EddyKernels.h

#include "hip/hip_runtime.h"
/////////////////////////////////////////////////////////////////////
///
/// \file EddyKernels.h
/// \brief Declarations of 
///
/// \author Jesper Andersson
/// \version 1.0b, Feb., 2013.
/// \Copyright (C) 2012 University of Oxford 
///
/////////////////////////////////////////////////////////////////////

#ifndef EddyKernels_h
#define EddyKernels_h

#include <string>
#include <hip/hip_runtime.h>

namespace EddyKernels {

#define MAX_IMA_SIZE 512
enum ExtrapType { CONSTANT = 0, PERIODIC = 1, MIRROR = 2};

__global__ void linear_ec_field(float *ec_field, 
				int xsz, int ysz, int zsz, 
				float xvxs, float yvxs, float zvxs,
				const float *ep, int npar,
				int max_id);

__global__ void quadratic_ec_field(float *ec_field, 
				   int xsz, int ysz, int zsz, 
				   float xvxs, float yvxs, float zvxs,
				   const float *ep, int npar,
				   int max_id);

__global__ void cubic_ec_field(float *ec_field, 
			       int xsz, int ysz, int zsz, 
			       float xvxs, float yvxs, float zvxs,
			       const float *ep, int npar,
			       int max_id);

__global__ void weighted_mean_ec_field(float *cur_field, float *prev_field, 
				       int xsz, int ysz, int zsz, 
				       int *mb_groups,                  // mb_groups[i] gives group # for slice i
				       float *cur_wgt, float *prev_wgt,
				       int max_id);

__global__ void make_coordinates(int xsz, int ysz, int zsz, 
				 float *xcoord, float *ycoord, float *zcoord, 
				 int max_id);

__global__ void affine_transform_coordinates(int   xsz, int   ysz, int   zsz,
					     float A11, float A12, float A13, float A14,
					     float A21, float A22, float A23, float A24,
					     float A31, float A32, float A33, float A34,
					     float *xcoord, float *ycoord, float *zcoord, 
					     bool tec, int   max_id);

__global__ void slice_wise_affine_transform_coordinates(int   xsz, int   ysz, int   zsz, const float *A,
							float *xcoord, float *ycoord, float *zcoord, 
							bool tec, int   max_id);

__global__ void general_transform_coordinates(int   xsz, int   ysz, int   zsz,
					      const float *xfield, const float *yfield, const float *zfield, 
					      float A11, float A12, float A13, float A14,
					      float A21, float A22, float A23, float A24,
					      float A31, float A32, float A33, float A34,
					      float M11, float M12, float M13, float M14, 
					      float M21, float M22, float M23, float M24, 
					      float M31, float M32, float M33, float M34, 
					      float *xcoord, float *ycoord, float *zcoord, 
					      bool tec, int   max_id);

__global__ void slice_wise_general_transform_coordinates(int   xsz, int   ysz, int   zsz,
							 const float *xfield, const float *yfield, 
							 const float *zfield, const float *A,
							 const float *M, float *xcoord, 
							 float *ycoord, float *zcoord, 
							 bool tec, int   max_id);

__global__ void slice_to_vol_xyz_coordinates(int   xsz, int   ysz, int   zsz,
					     const float *xfield, const float *yfield, 
					     const float *zfield, const float *M1,
					     const float *R, const float *M2, 
					     float *xcoord, float *ycoord, float *zcoord, 
					     float *zvolume, bool tec, int max_id);

__global__ void slice_to_vol_z_coordinates(int   xsz, int   ysz, int   zsz,
					   const float *xfield, const float *yfield, 
					   const float *zfield, const float *M1,
					   const float *R, const float *M2, 
					   float *xcoord, float *ycoord, float *zcoord, 
					   bool tec, int max_id);

__global__ void get_mask(int xsz, int ysz, int zsz,
			 int epvx, int epvy, int epvz, 
			 const float *xcoord, const float *ycoord, const float *zcoord, 
			 float *mask, 
			 int max_id);

__global__ void make_deriv(int xsz, int ysz, int zsz,
			   const float *xcoord, const float *ycoord, const float *zcoord, 
			   const float *xgrad, const float *ygrad, const float *zgrad,
			   const float *base, const float *jac, const float *basejac,
			   float dstep,
			   float *deriv, 
			   int max_id);

