#include "SUMA_suma.h"

void usage_SurfToSurf (SUMA_GENERIC_ARGV_PARSE *ps, int detail)
{
      static char FuncName[]={"usage_SurfToSurf"};
      char * s = NULL, *sio=NULL, *st = NULL, *sts = NULL;
      int i;
      s = SUMA_help_basics();
      sio  = SUMA_help_IO_Args(ps);
      printf ( 
"\n"
"Usage: SurfToSurf <-i_TYPE S1> [<-sv SV1>]\n"
"                  <-i_TYPE S2> [<-sv SV1>]\n"
"                  [<-prefix PREFIX>]\n"
"                  [<-output_params PARAM_LIST>]\n"
"                  [<-node_indices NODE_INDICES>]\n"
"                  [<-proj_dir PROJ_DIR>]\n"
"                  [<-data DATA>]\n"
"                  [<-node_debug NODE>]\n"
"                  [<-debug DBG_LEVEL>]\n"
"                  [-make_consistent]\n"
"                  [<-dset DSET>]\n"
"                  [<-mapfile MAP_INFO>]\n"
" \n"
"  This program is used to interpolate data from one surface (S2)\n"
" to another (S1), assuming the surfaces are quite similar in\n"
" shape but having different meshes (non-isotopic).\n"
" This is done by projecting each node (nj) of S1 along the normal\n"
" at nj and finding the closest triangle t of S2 that is intersected\n"
" by this projection. Projection is actually bidirectional.\n"
" If such a triangle t is found, the nodes (of S2) forming it are \n"
" considered to be the neighbors of nj.\n" 
" Values (arbitrary data, or coordinates) at these neighboring nodes\n"
" are then transferred to nj using barycentric interpolation or \n"
" nearest-node interpolation.\n"
" Nodes whose projections fail to intersect triangles in S2 are given\n"
" nonsensical values of -1 and 0.0 in the output.\n" 
"\n"
" Mandatory input:\n"
"  Two surfaces are required at input. See -i_TYPE options\n"
"  below for more information. \n"
"\n"
" Optional input:\n"
"  -prefix PREFIX: Specify the prefix of the output file.\n"
"                  The output file is in 1D format at the moment.\n"
"                  Default is SurfToSurf\n"
"  -output_params PARAM_LIST: Specify the list of mapping\n"
"                             parameters to include in output\n"
"     PARAM_LIST can have any or all of the following:\n"
"        NearestTriangleNodes: Use Barycentric interpolation (default)\n"
"                              and output indices of 3 nodes from S2\n"
"                              that neighbor nj of S1\n"
"        NearestNode: Use only the closest node from S2 (of the three \n"
"                     closest neighbors) to nj of S1 for interpolation\n"
"                     and output the index of that closest node.\n"
"        NearestTriangle: Output index of triangle t from S2 that\n"
"                         is the closest to nj along its projection\n"
"                         direction. \n"  
"        DistanceToSurf: Output distance (signed) from nj, along \n"
"                        projection direction to S2.\n"
"                        This is the parameter output by the precursor\n"
"                        program CompareSurfaces\n"
"        ProjectionOnSurf: Output coordinates of projection of nj onto \n"
"                          triangle t of S2.\n"
"        NearestNodeCoords: X Y Z coordinates of closest node on S2\n"
"        Data: Output the data from S2, interpolated onto S1\n"
"              If no data is specified via the -data option, then\n"
"              the XYZ coordinates of SO2's nodes are considered\n"
"              the data.\n"
"  -data DATA: 1D file containing data to be interpolated.\n"
"              Each row i contains data for node i of S2.\n"
"              You must have one row for each node making up S2.\n"
"              In other terms, if S2 has N nodes, you need N rows\n"
"              in DATA. \n"
"              Each column of DATA is processed separately (think\n"
"              sub-bricks, and spatial interpolation).\n"
"              You can use [] selectors to choose a subset \n"
"              of columns.\n"
"              If -data option is not specified and Data is in PARAM_LIST\n"
"              then the XYZ coordinates of SO2's nodes are the data.\n"
"  -dset DSET: Treat like -data, but works best with datasets, preserving\n"
"              header information in the output.\n"
"              -dset and -data are mutually exclusive.\n"
"              Also, -dset and parameter Data cannot be mixed.\n"
"  -node_indices NODE_INDICES: 1D file containing the indices of S1\n"
"                              to consider. The default is all of the\n"
"                              nodes in S1. Only one column of values is\n"
"                              allowed here, use [] selectors to choose\n"
"                              the column of node indices if NODE_INDICES\n"
"                              has multiple columns in it.\n"
"  -proj_dir PROJ_DIR: 1D file containing projection directions to use\n"
"                      instead of the node normals of S1.\n"
"                      Each row should contain one direction for each\n"
"                      of the nodes forming S1.\n"
"  -closest_possible OO: Flag allowing the substitution of the projection\n"
"                        result with the closest node that could be found\n"
"                        along any direction.\n"
"                        0: Don't do that, direction results only.\n"
"                        1: Use closest node if projection fails to hit target\n"
"                        2: Use closest node if it is at a closer distance.\n"
"                        3: Use closest and don't bother with projections.\n"
"  -make_consistent: Force a consistency check and correct triangle \n"
"                    orientation of S1 if needed. Triangles are also\n"
"                    oriented such that the majority of normals point\n"
"                    away from center of surface.\n"
"                    The program might not succeed in repairing some\n"
"                    meshes with inconsistent orientation.\n"
"  -mapfile MAP_INFO: Use the mapping from S2 to S1 that is stored in\n"
"                     MAP_INFO. MAP_INFO is a file containing the mapping\n"
"                     parameters between surfaces S2 and S1. \n"
"                     It is generated automatically by SurfToSurf when \n"
"                     -mapfile is not used, and saved under PREFIX.niml.M2M.\n"
"                     Reusing the MAP_INFO file allows for faster execution\n" 
"                     of SurfToSurf the next time around, assuming of course\n"
"                     that the two surfaces involved are the same, and that \n"
"                     only the input data differs.\n"
"               MAP_INFO is also generated by MapIcosahedron.\n"
"\n"
"  ----------------------------------------------------------------------\n"
"  Examples:\n"
"\n"
"    1. convert/interpolate original rh thickness data onto the std.60 mesh\n"
"       (apply the M2M map file originally generated by MapIcosahedron)\n"
"\n"
"       SurfToSurf -i rh.smoothwm.gii -i std.60.rh.smoothwm.gii \\\n"
"                  -mapfile std.60.sub-000_rh.niml.M2M          \\\n"
"                  -dset rh.thickness.gii.dset                  \\\n"
"                  -prefix my.std.60.sub-000.rh.thickness.\n"
"\n"
"       * consider '-output_params NearestNode' for integral data\n"
"\n"
"  ----------------------------------------------------------------------\n"
"%s"
"%s"
               "\n", sio,  s);
      SUMA_free(s); s = NULL; SUMA_free(st); st = NULL; SUMA_free(sio); sio = NULL;       
      s = SUMA_New_Additions(0, 1); printf("%s\n", s);SUMA_free(s); s = NULL;
      printf("       Ziad S. Saad SSCC/NIMH/NIH saadz@mail.nih.gov     \n"
             "       Shruti Japee LBC/NIMH/NIH  shruti@codon.nih.gov \n");
      exit(0);
}

