int gpuBufferSensePrepGadget::process(
GadgetContainerMessage<IsmrmrdReconData>* m1) {
IsmrmrdReconData* recondata= m1->getObjectPtr();
if (recondata->rbit_.size() != 1){
throw std::runtime_error("gpuBufferSensePrepGadget only support a single encoding space");
}
IsmrmrdReconBit& reconbit = recondata->rbit_[0];
GenericReconJob job;
IsmrmrdDataBuffered* buffer = &reconbit.data_;
//Use reference data if available.
if (reconbit.ref_){
GDEBUG("Using Reference data for CSM estimation\n");
buffer = reconbit.ref_.get_ptr();
}
size_t ncoils = buffer->headers_[0].active_channels;
std::vector<size_t> new_order = {0,1,2,4,5,6,3};
boost::shared_ptr<cuNDArray<float>> dcw;
boost::shared_ptr<cuNDArray<floatd2>> traj;
if (buffer->trajectory_){
auto & trajectory = *buffer->trajectory_;
if (buffer->headers_[0].trajectory_dimensions == 3){
auto traj_dcw = separate_traj_and_dcw(&trajectory);
dcw = boost::make_shared<cuNDArray<float>>(std::get<1>(traj_dcw).get());
traj = boost::make_shared<cuNDArray<floatd2>>(std::get<0>(traj_dcw).get());
} else if (buffer->headers_[0].trajectory_dimensions == 2){
auto old_traj_dims = *trajectory.get_dimensions();
std::vector<size_t> traj_dims (old_traj_dims.begin()+1,old_traj_dims.end()); //Remove first element
hoNDArray<floatd2> tmp_traj(traj_dims,(floatd2*)trajectory.get_data_ptr());
traj = boost::make_shared<cuNDArray<floatd2>>(tmp_traj);
} else {
throw std::runtime_error("Unsupported number of trajectory dimensions");
}
}
{
auto tmpdim = *buffer->data_.get_dimensions();
for (auto dim : tmpdim)
std::cout << dim << " ";
std::cout << std::endl;
auto permuted = permute((hoNDArray<float_complext>*)&buffer->data_,&new_order);
cuNDArray<float_complext> data(*permuted);
if (dcw){
float scale_factor = float(prod(image_dims_recon_os_))/asum(dcw.get());
*dcw *= scale_factor;
}
auto reg_images = reconstruct_regularization(&data,traj.get(),dcw.get(),ncoils);
//reg_images->squeeze();
auto csm = estimate_b1_map<float,2>(reg_images.get());
*reg_images *= *csm;
auto combined = sum(reg_images.get(),reg_images->get_number_of_dimensions()-1);
auto tmp_combined = abs(reg_images.get());
auto tmpcsm = abs(csm.get());
job.csm_host_ = csm->to_host();
job.reg_host_ = combined->to_host();
}
IsmrmrdDataBuffered* mainbuffer = &reconbit.data_;
//Permute as Sensegadgets expect last dimension to be coils. *Sigh*
job.dat_host_ =permute((hoNDArray<float_complext>*)&mainbuffer->data_,&new_order);
if (mainbuffer->trajectory_){
auto & trajectory = *mainbuffer->trajectory_;
if (mainbuffer->headers_[0].trajectory_dimensions >2 ){
auto traj_dcw = separate_traj_and_dcw(&trajectory);
job.tra_host_ = std::get<0>(traj_dcw);
job.dcw_host_ = std::get<1>(traj_dcw);
} else if (mainbuffer->headers_[0].trajectory_dimensions == 2){
auto old_traj_dims = *trajectory.get_dimensions();
std::vector<size_t> traj_dims (old_traj_dims.begin()+1,old_traj_dims.end()); //Remove first element
hoNDArray<floatd2> tmp_traj(traj_dims,(floatd2*)trajectory.get_data_ptr());
job.tra_host_ = boost::make_shared<hoNDArray<floatd2>>(tmp_traj);
auto host_dcw = boost::make_shared<hoNDArray<float>>(traj_dims);
fill(host_dcw.get(),1.0f);
job.dcw_host_ = host_dcw;
} else {
throw std::runtime_error("Unsupported number of trajectory dimensions");
}
}
{
float scale_factor = float(prod(image_dims_recon_os_))/asum(job.dcw_host_.get());
*job.dcw_host_ *= scale_factor;
}
auto data_dims = *job.dat_host_->get_dimensions();
//Sense gadgets expect only 1 dimension for encoding, so collapse the first
size_t elements = std::accumulate(data_dims.begin(),data_dims.end()-1,1,std::multiplies<size_t>());
std::vector<size_t> new_data_dims = {elements,data_dims.back()};
job.dat_host_->reshape(&new_data_dims);
size_t traj_elements = job.tra_host_->get_number_of_elements();
auto traj_dims = *job.tra_host_->get_dimensions();
size_t kpoints_per_frame = traj_dims[0]*profiles_per_frame_;
if (traj_elements%kpoints_per_frame){
std::stringstream ss;
ss << "Profiles per frame (" << profiles_per_frame_ << ") must be a divisor of total number of profiles (" << traj_elements/traj_dims[0] << ")";
throw std::runtime_error(ss.str());
}
std::vector<size_t> new_traj_dims ={kpoints_per_frame,traj_elements/kpoints_per_frame};
job.tra_host_->reshape(&new_traj_dims);
job.dcw_host_->reshape(&new_traj_dims);
//Let's invent some image headers!