__global__ void spline_interpolate(int         xsz,
				   int         ysz,
				   int         zsz,
				   const float *spcoef,
				   const float *xcoord, 
				   const float *ycoord, 
				   const float *zcoord, 
				   int         sizeT,
				   int         bc,
				   float       *ima);

__global__ void spline_interpolate(int   xsz,
				   int   ysz,
				   int   zsz,
				   const float *inima,
				   const float *xcoord, 
				   const float *ycoord, 
				   const float *zcoord, 
				   int         sizeT,
				   int         bc,
				   float       *oima,
				   float       *xd,
				   float       *yd,
				   float       *zd);

__global__ void linear_interpolate(int   xsz,
				   int   ysz,
				   int   zsz,
				   const float *inima,
				   const float *xcoord, 
				   const float *ycoord, 
				   const float *zcoord, 
				   int         sizeT,
				   int         bc,
				   float       *oima);

__global__ void linear_interpolate(int   xsz,
				   int   ysz,
				   int   zsz,
				   const float *inima,
				   const float *xcoord, 
				   const float *ycoord, 
				   const float *zcoord, 
				   int         sizeT,
				   int         bc,
				   float       *oima,
				   float       *xd,
				   float       *yd,
				   float       *zd);


__global__ void cubic_spline_deconvolution(float        *data, 
					   unsigned int xsize, 
					   unsigned int ysize,
					   unsigned int zsize,
					   unsigned int dir,
					   unsigned int initn,
					   int          bc,
					   int          max_id);

__global__ void convolve_1D(// Input
			    unsigned int xsz,
			    unsigned int ysz,
			    unsigned int zsz,
			    const float  *ima,
			    const float  *krnl,
			    unsigned int krnsz,
			    unsigned int dir,
			    int          max_id,
			    // Output
			    float        *cima);

/****************************************************************//**
*  								  
*  Inverts a displacement field (in voxel units) without reference
*  to any other inverse fields.
*  
*  \param[in] dfield Displacement field in units of voxels. It is 
*  assumed that the displacements are in the fastest changing direction (x)
*  \param[in] inmask Mask indicating where the dfield is valid
*  \param[in] xsz Size of fields in x-direction
*  \param[in] ysz Size of fields in y-direction
*  \param[out] idfield The inverted field in units of voxels
*  \param[out] omask Mask indicating where idfield is valid
*  \param[in] max_id xsz*zsz
*
********************************************************************/ 
__global__ void invert_displacement_field_x(const float  *dfield,
					    const float  *inmask,
					    unsigned int xsz, 
					    unsigned int ysz,
					    float        *idfield,
					    float        *omask,
					    int          max_id);

/****************************************************************//**
*  								  
*  Inverts a displacement field (in voxel units) _with_ reference
*  to another inverse field. The idea is that in "non-invertible" voxels
*  where there is some arbitrariness to what the "inverse" should be
*  we ensure consistency by setting the output inverse field to equal
*  the input inverse field.
*  
*  \param[in] dfield Displacement field in units of voxels. It is 
*  assumed that the displacements are in the fastest changing direction (x)
*  \param[in] inmask Mask indicating where the inidfield is valid
*  \param[in] inidfield Template inverse field. It will be used to 
*  bracket the inverse of dfield, and in the cases where the solution
*  doesn't fall in that brakcet idfield will be set to inidfield
*  \param[in] xsz Size of fields in x-direction
*  \param[in] ysz Size of fields in y-direction
*  \param[out] idfield The inverted field in units of voxels
*  \param[in] max_id xsz*zsz
*
********************************************************************/ 
__global__ void invert_displacement_field_x(const float  *dfield,
					    const float  *inmask,
					    const float  *inidfield,
					    unsigned int xsz, 
					    unsigned int ysz,
					    float        *idfield,
					    int          max_id);


/****************************************************************//**
*  								  
*  Inverts a displacement field (in voxel units) without reference
*  to any other inverse fields.
*  
*  \param[in] dfield Displacement field in units of voxels. It is 
*  assumed that the displacements are in the second fastest changing 
*  direction (y)
*  \param[in] inmask Mask indicating where the dfield is valid
*  \param[in] xsz Size of fields in x-direction
*  \param[in] ysz Size of fields in y-direction
*  \param[out] idfield The inverted field in units of voxels
*  \param[out] omask Mask indicating where idfield is valid
*  \param[in] max_id xsz*zsz
*
********************************************************************/ 
__global__ void invert_displacement_field_y(const float  *dfield,
					    const float  *inmask,
					    unsigned int xsz, 
					    unsigned int ysz,
					    float        *idfield,
					    float        *omask,
					    int          max_id);

