/* 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"
|
/* 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(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){
|
/* 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;
|
}
|
|
ts_bool xml_trisurf_footer(FILE *fh){
|
fprintf(fh, "</trisurf>\n");
|
return TS_SUCCESS;
|
}
|
|
ts_bool xml_trisurf_tria(ts_string *data, ts_triangle_list *tlist){
|
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,"</tria>");
|
return TS_SUCCESS;
|
}
|
|
ts_bool xml_trisurf_tria_neigh(ts_string *data, ts_triangle_list *tlist){
|
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,"</trianeigh>\n");
|
return TS_SUCCESS;
|
}
|
|
ts_bool xml_trisurf_vtx_neigh(ts_string *data, ts_vertex_list *vlist){
|
ts_uint i,j;
|
for(i=0;i<vlist->n;i++){
|
ts_sprintf(data,"<vtxn idx=\"%u\">",vlist->vtx[i]->idx);
|
for(j=0;j<vlist->vtx[i]->neigh_no;j++){
|
ts_sprintf(data,"%u ",vlist->vtx[i]->neigh[j]->idx);
|
}
|
ts_sprintf(data, "</vtxn>");
|
}
|
return TS_SUCCESS;
|
}
|
|
ts_bool xml_trisurf_vtx_tristar(ts_string *data, ts_vertex_list *vlist){
|
ts_uint i,j;
|
for(i=0;i<vlist->n;i++){
|
ts_sprintf(data,"<tristar idx=\"%u\">",vlist->vtx[i]->idx);
|
for(j=0;j<vlist->vtx[i]->tristar_no;j++){
|
ts_sprintf(data,"%u ",vlist->vtx[i]->tristar[j]->idx);
|
}
|
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);
|
}
|
