From dba66b4f8a25cb7eb18de5f7ffca97e179d7a5d9 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 19 Oct 2019 11:45:15 +0000
Subject: [PATCH] Moved compression/decompression routines to separate file
---
src/snapshot.c | 118 ++++++++++++++++++++++++++++++++++++++++++++++++----------
1 files changed, 97 insertions(+), 21 deletions(-)
diff --git a/src/snapshot.c b/src/snapshot.c
index c845e06..ee5a0d9 100644
--- a/src/snapshot.c
+++ b/src/snapshot.c
@@ -1,18 +1,81 @@
+/* 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);
+ ts_uint n=vsprintf(&(str->string[str->beg]),fmt,ap);
+ va_end(ap);
+ str->beg+=n;
+ 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(5120000*sizeof(char)); /*TODO: warning, can break if the string is to long */
+ data->beg=0;
+
xml_trisurf_header(fh, vesicle);
- xml_trisurf_tria(fh,vesicle->tlist);
- xml_trisurf_tria_neigh(fh,vesicle->tlist);
- xml_trisurf_vtx_neigh(fh,vesicle->vlist);
- xml_trisurf_vtx_tristar(fh,vesicle->vlist);
+ xml_trisurf_tria(data,vesicle->tlist);
+ xml_trisurf_tria_neigh(data,vesicle->tlist);
+ xml_trisurf_vtx_neigh(data,vesicle->vlist);
+ xml_trisurf_vtx_tristar(data,vesicle->vlist);
+ 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); /* 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;
}
@@ -21,47 +84,60 @@
return TS_SUCCESS;
}
-ts_bool xml_trisurf_tria(FILE *fh, ts_triangle_list *tlist){
+ts_bool xml_trisurf_tria(ts_string *data, ts_triangle_list *tlist){
ts_uint i;
- fprintf(fh,"<tria>\n");
+ ts_sprintf(data,"<tria>");
for(i=0; i<tlist->n;i++){
- fprintf(fh,"%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);
}
- fprintf(fh,"</tria>\n");
+ ts_sprintf(data,"</tria>");
return TS_SUCCESS;
}
-ts_bool xml_trisurf_tria_neigh(FILE *fh, ts_triangle_list *tlist){
+ts_bool xml_trisurf_tria_neigh(ts_string *data, ts_triangle_list *tlist){
ts_uint i;
- fprintf(fh,"<trianeigh>\n");
+ ts_sprintf(data,"<trianeigh>\n");
for(i=0; i<tlist->n;i++){
- fprintf(fh,"%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);
}
- fprintf(fh,"</trianeigh>\n");
+ ts_sprintf(data,"</trianeigh>\n");
return TS_SUCCESS;
}
-ts_bool xml_trisurf_vtx_neigh(FILE *fh, ts_vertex_list *vlist){
+ts_bool xml_trisurf_vtx_neigh(ts_string *data, ts_vertex_list *vlist){
ts_uint i,j;
for(i=0;i<vlist->n;i++){
- fprintf(fh,"<vtxn idx=\"%u\">",vlist->vtx[i]->idx);
+ ts_sprintf(data,"<vtxn idx=\"%u\">",vlist->vtx[i]->idx);
for(j=0;j<vlist->vtx[i]->neigh_no;j++){
- fprintf(fh,"%u ",vlist->vtx[i]->neigh[j]->idx);
+ ts_sprintf(data,"%u ",vlist->vtx[i]->neigh[j]->idx);
}
- fprintf(fh, "</vtxn>\n");
+ ts_sprintf(data, "</vtxn>");
}
return TS_SUCCESS;
}
-ts_bool xml_trisurf_vtx_tristar(FILE *fh, ts_vertex_list *vlist){
+ts_bool xml_trisurf_vtx_tristar(ts_string *data, ts_vertex_list *vlist){
ts_uint i,j;
for(i=0;i<vlist->n;i++){
- fprintf(fh,"<tristar idx=\"%u\">",vlist->vtx[i]->idx);
+ ts_sprintf(data,"<tristar idx=\"%u\">",vlist->vtx[i]->idx);
for(j=0;j<vlist->vtx[i]->tristar_no;j++){
- fprintf(fh,"%u ",vlist->vtx[i]->tristar[j]->idx);
+ ts_sprintf(data,"%u ",vlist->vtx[i]->tristar[j]->idx);
}
- fprintf(fh, "</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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