/* model.h Mark Woolrich FMRIB Image Analysis Group Copyright (C) 2002 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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You are not permitted under this Licence to use this Software commercially. Use for which any financial return is received shall be defined as commercial use, and includes (1) integration of all or part of the source code or the Software into a product for sale or license by or on behalf of Licensee to third parties or (2) use of the Software or any derivative of it for research with the final aim of developing software products for sale or license to a third party or (3) use of the Software or any derivative of it for research with the final aim of developing non-software products for sale or license to a third party, or (4) use of the Software to provide any service to an external organisation for which payment is received. If you are interested in using the Software commercially, please contact Isis Innovation Limited ("Isis"), the technology transfer company of the University, to negotiate a licence. Contact details are: innovation@isis.ox.ac.uk quoting reference DE/9564. */ #if !defined(model_h) #define model_h #include #include #include #include "utils/tracer_plus.h" #include "miscmaths/miscmaths.h" #ifndef M_PI #define M_PI 3.14159265358979323846 #endif #ifndef MAX_EN #define MAX_EN 1e16 #endif using namespace Utilities; using namespace MISCMATHS; namespace Bint { class Prior { public: Prior(){} virtual ~Prior(){} virtual float calc_energy(float value) const = 0; virtual float calc_gradient(float value) const = 0; private: }; class GaussPrior : public Prior { public: GaussPrior(float pmn,float pstd, float pmin = -1e16, float pmax = 1e16) : Prior(), mn(pmn),std(pstd),min(pmin),max(pmax) {} const GaussPrior& operator=(const GaussPrior& pin) { mn = pin.mn; std = pin.std; min = pin.min; max = pin.max; return *this; } GaussPrior(const GaussPrior& pin) { operator=(pin); } virtual ~GaussPrior(){} virtual float calc_energy(float value) const { float energy = MAX_EN; if(value > min && value < max) energy = pow(double((value-mn)/std),2.0)/2.0; return energy; } virtual float calc_gradient(float value) const { float grad = 0; if(value > min && value < max) grad = ((mn-value)/(std*std)); return grad; } private: GaussPrior(); float mn; float std; float min; float max; }; class UnifPrior : public Prior { public: UnifPrior(float pmin = -1e16, float pmax = 1e16) : Prior(), min(pmin),max(pmax) { en=-std::log( 1/(max-min) ); } const UnifPrior& operator=(const UnifPrior& pin) { min = pin.min; max = pin.max; en=-std::log( 1/(max-min) ); return *this; } UnifPrior(const UnifPrior& pin) { operator=(pin); } virtual ~UnifPrior(){} virtual float calc_energy(float value) const { float energy=MAX_EN; if(value >= min && value <= max ) energy=en; return energy; } virtual float calc_gradient(float value) const { float grad = 0; return grad; } private: UnifPrior(); float min; float max; float en; }; class GammaPrior : public Prior { public: // m=a/b, v=a/b^2, a=m^2/v, b=m/v GammaPrior(float pa,float pb, float pmin = 0, float pmax = 1e16) : Prior(), a(pa),b(pb),min(pmin),max(pmax) {} virtual ~GammaPrior(){} const GammaPrior& operator=(const GammaPrior& pin) { a = pin.a; b = pin.b; min = pin.min; max = pin.max; return *this; } GammaPrior(const GammaPrior& pin) { operator=(pin); } virtual float calc_energy(float value) const { float energy = MAX_EN; if(value > min && value < max) { energy = -(a-1)*std::log(value)+b*value; } return energy; } virtual float calc_gradient(float value) const { float grad = 0; if(value > min && value < max) { grad = -(a-1)/value+b; } return grad; } private: GammaPrior(); float a; float b; float min; float max; }; class SinPrior : public Prior { public: SinPrior(float pscale=1,float pmin=-1e16,float pmax=1e16) : Prior(), scale(pscale),min(pmin),max(pmax){} const SinPrior& operator=(const SinPrior& pin) { scale = pin.scale; min=pin.min; max=pin.max; return *this; } SinPrior(const SinPrior& pin) { operator=(pin); } virtual ~SinPrior(){} virtual float calc_energy(float value) const { float