void GadgetMessageImageExt::dump()
{
GDEBUG_STREAM("GadgetMessageImageExt" << std::endl);
GDEBUG_STREAM("----------------------------------------------------------" << std::endl);
//dumpInfo();
GDEBUG_STREAM("----------------------------------------------------------" << std::endl);
}
int GenericReconCartesianNonLinearSpirit2DTGadget::process_config(ACE_Message_Block* mb)
{
GADGET_CHECK_RETURN(BaseClass::process_config(mb) == GADGET_OK, GADGET_FAIL);
// -------------------------------------------------
ISMRMRD::IsmrmrdHeader h;
try
{
deserialize(mb->rd_ptr(), h);
}
catch (...)
{
GDEBUG("Error parsing ISMRMRD Header");
}
// -------------------------------------------------
// check the parameters
if(this->spirit_nl_iter_max.value()==0)
{
this->spirit_nl_iter_max.value(15);
GDEBUG_STREAM("spirit_iter_max: " << this->spirit_nl_iter_max.value());
}
if (this->spirit_nl_iter_thres.value()<FLT_EPSILON)
{
this->spirit_nl_iter_thres.value(0.004);
GDEBUG_STREAM("spirit_nl_iter_thres: " << this->spirit_nl_iter_thres.value());
}
if (this->spirit_image_reg_lamda.value() < FLT_EPSILON)
{
if(this->spirit_reg_proximity_across_cha.value())
{
this->spirit_image_reg_lamda.value(0.0002);
}
else
{
this->spirit_image_reg_lamda.value(0.00005);
}
GDEBUG_STREAM("spirit_image_reg_lamda: " << this->spirit_image_reg_lamda.value());
}
if (this->spirit_reg_N_weighting_ratio.value() < FLT_EPSILON)
{
if(acceFactorE1_[0]<=5)
{
this->spirit_reg_N_weighting_ratio.value(10.0);
}
else
{
this->spirit_reg_N_weighting_ratio.value(20.0);
}
GDEBUG_STREAM("spirit_reg_N_weighting_ratio: " << this->spirit_reg_N_weighting_ratio.value());
}
return GADGET_OK;
}
int CmrParametricT2MappingGadget::process_config(ACE_Message_Block* mb)
{
GADGET_CHECK_RETURN(BaseClass::process_config(mb) == GADGET_OK, GADGET_FAIL);
ISMRMRD::IsmrmrdHeader h;
try
{
deserialize(mb->rd_ptr(), h);
}
catch (...)
{
GDEBUG("Error parsing ISMRMRD Header");
}
if (!h.acquisitionSystemInformation)
{
GDEBUG("acquisitionSystemInformation not found in header. Bailing out");
return GADGET_FAIL;
}
GDEBUG_STREAM("Read prep times from from protocol : " << this->prep_times_.size() << " [ ");
// set num_T2prep_ to be number of SET
this->prep_times_.resize(this->meas_max_idx_.set + 1);
if (h.userParameters)
{
size_t i = 0;
if (h.userParameters->userParameterDouble.size() > 0)
{
std::vector<ISMRMRD::UserParameterDouble>::const_iterator iter = h.userParameters->userParameterDouble.begin();
for (; iter != h.userParameters->userParameterDouble.end(); iter++)
{
std::string usrParaName = iter->name;
double usrParaValue = iter->value;
std::stringstream str;
str << "T2PrepDuration_" << i;
if (usrParaName == str.str() && i < this->prep_times_.size())
{
this->prep_times_[i] = (float)usrParaValue;
GDEBUG_STREAM("CmrParametricT2MappingGadget, find T2 prep time : " << i << " - " << this->prep_times_[i]);
}
i++;
}
}
}
// -------------------------------------------------
return GADGET_OK;
}
int GenericReconFieldOfViewAdjustmentGadget::process(Gadgetron::GadgetContainerMessage< IsmrmrdImageArray >* m1)
{
if (perform_timing.value()) { gt_timer_.start("GenericReconFieldOfViewAdjustmentGadget::process"); }
GDEBUG_CONDITION_STREAM(verbose.value(), "GenericReconFieldOfViewAdjustmentGadget::process(...) starts ... ");
process_called_times_++;
IsmrmrdImageArray* recon_res_ = m1->getObjectPtr();
// print out recon info
if (verbose.value())
{
GDEBUG_STREAM("----> GenericReconFieldOfViewAdjustmentGadget::process(...) has been called " << process_called_times_ << " times ...");
std::stringstream os;
recon_res_->data_.print(os);
GDEBUG_STREAM(os.str());
}
if (!debug_folder_full_path_.empty()) { gt_exporter_.export_array_complex(recon_res_->data_, debug_folder_full_path_ + "data_before_FOV_adjustment"); }
// ----------------------------------------------------------
// FOV adjustment
// ----------------------------------------------------------
GADGET_CHECK_RETURN(this->adjust_FOV(*recon_res_) == GADGET_OK, GADGET_FAIL);
if (!debug_folder_full_path_.empty()) { gt_exporter_.export_array_complex(recon_res_->data_, debug_folder_full_path_ + "data_after_FOV_adjustment"); }
// make sure the image header is consistent with data
size_t N = recon_res_->headers_.get_number_of_elements();
for (size_t n = 0; n < N; n++)
{
recon_res_->headers_(n).matrix_size[0] = recon_res_->data_.get_size(0);
recon_res_->headers_(n).matrix_size[1] = recon_res_->data_.get_size(1);
recon_res_->headers_(n).matrix_size[2] = recon_res_->data_.get_size(2);
}
GDEBUG_CONDITION_STREAM(verbose.value(), "GenericReconFieldOfViewAdjustmentGadget::process(...) ends ... ");
// ----------------------------------------------------------
// send out results
// ----------------------------------------------------------
if (this->next()->putq(m1) == -1)
{
GERROR("GenericReconFieldOfViewAdjustmentGadget::process, passing data on to next gadget");
return GADGET_FAIL;
}
if (perform_timing.value()) { gt_timer_.stop(); }
return GADGET_OK;
}
GadgetMessageImageArray::GadgetMessageImageArray(int aSize[10])
{
try
{
unsigned int ii;
for ( ii=0; ii<10; ii++ )
{
matrix_size[ii] = aSize[ii];
}
unsigned int len = 1;
for ( ii=3; ii<10; ii++ )
{
len *= matrix_size[ii];
}
if ( len > 0 )
{
imageArray_ = new GadgetMessageImageExt[len];
}
kSpace_centre_col_no = matrix_size[0]/2;
kSpace_centre_line_no = matrix_size[1]/2;
kSpace_centre_partition_no = matrix_size[4]/2;
kSpace_max_acquired_col_no = matrix_size[0]-1;
kSpace_max_acquired_line_no = matrix_size[1]-1;
kSpace_max_acquired_partition_no = matrix_size[4]-1;
}
catch(...)
{
GDEBUG_STREAM("Failed in allocate imageArray_" << std::endl);
}
}
int GenericReconCartesianGrappaGadget::close(unsigned long flags) {
GDEBUG_CONDITION_STREAM(true, "GenericReconCartesianGrappaGadget - close(flags) : " << flags);
if (BaseClass::close(flags) != GADGET_OK) return GADGET_FAIL;
if (flags != 0) {
size_t e;
for (e = 0; e < recon_obj_.size(); e++) {
GDEBUG_STREAM("Clean recon_obj_ for encoding space " << e);
if (recon_obj_[e].recon_res_.data_.delete_data_on_destruct()) recon_obj_[e].recon_res_.data_.clear();
if (recon_obj_[e].recon_res_.headers_.delete_data_on_destruct()) recon_obj_[e].recon_res_.headers_.clear();
recon_obj_[e].recon_res_.meta_.clear();
if (recon_obj_[e].gfactor_.delete_data_on_destruct()) recon_obj_[e].gfactor_.clear();
if (recon_obj_[e].ref_calib_.delete_data_on_destruct()) recon_obj_[e].ref_calib_.clear();
if (recon_obj_[e].ref_calib_dst_.delete_data_on_destruct()) recon_obj_[e].ref_calib_dst_.clear();
if (recon_obj_[e].ref_coil_map_.delete_data_on_destruct()) recon_obj_[e].ref_coil_map_.clear();
if (recon_obj_[e].kernel_.delete_data_on_destruct()) recon_obj_[e].kernel_.clear();
if (recon_obj_[e].kernelIm_.delete_data_on_destruct()) recon_obj_[e].kernelIm_.clear();
if (recon_obj_[e].unmixing_coeff_.delete_data_on_destruct()) recon_obj_[e].unmixing_coeff_.clear();
if (recon_obj_[e].coil_map_.delete_data_on_destruct()) recon_obj_[e].coil_map_.clear();
}
}
return GADGET_OK;
}
void correct_time_stamp_with_fitting(hoNDArray<float>& time_stamp, size_t startE1, size_t endE1)
{
try
{
size_t E1 = time_stamp.get_size(0);
size_t N = time_stamp.get_size(1);
size_t rE1 = endE1 - startE1 + 1;
size_t e1, n;
size_t num_acq_read_outs = 0;
for ( n=0; n<N; n++ )
{
for ( e1=0; e1<E1; e1++ )
{
if ( time_stamp(e1, n) > 0 )
{
num_acq_read_outs++;
}
}
}
GDEBUG_STREAM(" Number of acquired lines : " << num_acq_read_outs);
float a, b; // y = a + b*x
{
std::vector<float> x(num_acq_read_outs), y(num_acq_read_outs);
size_t ind = 0;
for ( n=0; n<N; n++ )
{
for ( e1=startE1; e1<=endE1; e1++ )
{
float acq_time = time_stamp(e1, n);
if ( acq_time > 0 )
{
x[ind] = (float)(e1-startE1 + n*rE1);
y[ind] = acq_time;
ind++;
}
}
}
Gadgetron::simple_line_fit(x, y, a, b);
}
for ( n=0; n<N; n++ )
{
for ( e1=startE1; e1<=endE1; e1++ )
{
float x_v = (float)(e1-startE1 + n*rE1);
time_stamp(e1, n) = a + b*x_v;
}
}
}
catch(...)
{
GADGET_THROW("Exceptions happened in correct_time_stamp_with_fitting(...) ... ");
}
}
void GadgetMessageImageArray::extractMessageImageArrayForREP(int rep, GadgetMessageImageArray& imageArray)
{
if ( rep >= matrix_size[7] )
{
GDEBUG_STREAM("extractMessageImageArrayForSLC error - rep >= matrix_size[7] " << std::endl);
return;
}
int aSize[10];
unsigned int ii;
for ( ii=0; ii<10; ii++ )
{
aSize[ii] = matrix_size[ii];
}
aSize[7] = 1;
imageArray.resize(aSize);
imageArray.kSpace_centre_col_no = kSpace_centre_col_no;
imageArray.kSpace_centre_line_no = kSpace_centre_line_no;
imageArray.kSpace_centre_partition_no = kSpace_centre_partition_no;
imageArray.kSpace_max_acquired_col_no = kSpace_max_acquired_col_no;
imageArray.kSpace_max_acquired_line_no = kSpace_max_acquired_line_no;
imageArray.kSpace_max_acquired_partition_no = kSpace_max_acquired_partition_no;
int par, eco, phs, slc, set, seg;
int SLC = matrix_size[3];
int PAR = matrix_size[4];
int ECO = matrix_size[5];
int PHS = matrix_size[6];
int SET = matrix_size[8];
int SEG = matrix_size[9];
for ( seg=0; seg<SEG; seg++ )
{
for ( set=0; set<SET; set++ )
{
for ( slc=0; slc<SLC; slc++ )
{
for ( phs=0; phs<PHS; phs++ )
{
for ( eco=0; eco<ECO; eco++ )
{
for ( par=0; par<PAR; par++ )
{
int offset = this->get_offset(slc, par, eco, phs, rep, set, seg);
int offsetREP = imageArray.get_offset(slc, par, eco, phs, 0, set, seg);
imageArray.imageArray_[offsetREP] = imageArray_[offset];
}
}
}
}
}
}
}
fs::path get_gadgetron_home() {
const char *home = std::getenv("GADGETRON_HOME");
if (home != nullptr) {
return fs::path(home);
}
fs::path executable_path = get_executable_path();
GDEBUG_STREAM("Executable path: " << executable_path << std::endl);
fs::path gadgetron_home = executable_path
.parent_path()
.parent_path();
GDEBUG_STREAM("Gadgetron home: " << gadgetron_home << std::endl);
return gadgetron_home;
}
int GenericReconPartialFourierHandlingGadget::process_config(ACE_Message_Block* mb)
{
GADGET_CHECK_RETURN(BaseClass::process_config(mb) == GADGET_OK, GADGET_FAIL);
ISMRMRD::IsmrmrdHeader h;
try
{
deserialize(mb->rd_ptr(),h);
}
catch (...)
