#ifndef SUMA_GEOMCOMP_INCLUDED
#define SUMA_GEOMCOMP_INCLUDED
#ifndef MAX_NCODE
#define MAX_NCODE 111
#endif
typedef enum { SUMA_SMOOTH_NOT_SET, SUMA_EQUAL, SUMA_FUJIWARA, SUMA_DESBRUN } SUMA_TAUBIN_SMOOTH_OPTIONS;
static int SUMA_SSidbg=-1; /*!< Index of node for debug */
typedef struct {
int ni;
int layer;
float off;
} SUMA_OFFSET_LL_DATUM;
typedef struct {
int N_TriIndex; /*!< Number of triangles considered */
int *TriIndex; /*!< vector (N_TriIndex x 1) of 1D indices of triangles considered */
int **IntersectedVoxels; /*!< sparse matrix (N_TriIndex x N_InteresectedVoxels[i]) containing
1D indices of voxels intersected by the triangle. For example,
triangle of index TriIndex[i] intesects N_InteresectedVoxels[i]
whose 1D indices are stored in IntersectedVoxels[i] */
int *N_IntersectedVoxels; /*!< Number of voxels intersected by some triangle */
} SUMA_VTI; /*!< Voxel Triangle Intersection Structure. Create with SUMA_CreateVTI, Destroy with SUMA_FreeVTI*/
SUMA_VTI *SUMA_CreateVTI(int N_TriIndex, int *TriIndex);
SUMA_VTI * SUMA_FreeVTI(SUMA_VTI *vti);
SUMA_VTI *SUMA_GetVoxelsIntersectingTriangle( SUMA_SurfaceObject *SO, SUMA_VOLPAR *VolPar, float *NodeIJKlist,
SUMA_VTI *vti);
int SUMA_isSelfIntersect(SUMA_SurfaceObject *SO, int FullCount, byte * report);
int SUMA_VoxelNeighbors (int ijk, int ni, int nj, int nk, SUMA_VOX_NEIGHB_TYPES ntype, int *nl);
byte *SUMA_FillToVoxelMask(byte *ijkmask, int ijkseed, int ni, int nj, int nk, int *N_in, byte *usethisisin);
SUMA_Boolean SUMA_VoxelsInBox(int *voxelsijk, int *N_in, float *c1, float *c2);
SUMA_SurfaceObject *SUMA_Patch2Surf(float *NodeList, int N_NodeList, int *PatchFaces, int N_PatchFaces, int PatchDim);
SUMA_PATCH * SUMA_getPatch ( int *NodesSelected, int N_Nodes,
int *Full_FaceSetList, int N_Full_FaceSetList,
SUMA_MEMBER_FACE_SETS *Memb, int MinHits);
SUMA_Boolean SUMA_freePatch (SUMA_PATCH *Patch);
SUMA_Boolean *SUMA_MaskOfNodesInPatch(SUMA_SurfaceObject *SO, int *N_NodesUsedInPatch);
SUMA_BRANCH * SUMA_FindBranch (int ** InterMat, int N_InterMat, float ** InterNodes, int ** NodeLoc_in_InterMat, int verbose, int * WBsz);
SUMA_SURF_PLANE_INTERSECT *SUMA_Surf_Plane_Intersect (SUMA_SurfaceObject *SO, float *PlaneEq);
SUMA_ROI_DATUM *SUMA_Surf_Plane_Intersect_ROI (SUMA_SurfaceObject *SO, int Nfrom, int Nto, float *P);
void SUMA_WeldBranches ( SUMA_BRANCH *branch, int *sz_Branch, int brIndx1, int brIndx2 , int brEnd1, int brEnd2 );
float * SUMA_Plane_Equation (float * P1, float *P2, float *P3, float *thiseq);
int SUMA_Find_Edge_Nhost (SUMA_EDGE_LIST *EL, int *IsInter, int N_IsInter, int *kedge, int Nhost);
SUMA_Boolean SUMA_Mark_Tri (SUMA_EDGE_LIST *EL, int E1, int iBranch, int *TriBranch, int *IsInter, int *N_IsInter, int *VisitationOrder, int *ivisit);
int * SUMA_Dijkstra (SUMA_SurfaceObject *SO, int Nx, int Ny, SUMA_Boolean *isNodeInMesh, int *N_isNodeInMesh, int Method_Number, float *Lfinal, int *N_Path);
