From a8e354c7fad70eb7fdfda62ec83faf1be6c4ed44 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 24 Jan 2023 20:03:01 +0000
Subject: [PATCH] Changes in code and README for easier compilation. May break something
---
src/snapshot.c | 241 ++++++++++++++++++++++++++++++++++++++++++++----
1 files changed, 220 insertions(+), 21 deletions(-)
diff --git a/src/snapshot.c b/src/snapshot.c
index c845e06..81fb476 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 "io.h"
+#include "globals.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_string));
+ 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 +84,183 @@
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;
+}
+
+
+/* UTILITIES */
+
+/* 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;
+ 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 *));
+ defstream.avail_out = data_len+1;
+ defstream.next_out = (unsigned char *)compr;
+ deflateInit(&defstream, Z_BEST_COMPRESSION);
+ deflate(&defstream, Z_FINISH);
+ deflateEnd(&defstream);
+ /*base64 encode*/
+ size_t nbase;
+ *compressed=base64_encode((unsigned char *)compr,(size_t)defstream.total_out,&nbase);
+ //fwrite(base64, sizeof(unsigned char), nbase, fh);
+ free(compr);
+ 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',
+ 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P',
+ 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X',
+ 'Y', 'Z', 'a', 'b', 'c', 'd', 'e', 'f',
+ 'g', 'h', 'i', 'j', 'k', 'l', 'm', 'n',
+ 'o', 'p', 'q', 'r', 's', 't', 'u', 'v',
+ 'w', 'x', 'y', 'z', '0', '1', '2', '3',
+ '4', '5', '6', '7', '8', '9', '+', '/'};
+static char *decoding_table = NULL;
+static int mod_table[] = {0, 2, 1};
+
+
+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);
+ if (encoded_data == NULL) return NULL;
+
+ 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 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];
+ }
+
+ for (i = 0; i < mod_table[input_length % 3]; 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) {
+ int i,j;
+ if (decoding_table == NULL) build_decoding_table();
+
+ if (input_length % 4 != 0) return NULL;
+
+ *output_length = input_length / 4 * 3;
+ if (data[input_length - 1] == '=') (*output_length)--;
+ if (data[input_length - 2] == '=') (*output_length)--;
+
+ unsigned char *decoded_data = malloc(*output_length);
+ 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 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(decoding_table !=NULL) free(decoding_table);
+ return decoded_data;
+}
+
+
+void build_decoding_table() {
+
+ decoding_table = malloc(256);
+ int i;
+ for (i = 0; i < 64; i++)
+ decoding_table[(unsigned char) encoding_table[i]] = i;
+}
+
+
+void base64_cleanup() {
+ free(decoding_table);
+}
+
+
+
+
+
+
+
--
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