#include "SUMA_suma.h"

SUMA_SurfaceViewer *SUMAg_cSV = NULL; /*!< Global pointer to current Surface Viewer structure*/
SUMA_SurfaceViewer *SUMAg_SVv = NULL; /*!< Global pointer to the vector containing the various Surface Viewer Structures 
                                    SUMAg_SVv contains SUMA_MAX_SURF_VIEWERS structures */
int SUMAg_N_SVv = 0; /*!< Number of SVs realized by X */
SUMA_DO *SUMAg_DOv = NULL;   /*!< Global pointer to Displayable Object structure vector*/
int SUMAg_N_DOv = 0; /*!< Number of DOs stored in DOv */
SUMA_CommonFields *SUMAg_CF = NULL; /*!< Global pointer to structure containing info common to all viewers */

#define SURFQUAL_MAX_SURF 10  /*!< Maximum number of input surfaces */

void usage_SUMA_SurfQual ()
   {
      static char FuncName[]={"usage_SUMA_SurfQual"};
      char * s = NULL;
      s = SUMA_help_basics();
      printf ( "\nUsage: A program to check the quality of surfaces.\n"
               "  SurfQual <-spec SpecFile> <-surf_A insurf> <-surf_B insurf> ...\n"
               "             <-sphere> [-self_intersect] [-prefix OUTPREF]  \n"
               "\n"
               "  Mandatory parameters:\n"
               "     -spec SpecFile: Spec file containing input surfaces.\n"
               "     -surf_X: Name of input surface X where X is a character\n"
               "              from A to Z. If surfaces are specified using two\n"
               "              files, use the name of the node coordinate file.\n"
               "  Mesh winding consistency and 2-manifold checks are performed\n"
               "  on all surfaces.\n"
               "  Optional parameters:\n"
               "     -summary: Provide summary of results to stdout\n"
               "     -self_intersect: Check if surface is self intersecting.\n"
               "                      This option is rather slow, so be patient.\n"
               "                      In the presence of intersections, the output file\n"
               "                      OUTPREF_IntersNodes.1D.dset will contain the indices\n"
               "                      of nodes forming segments that intersect the surface.\n"
               "  Most other checks are specific to spherical surfaces (see option below).\n"
               "     -sphere: Indicates that surfaces read are spherical.\n"
               "              With this option you get the following output.\n"
               "              - Absolute deviation between the distance (d) of each\n"
               "                node from the surface's center and the estimated\n"
               "                radius(r). The distances, abs (d - r), are \n"
               "                and written to the file OUTPREF_Dist.1D.dset .\n"
               "                The first column represents node index and the \n"
               "                second is the absolute distance. A colorized \n"
               "                version of the distances is written to the file \n"
               "                OUTPREF_Dist.1D.col (node index followed \n"
               "                by r g b values). A list of the 10 largest absolute\n"
               "                distances is also output to the screen.\n"
               "              - Also computed is the cosine of the angle between \n"
               "                the normal at a node and the direction vector formed\n"
               "                formed by the center and that node. Since both vectors\n"
               "                are normalized, the cosine of the angle is the dot product.\n"
               "                On a sphere, the abs(dot product) should be 1 or pretty \n"
               "                close. Nodes where abs(dot product) < 0.9 are flagged as\n"
               "                bad and written out to the file OUTPREF_BadNodes.1D.dset .\n"
               "                The file OUTPREF_dotprod.1D.dset contains the dot product \n"
               "                values for all the nodes. The files with colorized results\n"
               "                are OUTPREF_BadNodes.1D.col and OUTPREF_dotprod.1D.col .\n"
               "                A list of the bad nodes is also output to the screen for\n"
               "                convenience. You can use the 'j' option in SUMA to have\n"
               "                the cross-hair go to a particular node. Use 'Alt+l' to\n"
               "                have the surface rotate and place the cross-hair at the\n"
               "                center of your screen.\n"
               "              NOTE: For detecting topological problems with spherical\n"
               "                surfaces, I find the dot product method to work best.\n"              
               "  Optional parameters:\n"
               "     -prefix OUTPREF: Prefix of output files. If more than one surface\n"
               "                      are entered, then the prefix will have _X added\n"
               "                      to it, where X is a character from A to Z.\n"
               "                      THIS PROGRAM WILL OVERWRITE EXISTING FILES.\n"
               "                      Default prefix is the surface's label.\n"
               "\n"
               "  Comments:\n"
               "     - The colorized (.col) files can be loaded into SUMA (with the 'c' \n"
               "     option. By focusing on the bright spots, you can find trouble spots\n"
               "     which would otherwise be very difficult to locate.\n"
               "     - You should also pay attention to the messages output when the \n"
               "     surfaces are being loaded, particularly to edges (segments that \n"
               "     join 2 nodes) are shared by more than 2 triangles. For a proper\n"
               "     closed surface, every segment should be shared by 2 triangles. \n"
               "     For cut surfaces, segments belonging to 1 triangle only form\n"
               "     the edge of that surface.\n"
               "     - There are no utilities within SUMA to correct these defects.\n"
               "     It is best to fix these problems with the surface creation\n"
               "     software you are using.\n"
               "     - Some warnings may be redundant. That should not hurt you.\n"
               "%s"
               "\n", s);
       SUMA_free(s); s = 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");
       exit (0);
   }