energy= MAX_EN; if(value > min && value < max){ if(!value==0){ energy=-std::log(fabs(std::sin(value/scale)/2)); } } return energy; } virtual float calc_gradient(float value) const { float grad = 0; if(value > min && value < max) { grad = sign(std::sin(value/scale))*(std::cos(value/scale)/scale)/(std::sin(value/scale)); } return grad; } private: SinPrior(); float scale; float min; float max; }; class GaussARDPrior : public Prior { public: GaussARDPrior() : Prior(){} const GaussARDPrior& operator=(const GaussARDPrior& pin) { return *this; } GaussARDPrior(const GaussARDPrior& pin) { operator=(pin); } virtual ~GaussARDPrior(){} virtual float calc_energy(float value) const { float energy= MAX_EN; if(value!=0){ energy=std::log(fabs(value)); } return energy; } virtual float calc_gradient(float value) const { float grad = 1; //Wooly thinks this is better than 0 if(value!=0){ grad =sign(value)/fabs(value);} return grad; } private: }; class Parameter { public: Parameter(const string& pname, float pinitvalue, float pinitstd, Prior& pprior, bool pallowtovary = true, bool psave = true) : name(pname), init_value(pinitvalue), init_std(pinitstd), priorobj(pprior), allowtovary(pallowtovary), save(psave) { } virtual ~Parameter(){} const string& getname() const {return name;} const Prior& getprior() const {return priorobj;} float getinitvalue() const {return init_value;} float getinitstd() const {return init_std;} bool getallowtovary() const {return allowtovary;} bool getsave() const { return save; } void setinitvalue(float pinitvalue) {init_value = pinitvalue;} protected: string name; float init_value; float init_std; Prior& priorobj; bool allowtovary; bool save; private: Parameter(); const Parameter& operator=(Parameter& par); Parameter(const Parameter&); }; class ForwardModel { public: ForwardModel(int pdebuglevel) : debuglevel(pdebuglevel), paramcount(0) {} virtual ~ForwardModel(){params.clear();priors.clear();} virtual ReturnMatrix nonlinearfunc(const ColumnVector& paramvalues) const = 0; virtual void setparams() = 0; virtual void initialise(const ColumnVector& data) = 0; // indexes from zero: Parameter& getparam(int p) {return *params[p];} int getnparams() const {return paramcount;} void clear_params() {params.clear();paramcount = 0;} void add_param(const string& pname, float pinit_value, float pinit_std, Prior* tmp, bool pallowtovary, bool psave) { paramcount++; priors.push_back(tmp); params.push_back(new Parameter(pname,pinit_value,pinit_std,*tmp,pallowtovary,psave)); } void add_param(const string& pname, float pinit_value, float pinit_std, GaussPrior& pprior, bool pallowtovary = true, bool psave = true) { add_param(pname,pinit_value,pinit_std,new GaussPrior(pprior),pallowtovary,psave); } void add_param(const string& pname, float pinit_value, float pinit_std, UnifPrior& pprior, bool pallowtovary = true, bool psave = true) { add_param(pname,pinit_value,pinit_std,new UnifPrior(pprior),pallowtovary,psave); } void add_param(const string& pname, float pinit_value, float pinit_std, GammaPrior& pprior, bool pallowtovary = true, bool psave = true) { add_param(pname,pinit_value,pinit_std,new GammaPrior(pprior),pallowtovary,psave); } void add_param(const string& pname, float pinit_value, float pinit_std, SinPrior& pprior, bool pallowtovary = true, bool psave = true) { add_param(pname,pinit_value,pinit_std,new SinPrior(pprior),pallowtovary,psave); } void add_param(const string& pname, float pinit_value, float pinit_std, GaussARDPrior& pprior, bool pallowtovary = true, bool psave = true) { add_param(pname,pinit_value,pinit_std,new GaussARDPrior(pprior),pallowtovary,psave); } protected: int debuglevel; vector params; int paramcount; vector priors; private: ForwardModel(); const ForwardModel& operator=(ForwardModel& par); ForwardModel(const ForwardModel&); }; class gForwardModel : public ForwardModel { public: gForwardModel(int pdebuglevel) : ForwardModel(pdebuglevel) {} virtual ~gForwardModel(){} // gradient virtual ReturnMatrix gradient(const ColumnVector& paramvalues) const = 0; private: gForwardModel(); const gForwardModel& operator=(gForwardModel& par); gForwardModel(const gForwardModel&); }; } #endif