size_t total_frames = profiles_per_frame_ > 0 ? mainbuffer->headers_.get_number_of_elements()/profiles_per_frame_ : 1 ;
job.image_headers_ = boost::shared_array<ISMRMRD::ImageHeader>(new ISMRMRD::ImageHeader[total_frames]);
for (size_t i = 0; i < total_frames; i++){
job.image_headers_[i] = create_image_header(mainbuffer->headers_[i*profiles_per_frame_],mainbuffer->sampling_,i,total_frames);
}
m1->release(); //We be done with everything now.
auto header_message = new GadgetContainerMessage<ISMRMRD::ImageHeader>(job.image_headers_[0]);
auto job_message = new GadgetContainerMessage<GenericReconJob>(job);
header_message->cont(job_message);
if (!this->next()->putq(header_message)){
GDEBUG("Failed to put message on que");
return GADGET_FAIL;
} else
return GADGET_OK;
//cuNDArray<float_complext> reg_images = reconstruct_regularization(reconbit.data_);
}
int gpuCSICoilEstimationGadget::process(
GadgetContainerMessage<IsmrmrdAcquisitionBucket>* m1) {
IsmrmrdAcquisitionBucket* bucket = m1->getObjectPtr();
auto cm1 = new GadgetContainerMessage<cuSenseData>();
auto senseData = cm1->getObjectPtr();
coils = bucket->data_.front().head_->getObjectPtr()->active_channels;
GDEBUG("Active channels %i \n",coils);
{
hoNDArray<std::complex<float>> * ho_data;
hoNDArray<float>* ho_traj;
std::tie(ho_data,ho_traj) = combine_data(bucket->data_);
if (skip_lines_ > 0){
auto cal_dims = *ho_data->get_dimensions();
cal_dims.back() = skip_lines_;
auto data_dims = *ho_data->get_dimensions();
data_dims.back() -= skip_lines_;
hoNDArray<float_complext> cal_view(cal_dims,(float_complext*) ho_data->get_data_ptr());
senseData->freq_calibration = boost::make_shared<cuNDArray<float_complext>>(cal_view);
senseData->freq_calibration->squeeze();
hoNDArray<float_complext> data_view(data_dims,(float_complext*)ho_data->get_data_ptr()+cal_view.get_number_of_elements());
senseData->data = boost::make_shared<cuNDArray<float_complext>>(data_view);
} else {
senseData->data = boost::make_shared<cuNDArray<float_complext>>(reinterpret_cast<hoNDArray<float_complext>*>(ho_data));
}
if (ho_traj->get_size(0) > 2){ //We have dcw
auto traj_dcw = separate_traj_and_dcw(ho_traj);
senseData->traj = boost::make_shared<cuNDArray<floatd2>>(*std::get<0>(traj_dcw));
senseData->dcw = boost::make_shared<cuNDArray<float>>(*std::get<1>(traj_dcw));
} else {
std::vector<size_t> tdims = *ho_traj->get_dimensions();
std::vector<size_t> tmp_dim(tdims.begin()+1,tdims.end());
hoNDArray<floatd2> tmp(tmp_dim,reinterpret_cast<floatd2*>(ho_traj->get_data_ptr()));
senseData->traj = boost::make_shared<cuNDArray<floatd2>>(tmp);
}
delete ho_data;
delete ho_traj;
}
//Remove Initial Spirals
boost::shared_ptr< cuNDArray<float_complext> > ref_data;
boost::shared_ptr< cuNDArray<floatd2> > ref_traj;
boost::shared_ptr<cuNDArray<float> > ref_dcw;
if (bucket->ref_.empty()){
ref_data = senseData->data;
ref_traj = senseData->traj;
ref_dcw = senseData->dcw;
} else {
hoNDArray<std::complex<float>> * ho_data;
hoNDArray<float>* ho_traj;
std::tie(ho_data,ho_traj) = combine_data(bucket->ref_);
ref_data = boost::make_shared<cuNDArray<float_complext>>(reinterpret_cast<hoNDArray<float_complext>*>(ho_data));
if (ho_traj->get_size(0) > 2){
auto traj_dcw = separate_traj_and_dcw(ho_traj);
ref_traj =boost::make_shared<cuNDArray<floatd2>>(*std::get<0>(traj_dcw));
ref_dcw = boost::make_shared<cuNDArray<float>>(*std::get<1>(traj_dcw));
} else {
std::vector<size_t> tdims = *ho_traj->get_dimensions();
std::vector<size_t> tmp_dim(tdims.begin()+1,tdims.end());
hoNDArray<floatd2> tmp(tmp_dim,reinterpret_cast<floatd2*>(ho_traj->get_data_ptr()));
ref_traj = boost::make_shared<cuNDArray<floatd2>>(tmp);
}
delete ho_data;
delete ho_traj;
}
senseData->csm = calculate_CSM(ref_data.get(),ref_traj.get(),ref_dcw.get());
if (this->next()->putq(cm1) == GADGET_FAIL){
GERROR("Failed to put message on que\n");
return GADGET_FAIL;
}
return GADGET_OK;
}