void SUMA_free_SPI (SUMA_SURF_PLANE_INTERSECT *SPI);
SUMA_SURF_PLANE_INTERSECT * SUMA_Allocate_SPI (SUMA_SurfaceObject *SO);
SUMA_TRI_BRANCH* SUMA_AssignTriBranch (SUMA_SurfaceObject *SO, SUMA_SURF_PLANE_INTERSECT *SPI, int Nx, int *BranchCount, SUMA_Boolean DoCopy);
SUMA_Boolean SUMA_show_STB (SUMA_TRI_BRANCH *B, FILE *Out);
void SUMA_free_STB (SUMA_TRI_BRANCH *Bv, int N_Bv);
SUMA_Boolean SUMA_Show_SPI (SUMA_SURF_PLANE_INTERSECT *SPI, FILE * Out, SUMA_SurfaceObject *SO);
int *SUMA_NodePath_to_EdgePath (SUMA_EDGE_LIST *EL, int *Path, int N_Path, int *N_Edge);
int *SUMA_NodePath_to_TriPath_Inters_OLD (SUMA_SurfaceObject *SO, SUMA_TRI_BRANCH *Bv, int *Path, int N_Path, int *N_Tri);
int *SUMA_NodePath_to_TriPath_Inters ( SUMA_SurfaceObject *SO, SUMA_SURF_PLANE_INTERSECT *SPI, int *nPath, int N_nPath, int *N_tPath);
int * SUMA_IntersectionStrip (SUMA_SurfaceObject *SO, SUMA_SURF_PLANE_INTERSECT *SPI, int *nPath, int N_nPath, float *dinters, float dmax, int *N_tPath);
SUMA_Boolean SUMA_FromIntEdgeToIntEdge (int Tri, int E1, int E2, SUMA_EDGE_LIST *EL, SUMA_SURF_PLANE_INTERSECT *SPI, int Ny, SUMA_Boolean *Visited, float *d, float dmax, int *tPath, int *N_tPath);
SUMA_Boolean SUMA_isSameEdge (SUMA_EDGE_LIST *EL, int E1, int E2);
SUMA_CONTOUR_EDGES *SUMA_GetContour (SUMA_SurfaceObject *SO, int *Nodes, int N_Node, int *N_ContEdges, int mode, SUMA_PATCH *UseThisPatch);
SUMA_Boolean SUMA_ShowPatch (SUMA_PATCH *Patch, FILE *Out) ;
void SUMA_Set_OffsetDebugNode (int d);
SUMA_Boolean SUMA_getoffsets (int n, SUMA_SurfaceObject *SO, float *Off, float lim);
SUMA_Boolean SUMA_getoffsets2 (int n, SUMA_SurfaceObject *SO, float lim, SUMA_GET_OFFSET_STRUCT *OffS, int * CoverThisNode, int N_CoverThisNode);
DList * SUMA_getoffsets_ll (int n, SUMA_SurfaceObject *SO, float lim, int *CoverThisNode, int N_CoverThisNode);
SUMA_GET_OFFSET_STRUCT *SUMA_Initialize_getoffsets (int N_Node);
SUMA_Boolean SUMA_AddNodeToLayer (int n, int LayInd, SUMA_GET_OFFSET_STRUCT *OffS);
SUMA_GET_OFFSET_STRUCT * SUMA_Free_getoffsets (SUMA_GET_OFFSET_STRUCT *OffS);
SUMA_Boolean SUMA_Recycle_getoffsets (SUMA_GET_OFFSET_STRUCT *OffS);
float ** SUMA_CalcNeighbDist (SUMA_SurfaceObject *SO);
float ** SUMA_Chung_Smooth_Weights (SUMA_SurfaceObject *SO);
float * SUMA_Chung_Smooth (SUMA_SurfaceObject *SO, float **wgt,
int N_iter, float FWHM, float *fin,
int vpn, SUMA_INDEXING_ORDER d_order, float *fout_user,
SUMA_COMM_STRUCT *cs, byte *nmask, byte strict_mask);
SUMA_Boolean SUMA_Chung_Smooth_dset (SUMA_SurfaceObject *SO, float **wgt,
int N_iter, float FWHM, SUMA_DSET *dset,
SUMA_COMM_STRUCT *cs, byte *nmask, byte strict_mask);
#define SUMA_CHUNG_KERNEL_NUMER(x,s) (exp(-(x)/(2.0*(s)*(s))))
float ** SUMA_Chung_Smooth_Weights_05 (SUMA_SurfaceObject *SO, float fwhm);
float * SUMA_Chung_Smooth_05 (SUMA_SurfaceObject *SO, float **wgt,
int N_iter, float FWHM, float *fin,
