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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 <unistd.h>
#include <fcntl.h>
#include "header.h"
#include "image_io/default.h"
#include "formats/list.h"
#include "formats/mrtrix_utils.h"
#include "file/ofstream.h"
#include "file/utils.h"
#include "file/entry.h"
#include "file/path.h"
#include "file/key_value.h"
#include "file/name_parser.h"
namespace MR
{
namespace Formats
{
// extensions are:
// mih: MRtrix Image Header
// mif: MRtrix Image File
std::unique_ptr<ImageIO::Base> MRtrix::read (Header& H) const
{
if (!Path::has_suffix (H.name(), ".mih") && !Path::has_suffix (H.name(), ".mif"))
return std::unique_ptr<ImageIO::Base>();
File::KeyValue::Reader kv (H.name(), "mrtrix image");
read_mrtrix_header (H, kv);
std::string fname;
size_t offset;
get_mrtrix_file_path (H, "file", fname, offset);
File::ParsedName::List list;
auto num = list.parse_scan_check (fname);
std::unique_ptr<ImageIO::Base> io_handler (new ImageIO::Default (H));
for (size_t n = 0; n < list.size(); ++n)
io_handler->files.push_back (File::Entry (list[n].name(), offset));
return io_handler;
}
bool MRtrix::check (Header& H, size_t num_axes) const
{
if (!Path::has_suffix (H.name(), ".mih") &&
!Path::has_suffix (H.name(), ".mif"))
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::create (Header& H) const
{
File::OFStream out (H.name(), std::ios::out | std::ios::binary);
out << "mrtrix image\n";
write_mrtrix_header (H, out);
bool single_file = Path::has_suffix (H.name(), ".mif");
int64_t offset = 0;
out << "file: ";
if (single_file) {
offset = int64_t(out.tellp()) + int64_t(18);
offset += ((4 - (offset % 4)) % 4);
out << ". " << offset << "\nEND\n";
}
else out << Path::basename (H.name().substr (0, H.name().size()-4) + ".dat") << "\n";
out.close();
std::unique_ptr<ImageIO::Base> io_handler (new ImageIO::Default (H));
if (single_file) {
File::resize (H.name(), offset + footprint(H));
io_handler->files.push_back (File::Entry (H.name(), offset));
}
else {
std::string data_file (H.name().substr (0, H.name().size()-4) + ".dat");
File::create (data_file, footprint(H));
io_handler->files.push_back (File::Entry (data_file));
}
return io_handler;
}
}
}
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