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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 "file/utils.h"
#include "file/entry.h"
#include "file/ofstream.h"
#include "file/path.h"
#include "file/key_value.h"
#include "file/name_parser.h"
#include "image_io/sparse.h"
#include "formats/list.h"
#include "formats/mrtrix_utils.h"
#include "fixel/legacy/keys.h"
namespace MR
{
namespace Formats
{
// extensions are:
// msh: MRtrix Sparse image Header
// msf: MRtrix Sparse image File
std::unique_ptr<ImageIO::Base> MRtrix_sparse::read (Header& H) const
{
if (!Path::has_suffix (H.name(), ".msh") && !Path::has_suffix (H.name(), ".msf"))
return std::unique_ptr<ImageIO::Base>();
File::KeyValue::Reader kv (H.name(), "mrtrix sparse image");
read_mrtrix_header (H, kv);
// Although the endianness of the image data itself (the sparse data offsets) actually doesn't matter
// (the Image class would deal with this conversion), the sparse data itself needs to have
// the correct endianness for the system. Since MRtrix_sparse::create() forces the endianness of the
// offset data to be native, this is the easiest way to verify that the sparse data also has the
// correct endianness
#ifdef MRTRIX_BYTE_ORDER_BIG_ENDIAN
const DataType dt = DataType::UInt64BE;
#else
const DataType dt = DataType::UInt64LE;
#endif
if (H.datatype() != dt)
throw Exception ("Cannot open sparse image file " + H.name() + " due to type mismatch; expect " + dt.description() + ", file is " + H.datatype().description());
const auto name_it = H.keyval().find (Fixel::Legacy::name_key);
if (name_it == H.keyval().end())
throw Exception ("sparse data class name not specified in sparse image header " + H.name());
const auto size_it = H.keyval().find (Fixel::Legacy::size_key);
if (size_it == H.keyval().end())
throw Exception ("sparse data class size not specified in sparse image header " + H.name());
std::string image_fname, sparse_fname;
size_t image_offset, sparse_offset;
get_mrtrix_file_path (H, "file", image_fname, image_offset);
File::ParsedName::List image_list;
image_list.parse_scan_check (image_fname);
get_mrtrix_file_path (H, "sparse_file", sparse_fname, sparse_offset);
std::unique_ptr<ImageIO::SparseLegacy> io_handler (new ImageIO::SparseLegacy (H, name_it->second, to<size_t>(size_it->second), File::Entry (sparse_fname, sparse_offset)));
for (size_t n = 0; n < image_list.size(); ++n)
io_handler->files.push_back (File::Entry (image_list[n].name(), image_offset));
return std::move (io_handler);
}
bool MRtrix_sparse::check (Header& H, size_t num_axes) const
{
if (!Path::has_suffix (H.name(), ".msh") &&
!Path::has_suffix (H.name(), ".msf"))
return false;
if (H.keyval().find (Fixel::Legacy::name_key) == H.keyval().end() ||
H.keyval().find (Fixel::Legacy::size_key) == H.keyval().end())
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_sparse::create (Header& H) const
{
const auto name_it = H.keyval().find (Fixel::Legacy::name_key);
if (name_it == H.keyval().end())
throw Exception ("Cannot create sparse image " + H.name() + "; no knowledge of underlying data class type");
const auto size_it = H.keyval().find (Fixel::Legacy::size_key);
if (size_it == H.keyval().end())
throw Exception ("Cannot create sparse image " + H.name() + "; no knowledge of underlying data class size");
H.datatype() = DataType::UInt64;
H.datatype().set_byte_order_native();
File::OFStream out (H.name(), std::ios::out | std::ios::binary);
out << "mrtrix sparse image\n";
write_mrtrix_header (H, out);
bool single_file = Path::has_suffix (H.name(), ".msf");
int64_t image_offset = 0, sparse_offset = 0;
std::string image_path, sparse_path;
if (single_file) {
image_offset = int64_t(out.tellp()) + int64_t(54);
image_offset += ((4 - (image_offset % 4)) % 4);
sparse_offset = image_offset + footprint(H);
out << "file: . " << image_offset << "\nsparse_file: . " << sparse_offset << "\nEND\n";
File::resize (H.name(), sparse_offset);
image_path = H.name();
sparse_path = H.name();
} else {
image_path = Path::basename (H.name().substr (0, H.name().size()-4) + ".dat");
sparse_path = Path::basename (H.name().substr (0, H.name().size()-4) + ".sdat");
out << "file: " << image_path << "\nsparse_file: " << sparse_path << "\nEND\n";
File::create (image_path, footprint(H));
File::create (sparse_path);
}
std::unique_ptr<ImageIO::SparseLegacy> io_handler (new ImageIO::SparseLegacy (H, name_it->second, to<size_t>(size_it->second), File::Entry (sparse_path, sparse_offset)));
io_handler->files.push_back (File::Entry (image_path, image_offset));
return std::move (io_handler);
}
}
}
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