typedef struct {
   SUMA_SO_File_Type iType;
   char *out_prefix;
   char *sv_name;
   char *surf_names[SURFQUAL_MAX_SURF];
   int N_surf;
   char *spec_file;
   char *surftype;
   int self_intersect;
   int DoSum;
} SUMA_SURFQUAL_OPTIONS;

/*!
   \brief parse the arguments for SurfQual program
   
   \param argv (char *)
   \param argc (int)
   \return Opt (SUMA_SURFQUAL_OPTIONS *) options structure.
               To free it, use 
               SUMA_free(Opt->out_prefix); 
               SUMA_free(Opt);
*/
SUMA_SURFQUAL_OPTIONS *SUMA_SurfQual_ParseInput (char *argv[], int argc)
{
   static char FuncName[]={"SUMA_SurfQual_ParseInput"}; 
   SUMA_SURFQUAL_OPTIONS *Opt=NULL;
   int kar, i, ind;
   char *outprefix;
   SUMA_Boolean brk = NOPE;
   SUMA_Boolean LocalHead = NOPE;

   SUMA_ENTRY;
   
   Opt = (SUMA_SURFQUAL_OPTIONS *)SUMA_malloc(sizeof(SUMA_SURFQUAL_OPTIONS));

   kar = 1;
   Opt->iType = SUMA_FT_NOT_SPECIFIED;
   Opt->out_prefix = NULL;
   Opt->sv_name = NULL;
   Opt->spec_file = NULL;
   Opt->N_surf = -1;
   Opt->surftype = NULL;
   Opt->self_intersect = 0;
   Opt->DoSum = 0;
   
   for (i=0; i<SURFQUAL_MAX_SURF; ++i) { Opt->surf_names[i] = NULL; }
	brk = NOPE;
   
	while (kar < argc) { /* loop accross command ine options */
		/*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
		if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
			 usage_SUMA_SurfQual();
          exit (0);
		}
		
      /* skip the options parsed in SUMA_ParseInput_basics_s */
		SUMA_SKIP_COMMON_OPTIONS(brk, kar);
      
      if (!brk && (strcmp(argv[kar], "-sphere") == 0)) {
			if (Opt->surftype) {
            SUMA_S_Err("Surface type already specified.\nOnly one type allowed.");
            exit(1);
         }
         Opt->surftype = argv[kar];
			brk = YUP;
		}
      
      if (!brk && (strcmp(argv[kar], "-self_intersect") == 0)) {
         Opt->self_intersect = 1;
			brk = YUP;
		}
      
      if (!brk && (strcmp(argv[kar], "-summary") == 0)) {
         Opt->DoSum = 1;
			brk = YUP;
		}
      
      if (!brk && (strcmp(argv[kar], "-spec") == 0)) {
         kar ++;
			if (kar >= argc)  {
		  		fprintf (SUMA_STDERR, "need argument after -spec \n");
				exit (1);
			}
			Opt->spec_file = argv[kar];
			brk = YUP;
		}
            