/****************************************************************//**
*  								  
*  Inverts a displacement field (in voxel units) _with_ reference
*  to another inverse field. The idea is that in "non-invertible" voxels
*  where there is some arbitrariness to what the "inverse" should be
*  we ensure consistency by setting the output inverse field to equal
*  the input inverse field.
*  
*  \param[in] dfield Displacement field in units of voxels. It is 
*  assumed that the displacements are in the second fastest changing 
*  direction (y)
*  \param[in] inmask Mask indicating where the inidfield is valid
*  \param[in] inidfield Template inverse field. It will be used to 
*  bracket the inverse of dfield, and in the cases where the solution
*  doesn't fall in that brakcet idfield will be set to inidfield
*  \param[in] xsz Size of fields in x-direction
*  \param[in] ysz Size of fields in y-direction
*  \param[out] idfield The inverted field in units of voxels
*  \param[in] max_id xsz*zsz
*
********************************************************************/ 
__global__ void invert_displacement_field_y(const float  *dfield,
					    const float  *inmask,
					    const float  *inidfield,
					    unsigned int xsz, 
					    unsigned int ysz,
					    float        *idfield,
					    int          max_id);

__global__ void invert_displacement_field(const float  *dfield, 
					  const float  *inmask,
					  unsigned int xsize, 
					  unsigned int ysize,
					  unsigned int zsize,
					  unsigned int dir,
					  float        *idfield,
					  float        *omask,
					  int          max_id);

__global__ void slice_modulate_deriv(const float  *inima,
				     const float  *mask,
				     unsigned int xsz,
				     unsigned int ysz,
				     unsigned int zsz,
				     const float  *mod,
				     float        *oima,
				     int          max_id);

__global__ void valid_voxels(unsigned int xsize,
			     unsigned int ysize,
			     unsigned int zsize,
			     bool         xval,
			     bool         yval,
			     bool         zval,
			     const float  *x,
			     const float  *y,
			     const float  *z,
			     int          max_id,
			     float        *mask);

__global__ void implicit_coord_sub(unsigned int xs,
				   unsigned int ys,
				   unsigned int zs,
				   float        *x,
				   float        *y,
				   float        *z,
				   int          max_id);

__global__ void subtract_multiply_and_add_to_me(const float  *pv,
						const float  *nv,
						float        a,
						int          max_id,
						float        *out);

__global__ void subtract_square_and_add_to_me(const float  *pv,
					      const float  *nv,
					      int          max_id,
					      float        *out);

__global__ void make_deriv_first_part(int xsz, int ysz, int zsz,
				      const float *xcoord, const float *ycoord, const float *zcoord, 
				      const float *xgrad, const float *ygrad, const float *zgrad,
				      const float *base, const float *jac, const float *basejac,
				      float dstep,
				      float *deriv, 
				      int max_id);

__global__ void make_deriv_second_part(int xsz, int ysz, int zsz,
				       const float *xcoord, const float *ycoord, const float *zcoord, 
				       const float *xgrad, const float *ygrad, const float *zgrad,
				       const float *base, const float *jac, const float *basejac,
				       float dstep,
				       float *deriv, 
				       int max_id);

__global__ void sample_derivs_along_x(int xsz, int ysz, int zsz, 
				      const float  *ima, 
				      bool         add_one,
				      ExtrapType   ep,
				      float        *deriv, 
				      int          max_id);

__global__ void masked_sample_derivs_along_x(int xsz, int ysz, int zsz, 
					     const float  *ima,
					     const float  *mask,
					     bool         add_one,
					     ExtrapType   ep,
					     float        *deriv, 
					     int          max_id);

__global__ void sample_derivs_along_y(int xsz, int ysz, int zsz, 
				      const float  *ima, 
				      bool         add_one,
				      ExtrapType   ep,
				      float        *deriv, 
				      int          max_id);

__global__ void masked_sample_derivs_along_y(int xsz, int ysz, int zsz, 
					     const float  *ima,
					     const float  *mask,
					     bool         add_one,
					     ExtrapType   ep,
					     float        *deriv, 
					     int          max_id);

__global__ void make_mask_from_stack(const float   *inmask,
				     const float   *zcoord,
				     unsigned int  xsz,
				     unsigned int  ysz,
				     unsigned int  zsz,
				     float         *omask);

