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/Makefile.am | 4
src/snapshot.c | 156 -------------------------
src/io.c | 2
src/b64zlib_compression.c | 158 ++++++++++++++++++++++++++
src/snapshot.h | 12 --
5 files changed, 162 insertions(+), 170 deletions(-)
diff --git a/src/Makefile.am b/src/Makefile.am
index c72d0d9..f660c95 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -14,7 +14,7 @@
#------------- LIBS ----------
lib_LTLIBRARIES= libtrisurf.la
-libtrisurf_la_SOURCES= general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c frame.c energy.c timestep.c vertexmove.c bondflip.c poly.c stats.c sh.c shcomplex.c constvol.c snapshot.c restore.c cluster.c
+libtrisurf_la_SOURCES= general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c frame.c energy.c timestep.c vertexmove.c bondflip.c poly.c stats.c sh.c shcomplex.c constvol.c snapshot.c restore.c cluster.c b64zlib_compression.c
#libtrisurf_la_CPPFLAGS = ${libxml2_CFLAGS}
libtrisurf_la_LIBADD=${libxml2_LIBS}
-pkginclude_HEADERS=general.h vertex.h bond.h triangle.h cell.h vesicle.h initial_distribution.h io.h frame.h energy.h timestep.h vertexmove.h bondflip.h poly.h stats.h sh.h shcomplex.h constvol.h snapshot.h restore.h cluster.h
+pkginclude_HEADERS=general.h vertex.h bond.h triangle.h cell.h vesicle.h initial_distribution.h io.h frame.h energy.h timestep.h vertexmove.h bondflip.h poly.h stats.h sh.h shcomplex.h constvol.h snapshot.h restore.h cluster.h b64zlib_compression.h
diff --git a/src/b64zlib_compression.c b/src/b64zlib_compression.c
new file mode 100644
index 0000000..5279725
--- /dev/null
+++ b/src/b64zlib_compression.c
@@ -0,0 +1,158 @@
+#include<stdio.h>
+#include<stdlib.h>
+#include<general.h>
+#include<string.h>
+#include<zlib.h>
+#include<inttypes.h>
+#include<b64zlib_compression.h>
+
+
+/* zlib compression base64 encoded */
+/* compressed must not be pre-malloced */
+/* taken from https://gist.github.com/arq5x/5315739 */
+/* This function is not to be used in compressing paraview data. See below. */
+ts_uint ts_compress_data(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, 6);
+// deflateInit(&defstream, Z_BEST_COMPRESSION);
+ deflate(&defstream, Z_FINISH);
+ deflateEnd(&defstream);
+ *compressed=compr;
+ return defstream.total_out;
+}
+
+ts_uint ts_compress_string64(char *data, ts_uint data_len, char **encoded_compressed){
+ size_t nbase;
+ char *compr;
+ size_t number_of_compressed_bytes=ts_compress_data(data, data_len, &compr);
+ *encoded_compressed=base64_encode((unsigned char *)compr,number_of_compressed_bytes,&nbase);
+ free(compr);
+ return nbase;
+}
+
+char *ts_compress(char *data, ts_uint data_len){
+ size_t nbase1, nbase2;
+ unsigned char *compr=(unsigned char *)malloc(data_len);
+ size_t number_of_compressed_bytes=data_len;
+
+ compress(compr,&number_of_compressed_bytes, (unsigned char *)data, data_len);
+// printf("Compressdion error code=%d, Z_OK=%d, Z_BUF_ERROR=%d", errcode, Z_OK, Z_BUF_ERROR);
+
+ char *encoded_compressed=base64_encode((unsigned char *)compr,number_of_compressed_bytes,&nbase1);
+
+ free(compr);
+
+ ts_uint header[4]={1, data_len, data_len, number_of_compressed_bytes};
+
+ char *encoded_header=(char *)base64_encode((unsigned char *)header, 4*sizeof(ts_uint), &nbase2);
+ char *return_value=malloc((nbase1+nbase2+1)*sizeof(char));
+ strncpy(return_value,encoded_header,nbase2);
+ strncpy(return_value+nbase2,encoded_compressed,nbase1);
+ *(return_value+nbase1+nbase2)=0;
+