      if (!brk && (strcmp(argv[kar], "-prefix") == 0)) {
         kar ++;
			if (kar >= argc)  {
		  		fprintf (SUMA_STDERR, "need argument after -prefix \n");
				exit (1);
			}
			Opt->out_prefix = SUMA_copy_string(argv[kar]);
			brk = YUP;
		}
            
      if (!brk && (strncmp(argv[kar], "-surf_", 6) == 0)) {
			if (kar + 1>= argc)  {
		  		fprintf (SUMA_STDERR, "need argument after -surf_X SURF_NAME \n");
				exit (1);
			}
			ind = argv[kar][6] - 'A';
         if (ind < 0 || ind >= SURFQUAL_MAX_SURF) {
            fprintf (SUMA_STDERR, "-surf_X SURF_NAME option is out of range.\n");
				exit (1);
         }
         kar ++;
         Opt->surf_names[ind] = argv[kar];
         Opt->N_surf = ind+1;
         brk = YUP;
		}
      
      
      if (!brk) {
			fprintf (SUMA_STDERR,"Error %s:\nOption %s not understood. Try -help for usage\n", FuncName, argv[kar]);
			exit (1);
		} else {	
			brk = NOPE;
			kar ++;
		}
      
   }
   
   if (Opt->N_surf < 1) {
      SUMA_SL_Err("No surface specified.");
      exit(1);
   }
      
   SUMA_RETURN (Opt);
     
}

int main (int argc,char *argv[])
{/* Main */    
   static char FuncName[]={"SurfQual"};
   char *OutName = NULL, ext[5], *prefix = NULL, *shist=NULL;
   SUMA_SURFQUAL_OPTIONS *Opt; 
   int SO_read = -1;
   int i, cnt, trouble, consistent = -1, eu = -1, nsi = -1;
   SUMA_SurfaceObject *SO = NULL;
   SUMA_SurfSpecFile Spec;
   void *SO_name = NULL;
   SUMA_Boolean DoConv = NOPE, DoSphQ = NOPE, DoSelfInt = NOPE;   
   SUMA_SPHERE_QUALITY SSQ;

   SUMA_Boolean LocalHead = NOPE;
	
   SUMA_STANDALONE_INIT;
   SUMA_mainENTRY;
   
   
	/* Allocate space for DO structure */
	SUMAg_DOv = SUMA_Alloc_DisplayObject_Struct (SUMA_MAX_DISPLAYABLE_OBJECTS);
   
   if (argc < 4)
       {
          usage_SUMA_SurfQual();
          exit (1);
       }
   
   Opt = SUMA_SurfQual_ParseInput (argv, argc);
   
   /* read all surfaces */
   if (!SUMA_AllocSpecFields(&Spec)) { SUMA_S_Err("Failed to initialize spec fields."); exit(1); }   
   if (!SUMA_Read_SpecFile (Opt->spec_file, &Spec)) {
		fprintf(SUMA_STDERR,"Error %s: Error in SUMA_Read_SpecFile\n", FuncName);
		exit(1);
	}
   SO_read = SUMA_spec_select_surfs(&Spec, Opt->surf_names, SURFQUAL_MAX_SURF, 0);
   if ( SO_read != Opt->N_surf )
   {
	   if (SO_read >=0 )
         fprintf(SUMA_STDERR,"Error %s:\nFound %d surfaces, expected %d.\n", FuncName,  SO_read, Opt->N_surf);
      exit(1);
   }
   /* now read into SUMAg_DOv */
   if (!SUMA_LoadSpec_eng(&Spec, SUMAg_DOv, &SUMAg_N_DOv, Opt->sv_name, 0, SUMAg_CF->DsetList) ) {
	   fprintf(SUMA_STDERR,"Error %s: Failed in SUMA_LoadSpec_eng\n", FuncName);
      exit(1);
   }
  
   if (Opt->self_intersect) DoSelfInt = YUP;