SUMA_GENERIC_PROG_OPTIONS_STRUCT *SUMA_SurfToSurf_ParseInput(
   char *argv[], int argc, SUMA_GENERIC_ARGV_PARSE *ps)
{
   static char FuncName[]={"SUMA_BrainWrap_ParseInput"}; 
   SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt=NULL;
   int kar;
   SUMA_Boolean brk, accepting_out;
   
   SUMA_Boolean LocalHead = NOPE;

   SUMA_ENTRY;
   
   Opt = SUMA_Alloc_Generic_Prog_Options_Struct();
   kar = 1;
   brk = NOPE;
   Opt->in_1D = NULL;
   Opt->NodeDbg = -1;
   Opt->debug = 0;
   Opt->NearestNode = 0;
   Opt->NearestTriangle = 0;
   Opt->DistanceToMesh = 0;
   Opt->ProjectionOnMesh = 0;
   Opt->NearestNodeCoords = 0;
   Opt->Data = 0;
   Opt->in_name = NULL;
   Opt->out_prefix = NULL;
   Opt->fix_winding = 0;
   Opt->iopt = 0;
   Opt->oform = SUMA_NO_DSET_FORMAT;
   accepting_out = NOPE;
   while (kar < argc) { /* loop across command line options */
      /*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
      
      if (!brk && accepting_out) { 
         /* make sure you have not begun with new options */
         if (*(argv[kar]) == '-') accepting_out = NOPE;
      }
      
      if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
          usage_SurfToSurf(ps, strlen(argv[kar]) > 3 ? 2:1);
          exit (0);
      }
      
      SUMA_SKIP_COMMON_OPTIONS(brk, kar);
      
      if (!brk && (strcmp(argv[kar], "-debug") == 0))
      {
         if (kar+1 >= argc)
         {
            fprintf (SUMA_STDERR, "need a number after -debug \n");
            exit (1);
         }
         
         Opt->debug = atoi(argv[++kar]);
         brk = YUP;
      }
      
      if (!brk && (strcmp(argv[kar], "-node_debug") == 0))
      {
         if (kar+1 >= argc)
         {
            fprintf (SUMA_STDERR, "need a number after -node_debug \n");
            exit (1);
         }
         
         Opt->NodeDbg = atoi(argv[++kar]);
         brk = YUP;
      }
      
      if (!brk && (strcmp(argv[kar], "-node_indices") == 0))
      {
         if (kar+1 >= argc)
         {
            fprintf (SUMA_STDERR, "need a parameter after -node_indices \n");
            exit (1);
         }
         
         Opt->in_nodeindices = argv[++kar];
         brk = YUP;
      }
      
      if (!brk && (strcmp(argv[kar], "-closest_possible") == 0))
      {
         if (kar+1 >= argc)
         {
            fprintf (SUMA_STDERR, "need a number after -closest_possible \n");
            exit (1);
         }
         