{
GDEBUG("Error parsing ISMRMRD Header");
}
if (!h.acquisitionSystemInformation)
{
GDEBUG("acquisitionSystemInformation not found in header. Bailing out");
return GADGET_FAIL;
}
// -------------------------------------------------
size_t NE = h.encoding.size();
num_encoding_spaces_ = NE;
GDEBUG_CONDITION_STREAM(verbose.value(), "Number of encoding spaces: " << NE);
acceFactorE1_.resize(NE, 1);
acceFactorE2_.resize(NE, 1);
size_t e;
for (e = 0; e < h.encoding.size(); e++)
{
if (!h.encoding[e].parallelImaging)
{
GDEBUG_STREAM("Parallel Imaging section not found in header for encoding " << e);
acceFactorE1_[e] = 1;
acceFactorE2_[e] = 1;
}
else
{
ISMRMRD::ParallelImaging p_imaging = *h.encoding[0].parallelImaging;
acceFactorE1_[e] = p_imaging.accelerationFactor.kspace_encoding_step_1;
acceFactorE2_[e] = p_imaging.accelerationFactor.kspace_encoding_step_2;
GDEBUG_CONDITION_STREAM(verbose.value(), "acceFactorE1 is " << acceFactorE1_[e]);
GDEBUG_CONDITION_STREAM(verbose.value(), "acceFactorE2 is " << acceFactorE2_[e]);
}
}
return GADGET_OK;
}
int PartialFourierAdjustROGadget::process_config(ACE_Message_Block* mb)
{
ISMRMRD::IsmrmrdHeader h;
deserialize(mb->rd_ptr(),h);
if (h.encoding.size() != 1) {
GDEBUG("Number of encoding spaces: %d\n", h.encoding.size());
GDEBUG("This partial fourier gadget only supports one encoding space\n");
return GADGET_FAIL;
}
ISMRMRD::EncodingSpaceType e_space = h.encoding[0].encodedSpace;
maxRO_ = e_space.matrixSize.x;
GDEBUG_STREAM("max RO : " << maxRO_);
return GADGET_OK;
}
int GenericReconPartialFourierHandlingGadget::process(Gadgetron::GadgetContainerMessage< IsmrmrdImageArray >* m1)
{
GDEBUG_CONDITION_STREAM(verbose.value(), "GenericReconPartialFourierHandlingGadget::process(...) starts ... ");
process_called_times_++;
IsmrmrdImageArray* recon_res_ = m1->getObjectPtr();
// print out recon info
if (verbose.value())
{
GDEBUG_STREAM("----> GenericReconPartialFourierHandlingGadget::process(...) has been called " << process_called_times_ << " times ...");
std::stringstream os;
recon_res_->data_.print(os);
GDEBUG_STREAM(os.str());
}
// some images do not need partial fourier handling processing
if (recon_res_->meta_[0].length(skip_processing_meta_field.value().c_str())>0)
{
if (this->next()->putq(m1) == -1)
{
GERROR("GenericReconPartialFourierHandlingGadget::process, passing incoming image array on to next gadget");
return GADGET_FAIL;
}
return GADGET_OK;
}
// call the partial foureir
size_t encoding = (size_t)recon_res_->meta_[0].as_long("encoding", 0);
GADGET_CHECK_RETURN(encoding<num_encoding_spaces_, GADGET_FAIL);
// perform SNR unit scaling
SamplingLimit sampling_limits[3];
sampling_limits[0].min_ = (uint16_t)recon_res_->meta_[0].as_long("sampling_limits_RO", 0);
sampling_limits[0].center_ = (uint16_t)recon_res_->meta_[0].as_long("sampling_limits_RO", 1);
sampling_limits[0].max_ = (uint16_t)recon_res_->meta_[0].as_long("sampling_limits_RO", 2);
sampling_limits[1].min_ = (uint16_t)recon_res_->meta_[0].as_long("sampling_limits_E1", 0);
sampling_limits[1].center_ = (uint16_t)recon_res_->meta_[0].as_long("sampling_limits_E1", 1);
sampling_limits[1].max_ = (uint16_t)recon_res_->meta_[0].as_long("sampling_limits_E1", 2);
sampling_limits[2].min_ = (uint16_t)recon_res_->meta_[0].as_long("sampling_limits_E2", 0);
sampling_limits[2].center_ = (uint16_t)recon_res_->meta_[0].as_long("sampling_limits_E2", 1);
sampling_limits[2].max_ = (uint16_t)recon_res_->meta_[0].as_long("sampling_limits_E2", 2);
size_t RO = recon_res_->data_.get_size(0);
size_t E1 = recon_res_->data_.get_size(1);
size_t E2 = recon_res_->data_.get_size(2);
size_t CHA = recon_res_->data_.get_size(3);
size_t N = recon_res_->data_.get_size(4);
size_t S = recon_res_->data_.get_size(5);
size_t SLC = recon_res_->data_.get_size(6);
// ----------------------------------------------------------
// pf kspace sampling range
// ----------------------------------------------------------
// if image padding is performed, those dimension may not need partial fourier handling
startRO_ = sampling_limits[0].min_;
endRO_ = sampling_limits[0].max_;
startE1_ = 0;
endE1_ = E1 - 1;
startE2_ = 0;
endE2_ = E2 - 1;
if (std::abs((double)(sampling_limits[1].max_ - E1 / 2) - (double)(E1 / 2 - sampling_limits[1].min_)) > acceFactorE1_[encoding])
{
startE1_ = sampling_limits[1].min_;
endE1_ = sampling_limits[1].max_;
}
if ((E2>1) && (std::abs((double)(sampling_limits[2].max_ - E2 / 2) - (double)(E2 / 2 - sampling_limits[2].min_)) > acceFactorE2_[encoding]))
{
startE2_ = sampling_limits[2].min_;
endE2_ = sampling_limits[2].max_;
}
long lenRO = endRO_ - startRO_ + 1;
long lenE1 = endE1_ - startE1_ + 1;
long lenE2 = endE2_ - startE2_ + 1;
if (lenRO == RO && lenE1 == E1 && lenE2 == E2)
{
GDEBUG_CONDITION_STREAM(verbose.value(), "lenRO == RO && lenE1 == E1 && lenE2 == E2");
if (this->next()->putq(m1) == -1)
{
GERROR("GenericReconPartialFourierHandlingGadget::process, passing data on to next gadget");
return GADGET_FAIL;
}
return GADGET_OK;
}
// ----------------------------------------------------------
// go to kspace
// ----------------------------------------------------------
if (E2 > 1)
{
Gadgetron::hoNDFFT<typename realType<T>::Type>::instance()->fft3c(recon_res_->data_, kspace_buf_);
}
else
{
Gadgetron::hoNDFFT<typename realType<T>::Type>::instance()->fft2c(recon_res_->data_, kspace_buf_);
}
/*if (!debug_folder_full_path_.empty())
{
gt_exporter_.exportArrayComplex(kspace_buf_, debug_folder_full_path_ + "kspace_before_pf");
}*/
// ----------------------------------------------------------
// pf handling
// ----------------------------------------------------------
GADGET_CHECK_RETURN(this->perform_partial_fourier_handling() == GADGET_OK, GADGET_FAIL);
/*if (!debug_folder_full_path_.empty())
{
gt_exporter_.exportArrayComplex(pf_res_, debug_folder_full_path_ + "kspace_after_pf");
}*/
// ----------------------------------------------------------
// go back to image domain
// ----------------------------------------------------------
if (E2 > 1)
{
Gadgetron::hoNDFFT<typename realType<T>::Type>::instance()->ifft3c(pf_res_, recon_res_->data_);
}
else
{
Gadgetron::hoNDFFT<typename realType<T>::Type>::instance()->ifft2c(pf_res_, recon_res_->data_);
}
/*if (!debug_folder_full_path_.empty())
{
gt_exporter_.exportArrayComplex(recon_res_->data_, debug_folder_full_path_ + "data_after_pf");
}*/
GDEBUG_CONDITION_STREAM(verbose.value(), "GenericReconPartialFourierHandlingGadget::process(...) ends ... ");
// ----------------------------------------------------------
// send out results
// ----------------------------------------------------------
if (this->next()->putq(m1) == -1)
{
GERROR("GenericReconPartialFourierHandlingGadget::process, passing data on to next gadget");
return GADGET_FAIL;
}
return GADGET_OK;
}
void BucketToBufferGadget::fillSamplingDescription(SamplingDescription & sampling, ISMRMRD::Encoding & encoding, IsmrmrdAcquisitionBucketStats & stats, ISMRMRD::AcquisitionHeader& acqhdr, bool forref)
{
// For cartesian trajectories, assume that any oversampling has been removed.
if (encoding.trajectory == ISMRMRD::TrajectoryType::CARTESIAN) {
sampling.encoded_FOV_[0] = encoding.reconSpace.fieldOfView_mm.x;
sampling.encoded_matrix_[0] = encoding.reconSpace.matrixSize.x;
} else {
sampling.encoded_FOV_[0] = encoding.encodedSpace.fieldOfView_mm.x;
sampling.encoded_matrix_[0] = encoding.encodedSpace.matrixSize.x;
}
sampling.encoded_FOV_[1] = encoding.encodedSpace.fieldOfView_mm.y;
sampling.encoded_FOV_[2] = encoding.encodedSpace.fieldOfView_mm.z;
sampling.encoded_matrix_[1] = encoding.encodedSpace.matrixSize.y;
sampling.encoded_matrix_[2] = encoding.encodedSpace.matrixSize.z;
sampling.recon_FOV_[0] = encoding.reconSpace.fieldOfView_mm.x;
sampling.recon_FOV_[1] = encoding.reconSpace.fieldOfView_mm.y;
sampling.recon_FOV_[2] = encoding.reconSpace.fieldOfView_mm.z;
sampling.recon_matrix_[0] = encoding.reconSpace.matrixSize.x;
sampling.recon_matrix_[1] = encoding.reconSpace.matrixSize.y;
sampling.recon_matrix_[2] = encoding.reconSpace.matrixSize.z;
// For cartesian trajectories, assume that any oversampling has been removed.
if ( ((encoding.trajectory == ISMRMRD::TrajectoryType::CARTESIAN)) || (encoding.trajectory == ISMRMRD::TrajectoryType::EPI) )
{
sampling.sampling_limits_[0].min_ = acqhdr.discard_pre;
sampling.sampling_limits_[0].max_ = acqhdr.number_of_samples - acqhdr.discard_post - 1;
sampling.sampling_limits_[0].center_ = acqhdr.number_of_samples / 2;
} else {
sampling.sampling_limits_[0].min_ = 0;
sampling.sampling_limits_[0].max_ = encoding.encodedSpace.matrixSize.x - 1;
sampling.sampling_limits_[0].center_ = encoding.encodedSpace.matrixSize.x / 2;
}
// if the scan is cartesian
if ( ( (encoding.trajectory == ISMRMRD::TrajectoryType::CARTESIAN) && (!forref || (forref && (encoding.parallelImaging.get().calibrationMode.get() == "embedded"))) )
|| ( (encoding.trajectory == ISMRMRD::TrajectoryType::EPI) && !forref) )
{
int16_t space_matrix_offset_E1 = 0;
if (encoding.encodingLimits.kspace_encoding_step_1.is_present())
{
space_matrix_offset_E1 = (int16_t)encoding.encodedSpace.matrixSize.y / 2 - (int16_t)encoding.encodingLimits.kspace_encoding_step_1->center;
}
int16_t space_matrix_offset_E2 = 0;
if (encoding.encodingLimits.kspace_encoding_step_2.is_present() && encoding.encodedSpace.matrixSize.z > 1)
{
space_matrix_offset_E2 = (int16_t)encoding.encodedSpace.matrixSize.z / 2 - (int16_t)encoding.encodingLimits.kspace_encoding_step_2->center;
}
// E1
sampling.sampling_limits_[1].min_ = encoding.encodingLimits.kspace_encoding_step_1->minimum + space_matrix_offset_E1;
sampling.sampling_limits_[1].max_ = encoding.encodingLimits.kspace_encoding_step_1->maximum + space_matrix_offset_E1;
sampling.sampling_limits_[1].center_ = sampling.encoded_matrix_[1] / 2;
GADGET_CHECK_THROW(sampling.sampling_limits_[1].min_ < encoding.encodedSpace.matrixSize.y);
GADGET_CHECK_THROW(sampling.sampling_limits_[1].max_ >= sampling.sampling_limits_[1].min_);
GADGET_CHECK_THROW(sampling.sampling_limits_[1].center_ >= sampling.sampling_limits_[1].min_);
GADGET_CHECK_THROW(sampling.sampling_limits_[1].center_ <= sampling.sampling_limits_[1].max_);
// E2
sampling.sampling_limits_[2].min_ = encoding.encodingLimits.kspace_encoding_step_2->minimum + space_matrix_offset_E2;
sampling.sampling_limits_[2].max_ = encoding.encodingLimits.kspace_encoding_step_2->maximum + space_matrix_offset_E2;
sampling.sampling_limits_[2].center_ = sampling.encoded_matrix_[2] / 2;
GADGET_CHECK_THROW(sampling.sampling_limits_[2].min_ < encoding.encodedSpace.matrixSize.y);
GADGET_CHECK_THROW(sampling.sampling_limits_[2].max_ >= sampling.sampling_limits_[2].min_);
GADGET_CHECK_THROW(sampling.sampling_limits_[2].center_ >= sampling.sampling_limits_[2].min_);
GADGET_CHECK_THROW(sampling.sampling_limits_[2].center_ <= sampling.sampling_limits_[2].max_);
}
else
{
sampling.sampling_limits_[1].min_ = encoding.encodingLimits.kspace_encoding_step_1->minimum;
sampling.sampling_limits_[1].max_ = encoding.encodingLimits.kspace_encoding_step_1->maximum;
sampling.sampling_limits_[1].center_ = encoding.encodingLimits.kspace_encoding_step_1->center;
sampling.sampling_limits_[2].min_ = encoding.encodingLimits.kspace_encoding_step_2->minimum;
sampling.sampling_limits_[2].max_ = encoding.encodingLimits.kspace_encoding_step_2->maximum;
sampling.sampling_limits_[2].center_ = encoding.encodingLimits.kspace_encoding_step_2->center;
}
if (verbose.value())
{
GDEBUG_STREAM("Encoding space : " << int(encoding.trajectory)
<< " - FOV : [ " << encoding.encodedSpace.fieldOfView_mm.x << " " << encoding.encodedSpace.fieldOfView_mm.y << " " << encoding.encodedSpace.fieldOfView_mm.z << " ] "
<< " - Matris size : [ " << encoding.encodedSpace.matrixSize.x << " " << encoding.encodedSpace.matrixSize.y << " " << encoding.encodedSpace.matrixSize.z << " ] ");
GDEBUG_STREAM("Sampling limits : "
<< "- RO : [ " << sampling.sampling_limits_[0].min_ << " " << sampling.sampling_limits_[0].center_ << " " << sampling.sampling_limits_[0].max_
<< " ] - E1 : [ " << sampling.sampling_limits_[1].min_ << " " << sampling.sampling_limits_[1].center_ << " " << sampling.sampling_limits_[1].max_
<< " ] - E2 : [ " << sampling.sampling_limits_[2].min_ << " " << sampling.sampling_limits_[2].center_ << " " << sampling.sampling_limits_[2].max_ << " ]");
}
}
int WhiteNoiseInjectorGadget::process(GadgetContainerMessage<ISMRMRD::AcquisitionHeader>* m1, GadgetContainerMessage< hoNDArray< std::complex<float> > >* m2)
{
bool is_noise = ISMRMRD::FlagBit(ISMRMRD::ISMRMRD_ACQ_IS_NOISE_MEASUREMENT).isSet(m1->getObjectPtr()->flags);
bool is_scc_correction = ISMRMRD::FlagBit(ISMRMRD::ISMRMRD_ACQ_IS_SURFACECOILCORRECTIONSCAN_DATA).isSet(m1->getObjectPtr()->flags);
bool is_ref = ISMRMRD::FlagBit(ISMRMRD::ISMRMRD_ACQ_IS_PARALLEL_CALIBRATION).isSet(m1->getObjectPtr()->flags);
bool is_ref_kspace = ISMRMRD::FlagBit(ISMRMRD::ISMRMRD_ACQ_IS_PARALLEL_CALIBRATION_AND_IMAGING).isSet(m1->getObjectPtr()->flags);
size_t channels = m1->getObjectPtr()->active_channels;
size_t samples = m1->getObjectPtr()->number_of_samples;
if (!is_noise && !is_scc_correction )
{
bool add_noise = true;
if ( is_ref && !is_ref_kspace && (is_seperate_||is_external_) )
{
add_noise = add_noise_ref_;
if ( !add_noise )
{
GDEBUG_STREAM("WhiteNoiseInjectorGadget, noise is not added to the ref acquisitions ... ");
}
}
if ( add_noise )
{
if ( !noise_.dimensions_equal(m2->getObjectPtr()) )
{
noise_.create(m2->getObjectPtr()->get_dimensions());
noise_fl_.create(m2->getObjectPtr()->get_dimensions());
}
if ( !randn_->gen(noise_) )
{
GERROR_STREAM("WhiteNoiseInjectorGadget, randn_->gen(noise_) failed ... ");
return GADGET_FAIL;
}
if ( !noise_fl_.copyFrom(noise_) )
{
GERROR_STREAM("WhiteNoiseInjectorGadget, noise_fl_.copyFrom(noise_) failed ... ");
return GADGET_FAIL;
}
try
{
Gadgetron::add(*m2->getObjectPtr(), noise_fl_, *m2->getObjectPtr());
}
catch(...)
{
GERROR_STREAM("WhiteNoiseInjectorGadget, Gadgetron::add(*m2->getObjectPtr(), noise_, *m2->getObjectPtr()) failed ... ");
return GADGET_FAIL;
}
}
}
if (this->next()->putq(m1) == -1)
{
GERROR("WhiteNoiseInjectorGadget::process, passing data on to next gadget");
return -1;
}
return GADGET_OK;
}
bool prepOpenMP()
{
try
{
GDEBUG_STREAM("--> OpenMP info <--");
GDEBUG_STREAM("--------------------------------------------------------");
int numOpenMPProcs = omp_get_num_procs();
GDEBUG_STREAM("GtPlusRecon, numOpenMPProcs : " << numOpenMPProcs);
#ifndef WIN32
int maxOpenMPLevels = omp_get_max_active_levels();
GDEBUG_STREAM("GtPlusRecon, maxOpenMPLevels : " << maxOpenMPLevels);
#endif // WIN32
int maxOpenMPThreads = omp_get_max_threads();
GDEBUG_STREAM("GtPlusRecon, maxOpenMPThreads : " << maxOpenMPThreads);
if ( numOpenMPProcs != maxOpenMPThreads )
{
GDEBUG_STREAM("GtPlusRecon, numOpenMPProcs != maxOpenMPThreads , hyperthreading must be disabled ... ");
omp_set_num_threads(numOpenMPProcs);
}
// omp_set_nested(1);
int allowOpenMPNested = omp_get_nested();
GDEBUG_STREAM("GtPlusRecon, allowOpenMPNested : " << allowOpenMPNested);
#ifdef WIN32
GDEBUG_STREAM("----------------------------------");
GDEBUG_STREAM("GtPlus, set thread affinity ... ");
/// lock the threads
#pragma omp parallel default(shared)
{
int tid = omp_get_thread_num();
DWORD_PTR mask = (1 << tid);
GDEBUG_STREAM("thread id : " << tid << " - mask : " << mask);
SetThreadAffinityMask( GetCurrentThread(), mask );
}
#endif // WIN32
GDEBUG_STREAM("--------------------------------------------------------");
}
catch(...)
