIMAGE::volume *mask); // Calculates the Hessian of the cost-function with // respect to the parameters determining the scaling. virtual boost::shared_ptr Hessian(const NEWIMAGE::volume& ref, const NEWIMAGE::volume *mask, MISCMATHS::BFMatrixPrecisionType prec=BFMatrixDoublePrecision) const; // Calculates the cross-terms (off-diagonal) of the Hessian // of the cost-function. I.e. the mixed partial derivatives // where the differentiation is w.r.t. one displacement parameter // and one scaling parameter. virtual boost::shared_ptr CrossHessian(const BASISFIELD::basisfield& dfield, const NEWIMAGE::volume& dima, const NEWIMAGE::volume& ref, const NEWIMAGE::volume *mask, MISCMATHS::BFMatrixPrecisionType prec) const; protected: enum MappingType {NO_SCALING, GLOBAL_LINEAR, GLOBAL_NON_LINEAR, LOCAL_LINEAR, LOCAL_BIAS_WITH_GLOBAL_NON_LINEAR, LOCAL_NON_LINEAR}; std::vector _sfac; // Vector of coefficients for global mapping std::vector _presc; // "pre-scaling" to improve condition # of Hessian // _presc is _only_ used by global_non_linear model std::vector > _sfld; // Vector of fields for local mapping double _lambda; // Weighting of membrane-energy of field/fields const MappingType _mt; // Flag to determine the current mapping type bool _fixed; // True if mapping should be kept fixed }; /////////////////////////////////////////////////////////////////////////////////////////////// // // The SSDIntensityMapper is a sub-class of IntensityMapper. It provides instances of the // gradient and hessian methods that are relevent/suitable for sum-of-squared differences // type cost-functions. // /////////////////////////////////////////////////////////////////////////////////////////////// class SSDIntensityMapper : public IntensityMapper { public: // Constructors and destructor // Constructor for no scaling SSDIntensityMapper() : IntensityMapper() {} // Constructor for global linear mapping SSDIntensityMapper(double sfac) : IntensityMapper(sfac) {} // Constructor for global non-linear mapping SSDIntensityMapper(const std::vector& sfac) : IntensityMapper(sfac) {} // Constructor for local linear mapping SSDIntensityMapper(boost::shared_ptr& sfld, double lambda=1000.0) : IntensityMapper(sfld,lambda) {} // Constructor for global non-linear mapping with local bias-field SSDIntensityMapper(const std::vector& sfac, const boost::shared_ptr& sfld, double lambda=1000.0) : IntensityMapper(sfac,sfld,lambda) {} // Constructor for local non-linear mapping SSDIntensityMapper(const std::vector >& sfld, double lambda=1000.0) : IntensityMapper(sfld,lambda) {} ~SSDIntensityMapper() {} // Thanks to boost // Calculates the gradient of the cost-function with // respect to the parameters determining the scaling. virtual NEWMAT::ReturnMatrix Gradient(const NEWIMAGE::volume& ref, const NEWIMAGE::volume& diff, const NEWIMAGE::volume *mask); // Calculates the Hessian of the cost-function with // respect to the parameters determining the scaling. virtual boost::shared_ptr Hessian(const NEWIMAGE::volume& ref, const NEWIMAGE::volume *mask, MISCMATHS::BFMatrixPrecisionType prec) const; // Calculates the cross-terms (off-diagonal) of the Hessian // of the cost-function. I.e. the mixed partial derivatives // where the differentiation is w.r.t. one displacement parameter // and one scaling parameter. virtual boost::shared_ptr CrossHessian(const BASISFIELD::basisfield& dfield, const NEWIMAGE::volume& dima, const NEWIMAGE::volume& ref, const NEWIMAGE::volume *mask, MISCMATHS::BFMatrixPrecisionType prec) const; private: // Utility function that returns mean of a vector, possibly ignoring zeros. double vector_mean(const NEWMAT::ColumnVector& vec, bool exclude_zeros=true) const; // Utility function that calculates some sums of elementwise products // of images. If you consider vol1, vol2 and vol3 below as column vectors // then it returns ((v1.^n).*v2)'*v3 double funny_dotproduct(const NEWIMAGE::volume& vol1, unsigned int n, const NEWIMAGE::volume& vol2, const NEWIMAGE::volume& vol3, const NEWIMAGE::volume& mask) const; double funny_dotproduct(const NEWIMAGE::volume& vol1, unsigned int n, const NEWIMAGE::volume& vol2, const NEWIMAGE::volume& vol3) const; double funny_dotproduct(const NEWIMAGE::volume& vol1, unsigned int n, const NEWIMAGE::volume& vol2, const NEWIMAGE::volume& vol3, const NEWIMAGE::volume *mask) const; }; /////////////////////////////////////////////////////////////////////////////////////////////// // // Class used for reading intensity mapping info from file. // /////////////////////////////////////////////////////////////////////////////////////////////// class IntensityMapperReaderException: public std::exception { private: std::string m_msg; public: IntensityMapperReaderException(const std::string& msg) throw(): m_msg(msg) {} virtual const char * what() const throw() { return string("IntensityMapperReader:: msg=" + m_msg).c_str(); } ~IntensityMapperReaderException() throw() {} }; class IntensityMapperReader { public: IntensityMapperReader() : _has_global(false), _has_local(false) {} IntensityMapperReader(const std::string& fname) : _has_global(false), _has_local(false) {common_read(fname);} void Read(const std::string& fname) {common_read(fname);} bool HasGlobal() const {return(_has_global);} bool HasLocal() const {return(_has_local);} std::vector LocalFieldSize() const; std::vector LocalFieldVoxelSize() const; unsigned int NLocalFields() const {return(_local.tsize());} unsigned int GlobalN() const {return(_global.size());} std::vector GetGlobal() const {return(_global);} std::vector > GetLocalAsSplinefieldVector(const std::vector& ksp) const; BASISFIELD::splinefield GetLocalAsSingleSplinefield(const std::vector& ksp, unsigned int indx=0) const; protected: void common_read(const std::string& fname); private: std::string _fname; std::vector _global; bool _has_global; NEWIMAGE::volume4D _local; bool _has_local; }; } // End namespace FNIRT #endif // end #ifndef intensity_mappers_h