RefPtr<Handler::Base> MRtrix_GZ::read (Header& H) const
{
if (!Path::has_suffix (H.name(), ".mif.gz"))
return RefPtr<Handler::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;
get_mrtrix_file_path (H, "file", fname, 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);
offset = header.str().size() + size_t(24);
offset += ((4 - (offset % 4)) % 4);
header << "file: . " << offset << "\nEND\n";
RefPtr<Handler::Base> handler (new Handler::GZ (H, offset));
memcpy (reinterpret_cast<Handler::GZ*>((Handler::Base*)handler)->header(), header.str().c_str(), header.str().size());
memset (reinterpret_cast<Handler::GZ*>((Handler::Base*)handler)->header() + header.str().size(), 0, offset - header.str().size());
handler->files.push_back (File::Entry (H.name(), offset));
return handler;
}
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 = 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;
}
std::shared_ptr<Handler::Base> MRtrix_sparse::create (Header& H) const
{
Header::const_iterator name_it = H.find (Image::Sparse::name_key);
if (name_it == H.end())
throw Exception ("Cannot create sparse image " + H.name() + "; no knowledge of underlying data class type");
Header::const_iterator size_it = H.find (Image::Sparse::size_key);
if (size_it == H.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 = out.tellp() + int64_t(54);
image_offset += ((4 - (image_offset % 4)) % 4);
sparse_offset = image_offset + Image::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, Image::footprint(H));
File::create (sparse_path);
}
Handler::Default base_handler (H);
base_handler.files.push_back (File::Entry (image_path, image_offset));
std::shared_ptr<Handler::Base> handler (new Handler::Sparse (base_handler, name_it->second, to<size_t>(size_it->second), File::Entry (sparse_path, sparse_offset)));
return handler;
}
RefPtr<Image::Handler::Base> MRtrix_GZ::create (Header& H) const
{
std::stringstream header;
header << "mrtrix image\n";
write_mrtrix_header (H, header);
int64_t offset = header.tellp() + int64_t(24);
offset += ((4 - (offset % 4)) % 4);
header << "file: . " << offset << "\nEND\n";
while (header.tellp() < offset)
header << '\0';
RefPtr<Handler::GZ> handler (new Handler::GZ (H, offset));
memcpy (handler->header(), header.str().c_str(), offset);
File::create (H.name());
handler->files.push_back (File::Entry (H.name(), offset));
return handler;
}
RefPtr<Handler::Base> MRtrix::create (Header& H) const
{
if (!File::is_tempfile (H.name()))
File::create (H.name());
std::ofstream out (H.name().c_str(), std::ios::out | std::ios::binary);
if (!out)
throw Exception ("error creating file \"" + H.name() + "\":" + strerror (errno));
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 = 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();
RefPtr<Handler::Base> handler (new Handler::Default (H));
if (single_file) {
File::resize (H.name(), offset + Image::footprint(H));
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, Image::footprint(H));
handler->files.push_back (File::Entry (data_file));
}
return handler;
}