{
GERROR_STREAM("Errors in GtPlus prepOpenMP() ... ");
return false;
}
return true;
}
int DistributeGadget::process(ACE_Message_Block* m)
{
int node_index = this->node_index(m);
if (single_package_mode.value()) {
node_index = ++started_nodes_;
}
if (node_index < 0) {
GERROR("Negative node index received");
return GADGET_FAIL;
}
//If we are not supposed to use this node for compute, add one to make sure we are not on node 0
//if (!use_this_node_for_compute.value()) {
// node_index = node_index+1;
//}
// instead of sending down the stream, processing is done by making connections
//if (node_index == 0) { //process locally
// if (this->next()->putq(m) == -1) {
// m->release();
// GERROR("DistributeGadget::process, passing data on to next gadget\n");
// return GADGET_FAIL;
// }
// return GADGET_OK;
//}
//At this point, the node index is positive, so we need to find a suitable connector.
mtx_.acquire();
auto n = node_map_.find(node_index);
mtx_.release();
GadgetronConnector* con = 0;
if (n != node_map_.end()) { //We have a suitable connection already.
con = n->second;
} else {
std::vector<GadgetronNodeInfo> nl;
CloudBus::instance()->get_node_info(nl);
GDEBUG("Number of network nodes found: %d\n", nl.size());
GadgetronNodeInfo me;
me.address = "127.0.0.1";//We may have to update this
me.port = CloudBus::instance()->port();
me.uuid = CloudBus::instance()->uuid();
me.active_reconstructions = CloudBus::instance()->active_reconstructions();
//This would give the current node the lowest possible priority
if (!use_this_node_for_compute.value()) {
me.active_reconstructions = UINT32_MAX;
}
for (auto it = nl.begin(); it != nl.end(); it++) {
if (it->active_reconstructions < me.active_reconstructions) {
me = *it;
}
//Is this a free node
if (me.active_reconstructions == 0) break;
}
// first job, send to current node if required
if (use_this_node_for_compute.value() && node_index==0)
{
size_t num_of_ip = local_address_.size();
for (auto it = nl.begin(); it != nl.end(); it++)
{
for (size_t ii=0; ii<num_of_ip; ii++)
{
if (it->address == local_address_[ii])
{
me = *it;
}
}
}
GDEBUG_STREAM("Send first job to current node : " << me.address);
}
con = new DistributionConnector(this);
GadgetronXML::GadgetStreamConfiguration cfg;
try {
deserialize(node_xml_config_.c_str(), cfg);
} catch (const std::runtime_error& e) {
GERROR("Failed to parse Node Gadget Stream Configuration: %s\n", e.what());
return GADGET_FAIL;
}
//Configuration of readers
for (auto i = cfg.reader.begin(); i != cfg.reader.end(); ++i) {
GadgetMessageReader* r =
controller_->load_dll_component<GadgetMessageReader>(i->dll.c_str(),
i->classname.c_str());
if (!r) {
GERROR("Failed to load GadgetMessageReader from DLL\n");
return GADGET_FAIL;
}
con->register_reader(i->slot, r);
}
for (auto i = cfg.writer.begin(); i != cfg.writer.end(); ++i) {
GadgetMessageWriter* w =
controller_->load_dll_component<GadgetMessageWriter>(i->dll.c_str(),
i->classname.c_str());
if (!w) {
GERROR("Failed to load GadgetMessageWriter from DLL\n");
return GADGET_FAIL;
}
con->register_writer(i->slot, w);
}
char buffer[10];
sprintf(buffer,"%d",me.port);
if (con->open(me.address,std::string(buffer)) != 0) {
GERROR("Failed to open connection to node %s : %d\n", me.address.c_str(), me.port);
return GADGET_FAIL;
}
if (con->send_gadgetron_configuration_script(node_xml_config_) != 0) {
GERROR("Failed to send XML configuration to compute node\n");
return GADGET_FAIL;
}
if (con->send_gadgetron_parameters(node_parameters_) != 0) {
GERROR("Failed to send XML parameters to compute node\n");
return GADGET_FAIL;
}
mtx_.acquire();
node_map_[node_index] = con;
mtx_.release();
}
if (!con) {
//Zero pointer for the connection means that either a) connection creation failed or b) using local chain.
//Either way, we will send it down the chain.
if (!use_this_node_for_compute.value()) {
GERROR("This node cannot be used for computing and no other node is available\n");
m->release();
return GADGET_FAIL;
}
if (this->next()->putq(m) == -1) {
m->release();
GERROR("DistributeGadget::process, passing data on to next gadget\n");
return GADGET_FAIL;
} else {
return GADGET_OK;
}
} else {
//Let's make sure that we did not send a close message to this connector already
auto c = std::find(closed_connectors_.begin(),closed_connectors_.end(),con);
if (c != closed_connectors_.end()) {
//This is a bad situation, we need to bail out.
m->release();
GERROR("The valid connection for incoming data has already been closed. Distribute Gadget is not configured properly for this type of data\n");
return GADGET_FAIL;
}
//If nodes receive their data sequentially (default), we should see if we should be closing the previos connection
if (nodes_used_sequentially.value() && !single_package_mode.value()) {
//Is this a new connection, if so, send previous one a close
if (prev_connector_ && prev_connector_ != con) {
GDEBUG("Sending close to previous connector, not expecting any more data for this one\n");
auto mc = new GadgetContainerMessage<GadgetMessageIdentifier>();
mc->getObjectPtr()->id = GADGET_MESSAGE_CLOSE;
if (prev_connector_->putq(mc) == -1) {
GERROR("Unable to put CLOSE package on queue of previous connection\n");
return -1;
}
closed_connectors_.push_back(prev_connector_);
}
}
//Update previous connection
prev_connector_ = con;
//We have a valid connector
auto m1 = new GadgetContainerMessage<GadgetMessageIdentifier>();
m1->getObjectPtr()->id = message_id(m);
m1->cont(m);
if (con->putq(m1) == -1) {
GERROR("Unable to put package on connector queue\n");
m1->release();
return GADGET_FAIL;
}
if (single_package_mode.value()) {
auto m2 = new GadgetContainerMessage<GadgetMessageIdentifier>();
m2->getObjectPtr()->id = GADGET_MESSAGE_CLOSE;
if (con->putq(m2) == -1) {
GERROR("Unable to put CLOSE package on queue\n");
return -1;
}
closed_connectors_.push_back(con);
}
}
return 0;
}
int GenericReconFieldOfViewAdjustmentGadget::adjust_FOV(IsmrmrdImageArray& recon_res)
{
try
{
size_t RO = recon_res.data_.get_size(0);
size_t E1 = recon_res.data_.get_size(1);
size_t E2 = recon_res.data_.get_size(2);
double encodingFOV_RO = recon_res.meta_[0].as_double("encoding_FOV", 0);
double encodingFOV_E1 = recon_res.meta_[0].as_double("encoding_FOV", 1);
double encodingFOV_E2 = recon_res.meta_[0].as_double("encoding_FOV", 2);
double reconFOV_RO = recon_res.meta_[0].as_double("recon_FOV", 0);
double reconFOV_E1 = recon_res.meta_[0].as_double("recon_FOV", 1);
double reconFOV_E2 = recon_res.meta_[0].as_double("recon_FOV", 2);
long encoding = recon_res.meta_[0].as_long("encoding", 0);
size_t reconSizeRO = recon_size_[encoding][0];
size_t reconSizeE1 = recon_size_[encoding][1];
size_t reconSizeE2 = recon_size_[encoding][2];
// if 2D reconstruction, no need to process along E2
if (E2 <= 1)
{
reconSizeE2 = E2;
reconFOV_E2 = encodingFOV_E2;
}
// if encoded FOV are the same as recon FOV
if ((std::abs(encodingFOV_RO / 2 - reconFOV_RO)<0.1) && (std::abs(encodingFOV_E1 - reconFOV_E1)<0.1) && (std::abs(encodingFOV_E2 - reconFOV_E2)<0.1))
{
if (RO <= reconSizeRO && E1 <= reconSizeE1 && E2 <= reconSizeE2)
{
Gadgetron::zero_pad_resize(recon_res.data_, reconSizeRO, reconSizeE1, reconSizeE2, res_);
}
else if (RO >= reconSizeRO && E1 >= reconSizeE1 && E2 >= reconSizeE2)
{
this->perform_fft(E2, recon_res.data_, kspace_buf_);
Gadgetron::crop(reconSizeRO, reconSizeE1, reconSizeE2, &kspace_buf_, &res_);
this->perform_ifft(E2, res_, recon_res.data_);
}
else
{
GDEBUG_STREAM("Inconsistent image size [" << RO << " " << E1 << " " << E2 << "]; recon image size [" << reconSizeRO << " " << reconSizeE1 << " " << reconSizeE2 << "] ... ");
return GADGET_FAIL;
}
}
else if ((encodingFOV_E1 >= reconFOV_E1) && (encodingFOV_E2 >= reconFOV_E2))
{
size_t encodingE1 = reconSizeE1;
if (encodingFOV_E1 > reconFOV_E1)
{
double spacingE1 = reconFOV_E1 / reconSizeE1;
encodingE1 = (size_t)std::floor(encodingFOV_E1 / spacingE1 + 0.5);
}
size_t encodingE2 = reconSizeE2;
if (encodingFOV_E2 > reconFOV_E2)
{
double spacingE2 = reconFOV_E2 / reconSizeE2;
encodingE2 = (size_t)std::floor(encodingFOV_E2 / spacingE2 + 0.5);
}
hoNDArray< std::complex<float> >* pSrc = &recon_res.data_;
hoNDArray< std::complex<float> >* pDst = &res_;
hoNDArray< std::complex<float> >* pTmp;
// adjust E1
if (encodingE1 >= E1 + 1)
{
Gadgetron::zero_pad_resize(*pSrc, RO, encodingE1, E2, *pDst);
pTmp = pSrc; pSrc = pDst; pDst = pTmp;
}
else if (encodingE1 <= E1 - 1)
{
this->perform_fft(E2, *pSrc, kspace_buf_);
Gadgetron::crop(RO, encodingE1, E2, &kspace_buf_, pDst);
this->perform_ifft(E2, *pDst, *pDst);
pTmp = pSrc; pSrc = pDst; pDst = pTmp;
}
// adjust E2
if (encodingE2 >= E2 + 1)
{
Gadgetron::zero_pad_resize(*pSrc, RO, pSrc->get_size(1), encodingE2, *pDst);
pTmp = pSrc; pSrc = pDst; pDst = pTmp;
}
else if (encodingE2 <= E2 - 1)
{
this->perform_fft(E2, *pSrc, kspace_buf_);
Gadgetron::crop(RO, pSrc->get_size(1), encodingE2, &kspace_buf_, pDst);
this->perform_ifft(E2, *pDst, *pDst);
pTmp = pSrc; pSrc = pDst; pDst = pTmp;
}
//adjust RO
if (RO < reconSizeRO)
{
Gadgetron::zero_pad_resize(*pSrc, reconSizeRO, pSrc->get_size(1), pSrc->get_size(2), *pDst);
pTmp = pSrc; pSrc = pDst; pDst = pTmp;
}
else if (RO > reconSizeRO)
{
this->perform_fft(E2, *pSrc, kspace_buf_);
Gadgetron::crop(reconSizeRO, pSrc->get_size(1), pSrc->get_size(2), &kspace_buf_, pDst);
this->perform_ifft(E2, *pDst, *pDst);
pTmp = pSrc; pSrc = pDst; pDst = pTmp;
}
// final cut on image
GADGET_CHECK_EXCEPTION_RETURN_FALSE(Gadgetron::crop(reconSizeRO, reconSizeE1, reconSizeE2, pSrc, pDst));
if (pDst != &recon_res.data_)
{
recon_res.data_ = *pDst;
}
}
}
catch (...)
{
GERROR_STREAM("Errors in GenericReconFieldOfViewAdjustmentGadget::adjust_FOV(IsmrmrdImageArray& data) ... ");
return GADGET_FAIL;
}
return GADGET_OK;
}
int GenericReconEigenChannelGadget::process_config(ACE_Message_Block* mb)
{
ISMRMRD::IsmrmrdHeader h;
try
{
deserialize(mb->rd_ptr(), h);
}
catch (...)