   DoConv = NOPE;
   DoSphQ = NOPE;   
   if (Opt->surftype) {
      if (!strcmp(Opt->surftype, "-sphere")) { 
         DoSphQ = YUP;
      }else {
         /* Don't complain anymore, maybe winding checking is all users need */
      }
   }
   
   for (i=0; i < Opt->N_surf; ++i) {/* loop to read in surfaces */
      /* now identify surface needed */
      SO = SUMA_find_named_SOp_inDOv(Opt->surf_names[i], SUMAg_DOv, SUMAg_N_DOv);
      if (!SO) {
         fprintf (SUMA_STDERR,"Error %s:\n"
                              "Failed to find surface %s\n"
                              "in spec file. Use full name.\n",
                              FuncName, Opt->surf_names[i]);
         exit(1);
      }
      
      if (!SO->EL) SUMA_SurfaceMetrics(SO, "EdgeList", NULL);
      if (!SO->MF) SUMA_SurfaceMetrics(SO, "MemberFace", NULL);
      if (!SO->Label) SUMA_SurfaceFileName(SO, NOPE);
      
      
      /* do the quality thing based on the Opt->surftype */
      if (!Opt->out_prefix) prefix = SUMA_copy_string(SO->Label);
      else prefix = SUMA_copy_string (Opt->out_prefix);
      
      /* check the winding */
      if (!SUMA_MakeConsistent (SO->FaceSetList, SO->N_FaceSet, SO->EL, 0, &trouble)) {
         SUMA_S_Warn("Failed to make sure surface's mesh is consistently wound.\n"
                     "You should fix the mesh.\n");
         consistent = 0;
      } 
      
      if (DoConv) {
         float *Cx = NULL;
         if (Opt->N_surf > 1) {
            sprintf(ext,"_%c", 65+i);
            OutName = SUMA_append_replace_string (prefix, "_Conv_detail.1D.dset", ext, 0);
         } else { 
            OutName = SUMA_append_string (prefix, "_Conv_detail.1D.dset");
         }
         Cx = SUMA_Convexity_Engine ( SO->NodeList, SO->N_Node, 
                                      SO->NodeNormList, SO->FN, OutName);
         if (Cx) SUMA_free(Cx); Cx = NULL;
         if (OutName) SUMA_free(OutName); OutName = NULL;
      } 
      
      if (DoSphQ) {
         if (Opt->N_surf > 1) {
            sprintf(ext,"_%c", 65+i);
            OutName = SUMA_append_string (prefix, ext);
         } else { 
            OutName = SUMA_copy_string (prefix);
         }
         shist = SUMA_HistString (NULL, argc, argv, NULL);
         SSQ = SUMA_SphereQuality (SO, OutName, shist);   
         if (shist) SUMA_free(shist); shist = NULL;
         if (OutName) SUMA_free(OutName); OutName = NULL;
      }
      
   }
   
  
   if (trouble) { /* put winding problem here to make it visible */
      fprintf (SUMA_STDERR,"\n");
      SUMA_S_Warn("Mesh is not consistent, use ConvertSurface's -make_consistent \n"
                  "option to fix the problem before proceeding further.\n"
                  "Other results reported by this and other programs\n"
                  "may be incorrect if mesh is not consistently wound.\n" ); 
      consistent = 0;
   } else {
      consistent = 1;
      fprintf (SUMA_STDERR,"\n");
      fprintf (SUMA_STDERR,"Surface is consistently wound\n");
   }
   { 
      SUMA_EULER_SO(SO, eu);
      fprintf (SUMA_STDERR,"\n");
      fprintf(SUMA_STDERR,"Surface Euler number is: %d\n", eu);
   }
   if ((SO->EL->min_N_Hosts == 1 || SO->EL->max_N_Hosts == 1)) {
         fprintf (SUMA_STDERR,"\n");
         fprintf(SUMA_STDERR,"Warning %s:\n Min/Max number of edge hosting triangles: [%d/%d] \n", FuncName, SO->EL->min_N_Hosts, SO->EL->max_N_Hosts);
         fprintf(SUMA_STDERR," You have edges that form a border in the surface.\n");
   }
   if (SO->EL->min_N_Hosts == 2 && SO->EL->max_N_Hosts == 2) {
      fprintf (SUMA_STDERR,"\n");
      fprintf(SUMA_STDERR,"Surface is closed and is a 2-manifold.");
   }
   if (SO->EL->min_N_Hosts > 2 || SO->EL->max_N_Hosts > 2) {
      fprintf (SUMA_STDERR,"\n");
      fprintf(SUMA_STDERR, "Warning %s:\n"
                           "Min/Max number of edge hosting triangles: [%d/%d] \n", FuncName, SO->EL->min_N_Hosts, SO->EL->max_N_Hosts);
      fprintf(SUMA_STDERR, "Warning %s:\n"
                           " You have edges that belong to more than two triangles.\n"
                           " Bad for analysis assuming surface is a 2-manifold.\n", FuncName);
      if (1) {
         int iii=0;
         fprintf(SUMA_STDERR, " These edges are formed by the following nodes:\n");
         for (iii = 0; iii < SO->EL->N_EL; ++iii) { 
            if (SO->EL->ELps[iii][2] > 2) fprintf (SUMA_STDERR," %d: Edge [%d %d] shared by %d triangles.\n", 
                                             iii+1, SO->EL->EL[iii][0], SO->EL->EL[iii][1] , SO->EL->ELps[iii][2] );
         }
      }
   }
   