         Opt->iopt = atoi(argv[++kar]);
         if (Opt->iopt != 0 && Opt->iopt != 1 && Opt->iopt != 2 && 
             Opt->iopt != 3) {
            SUMA_S_Errv("Must choose from 0, 1, 2, or 3 for -closest_possible."
                        " Have %d\n",
                         Opt->iopt);
            exit (1);
         } 
         brk = YUP;
      }
      
      if (!brk && (strcmp(argv[kar], "-output_params") == 0))
      {
         if (kar+1 >= argc)
         {
            fprintf (SUMA_STDERR, 
                     "need at least one parameter after output_params \n");
            exit (1);
         }
         
         accepting_out = YUP;
         brk = YUP;
      }
      
      if (!brk && accepting_out && (strcmp(argv[kar], "NearestNode") == 0)) {
         if (Opt->NearestNode < 1) Opt->NearestNode = 1;
         brk = YUP;
      }
      
      if (!brk && accepting_out && 
            (strcmp(argv[kar], "NearestTriangleNodes") == 0)) {
         if (Opt->NearestNode < 3) Opt->NearestNode = 3;
         brk = YUP;
      }
      
      if (!brk && accepting_out && (strcmp(argv[kar], "NearestTriangle") == 0)) {
         if (Opt->NearestTriangle < 1) Opt->NearestTriangle = 1;
         brk = YUP;
      }
      
      if (!brk && accepting_out && (strcmp(argv[kar], "DistanceToSurf") == 0)) {
         Opt->DistanceToMesh = 1;
         brk = YUP;
      }
      
      if (!brk && accepting_out && 
            (strcmp(argv[kar], "ProjectionOnSurf") == 0)) {
         Opt->ProjectionOnMesh = 1;
         brk = YUP;
      }
      
      if (!brk && accepting_out && 
            (strcmp(argv[kar], "NearestNodeCoords") == 0)) {
         Opt->NearestNodeCoords = 1;
         brk = YUP;
      }
      
      if (!brk && accepting_out && 
            (strcmp(argv[kar], "Data") == 0)) {
         if (Opt->Data < 0) {
            fprintf (SUMA_STDERR, 
                     "Cannot mix parameter Data with -dset option \n");
            exit (1);   
         }
         Opt->Data = 1;
         brk = YUP;
      }
      
      if (!brk && (strcmp(argv[kar], "-data") == 0))
      {
         if (kar+1 >= argc)
         {
            fprintf (SUMA_STDERR, "need a name after -data \n");
            exit (1);
         }
         ++kar;
         if (strcmp(argv[kar],"_XYZ_") == 0) { 
            /* default Opt->in_name = NULL*/
            if (Opt->in_name) {
               SUMA_SL_Err("Input already specified."
                           "Do not mix -data and -dset");
               exit (1);
            }
         } else {
            Opt->in_name = SUMA_copy_string(argv[kar]);
         }
         Opt->Data = 1;
         brk = YUP;
      }
      
      if (!brk && (strcmp(argv[kar], "-dset") == 0))
      {
         if (kar+1 >= argc)
         {
            fprintf (SUMA_STDERR, "need a name after -dset \n");
            exit (1);
         }
         ++kar;
         if (strcmp(argv[kar],"_XYZ_") == 0 || Opt->Data > 0) { 
            /* default Opt->in_name = NULL*/
            if (Opt->in_name || Opt->Data > 0) {
               SUMA_SL_Err("Input already specified."
                           "Do not mix -data and -dset."
                           "Or use parameter DATA with -dset");
               exit (1);
            }
         } else {
            Opt->in_name = SUMA_copy_string(argv[kar]);
         }
         Opt->Data = -1;
         brk = YUP;
      }
      
      if (!brk && (strcmp(argv[kar], "-prefix") == 0))
      {
         if (kar+1 >= argc)
         {
            fprintf (SUMA_STDERR, "need a name after -prefix \n");
            exit (1);
         }
         
         Opt->out_prefix = SUMA_RemoveDsetExtension_eng(argv[++kar],
                                                      &(Opt->oform));
         brk = YUP;
      }

      if (!brk && (strcmp(argv[kar], "-mapfile") == 0))
      {
         if (kar+1 >= argc)
         {
            fprintf (SUMA_STDERR, "need a name after -mapfile \n");
            exit (1);
         }
         
         Opt->s = SUMA_Extension(argv[++kar],".niml.M2M", NOPE);
         if (!SUMA_filexists(Opt->s)) {
            SUMA_S_Errv("File %s not found\n"
                         , Opt->s);
            exit(1);
         }
         brk = YUP;
      }
      
      if (!brk && (strcmp(argv[kar], "-proj_dir") == 0))
      {
         if (kar+1 >= argc)
         {
            fprintf (SUMA_STDERR, "need a name after -proj_dir \n");
            exit (1);
         }
         
         Opt->in_1D = argv[++kar];
         brk = YUP;
      }
      if (!brk && (strcmp(argv[kar], "-make_consistent") == 0))
      {
         Opt->fix_winding = 1;
         brk = YUP;
      }
      if (!brk && !ps->arg_checked[kar]) {
         fprintf (SUMA_STDERR,
                  "Error %s:\n"
                  "Option %s not understood. Try -help for usage\n", 
                  FuncName, argv[kar]);
         suggest_best_prog_option(argv[0], argv[kar]);
         exit (1);
      } else { 
         brk = NOPE;
         kar ++;
      }
   }
   