{
GDEBUG("Error parsing ISMRMRD Header");
}
if (!h.acquisitionSystemInformation)
{
GDEBUG("acquisitionSystemInformation not found in header. Bailing out");
return GADGET_FAIL;
}
// -------------------------------------------------
size_t NE = h.encoding.size();
num_encoding_spaces_ = NE;
GDEBUG_CONDITION_STREAM(verbose.value(), "Number of encoding spaces: " << NE);
calib_mode_.resize(NE, ISMRMRD_noacceleration);
KLT_.resize(NE);
for (size_t e = 0; e < h.encoding.size(); e++)
{
ISMRMRD::EncodingSpace e_space = h.encoding[e].encodedSpace;
ISMRMRD::EncodingSpace r_space = h.encoding[e].reconSpace;
ISMRMRD::EncodingLimits e_limits = h.encoding[e].encodingLimits;
if (!h.encoding[e].parallelImaging)
{
GDEBUG_STREAM("Parallel Imaging section not found in header");
calib_mode_[e] = ISMRMRD_noacceleration;
}
else
{
ISMRMRD::ParallelImaging p_imaging = *h.encoding[0].parallelImaging;
std::string calib = *p_imaging.calibrationMode;
bool separate = (calib.compare("separate") == 0);
bool embedded = (calib.compare("embedded") == 0);
bool external = (calib.compare("external") == 0);
bool interleaved = (calib.compare("interleaved") == 0);
bool other = (calib.compare("other") == 0);
calib_mode_[e] = Gadgetron::ISMRMRD_noacceleration;
if (p_imaging.accelerationFactor.kspace_encoding_step_1 > 1 || p_imaging.accelerationFactor.kspace_encoding_step_2 > 1)
{
if (interleaved)
calib_mode_[e] = Gadgetron::ISMRMRD_interleaved;
else if (embedded)
calib_mode_[e] = Gadgetron::ISMRMRD_embedded;
else if (separate)
calib_mode_[e] = Gadgetron::ISMRMRD_separate;
else if (external)
calib_mode_[e] = Gadgetron::ISMRMRD_external;
else if (other)
calib_mode_[e] = Gadgetron::ISMRMRD_other;
}
}
}
// ---------------------------------------------------------------------------------------------------------
/*if (!debug_folder.value().empty())
{
Gadgetron::get_debug_folder_path(debug_folder.value(), debug_folder_full_path_);
GDEBUG_CONDITION_STREAM(verbose.value(), "Debug folder is " << debug_folder_full_path_);
}
else
{
GDEBUG_CONDITION_STREAM(verbose.value(), "Debug folder is not set ... ");
}*/
return GADGET_OK;
}
int WhiteNoiseInjectorGadget::process_config(ACE_Message_Block* mb)
{
noise_mean_ = noise_mean.value();
noise_std_ = noise_std.value();
add_noise_ref_ = add_noise_ref.value();
GDEBUG_STREAM("noise mean is " << noise_mean_);
GDEBUG_STREAM("noise std is " << noise_std_);
GDEBUG_STREAM("add_noise_ref is " << add_noise_ref_);
randn_->setPara(noise_mean_, noise_std_);
// get the current time and generate a seed
time_t rawtime;
struct tm * timeinfo;
time ( &rawtime );
timeinfo = localtime ( &rawtime );
long long seed = (long long)(1e10*(timeinfo->tm_year+1900) + 1e8*(timeinfo->tm_mon+1) + 1e6*timeinfo->tm_mday + 1e4*timeinfo->tm_hour + 1e2*timeinfo->tm_min + timeinfo->tm_sec + std::rand());
std::array<unsigned int, 10> sequence;
sequence[0] = (unsigned int)(1e10*(timeinfo->tm_year+1900));
sequence[1] = (unsigned int)(1e8*(timeinfo->tm_mon+1));
sequence[2] = (unsigned int)(1e6*timeinfo->tm_mday);
sequence[3] = (unsigned int)(1e4*timeinfo->tm_hour);
sequence[4] = (unsigned int)(1e2*timeinfo->tm_min);
sequence[5] = (unsigned int)(timeinfo->tm_sec);
std::srand( (unsigned int)seed );
sequence[6] = (unsigned int)(std::rand());
sequence[7] = (unsigned int)(std::rand());
sequence[8] = (unsigned int)(std::rand());
sequence[9] = (unsigned int)(std::rand());
std::seed_seq seedSeq(sequence.begin(), sequence.end());
randn_->getRandomer().seed(seedSeq);
randn_->seed( (unsigned long)seed );
// ---------------------------------------------------------------------------------------------------------
ISMRMRD::IsmrmrdHeader h;
try {
deserialize(mb->rd_ptr(),h);
} catch (...) {
GDEBUG("Error parsing ISMRMRD Header");
throw;
return GADGET_FAIL;
}
if( h.encoding.size() != 1)
{
GDEBUG("Number of encoding spaces: %d\n", h.encoding.size());
GDEBUG("This simple WhiteNoiseInjectorGadget only supports one encoding space\n");
return GADGET_FAIL;
}
if (!h.encoding[0].parallelImaging) {
GDEBUG("Parallel Imaging section not found in header");
return GADGET_FAIL;
}
ISMRMRD::ParallelImaging p_imaging = *h.encoding[0].parallelImaging;
acceFactorE1_ = (double)(p_imaging.accelerationFactor.kspace_encoding_step_1);
acceFactorE2_ = (double)(p_imaging.accelerationFactor.kspace_encoding_step_2);
GDEBUG_STREAM("acceFactorE1_ is " << acceFactorE1_);
GDEBUG_STREAM("acceFactorE2_ is " << acceFactorE2_);
if ( !p_imaging.calibrationMode.is_present() )
{
GDEBUG("Parallel Imaging calibrationMode not found in header");
return GADGET_FAIL;
}
std::string calib = *p_imaging.calibrationMode;
if ( calib.compare("interleaved") == 0 )
{
is_interleaved_ = true;
GDEBUG_STREAM("Calibration mode is interleaved");
} else if ( calib.compare("embedded") == 0 ) {
is_embeded_ = true;
GDEBUG_STREAM("Calibration mode is embedded");
} else if ( calib.compare("separate") == 0 ) {
is_seperate_ = true;
GDEBUG_STREAM("Calibration mode is separate");
} else if ( calib.compare("external") == 0 ) {
is_external_ = true;
GDEBUG_STREAM("Calibration mode is external");
} else if ( (calib.compare("other") == 0)) {
is_other_ = true;
GDEBUG_STREAM("Calibration mode is other");
} else {
GDEBUG("Failed to process parallel imaging calibration mode");
return GADGET_FAIL;
}
return GADGET_OK;
}
int GenericReconCartesianGrappaGadget::process(Gadgetron::GadgetContainerMessage<IsmrmrdReconData> *m1) {
if (perform_timing.value()) { gt_timer_local_.start("GenericReconCartesianGrappaGadget::process"); }
process_called_times_++;
IsmrmrdReconData *recon_bit_ = m1->getObjectPtr();
if (recon_bit_->rbit_.size() > num_encoding_spaces_) {
GWARN_STREAM("Incoming recon_bit has more encoding spaces than the protocol : " << recon_bit_->rbit_.size()
<< " instead of "
<< num_encoding_spaces_);
}
GadgetContainerMessage< std::vector<ISMRMRD::Waveform> > * wav = AsContainerMessage< std::vector<ISMRMRD::Waveform> >(m1->cont());
if (wav)
{
if (verbose.value())
{
GDEBUG_STREAM("Incoming recon_bit with " << wav->getObjectPtr()->size() << " wave form samples ");
}
}
// for every encoding space
for (size_t e = 0; e < recon_bit_->rbit_.size(); e++) {
std::stringstream os;
os << "_encoding_" << e << "_" << process_called_times_;
GDEBUG_CONDITION_STREAM(verbose.value(),
"Calling " << process_called_times_ << " , encoding space : " << e);
GDEBUG_CONDITION_STREAM(verbose.value(),
"======================================================================");
// ---------------------------------------------------------------
// export incoming data
if (!debug_folder_full_path_.empty()) {
gt_exporter_.export_array_complex(recon_bit_->rbit_[e].data_.data_,
debug_folder_full_path_ + "data" + os.str());
}
if (!debug_folder_full_path_.empty() && recon_bit_->rbit_[e].data_.trajectory_) {
if (recon_bit_->rbit_[e].ref_->trajectory_->get_number_of_elements() > 0) {
gt_exporter_.export_array(*(recon_bit_->rbit_[e].data_.trajectory_),
debug_folder_full_path_ + "data_traj" + os.str());
}
}
// ---------------------------------------------------------------
if (recon_bit_->rbit_[e].ref_) {
if (!debug_folder_full_path_.empty()) {
gt_exporter_.export_array_complex(recon_bit_->rbit_[e].ref_->data_,
debug_folder_full_path_ + "ref" + os.str());
}
if (!debug_folder_full_path_.empty() && recon_bit_->rbit_[e].ref_->trajectory_) {
if (recon_bit_->rbit_[e].ref_->trajectory_->get_number_of_elements() > 0) {
gt_exporter_.export_array(*(recon_bit_->rbit_[e].ref_->trajectory_),
debug_folder_full_path_ + "ref_traj" + os.str());
}
}
// ---------------------------------------------------------------
// after this step, the recon_obj_[e].ref_calib_ and recon_obj_[e].ref_coil_map_ are set
if (perform_timing.value()) { gt_timer_.start("GenericReconCartesianGrappaGadget::make_ref_coil_map"); }
this->make_ref_coil_map(*recon_bit_->rbit_[e].ref_, *recon_bit_->rbit_[e].data_.data_.get_dimensions(),
recon_obj_[e].ref_calib_, recon_obj_[e].ref_coil_map_, e);
if (perform_timing.value()) { gt_timer_.stop(); }
// ----------------------------------------------------------
// export prepared ref for calibration and coil map
if (!debug_folder_full_path_.empty()) {
this->gt_exporter_.export_array_complex(recon_obj_[e].ref_calib_,
debug_folder_full_path_ + "ref_calib" + os.str());
}
if (!debug_folder_full_path_.empty()) {
this->gt_exporter_.export_array_complex(recon_obj_[e].ref_coil_map_,
debug_folder_full_path_ + "ref_coil_map" + os.str());
}
// ---------------------------------------------------------------
// after this step, the recon_obj_[e].ref_calib_dst_ and recon_obj_[e].ref_coil_map_ are modified
if (perform_timing.value()) {
gt_timer_.start("GenericReconCartesianGrappaGadget::prepare_down_stream_coil_compression_ref_data");
}
this->prepare_down_stream_coil_compression_ref_data(recon_obj_[e].ref_calib_,
recon_obj_[e].ref_coil_map_,
recon_obj_[e].ref_calib_dst_, e);
if (perform_timing.value()) { gt_timer_.stop(); }
if (!debug_folder_full_path_.empty()) {
this->gt_exporter_.export_array_complex(recon_obj_[e].ref_calib_dst_,
debug_folder_full_path_ + "ref_calib_dst" + os.str());
}
if (!debug_folder_full_path_.empty()) {
this->gt_exporter_.export_array_complex(recon_obj_[e].ref_coil_map_,
debug_folder_full_path_ + "ref_coil_map_dst" + os.str());
}
// ---------------------------------------------------------------
// after this step, coil map is computed and stored in recon_obj_[e].coil_map_
if (perform_timing.value()) {
gt_timer_.start("GenericReconCartesianGrappaGadget::perform_coil_map_estimation");
}
this->perform_coil_map_estimation(recon_obj_[e].ref_coil_map_, recon_obj_[e].coil_map_, e);
if (perform_timing.value()) { gt_timer_.stop(); }
// ---------------------------------------------------------------
// after this step, recon_obj_[e].kernel_, recon_obj_[e].kernelIm_, recon_obj_[e].unmixing_coeff_ are filled
// gfactor is computed too
if (perform_timing.value()) { gt_timer_.start("GenericReconCartesianGrappaGadget::perform_calib"); }
this->perform_calib(recon_bit_->rbit_[e], recon_obj_[e], e);
if (perform_timing.value()) { gt_timer_.stop(); }
// ---------------------------------------------------------------
recon_bit_->rbit_[e].ref_->clear();
recon_bit_->rbit_[e].ref_ = boost::none;
}
if (recon_bit_->rbit_[e].data_.data_.get_number_of_elements() > 0) {
if (!debug_folder_full_path_.empty()) {
gt_exporter_.export_array_complex(recon_bit_->rbit_[e].data_.data_,
debug_folder_full_path_ + "data_before_unwrapping" + os.str());
}
if (!debug_folder_full_path_.empty() && recon_bit_->rbit_[e].data_.trajectory_) {
if (recon_bit_->rbit_[e].data_.trajectory_->get_number_of_elements() > 0) {
gt_exporter_.export_array(*(recon_bit_->rbit_[e].data_.trajectory_),
debug_folder_full_path_ + "data_before_unwrapping_traj" + os.str());
}
}
// ---------------------------------------------------------------
if (perform_timing.value()) {
gt_timer_.start("GenericReconCartesianGrappaGadget::perform_unwrapping");
}
this->perform_unwrapping(recon_bit_->rbit_[e], recon_obj_[e], e);
if (perform_timing.value()) { gt_timer_.stop(); }
// ---------------------------------------------------------------
if (perform_timing.value()) {
gt_timer_.start("GenericReconCartesianGrappaGadget::compute_image_header");
}
this->compute_image_header(recon_bit_->rbit_[e], recon_obj_[e].recon_res_, e);
if (perform_timing.value()) { gt_timer_.stop(); }
// ---------------------------------------------------------------
// pass down waveform
if(wav) recon_obj_[e].recon_res_.waveform_ = *wav->getObjectPtr();
recon_obj_[e].recon_res_.acq_headers_ = recon_bit_->rbit_[e].data_.headers_;
// ---------------------------------------------------------------
if (!debug_folder_full_path_.empty()) {
this->gt_exporter_.export_array_complex(recon_obj_[e].recon_res_.data_,
debug_folder_full_path_ + "recon_res" + os.str());
}
if (perform_timing.value()) {
gt_timer_.start("GenericReconCartesianGrappaGadget::send_out_image_array");
}
this->send_out_image_array(recon_obj_[e].recon_res_, e,
image_series.value() + ((int) e + 1), GADGETRON_IMAGE_REGULAR);
if (perform_timing.value()) { gt_timer_.stop(); }
// ---------------------------------------------------------------
if (send_out_gfactor.value() && recon_obj_[e].gfactor_.get_number_of_elements() > 0 &&
(acceFactorE1_[e] * acceFactorE2_[e] > 1)) {
IsmrmrdImageArray res;
Gadgetron::real_to_complex(recon_obj_[e].gfactor_, res.data_);
res.headers_ = recon_obj_[e].recon_res_.headers_;
res.meta_ = recon_obj_[e].recon_res_.meta_;
if (perform_timing.value()) {
gt_timer_.start("GenericReconCartesianGrappaGadget::send_out_image_array, gfactor");
}
this->send_out_image_array(res, e, image_series.value() + 10 * ((int) e + 2),
GADGETRON_IMAGE_GFACTOR);
if (perform_timing.value()) { gt_timer_.stop(); }
}
// ---------------------------------------------------------------
if (send_out_snr_map.value()) {
hoNDArray<std::complex<float> > snr_map;
if (calib_mode_[e] == Gadgetron::ISMRMRD_noacceleration) {
snr_map = recon_obj_[e].recon_res_.data_;
} else {
if (recon_obj_[e].gfactor_.get_number_of_elements() > 0) {
if (perform_timing.value()) { gt_timer_.start("compute SNR map array"); }
this->compute_snr_map(recon_obj_[e], snr_map);
if (perform_timing.value()) { gt_timer_.stop(); }
}
}
if (snr_map.get_number_of_elements() > 0) {
if (!debug_folder_full_path_.empty()) {
this->gt_exporter_.export_array_complex(snr_map,
debug_folder_full_path_ + "snr_map" + os.str());
}
if (perform_timing.value()) { gt_timer_.start("send out gfactor array, snr map"); }
IsmrmrdImageArray res;
res.data_ = snr_map;
res.headers_ = recon_obj_[e].recon_res_.headers_;
res.meta_ = recon_obj_[e].recon_res_.meta_;
res.acq_headers_ = recon_bit_->rbit_[e].data_.headers_;
this->send_out_image_array(res, e,
image_series.value() + 100 * ((int) e + 3), GADGETRON_IMAGE_SNR_MAP);
if (perform_timing.value()) { gt_timer_.stop(); }
}
}
}
recon_obj_[e].recon_res_.data_.clear();
recon_obj_[e].gfactor_.clear();
recon_obj_[e].recon_res_.headers_.clear();
recon_obj_[e].recon_res_.meta_.clear();
}
m1->release();
if (perform_timing.value()) { gt_timer_local_.stop(); }
return GADGET_OK;
}
void GadgetMessageImageArray::dump()
{
unsigned int ii;
GDEBUG_STREAM("GadgetMessageImageArray" << std::endl);
GDEBUG_STREAM("==========================================================" << std::endl);
GDEBUG_STREAM("matrix_size : ");
for ( ii=0; ii<10; ii++ )
{
GDEBUG_STREAM(matrix_size[ii] << " ");
}
GDEBUG_STREAM(std::endl);
GDEBUG_STREAM("----------------------------------------------------------" << std::endl);
GDEBUG_STREAM("kSpace_centre_col_no : " << kSpace_centre_col_no << std::endl);
GDEBUG_STREAM("kSpace_max_acquired_col_no : " << kSpace_max_acquired_col_no << std::endl);
GDEBUG_STREAM("----------------------------------------------------------" << std::endl);
GDEBUG_STREAM("kSpace_centre_line_no : " << kSpace_centre_line_no << std::endl);
GDEBUG_STREAM("kSpace_max_acquired_line_no : " << kSpace_max_acquired_line_no << std::endl);
GDEBUG_STREAM("----------------------------------------------------------" << std::endl);
GDEBUG_STREAM("kSpace_centre_partition_no : " << kSpace_centre_partition_no << std::endl);
GDEBUG_STREAM("kSpace_max_acquired_partition_no : " << kSpace_max_acquired_partition_no << std::endl);
GDEBUG_STREAM("----------------------------------------------------------" << std::endl);
if ( imageArray_ )
{
int slc, par, eco, phs, rep, set, seg;
for ( seg=0; seg<matrix_size[9]; seg++ )
{
for ( set=0; set<matrix_size[8]; set++ )
{
for ( rep=0; rep<matrix_size[7]; rep++ )
{
for ( phs=0; phs<matrix_size[6]; phs++ )
{
for ( eco=0; eco<matrix_size[5]; eco++ )
{
for ( par=0; par<matrix_size[4]; par++ )
{
for ( slc=0; slc<matrix_size[3]; slc++ )
{
int offset = get_offset(slc, par, eco, phs, rep, set, seg);
std::cout << "[Slice Partition Echo Phase Rep Set Seg] = ["
<< " " << slc
<< " " << par
<< " " << eco
<< " " << phs
<< " " << rep
<< " " << set
<< " " << seg << "]" << std::endl;
imageArray_[offset].dump();
}
}
}
}
}
}
}
}
GDEBUG_STREAM("==========================================================" << std::endl);
}
int GenericReconCartesianReferencePrepGadget::process_config(ACE_Message_Block* mb)
{
ISMRMRD::IsmrmrdHeader h;
try
{
deserialize(mb->rd_ptr(), h);
}
catch (...)
