Added examples to help

Samo Penic

2016-05-27 c4178cb8b767cd8a6b32f0bfe7c9dbe061cdebfd

 src/restore.c

@@ -1,3 +1,4 @@
/* vim: set ts=4 sts=4 sw=4 noet : */
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
@@ -16,7 +17,7 @@
#include "initial_distribution.h"
#include "io.h"

ts_bool parseDump(char *dumpfname) {
ts_vesicle *parseDump(char *dumpfname) {
   xmlDocPtr doc;
   xmlNodePtr cur, cur1,cur2;
   ts_vesicle *vesicle=NULL;
@@ -54,12 +55,13 @@
               cur2=cur1->xmlChildrenNode;
               while(cur2!=NULL){
                  if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Points"))){
                     fprintf(stderr,"Found point data\n");
                     //fprintf(stderr,"Found point data\n");
                     if(vesicle!=NULL)
                        //fprintf(stderr,"Fils: %ld, Nfono: %ld\n", vesicle->tape->nfil, vesicle->tape->nfono);
                        parseXMLVertexPosition(vesicle, doc, cur2);
                  }
                  if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Cells"))){
                  fprintf(stderr,"Found cell(Bonds) data\n");
                  //fprintf(stderr,"Found cell(Bonds) data\n");
                     if(vesicle!=NULL)
                        parseXMLBonds(vesicle, doc, cur2);
                  }
@@ -75,18 +77,18 @@
   
   xmlFreeDoc(doc);

   vesicle->poly_list=init_poly_list(0, 0, vesicle->vlist, vesicle);
//   vesicle->poly_list=init_poly_list(0, 0, vesicle->vlist, vesicle);

   init_normal_vectors(vesicle->tlist);
   mean_curvature_and_energy(vesicle);

/* TODO: cells, polymeres, filaments, core, tape */
/* TODO: filaments */

   fprintf(stderr,"Restoration completed\n");
//   ts_fprintf(stdout,"Restoration completed\n");
//   write_vertex_xml_file(vesicle,999);
   vesicle_free(vesicle);
   exit(0);
   return TS_SUCCESS;
//   vesicle_free(vesicle);
//   exit(0);
   return vesicle;
}

ts_bool setGlobalTapeTXTfromTapeTag(xmlDocPtr doc, xmlNodePtr cur){
@@ -99,7 +101,7 @@

/* this is a parser of additional data in xml */
ts_vesicle *parseTrisurfTag(xmlDocPtr doc, xmlNodePtr cur){
   fprintf(stderr,"Parsing trisurf tag\n");
   //fprintf(stderr,"Parsing trisurf tag\n");
   xmlNodePtr child;

#ifdef COMPRESS
@@ -129,17 +131,17 @@
       inflateInit(&infstream);
       inflate(&infstream, Z_NO_FLUSH);
       inflateEnd(&infstream);   
   fprintf(stderr,"%lu\n",cLen);
   //fprintf(stderr,"%lu\n",cLen);
   subtree[infstream.total_out]='\0'; //zero terminate string   
   fprintf(stderr,"%s\n",subtree);
   //fprintf(stderr,"%s\n",subtree);
   
   free(subtree);
#endif
   /*parse xml subtree */
   xmlChar *nvtx, *npoly, *nfono;
   xmlChar *nvtx, *npoly, *nmono;
   nvtx = xmlGetProp(cur, (xmlChar *)"nvtx");
   npoly=xmlGetProp(cur, (xmlChar *)"npoly");
   nfono=xmlGetProp(cur, (xmlChar *)"nfono");
   nmono=xmlGetProp(cur, (xmlChar *)"nmono");
   ts_tape *tape=parsetapebuffer(tapetxt);
   //fprintf(stderr,"nvtx=%u\n",atoi((char *)nvtx));
   //TODO: check if nvtx is in agreement with nshell from tape
@@ -147,7 +149,7 @@
   //vesicle->poly_list=init_poly_list(atoi((char *)npoly),atoi((char *)nmono), vesicle->vlist, vesicle);
   xmlFree(nvtx);
   xmlFree(npoly);
   xmlFree(nfono);
   xmlFree(nmono);

   child = cur->xmlChildrenNode;
   while (child != NULL) {
@@ -221,7 +223,7 @@
      for(i=0;i<3;i++)   vtx[i]=strtok(NULL," ");
      j++;
   }   
   fprintf(stderr,"Parsing triangles %s j=%d\n",triangles,j);	
   //fprintf(stderr,"Parsing triangles %s j=%d\n",triangles,j);	

