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/*
* generate_cartesian_shepp_logan.cpp
*
* Created on: Apr 1, 2013
* Author: Michael S. Hansen
*
*/
#include <iostream>
#include <boost/uuid/uuid.hpp>
#include <boost/uuid/uuid_generators.hpp>
#include <boost/uuid/uuid_io.hpp>
#include "ismrmrd/ismrmrd.h"
#include "ismrmrd/xml.h"
#include "ismrmrd/dataset.h"
#include "ismrmrd/version.h"
#include "ismrmrd_phantom.h"
#include "ismrmrd_fftw.h"
#include <boost/program_options.hpp>
using namespace ISMRMRD;
namespace po = boost::program_options;
// MAIN APPLICATION
int main(int argc, char** argv)
{
/** TODO
*
* Noise samples
* Acceleration
* k-space coordinates
*
*/
unsigned int matrix_size; //Matrix size
uint16_t ncoils; //Number of coils
unsigned int ros; //Readout ovesampling
unsigned int repetitions;
unsigned int acc_factor;
unsigned int cal_width; // Calibration area width (readouts)
float noise_level;
std::string outfile;
std::string dataset;
bool store_coordinates = false;
bool noise_calibration = false;
po::options_description desc("Allowed options");
desc.add_options()
("help,h", "produce help message")
("matrix,m", po::value<unsigned int>(&matrix_size)->default_value(256), "Matrix Size")
("coils,c", po::value<uint16_t>(&ncoils)->default_value(8), "Number of Coils")
("oversampling,O", po::value<unsigned int>(&ros)->default_value(2), "Readout oversampling")
("repetitions,r", po::value<unsigned int>(&repetitions)->default_value(1), "Repetitions")
("acceleration,a", po::value<unsigned int>(&acc_factor)->default_value(1), "Acceleration factor")
("calibration-width,w", po::value<unsigned int>(&cal_width)->default_value(0), "Calibration area width")
("noise-level,n", po::value<float>(&noise_level)->default_value(0.05f,"0.05"), "Noise Level")
("output,o", po::value<std::string>(&outfile)->default_value("testdata.h5"), "Output File Name")
("dataset,d", po::value<std::string>(&dataset)->default_value("dataset"), "Output Dataset Name")
("noise-calibration,C", po::value<bool>(&noise_calibration)->zero_tokens(), "Add noise calibration")
("k-coordinates,k", po::value<bool>(&store_coordinates)->zero_tokens(), "Store k-space coordinates")
;
po::variables_map vm;
po::store(po::parse_command_line(argc, argv, desc), vm);
po::notify(vm);
if (vm.count("help")) {
std::cout << desc << "\n";
return 1;
}
std::cout << "Generating Cartesian Shepp Logan Phantom!!!" << std::endl;
std::cout << "Acceleration: " << acc_factor << std::endl;
boost::shared_ptr<NDArray<complex_float_t> > phantom = shepp_logan_phantom(matrix_size);
boost::shared_ptr<NDArray<complex_float_t> > coils = generate_birdcage_sensitivities(matrix_size, ncoils, 1.5);
std::vector<size_t> dims;
dims.push_back(matrix_size*ros); //oversampling in the readout direction
dims.push_back(matrix_size);
dims.push_back(ncoils);
NDArray<complex_float_t> coil_images(dims);
std::fill(coil_images.begin(), coil_images.end(), complex_float_t(0.0f, 0.0f));
for (unsigned int c = 0; c < ncoils; c++) {
for (unsigned int y = 0; y < matrix_size; y++) {
for (unsigned int x = 0; x < matrix_size; x++) {
uint16_t xout = x + (matrix_size*ros-matrix_size)/2;
coil_images(xout,y,c) = (*phantom)(x,y) * (*coils)(x,y,c);
}
}
}
//Let's append the data to the file
//Create if needed
Dataset d(outfile.c_str(),dataset.c_str(), true);
Acquisition acq;
uint16_t readout = static_cast<uint16_t>(matrix_size*ros);
if (noise_calibration)
{
acq.resize(readout, ncoils);
memset((void *)acq.getDataPtr(), 0, acq.getDataSize());
acq.setFlag(ISMRMRD_ACQ_IS_NOISE_MEASUREMENT);
add_noise(acq,noise_level);
acq.sample_time_us() = 5.0;
d.appendAcquisition(acq);
}
if (store_coordinates) {
