/* CCOPYRIGHT */ /* 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"). The Software is distributed "AS IS" under this Licence solely for non-commercial use in the hope that it will be useful, but in order that the University as a charitable foundation protects its assets for the benefit of its educational and research purposes, the University makes clear that no condition is made or to be implied, nor is any warranty given or to be implied, as to the accuracy of the Software, or that it will be suitable for any particular purpose or for use under any specific conditions. Furthermore, the University disclaims all responsibility for the use which is made of the Software. It further disclaims any liability for the outcomes arising from using the Software. The Licensee agrees to indemnify the University and hold the University harmless from and against any and all claims, damages and liabilities asserted by third parties (including claims for negligence) which arise directly or indirectly from the use of the Software or the sale of any products based on the Software. No part of the Software may be reproduced, modified, transmitted or transferred in any form or by any means, electronic or mechanical, without the express permission of the University. The permission of the University is not required if the said reproduction, modification, transmission or transference is done without financial return, the conditions of this Licence are imposed upon the receiver of the product, and all original and amended source code is included in any transmitted product. You may be held legally responsible for any copyright infringement that is caused or encouraged by your failure to abide by these terms and conditions. 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. */ #ifndef __splines_h #define __splines_h #ifdef __cplusplus extern "C" { #endif /* Silly little macros. */ /* Get index into C-type array given 3D subscript and array of given dimensions. */ #ifndef index #define index(A,B,C,DIM) ((C)*DIM[0]*DIM[1] + (B)*DIM[0] + (A)) #endif #ifndef MIN #define MIN(A,B) ((A) > (B) ? (B) : (A)) #endif #ifndef MAX #define MAX(A,B) ((A) > (B) ? (A) : (B)) #endif /* The following 2 macros are used to obtain start and end indicies into (C-type 0 offset) image-matrix given knot spacing and spline-coefficient index. */ #ifndef k2strt #define k2strt(K,KSP) (1+(KSP)*((K)-4))) #endif #ifndef k2end #define k2end(K,KSP) ((K)*(KSP)-1) #endif /* The following 2 macros are used to go between knot-spacing and spline kernel size. */ #ifndef sz2ksp #define sz2ksp(SZ) (((SZ)+1)/4) #endif #ifndef ksp2sz #define ksp2sz(KSP) (4*(KSP)-1) #endif /* These are to ensure that right memory allocation routines are used depending on wether the routines are linked to mex-files or to C++. */ #ifdef MEX #define my_calloc mxCalloc #define my_realloc mxRealloc #define my_free mxFree #else #define my_calloc calloc #define my_realloc realloc #define my_free free #endif void please_free(void *ptr); int spline_kron(/* Input */ int ndim, /* Dimensionality of spline. */ int dim[3], /* Size of spline in the different directions. */ double *sp1d[3], /* Set of 1D splines. */ /* Output */ double *spline); /* nD (n>0 & n<4) spline. */ int get_1D_spline(/* Input */ int knsp, /* Knot-spacing (in # of voxels) */ /* Output */ double **spline); /* 1D spline function */ int get_1D_spline_d(/* Input */ int knsp, /* Knot-spacing (in # of voxels) */ /* Output */ double **spline); /* 1D spline function */ int get_1D_spline_dd(/* Input */ int knsp, /* Knot-spacing (in # of voxels) */ /* Output */ double **spline); /* 1D spline function */ int zoom_field(/* input */ int ndim, int oksp[3], int nksp[3], int idim[3], double *oc, /* Output */ double *nc); int zoom_field_by2(/* Input */ int ndim, int ksp[3], int idim[3], int zdim, double *oc, /* Output */ double **nc); int get_field(/* Input */ int ndim, int cdim[3], double *c, int sdim[3], double *sp, int fdim[3], /* Output */ double *f); int get_range(/* Input */ int k, int ssz, int fsz, /* Output */ int *fs, int *fe, int *ks); int no_of_knots(int ksp, int msz); int make_A(/* Input. */ int ndim, int kdim[3], int sdim[3], double *spl, int idim[3], double *ima, /* Output. */ int *irp, int *jcp, double *sp); int make_Aty(/* Input. */ int ndim, /* Actual dimensionality of problem (1, 2 or 3). */ int cdim[3], /* # of knots in the three dimensions. */ int sdim[3], /* Size of spline kernel in the three dimensions. */ double *spl, /* Spline kernel. */ int idim[3], /* Size of image matrix. */ double *ima, /* Image. */ double *y, /* y-vector. */ /* Output. */ double *aty); /* Resulting vector */ int make_AtA(/* Input. */ int ndim, /* Actual dimensionality of problem (1, 2 or 3). */ int cdim[3], /* # of knots in the three dimensions. */ int sdim[3], /* Size of spline kernel in the three dimensions. */ double *spl, /* Spline kernel. */ int idim[3], /* Size of image matrix. */ double *ima, /* Image. */ /* Output. */ int *irp, /* Array of row-indicies. */ int *jcp, /* Array of pointers into column-starts in irp. */ double *sp); /* Array of non-zero values in sparse matric. */ int make_AtB(/* Input. */ int ndim, /* Actual dimensionality of problem (1, 2 or 3). */ int cdim[3], /* # of knots in the three dimensions. */ int sdim[3], /* Size of spline kernel in the three dimensions. */ double *splB, /* Spline kernel for B. */ double *splA, /* Spline kernel for A. */ int idim[3], /* Size of image matrix. */ double *imaB, /* Image for B. */ double *imaA, /* Image for A. */ /* Output. */ int *irp, /* Array of row-indicies. */ int *jcp, /* Array of pointers into column-starts in irp. */ double *sp); /* Array of non-zero values in sparse matric. */ int get_memen_grad(/* Input. */ int ndim, /* # of dimensions (1,2 or 3) */ const int cdim[3], /* Size of coefficient array. */ const int ksp[3], /* Knot-spacings. */ const double *beta, /* Coefficients. */ /* Output.*/ double *grad); double get_memen(/* Input. */ int ndim, /* # of dimensions (1,2 or 3) */ const int cdim[3], /* Size of coefficient array. */ const int ksp[3], /* Knot-spacings. */ const double *beta); /* Coefficients. */ double *memen_AtAb(/* Input. */ int ndim, /* # of dimensions (1,2 or 3). */ const int cdim[3], /* Size of coeffient array. */ const int ksp[3], /* Knot-spacing. */ const int sdim[3], /* Kernel dimensions. */ const double *spl, /* Spline kernel. */ const double *beta, /* Spline coefficients. */ int what, /* 0->A*b, 1->A'*A*b */ /* Output. */ int *sz, /* Length of output vector */ double **ovec); /* Output vector */ int make_memen_H(/* Input. */ const int ndim, /* Actual dimensionality of problem (1, 2 or 3). */ int cdim[3], /* # of knots in the three dimensions. */ const int ksp[3], /* Knot spacing in the three dimensions. */ /* Output. */ int *irp, /* Array of row-indicies. */ int *jcp, /* Array of pointers into column-starts in irp. */ double *sp); /* Array of non-zero values in sparse matric. */ double dot_prod(int i1, /* [i1 j1 k1] is index of first spline kernel/coef. */ int j1, int k1, int i2, /* [i2 j2 k2] is index of second spline kernel/coef. */ int j2, int k2, int sdim[3], /* Size of spline kernel (common to s1 and s2). */ int idim[3], /* Size of image. */ double *s2, /* Second spline kernel. */ double *ima, /* Image. */ double *s1, /* First spline kernel (pre-multiplied with image. */ int is1[3], /* Start indices of first spline kernel in image. */ int ie1[3], /* End indices of first spline kernel in image. */ int ss1[3]); /* Offset into first spline kernel (to handle edges). */ double dot_prod_H(int i1, /* [i1 j1 k1] is index of first spline kernel/coef. */ int j1, int k1, int i2, /* [i2 j2 k2] is index of second spline kernel/coef. */ int j2, int k2, int sdim[3], /* Size of spline kernel (common to s1 and s2). */ double *s1, /* First spline kernel. */ double *s2); /* Second spline kernel. */ double get_s_by_i(/* Input */ int i, /* [i j k] index of spline kernel/coef. */ int j, int k, int sdim[3], /* Size of spline kernel. */ int idim[3], /* Size of image. */ double *spl, /* Spline. */ double *ima, /* Image. */ /* Output */ double *sbyi); /* Spline multiplied with appuretenant values in image. */ int get_nabos(/* Input. */ int i, /* Index (in one dimension) of spline-coef. */ int csz, /* Total # of spline-coef. */ int ssz, /* Size of spline kernel. */ /* Output. */ int *ns, /* Lowest index of overlapping neighbour. */ int *ne); /* Highest index of overlapping neighbour. */ int get_A_nzmax(/* Input. */ int ndim, int kdim[3], int sdim[3], int idim[3]); int get_AtA_nzmax(int ndim, const int nknot[3], const int ksp[3]); int n_nabo(int i, int n, int ksp); int AtranspA(/* Input. */ int *ir_in, int *jc_in, double *s_in, int m, int n, int nzmax, /* Output. */ int **ir_out_orig, /* These have to be pointers */ int *jc_out, /* to pointers to allow for */ double **s_out_orig); /* realloc. */ int AtranspB(/* Input. */ int *ir_inA, int *jc_inA, double *s_inA, int mA, int nA, int *ir_inB, int *jc_inB, double *s_inB, int mB, int nB, int nzmax, /* Output. */ int **ir_out_orig, /* These have to be pointers */ int *jc_out, /* to pointers to allow for */ double **s_out_orig); /* realloc. */ double find_val(int *a, int n, int key, double *val); int cmpf(const void *el1, const void *el2); int fnirt_zoom_field(/* input */ int ndim, int oksp[3], int ocdim[3], int nksp[3], int idim[3], double *oc, /* Output */ double *nc); int fnirt_zoom_field_by2(/* Input */ int ndim, int ksp[3], int ocdim[3], int idim[3], int zdim, double *oc, /* Output */ double **nc); #ifdef __cplusplus } #endif #endif