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#include "ismrmrd/dataset.h"
#include "ismrmrd/serialization.h"
#include "ismrmrd/serialization_iostream.h"
#include "ismrmrd_io_utils.h"
#include <boost/program_options.hpp>
#include <fstream>
#include <iostream>
#include <string>
namespace po = boost::program_options;
void serialize_to_stream(const std::string &input_file, const std::string &groupname, const std::vector<std::string> &image_series, std::ostream &os, std::string config_file, std::string config_text) {
ISMRMRD::Dataset d(input_file.c_str(), groupname.c_str(), false);
ISMRMRD::OStreamView ws(os);
ISMRMRD::ProtocolSerializer serializer(ws);
if (config_file.size()) {
ISMRMRD::ConfigFile cfg;
strcpy(cfg.config, config_file.c_str());
serializer.serialize(cfg);
}
if (config_text.size()) {
ISMRMRD::ConfigText cfg;
cfg.config_text = config_text;
serializer.serialize(cfg);
}
try {
std::string xml;
d.readHeader(xml);
ISMRMRD::IsmrmrdHeader hdr;
ISMRMRD::deserialize(xml.c_str(), hdr);
serializer.serialize(hdr);
} catch (std::exception &) {
if (image_series.empty()) {
// rethrow exception if image series not specified
throw;
}
}
// If user has asked for image series, we will only send images,
// otherwise we will send acquisitions and waveforms.
if (!image_series.empty()) {
for (size_t s = 0; s < image_series.size(); s++) {
unsigned int number_of_images = d.getNumberOfImages(image_series[s].c_str());
for (unsigned int i = 0; i < number_of_images; i++) {
// Danger: Here we will take advantage of the fact that the
// C++ wrapper calls ismrmrd_read_image (C API) without checking
// that the type is correct. This is a bug in the C++ wrapper.
ISMRMRD::Image<complex_double_t> img;
d.readImage(image_series[s].c_str(), i, img);
if (img.getHead().data_type == ISMRMRD::ISMRMRD_USHORT) {
ISMRMRD::Image<unsigned short> *img_ushort = reinterpret_cast<ISMRMRD::Image<unsigned short> *>(&img);
serializer.serialize(*img_ushort);
} else if (img.getHead().data_type == ISMRMRD::ISMRMRD_SHORT) {
ISMRMRD::Image<short> *img_short = reinterpret_cast<ISMRMRD::Image<short> *>(&img);
serializer.serialize(*img_short);
} else if (img.getHead().data_type == ISMRMRD::ISMRMRD_UINT) {
ISMRMRD::Image<unsigned int> *img_uint = reinterpret_cast<ISMRMRD::Image<unsigned int> *>(&img);
serializer.serialize(*img_uint);
} else if (img.getHead().data_type == ISMRMRD::ISMRMRD_INT) {
ISMRMRD::Image<int> *img_int = reinterpret_cast<ISMRMRD::Image<int> *>(&img);
serializer.serialize(*img_int);
} else if (img.getHead().data_type == ISMRMRD::ISMRMRD_FLOAT) {
ISMRMRD::Image<float> *img_float = reinterpret_cast<ISMRMRD::Image<float> *>(&img);
serializer.serialize(*img_float);
} else if (img.getHead().data_type == ISMRMRD::ISMRMRD_DOUBLE) {
ISMRMRD::Image<double> *img_double = reinterpret_cast<ISMRMRD::Image<double> *>(&img);
serializer.serialize(*img_double);
} else if (img.getHead().data_type == ISMRMRD::ISMRMRD_CXFLOAT) {
ISMRMRD::Image<complex_float_t> *img_cxfloat = reinterpret_cast<ISMRMRD::Image<complex_float_t> *>(&img);
serializer.serialize(*img_cxfloat);
} else if (img.getHead().data_type == ISMRMRD::ISMRMRD_CXDOUBLE) {
serializer.serialize(img);
} else {
throw std::runtime_error("Unknown data type");
}
}
}
} else {
// Here we implement the pattern of merge sorting acquisitions and waveforms based on timestamp.
// For each dataset of waveforms and acquisitions, we will assume that they are sorted by timestamp.
unsigned int number_of_acquisitions = d.getNumberOfAcquisitions();
unsigned int number_of_waveforms = d.getNumberOfWaveforms();
unsigned int a = 0, a_fetched = number_of_acquisitions, w = 0, w_fetched = number_of_waveforms;
ISMRMRD::Acquisition acq;
ISMRMRD::Waveform wfm;
while (a < number_of_acquisitions || w < number_of_waveforms) {
if (a < number_of_acquisitions && a_fetched != a) {
d.readAcquisition(a, acq);
a_fetched = a;
}
if (w < number_of_waveforms && w_fetched != w) {
d.readWaveform(w, wfm);
w_fetched = w;
}
// If we have both acquisitions and waveforms, advance the one with the
// smaller timestamp, otherwise advance the one that exists
if (a < number_of_acquisitions && w < number_of_waveforms) {
if (acq.getHead().acquisition_time_stamp < wfm.head.time_stamp) {
serializer.serialize(acq);
a++;
} else {
serializer.serialize(wfm);
w++;
}
} else if (a < number_of_acquisitions) {
serializer.serialize(acq);
a++;
} else {
serializer.serialize(wfm);
w++;
}
}
}
serializer.close();
}
int main(int argc, char **argv) {
// Parse arguments using boost program options
po::options_description desc("Allowed options");
// Arguments
std::string config_file = "";
std::string local_config_file = "";
std::string config_text = "";
std::string input_file;
std::string output_file = "";
bool use_stdout = false;
std::vector<std::string> image_series;
std::string groupname;
// clang-format off
desc.add_options()
("help,h", "produce help message")
("input,i", po::value<std::string>(&input_file)->required(),"input ISMRMRD HDF5 file")
("output,o", po::value<std::string>(&output_file),"Binary output file")
("use-stdout", po::bool_switch(&use_stdout), "Use stdout for output")
("group,g", po::value<std::string>(&groupname)->default_value("dataset"), "group name")
("image-series,s", po::value<std::vector<std::string> >(&image_series)->multitoken(), "image series to extract")
("config-file,c", po::value<std::string>(&config_file), "Configuration name (aka config file)")
("local-config-file,C", po::value<std::string>(&local_config_file), "Configuration text file");
// 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("help")) {
std::cerr << desc << "\n";
return 1;
}
if (vm.count("output") && use_stdout) {
std::cerr << "Error: Cannot specify both output file and use-stdout" << std::endl;
return 1;
}
if (vm.count("config-file") && vm.count("local-config-file")) {
std::cerr << "Error: Cannot specify both config-name and config-text-file" << std::endl;
return 1;
}
// Read config text file into string
if (vm.count("local-config-file")) {
std::ifstream f(local_config_file.c_str());
std::stringstream buffer;
buffer << f.rdbuf();
config_text = buffer.str();
}
if (use_stdout) {
ISMRMRD::set_binary_io();
serialize_to_stream(input_file, groupname, image_series, std::cout, config_file, config_text);
} else if (output_file != "") {
std::ofstream out(output_file.c_str(), std::ios::out | std::ios::binary);
serialize_to_stream(input_file, groupname, image_series, out, config_file, config_text);
} else {
std::cerr << "Error: Must specify either output file or use-stdout" << std::endl;
return 1;
}
return 0;
}
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