Done and implemented compression. It doesn't segfaults at the moment

Samo Penic

2019-10-18 842378276ab4c4a8dabd02324bb24b8da39c4384

 src/snapshot.c

@@ -9,6 +9,7 @@
#include<inttypes.h>
#include<config.h>
#include <time.h>
#include <string.h>
#include "io.h"
/* a helper function that utilizes ts_string data structure and performs same as sprintf */
ts_uint ts_sprintf(ts_string *str, char *fmt, ...){
@@ -24,7 +25,7 @@
ts_bool xml_trisurf_data(FILE *fh, ts_vesicle *vesicle){

   ts_string *data=(ts_string *)malloc(sizeof(ts_sprintf));
   data->string=(char *)malloc(512000*sizeof(char)); /*TODO: warning, can break if the string is to long */
   data->string=(char *)malloc(5120000*sizeof(char)); /*TODO: warning, can break if the string is to long */
   data->beg=0;
   
   xml_trisurf_header(fh, vesicle);
@@ -32,14 +33,16 @@
   xml_trisurf_tria_neigh(data,vesicle->tlist);
   xml_trisurf_vtx_neigh(data,vesicle->vlist);   
   xml_trisurf_vtx_tristar(data,vesicle->vlist);
#ifdef COMPRESSION
   xml_trisurf_nucleus(data,vesicle);
   xml_trisurf_constvolarea(data,V0,A0);
//#ifdef COMPRESSION
   char *compressed;
   ts_uint nbytes=ts_compress_string64(data->string, data->beg-1, &compressed); //suppress null character at the end with by substracting 1
   fwrite(compressed, sizeof(unsigned char), nbytes, fh);
   free (compressed);
#else
   fprintf(fh,"%s", data->string);
#endif
//#else
//   fprintf(fh,"%s", data->string);
//#endif
   free(data->string);  /* TODO: valgrind is not ok with this! */
   free(data);
   xml_trisurf_footer(fh);
@@ -57,7 +60,7 @@
   fprintf(fh, "<trisurfversion>Trisurf (commit %s), compiled on %s %s</trisurfversion>\n",TS_VERSION, __DATE__,  __TIME__);
   fprintf(fh, "<dumpdate>%s</dumpdate>\n", c_time_string);

   fprintf(fh, "<tape>\n");
   fprintf(fh, "<tape>");
      fprintf(fh,"%s",tapetxt);   
   fprintf(fh, "</tape>\n");
   if(vesicle->poly_list!=NULL){
@@ -124,7 +127,18 @@
   return TS_SUCCESS;
}

ts_bool xml_trisurf_nucleus(ts_string *data, ts_vesicle* vesicle){
   if(vesicle->R_nucleus>0.0 || (vesicle->R_nucleusX>0.0 && vesicle->R_nucleusY>0.0 && vesicle->R_nucleusZ>0.0)){
      ts_sprintf(data,"<nucleus>%.17e %.17e %.17e</nucleus>",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);
   }
   return TS_SUCCESS;
}
ts_bool xml_trisurf_constvolarea(ts_string *data, ts_double volume, ts_double area){
   ts_sprintf(data,"<constant_volume>%.17e</constant_volume>",volume);
   ts_sprintf(data,"<constant_area>%.17e</constant_area>",area);

   return TS_SUCCESS;
}


/* UTILITIES */
@@ -132,27 +146,59 @@
/* zlib compression base64 encoded */
/* compressed must not be pre-malloced */
/* taken from https://gist.github.com/arq5x/5315739 */
ts_uint ts_compress_string64(char *data, ts_uint data_len, char **compressed){
ts_uint ts_compress_data(char *data, ts_uint data_len, char **compressed){
   z_stream defstream;
   defstream.zalloc = Z_NULL;
   defstream.zfree = Z_NULL;
   defstream.opaque = Z_NULL;
   defstream.avail_in = data_len+1;
   defstream.next_in = (unsigned char *)data;   
   char *compr=(char *)malloc(data_len*sizeof(char *));
   char *compr=(char *)malloc(data_len*sizeof(char));
   defstream.avail_out = data_len+1;
   defstream.next_out = (unsigned char *)compr;
   deflateInit(&defstream, Z_BEST_COMPRESSION);
   deflateInit(&defstream, 6);
//   deflateInit(&defstream, Z_BEST_COMPRESSION);
       deflate(&defstream, Z_FINISH);
       deflateEnd(&defstream);
   /*base64 encode*/
   *compressed=compr;
   return defstream.total_out;
}

ts_uint ts_compress_string64(char *data, ts_uint data_len, char **encoded_compressed){
   size_t nbase;
   *compressed=base64_encode((unsigned char *)compr,(size_t)defstream.total_out,&nbase);
   //fwrite(base64, sizeof(unsigned char), nbase, fh);
   char *compr;
   size_t number_of_compressed_bytes=ts_compress_data(data, data_len, &compr);
   *encoded_compressed=base64_encode((unsigned char *)compr,number_of_compressed_bytes,&nbase);
   free(compr);
   return nbase;
}

char *ts_compress(char *data, ts_uint data_len){
   size_t nbase1, nbase2;
   unsigned char *compr=(unsigned char *)malloc(data_len);
   size_t number_of_compressed_bytes=data_len;

   compress(compr,&number_of_compressed_bytes, (unsigned char *)data, data_len);
//   printf("Compressdion error code=%d, Z_OK=%d, Z_BUF_ERROR=%d", errcode, Z_OK, Z_BUF_ERROR);

   char *encoded_compressed=base64_encode((unsigned char *)compr,number_of_compressed_bytes,&nbase1);

   free(compr);

   ts_uint header[4]={1, data_len, data_len, number_of_compressed_bytes};

   char *encoded_header=(char *)base64_encode((unsigned char *)header, 4*sizeof(ts_uint), &nbase2);
   char *return_value=malloc((nbase1+nbase2+1)*sizeof(char));
   strncpy(return_value,encoded_header,nbase2);
   strncpy(return_value+nbase2,encoded_compressed,nbase1);
   *(return_value+nbase1+nbase2)=0;

//   printf("Compressed size in bytes= %ld, size of encoded header= %ld, size of encoded compressed= %ld.\n",number_of_compressed_bytes, nbase2, nbase1);
   free(encoded_compressed);
   free(encoded_header);
   return return_value;
}

ts_uint ts_decompress_string64(char *b64, ts_uint data_len, char **decompressed){
return TS_SUCCESS;