Commiting old changes

Samo Penic

2020-04-09 4f5ffcfd5ba38b6b7dd6d3b15de8bb8677537b9f

 src/restore.c

@@ -7,7 +7,7 @@
#include <general.h>
#include <restore.h>
#include <snapshot.h>
#include <zlib.h>
#include <b64zlib_compression.h>
#include "vesicle.h"
#include "vertex.h"
#include "triangle.h"
@@ -332,8 +332,8 @@
   xmlNodePtr child = cur->xmlChildrenNode;
   xmlChar *property_name;
   xmlChar *values;
   char *vals;
   char *token;
//   char *vals;
//   char *token;
   int idx, polyidx, monoidx, filidx, fonoidx;
   while (child != NULL) {
      if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
@@ -341,26 +341,31 @@
      //   fprintf(stderr,"Name: %s\n", property_name);
         if(!xmlStrcmp(property_name,(const xmlChar *)"spontaneous_curvature")){
            values=xmlNodeListGetString(doc,child->xmlChildrenNode,1);
            vals=(char *)values;
            token=strtok(vals," ");
            idx=0;
            while(token!=NULL){
//            vals=(char *)values;
            unsigned long data_len=0;
            ts_double *curv_values=(double *)ts_decompress((unsigned char *)values,strlen((char *)values), &data_len);
            data_len=data_len/sizeof(ts_double);
//            token=strtok(vals," ");
            for(idx=0;idx<data_len;idx++){
//            while(token!=NULL){
               if(idx<vesicle->vlist->n){
                  vesicle->vlist->vtx[idx]->c=atof(token);
                  vesicle->vlist->vtx[idx]->c=curv_values[idx]; //atof(token);
               } 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]->c=atof(token);
                  vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->c=curv_values[idx];//atof(token);
               } 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]->c=atof(token);
                  vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->c=curv_values[idx];//atof(token);
               }
               idx++;
               token=strtok(NULL," ");
               //idx++;
               //token=strtok(NULL," ");
            }
				
            xmlFree(values);      
            free(curv_values);
         }
         xmlFree(property_name);
      }
@@ -373,41 +378,45 @@
ts_bool parseXMLVertexPosition(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
   xmlNodePtr child = cur->xmlChildrenNode;
   xmlChar *points;
   char *pts;
   int i, idx, polyidx, monoidx, filidx, fonoidx;
   char *token[3];
//   char *pts;
   int i,idx, polyidx, monoidx, filidx, fonoidx;
//   char *token[3];
   while (child != NULL) {
      if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
         points = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
         pts=(char *)points;
         token[0]=strtok(pts," ");
         token[1]=strtok(NULL," ");
         token[2]=strtok(NULL,"\n");
         idx=0;
         while(token[0]!=NULL){
         unsigned long data_len=0;
         ts_double *coords=(double *)ts_decompress((unsigned char *)points,strlen((char *)points), &data_len);
         data_len=data_len/sizeof(ts_double);
         //pts=(char *)points;
         //token[0]=strtok(pts," ");
         //token[1]=strtok(NULL," ");
         //token[2]=strtok(NULL,"\n");
         for(i=0,idx=0;i<data_len;i+=3,idx++){
//         while(token[0]!=NULL){
            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]);
               vesicle->vlist->vtx[idx]->x=coords[i];//atof(token[0]);
               vesicle->vlist->vtx[idx]->y=coords[i+1];//atof(token[1]);
               vesicle->vlist->vtx[idx]->z=coords[i+2];//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]);
               vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->x=coords[i];//atof(token[0]);
               vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->y=coords[i+1];//atof(token[1]);
               vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->z=coords[i+2];//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]);
               vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->x=coords[i];//atof(token[0]);
               vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->y=coords[i+1];//atof(token[1]);
               vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->z=coords[i+2];//atof(token[2]);
            }
            for(i=0;i<2;i++)   token[i]=strtok(NULL," ");	
            token[2]=strtok(NULL,"\n");
            idx++;
            //for(i=0;i<2;i++)   token[i]=strtok(NULL," ");	
            //token[2]=strtok(NULL,"\n");
            //idx++;
         }
         xmlFree(points);
         free(coords);
      }
      child=child->next;
   }
@@ -419,41 +428,41 @@
ts_bool parseXMLBonds(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
   xmlNodePtr child = cur->xmlChildrenNode;
   xmlChar *bonds, *conname;
   char *b;
//   char *b;
   int idx, polyidx;
   char *token[2];
   int temp_cnt=0;
//   char *token[2];
//   int temp_cnt=0;
   while (child != NULL) {
      conname=xmlGetProp(child, (xmlChar *)"Name");
      if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray")) && !xmlStrcmp(conname, (const xmlChar *)"connectivity") ){
         bonds = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
         b=(char *)bonds;
         token[0]=strtok(b," ");
         token[1]=strtok(NULL,"\n");
         idx=0;
         while(token[0]!=NULL){
         unsigned long data_len=0;
         unsigned long *conn=(unsigned long *)ts_decompress((unsigned char *)bonds,strlen((char *)bonds), &data_len);
         data_len=data_len/sizeof(unsigned long);
         //token[0]=strtok(b," ");
         //token[1]=strtok(NULL,"\n");
         for(idx=0;idx<data_len;idx+=2){
//         while(token[0]!=NULL){
            if(idx<3*(vesicle->vlist->n-2)){
               bond_add(vesicle->blist, vesicle->vlist->vtx[atoi(token[0])], vesicle->vlist->vtx[atoi(token[1])]);
               bond_add(vesicle->blist, vesicle->vlist->vtx[conn[idx]], vesicle->vlist->vtx[conn[idx+1]]);
               //fprintf(stderr,"Bonds in vesicle count idx=%d\n",idx);
            }
            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)){
                  temp_cnt++;
//                  temp_cnt++;
                  //fprintf(stderr,"%d: Bonds in poly count idx=%d, t1=%s t2=%s\n",temp_cnt,idx, token[0], token[1]);
                  
                  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];
                  vesicle->poly_list->poly[polyidx]->grafted_vtx=vesicle->vlist->vtx[conn[idx]];
                  vesicle->vlist->vtx[conn[idx]]->grafted_poly=vesicle->poly_list->poly[polyidx];
               }
            }
            token[0]=strtok(NULL," ");	
            token[1]=strtok(NULL,"\n");	
            idx++;
         }
         xmlFree(bonds);
         free(conn);
      }
      xmlFree(conname);
      child=child->next;