// ==================================================================================================================
// BEGIN: main
// ==================================================================================================================
int main(int argc, char *argv[])
{
OptionsParser op;
if (!op.ParseOptions(argc, argv))
return -1;
std::string outputDir = utils::GetParentDirectory(op.outputFilename);
communicator_type com;
com.allocateGPU();
agile::GPUTimer timer;
timer.start();
agile::GPUEnvironment::printInformation(std::cout);
std::cout << std::endl;
// kdata
CVector kdata;
// kspace mask/trajectory
RVector mask;
// density compensation in case of nonuniform data
RVector w(0);
// get data dimensions
std::string extension = utils::GetFileExtension(op.kdataFilename);
std::cout << "Extension:" << extension << std::endl;
Dimension dims; // = op.dims;
if (extension.compare(".bin") == 0)
dims = op.dims;
else if (extension.compare(".cfl") == 0)
{
long dimensions[4];
utils::ReadCflHeader(op.kdataFilename, dimensions);
dims.width=dimensions[0];
dims.height=dimensions[1];
dims.depth=dimensions[2];
dims.readouts=dimensions[0];
dims.encodings=dimensions[1];
dims.encodings2=dimensions[2];
dims.coils=dimensions[3];
dims.frames=dimensions[3];
std::cout << "DIMS main; nx: " << dims.width << " / ny:" << dims.height << " / nz:" << dims.depth << " / nc:" << dims.coils << std::endl;
std::cout << "DIMS main; nRO: " << dims.readouts << " / nENC1:" << dims.encodings << " / nENC2:" << dims.encodings2 << " / nframes:" << dims.frames << std::endl;
}
if (op.rawdata)
{
PerformRawDataPreparation(dims, op, kdata, mask, w);
}
else
{
std::cout << "Binary files defined...." << std::endl;
if (!LoadGPUVectorFromFile(op.kdataFilename, kdata))
return -1;
else
std::cout << "Data File " << op.kdataFilename << " successfully loaded." << std::endl;
if (!LoadGPUVectorFromFile(op.maskFilename, mask))
return -1;
else
std::cout << "Mask File " << op.maskFilename << " successfully loaded." << std::endl;
// set values in data-array to zero according to mask
if (!op.nonuniform)
{
if (op.method==TGV2_3D)
{
for (unsigned coil = 0; coil < dims.coils; coil++)
{
unsigned offset = dims.width * dims.height * dims.depth * coil;
agile::lowlevel::multiplyElementwise(
kdata.data() + offset, mask.data(),
kdata.data() + offset, dims.width * dims.height * dims.depth);
}
}
else
{
for (unsigned frame = 0; frame < dims.frames; frame++)
{
unsigned offset = dims.width * dims.height * dims.coils * frame;
for (unsigned coil = 0; coil < dims.coils; coil++)
{
unsigned int x_offset = offset + coil * dims.width * dims.height;
agile::lowlevel::multiplyElementwise(
kdata.data() + x_offset, mask.data() + dims.width * dims.height * frame,
kdata.data() + x_offset, dims.width * dims.height);
}
}
}
}
}
BaseOperator *baseOp = NULL;
unsigned N;
if (op.method==TGV2_3D)
N = dims.width * dims.height * dims.depth;
else
N = dims.width * dims.height;
CVector b1, u0;
// init b1 and u0
b1 = CVector(N * dims.coils);
b1.assign(N * dims.coils, 1.0);
u0 = CVector(N);
u0.assign(N, 0.0);
// check if b1 and u0 data is provided
if (LoadGPUVectorFromFile(op.sensitivitiesFilename, b1))
{
std::cout << "B1 File " << op.sensitivitiesFilename
<< " successfully loaded." << std::endl;
if (LoadGPUVectorFromFile(op.u0Filename, u0))
{
std::cout << " initial solution (u0) file " << op.u0Filename
<< " successfully loaded." << std::endl;
}
else
{
std::cout << "no initial solution (u0) data provided!" << std::endl;
}
}
else
{
if (op.method==TGV2_3D)
{
std::cerr << "Coil Construction for 3D reconstruction not implemented! Provide b1 seperately!"