+// printf("Compressed size in bytes= %ld, size of encoded header= %ld, size of encoded compressed= %ld.\n",number_of_compressed_bytes, nbase2, nbase1);
+ free(encoded_compressed);
+ free(encoded_header);
+ return return_value;
+}
+
+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);
+}
+
+
+
diff --git a/src/io.c b/src/io.c
index 0d22aa7..0dd022c 100644
--- a/src/io.c
+++ b/src/io.c
@@ -17,7 +17,7 @@
#include <dirent.h>
#include <errno.h>
#include <snapshot.h>
-
+#include <b64zlib_compression.h>
ts_bool parse_args(int argc, char **argv){
int c, retval;
diff --git a/src/snapshot.c b/src/snapshot.c
index 3a4de89..ee5a0d9 100644
--- a/src/snapshot.c
+++ b/src/snapshot.c
@@ -11,6 +11,7 @@
#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;
@@ -139,159 +140,4 @@
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_data(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, 6);
-// deflateInit(&defstream, Z_BEST_COMPRESSION);
- deflate(&defstream, Z_FINISH);
- deflateEnd(&defstream);
- *compressed=compr;
- return defstream.total_out;
-}
-
-ts_uint ts_compress_string64(char *data, ts_uint data_len, char **encoded_compressed){
- size_t nbase;
- char *compr;
- size_t number_of_compressed_bytes=ts_compress_data(data, data_len, &compr);
- *encoded_compressed=base64_encode((unsigned char *)compr,number_of_compressed_bytes,&nbase);
- free(compr);
- return nbase;
-}
-
-char *ts_compress(char *data, ts_uint data_len){
- size_t nbase1, nbase2;
- unsigned char *compr=(unsigned char *)malloc(data_len);
- size_t number_of_compressed_bytes=data_len;
-
- compress(compr,&number_of_compressed_bytes, (unsigned char *)data, data_len);
-// printf("Compressdion error code=%d, Z_OK=%d, Z_BUF_ERROR=%d", errcode, Z_OK, Z_BUF_ERROR);
-
- char *encoded_compressed=base64_encode((unsigned char *)compr,number_of_compressed_bytes,&nbase1);
-
- free(compr);
-
- ts_uint header[4]={1, data_len, data_len, number_of_compressed_bytes};
-
- char *encoded_header=(char *)base64_encode((unsigned char *)header, 4*sizeof(ts_uint), &nbase2);
- char *return_value=malloc((nbase1+nbase2+1)*sizeof(char));
- strncpy(return_value,encoded_header,nbase2);
- strncpy(return_value+nbase2,encoded_compressed,nbase1);
- *(return_value+nbase1+nbase2)=0;
-
-// printf("Compressed size in bytes= %ld, size of encoded header= %ld, size of encoded compressed= %ld.\n",number_of_compressed_bytes, nbase2, nbase1);
- free(encoded_compressed);
- free(encoded_header);
- return return_value;
-}
-
-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);
-}
-
-
-
-
-
-
diff --git a/src/snapshot.h b/src/snapshot.h
index 452202e..eda09ae 100644
--- a/src/snapshot.h
+++ b/src/snapshot.h
@@ -1,16 +1,11 @@
/* vim: set ts=4 sts=4 sw=4 noet : */
#ifndef _H_SNAPSHOT
#define _H_SNAPSHOT
-
-
-
typedef struct{
char *string;
ts_uint beg;
} ts_string;
-
//#define COMPRESSION
-
ts_bool xml_trisurf_data(FILE *fh, ts_vesicle *vesicle);
ts_bool xml_trisurf_header(FILE *fh, ts_vesicle *vesicle);
ts_bool xml_trisurf_footer(FILE *fh);
@@ -20,11 +15,4 @@
ts_bool xml_trisurf_vtx_tristar(ts_string *data, ts_vertex_list *vlist);
ts_bool xml_trisurf_nucleus(ts_string *data, ts_vesicle* vesicle);
ts_bool xml_trisurf_constvolarea(ts_string *data, ts_double volume, ts_double area);
-/* UTILITIES */
-char *base64_encode(const unsigned 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);
-void build_decoding_table();
-void base64_cleanup();
-ts_uint ts_compress_string64(char *data, ts_uint data_len, char **compressed);
-char *ts_compress(char *data, ts_uint data_len);
#endif
--
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