/* costfns.h Mark Jenkinson, FMRIB Image Analysis Group Copyright (C) 2001 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. */ #if !defined(__costfns_h) #define __costfns_h #include "newimageall.h" using namespace NEWIMAGE; namespace NEWIMAGE { enum costfns { Woods, CorrRatio, MutualInfo, NormCorr, NormMI, LeastSq, LabelDiff, NormCorrSinc, BBR, Unknown }; costfns costfn_type(const string& cname); class Costfn { public: const volume &refvol; const volume &testvol; const volume &rweight; const volume &tweight; volume wmseg; // WM segmentation (or any useful boundary) for BBR volume fmap; // fieldmap for BBR volume fmap_mask; // fieldmap mask for BBR //volume4D nonlin_basis; mutable volume4D debugvol; private: int *bindex; int no_bins; ColumnVector plnp; int *jointhist; int *marghist1; int *marghist2; float *fjointhist; float *fmarghist1; float *fmarghist2; mutable int p_count; costfns p_costtype; bool validweights; float bin_a0; float bin_a1; float bbr_dist; // in mm float bbr_offset; float bbr_slope; Matrix bbr_pts; // in mm coords Matrix bbr_norms; // in mm coords pointing from wm to other float *gm_coord_x; // in mm coords float *gm_coord_y; float *gm_coord_z; float *wm_coord_x; float *wm_coord_y; float *wm_coord_z; int no_coords; int vertex_step; int pe_dir; // for fieldmap application string bbr_type; bool debug_mode; public: float smoothsize; float fuzzyfrac; public: // Publicly available calls Costfn(const volume& refv, const volume& inputv); Costfn(const volume& refv, const volume& inputv, const volume& refweight, const volume& inweight); ~Costfn(); void set_debug_mode(bool debug_flag=true); void set_costfn(const costfns& costtype) { p_costtype = costtype; } costfns get_costfn(void) { return p_costtype; } void set_no_bins(int n_bins); int set_bbr_seg(const volume& bbr_seg); int set_bbr_coords(const Matrix& coords, const Matrix& norms); int set_bbr_type(const string& typenm); int set_bbr_step(int step); int set_bbr_slope(float slope); int set_bbr_fmap(const volume& fieldmap, int phase_encode_direction); int set_bbr_fmap(const volume& fieldmap, const volume& fieldmap_mask, int phase_encode_direction); int count() const { return p_count; } // General cost function call float cost(const Matrix& affmat) const; // affmat is voxel to voxel // affmat is voxel to voxel and non-linear parameters are arbitrary float cost(const Matrix& affmat, const ColumnVector& nonlin_params) const; // in the following, all warps are mm to mm float cost(const volume4D& warp) const; float cost_gradient(volume4D& gradvec, const volume4D& warp, bool nullbc) const; // some basic entropy calls float ref_entropy(const Matrix& aff) const; float test_entropy(const Matrix& aff) const; float joint_entropy(const Matrix& aff) const; volume image_mapper(const Matrix& affmat) const; // affmat is voxel to voxel Matrix mappingfn(const Matrix& affmat) const; // affmat is voxel to voxel float get_bin_intensity(int bin_number) const; float get_bin_number(float intensity) const; bool is_bbr_set(void) const; // a resampling function (since it is logical to keep it with the general cost processing for bbr) float bbr_resamp(const Matrix& aff, const ColumnVector& nonlin_params, volume& resampvol) const; private: // Prevent default behaviours Costfn(); Costfn operator=(const Costfn&); Costfn(const Costfn&); // Internal functions available float normcorr(const Matrix& aff) const; float normcorr_smoothed(const Matrix& aff) const; float normcorr_smoothed_sinc(const Matrix& aff) const; float normcorr_fully_weighted(const Matrix& aff, const volume& refweight, const volume& testweight) const; float leastsquares(const Matrix& aff) const; float leastsquares_smoothed(const Matrix& aff) const; float leastsquares_fully_weighted(const Matrix& aff, const volume& refweight, const volume& testweight) const; float labeldiff(const Matrix& aff) const; float labeldiff_smoothed(const Matrix& aff) const; float labeldiff_fully_weighted(const Matrix& aff, const volume& refweight, const volume& testweight) const; float bbr(const Matrix& aff) const; float bbr(const Matrix& aff, const ColumnVector& nonlin_params) const; float bbr(const Matrix& aff, const ColumnVector& nonlin_params, volume& resampvol, bool resampling_required) const; float fmap_extrap(const double& x_vox, const double& y_vox, const double& z_vox, const ColumnVector& v_pe) const; int vox_coord_calc(ColumnVector& tvc, ColumnVector& rvc, const Matrix& aff, const ColumnVector& nonlin_params, const Matrix& iaffbig, const Matrix& mm2vox, const ColumnVector& pe_dir_vec) const; float woods_fn(const Matrix& aff) const; float woods_fn_smoothed(const Matrix& aff) const; float corr_ratio(const Matrix& aff) const; float corr_ratio_smoothed(const Matrix& aff) const; float corr_ratio_fully_weighted(const Matrix& aff, const volume& refweight, const volume& testweight) const; float corr_ratio_fully_weighted(const volume4D& warpvol, const volume& refweight, const volume& testweight) const; float corr_ratio_gradient_fully_weighted(volume4D& gradvec, const volume4D& warpvol, const volume& refweight, const volume& testweight, bool nullbc) const; float mutual_info(const Matrix& aff) const; float mutual_info_smoothed(const Matrix& aff) const; float mutual_info_fully_weighted(const Matrix& aff, const volume& refweight, const volume& testweight) const; float normalised_mutual_info(const Matrix& aff) const; float normalised_mutual_info_smoothed(const Matrix& aff) const; float normalised_mutual_info_fully_weighted(const Matrix& aff, const volume& refweight, const volume& testweight) const; float cost(const Matrix& affmat, const volume& refweight, const volume& testweight) const; float cost(const Matrix& affmat, const ColumnVector& nonlin_params, const volume& refweight, const volume& testweight) const; float cost(const volume4D& warp, const volume& refweight, const volume& testweight) const; float cost_gradient(volume4D& gradvec, const volume4D& warp, const volume& refweight, const volume& testweight, bool nullbc=false) const; int p_corr_ratio_image_mapper(volume& vout, Matrix& mappingfn, const volume& vref, const volume& vtest, const volume& refweight, const volume& testweight, int *bindex, const Matrix& aff, const int no_bins, const float smoothsize) const; }; ////////////////////////////////////////////////////////////////////////// } #endif