{
GDEBUG("Error parsing ISMRMRD Header");
}
if (!h.acquisitionSystemInformation)
{
GDEBUG("acquisitionSystemInformation not found in header. Bailing out");
return GADGET_FAIL;
}
// -------------------------------------------------
size_t NE = h.encoding.size();
num_encoding_spaces_ = NE;
GDEBUG_CONDITION_STREAM(verbose.value(), "Number of encoding spaces: " << NE);
calib_mode_.resize(NE, ISMRMRD_noacceleration);
ref_prepared_.resize(NE, false);
for (size_t e = 0; e < h.encoding.size(); e++)
{
ISMRMRD::EncodingSpace e_space = h.encoding[e].encodedSpace;
ISMRMRD::EncodingSpace r_space = h.encoding[e].reconSpace;
ISMRMRD::EncodingLimits e_limits = h.encoding[e].encodingLimits;
GDEBUG_CONDITION_STREAM(verbose.value(), "---> Encoding space : " << e << " <---");
GDEBUG_CONDITION_STREAM(verbose.value(), "Encoding matrix size: " << e_space.matrixSize.x << " " << e_space.matrixSize.y << " " << e_space.matrixSize.z);
GDEBUG_CONDITION_STREAM(verbose.value(), "Encoding field_of_view : " << e_space.fieldOfView_mm.x << " " << e_space.fieldOfView_mm.y << " " << e_space.fieldOfView_mm.z);
GDEBUG_CONDITION_STREAM(verbose.value(), "Recon matrix size : " << r_space.matrixSize.x << " " << r_space.matrixSize.y << " " << r_space.matrixSize.z);
GDEBUG_CONDITION_STREAM(verbose.value(), "Recon field_of_view : " << r_space.fieldOfView_mm.x << " " << r_space.fieldOfView_mm.y << " " << r_space.fieldOfView_mm.z);
if (!h.encoding[e].parallelImaging)
{
GDEBUG_STREAM("Parallel Imaging section not found in header");
calib_mode_[e] = ISMRMRD_noacceleration;
}
else
{
ISMRMRD::ParallelImaging p_imaging = *h.encoding[0].parallelImaging;
GDEBUG_CONDITION_STREAM(verbose.value(), "acceFactorE1 is " << p_imaging.accelerationFactor.kspace_encoding_step_1);
GDEBUG_CONDITION_STREAM(verbose.value(), "acceFactorE2 is " << p_imaging.accelerationFactor.kspace_encoding_step_2);
std::string calib = *p_imaging.calibrationMode;
bool separate = (calib.compare("separate") == 0);
bool embedded = (calib.compare("embedded") == 0);
bool external = (calib.compare("external") == 0);
bool interleaved = (calib.compare("interleaved") == 0);
bool other = (calib.compare("other") == 0);
calib_mode_[e] = Gadgetron::ISMRMRD_noacceleration;
if (p_imaging.accelerationFactor.kspace_encoding_step_1 > 1 || p_imaging.accelerationFactor.kspace_encoding_step_2 > 1)
{
if (interleaved)
calib_mode_[e] = Gadgetron::ISMRMRD_interleaved;
else if (embedded)
calib_mode_[e] = Gadgetron::ISMRMRD_embedded;
else if (separate)
calib_mode_[e] = Gadgetron::ISMRMRD_separate;
else if (external)
calib_mode_[e] = Gadgetron::ISMRMRD_external;
else if (other)
calib_mode_[e] = Gadgetron::ISMRMRD_other;
}
}
}
// ---------------------------------------------------------------------------------------------------------
return GADGET_OK;
}
int CmrParametricT2MappingGadget::perform_mapping(IsmrmrdImageArray& data, IsmrmrdImageArray& map, IsmrmrdImageArray& para, IsmrmrdImageArray& map_sd, IsmrmrdImageArray& para_sd)
{
try
{
if (perform_timing.value()) { gt_timer_.start("CmrParametricT2MappingGadget::perform_mapping"); }
GDEBUG_CONDITION_STREAM(verbose.value(), "CmrParametricT2MappingGadget::perform_mapping(...) starts ... ");
size_t RO = data.data_.get_size(0);
size_t E1 = data.data_.get_size(1);
size_t E2 = data.data_.get_size(2);
size_t CHA = data.data_.get_size(3);
size_t N = data.data_.get_size(4);
size_t S = data.data_.get_size(5);
size_t SLC = data.data_.get_size(6);
size_t ro, e1, s, slc, p;
GADGET_CHECK_RETURN(E2 == 1, GADGET_FAIL);
GADGET_CHECK_RETURN(CHA == 1, GADGET_FAIL);
GADGET_CHECK_RETURN(this->prep_times_.size() >= N, GADGET_FAIL);
hoNDArray<float> mag;
Gadgetron::abs(data.data_, mag);
if (!debug_folder_full_path_.empty())
{
gt_exporter_.export_array(mag, debug_folder_full_path_ + "CmrParametricT2Mapping_data_mag");
}
bool need_sd_map = send_sd_map.value();
Gadgetron::GadgetronTimer gt_timer(false);
// -------------------------------------------------------------
// set mapping parameters
Gadgetron::CmrT2Mapping<float> t2_mapper;
t2_mapper.fill_holes_in_maps_ = perform_hole_filling.value();
t2_mapper.max_size_of_holes_ = max_size_hole.value();
t2_mapper.compute_SD_maps_ = need_sd_map;
t2_mapper.ti_.resize(N, 0);
memcpy(&(t2_mapper.ti_)[0], &this->prep_times_[0], sizeof(float)*N);
t2_mapper.data_.create(RO, E1, N, S, SLC, mag.begin());
t2_mapper.max_iter_ = max_iter.value();
t2_mapper.thres_fun_ = thres_func.value();
t2_mapper.max_map_value_ = max_T2.value();
t2_mapper.verbose_ = verbose.value();
t2_mapper.debug_folder_ = debug_folder_full_path_;
t2_mapper.perform_timing_ = perform_timing.value();
// -------------------------------------------------------------
// compute mask if needed
if (mapping_with_masking.value())
{
t2_mapper.mask_for_mapping_.create(RO, E1, SLC);
// get the image with shortest prep time
hoNDArray<float> mag_shortest_TE;
mag_shortest_TE.create(RO, E1, SLC);
for (slc = 0; slc < SLC; slc++)
{
size_t ind = 0;
float min_te = this->prep_times_[0];
for (size_t n = 1; n < this->prep_times_.size(); n++)
{
if(this->prep_times_[n]<min_te)
{
min_te = this->prep_times_[n];
ind = n;
}
}
memcpy(&mag_shortest_TE(0, 0, slc), &mag(0, 0, ind, 0, slc), sizeof(float)*RO*E1);
}
if (!debug_folder_full_path_.empty())
{
gt_exporter_.export_array(mag_shortest_TE, debug_folder_full_path_ + "CmrParametricT2Mapping_mag_shortest_TE");
}
double scale_factor = 1.0;
if (data.meta_[0].length(GADGETRON_IMAGE_SCALE_RATIO) > 0)
{
scale_factor = data.meta_[0].as_double(GADGETRON_IMAGE_SCALE_RATIO);
}
GDEBUG_STREAM("CmrParametricT2MappingGadget, find incoming image has scale factor of " << scale_factor);
if (perform_timing.value()) { gt_timer.start("CmrParametricT2MappingGadget::compute_mask_for_mapping"); }
this->compute_mask_for_mapping(mag, t2_mapper.mask_for_mapping_, (float)scale_factor);
if (perform_timing.value()) { gt_timer.stop(); }
if (!debug_folder_full_path_.empty())
{
gt_exporter_.export_array(t2_mapper.mask_for_mapping_, debug_folder_full_path_ + "CmrParametricT2Mapping_mask_for_mapping");
}
}
// -------------------------------------------------------------
// perform mapping
if (perform_timing.value()) { gt_timer.start("CmrParametricT2MappingGadget, t2_mapper.perform_parametric_mapping"); }
t2_mapper.perform_parametric_mapping();
if (perform_timing.value()) { gt_timer.stop(); }
size_t num_para = t2_mapper.get_num_of_paras();
// -------------------------------------------------------------
// get the results
map.data_.create(RO, E1, E2, CHA, 1, S, SLC);
Gadgetron::clear(map.data_);
map.headers_.create(1, S, SLC);
map.meta_.resize(S*SLC);
para.data_.create(RO, E1, E2, CHA, num_para, S, SLC);
Gadgetron::clear(para.data_);
para.headers_.create(num_para, S, SLC);
para.meta_.resize(num_para*S*SLC);
if (need_sd_map)
{
map_sd.data_.create(RO, E1, E2, CHA, 1, S, SLC);
Gadgetron::clear(map_sd.data_);
map_sd.headers_.create(1, S, SLC);
map_sd.meta_.resize(S*SLC);
para_sd.data_.create(RO, E1, E2, CHA, num_para, S, SLC);
Gadgetron::clear(para_sd.data_);
para_sd.headers_.create(num_para, S, SLC);
para_sd.meta_.resize(num_para*S*SLC);
}
for (slc = 0; slc < SLC; slc++)
{
for (s = 0; s < S; s++)
{
for (e1 = 0; e1 < E1; e1++)
{
for (ro = 0; ro < RO; ro++)
{
map.data_(ro, e1, 0, 0, 0, s, slc) = t2_mapper.map_(ro, e1, s, slc);
if (need_sd_map)
{
map_sd.data_(ro, e1, 0, 0, 0, s, slc) = t2_mapper.sd_map_(ro, e1, s, slc);
}
for (p = 0; p < num_para; p++)
{
para.data_(ro, e1, 0, 0, p, s, slc) = t2_mapper.para_(ro, e1, p, s, slc);
if (need_sd_map)
{
para_sd.data_(ro, e1, 0, 0, p, s, slc) = t2_mapper.sd_para_(ro, e1, p, s, slc);
}
}
}
}
size_t slc_ind = data.headers_(0, s, slc).slice;
map.headers_(0, s, slc) = data.headers_(0, s, slc);
map.headers_(0, s, slc).image_index = 1 + slc_ind;
map.headers_(0, s, slc).image_series_index = 11;
map.meta_[s+slc*S] = data.meta_[s + slc*S];
map.meta_[s + slc*S].set(GADGETRON_DATA_ROLE, GADGETRON_IMAGE_T2MAP);
map.meta_[s + slc*S].append(GADGETRON_SEQUENCEDESCRIPTION, GADGETRON_IMAGE_T2MAP);
map.meta_[s + slc*S].append(GADGETRON_IMAGEPROCESSINGHISTORY, GADGETRON_IMAGE_T2MAP);
map_sd.headers_(0, s, slc) = data.headers_(0, s, slc);
map_sd.headers_(0, s, slc).image_index = 1 + slc_ind;
map_sd.headers_(0, s, slc).image_series_index = 12;
map_sd.meta_[s + slc*S] = data.meta_[s + slc*S];
map_sd.meta_[s + slc*S].set(GADGETRON_DATA_ROLE, GADGETRON_IMAGE_T2SDMAP);
map_sd.meta_[s + slc*S].append(GADGETRON_SEQUENCEDESCRIPTION, GADGETRON_IMAGE_T2SDMAP);
map_sd.meta_[s + slc*S].append(GADGETRON_IMAGEPROCESSINGHISTORY, GADGETRON_IMAGE_T2SDMAP);
if (need_sd_map)
{
for (p = 0; p < num_para; p++)
{
para.headers_(p, s, slc) = data.headers_(0, s, slc);
para.headers_(p, s, slc).image_index = 1 + p + slc_ind*num_para;
para.meta_[p + s*num_para + slc*num_para*S] = data.meta_[s + slc*S];
para_sd.headers_(p, s, slc) = data.headers_(0, s, slc);
para_sd.headers_(p, s, slc).image_index = 1 + p + slc_ind*num_para;
para_sd.meta_[p + s*num_para + slc*num_para*S] = data.meta_[s + slc*S];
}
}
}
}
// -------------------------------------------------------------
if (perform_timing.value()) { gt_timer_.stop(); }
}
catch (...)
{
GERROR_STREAM("Exceptions happened in CmrParametricT2MappingGadget::perform_mapping(...) ... ");
return GADGET_FAIL;
}
return GADGET_OK;
}
int MultiChannelCartesianGrappaReconGadget::send_out_image_array(IsmrmrdReconBit& recon_bit, IsmrmrdImageArray& res, size_t encoding, int series_num, const std::string& data_role)
{
try
{
size_t RO = res.data_.get_size(0);
size_t E1 = res.data_.get_size(1);
size_t E2 = res.data_.get_size(2);
size_t CHA = res.data_.get_size(3);
size_t N = res.data_.get_size(4);
size_t S = res.data_.get_size(5);
size_t SLC = res.data_.get_size(6);
GDEBUG_CONDITION_STREAM(true, "sending out image array, acquisition boundary [RO E1 E2 CHA N S SLC] = [" << RO << " " << E1 << " " << E2 << " " << CHA << " " << N << " " << S << " " << SLC << "] ");
// compute image numbers and fill the image meta
size_t n, s, slc;
for (slc = 0; slc < SLC; slc++)
{
for (s = 0; s < S; s++)
{
for (n = 0; n < N; n++)
{
ISMRMRD::ImageHeader header = res.headers_(n, s, slc);
if (header.measurement_uid == 0) continue;
res.headers_(n, s, slc).image_index = (uint16_t)this->compute_image_number(res.headers_(n, s, slc), encoding, CHA, 0, E2);
res.headers_(n, s, slc).image_series_index = series_num;
size_t offset = n + s*N + slc*N*S;
res.meta_[offset].set(GADGETRON_IMAGENUMBER, (long)res.headers_(n, s, slc).image_index);
res.meta_[offset].set(GADGETRON_IMAGEPROCESSINGHISTORY, "GT");
if (data_role == GADGETRON_IMAGE_REGULAR)
{
res.headers_(n, s, slc).image_type = ISMRMRD::ISMRMRD_IMTYPE_MAGNITUDE;
res.meta_[offset].append(GADGETRON_IMAGECOMMENT, "GT");
res.meta_[offset].append(GADGETRON_SEQUENCEDESCRIPTION, "_GT");
res.meta_[offset].set(GADGETRON_DATA_ROLE, GADGETRON_IMAGE_REGULAR);
}
else if (data_role == GADGETRON_IMAGE_GFACTOR)
{
res.headers_(n, s, slc).image_type = ISMRMRD::ISMRMRD_IMTYPE_MAGNITUDE;
res.meta_[offset].append(GADGETRON_IMAGECOMMENT, GADGETRON_IMAGE_GFACTOR);
res.meta_[offset].append(GADGETRON_SEQUENCEDESCRIPTION, GADGETRON_IMAGE_GFACTOR);
res.meta_[offset].set(GADGETRON_DATA_ROLE, GADGETRON_IMAGE_GFACTOR);
// set the skip processing flag, so gfactor map will not be processed during e.g. partial fourier handling or kspace filter gadgets
res.meta_[offset].set(GADGETRON_SKIP_PROCESSING_AFTER_RECON, (long)1);
// set the flag to use dedicated scaling factor
res.meta_[offset].set(GADGETRON_USE_DEDICATED_SCALING_FACTOR, (long)1);
}
if (verbose.value())
{
for (size_t cha = 0; cha < CHA; cha++)
{
GDEBUG_STREAM("sending out " << data_role << " image [CHA SLC CON PHS REP SET AVE] = [" << cha << " "<< res.headers_(n, s, slc).slice << " " << res.headers_(n, s, slc).contrast << " "<< res.headers_(n, s, slc).phase << " " << res.headers_(n, s, slc).repetition << " " << res.headers_(n, s, slc).set << " " << res.headers_(n, s, slc).average << " " << "] "<< " -- Image number -- " << res.headers_(n, s, slc).image_index);
}
}
}
}
}
// send out the images
Gadgetron::GadgetContainerMessage<IsmrmrdImageArray>* cm1 = new Gadgetron::GadgetContainerMessage<IsmrmrdImageArray>();
*(cm1->getObjectPtr()) = res;
if (this->next()->putq(cm1) < 0)
{
GERROR_STREAM("Put image array to Q failed ... ");
return GADGET_FAIL;
}
}
catch (...)