   if (DoSelfInt) {
      int iii;
      FILE *fout=NULL;
      byte *report = (byte *)SUMA_calloc(SO->N_Node, sizeof(byte));
      if (!report) {
         SUMA_SL_Crit("Failed to allocate for report");
         report = NULL;
      }  
      fprintf( SUMA_STDERR, "\n\nChecking for intersections...:\n");
      nsi = SUMA_isSelfIntersect(SO, 500, report);
      if (nsi) {
         fprintf(SUMA_STDERR, " Surface is self intersecting.\n%d segments were found to intersect the surface.\n", nsi);
         if (nsi >= 500) {
            fprintf(SUMA_STDERR, " It is possible that you have additional segments intersecting the surface.\n");
         }
         if (report) {
            if (Opt->N_surf > 1) {
               sprintf(ext,"_%c", 65+i);
               OutName = SUMA_append_replace_string (prefix, "_IntersNodes.1D.dset", ext, 0);
            } else { 
               OutName = SUMA_append_string (prefix, "_IntersNodes.1D.dset");
            }
            fout = fopen(OutName, "w");
            if (fout) {
               fprintf(fout,  "#List of nodes that are part of segments which intersect the surface\n"
                              "#%s\n"
                              "#A total of %d segments (search limit is 500) were found to intersect the surface.\n"
                              "#Col.1 : Node index\n"
                              "#Col.2 : Dummny flag, always 1\n", SUMA_CHECK_NULL_STR(SO->Label), nsi );
               for (iii=0; iii<SO->N_Node; ++iii) if (report[iii]) fprintf(fout, "%d\t1\n", iii);
               fclose(fout); fout = NULL;
            } else {
               SUMA_SL_Err("Failed to open file for output.");
            }
            if (OutName) SUMA_free(OutName);
         }         
      }else {
         fprintf(SUMA_STDERR, " Surface is not self intersecting.\n");
      }   
      if (report) SUMA_free(report); report = NULL;
   }
   
   fprintf (SUMA_STDERR,"\n");
   
   if (Opt->DoSum) {   /* do not change syntax, scripts depend on this */
                     fprintf(stdout,"Summary:\n");
                     fprintf(stdout,"Euler_No %d\n", eu);
                     fprintf(stdout,"Consistent_Winding %d\n", consistent);
      if (DoSphQ) {
                     fprintf(stdout,"Folding_Triangles %d\n", SSQ.N_bad_facesets);
                     fprintf(stdout,"Sketchy_nodes %d\n", SSQ.N_bad_nodes);
                  }
      if (DoSelfInt) fprintf(stdout,"Self_Intersections %d\n", nsi);
                     fprintf(stdout,"\n");
   }
   
   SUMA_LH("clean up");
   if (!SUMA_FreeSpecFields(&Spec)) { SUMA_S_Err("Failed to free spec fields"); }
   if (prefix) SUMA_free(prefix); prefix = NULL;
   if (Opt->out_prefix) SUMA_free(Opt->out_prefix); Opt->out_prefix = NULL;
   if (Opt) SUMA_free(Opt);   
   if (!SUMA_Free_Displayable_Object_Vect (SUMAg_DOv, SUMAg_N_DOv)) {
      SUMA_SL_Err("DO Cleanup Failed!");
   }
   if (!SUMA_Free_CommonFields(SUMAg_CF)) SUMA_error_message(FuncName,"SUMAg_CF Cleanup Failed!",1);
   
   SUMA_RETURN(0);
}