int vpn, SUMA_INDEXING_ORDER d_order, float *fout_user,
SUMA_COMM_STRUCT *cs, byte *nmask, byte strict_mask);
SUMA_Boolean SUMA_Chung_Smooth_05_dset (SUMA_SurfaceObject *SO, float **wgt,
int N_iter, float FWHM, SUMA_DSET *dset,
SUMA_COMM_STRUCT *cs, byte *nmask, byte strict_mask);
SUMA_Boolean SUMA_Taubin_Smooth_TransferFunc (float l, float m, int N, FILE *Out);
SUMA_Boolean SUMA_Taubin_Smooth_Coef (float k, float *l, float *m);
void SUMA_Set_Taubin_Weights(SUMA_TAUBIN_SMOOTH_OPTIONS tb);
byte SUMA_Get_Taubin_Weights(void);
void SUMA_Set_SurfSmooth_NodeDebug(int n);
float ** SUMA_Taubin_Desbrun_Smooth_Weights (SUMA_SurfaceObject *SO, float *NewNodeList, float ***UseThisWeight);
float ** SUMA_Taubin_Fujiwara_Smooth_Weights (SUMA_SurfaceObject *SO, float *NewNodeList, float ***UseThisWeight);
float * SUMA_Taubin_Smooth (SUMA_SurfaceObject *SO, float **wgt,
float lambda, float mu, float *fin,
int N_iter, int vpn, SUMA_INDEXING_ORDER d_order,
float *fout_user, SUMA_COMM_STRUCT *cs,
byte *nmask, byte strict_mask);
SUMA_Boolean SUMA_ApplyAffine (float *NodeList, int N_Node, float M[][4], float *center);
float *SUMA_NN_GeomSmooth( SUMA_SurfaceObject *SO, int Niter, float *fin_orig,
int vpn, SUMA_INDEXING_ORDER d_order, float *fout_final_user,
SUMA_COMM_STRUCT *cs, byte *nmask, byte strict_mask);
SUMA_Boolean SUMA_EquateSurfaceSize(SUMA_SurfaceObject *SO, SUMA_SurfaceObject *SOref, float max_off, SUMA_COMM_STRUCT *cs);
SUMA_Boolean SUMA_EquateSurfaceVolumes(SUMA_SurfaceObject *SO, SUMA_SurfaceObject *SOref, float perc_tol, SUMA_COMM_STRUCT *cs);
SUMA_Boolean SUMA_EquateSurfaceAreas(SUMA_SurfaceObject *SO, SUMA_SurfaceObject *SOref, float perc_tol, SUMA_COMM_STRUCT *cs);
double SUMA_Mesh_Volume(SUMA_SurfaceObject *SO, int *FSI, int N_FaceSet) ;
double SUMA_Mesh_Area(SUMA_SurfaceObject *SO, int *FSI, int N_FaceSet) ;
double SUMA_Pattie_Volume (SUMA_SurfaceObject *SO1, SUMA_SurfaceObject *SO2, int *Nodes, int N_Node, SUMA_SurfaceObject *UseThisSO, int minhits);
double SUMA_NewAreaAtRadius(SUMA_SurfaceObject *SO, double r, double Rref, float *tmpList);
SUMA_Boolean SUMA_ProjectSurfaceToSphere(SUMA_SurfaceObject *SO, SUMA_SurfaceObject *SOref, float radius, SUMA_COMM_STRUCT *cs);
SUMA_OFFSET_STRUCT *SUMA_FormNeighbOffset ( SUMA_SurfaceObject *SO, float OffsetLim, const char *opts, byte *nmask, float FWHM);
SUMA_OFFSET_STRUCT * SUMA_free_NeighbOffset (SUMA_SurfaceObject *SO, SUMA_OFFSET_STRUCT *OffS_out);
float *SUMA_Offset_GeomSmooth( SUMA_SurfaceObject *SO, int N_iter, float Offestlim, float *fin_orig,
int vpn, SUMA_INDEXING_ORDER d_order, float *fout_final_user,
SUMA_COMM_STRUCT *cs);
SUMA_Boolean SUMA_GetOffset2Offset (SUMA_GET_OFFSET_STRUCT *GOS, SUMA_OFFSET_STRUCT *OS);
char * SUMA_ShowOffset_ll_Info (DList *list, int detail);
char * SUMA_ShowOffset_Info (SUMA_GET_OFFSET_STRUCT *OffS, int detail);
/* Begin function prototypes for VolData.c */
