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#include "ismrmrd/dataset.h"
#include "ismrmrd/serialization_iostream.h"
#include "ismrmrd_io_utils.h"
#include <boost/program_options.hpp>
#include <fstream>
#include <iostream>
namespace po = boost::program_options;
template <typename T>
std::string create_image_series_name(const ISMRMRD::Image<T> &img) {
std::stringstream ss;
ss.imbue(std::locale::classic());
ss << "image_" << img.getHead().image_series_index;
return ss.str();
}
template <typename T>
std::string create_nd_array_name(const ISMRMRD::NDArray<T> &arr) {
std::stringstream ss;
ss.imbue(std::locale::classic());
ss << "array_ver_" << arr.getVersion() << "_dim_";
for (uint16_t ii=0; ii<arr.getNDim(); ii++) ss << arr.getDims()[ii] << "_";
ss << "datatype_" << arr.getDataType();
return ss.str();
}
void convert_stream_to_hdf5(std::string output_file, std::string groupname, std::istream &is) {
ISMRMRD::Dataset d(output_file.c_str(), groupname.c_str(), true);
ISMRMRD::IStreamView rs(is);
ISMRMRD::ProtocolDeserializer deserializer(rs);
// Some reconstructions return the header but it is not required.
if (deserializer.peek() == ISMRMRD::ISMRMRD_MESSAGE_HEADER) {
ISMRMRD::IsmrmrdHeader hdr;
deserializer.deserialize(hdr);
// We will convert the XML header to a string and write it to the HDF5 file
std::stringstream xmlstream(std::ios::out | std::ios::binary);
ISMRMRD::serialize(hdr, xmlstream);
d.writeHeader(xmlstream.str());
}
while (deserializer.peek() != ISMRMRD::ISMRMRD_MESSAGE_CLOSE) {
if (deserializer.peek() == ISMRMRD::ISMRMRD_MESSAGE_ACQUISITION) {
ISMRMRD::Acquisition acq;
deserializer.deserialize(acq);
d.appendAcquisition(acq);
} else if (deserializer.peek() == ISMRMRD::ISMRMRD_MESSAGE_IMAGE) {
if (deserializer.peek_image_data_type() == ISMRMRD::ISMRMRD_USHORT) {
ISMRMRD::Image<unsigned short> img;
deserializer.deserialize(img);
d.appendImage(create_image_series_name(img), img);
} else if (deserializer.peek_image_data_type() == ISMRMRD::ISMRMRD_SHORT) {
ISMRMRD::Image<short> img;
deserializer.deserialize(img);
d.appendImage(create_image_series_name(img), img);
} else if (deserializer.peek_image_data_type() == ISMRMRD::ISMRMRD_UINT) {
ISMRMRD::Image<unsigned int> img;
deserializer.deserialize(img);
d.appendImage(create_image_series_name(img), img);
} else if (deserializer.peek_image_data_type() == ISMRMRD::ISMRMRD_INT) {
ISMRMRD::Image<int> img;
deserializer.deserialize(img);
d.appendImage(create_image_series_name(img), img);
} else if (deserializer.peek_image_data_type() == ISMRMRD::ISMRMRD_FLOAT) {
ISMRMRD::Image<float> img;
deserializer.deserialize(img);
d.appendImage(create_image_series_name(img), img);
} else if (deserializer.peek_image_data_type() == ISMRMRD::ISMRMRD_DOUBLE) {
ISMRMRD::Image<double> img;
deserializer.deserialize(img);
d.appendImage(create_image_series_name(img), img);
} else if (deserializer.peek_image_data_type() == ISMRMRD::ISMRMRD_CXFLOAT) {
ISMRMRD::Image<std::complex<float> > img;
deserializer.deserialize(img);
d.appendImage(create_image_series_name(img), img);
} else if (deserializer.peek_image_data_type() == ISMRMRD::ISMRMRD_CXDOUBLE) {
ISMRMRD::Image<std::complex<double> > img;
deserializer.deserialize(img);
d.appendImage(create_image_series_name(img), img);
} else {
throw std::runtime_error("Unknown image type");
}
} else if (deserializer.peek() == ISMRMRD::ISMRMRD_MESSAGE_WAVEFORM) {
ISMRMRD::Waveform wfm;
deserializer.deserialize(wfm);
d.appendWaveform(wfm);
} else if (deserializer.peek() == ISMRMRD::ISMRMRD_MESSAGE_NDARRAY) {
if (deserializer.peek_ndarray_data_type() == ISMRMRD::ISMRMRD_USHORT) {