   xmlFree(triangles);
   return TS_SUCCESS;
@@ -245,7 +247,7 @@
      j++;
      for(i=0;i<3;i++)   ntria[i]=strtok(NULL," ");
   }   
   fprintf(stderr,"Parsing triangle neighbors j=%d\n",j);	
   //fprintf(stderr,"Parsing triangle neighbors j=%d\n",j);	

   xmlFree(triangles);
   return TS_SUCCESS;
@@ -285,7 +287,7 @@
   xmlNodePtr child = cur->xmlChildrenNode;
   xmlChar *points;
   char *pts;
   int i, idx;
   int i, idx, polyidx, monoidx, filidx, fonoidx;
   char *token[3];
   while (child != NULL) {
      if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
@@ -296,9 +298,24 @@
         token[2]=strtok(NULL,"\n");
         idx=0;
         while(token[0]!=NULL){
            vesicle->vlist->vtx[idx]->x=atof(token[0]);
            vesicle->vlist->vtx[idx]->y=atof(token[1]);
            vesicle->vlist->vtx[idx]->z=atof(token[2]);
            if(idx<vesicle->vlist->n){
               vesicle->vlist->vtx[idx]->x=atof(token[0]);
               vesicle->vlist->vtx[idx]->y=atof(token[1]);
               vesicle->vlist->vtx[idx]->z=atof(token[2]);
            } else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) {
               polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono;
               monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono;
               vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->x=atof(token[0]);
               vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->y=atof(token[1]);
               vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->z=atof(token[2]);
            } else {
               filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono;
               fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono;
               //fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]);
               vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->x=atof(token[0]);
               vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->y=atof(token[1]);
               vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->z=atof(token[2]);
            }
            for(i=0;i<2;i++)   token[i]=strtok(NULL," ");   
            token[2]=strtok(NULL,"\n");
            idx++;
@@ -307,7 +324,8 @@
      }
      child=child->next;
   }
   fprintf(stderr,"Vertices position j=%d\n",idx);	
   //fprintf(stderr,"Came here\n");
   //fprintf(stderr,"Vertices position j=%d\n",idx);	

   return TS_SUCCESS;
}
@@ -315,7 +333,7 @@
   xmlNodePtr child = cur->xmlChildrenNode;
   xmlChar *bonds, *conname;
   char *b;
   int idx;
   int idx, polyidx;
   char *token[2];
   while (child != NULL) {
      conname=xmlGetProp(child, (xmlChar *)"Name");
@@ -326,7 +344,19 @@
         token[1]=strtok(NULL,"\n");
         idx=0;
         while(token[0]!=NULL){
            bond_add(vesicle->blist, vesicle->vlist->vtx[atoi(token[0])], vesicle->vlist->vtx[atoi(token[1])]);
            if(idx<3*(vesicle->vlist->n-2)){
               bond_add(vesicle->blist, vesicle->vlist->vtx[atoi(token[0])], vesicle->vlist->vtx[atoi(token[1])]);
            }
            else {
            //find grafted vtx
               if(vesicle->tape->npoly && vesicle->tape->nmono && (vesicle->tape->nmono-1)==(idx-3*(vesicle->vlist->n-2))%(vesicle->tape->nmono)
                  && idx<(3*vesicle->vlist->n-2+vesicle->tape->nmono*vesicle->tape->npoly+vesicle->tape->npoly)){
                  polyidx=(idx-3*(vesicle->vlist->n-2))/(vesicle->tape->nmono);
                  //fprintf(stderr,"poly=%d, vertex=%d\n",polyidx,atoi(token[0]));
                  vesicle->poly_list->poly[polyidx]->grafted_vtx=vesicle->vlist->vtx[atoi(token[0])];
                  vesicle->vlist->vtx[atoi(token[0])]->grafted_poly=vesicle->poly_list->poly[polyidx];
               }
            }
            token[0]=strtok(NULL," ");   
            token[1]=strtok(NULL,"\n");   
            idx++;
@@ -336,7 +366,7 @@
      xmlFree(conname);
      child=child->next;
   }
   fprintf(stderr,"Bond data j=%d\n",idx);	
   //fprintf(stderr,"Bond data j=%d\n",idx);	
   return TS_SUCCESS;
}