From 86b69b3803b1b31c040cede6b47bf617561b3b81 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 01 Mar 2016 08:36:37 +0000
Subject: [PATCH] Polymeres are restored

---
 src/snapshot.c |   48 +++++++++++++++++++++++++++++++++++++-----------
 1 files changed, 37 insertions(+), 11 deletions(-)

diff --git a/src/snapshot.c b/src/snapshot.c
index a39ff87..9dc23a9 100644
--- a/src/snapshot.c
+++ b/src/snapshot.c
@@ -5,7 +5,10 @@
 #include<stdarg.h>
 #include <zlib.h>
 #include<inttypes.h>
-
+#include<config.h>
+#include <time.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, ...){
 	va_list ap;
 	va_start(ap,fmt);
@@ -15,7 +18,7 @@
 	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));
@@ -35,20 +38,38 @@
 #else
 	fprintf(fh,"%s", data->string);
 #endif
-	free(data->string);
+	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, "<trisurfversion></trisurfversion>\n");
-	fprintf(fh, "<trisurfdate></trisurfdate>\n");
-	fprintf(fh, "<dumpdate></dumpdate>\n");
+/* format current time */
+	time_t current_time;
+    	char *c_time_string;
+	current_time = time(NULL);
+	c_time_string = ctime(&current_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>\n");
-	
+		fprintf(fh,"%s",tapetxt);	
 	fprintf(fh, "</tape>\n");
-	fprintf(fh, "<trisurf nvtx=\"%u\" npoly=\"%u\" nfono=\"%u\">\n", vesicle->vlist->n, vesicle->poly_list->n, vesicle->poly_list->poly[0]->vlist->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;
 }
 
@@ -61,7 +82,7 @@
 	ts_uint i;
 	ts_sprintf(data,"<tria>");
 	for(i=0; i<tlist->n;i++){
-		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,"%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>");
 	return TS_SUCCESS;
@@ -71,7 +92,7 @@
 	ts_uint i;
 	ts_sprintf(data,"<trianeigh>\n");
 	for(i=0; i<tlist->n;i++){
-		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,"%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;
@@ -108,6 +129,7 @@
 
 /* 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){
 	z_stream defstream;
 	defstream.zalloc = Z_NULL;
@@ -129,6 +151,10 @@
 	return nbase;
 }
 
+ts_uint ts_decompress_string64(char *b64, ts_uint data_len, char **decompressed){
+return TS_SUCCESS;
+
+}
 
 /* base64 encoding, taken from http://stackoverflow.com/questions/342409/how-do-i-base64-encode-decode-in-c */
 static char encoding_table[] = {'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H',
@@ -205,7 +231,7 @@
         	if (j < *output_length) decoded_data[j++] = (triple >> 1 * 8) & 0xFF;
         	if (j < *output_length) decoded_data[j++] = (triple >> 0 * 8) & 0xFF;
     }
-
+	if(decoding_table !=NULL) free(decoding_table);
     return decoded_data;
 }
 

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