From c14bd6e408bec0634a7cac3aa87e177562430afe Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Mon, 07 Mar 2016 14:04:32 +0000
Subject: [PATCH] Working on script for executing trisurf. Added directory generation, started working on start code. Started reading statistics CSV file for generating report on running simulation
---
src/snapshot.c | 108 ++++++++++++++++++++++++++++++++----------------------
1 files changed, 64 insertions(+), 44 deletions(-)
diff --git a/src/snapshot.c b/src/snapshot.c
index 6bbefdb..370ce4c 100644
--- a/src/snapshot.c
+++ b/src/snapshot.c
@@ -1,3 +1,5 @@
+/* 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>
@@ -5,7 +7,10 @@
#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 +20,7 @@
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));
@@ -29,26 +34,44 @@
xml_trisurf_vtx_tristar(data,vesicle->vlist);
#ifdef COMPRESSION
char *compressed;
- ts_uint nbytes=ts_compress_string64(data->string, data->beg, &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);
+ 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(¤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>\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;
}
@@ -59,11 +82,11 @@
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;
}
@@ -71,7 +94,7 @@
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;
@@ -84,7 +107,7 @@
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;
}
@@ -96,7 +119,7 @@
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;
}
@@ -108,6 +131,7 @@
/* 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 +153,10 @@
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',
@@ -143,10 +171,7 @@
static int mod_table[] = {0, 2, 1};
-char *base64_encode(const unsigned char *data,
- size_t input_length,
- size_t *output_length) {
-
+char *base64_encode(const unsigned char *data, size_t input_length, size_t *output_length) {
*output_length = 4 * ((input_length + 2) / 3);
int i,j;
char *encoded_data = malloc(*output_length);
@@ -154,29 +179,25 @@
for (i = 0, j = 0; i < input_length;) {
- uint32_t octet_a = i < input_length ? (unsigned char)data[i++] : 0;
- uint32_t octet_b = i < input_length ? (unsigned char)data[i++] : 0;
- uint32_t octet_c = i < input_length ? (unsigned char)data[i++] : 0;
+ uint32_t octet_a = i < input_length ? (unsigned char)data[i++] : 0;
+ uint32_t octet_b = i < input_length ? (unsigned char)data[i++] : 0;
+ uint32_t octet_c = i < input_length ? (unsigned char)data[i++] : 0;
+ uint32_t triple = (octet_a << 0x10) + (octet_b << 0x08) + octet_c;
- uint32_t triple = (octet_a << 0x10) + (octet_b << 0x08) + octet_c;
-
- encoded_data[j++] = encoding_table[(triple >> 3 * 6) & 0x3F];
- encoded_data[j++] = encoding_table[(triple >> 2 * 6) & 0x3F];
- encoded_data[j++] = encoding_table[(triple >> 1 * 6) & 0x3F];
- encoded_data[j++] = encoding_table[(triple >> 0 * 6) & 0x3F];
+ encoded_data[j++] = encoding_table[(triple >> 3 * 6) & 0x3F];
+ encoded_data[j++] = encoding_table[(triple >> 2 * 6) & 0x3F];
+ encoded_data[j++] = encoding_table[(triple >> 1 * 6) & 0x3F];
+ encoded_data[j++] = encoding_table[(triple >> 0 * 6) & 0x3F];
}
for (i = 0; i < mod_table[input_length % 3]; i++)
- encoded_data[*output_length - 1 - i] = '=';
+ encoded_data[*output_length - 1 - i] = '=';
return encoded_data;
}
-unsigned char *base64_decode(const char *data,
- size_t input_length,
- size_t *output_length) {
-
+unsigned char *base64_decode(const char *data, size_t input_length, size_t *output_length) {
int i,j;
if (decoding_table == NULL) build_decoding_table();
@@ -190,22 +211,21 @@
if (decoded_data == NULL) return NULL;
for (i = 0, j = 0; i < input_length;) {
+ uint32_t sextet_a = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
+ uint32_t sextet_b = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
+ uint32_t sextet_c = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
+ uint32_t sextet_d = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
- uint32_t sextet_a = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
- uint32_t sextet_b = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
- uint32_t sextet_c = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
- uint32_t sextet_d = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
-
- uint32_t triple = (sextet_a << 3 * 6)
+ uint32_t triple = (sextet_a << 3 * 6)
+ (sextet_b << 2 * 6)
+ (sextet_c << 1 * 6)
+ (sextet_d << 0 * 6);
- if (j < *output_length) decoded_data[j++] = (triple >> 2 * 8) & 0xFF;
- if (j < *output_length) decoded_data[j++] = (triple >> 1 * 8) & 0xFF;
- if (j < *output_length) decoded_data[j++] = (triple >> 0 * 8) & 0xFF;
+ if (j < *output_length) decoded_data[j++] = (triple >> 2 * 8) & 0xFF;
+ 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;
}
@@ -215,7 +235,7 @@
decoding_table = malloc(256);
int i;
for (i = 0; i < 64; i++)
- decoding_table[(unsigned char) encoding_table[i]] = i;
+ decoding_table[(unsigned char) encoding_table[i]] = i;
}
--
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