/* fwdmodel_simple.h - Implements the simplified ASL model Adrian Groves, 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. */ #include "fwdmodel.h" #include "inference.h" #include using namespace std; class SimpleFwdModelIdStruct { public: SimpleFwdModelIdStruct() { Nbasis = 0; } void Define( int NumBasisFcns ) { assert(Nbasis==0); assert(NumBasisFcns>0); Nbasis = NumBasisFcns; } // virtual void DumpVector(const ColumnVector& vec, const string& indent = ""); // virtual ~SimpleFwdModelIdStruct() { return; } // N=3: 1=Q0 2=Q1 3=Q2 4=Q3 5=U0 6=U1 7=U2 8=U3 9=R0 10=R1 11=R2 12=R3 double Q0(const ColumnVector& p) const { return p(1); } ReturnMatrix Qn(const ColumnVector& p) const { AssertValid(p); ColumnVector tmp = p.Rows(2,Nbasis+1); return tmp; } double U0(const ColumnVector& p) const { return p(2+Nbasis); } ReturnMatrix Un(const ColumnVector& p) const { AssertValid(p); ColumnVector tmp = p.Rows(3+Nbasis,2+2*Nbasis); return tmp; } double R0(const ColumnVector& p) const { AssertValid(p); return p(3+2*Nbasis); } ReturnMatrix Rn(const ColumnVector& p) const { AssertValid(p); ColumnVector tmp = p.Rows(4+2*Nbasis,3+3*Nbasis); return tmp; } void NameParams(vector& names) const; private: int Nbasis; void AssertValid(const ColumnVector& p) const { assert(Nbasis>0); assert(p.Nrows() == 3 + 3*Nbasis); } }; class SimpleFwdModel : public FwdModel { public: // Virtual function overrides virtual void Evaluate(const ColumnVector& params, ColumnVector& result) const; virtual void DumpParameters(const ColumnVector& vec, const string& indents = "") const; virtual void NameParams(vector& names) const { id.NameParams(names); } virtual int NumParams() const { return 3 + 3*basis.Ncols(); } string ModelVersion() const; virtual ~SimpleFwdModel() { return; } virtual void HardcodedInitialDists(MVNDist& prior, MVNDist& posterior) const { prior.means = 0; prior.SetPrecisions(IdentityMatrix(NumParams()) * 1e-12); posterior = prior; // Informative starting points // I'm not very happy with this whole setup... the physical arrangment // of elements in the vector should only appear once. posterior.means(1) = 50; posterior.means(2+basis.Ncols()) = 1.5e4; posterior.means(3+2*basis.Ncols()) = 25; assert(id.Q0(posterior.means) == 50); assert(id.U0(posterior.means) == 1.5e4); assert(id.R0(posterior.means) == 25); } // Constructor SimpleFwdModel(ArgsType& args); // SimpleFwdModel(const SimpleFwdModel& from); // copy constructor - default ok? protected: // Constants ColumnVector echoTime; Matrix basis; // basis in columns? ColumnVector rho; SimpleFwdModelIdStruct id; };