   /* set default for NearestNode if nothing has been set */
   if (Opt->NearestNode < 1) Opt->NearestNode = 3;
   
   if (!Opt->out_prefix) Opt->out_prefix = SUMA_copy_string("SurfToSurf"); 
   if (Opt->in_1D && Opt->s) {
      SUMA_S_Err("Cannot use -proj_dir along with -mapfile");
      exit(1);
   }
   SUMA_RETURN(Opt);
}

int main (int argc,char *argv[])
{/* Main */    
   static char FuncName[]={"SurfToSurf"}; 
   SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt;  
   SUMA_GENERIC_ARGV_PARSE *ps=NULL;
   SUMA_SurfaceObject *SO1=NULL, *SO2 = NULL;
   SUMA_SurfSpecFile *Spec = NULL;
   SUMA_M2M_STRUCT *M2M = NULL;
   int N_Spec=0, *nodeind = NULL, N_nodeind, icol, i, j;
   MRI_IMAGE *im = NULL, *im_data=NULL;
   int nvec=0, ncol=0, nvec_data=0, ncol_data=0, Nchar=0;
   float *far = NULL, *far_data=NULL, *dt = NULL, *projdir=NULL;
   char *outname = NULL, *s=NULL, sbuf[100];
   void *SO_name = NULL;   
   FILE *outptr=NULL;
   SUMA_Boolean exists = NOPE;
   SUMA_INDEXING_ORDER d_order = SUMA_NO_ORDER;
   SUMA_STRING *SS=NULL;
   SUMA_Boolean LocalHead = NOPE;

   SUMA_STANDALONE_INIT;
   SUMA_mainENTRY;

   /* Allocate space for DO structure */
   SUMAg_DOv = SUMA_Alloc_DisplayObject_Struct (SUMA_MAX_DISPLAYABLE_OBJECTS);
   ps = SUMA_Parse_IO_Args(argc, argv, "-i;-t;-spec;-s;-sv;-o;");
   
   Opt = SUMA_SurfToSurf_ParseInput (argv, argc, ps);
   if (argc < 2) {
      SUMA_S_Err("Too few options");
      usage_SurfToSurf(ps, 0);
      exit (1);
   }
   

   /* if output surface requested, check on pre-existing file */
   if (ps->o_N_surfnames) {
      SO_name = SUMA_Prefix2SurfaceName(ps->o_surfnames[0], 
                                        NULL, NULL, ps->o_FT[0], &exists);
      if (exists) {
         fprintf(SUMA_STDERR,
                  "Error %s:\nOutput file(s) %s* on disk.\n"
                  "Will not overwrite.\n", FuncName, ps->o_surfnames[0]);
         exit(1);
      }
   } 
   
   if (Opt->debug > 2) LocalHead = YUP;
   outname = SUMA_append_extension(Opt->out_prefix,".1D");
   if (SUMA_filexists(outname) && !THD_ok_overwrite()) {
      fprintf(SUMA_STDERR,"Output file %s exists.\n", outname);
      exit(1);
   }
   
   /* Load the surfaces from command line*/
   Spec = SUMA_IO_args_2_spec(ps, &N_Spec);
   if (N_Spec != 1) {
      SUMA_S_Err( "Multiple spec at input.\n"
                  "Do not mix surface input types together\n");
      exit(1);
   }

      if (Spec->N_Surfs != 2) {
      SUMA_S_Err("2 surfaces expected.");
      exit(1);
   }
   
   SO1 = SUMA_Load_Spec_Surf(Spec, 0, ps->sv[0], 0);
   if (!SO1) {
         fprintf (SUMA_STDERR,"Error %s:\n"
                              "Failed to find surface\n"
                              "in spec file. \n",
                              FuncName );
         exit(1);
   }
   if (!SUMA_SurfaceMetrics(SO1, "EdgeList|MemberFace", NULL)) { 
      SUMA_SL_Err("Failed to create edge list for SO1"); 
      exit(1);  
   }
   if (Opt->fix_winding) {
      int orient, trouble;
      if (LocalHead) 
         fprintf(SUMA_STDERR,
                  "%s: Making sure S1 is consistently orientated\n", FuncName);
      if (!SUMA_MakeConsistent (SO1->FaceSetList, SO1->N_FaceSet, 
                                SO1->EL, Opt->debug, &trouble)) {
         SUMA_SL_Err("Failed in SUMA_MakeConsistent");
      }
      if (trouble && LocalHead) {
         fprintf(SUMA_STDERR,
                     "%s: trouble value of %d from SUMA_MakeConsistent.\n"
                     "Inconsistencies were found and corrected unless \n"
                     "stderr output messages from SUMA_MakeConsistent\n"
                     "indicate otherwise.\n", FuncName, trouble);
      }
      if (LocalHead) 
         fprintf(SUMA_STDERR,"%s: Checking orientation.\n", FuncName);
      orient = SUMA_OrientTriangles (SO1->NodeList, SO1->N_Node, 
                                     SO1->FaceSetList, SO1->N_FaceSet, 
                                     1, 0, NULL, NULL);
      if (orient < 0) { 
         /* flipping was done, dump the edge list since it is not 
            automatically updated (should do that in function, 
            just like in SUMA_MakeConsistent,  shame on you) 
            