__global__ void transfer_y_hat_to_volume(const float   *yhat,
					 unsigned int  xsz,
					 unsigned int  ysz,
					 unsigned int  zsz,
					 unsigned int  y,
					 float         *vol);

__global__ void TransferAndCheckSorting(const float  *origz,
					unsigned int xsz,
					unsigned int ysz,
					unsigned int zsz,
					float        *sortz,
					unsigned int *flags);

__global__ void TransferVolumeToVectors(const float  *orig,
					unsigned int xsz,
					unsigned int ysz,
					unsigned int zsz,
					float        *trgt);

__global__ void SortVectors(const unsigned int  *indx,
			    unsigned int        nindx,
			    unsigned int        zsz,
			    float               *key,
			    float               *vec2);

__global__ void LinearInterpolate(const float    *zcoord,
				  const float    *val,
				  unsigned int   zsz,
				  float          *ival);

__global__ void TransferColumnsToVolume(const float    *zcols,
					unsigned int   xsz,
					unsigned int   ysz,
					unsigned int   zsz,
					float          *vol);

__global__ void MakeWeights(const float  *zcoord,
			    unsigned int xsz,
			    unsigned int zsz,
			    unsigned int j,
			    float        *weight);

__global__ void InsertWeights(const float  *wvec,
			      unsigned int j,
			      unsigned int xsz,
			      unsigned int ysz,
			      unsigned int zsz,
			      float        *wvol);

__global__ void MakeDiagwpVecs(const float *pred,
			       const float *wgts,
			       unsigned int xsz,
			       unsigned int ysz,
			       unsigned int zsz,
			       unsigned int j,
			       float        *diagwp);

__global__ void CopyAndMultiply(const float *src,
				int         max_id,
				float       val,
				float       *trgt);

} // End namespace EddyKernels

// Dead code

/*

__global__ void x_modulate_deriv(const float  *inima,
				 const float  *mask,
				 unsigned int xsz,
				 unsigned int ysz,
				 unsigned int zsz,
				 float        vxs,
				 float        *oima,
				 int          max_id);

__global__ void y_modulate_deriv(const float  *inima,
				 const float  *mask,
				 unsigned int xsz,
				 unsigned int ysz,
				 unsigned int zsz,
				 float        vxs,
				 float        *oima,
				 int          max_id);

__global__ void z_modulate_deriv(const float  *inima,
				 const float  *mask,
				 unsigned int xsz,
				 unsigned int ysz,
				 unsigned int zsz,
				 float        vxs,
				 float        *oima,
				 int          max_id);

__global__ void get_lower_bound_of_inverse_x(const float  *dfield,
					     const float  *inmask,
					     unsigned int xsz, 
					     unsigned int ysz,
					     unsigned int zsz,
					     int          *lb,
					     float        *omask,
					     int          max_id);

__global__ void get_lower_bound_of_inverse_y(const float  *dfield,
					     const float  *inmask,
					     unsigned int xsz, 
					     unsigned int ysz,
					     unsigned int zsz,
					     int          *lb,
					     float        *omask,
					     int          max_id);

__global__ void invert_displacement_field_x(const float  *dfield,
					    const float  *inmask,
					    const int    *lb,
					    unsigned int xsz, 
					    unsigned int ysz,
					    unsigned int zsz,
					    float        *idfield,
					    int          max_id);

__global__ void invert_displacement_field_y(const float  *dfield,
					    const float  *inmask,
					    const int    *lb,
					    unsigned int xsz, 
					    unsigned int ysz,
					    unsigned int zsz,
					    float        *idfield,
					    int          max_id);

__global__ void make_deriv_first_part(int xsz, int ysz, int zsz,
				      const float *xcoord, const float *ycoord, const float *zcoord, 
				      const float *xgrad, const float *ygrad, const float *zgrad,
				      const float *base, const float *jac, const float *basejac,
				      float dstep,
				      float *deriv, 
				      int max_id);

__global__ void make_deriv_second_part(int xsz, int ysz, int zsz,
				       const float *xcoord, const float *ycoord, const float *zcoord, 
				       const float *xgrad, const float *ygrad, const float *zgrad,
				       const float *base, const float *jac, const float *basejac,
				       float dstep,
				       float *deriv, 
				       int max_id);

__global__ void XtX(unsigned int        nima,
		    unsigned int        nvox,
		    const float* const  *iptrv,
		    const float         *mask,
		    float               *XtX,
		    int                 max_id);

*/

#endif // End #ifndef EddyKernels_h