{
GERROR_STREAM("Errors in MultiChannelCartesianGrappaReconGadget::send_out_image_array(...) ... ");
return GADGET_FAIL;
}
return GADGET_OK;
}
void GenericReconCartesianGrappaGadget::perform_unwrapping(IsmrmrdReconBit &recon_bit, ReconObjType &recon_obj,
size_t e) {
typedef std::complex<float> T;
typedef std::complex<float> T;
size_t RO = recon_bit.data_.data_.get_size(0);
size_t E1 = recon_bit.data_.data_.get_size(1);
size_t E2 = recon_bit.data_.data_.get_size(2);
size_t dstCHA = recon_bit.data_.data_.get_size(3);
size_t N = recon_bit.data_.data_.get_size(4);
size_t S = recon_bit.data_.data_.get_size(5);
size_t SLC = recon_bit.data_.data_.get_size(6);
hoNDArray<std::complex<float> > &src = recon_obj.ref_calib_;
size_t ref_RO = src.get_size(0);
size_t ref_E1 = src.get_size(1);
size_t ref_E2 = src.get_size(2);
size_t srcCHA = src.get_size(3);
size_t ref_N = src.get_size(4);
size_t ref_S = src.get_size(5);
size_t ref_SLC = src.get_size(6);
size_t unmixingCoeff_CHA = recon_obj.unmixing_coeff_.get_size(3);
size_t convkRO = recon_obj.kernel_.get_size(0);
size_t convkE1 = recon_obj.kernel_.get_size(1);
size_t convkE2 = recon_obj.kernel_.get_size(2);
recon_obj.recon_res_.data_.create(RO, E1, E2, 1, N, S, SLC);
if (!debug_folder_full_path_.empty()) {
std::stringstream os;
os << "encoding_" << e;
std::string suffix = os.str();
gt_exporter_.export_array_complex(recon_bit.data_.data_, debug_folder_full_path_ + "data_src_" + suffix);
}
// compute aliased images
data_recon_buf_.create(RO, E1, E2, dstCHA, N, S, SLC);
if (E2 > 1) {
Gadgetron::hoNDFFT<float>::instance()->ifft3c(recon_bit.data_.data_, complex_im_recon_buf_,
data_recon_buf_);
} else {
Gadgetron::hoNDFFT<float>::instance()->ifft2c(recon_bit.data_.data_, complex_im_recon_buf_,
data_recon_buf_);
}
// SNR unit scaling
float effective_acce_factor(1), snr_scaling_ratio(1);
this->compute_snr_scaling_factor(recon_bit, effective_acce_factor, snr_scaling_ratio);
if (effective_acce_factor > 1) {
// since the grappa in gadgetron is doing signal preserving scaling, to perserve noise level, we need this compensation factor
double grappaKernelCompensationFactor = 1.0 / (acceFactorE1_[e] * acceFactorE2_[e]);
Gadgetron::scal((float) (grappaKernelCompensationFactor * snr_scaling_ratio), complex_im_recon_buf_);
if (this->verbose.value()) GDEBUG_STREAM(
"GenericReconCartesianGrappaGadget, grappaKernelCompensationFactor*snr_scaling_ratio : "
<< grappaKernelCompensationFactor * snr_scaling_ratio);
}
if (!debug_folder_full_path_.empty()) {
std::stringstream os;
os << "encoding_" << e;
std::string suffix = os.str();
gt_exporter_.export_array_complex(complex_im_recon_buf_, debug_folder_full_path_ + "aliasedIm_" + suffix);
}
// unwrapping
long long num = N * S * SLC;
long long ii;
#pragma omp parallel default(none) private(ii) shared(num, N, S, RO, E1, E2, srcCHA, convkRO, convkE1, convkE2, ref_N, ref_S, recon_obj, dstCHA, unmixingCoeff_CHA, e) if(num>1)
{
#pragma omp for
for (ii = 0; ii < num; ii++) {
size_t slc = ii / (N * S);
size_t s = (ii - slc * N * S) / N;
size_t n = ii - slc * N * S - s * N;
// combined channels
T *pIm = &(complex_im_recon_buf_(0, 0, 0, 0, n, s, slc));
size_t usedN = n;
if (n >= ref_N) usedN = ref_N - 1;
size_t usedS = s;
if (s >= ref_S) usedS = ref_S - 1;
T *pUnmix = &(recon_obj.unmixing_coeff_(0, 0, 0, 0, usedN, usedS, slc));
T *pRes = &(recon_obj.recon_res_.data_(0, 0, 0, 0, n, s, slc));
hoNDArray<std::complex<float> > res(RO, E1, E2, 1, pRes);
hoNDArray<std::complex<float> > unmixing(RO, E1, E2, unmixingCoeff_CHA, pUnmix);
hoNDArray<std::complex<float> > aliasedIm(RO, E1, E2,
((unmixingCoeff_CHA <= srcCHA) ? unmixingCoeff_CHA : srcCHA),
1, pIm);
Gadgetron::apply_unmix_coeff_aliased_image_3D(aliasedIm, unmixing, res);
}
}
if (!debug_folder_full_path_.empty()) {
std::stringstream os;
os << "encoding_" << e;
std::string suffix = os.str();
gt_exporter_.export_array_complex(recon_obj.recon_res_.data_,
debug_folder_full_path_ + "unwrappedIm_" + suffix);
}
}
int MultiChannelCartesianGrappaReconGadget::process_config(ACE_Message_Block* mb)
{
ISMRMRD::IsmrmrdHeader h;
try
{
deserialize(mb->rd_ptr(), h);
}
catch (...)
{
GDEBUG("Error parsing ISMRMRD Header");
}
if (!h.acquisitionSystemInformation)
{
GDEBUG("acquisitionSystemInformation not found in header. Bailing out");
return GADGET_FAIL;
}
// -------------------------------------------------
size_t NE = h.encoding.size();
num_encoding_spaces_ = NE;
GDEBUG_CONDITION_STREAM(verbose.value(), "Number of encoding spaces: " << NE);
meas_max_idx_.resize(NE);
acceFactorE1_.resize(NE, 1);
acceFactorE2_.resize(NE, 1);
calib_mode_.resize(NE, ISMRMRD_noacceleration);
recon_obj_.resize(NE);
size_t e;
for (e = 0; e < h.encoding.size(); e++)
{
ISMRMRD::EncodingSpace e_space = h.encoding[e].encodedSpace;
ISMRMRD::EncodingSpace r_space = h.encoding[e].reconSpace;
ISMRMRD::EncodingLimits e_limits = h.encoding[e].encodingLimits;
GDEBUG_CONDITION_STREAM(verbose.value(), "---> Encoding space : " << e << " <---");
GDEBUG_CONDITION_STREAM(verbose.value(), "Encoding matrix size: " << e_space.matrixSize.x << " " << e_space.matrixSize.y << " " << e_space.matrixSize.z);
GDEBUG_CONDITION_STREAM(verbose.value(), "Encoding field_of_view : " << e_space.fieldOfView_mm.x << " " << e_space.fieldOfView_mm.y << " " << e_space.fieldOfView_mm.z);
GDEBUG_CONDITION_STREAM(verbose.value(), "Recon matrix size : " << r_space.matrixSize.x << " " << r_space.matrixSize.y << " " << r_space.matrixSize.z);
GDEBUG_CONDITION_STREAM(verbose.value(), "Recon field_of_view : " << r_space.fieldOfView_mm.x << " " << r_space.fieldOfView_mm.y << " " << r_space.fieldOfView_mm.z);
meas_max_idx_[e].kspace_encode_step_1 = (uint16_t)e_space.matrixSize.y - 1;
meas_max_idx_[e].set = (e_limits.set && (e_limits.set->maximum > 0)) ? e_limits.set->maximum : 0;
meas_max_idx_[e].phase = (e_limits.phase && (e_limits.phase->maximum > 0)) ? e_limits.phase->maximum : 0;
meas_max_idx_[e].kspace_encode_step_2 = (uint16_t)e_space.matrixSize.z - 1;
meas_max_idx_[e].contrast = (e_limits.contrast && (e_limits.contrast->maximum > 0)) ? e_limits.contrast->maximum : 0;
meas_max_idx_[e].slice = (e_limits.slice && (e_limits.slice->maximum > 0)) ? e_limits.slice->maximum : 0;
meas_max_idx_[e].repetition = e_limits.repetition ? e_limits.repetition->maximum : 0;
meas_max_idx_[e].slice = (e_limits.slice && (e_limits.slice->maximum > 0)) ? e_limits.slice->maximum : 0;
meas_max_idx_[e].average = e_limits.average ? e_limits.average->maximum : 0;
meas_max_idx_[e].segment = 0;
if (!h.encoding[e].parallelImaging)
{
GDEBUG_STREAM("Parallel Imaging section not found in header");
calib_mode_[e] = ISMRMRD_noacceleration;
acceFactorE1_[e] = 1;
acceFactorE2_[e] = 1;
}
else
{
ISMRMRD::ParallelImaging p_imaging = *h.encoding[0].parallelImaging;
acceFactorE1_[e] = p_imaging.accelerationFactor.kspace_encoding_step_1;
acceFactorE2_[e] = p_imaging.accelerationFactor.kspace_encoding_step_2;
GDEBUG_CONDITION_STREAM(verbose.value(), "acceFactorE1 is " << acceFactorE1_[e]);
GDEBUG_CONDITION_STREAM(verbose.value(), "acceFactorE2 is " << acceFactorE2_[e]);
std::string calib = *p_imaging.calibrationMode;
bool separate = (calib.compare("separate") == 0);
bool embedded = (calib.compare("embedded") == 0);
bool external = (calib.compare("external") == 0);
bool interleaved = (calib.compare("interleaved") == 0);
bool other = (calib.compare("other") == 0);
calib_mode_[e] = Gadgetron::ISMRMRD_noacceleration;
if (acceFactorE1_[e] > 1 || acceFactorE2_[e] > 1)
{
if (interleaved)
calib_mode_[e] = Gadgetron::ISMRMRD_interleaved;
else if (embedded)
calib_mode_[e] = Gadgetron::ISMRMRD_embedded;
else if (separate)
calib_mode_[e] = Gadgetron::ISMRMRD_separate;
else if (external)
calib_mode_[e] = Gadgetron::ISMRMRD_external;
else if (other)
calib_mode_[e] = Gadgetron::ISMRMRD_other;
}
}
}
// ---------------------------------------------------------------------------------------------------------
/*if (!debug_folder.value().empty())
{
Gadgetron::get_debug_folder_path(debug_folder.value(), debug_folder_full_path_);
GDEBUG_CONDITION_STREAM(verbose.value(), "Debug folder is " << debug_folder_full_path_);
}
else
{
GDEBUG_CONDITION_STREAM(verbose.value(), "Debug folder is not set ... ");
}*/
return GADGET_OK;
}
int GenericReconEigenChannelGadget::process(Gadgetron::GadgetContainerMessage< IsmrmrdReconData >* m1)
{
if (perform_timing.value()) { gt_timer_.start("GenericReconEigenChannelGadget::process"); }
process_called_times_++;
IsmrmrdReconData* recon_bit_ = m1->getObjectPtr();
if (recon_bit_->rbit_.size() > num_encoding_spaces_)
{
GWARN_STREAM("Incoming recon_bit has more encoding spaces than the protocol : " << recon_bit_->rbit_.size() << " instead of " << num_encoding_spaces_);
}
// for every encoding space, prepare the recon_bit_->rbit_[e].ref_
size_t e, n, s, slc;
for (e = 0; e < recon_bit_->rbit_.size(); e++)
{
auto & rbit = recon_bit_->rbit_[e];
std::stringstream os;
os << "_encoding_" << e;
hoNDArray< std::complex<float> >& data = recon_bit_->rbit_[e].data_.data_;
size_t RO = data.get_size(0);
size_t E1 = data.get_size(1);
size_t E2 = data.get_size(2);
size_t CHA = data.get_size(3);
size_t N = data.get_size(4);
size_t S = data.get_size(5);
size_t SLC = data.get_size(6);
GDEBUG_CONDITION_STREAM(verbose.value(), "GenericReconEigenChannelGadget - incoming data array : [RO E1 E2 CHA N S SLC] - [" << RO << " " << E1 << " " << E2 << " " << CHA << " " << N << " " << S << " " << SLC << "]");
// whether it is needed to update coefficients
bool recompute_coeff = false;
if ( (KLT_[e].size()!=SLC) || update_eigen_channel_coefficients.value() )
{
recompute_coeff = true;
}
else
{
if(KLT_[e].size() == SLC)
{
for (slc = 0; slc < SLC; slc++)
{
if (KLT_[e][slc].size() != S)
{
recompute_coeff = true;
break;
}
else
{
for (s = 0; s < S; s++)
{
if (KLT_[e][slc][s].size() != N)
{
recompute_coeff = true;
break;
}
}
}
}
}
}
if(recompute_coeff)
{
bool average_N = average_all_ref_N.value();
bool average_S = average_all_ref_S.value();
if(rbit.ref_)
{
// use ref to compute coefficients
Gadgetron::compute_eigen_channel_coefficients(rbit.ref_->data_, average_N, average_S,
(calib_mode_[e] == Gadgetron::ISMRMRD_interleaved), N, S, upstream_coil_compression_thres.value(), upstream_coil_compression_num_modesKept.value(), KLT_[e]);
}
else
{
// use data to compute coefficients
Gadgetron::compute_eigen_channel_coefficients(rbit.data_.data_, average_N, average_S,
(calib_mode_[e] == Gadgetron::ISMRMRD_interleaved), N, S, upstream_coil_compression_thres.value(), upstream_coil_compression_num_modesKept.value(), KLT_[e]);
}
if (verbose.value())
{
hoNDArray< std::complex<float> > E;
for (slc = 0; slc < SLC; slc++)
{
for (s = 0; s < S; s++)
{
for (n = 0; n < N; n++)
{
KLT_[e][slc][s][n].eigen_value(E);
GDEBUG_STREAM("Number of modes kept: " << KLT_[e][slc][s][n].output_length() << "; Eigen value, slc - " << slc << ", S - " << s << ", N - " << n << " : [");
for (size_t c = 0; c < E.get_size(0); c++)
{
GDEBUG_STREAM(" " << E(c));
}
GDEBUG_STREAM("]");
}
}
}
}
}
/*if (!debug_folder_full_path_.empty())
{
gt_exporter_.exportArrayComplex(rbit.data_.data_, debug_folder_full_path_ + "data_before_KLT" + os.str());
}*/