            If you revisit this section, use the newer:
            SUMA_OrientSOTriangles
         */ 
         if (SO1->EL) SUMA_free_Edge_List(SO1->EL); SO1->EL = NULL; 
         if (!SUMA_SurfaceMetrics(SO1, "EdgeList", NULL)) { 
            SUMA_SL_Err("Failed to create edge list for SO1"); exit(1);  
         }
         /* free normals, new ones needed (Normals should be flipped inside  of 
            SUMA_OrientTriangles! (just like in SUMA_MakeConsistent) ) */
         if (SO1->NodeNormList) SUMA_free(SO1->NodeNormList); 
            SO1->NodeNormList = NULL;
         if (SO1->FaceNormList) SUMA_free(SO1->FaceNormList); 
            SO1->FaceNormList = NULL;
      }
      if (!orient) { 
         fprintf(SUMA_STDERR,
                  "Error %s:\nFailed in SUMA_OrientTriangles\n", FuncName); 
      }
      if (LocalHead) {
         if (orient < 0) { SUMA_SL_Note("S1 was reoriented"); }
         else { SUMA_SL_Note("S1 was properly oriented"); }
      }
   }
  
   
   if (!SO1->NodeNormList || !SO1->FaceNormList) { 
      SUMA_LH("Node Normals"); SUMA_RECOMPUTE_NORMALS(SO1); 
   }
   if (Opt->NodeDbg >= SO1->N_Node) {
      SUMA_SL_Warn(  "node_debug index is larger than number "
                     "of nodes in surface, ignoring -node_debug.");
      Opt->NodeDbg = -1;
   }
      
   SO2 = SUMA_Load_Spec_Surf(Spec, 1, ps->sv[1], 0);
   if (!SO2) {
      fprintf (SUMA_STDERR,"Error %s:\n"
                           "Failed to find surface\n"
                           "in spec file. \n",
                           FuncName );
      exit(1);
   }  
   if (!SUMA_SurfaceMetrics(SO2, "EdgeList|MemberFace", NULL)) { 
      SUMA_SL_Err("Failed to create edge list for SO2"); exit(1);  
   }
   if (!SO2->NodeNormList || !SO2->FaceNormList) { 
      SUMA_LH("Node Normals"); SUMA_RECOMPUTE_NORMALS(SO2); 
   }
   
   if (LocalHead) { 
      SUMA_LH("Surf1");
      SUMA_Print_Surface_Object(SO1, NULL);
      SUMA_LH("Surf2");
      SUMA_Print_Surface_Object(SO2, NULL);
   }
   
   /* a select list of nodes? */
   nodeind = NULL; N_nodeind = 0;
   if (Opt->in_nodeindices) {
      im = mri_read_1D(Opt->in_nodeindices);
      if (!im) { SUMA_SL_Err("Failed to read 1D file of node indices"); exit(1);}
      far = MRI_FLOAT_PTR(im);
      N_nodeind = nvec = im->nx;
      ncol = im->ny;
      if (ncol != 1) { 
         SUMA_SL_Err("More than one column in node index input file."); exit(1);
      }
      nodeind = (int *)SUMA_calloc(nvec, sizeof(int));
      if (!nodeind) { SUMA_SL_Crit("Failed to allocate"); exit(1); }
      for (i=0;i<nvec;++i) { 
         nodeind[i] = (int)far[i]; 
         if (nodeind[i] < 0 || nodeind[i] >= SO1->N_Node) {
            fprintf(SUMA_STDERR, 
                    "Error %s:\n"
                    "A node index of %d was found in input file %s, entry %d.\n"
                    "Acceptable indices are positive and less than %d\n", 
                    FuncName, nodeind[i], Opt->in_nodeindices, i, SO1->N_Node);
            exit(1);
         }
      } 
      mri_free(im); im = NULL;   /* done with that baby */
   }
   
   /* a preset directions vector ?*/
   projdir = NULL; 
   if (Opt->in_1D) {
      im = mri_read_1D(Opt->in_1D);
      if (!im) { 
         SUMA_SL_Err("Failed to read 1D file of projection directions"); exit(1);
      }
      far = MRI_FLOAT_PTR(im);
      if (im->ny != 3) { 
         SUMA_SL_Err("Need three columns in projection directions file."); 
         exit(1); 
      }
      if (im->nx != SO1->N_Node) {
         fprintf(SUMA_STDERR, 
                  "Error %s: You must have a direction for each node in SO1.\n"
                  "%d directions found but SO1 has %d nodes.\n", 
                  FuncName, im->nx, SO1->N_Node);
         exit(1);
      }

      /* change to row major major and make it match nodeind */
      projdir = (float *)SUMA_calloc(SO1->N_Node*3, sizeof(float));
      if (!projdir) { SUMA_SL_Crit("Failed to allocate"); exit(1); }
      for (i=0; i<SO1->N_Node; ++i) {
         projdir[3*i  ] = far[i              ];
         projdir[3*i+1] = far[i+  SO1->N_Node];
         projdir[3*i+2] = far[i+2*SO1->N_Node];
      }
      mri_free(im); im = NULL;   /* done with that baby */