THD_fvec3 SUMA_THD_3dfind_to_3dmm( SUMA_SurfaceObject *SO, THD_fvec3 iv );
THD_fvec3 SUMA_THD_3dfind_to_3dmm_vp( SUMA_VOLPAR *vp, THD_fvec3 iv );
THD_fvec3 SUMA_THD_3dind_to_3dmm( SUMA_SurfaceObject *SO, THD_ivec3 iv );
THD_fvec3 SUMA_THD_3dmm_to_3dfind( SUMA_SurfaceObject *SO , THD_fvec3 fv );
THD_ivec3 SUMA_THD_3dmm_to_3dind( SUMA_SurfaceObject *SO , THD_fvec3 fv );
THD_ivec3 SUMA_THD_3dmm_to_3dind_warn( SUMA_SurfaceObject *SO , THD_fvec3 fv, int *out );
THD_fvec3 SUMA_THD_3dmm_to_dicomm( int xxorient, int yyorient, int zzorient , THD_fvec3 imv );
THD_fvec3 SUMA_THD_dicomm_to_3dmm( SUMA_SurfaceObject *SO , THD_fvec3 dicv );
void SUMA_orcode_to_orstring (int xxorient, int yyorient, int zzorient, char *orstr);
void SUMA_sizeto3d_2_deltaHEAD(THD_ivec3 orient, THD_fvec3 *delta);
void SUMA_originto3d_2_originHEAD(THD_ivec3 orient, THD_fvec3 *origin);
SUMA_Boolean SUMA_vec_3dfind_to_3dmm (float *NodeList, int N_Node, SUMA_VOLPAR *VolPar);
SUMA_Boolean SUMA_vec_3dmm_to_3dfind (float *NodeList, int N_Node, SUMA_VOLPAR *VolPar);
SUMA_Boolean SUMA_vec_dicomm_to_3dfind (float *NodeList, int N_Node, SUMA_VOLPAR *VolPar);
SUMA_Boolean SUMA_vec_3dfind_to_dicomm (float *NodeList, int N_Node, SUMA_VOLPAR *VolPar);
SUMA_Boolean SUMA_vec_3dmm_to_dicomm (float *NodeList, int N_Node, SUMA_VOLPAR *VolPar);
SUMA_Boolean SUMA_vec_dicomm_to_3dmm (float *NodeList, int N_Node, SUMA_VOLPAR *VolPar);
SUMA_Boolean SUMA_CoordChange (char *orc_in, char *orc_out, float *XYZ, int N_xyz);
int SUMA_flip_orient(int xxorient);
int SUMA_ok_orstring (char *orstr);
SUMA_Boolean SUMA_orstring_to_orcode (char *orstr, int *orient);
int SUMA_Subdivide_Mesh(float **NodeListp, int *N_Node, int **FaceSetListp, int *N_FaceSet, float maxarea);
int SUMA_OrientTriangles (float *NodeList, int N_Node, int *FaceSetList, int N_FaceSet, int orient, int Force);
SUMA_Boolean SUMA_Offset_Smooth_dset( SUMA_SurfaceObject *SO,
float FWHM, float OffsetLim,
int N_iter,
SUMA_DSET *dset,
SUMA_COMM_STRUCT *cs, byte *nmask, byte strict_mask);
float SUMA_estimate_FWHM_1dif( SUMA_SurfaceObject *SO, float *fim , byte *nmask, int nodup );
float *SUMA_estimate_dset_FWHM_1dif(SUMA_SurfaceObject *SO, SUMA_DSET *dset,
int *icols, int N_icols, byte *nmask,
int nodup, char *options);
SUMA_Boolean SUMA_NewSurfaceRadius(SUMA_SurfaceObject *SO, double r, float *Center);
void SUMA_SetDbgFWHM(int i);
int SUMA_GetDbgFWHM(void);
SUMA_Boolean SUMA_CenterOfSphere(double *p1, double *p2, double *p3, double *p4, double *c);
SUMA_Boolean SUMA_GetCenterOfSphereSurface(SUMA_SurfaceObject *SO, int Nquads, double *cs, double *cm);
/* End function prototypes for VolData.c */
/* Begin function prototypes for SUMA_ConvexHull.c */
int SUMA_qhull_wrap( int npt , float * xyz , int ** ijk , int fliporient);
/* End function prototypes for SUMA_ConvexHull.c */
#endif
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