<< std::endl;
return -1;
}
std::cout << "Performing Coil Construction!" << std::endl;
CVector u(N * dims.coils);
u.assign(N * dims.coils, 0.0);
if (op.nonuniform)
{
PerformNonCartesianCoilConstruction(dims, op, kdata, u, b1, mask, w, com);
}
else
{
PerformCartesianCoilConstruction(dims, op, kdata, u, b1, mask, com);
}
utils::GetSubVector(u, u0, dims.coils - 1, N);
ExportAdditionalResultsToMatlabBin(outputDir.c_str(),
"b1_reconstructed.bin", b1);
ExportAdditionalResultsToMatlabBin(outputDir.c_str(),
"u0_reconstructed.bin", u0);
}
if (op.nonuniform)
{
unsigned nFE = dims.readouts;
unsigned spokesPerFrame = dims.encodings;
std::cout << "Init NonCartesian Operator using kernelWidth:"
<< op.gpuNUFFTParams.kernelWidth
<< " sectorWidth:" << op.gpuNUFFTParams.sectorWidth
<< " OSF:" << op.gpuNUFFTParams.osf << std::endl;
// Create 2d-t MR Operator
baseOp = new NoncartesianOperator(
dims.width, dims.height, dims.coils, dims.frames,
spokesPerFrame * dims.frames, nFE, spokesPerFrame, mask, w, b1,
op.gpuNUFFTParams.kernelWidth, op.gpuNUFFTParams.sectorWidth,
op.gpuNUFFTParams.osf);
}
else
{
// Create 3d MR Operator
if (op.method==TGV2_3D)
{
baseOp = new CartesianOperator3D(dims.width, dims.height, dims.depth,
dims.coils, mask, false);
}
else
{
baseOp = new CartesianOperator(dims.width, dims.height, dims.coils,
dims.frames, mask, false);
}
}
// ==================================================================================================================
// BEGIN: Perform iterative (TV, TGV2, TGV_3D, ICTGV2) reconstruction
// ==================================================================================================================
PDRecon *recon = NULL;
GenerateReconOperator(&recon, op, baseOp);
CVector x(0); // resize at runtime
if (op.method==TGV2_3D)
{
x.resize(N, 0.0);
agile::copy(u0, x);
}
else
{
x.resize(N * dims.frames, 0.0);
for (unsigned frame = 0; frame < dims.frames; frame++)
{
utils::SetSubVector(u0, x, frame, N);
}
}
std::cout << "Initialization time: " << timer.stop() / 1000 << "s"
<< std::endl;
timer.start();
// run reconstruction
recon->IterativeReconstruction(kdata, x, b1);
std::cout << "Execution time: " << timer.stop() / 1000 << "s" << std::endl;
// ==================================================================================================================
// END: Perform iterative (TV, TGV2, TGV_3D, ICTGV2) reconstruction
// ==================================================================================================================
// ==================================================================================================================
// BEGIN: Define output
// ==================================================================================================================
std::string extension_out = utils::GetFileExtension(op.outputFilename);
std::vector<CType> xHost;
x.copyToHost(xHost);
// write reconstruction to bin file
if (extension_out.compare(".bin") == 0)
{
std::cout << "writing output file to: " << op.outputFilename << std::endl;
agile::writeVectorFile(op.outputFilename.c_str(), xHost);
}
// write reconstruction to h5 file
else if (extension_out.compare(".h5") == 0)
{
std::vector<size_t> dimVec;
dimVec.push_back(dims.width);
dimVec.push_back(dims.height);
dimVec.push_back(dims.frames);
utils::WriteH5File(op.outputFilename, "recon", dimVec, xHost);
}
// write reconstruction to dicom file
else if (extension_out.compare(".dcm") == 0)
{
agile::DICOM dicomfile;
std::string filenamewoe = utils::GetFilename(op.outputFilename);
std::ostringstream ss;
for (unsigned frame = 0; frame < dims.frames; frame++)
{
std::vector<float> xoutmag;
std::vector<float> xoutphs;
for( unsigned i = N*frame; i < N*(frame+1); i++ )
{
xoutmag.push_back( (float)std::sqrt( pow(real(xHost[i]),2) + pow(std::imag(xHost[i]),2) ) ) ;
xoutphs.push_back( (float)std::atan2( real(xHost[i]),std::imag(xHost[i]) ) );
}
ss << std::setw(3) << std::setfill('0') << frame;
// magnitude
const std::string str = ss.str();
std::string outputPath1 = boost::lexical_cast<std::string>(outputDir) + "/" + filenamewoe + "_magframe" + ss.str() + ".dcm";
std::cout << "writing dicom file to: " << outputPath1 << std::endl;
//dicomfile.set_dicominfo(_in_dicomfile.get_dicominfo());
dicomfile.gendicom(outputPath1.c_str(), xoutmag, dims.height, dims.width);
// phase
std::string outputPath2 = boost::lexical_cast<std::string>(outputDir) + "/" + filenamewoe + "_phsframe" + ss.str() + ".dcm";
std::cout << "writing dicom file to: " << outputPath2 << std::endl;
//dicomfile.set_dicominfo(_in_dicomfile.get_dicominfo());
dicomfile.gendicom(outputPath2.c_str(), xoutphs, dims.height, dims.width);
ss.str("");
}
}
else
{
// write reconstruction to binary file
agile::writeVectorFile(op.outputFilename.c_str(), xHost);
}
// export additional information (pdgap, ictgv-component)
if (op.extradata)
recon->ExportAdditionalResults(outputDir.c_str(),
&ExportAdditionalResultsToMatlabBin);
// ==================================================================================================================
// END: Define output
// ==================================================================================================================
delete recon;
delete baseOp;
}