   }
   
   if (SO_name) {
      /* user is interpolating surface coords, check on other input insanity */
      if (nodeind) {
         fprintf( SUMA_STDERR, 
                  "Error %s: You cannot combine "
                  "option -o_TYPE with -node_indices", FuncName);
         exit(1);
      }
      if (Opt->in_name) {
         fprintf(SUMA_STDERR, 
                  "Error %s: You cannot combine option -o_TYPE with -data", 
                  FuncName);
         exit(1);
      }
   } 
   /* a 1D file containing data, or Data parameter (for XYZ)? */
   if (Opt->Data > 0) {
      if (Opt->in_name) {
         /* When you are ready to work with dsets, you should 
         checkout the function morphDsetToStd. It uses M2M */
         im_data = mri_read_1D(Opt->in_name);
         if (!im_data) { 
            SUMA_SL_Err("Failed to read 1D file of data"); exit(1);}
         far_data = MRI_FLOAT_PTR(im_data);
         nvec_data = im_data->nx;
         ncol_data = im_data->ny;
         if (nvec_data != SO2->N_Node) {
            SUMA_SL_Err("Your data file must have one row "
                        "for each node in surface 2.\n"); exit(1);
         }
         d_order = SUMA_COLUMN_MAJOR;
      } else { 
         im_data = NULL;
         far_data = SO2->NodeList;
         nvec_data = SO2->N_Node;
         ncol_data = 3;
         d_order = SUMA_ROW_MAJOR;
      }
   } else {
      /* just -dset */
   }
   
     

   
   if (!Opt->s) {
      SUMA_LH("Going for the mapping of SO1 --> SO2");
      M2M = SUMA_GetM2M_NN( SO1, SO2, nodeind, N_nodeind, 
                            projdir, 0, Opt->NodeDbg, Opt->iopt);
      SUMA_S_Notev("Saving M2M into %s\n\n",
               Opt->out_prefix);
      if (!(SUMA_Save_M2M(Opt->out_prefix, M2M))) {
         SUMA_S_Err("Failed to save M2M");
         exit(1);
      }
   } else {
      SUMA_S_Notev("Reusing mapping of SO1 --> SO2 from %s\n\n", 
               Opt->s);   
      if (!(M2M = SUMA_Load_M2M(Opt->s))) {
         SUMA_S_Errv("Failed to load %s\n", Opt->s);
         exit(1);
      }
   }

   /* Now show the mapping results for a debug node ? */
   if (Opt->NodeDbg >= 0) {
      char *s = NULL;
      s = SUMA_M2M_node_Info(M2M, Opt->NodeDbg);
      fprintf(SUMA_STDERR,"%s: Debug for node %d ([%f, %f, %f])of SO1:\n%s\n\n", 
                           FuncName, Opt->NodeDbg, 
                           SO1->NodeList[3*Opt->NodeDbg], 
                           SO1->NodeList[3*Opt->NodeDbg+1], 
                           SO1->NodeList[3*Opt->NodeDbg+2],
                           s); 
      SUMA_free(s); s = NULL;
   }
   
   /* Now please do the interpolation */
   if (Opt->Data > 0) {
      if (Opt->NearestNode > 1) 
         dt = SUMA_M2M_interpolate( M2M, far_data, ncol_data, 
                                    nvec_data, d_order, 0 );
      else if (Opt->NearestNode == 1) 
         dt = SUMA_M2M_interpolate( M2M, far_data, ncol_data, 
                                    nvec_data, d_order, 1 );
      if (!dt) {
         SUMA_SL_Err("Failed to interpolate");
         exit(1);
      }
   } else if (Opt->Data < 0) {
         SUMA_DSET *dset=NULL, *dseto=NULL;
         char *oname=NULL, *uname=NULL, *s1=NULL, *s2=NULL;
         int iform=SUMA_NO_DSET_FORMAT;
         if (Opt->NodeDbg>= 0) {
            SUMA_S_Notev("Processing dset %s\n", Opt->in_name);
         }
         iform = SUMA_NO_DSET_FORMAT;
         if (!(dset = SUMA_LoadDset_s (Opt->in_name, &iform, 0))) {
            SUMA_S_Errv("Failed to load %s\n", Opt->in_name);
            exit(1);
         }
         if (!(dseto = SUMA_morphDsetToStd ( dset, M2M, 
                                             Opt->NearestNode == 1 ? 1:0))) {
            SUMA_S_Errv("Failed to map %s\n", Opt->in_name);
            exit(1);
         }
         if (0 && !strchr(Opt->out_prefix,'/') ){
            /* Don't know what made me think that appending the
               path of the input was a good idea... */
            s1 = SUMA_append_string(
                  SUMA_FnameGet(Opt->in_name,"pa", SUMAg_CF->cwd),
                  Opt->out_prefix); 
         } else {
            s1 = SUMA_copy_string(Opt->out_prefix); 
         }
         s2 = SUMA_RemoveDsetExtension_s(
               SUMA_FnameGet(Opt->in_name,"l",SUMAg_CF->cwd), 
               SUMA_NO_DSET_FORMAT);
         uname = SUMA_append_extension(s1,s2);      
         SUMA_free(s1); SUMA_free(s2);
         oname = SUMA_WriteDset_s (uname, dseto, Opt->oform, 1, 1);
         if (Opt->NodeDbg>= 0) SUMA_S_Notev("Wrote %s\n", oname);
         if (oname) SUMA_free(oname); oname=NULL;
         if (uname) SUMA_free(uname); oname=NULL;
         if (dseto) SUMA_FreeDset(dseto); dseto = NULL;
         if (dset) SUMA_FreeDset(dset); dset = NULL;      
   }
   
