From 842378276ab4c4a8dabd02324bb24b8da39c4384 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 18 Oct 2019 10:28:34 +0000
Subject: [PATCH] Done and implemented compression. It doesn't segfaults at the moment
---
src/snapshot.c | 68 ++++++++++++++++++++++++++++-----
1 files changed, 57 insertions(+), 11 deletions(-)
diff --git a/src/snapshot.c b/src/snapshot.c
index cabb1f8..3a4de89 100644
--- a/src/snapshot.c
+++ b/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);
@@ -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;
--
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