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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/.
*/
#include "file/utils.h"
#include "file/path.h"
#include "file/gz.h"
#include "header.h"
#include "image_io/gz.h"
#include "formats/list.h"
#include "formats/mrtrix_utils.h"
namespace MR
{
namespace Formats
{
std::unique_ptr<ImageIO::Base> MRtrix_GZ::read (Header& H) const
{
if (!Path::has_suffix (H.name(), ".mif.gz"))
return std::unique_ptr<ImageIO::Base>();
File::GZ zf (H.name(), "r");
std::string first_line = zf.getline();
if (first_line != "mrtrix image") {
zf.close();
throw Exception ("invalid first line for compressed image \"" + H.name() + "\" (expected \"mrtrix image\", read \"" + first_line + "\")");
}
read_mrtrix_header (H, zf);
zf.close();
std::string fname;
size_t offset, write_offset;
get_mrtrix_file_path (H, "file", fname, offset);
write_offset = offset;
if (fname != H.name())
throw Exception ("GZip-compressed MRtrix format images must have image data within the same file as the header");
std::stringstream header;
header << "mrtrix image\n";
write_mrtrix_header (H, header);
write_offset = header.str().size() + size_t(24);
write_offset += ((4 - (offset % 4)) % 4);
header << "file: . " << write_offset << "\nEND\n";
std::unique_ptr<ImageIO::GZ> io_handler (new ImageIO::GZ (H, write_offset));
memcpy (io_handler.get()->header(), header.str().c_str(), header.str().size());
memset (io_handler.get()->header() + header.str().size(), 0, write_offset - header.str().size());
io_handler->files.push_back (File::Entry (H.name(), offset));
return std::move (io_handler);
}
bool MRtrix_GZ::check (Header& H, size_t num_axes) const
{
if (!Path::has_suffix (H.name(), ".mif.gz"))
return false;
H.ndim() = num_axes;
for (size_t i = 0; i < H.ndim(); i++)
if (H.size (i) < 1)
H.size(i) = 1;
return true;
}
std::unique_ptr<ImageIO::Base> MRtrix_GZ::create (Header& H) const
{
std::stringstream header;
header << "mrtrix image\n";
write_mrtrix_header (H, header);
int64_t offset = int64_t(header.tellp()) + int64_t(24);
offset += ((4 - (offset % 4)) % 4);
header << "file: . " << offset << "\nEND\n";
while (int64_t(header.tellp()) < offset)
header << '\0';
std::unique_ptr<ImageIO::GZ> io_handler (new ImageIO::GZ (H, offset));
memcpy (io_handler->header(), header.str().c_str(), offset);
File::create (H.name());
io_handler->files.push_back (File::Entry (H.name(), offset));
return std::move (io_handler);
}
}
}
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