   SUMA_LH("Forming the remaining output");
   outptr = fopen(outname,"w");
   if (!outptr) {
      SUMA_SL_Err("Failed to open file for output.\n");
      exit(1);
   }
   
   /* first create the header of the output */
   SS = SUMA_StringAppend(NULL, NULL);
   SS = SUMA_StringAppend_va(SS, 
      "#Mapping from nodes on surf 1 (S1) to nodes on surf 2 (S2)\n"
      "#  Surf 1 is labeled %s, idcode:%s\n"
      "#  Surf 2 is labeled %s, idcode:%s\n",
      SO1->Label, SO1->idcode_str, SO2->Label, SO2->idcode_str);
   icol = 0;
   SS = SUMA_StringAppend_va(SS, "#Col. %d:\n"
                                 "#     S1n (or nj): Index of node on S1\n"
                                 , icol); 
   ++icol;
   if (Opt->NearestNode > 1) {
      SS = SUMA_StringAppend_va(SS, 
         "#Col. %d..%d:\n"
         "#     S2ne_S1n: Indices of %d nodes on S2 \n"
         "#     that are closest neighbors of nj.\n"
         "#     The first index is that of the node on S2 that is closest \n"
         "#     to nj. If -1 then these values should be ignored because\n"
         "#     in such cases, nj's projection failed.\n" 
         , icol, icol+Opt->NearestNode-1, Opt->NearestNode); 
      icol += Opt->NearestNode;
      SS = SUMA_StringAppend_va(SS, 
         "#Col. %d..%d:\n"
         "#     S2we_S1n: Weights assigned to nodes on surf 2 (S2) \n"
         "#     that are closest neighbors of nj.\n"
         , icol, icol+Opt->NearestNode-1, Opt->NearestNode); 
      icol += Opt->NearestNode;
   } else if (Opt->NearestNode == 1) {
      SS = SUMA_StringAppend_va(SS, 
         "#Col. %d:\n"
         "#     S2ne_S1n: Index of the node on S2 (label:%s idcode:%s)\n"
         "#     that is the closest neighbor of nj.\n"
         "#     If -1 then this value should be ignored because\n"
         "#     nj's projection failed.\n" 
         , icol, SO2->Label, SO2->idcode_str); 
      ++icol;
   }
   if (Opt->NearestTriangle) { 
      SS = SUMA_StringAppend_va(SS, 
         "#Col. %d:\n"
         "#     S2t_S1n: Index of the S2 triangle that hosts node nj on S1.\n"
         "#     In other words, nj's closest projection onto S2 falls on \n"
         "#     triangle S2t_S1n\n"
         "#     If -1 then this value should be ignored because \n"
         "#     nj's projection failed.\n" 
         , icol); 
      ++icol; 
   }
   if (Opt->ProjectionOnMesh) { 
      SS = SUMA_StringAppend_va(SS, 
         "#Col. %d..%d:\n"
         "#     S2p_S1n: Coordinates of projection of nj onto S2\n"
         , icol, icol+2); 
      icol += 3; 
   }
   if (Opt->DistanceToMesh) {
      SS = SUMA_StringAppend_va(SS, 
         "#Col. %d:\n"
         "#     Closest distance from nj to S2\n"
         , icol); 
         ++icol;
   }
   if (Opt->NearestNodeCoords) {
      SS = SUMA_StringAppend_va(SS, 
         "#Col. %d .. %d:\n"
         "#     X Y Z coords of nearest node\n"
         , icol,  icol+2); 
      icol += 3; 
   }
   if (Opt->Data > 0) {
      if (!Opt->in_name) {
         SS = SUMA_StringAppend_va(SS, 
      "#Col. %d..%d:\n"
      "#     Interpolation using XYZ coordinates of S2 nodes that neighbor nj\n"
      "#     (same as coordinates of node's projection onto triangle in S2, \n"
      "#     if using barycentric interpolation)\n"
         , icol, icol+2); 
      icol += 3; 
} else {
SS = SUMA_StringAppend_va(SS, 
         "#Col. %d..%d:\n"
         "#     Interpolation of data at nodes on S2 that neighbor nj\n"
         "#     Data obtained from %s\n"
         , icol, icol+ncol_data-1, Opt->in_name);  icol += ncol_data;
      }
   } 
   s = SUMA_HistString("SurfToSurf", argc, argv, NULL);
   SS = SUMA_StringAppend_va(SS, 
                                "#History:\n"
                                "#%s\n", s); SUMA_free(s); s = NULL;
   SUMA_SS2S(SS,s);
   fprintf(outptr,"%s\n",s); SUMA_free(s); s = NULL;
   
   /* put headers atop columns */
   Nchar = 6; /* if you change this number you'll need to fix  formats below */
   for (i=0; i<icol; ++i) { 
      sprintf(sbuf,"#%s", MV_format_fval2(i, Nchar -1)); 
      fprintf(outptr,"%6s   ", sbuf); 
   }
   fprintf(outptr,"\n");
   
