gz.h

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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