// apply KL coefficients
Gadgetron::apply_eigen_channel_coefficients(KLT_[e], rbit.data_.data_);
/*if (!debug_folder_full_path_.empty())
{
gt_exporter_.exportArrayComplex(rbit.data_.data_, debug_folder_full_path_ + "data_after_KLT" + os.str());
}*/
if (rbit.ref_)
{
/*if (!debug_folder_full_path_.empty())
{
gt_exporter_.exportArrayComplex(rbit.ref_->data_, debug_folder_full_path_ + "ref_before_KLT" + os.str());
}*/
Gadgetron::apply_eigen_channel_coefficients(KLT_[e], rbit.ref_->data_);
/*if (!debug_folder_full_path_.empty())
{
gt_exporter_.exportArrayComplex(rbit.ref_->data_, debug_folder_full_path_ + "ref_after_KLT" + os.str());
}*/
}
}
if (perform_timing.value()) { gt_timer_.stop(); }
if (this->next()->putq(m1) < 0)
{
GERROR_STREAM("Put IsmrmrdReconData to Q failed ... ");
return GADGET_FAIL;
}
return GADGET_OK;
}
void GenericReconCartesianNonLinearSpirit2DTGadget::perform_nonlinear_spirit_unwrapping(hoNDArray< std::complex<float> >& kspace,
hoNDArray< std::complex<float> >& kerIm, hoNDArray< std::complex<float> >& ref2DT, hoNDArray< std::complex<float> >& coilMap2DT, hoNDArray< std::complex<float> >& res, size_t e)
{
try
{
bool print_iter = this->spirit_print_iter.value();
size_t RO = kspace.get_size(0);
size_t E1 = kspace.get_size(1);
size_t E2 = kspace.get_size(2);
size_t CHA = kspace.get_size(3);
size_t N = kspace.get_size(4);
size_t S = kspace.get_size(5);
size_t SLC = kspace.get_size(6);
size_t ref_N = kerIm.get_size(4);
size_t ref_S = kerIm.get_size(5);
hoNDArray< std::complex<float> > kspaceLinear(kspace);
res = kspace;
// detect whether random sampling is used
bool use_random_sampling = false;
std::vector<long long> sampled_step_size;
long long n, e1;
for (n=0; n<(long long)N; n++)
{
long long prev_sampled_line = -1;
for (e1=0; e1<(long long)E1; e1++)
{
if(std::abs(kspace(RO/2, e1, 0, 0, 0, 0, 0))>0 && std::abs(kspace(RO/2, e1, 0, CHA-1, 0, 0, 0))>0)
{
if(prev_sampled_line>0)
{
sampled_step_size.push_back(e1 - prev_sampled_line);
}
prev_sampled_line = e1;
}
}
}
if(sampled_step_size.size()>4)
{
size_t s;
for (s=2; s<sampled_step_size.size()-1; s++)
{
if(sampled_step_size[s]!=sampled_step_size[s-1])
{
use_random_sampling = true;
break;
}
}
}
if(use_random_sampling)
{
GDEBUG_STREAM("SPIRIT Non linear, random sampling is detected ... ");
}
Gadgetron::GadgetronTimer timer(false);
// compute linear solution as the initialization
if(use_random_sampling)
{
if (this->perform_timing.value()) timer.start("SPIRIT Non linear, perform linear spirit recon ... ");
this->perform_spirit_unwrapping(kspace, kerIm, kspaceLinear);
if (this->perform_timing.value()) timer.stop();
}
else
{
if (this->perform_timing.value()) timer.start("SPIRIT Non linear, perform linear recon ... ");
size_t ref2DT_RO = ref2DT.get_size(0);
size_t ref2DT_E1 = ref2DT.get_size(1);
// mean over N
hoNDArray< std::complex<float> > meanKSpace;
Gadgetron::sum_over_dimension(ref2DT, meanKSpace, 4);
// if (!debug_folder_full_path_.empty()) { gt_exporter_.export_array_complex(meanKSpace, debug_folder_full_path_ + "spirit_nl_2DT_meanKSpace"); }
hoNDArray< std::complex<float> > acsSrc(ref2DT_RO, ref2DT_E1, CHA, meanKSpace.begin());
hoNDArray< std::complex<float> > acsDst(ref2DT_RO, ref2DT_E1, CHA, meanKSpace.begin());
double grappa_reg_lamda = 0.0005;
size_t kRO = 5;
size_t kE1 = 4;
hoNDArray< std::complex<float> > convKer;
hoNDArray< std::complex<float> > kIm(RO, E1, CHA, CHA);
Gadgetron::grappa2d_calib_convolution_kernel(acsSrc, acsDst, (size_t)this->acceFactorE1_[e], grappa_reg_lamda, kRO, kE1, convKer);
Gadgetron::grappa2d_image_domain_kernel(convKer, RO, E1, kIm);
// if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(kIm, debug_folder_full_path_ + "spirit_nl_2DT_kIm");
Gadgetron::hoNDFFT<float>::instance()->ifft2c(kspace, complex_im_recon_buf_);
// if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(complex_im_recon_buf_, debug_folder_full_path_ + "spirit_nl_2DT_aliasedImage");
hoNDArray< std::complex<float> > resKSpace(RO, E1, CHA, N);
hoNDArray< std::complex<float> > aliasedImage(RO, E1, CHA, N, complex_im_recon_buf_.begin());
Gadgetron::grappa2d_image_domain_unwrapping_aliased_image(aliasedImage, kIm, resKSpace);
// if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(resKSpace, debug_folder_full_path_ + "spirit_nl_2DT_linearImage");
Gadgetron::hoNDFFT<float>::instance()->fft2c(resKSpace);
memcpy(kspaceLinear.begin(), resKSpace.begin(), resKSpace.get_number_of_bytes());
if (this->perform_timing.value()) timer.stop();
}
// if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(kspaceLinear, debug_folder_full_path_ + "spirit_nl_2DT_kspaceLinear");
// perform nonlinear reconstruction
{
boost::shared_ptr< hoNDArray< std::complex<float> > > coilMap;
bool hasCoilMap = false;
if (coilMap2DT.get_size(0) == RO && coilMap2DT.get_size(1) == E1 && coilMap2DT.get_size(3)==CHA)
{
if (ref_N < N)
{
coilMap = boost::shared_ptr< hoNDArray< std::complex<float> > >(new hoNDArray< std::complex<float> >(RO, E1, CHA, coilMap2DT.begin()));
}
else
{
coilMap = boost::shared_ptr< hoNDArray< std::complex<float> > >(new hoNDArray< std::complex<float> >(RO, E1, CHA, ref_N, coilMap2DT.begin()));
}
hasCoilMap = true;
}
boost::shared_ptr<hoNDArray< std::complex<float> > > ker(new hoNDArray< std::complex<float> >(RO, E1, CHA, CHA, ref_N, kerIm.begin()));
boost::shared_ptr<hoNDArray< std::complex<float> > > acq(new hoNDArray< std::complex<float> >(RO, E1, CHA, N, kspace.begin()));
hoNDArray< std::complex<float> > kspaceInitial(RO, E1, CHA, N, kspaceLinear.begin());
hoNDArray< std::complex<float> > res2DT(RO, E1, CHA, N, res.begin());
if (this->spirit_data_fidelity_lamda.value() > 0)
{
GDEBUG_STREAM("Start the NL SPIRIT data fidelity iteration - regularization strength : "
<< this->spirit_image_reg_lamda.value()
<< " - number of iteration : " << this->spirit_nl_iter_max.value()
<< " - proximity across cha : " << this->spirit_reg_proximity_across_cha.value()
<< " - redundant dimension weighting ratio : " << this->spirit_reg_N_weighting_ratio.value()
<< " - using coil sen map : " << this->spirit_reg_use_coil_sen_map.value()
<< " - iter thres : " << this->spirit_nl_iter_thres.value());
typedef hoGdSolver< hoNDArray< std::complex<float> >, hoWavelet2DTOperator< std::complex<float> > > SolverType;
SolverType solver;
solver.iterations_ = this->spirit_nl_iter_max.value();
solver.set_output_mode(this->spirit_print_iter.value() ? SolverType::OUTPUT_VERBOSE : SolverType::OUTPUT_SILENT);
solver.grad_thres_ = this->spirit_nl_iter_thres.value();
solver.proximal_strength_ratio_ = this->spirit_image_reg_lamda.value();
boost::shared_ptr< hoNDArray< std::complex<float> > > x0 = boost::make_shared< hoNDArray< std::complex<float> > >(kspaceInitial);
solver.set_x0(x0);
// parallel imaging term
std::vector<size_t> dims;
acq->get_dimensions(dims);
hoSPIRIT2DTDataFidelityOperator< std::complex<float> > spirit(&dims);
spirit.set_forward_kernel(*ker, false);
spirit.set_acquired_points(*acq);
// image reg term
hoWavelet2DTOperator< std::complex<float> > wav3DOperator(&dims);
wav3DOperator.set_acquired_points(*acq);
wav3DOperator.scale_factor_first_dimension_ = this->spirit_reg_RO_weighting_ratio.value();
wav3DOperator.scale_factor_second_dimension_ = this->spirit_reg_E1_weighting_ratio.value();
wav3DOperator.scale_factor_third_dimension_ = this->spirit_reg_N_weighting_ratio.value();
wav3DOperator.with_approx_coeff_ = !this->spirit_reg_keep_approx_coeff.value();
wav3DOperator.change_coeffcients_third_dimension_boundary_ = !this->spirit_reg_keep_redundant_dimension_coeff.value();
wav3DOperator.proximity_across_cha_ = this->spirit_reg_proximity_across_cha.value();
wav3DOperator.no_null_space_ = true;
wav3DOperator.input_in_kspace_ = true;
if (this->spirit_reg_use_coil_sen_map.value() && hasCoilMap)
{
wav3DOperator.coil_map_ = *coilMap;
}
// set operators
solver.oper_system_ = &spirit;
solver.oper_reg_ = &wav3DOperator;
if (this->perform_timing.value()) timer.start("NonLinear SPIRIT solver for 2DT with data fidelity ... ");
solver.solve(*acq, res2DT);
if (this->perform_timing.value()) timer.stop();
// if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(res2DT, debug_folder_full_path_ + "spirit_nl_2DT_data_fidelity_res");
}
else
{
GDEBUG_STREAM("Start the NL SPIRIT iteration with regularization strength : "
<< this->spirit_image_reg_lamda.value()
<< " - number of iteration : " << this->spirit_nl_iter_max.value()
<< " - proximity across cha : " << this->spirit_reg_proximity_across_cha.value()
<< " - redundant dimension weighting ratio : " << this->spirit_reg_N_weighting_ratio.value()
<< " - using coil sen map : " << this->spirit_reg_use_coil_sen_map.value()
<< " - iter thres : " << this->spirit_nl_iter_thres.value());
typedef hoGdSolver< hoNDArray< std::complex<float> >, hoWavelet2DTOperator< std::complex<float> > > SolverType;
SolverType solver;
solver.iterations_ = this->spirit_nl_iter_max.value();
solver.set_output_mode(this->spirit_print_iter.value() ? SolverType::OUTPUT_VERBOSE : SolverType::OUTPUT_SILENT);
solver.grad_thres_ = this->spirit_nl_iter_thres.value();
solver.proximal_strength_ratio_ = this->spirit_image_reg_lamda.value();
boost::shared_ptr< hoNDArray< std::complex<float> > > x0 = boost::make_shared< hoNDArray< std::complex<float> > >(kspaceInitial);
solver.set_x0(x0);
// parallel imaging term
std::vector<size_t> dims;
acq->get_dimensions(dims);
hoSPIRIT2DTOperator< std::complex<float> > spirit(&dims);
spirit.set_forward_kernel(*ker, false);
spirit.set_acquired_points(*acq);
spirit.no_null_space_ = true;
spirit.use_non_centered_fft_ = false;
// image reg term
std::vector<size_t> dim;
acq->get_dimensions(dim);
hoWavelet2DTOperator< std::complex<float> > wav3DOperator(&dim);
wav3DOperator.set_acquired_points(*acq);
wav3DOperator.scale_factor_first_dimension_ = this->spirit_reg_RO_weighting_ratio.value();
wav3DOperator.scale_factor_second_dimension_ = this->spirit_reg_E1_weighting_ratio.value();
wav3DOperator.scale_factor_third_dimension_ = this->spirit_reg_N_weighting_ratio.value();
wav3DOperator.with_approx_coeff_ = !this->spirit_reg_keep_approx_coeff.value();
wav3DOperator.change_coeffcients_third_dimension_boundary_ = !this->spirit_reg_keep_redundant_dimension_coeff.value();
wav3DOperator.proximity_across_cha_ = this->spirit_reg_proximity_across_cha.value();
wav3DOperator.no_null_space_ = true;
wav3DOperator.input_in_kspace_ = true;
if (this->spirit_reg_use_coil_sen_map.value() && hasCoilMap)
{
wav3DOperator.coil_map_ = *coilMap;
}
// set operators
solver.oper_system_ = &spirit;
solver.oper_reg_ = &wav3DOperator;
// set call back
solverCallBack cb;
cb.solver_ = &solver;
solver.call_back_ = &cb;
hoNDArray< std::complex<float> > b(kspaceInitial);
Gadgetron::clear(b);
if (this->perform_timing.value()) timer.start("NonLinear SPIRIT solver for 2DT ... ");
solver.solve(b, res2DT);
if (this->perform_timing.value()) timer.stop();
// if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(res2DT, debug_folder_full_path_ + "spirit_nl_2DT_res");
spirit.restore_acquired_kspace(kspace, res2DT);
// if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(res2DT, debug_folder_full_path_ + "spirit_nl_2DT_res_restored");
}
}
}
catch (...)