ISMRMRD::NDArray<unsigned short> arr;
deserializer.deserialize(arr);
d.appendNDArray(create_nd_array_name(arr), arr);
} else if (deserializer.peek_ndarray_data_type() == ISMRMRD::ISMRMRD_SHORT) {
ISMRMRD::NDArray<short> arr;
deserializer.deserialize(arr);
d.appendNDArray(create_nd_array_name(arr), arr);
} else if (deserializer.peek_ndarray_data_type() == ISMRMRD::ISMRMRD_UINT) {
ISMRMRD::NDArray<unsigned int> arr;
deserializer.deserialize(arr);
d.appendNDArray(create_nd_array_name(arr), arr);
} else if (deserializer.peek_ndarray_data_type() == ISMRMRD::ISMRMRD_INT) {
ISMRMRD::NDArray<int> arr;
deserializer.deserialize(arr);
d.appendNDArray(create_nd_array_name(arr), arr);
} else if (deserializer.peek_ndarray_data_type() == ISMRMRD::ISMRMRD_FLOAT) {
ISMRMRD::NDArray<float> arr;
deserializer.deserialize(arr);
d.appendNDArray(create_nd_array_name(arr), arr);
} else if (deserializer.peek_ndarray_data_type() == ISMRMRD::ISMRMRD_DOUBLE) {
ISMRMRD::NDArray<double> arr;
deserializer.deserialize(arr);
d.appendNDArray(create_nd_array_name(arr), arr);
} else if (deserializer.peek_ndarray_data_type() == ISMRMRD::ISMRMRD_CXFLOAT) {
ISMRMRD::NDArray<std::complex<float> > arr;
deserializer.deserialize(arr);
d.appendNDArray(create_nd_array_name(arr), arr);
} else if (deserializer.peek_ndarray_data_type() == ISMRMRD::ISMRMRD_CXDOUBLE) {
ISMRMRD::NDArray<std::complex<double> > arr;
deserializer.deserialize(arr);
d.appendNDArray(create_nd_array_name(arr), arr);
} else {
throw std::runtime_error("Unknown nd array type");
}
} else if (deserializer.peek() == ISMRMRD::ISMRMRD_MESSAGE_TEXT) {
ISMRMRD::TextMessage txt;
deserializer.deserialize(txt);
std::cerr << "TEXT MESSAGE: " << txt.message << std::endl;
} else {
std::stringstream ss;
ss << "Unknown message type " << deserializer.peek();
throw std::runtime_error(ss.str());
}
}
// If we can read any more at this point, it is an error
if (is.get() != EOF) {
throw std::runtime_error("Extra data after ISMRMRD_CLOSE");
}
}
int main(int argc, char **argv) {
// Arguments
std::string input_file = "";
std::string output_file;
std::string groupname;
bool use_stdin = false;
// Parse arguments using boost program options
po::options_description desc("Allowed options");
// clang-format off
desc.add_options()
("help,h", "produce help message")
("input,i", po::value<std::string>(&input_file),"Binary input file")
("output,o", po::value<std::string>(&output_file)->required(),"ISMRMRD HDF5 output file")
("use-stdin", po::bool_switch(&use_stdin), "Use stdout for output")
("group,g", po::value<std::string>(&groupname)->default_value("dataset"), "group name");
// clang-format on
po::variables_map vm;
try {
po::store(po::parse_command_line(argc, argv, desc), vm);
po::notify(vm);
} catch (boost::wrapexcept<po::required_option> &e) {
std::cerr << "Error: " << e.what() << std::endl;
std::cerr << desc << std::endl;
return 1;
}
if (vm.count("input") && use_stdin) {
std::cerr << "Error: Cannot specify both output file and use-stdout" << std::endl;
return 1;
}
if (vm.count("help")) {
std::cerr << desc << "\n";
return 1;
}
if (vm.count("input")) {
std::ifstream is(input_file.c_str(), std::ios::binary);
if (!is) {
std::cerr << "Error: Could not open input file " << input_file << std::endl;
return 1;
}
convert_stream_to_hdf5(output_file, groupname, is);
} else if (use_stdin) {
ISMRMRD::set_binary_io();
convert_stream_to_hdf5(output_file, groupname, std::cin);
} else {
std::cerr << "Error: Must specify either input file or use-stdin" << std::endl;
return 1;
}
return 0;
}
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