From 4ca00dc38c72f67dc714fbb45b3006afec097c9c Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 19 Oct 2019 13:26:56 +0000
Subject: [PATCH] Compression except of trisurf header is done. Preparing for decompression
---
src/snapshot.c | 94 ++++++++++++++++++++++++++++++++--------------
1 files changed, 65 insertions(+), 29 deletions(-)
diff --git a/src/snapshot.c b/src/snapshot.c
index ee735f8..d21b864 100644
--- a/src/snapshot.c
+++ b/src/snapshot.c
@@ -1,9 +1,18 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdio.h>
#include<general.h>
#include<snapshot.h>
#include<stdlib.h>
#include<stdarg.h>
#include <zlib.h>
+#include<inttypes.h>
+#include<config.h>
+#include <time.h>
+#include <string.h>
+#include "io.h"
+#include <b64zlib_compression.h>
+/* a helper function that utilizes ts_string data structure and performs same as sprintf */
ts_uint ts_sprintf(ts_string *str, char *fmt, ...){
va_list ap;
va_start(ap,fmt);
@@ -13,11 +22,11 @@
return n;
}
-
+/* outputs additional data into paraview xml file */
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);
@@ -25,34 +34,48 @@
xml_trisurf_tria_neigh(data,vesicle->tlist);
xml_trisurf_vtx_neigh(data,vesicle->vlist);
xml_trisurf_vtx_tristar(data,vesicle->vlist);
-#ifdef COMPRESSION
- z_stream defstream;
- defstream.zalloc = Z_NULL;
- defstream.zfree = Z_NULL;
- defstream.opaque = Z_NULL;
- defstream.avail_in = data->beg+1;
- defstream.next_in = (unsigned char *)data->string;
- char *compr=(char *)malloc((data->beg+1)*sizeof(char *));
- defstream.avail_out = data->beg+1;
- defstream.next_out = (unsigned char *)compr;
- deflateInit(&defstream, Z_BEST_COMPRESSION);
- deflate(&defstream, Z_FINISH);
- deflateEnd(&defstream);
- fwrite(compr, sizeof(unsigned char), defstream.total_out, fh);
-// fprintf(fh,"%s",compr);
-//printf("Uncompressed size is: %lu\n", defstream.total_out);
- free(compr);
-#else
+ 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
- free(data->string);
+//#endif
+ free(data->string); /* TODO: valgrind is not ok with this! */
free(data);
xml_trisurf_footer(fh);
return TS_SUCCESS;
}
ts_bool xml_trisurf_header(FILE *fh, ts_vesicle *vesicle){
- fprintf(fh, "<trisurf nvtx=\"%u\" npoly=\"%u\" nfono=\"%u\">\n", vesicle->vlist->n, vesicle->poly_list->n, vesicle->poly_list->poly[0]->vlist->n);
+/* format current time */
+ time_t current_time;
+ char *c_time_string;
+ current_time = time(NULL);
+ c_time_string = ctime(¤t_time);
+ int npoly, nfono;
+
+ 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>");
+ fprintf(fh,"%s",tapetxt);
+ fprintf(fh, "</tape>\n");
+ if(vesicle->poly_list!=NULL){
+ npoly=vesicle->poly_list->n;
+ if(npoly!=0){
+ nfono=vesicle->poly_list->poly[0]->vlist->n;
+ } else {
+ nfono=0;
+ }
+ } else {
+ npoly=0;
+ nfono=0;
+ }
+ fprintf(fh, "<trisurf nvtx=\"%u\" npoly=\"%u\" nmono=\"%u\" compressed=\"false\">\n", vesicle->vlist->n, npoly, nfono);
return TS_SUCCESS;
}
@@ -63,11 +86,11 @@
ts_bool xml_trisurf_tria(ts_string *data, ts_triangle_list *tlist){
ts_uint i;
- ts_sprintf(data,"<tria>\n");
+ ts_sprintf(data,"<tria>");
for(i=0; i<tlist->n;i++){
- ts_sprintf(data,"%u %u %u\n",tlist->tria[i]->vertex[0]->idx, tlist->tria[i]->vertex[1]->idx, tlist->tria[i]->vertex[2]->idx);
+ ts_sprintf(data,"%u %u %u ",tlist->tria[i]->vertex[0]->idx, tlist->tria[i]->vertex[1]->idx, tlist->tria[i]->vertex[2]->idx);
}
- ts_sprintf(data,"</tria>\n");
+ ts_sprintf(data,"</tria>");
return TS_SUCCESS;
}
@@ -75,7 +98,7 @@
ts_uint i;
ts_sprintf(data,"<trianeigh>\n");
for(i=0; i<tlist->n;i++){
- ts_sprintf(data,"%u %u %u\n",tlist->tria[i]->neigh[0]->idx, tlist->tria[i]->neigh[1]->idx, tlist->tria[i]->neigh[2]->idx);
+ ts_sprintf(data,"%u %u %u ",tlist->tria[i]->neigh[0]->idx, tlist->tria[i]->neigh[1]->idx, tlist->tria[i]->neigh[2]->idx);
}
ts_sprintf(data,"</trianeigh>\n");
return TS_SUCCESS;
@@ -88,7 +111,7 @@
for(j=0;j<vlist->vtx[i]->neigh_no;j++){
ts_sprintf(data,"%u ",vlist->vtx[i]->neigh[j]->idx);
}
- ts_sprintf(data, "</vtxn>\n");
+ ts_sprintf(data, "</vtxn>");
}
return TS_SUCCESS;
}
@@ -100,8 +123,21 @@
for(j=0;j<vlist->vtx[i]->tristar_no;j++){
ts_sprintf(data,"%u ",vlist->vtx[i]->tristar[j]->idx);
}
- ts_sprintf(data, "</tristar>\n");
+ ts_sprintf(data, "</tristar>");
}
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;
+}
+
--
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