std::shared_ptr<Handler::Base> MRtrix_sparse::read (Header& H) const
{
if (!Path::has_suffix (H.name(), ".msh") && !Path::has_suffix (H.name(), ".msf"))
return std::shared_ptr<Handler::Base>();
File::KeyValue 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::Buffer<> 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());
Header::const_iterator name_it = H.find (Image::Sparse::name_key);
if (name_it == H.end())
throw Exception ("sparse data class name not specified in sparse image header " + H.name());
Header::const_iterator size_it = H.find (Image::Sparse::size_key);
if (size_it == H.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);
ParsedName::List image_list;
std::vector<int> image_num = image_list.parse_scan_check (image_fname);
get_mrtrix_file_path (H, "sparse_file", sparse_fname, sparse_offset);
Handler::Default base_handler (H);
for (size_t n = 0; n < image_list.size(); ++n)
base_handler.files.push_back (File::Entry (image_list[n].name(), 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_fname, sparse_offset)));
return handler;
}
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;
}
RefPtr<Handler::Base> MRtrix::read (Header& H) const
{
if (!Path::has_suffix (H.name(), ".mih") && !Path::has_suffix (H.name(), ".mif"))
return RefPtr<Handler::Base>();
File::KeyValue kv (H.name(), "mrtrix image");
read_mrtrix_header (H, kv);
std::string fname;
size_t offset;
get_mrtrix_file_path (H, "file", fname, offset);
ParsedName::List list;
std::vector<int> num = list.parse_scan_check (fname);
RefPtr<Handler::Base> handler (new Handler::Default (H));
for (size_t n = 0; n < list.size(); ++n)
handler->files.push_back (File::Entry (list[n].name(), offset));
return handler;
}