/* noisemodel_ar.cc - Class implementation for the AR(1) noise model Adrian Groves and Michael Chappell, FMRIB Image Analysis Group Copyright (C) 2007-2008 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 "noisemodel.h" #include "dist_gamma.h" #include using namespace std; class Ar1cParams; // Helper class -- caches some of the AR matrices class Ar1cMatrixCache { public: const SymmetricBandMatrix& GetMatrix(unsigned n, unsigned a12pow, unsigned a3pow) const; const SymmetricBandMatrix& GetMarginal(unsigned n) const; void Update(const Ar1cParams& dist, int nTimes); Ar1cMatrixCache(int numPhis) : nPhis(numPhis) { return; } Ar1cMatrixCache(const Ar1cMatrixCache& from) : alphaMarginals(from.alphaMarginals), alphaMatrices(from.alphaMatrices), nPhis(from.nPhis) { return; } private: vector alphaMarginals; // recalculated whenever alpha changes unsigned FlattenIndex(unsigned n, unsigned a12pow, unsigned a34pow) const { assert(n==1 || n==2 && a12pow<=2 && a34pow<=2); return n-1 + 2*( a12pow + 3*(a34pow) ); } vector alphaMatrices; // should only be calculated once // Note that if more than one model is being inferred upon at a time, // this will be unnecessarily duplicated in every one of them -- // might speed things up considerably by sharing. int nPhis; }; // Parameter-storage class -- it's really just an enhanced structure class Ar1cParams : public NoiseParams { public: virtual Ar1cParams* Clone() const { return new Ar1cParams(*this); } virtual const Ar1cParams& operator=(const NoiseParams& in) { const Ar1cParams& from = dynamic_cast(in); alpha = from.alpha; phis = from.phis; alphaMat = from.alphaMat; return *this; } virtual const MVNDist OutputAsMVN() const; virtual void InputFromMVN(const MVNDist& mvn); // Human-readable debug output (dump internal state to LOG) virtual void Dump(const string indent = "") const; // Constructor/destructor Ar1cParams(int nAlpha, int nPhi) : alpha(nAlpha), phis(nPhi), alphaMat(nPhi) { return; } Ar1cParams(const Ar1cParams& from) : alpha(from.alpha), phis(from.phis), alphaMat(from.alphaMat) { return; } virtual ~Ar1cParams() { return; } private: friend class Ar1cNoiseModel; // Needs to use this class like it's a structure friend class Ar1cMatrixCache; MVNDist alpha; vector phis; Ar1cMatrixCache alphaMat; }; class Ar1cNoiseModel : public NoiseModel { public: // virtual Ar1cNoiseModel* Clone() const; // makes a new identical copy of this object virtual Ar1cParams* NewParams() const { return new Ar1cParams( NumAlphas(), nPhis ); } virtual void HardcodedInitialDists(NoiseParams& prior, NoiseParams& posterior) const; // virtual void LoadPrior( const string& filename ); // loads priors from file, and also initializes posteriors virtual void Precalculate( NoiseParams& noise, const NoiseParams& noisePrior, const ColumnVector& sampleData ) const; // Used to pre-evaluate the alpha matrices in the cache // virtual void AdjustPrior(...) might be needed for multi-voxel methods... // probably best for that to go in a derived class. // virtual void Dump(const string indent = "") const; // virtual void DumpPrior(const string indent = "") const; // virtual void DumpPosterior(const string indent = "") const; // human-readable debug output // virtual const MVNDist GetResultsAsMVN() const; // Constructor/destructor Ar1cNoiseModel(const string& ar1CrossTerms, int numPhis ); // ar1CrossTerms must be either "none", "dual", or "same". virtual ~Ar1cNoiseModel() { return; } // VB Updates virtual void UpdateNoise( NoiseParams& noise, const NoiseParams& noisePrior, const MVNDist& theta, const LinearFwdModel& linear, const ColumnVector& data) const { UpdateAlpha(noise, noisePrior, theta, linear, data); UpdatePhi(noise, noisePrior, theta, linear, data); } virtual void UpdateAlpha( NoiseParams& noise, const NoiseParams& noisePrior, const MVNDist& theta, const LinearFwdModel& model, const ColumnVector& data) const; virtual void UpdatePhi( NoiseParams& noise, const NoiseParams& noisePrior, const MVNDist& theta, const LinearFwdModel& model, const ColumnVector& data) const; virtual void UpdateTheta( const NoiseParams& noise, // const NoiseParams& noisePrior, MVNDist& theta, const MVNDist& thetaPrior, const LinearFwdModel& model, const ColumnVector& data, MVNDist* thetaWithoutPrior = NULL, float LMalpha = 0 ) const; virtual double CalcFreeEnergy( const NoiseParams& noise, const NoiseParams& noisePrior, const MVNDist& theta, const MVNDist& thetaPrior, const LinearFwdModel& model, const ColumnVector& data) const; // void SaveParams(const MVNDist& theta) {}; // void RevertParams(MVNDist& theta) {}; protected: // Ar1cParameters* prior; // Ar1cParameters* posterior; // Whenever this changes, call alphaMat.Update! // Ar1cMatrixCache alphaMat; const string ar1Type; int NumAlphas() const; // converts the above string into a number const int nPhis; };