acq.resize(readout, ncoils, 2);
}
else {
acq.resize(readout, ncoils);
}
memset((void*)acq.getDataPtr(), 0, acq.getDataSize());
acq.available_channels() = ncoils;
acq.center_sample() = (readout>>1);
int hw = cal_width/2;
int from = matrix_size / 2 - hw;
int till = matrix_size / 2 + hw - 1;
for (unsigned int r = 0; r < repetitions; r++) {
for (unsigned int a = 0; a < acc_factor; a++) {
NDArray<complex_float_t> cm = coil_images;
fft2c(cm);
add_noise(cm,noise_level);
for (int64_t i = 0; i < matrix_size; i++) {
if ((i - a)%acc_factor && !(i >= from && i <= till))
continue; // skip this readout
//Set some flags
acq.clearAllFlags();
if (i == a) {
acq.setFlag(ISMRMRD_ACQ_FIRST_IN_SLICE);
}
else if (i >= (matrix_size-acc_factor)) {
acq.setFlag(ISMRMRD_ACQ_LAST_IN_SLICE);
}
else if (i >= from && i <= till) {
if ((i - a) % acc_factor)
acq.setFlag(ISMRMRD_ACQ_IS_PARALLEL_CALIBRATION);
else
acq.setFlag(ISMRMRD_ACQ_IS_PARALLEL_CALIBRATION_AND_IMAGING);
}
acq.idx().kspace_encode_step_1 = static_cast<uint16_t>(i);
acq.idx().repetition = r*acc_factor + a;
acq.sample_time_us() = 5.0;
for (uint16_t c = 0; c < ncoils; c++) {
for (uint16_t s = 0; s < readout; s++) {
acq.data(s,c) = cm(s, static_cast<uint16_t>(i), c);
}
}
if (store_coordinates) {
float ky = (1.0f*i-(matrix_size>>1))/(1.0f*matrix_size);
for (uint16_t x = 0; x < readout; x++) {
float kx = (1.0f*x-(readout>>1))/(1.0f*readout);
acq.traj(0,x) = kx;
acq.traj(1,x) = ky;
}
}
d.appendAcquisition(acq);
}
}
}
//Let's create a header, we will use the C++ classes in ismrmrd/xml.h
IsmrmrdHeader h;
h.version = ISMRMRD_XMLHDR_VERSION;
h.experimentalConditions.H1resonanceFrequency_Hz = 63500000; //~1.5T
AcquisitionSystemInformation sys;
sys.institutionName = "ISMRM Synthetic Imaging Lab";
sys.receiverChannels = ncoils;
h.acquisitionSystemInformation = sys;
SubjectInformation subject;
subject.patientID = "ISMRMRDSheppLoganPhantom";
h.subjectInformation = subject;
MeasurementInformation meas;
boost::uuids::random_generator uuidGenerator;
meas.measurementID = boost::uuids::to_string(uuidGenerator());
meas.patientPosition = "HFS";
h.measurementInformation = meas;
//Create an encoding section
Encoding e;
e.encodedSpace.matrixSize.x = readout;
e.encodedSpace.matrixSize.y = matrix_size;
e.encodedSpace.matrixSize.z = 1;
e.encodedSpace.fieldOfView_mm.x = 600;
e.encodedSpace.fieldOfView_mm.y = 300;
e.encodedSpace.fieldOfView_mm.z = 6;
e.reconSpace.matrixSize.x = readout/2;
e.reconSpace.matrixSize.y = matrix_size;
e.reconSpace.matrixSize.z = 1;
e.reconSpace.fieldOfView_mm.x = 300;
e.reconSpace.fieldOfView_mm.y = 300;
e.reconSpace.fieldOfView_mm.z = 6;
e.trajectory = TrajectoryType::CARTESIAN;
e.encodingLimits.kspace_encoding_step_1 = Limit(0, matrix_size-1,(matrix_size>>1));
e.encodingLimits.repetition = Limit(0, repetitions*acc_factor - 1,0);
//e.g. parallel imaging
if (acc_factor > 1) {
ParallelImaging parallel;
parallel.accelerationFactor.kspace_encoding_step_1 = acc_factor;
parallel.accelerationFactor.kspace_encoding_step_2 = 1;
parallel.calibrationMode = "interleaved";
e.parallelImaging = parallel;
}
//Add the encoding section to the header
h.encoding.push_back(e);
//Add any additional fields that you may want would go here....
//Serialize the header
std::stringstream str;
ISMRMRD::serialize( h, str);
std::string xml_header = str.str();
//std::cout << xml_header << std::endl;
//Write the header to the data file.
d.writeHeader(xml_header);
//Write out some arrays for convenience
d.appendNDArray("phantom", *phantom);
d.appendNDArray("csm", *coils);
d.appendNDArray("coil_images", coil_images);
return 0;
}
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