   /* Now put in the values, make sure you parallel columns above! */
   for (i=0; i<M2M->M1Nn; ++i) {
      fprintf(outptr,"%6s   ", MV_format_fval2(M2M->M1n[i], Nchar));
      if (Opt->NearestNode > 0) {
         for (j=0; j<Opt->NearestNode; ++j) { 
            if (j < M2M->M2Nne_M1n[i]) 
               fprintf(outptr,"%6s   ", 
                  MV_format_fval2(M2M->M2ne_M1n[i][j], Nchar)); 
            else fprintf(outptr,"%6s   ", "-1"); 
         } /* Neighboring nodes */
      } 
      if (Opt->NearestNode > 1) { /* add the weights */
         for (j=0; j<Opt->NearestNode; ++j) { 
            if (j < M2M->M2Nne_M1n[i]) 
               fprintf(outptr,"%6s   ", 
                  MV_format_fval2(M2M->M2we_M1n[i][j], Nchar)); 
            else fprintf(outptr,"%6s   ", "0.0"); 
         } 
      }
      if (Opt->NearestTriangle) {
         fprintf(outptr,"%6s   ", MV_format_fval2(M2M->M2t_M1n[i], Nchar)); 
      }
      if (Opt->ProjectionOnMesh) {
         fprintf(outptr,"%6s   ", MV_format_fval2(M2M->M2p_M1n[3*i], Nchar));
         fprintf(outptr,"%6s   ", MV_format_fval2(M2M->M2p_M1n[3*i+1], Nchar));
         fprintf(outptr,"%6s   ", MV_format_fval2(M2M->M2p_M1n[3*i+2], Nchar)); 
      }
      if (Opt->DistanceToMesh) { 
         fprintf(outptr,"%6s   ", MV_format_fval2(M2M->PD[i], Nchar)); 
      }
      if (Opt->NearestNodeCoords) {
         float x=0.0,y=0.0,z=0.0;
         int n = M2M->M2ne_M1n[i][0];
         if (n>0) {
            n = n * SO2->NodeDim;
            x = SO2->NodeList[n];
            y = SO2->NodeList[n+1];
            z = SO2->NodeList[n+2];
         }
         fprintf(outptr,"%6s   ", MV_format_fval2(x, Nchar)); 
         fprintf(outptr,"%6s   ", MV_format_fval2(y, Nchar)); 
         fprintf(outptr,"%6s   ", MV_format_fval2(z, Nchar)); 
      }
      if (dt && Opt->Data > 0) {
         if (!Opt->in_name) {
            fprintf(outptr,"%6s   ", MV_format_fval2(dt[3*i], Nchar));
            fprintf(outptr,"%6s   ", MV_format_fval2(dt[3*i+1], Nchar));
            fprintf(outptr,"%6s   ", MV_format_fval2(dt[3*i+2], Nchar));
         } else { /* Column major business */
            for (j=0; j<ncol_data; ++j) { 
               fprintf(outptr,"%6s   ", 
                     MV_format_fval2(dt[i+j*M2M->M1Nn], Nchar)); }
         }
      }
      fprintf(outptr,"\n");
   }
   
   /* do they want an output surface ? */
   if (SO_name) {
      float *tmpfv = NULL;
      SUMA_LH("Writing surface");
      tmpfv = SO1->NodeList;
      SO1->NodeList = dt;
      if (!SUMA_Save_Surface_Object (SO_name, SO1, 
                                     ps->o_FT[0], ps->o_FF[0], NULL)) {
         SUMA_S_Err("Failed to write surface object.\n");
         exit (1);
      }
      SO1->NodeList = tmpfv; tmpfv = NULL;
   }
   
   if (N_Spec) {
      int k=0; 
      for (k=0; k<N_Spec; ++k) {
         if (!SUMA_FreeSpecFields(&(Spec[k]))) {
            SUMA_S_Err("Failed to free spec fields");
         } 
      }
      SUMA_free(Spec); Spec = NULL; N_Spec = 0;
   }

   if (projdir) SUMA_free(projdir); projdir = NULL;
   if (SO_name) SUMA_free(SO_name); SO_name = NULL;   
   if (outptr) fclose(outptr); outptr = NULL;
   if (dt) SUMA_free(dt); dt = NULL;
   if (s) SUMA_free(s); s = NULL;
   if (im_data) mri_free(im_data); im_data = NULL;   /* done with the data */
   if (nodeind) SUMA_free(nodeind); nodeind = NULL;
   if (M2M) M2M = SUMA_FreeM2M(M2M);
   if (SO1) SUMA_Free_Surface_Object(SO1); SO1 = NULL;
   if (SO2) SUMA_Free_Surface_Object(SO2); SO2 = NULL;
   if (Spec) SUMA_free(Spec); Spec = NULL;
   if (ps) SUMA_FreeGenericArgParse(ps); ps = NULL;
   if (Opt) Opt = SUMA_Free_Generic_Prog_Options_Struct(Opt);
   if (!SUMA_Free_CommonFields(SUMAg_CF)) SUMA_error_message(FuncName,"SUMAg_CF Cleanup Failed!",1);
   exit(0);
   
} 
