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#include "fftw3.h"
#include "ismrmrd/meta.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;
// Helper function for the FFTW library
void circshift(complex_float_t *out, const complex_float_t *in, int xdim, int ydim, int xshift, int yshift) {
for (int i = 0; i < ydim; i++) {
int ii = (i + yshift) % ydim;
for (int j = 0; j < xdim; j++) {
int jj = (j + xshift) % xdim;
out[ii * xdim + jj] = in[i * xdim + j];
}
}
}
#define fftshift(out, in, x, y) circshift(out, in, x, y, (x / 2), (y / 2))
void reconstruct(std::istream &in, std::ostream &out, bool magnitude = false) {
ISMRMRD::IStreamView rs(in);
ISMRMRD::OStreamView ws(out);
ISMRMRD::ProtocolDeserializer deserializer(rs);
ISMRMRD::ProtocolSerializer serializer(ws);
if (deserializer.peek() == ISMRMRD::ISMRMRD_MESSAGE_CONFIG_FILE) {
ISMRMRD::ConfigFile cfg;
deserializer.deserialize(cfg);
std::string config_name(cfg.config);
std::cerr << "Reconstruction received config file: " << config_name << std::endl;
std::cerr << "Configuration file is ignored in this sample reconstruction" << std::endl;
}
if (deserializer.peek() == ISMRMRD::ISMRMRD_MESSAGE_TEXT) {
ISMRMRD::TextMessage msg;
deserializer.deserialize(msg);
std::cerr << "Reconstruction received text message prior to config: " << std::endl
<< msg.message << std::endl;
}
ISMRMRD::IsmrmrdHeader hdr;
deserializer.deserialize(hdr);
if (hdr.encoding.size() != 1) {
throw std::runtime_error("This simple reconstruction application only supports one encoding space");
}
ISMRMRD::EncodingSpace e_space = hdr.encoding[0].encodedSpace;
ISMRMRD::EncodingSpace r_space = hdr.encoding[0].reconSpace;
if (e_space.matrixSize.z != 1) {
throw std::runtime_error("This simple reconstruction application only supports 2D encoding spaces");
}
uint16_t nX = e_space.matrixSize.x;
uint16_t nY = e_space.matrixSize.y;
uint16_t nCoils = 0;
ISMRMRD::NDArray<complex_float_t> buffer;
ISMRMRD::AcquisitionHeader acqhdr;
while (std::cin) {
ISMRMRD::Acquisition acq;
try {
deserializer.deserialize(acq);
} catch (ISMRMRD::ProtocolStreamClosed &) {
break;
}
if (!nCoils) {
nCoils = acq.active_channels();
acqhdr = acq.getHead();
// Allocate a buffer for the data
std::vector<size_t> dims;
dims.push_back(nX);
dims.push_back(nY);
dims.push_back(nCoils);
buffer = ISMRMRD::NDArray<complex_float_t>(dims);
std::fill(buffer.begin(), buffer.end(), complex_float_t(0.0f, 0.0f));
}
for (uint16_t c = 0; c < nCoils; c++) {
memcpy(&buffer(0, acq.idx().kspace_encode_step_1, c), &acq.data(0, c), sizeof(complex_float_t) * nX);
}
}
for (uint16_t c = 0; c < nCoils; c++) {
fftwf_complex *tmp = (fftwf_complex *)fftwf_malloc(sizeof(fftwf_complex) * (nX * nY));
if (!tmp) {
throw std::runtime_error("Error allocating temporary storage for FFTW");
}
fftwf_plan p = fftwf_plan_dft_2d(nY, nX, tmp, tmp, FFTW_BACKWARD, FFTW_ESTIMATE);
fftshift(reinterpret_cast<complex_float_t *>(tmp), &buffer(0, 0, c), nX, nY);
fftwf_execute(p);
fftshift(&buffer(0, 0, c), reinterpret_cast<std::complex<float> *>(tmp), nX, nY);
fftwf_destroy_plan(p);
fftwf_free(tmp);
}
// Allocate an image
ISMRMRD::Image<std::complex<float> > img_out(r_space.matrixSize.x, r_space.matrixSize.y, 1, 1);
std::fill(img_out.begin(), img_out.end(), std::complex<float>(0.0f, 0.0f));
// if there is oversampling in the readout direction remove it
uint16_t offset = ((e_space.matrixSize.x - r_space.matrixSize.x) >> 1);
// Take the sqrt of the sum of squares
for (uint16_t y = 0; y < r_space.matrixSize.y; y++) {
for (uint16_t x = 0; x < r_space.matrixSize.x; x++) {
float mag = 0;
float phase = 0;
for (uint16_t c = 0; c < nCoils; c++) {
std::complex<float> val = buffer(x + offset, y, c);
float w = std::abs(val) * std::abs(val);
mag += w;
phase += std::arg(val) * w;
}
img_out(x, y) = std::polar<float>(std::sqrt(mag), phase / mag);
