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/* Copyright (c) 2008-2022 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "as is"
* basis, without warranty of any kind, either expressed, implied, or
* statutory, including, without limitation, warranties that the
* Covered Software is free of defects, merchantable, fit for a
* particular purpose or non-infringing.
* See the Mozilla Public License v. 2.0 for more details.
*
* For more details, see http://www.mrtrix.org/.
*/
#ifndef __file_gz_h__
#define __file_gz_h__
#include <cassert>
#include <cstring>
#include <cstdio>
#include <sys/types.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <zlib.h>
#include "debug.h"
#include "mrtrix.h"
#include "types.h"
#include "exception.h"
#include "file/path.h"
namespace MR
{
namespace File
{
class GZ { NOMEMALIGN
public:
GZ () : gz (NULL) { }
GZ (const std::string& fname, const char* mode) : gz (NULL) {
open (fname, mode);
}
~GZ () {
try {
close();
} catch (...) {
FAIL ("error closing GZ file \"" + filename + "\": " + error());
App::exit_error_code = 1;
}
}
const std::string& name () const {
return filename;
}
void open (const std::string& fname, const char* mode) {
close();
filename = fname;
if (!MR::Path::exists (filename))
throw Exception ("cannot access file \"" + filename + "\": No such file or directory");
gz = gzopen (filename.c_str(), mode);
if (!gz)
throw Exception ("error opening file \"" + filename + "\": " + strerror(errno));
}
void close () {
if (gz) {
if (gzclose (gz))
throw Exception ("error closing GZ file \"" + filename + "\": " + error());
filename.clear();
gz = NULL;
}
}
bool is_open () const {
return gz;
}
bool eof () const {
assert (gz);
return gzeof (gz);
}
int64_t tell () const {
assert (gz);
return gztell (gz);
}
int64_t tellg () const {
return tell();
}
void seek (int64_t offset) {
assert (gz);
z_off_t pos = gzseek (gz, offset, SEEK_SET);
if (pos < 0)
throw Exception ("error seeking in GZ file \"" + filename + "\": " + error());
}
int read (char* s, size_t n) {
assert (gz);
int n_read = gzread (gz, s, n);
if (n_read < 0)
throw Exception ("error uncompressing GZ file \"" + filename + "\": " + error());
return n_read;
}
void write (const char* s, size_t n) {
assert (gz);
if (gzwrite (gz, s, n) <= 0)
throw Exception ("error writing to GZ file \"" + filename + "\": " + error());
}
void write (const std::string& s) {
assert (gz);
if (gzputs (gz, s.c_str()) < 0)
throw Exception ("error writing to GZ file \"" + filename + "\": " + error());
}
std::string getline () {
assert (gz);
std::string string;
int c = 0;
do {
c = gzgetc (gz);
if (c < 0) {
if (eof()) break;
throw Exception ("error uncompressing GZ file \"" + filename + "\": " + error());
}
string += char (c);
}
while (c != '\n');
if (string.size() && (string[string.size()-1] == 015 || string[string.size()-1] == '\n'))
string.resize (string.size()-1);
return string;
}
template <typename T> T get () {
T val;
if (read (&val, sizeof (T)) != sizeof (T))
throw Exception ("error uncompressing GZ file \"" + filename + "\": " + error());
return val;
}
template <typename T> T get (int64_t offset) {
seek (offset);
return get<T>();
}
template <typename T> T* get (T* buf, size_t n) {
if (read (buf, n*sizeof (T)) != n*sizeof (T))
throw Exception ("error uncompressing GZ file \"" + filename + "\": " + error());
return buf;
}
template <typename T> T* get (int64_t offset, T* buf, size_t n) {
seek (offset);
return get<T> (buf, n);
}
protected:
gzFile gz;
std::string filename;
const char* error () {
int error_number;
const char* s = gzerror (gz, &error_number);
if (error_number == Z_ERRNO) s = strerror (errno);
return s;
}
};
}
}
#endif
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