From 1eb75bcca71b97196c1ad29da5d082a21b12cf00 Mon Sep 17 00:00:00 2001 From: Samo Penic <samo.penic@gmail.com> Date: Sat, 19 Oct 2019 15:30:09 +0000 Subject: [PATCH] Did restore. Segfaults. --- src/b64zlib_compression.c | 6 ++- src/restore.c | 98 +++++++++++++++++++++++++------------------------ 2 files changed, 54 insertions(+), 50 deletions(-) diff --git a/src/b64zlib_compression.c b/src/b64zlib_compression.c index 5f51a97..013897e 100644 --- a/src/b64zlib_compression.c +++ b/src/b64zlib_compression.c @@ -98,17 +98,19 @@ return return_value; } -char *ts_decompress(unsigned char *compressed_data, unsigned int data_len, unsigned int result_len){ +char *ts_decompress(unsigned char *compressed_data, unsigned int data_len, size_t *decompressed_length){ const size_t encoded_header_len=24; ts_uint *header; size_t nbase1=0,nbase2=0; header=(ts_uint *)base64_decode((const char *)compressed_data, encoded_header_len, &nbase2); if(header==NULL) fprintf(stderr, "Error decoding header\n"); //fprintf(stderr,"Header=%d, %d, %d, %d\n", header[0],header[1], header[2], header[3]); + unsigned long result_len=header[2]; unsigned char *decoded_data=base64_decode((const char *)&compressed_data[encoded_header_len], data_len-encoded_header_len, &nbase1); if(decoded_data==NULL) fprintf(stderr, "Error decoding compressed data\n"); unsigned char *return_value=(unsigned char *)malloc(result_len*sizeof(char)); - uncompress(return_value, (unsigned long *)&result_len, decoded_data, header[3]); + uncompress(return_value, &result_len, decoded_data, header[3]); + *decompressed_length=result_len; free(decoded_data); free(header); return (char *)return_value; diff --git a/src/restore.c b/src/restore.c index 6e12c1e..a1211ea 100644 --- a/src/restore.c +++ b/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"))){ @@ -341,24 +341,26 @@ // 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); +// 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); } @@ -373,39 +375,41 @@ 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 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); + //pts=(char *)points; + //token[0]=strtok(pts," "); + //token[1]=strtok(NULL," "); + //token[2]=strtok(NULL,"\n"); + for(idx=0;idx<data_len;idx+=3){ +// 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[idx];//atof(token[0]); + vesicle->vlist->vtx[idx]->y=coords[idx+1];//atof(token[1]); + vesicle->vlist->vtx[idx]->z=coords[idx+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[idx];//atof(token[0]); + vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->y=coords[idx+1];//atof(token[1]); + vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->z=coords[idx+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[idx];//atof(token[0]); + vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->y=coords[idx+1];//atof(token[1]); + vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->z=coords[idx+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); } @@ -419,39 +423,37 @@ 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); + //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); } -- Gitblit v1.9.3