}
}
img_out.setImageType(ISMRMRD::ISMRMRD_IMTYPE_COMPLEX);
img_out.setSlice(0);
img_out.setFieldOfView(r_space.fieldOfView_mm.x, r_space.fieldOfView_mm.y, r_space.fieldOfView_mm.z);
img_out.setPosition(acqhdr.position[0], acqhdr.position[1], acqhdr.position[2]);
img_out.setPatientTablePosition(acqhdr.patient_table_position[0], acqhdr.patient_table_position[1], acqhdr.patient_table_position[2]);
img_out.setReadDirection(acqhdr.read_dir[0], acqhdr.read_dir[1], acqhdr.read_dir[2]);
img_out.setPhaseDirection(acqhdr.phase_dir[0], acqhdr.phase_dir[1], acqhdr.phase_dir[2]);
img_out.setSliceDirection(acqhdr.slice_dir[0], acqhdr.slice_dir[1], acqhdr.slice_dir[2]);
ISMRMRD::MetaContainer meta;
meta.append("ImageRowDir", acqhdr.read_dir[0]);
meta.append("ImageRowDir", acqhdr.read_dir[1]);
meta.append("ImageRowDir", acqhdr.read_dir[2]);
meta.append("ImageColumnDir", acqhdr.phase_dir[0]);
meta.append("ImageColumnDir", acqhdr.phase_dir[1]);
meta.append("ImageColumnDir", acqhdr.phase_dir[2]);
std::stringstream meta_string_stream;
ISMRMRD::serialize(meta, meta_string_stream);
img_out.setAttributeString(meta_string_stream.str().c_str());
// If this we want magnitude:
if (magnitude) {
ISMRMRD::Image<float> float_img_out(img_out.getMatrixSizeX(), img_out.getMatrixSizeY(), 1, 1);
ISMRMRD::ImageHeader head = img_out.getHead();
head.image_type = ISMRMRD::ISMRMRD_IMTYPE_MAGNITUDE;
head.data_type = ISMRMRD::ISMRMRD_FLOAT;
float_img_out.setHead(head);
float_img_out.setAttributeString(meta_string_stream.str().c_str());
for (size_t i = 0; i < img_out.getNumberOfDataElements(); i++) {
float_img_out.getDataPtr()[i] = std::abs(img_out.getDataPtr()[i]);
}
serializer.serialize(float_img_out);
} else {
serializer.serialize(img_out);
}
serializer.close();
}
int main(int argc, char **argv) {
// Parse arguments using boost program options
po::options_description desc("Allowed options");
// Arguments
std::string input_file = "";
std::string output_file = "";
bool use_stdin = false;
bool use_stdout = false;
bool output_magnitude = false; // Default output images is complex float
// clang-format off
desc.add_options()
("help,h", "produce help message")
("input,i", po::value<std::string>(&input_file),"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")
("use-stdin", po::bool_switch(&use_stdin), "Use stdout for output")
("output-magnitude", po::bool_switch(&output_magnitude), "Output magnitude images");
// clang-format on
po::variables_map vm;
po::store(po::parse_command_line(argc, argv, desc), vm);
po::notify(vm);
if (vm.count("help")) {
std::cerr << desc << "\n";
return 1;
}
if (vm.count("input") && use_stdin) {
std::cerr << "Error: Cannot specify both input file and use-stdin" << std::endl;
return 1;
}
if (vm.count("output") && use_stdout) {
std::cerr << "Error: Cannot specify both output file and use-stdout" << std::endl;
return 1;
}
if (use_stdin && use_stdout) {
ISMRMRD::set_binary_io();
reconstruct(std::cin, std::cout, output_magnitude);
} else if (input_file.size() && output_file.size()) {
std::ifstream input(input_file.c_str(), std::ios::in | std::ios::binary);
std::ofstream output(output_file.c_str(), std::ios::out | std::ios::binary);
reconstruct(input, output, output_magnitude);
} else if (input_file.size() && use_stdout) {
ISMRMRD::set_binary_io();
std::ifstream input(input_file.c_str(), std::ios::in | std::ios::binary);
reconstruct(input, std::cout, output_magnitude);
} else if (output_file.size() && use_stdin) {
ISMRMRD::set_binary_io();
std::ofstream output(output_file.c_str(), std::ios::out | std::ios::binary);
reconstruct(std::cin, output, output_magnitude);
} else {
std::cerr << "Error: Must specify either input file and output file or use-stdin and use-stdout" << std::endl;
return 1;
}
return 0;
}
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