{
GADGET_THROW("Errors happened in GenericReconCartesianNonLinearSpirit2DTGadget::perform_nonlinear_spirit_unwrapping(...) ... ");
}
}
void GenericReconCartesianNonLinearSpirit2DTGadget::perform_nonlinear_spirit_unwrapping(hoNDArray< std::complex<float> >& kspace,
hoNDArray< std::complex<float> >& kerIm, hoNDArray< std::complex<float> >& ref2DT, hoNDArray< std::complex<float> >& coilMap2DT, hoNDArray< std::complex<float> >& res, size_t e)
{
try
{
bool print_iter = this->spirit_print_iter.value();
size_t RO = kspace.get_size(0);
size_t E1 = kspace.get_size(1);
size_t E2 = kspace.get_size(2);
size_t CHA = kspace.get_size(3);
size_t N = kspace.get_size(4);
size_t S = kspace.get_size(5);
size_t SLC = kspace.get_size(6);
size_t ref_N = kerIm.get_size(4);
size_t ref_S = kerIm.get_size(5);
hoNDArray< std::complex<float> > kspaceLinear(kspace);
res = kspace;
// detect whether random sampling is used
bool use_random_sampling = false;
std::vector<long long> sampled_step_size;
long long n, e1;
for (n=0; n<(long long)N; n++)
{
long long prev_sampled_line = -1;
for (e1=0; e1<(long long)E1; e1++)
{
if(std::abs(kspace(RO/2, e1, 0, 0, 0, 0, 0))>0 && std::abs(kspace(RO/2, e1, 0, CHA-1, 0, 0, 0))>0)
{
if(prev_sampled_line>0)
{
sampled_step_size.push_back(e1 - prev_sampled_line);
}
prev_sampled_line = e1;
}
}
}
if(sampled_step_size.size()>4)
{
size_t s;
for (s=2; s<sampled_step_size.size()-1; s++)
{
if(sampled_step_size[s]!=sampled_step_size[s-1])
{
use_random_sampling = true;
break;
}
}
}
if(use_random_sampling)
{
GDEBUG_STREAM("SPIRIT Non linear, random sampling is detected ... ");
}
Gadgetron::GadgetronTimer timer(false);
boost::shared_ptr< hoNDArray< std::complex<float> > > coilMap;
bool hasCoilMap = false;
if (coilMap2DT.get_size(0) == RO && coilMap2DT.get_size(1) == E1 && coilMap2DT.get_size(3)==CHA)
{
if (ref_N < N)
{
coilMap = boost::shared_ptr< hoNDArray< std::complex<float> > >(new hoNDArray< std::complex<float> >(RO, E1, CHA, coilMap2DT.begin()));
}
else
{
coilMap = boost::shared_ptr< hoNDArray< std::complex<float> > >(new hoNDArray< std::complex<float> >(RO, E1, CHA, ref_N, coilMap2DT.begin()));
}
hasCoilMap = true;
}
hoNDArray<float> gFactor;
float gfactorMedian = 0;
float smallest_eigen_value(0);
// -----------------------------------------------------
// estimate gfactor
// -----------------------------------------------------
// mean over N
hoNDArray< std::complex<float> > meanKSpace;
if(calib_mode_[e]==ISMRMRD_interleaved)
{
Gadgetron::compute_averaged_data_N_S(kspace, true, true, true, meanKSpace);
}
else
{
Gadgetron::compute_averaged_data_N_S(ref2DT, true, true, true, meanKSpace);
}
if (!debug_folder_full_path_.empty()) { gt_exporter_.export_array_complex(meanKSpace, debug_folder_full_path_ + "spirit_nl_2DT_meanKSpace"); }
hoNDArray< std::complex<float> > acsSrc(meanKSpace.get_size(0), meanKSpace.get_size(1), CHA, meanKSpace.begin());
hoNDArray< std::complex<float> > acsDst(meanKSpace.get_size(0), meanKSpace.get_size(1), CHA, meanKSpace.begin());
double grappa_reg_lamda = 0.0005;
size_t kRO = 5;
size_t kE1 = 4;
hoNDArray< std::complex<float> > convKer;
hoNDArray< std::complex<float> > kIm(RO, E1, CHA, CHA);
Gadgetron::grappa2d_calib_convolution_kernel(acsSrc, acsDst, (size_t)this->acceFactorE1_[e], grappa_reg_lamda, kRO, kE1, convKer);
Gadgetron::grappa2d_image_domain_kernel(convKer, RO, E1, kIm);
hoNDArray< std::complex<float> > unmixC;
if(hasCoilMap)
{
Gadgetron::grappa2d_unmixing_coeff(kIm, *coilMap, (size_t)acceFactorE1_[e], unmixC, gFactor);
if (!debug_folder_full_path_.empty()) gt_exporter_.export_array(gFactor, debug_folder_full_path_ + "spirit_nl_2DT_gFactor");
hoNDArray<float> gfactorSorted(gFactor);
std::sort(gfactorSorted.begin(), gfactorSorted.begin()+RO*E1);
gfactorMedian = gFactor((RO*E1 / 2));
GDEBUG_STREAM("SPIRIT Non linear, the median gfactor is found to be : " << gfactorMedian);
}
if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(kIm, debug_folder_full_path_ + "spirit_nl_2DT_kIm");
hoNDArray< std::complex<float> > complexIm;
// compute linear solution as the initialization
if(use_random_sampling)
{
if (this->perform_timing.value()) timer.start("SPIRIT Non linear, perform linear spirit recon ... ");
this->perform_spirit_unwrapping(kspace, kerIm, kspaceLinear);
if (this->perform_timing.value()) timer.stop();
}
else
{
if (this->perform_timing.value()) timer.start("SPIRIT Non linear, perform linear recon ... ");
//size_t ref2DT_RO = ref2DT.get_size(0);
//size_t ref2DT_E1 = ref2DT.get_size(1);
//// mean over N
//hoNDArray< std::complex<float> > meanKSpace;
//Gadgetron::sum_over_dimension(ref2DT, meanKSpace, 4);
//if (!debug_folder_full_path_.empty()) { gt_exporter_.export_array_complex(meanKSpace, debug_folder_full_path_ + "spirit_nl_2DT_meanKSpace"); }
//hoNDArray< std::complex<float> > acsSrc(ref2DT_RO, ref2DT_E1, CHA, meanKSpace.begin());
//hoNDArray< std::complex<float> > acsDst(ref2DT_RO, ref2DT_E1, CHA, meanKSpace.begin());
//double grappa_reg_lamda = 0.0005;
//size_t kRO = 5;
//size_t kE1 = 4;
//hoNDArray< std::complex<float> > convKer;
//hoNDArray< std::complex<float> > kIm(RO, E1, CHA, CHA);
//Gadgetron::grappa2d_calib_convolution_kernel(acsSrc, acsDst, (size_t)this->acceFactorE1_[e], grappa_reg_lamda, kRO, kE1, convKer);
//Gadgetron::grappa2d_image_domain_kernel(convKer, RO, E1, kIm);
//if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(kIm, debug_folder_full_path_ + "spirit_nl_2DT_kIm");
Gadgetron::hoNDFFT<float>::instance()->ifft2c(kspace, complex_im_recon_buf_);
if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(complex_im_recon_buf_, debug_folder_full_path_ + "spirit_nl_2DT_aliasedImage");
hoNDArray< std::complex<float> > resKSpace(RO, E1, CHA, N);
hoNDArray< std::complex<float> > aliasedImage(RO, E1, CHA, N, complex_im_recon_buf_.begin());
Gadgetron::grappa2d_image_domain_unwrapping_aliased_image(aliasedImage, kIm, resKSpace);
if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(resKSpace, debug_folder_full_path_ + "spirit_nl_2DT_linearImage");
Gadgetron::hoNDFFT<float>::instance()->fft2c(resKSpace);
memcpy(kspaceLinear.begin(), resKSpace.begin(), resKSpace.get_number_of_bytes());
Gadgetron::apply_unmix_coeff_aliased_image(aliasedImage, unmixC, complexIm);
if (this->perform_timing.value()) timer.stop();
}
if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(kspaceLinear, debug_folder_full_path_ + "spirit_nl_2DT_kspaceLinear");
if(hasCoilMap)
{
if(N>=spirit_reg_minimal_num_images_for_noise_floor.value())
{
// estimate the noise level
if(use_random_sampling)
{
Gadgetron::hoNDFFT<float>::instance()->ifft2c(kspaceLinear, complex_im_recon_buf_);
hoNDArray< std::complex<float> > complexLinearImage(RO, E1, CHA, N, complex_im_recon_buf_.begin());
Gadgetron::coil_combine(complexLinearImage, *coilMap, 2, complexIm);
}
if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(complexIm, debug_folder_full_path_ + "spirit_nl_2DT_linearImage_complexIm");
// if N is sufficiently large, we can estimate the noise floor by the smallest eigen value
hoMatrix< std::complex<float> > data;
data.createMatrix(RO*E1, N, complexIm.begin(), false);
hoNDArray< std::complex<float> > eigenVectors, eigenValues, eigenVectorsPruned;
// compute eigen
hoNDKLT< std::complex<float> > klt;
klt.prepare(data, (size_t)1, (size_t)0);
klt.eigen_value(eigenValues);
if (this->verbose.value())
{
GDEBUG_STREAM("SPIRIT Non linear, computes eigen values for all 2D kspaces ... ");
eigenValues.print(std::cout);
for (size_t i = 0; i<eigenValues.get_size(0); i++)
{
GDEBUG_STREAM(i << " = " << eigenValues(i));
}
}
smallest_eigen_value = std::sqrt( std::abs(eigenValues(N - 1).real()) / (RO*E1) );
GDEBUG_STREAM("SPIRIT Non linear, the smallest eigen value is : " << smallest_eigen_value);
}
}
// perform nonlinear reconstruction
{
boost::shared_ptr<hoNDArray< std::complex<float> > > ker(new hoNDArray< std::complex<float> >(RO, E1, CHA, CHA, ref_N, kerIm.begin()));
boost::shared_ptr<hoNDArray< std::complex<float> > > acq(new hoNDArray< std::complex<float> >(RO, E1, CHA, N, kspace.begin()));
hoNDArray< std::complex<float> > kspaceInitial(RO, E1, CHA, N, kspaceLinear.begin());
hoNDArray< std::complex<float> > res2DT(RO, E1, CHA, N, res.begin());
if (this->spirit_data_fidelity_lamda.value() > 0)
{
GDEBUG_STREAM("Start the NL SPIRIT data fidelity iteration - regularization strength : " << this->spirit_image_reg_lamda.value()
<< " - number of iteration : " << this->spirit_nl_iter_max.value()
<< " - proximity across cha : " << this->spirit_reg_proximity_across_cha.value()
<< " - redundant dimension weighting ratio : " << this->spirit_reg_N_weighting_ratio.value()
<< " - using coil sen map : " << this->spirit_reg_use_coil_sen_map.value()
<< " - iter thres : " << this->spirit_nl_iter_thres.value()
<< " - wavelet name : " << this->spirit_reg_name.value()
);
typedef hoGdSolver< hoNDArray< std::complex<float> >, hoWavelet2DTOperator< std::complex<float> > > SolverType;
SolverType solver;
solver.iterations_ = this->spirit_nl_iter_max.value();
solver.set_output_mode(this->spirit_print_iter.value() ? SolverType::OUTPUT_VERBOSE : SolverType::OUTPUT_SILENT);
solver.grad_thres_ = this->spirit_nl_iter_thres.value();
if(spirit_reg_estimate_noise_floor.value() && std::abs(smallest_eigen_value)>0)
{
solver.scale_factor_ = smallest_eigen_value;
solver.proximal_strength_ratio_ = this->spirit_image_reg_lamda.value() * gfactorMedian;
GDEBUG_STREAM("SPIRIT Non linear, eigen value is used to derive the regularization strength : " << solver.proximal_strength_ratio_ << " - smallest eigen value : " << solver.scale_factor_);
}
else
{
solver.proximal_strength_ratio_ = this->spirit_image_reg_lamda.value();
}
boost::shared_ptr< hoNDArray< std::complex<float> > > x0 = boost::make_shared< hoNDArray< std::complex<float> > >(kspaceInitial);
solver.set_x0(x0);
// parallel imaging term
std::vector<size_t> dims;
acq->get_dimensions(dims);
hoSPIRIT2DTDataFidelityOperator< std::complex<float> > spirit(&dims);
spirit.set_forward_kernel(*ker, false);
spirit.set_acquired_points(*acq);
// image reg term
hoWavelet2DTOperator< std::complex<float> > wav3DOperator(&dims);
wav3DOperator.set_acquired_points(*acq);
wav3DOperator.scale_factor_first_dimension_ = this->spirit_reg_RO_weighting_ratio.value();
wav3DOperator.scale_factor_second_dimension_ = this->spirit_reg_E1_weighting_ratio.value();
wav3DOperator.scale_factor_third_dimension_ = this->spirit_reg_N_weighting_ratio.value();
wav3DOperator.with_approx_coeff_ = !this->spirit_reg_keep_approx_coeff.value();
wav3DOperator.change_coeffcients_third_dimension_boundary_ = !this->spirit_reg_keep_redundant_dimension_coeff.value();
wav3DOperator.proximity_across_cha_ = this->spirit_reg_proximity_across_cha.value();
wav3DOperator.no_null_space_ = true;
wav3DOperator.input_in_kspace_ = true;
wav3DOperator.select_wavelet(this->spirit_reg_name.value());
if (this->spirit_reg_use_coil_sen_map.value() && hasCoilMap)
{
wav3DOperator.coil_map_ = *coilMap;
}
// set operators
solver.oper_system_ = &spirit;
solver.oper_reg_ = &wav3DOperator;
if (this->perform_timing.value()) timer.start("NonLinear SPIRIT solver for 2DT with data fidelity ... ");
solver.solve(*acq, res2DT);
if (this->perform_timing.value()) timer.stop();
if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(res2DT, debug_folder_full_path_ + "spirit_nl_2DT_data_fidelity_res");
}
else
{
GDEBUG_STREAM("Start the NL SPIRIT iteration with regularization strength : "<< this->spirit_image_reg_lamda.value()
<< " - number of iteration : " << this->spirit_nl_iter_max.value()
<< " - proximity across cha : " << this->spirit_reg_proximity_across_cha.value()
<< " - redundant dimension weighting ratio : " << this->spirit_reg_N_weighting_ratio.value()
<< " - using coil sen map : " << this->spirit_reg_use_coil_sen_map.value()
<< " - iter thres : " << this->spirit_nl_iter_thres.value()
<< " - wavelet name : " << this->spirit_reg_name.value()
);
typedef hoGdSolver< hoNDArray< std::complex<float> >, hoWavelet2DTOperator< std::complex<float> > > SolverType;
SolverType solver;
solver.iterations_ = this->spirit_nl_iter_max.value();
solver.set_output_mode(this->spirit_print_iter.value() ? SolverType::OUTPUT_VERBOSE : SolverType::OUTPUT_SILENT);
solver.grad_thres_ = this->spirit_nl_iter_thres.value();
if(spirit_reg_estimate_noise_floor.value() && std::abs(smallest_eigen_value)>0)
{
solver.scale_factor_ = smallest_eigen_value;
solver.proximal_strength_ratio_ = this->spirit_image_reg_lamda.value() * gfactorMedian;
GDEBUG_STREAM("SPIRIT Non linear, eigen value is used to derive the regularization strength : " << solver.proximal_strength_ratio_ << " - smallest eigen value : " << solver.scale_factor_);
}
else
{
solver.proximal_strength_ratio_ = this->spirit_image_reg_lamda.value();
}
boost::shared_ptr< hoNDArray< std::complex<float> > > x0 = boost::make_shared< hoNDArray< std::complex<float> > >(kspaceInitial);
solver.set_x0(x0);
// parallel imaging term
std::vector<size_t> dims;
acq->get_dimensions(dims);
hoSPIRIT2DTOperator< std::complex<float> > spirit(&dims);
spirit.set_forward_kernel(*ker, false);
spirit.set_acquired_points(*acq);
spirit.no_null_space_ = true;
spirit.use_non_centered_fft_ = false;
// image reg term
std::vector<size_t> dim;
acq->get_dimensions(dim);
hoWavelet2DTOperator< std::complex<float> > wav3DOperator(&dim);
wav3DOperator.set_acquired_points(*acq);
wav3DOperator.scale_factor_first_dimension_ = this->spirit_reg_RO_weighting_ratio.value();
wav3DOperator.scale_factor_second_dimension_ = this->spirit_reg_E1_weighting_ratio.value();
wav3DOperator.scale_factor_third_dimension_ = this->spirit_reg_N_weighting_ratio.value();
wav3DOperator.with_approx_coeff_ = !this->spirit_reg_keep_approx_coeff.value();
wav3DOperator.change_coeffcients_third_dimension_boundary_ = !this->spirit_reg_keep_redundant_dimension_coeff.value();
wav3DOperator.proximity_across_cha_ = this->spirit_reg_proximity_across_cha.value();
wav3DOperator.no_null_space_ = true;
wav3DOperator.input_in_kspace_ = true;
wav3DOperator.select_wavelet(this->spirit_reg_name.value());
if (this->spirit_reg_use_coil_sen_map.value() && hasCoilMap)
{
wav3DOperator.coil_map_ = *coilMap;
}
// set operators
solver.oper_system_ = &spirit;
solver.oper_reg_ = &wav3DOperator;
// set call back
solverCallBack cb;
cb.solver_ = &solver;
solver.call_back_ = &cb;
hoNDArray< std::complex<float> > b(kspaceInitial);
Gadgetron::clear(b);
if (this->perform_timing.value()) timer.start("NonLinear SPIRIT solver for 2DT ... ");
solver.solve(b, res2DT);
if (this->perform_timing.value()) timer.stop();
if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(res2DT, debug_folder_full_path_ + "spirit_nl_2DT_res");
spirit.restore_acquired_kspace(kspace, res2DT);
if (!debug_folder_full_path_.empty()) gt_exporter_.export_array_complex(res2DT, debug_folder_full_path_ + "spirit_nl_2DT_res_restored");
}
}
}
catch (...)
{
GADGET_THROW("Errors happened in GenericReconCartesianNonLinearSpirit2DTGadget::perform_nonlinear_spirit_unwrapping(...) ... ");
}
}
int DistributeGadget::process_config(ACE_Message_Block* m)
{
started_nodes_ = 0;
node_parameters_ = std::string(m->rd_ptr());
//Grab the original XML conifguration
std::string xml = controller_->get_xml_configuration();
GadgetronXML::GadgetStreamConfiguration cfg;
GadgetronXML::deserialize(xml.c_str(),cfg);
//Delete Gadgets up to this Gadget
std::vector<GadgetronXML::Gadget>::iterator it = cfg.gadget.begin();
while ((it->name != std::string(this->module()->name())) && (it != cfg.gadget.end())) it++; it++;
cfg.gadget.erase(cfg.gadget.begin(),it);
//Delete Gadgets after collector
it = cfg.gadget.begin();
while ((it->name != collector.value()) && (it != cfg.gadget.end())) it++; it++;
cfg.gadget.erase(it,cfg.gadget.end());
std::stringstream o;
GadgetronXML::serialize(cfg,o);
node_xml_config_ = o.str();
Gadget* tmp = this;
while (tmp->next()) {
if (std::string(tmp->module()->name()) == collector.value()) break;
tmp = dynamic_cast<Gadget*>(tmp->next());
}
collect_gadget_ = tmp;
if (!collect_gadget_) {
GERROR("Failed to locate collector Gadget with name %s\n", collector.value().c_str());
return GADGET_FAIL;
} else {
collect_gadget_->set_parameter("pass_through_mode","true");
}
// get current node ip addresses
ACE_INET_Addr* the_addr_array = NULL;
size_t num_of_ip = 0;
int rc = ACE::get_ip_interfaces (num_of_ip, the_addr_array);
if (rc != 0)
{
GERROR_STREAM("Retreive local ip addresses failed ... ");
num_of_ip = 0;
}
if (the_addr_array!=NULL ) delete [] the_addr_array;
for (size_t ii=0; ii<num_of_ip; ii++)
{
std::string ip = std::string(the_addr_array[ii].get_host_addr());
local_address_.push_back(ip);
GDEBUG_STREAM("--> Local address : " << ip);
}
return GADGET_OK;
}
