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AddTrajInfoGadget.cpp
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AddTrajInfoGadget.cpp
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#include "AddTrajInfoGadget.h"
#include "hoNDFFT.h"
#include "hoNDArray_math.h"
#include "hoNDArray_utils.h"
namespace Gadgetron
{
AddTrajInfoGadget::AddTrajInfoGadget()
: image_counter_(0)
{
}
int AddTrajInfoGadget::process_config(ACE_Message_Block *mb)
{
try
{
deserialize(mb->rd_ptr(), MeasHeader);
}
catch (...)
{
GDEBUG("Error parsing ISMRMRD Header");
}
if (!MeasHeader.acquisitionSystemInformation)
{
GDEBUG("acquisitionSystemInformation not found in header. Bailing out");
return GADGET_FAIL;
}
SpiralTraj = Spiral::spiraltraj_gadgetron(MeasHeader);
SpiralTraj.setDelayParams(grad_delay.value(),ADC_shift.value());
return GADGET_OK;
}
int AddTrajInfoGadget::process(GadgetContainerMessage<IsmrmrdReconData> *m1)
{
// Iterate over all the recon bits
for (std::vector<IsmrmrdReconBit>::iterator it = m1->getObjectPtr()->rbit_.begin();
it != m1->getObjectPtr()->rbit_.end(); ++it)
{
// Grab a reference to the buffer containing the imaging data
// We are ignoring the reference data
// IsmrmrdDataBuffered & dbuff2 = it->data_;
IsmrmrdReconBit &rbit = *it;
IsmrmrdDataBuffered &dbuff = it->data_;
// trajectories are -0.5 to 0.5 scaled with dim (Grad_Axis=2,ADC_points, Interleaves/E1)
auto traj = SpiralTraj.calculate_trajectories_and_weight(dbuff.headers_[0].number_of_samples);
GDEBUG("done calculating trajectories\n");
dbuff.trajectory_ = traj.first;
dbuff.density_ = traj.second;
if (calc_3D_traj.value())
{
// trajectories are -0.5 to 0.5 scaled with dim (Grad_Axis=3,ADC_points, Interleaves/E1,Partitions/E2)
CalcTrajectory3D(dbuff);
}
RemoveUnacquiredData(dbuff);
PerformFOVShift(dbuff.data_, dbuff.headers_[0], dbuff.trajectory_.value());
} // reconbit iteration
if (this->next()->putq(m1) < 0)
{
GERROR_STREAM("Put IsmrmrdReconData to Q failed ... ");
return GADGET_FAIL;
}
return GADGET_OK;
} // process()
bool AddTrajInfoGadget::PerformFOVShift(Gadgetron::hoNDArray<complex_float_t> &ksp_data, ISMRMRD::AcquisitionHeader &acq_hdr, Gadgetron::hoNDArray<float> &kTraj)
{
using namespace Gadgetron::Indexing;
// ksp_data 2 dimensional COLx CHA
// kTRaj 2 dimensional COLxLIN
const float pi = std::acos(-1);
float kmax = (2.f * pi) * SpiralTraj.getKmax(); // 1/m
auto sz = ksp_data.dimensions();
auto sz1 = kTraj.dimensions();
auto slcPos = acq_hdr.position; // mm
// if (acq_hdr.isFlagSet(ISMRMRD::ISMRMRD_ACQ_FIRST_IN_REPETITION))
GDEBUG_STREAM("RPOS " << slcPos[0] << " PhPos " << slcPos[1] << " slcPos " << slcPos[2]);
size_t E0 = ksp_data.get_size(0);
size_t E1 = ksp_data.get_size(1);
size_t E2 = ksp_data.get_size(2);
size_t CHA = ksp_data.get_size(3);
size_t N = ksp_data.get_size(4);
size_t S = ksp_data.get_size(5);
size_t LOC = ksp_data.get_size(6);
//calculate the signal phase modulation because of off-center shift
const std::complex<float> imagi(0, 1); // 0+1i
Gadgetron::hoNDArray<complex_float_t> B0mod(kTraj.get_size(1), kTraj.get_size(2));
size_t traj_dim=kTraj.get_size(0);
size_t ELEM = E0 * E1 *traj_dim;
for (uint32_t i = 0; i < ELEM; i += traj_dim)
{
B0mod[i / traj_dim] = (imagi * ((kTraj[i + 1] * slcPos[0] * 1e-3f + kTraj[i] * slcPos[1] * -1e-3f) * (2.f * kmax)));
}
// std::transform(test.begin(),test.end(),B0mod.begin(),[kmax,slcPos,pi,imagi](auto x){return (imagi*((2.f*pi)*(x[0]*slcPos[0]*1e-3f+x[1]*slcPos[1]*-1e-3f)*(2.f*kmax)));});
// apply that off-center shift to the data;
for (uint16_t loc = 0; loc < LOC; loc++)
{
for (uint16_t s = 0; s < S; s++)
{
for (uint16_t n = 0; n < N; n++)
{
for (uint16_t cha = 0; cha < CHA; cha++)
{
for (uint16_t e2 = 0; e2 < E2; e2++)
{
complex_float_t *startPtr = &ksp_data(0, 0, e2, cha, n, s, loc);
for (auto elem = 0; elem < E0 * E1; ++elem)
{
startPtr[elem] = startPtr[elem] * std::exp(B0mod[elem]);
}
}
}
}
}
}
return true;
}
bool AddTrajInfoGadget::RemoveUnacquiredData(IsmrmrdDataBuffered &dbuff)
{
if (!MeasHeader.encoding[0].parallelImaging.has_value())
return false;
auto R_E1 = MeasHeader.encoding[0].parallelImaging.value().accelerationFactor.kspace_encoding_step_1;
auto R_E2 = MeasHeader.encoding[0].parallelImaging.value().accelerationFactor.kspace_encoding_step_2;
if(R_E1*R_E2 ==1)
return false;
GDEBUG_STREAM("Trying to remove unacquired datapoints: R_E1= "<<R_E1 <<" ,R_E2= "<<R_E2<<std::endl);
auto &h = dbuff.headers_;
auto &traj = dbuff.trajectory_.value();
auto &dcw = dbuff.density_.value();
auto &data = dbuff.data_;
size_t E0 = 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 LOC = data.get_size(6);
auto new_headers=hoNDArray<ISMRMRD::AcquisitionHeader>(E1/R_E1,E2/R_E2,N,S,LOC);
auto new_data=hoNDArray<complex_float_t>(E0,E1/R_E1,E2/R_E2,CHA,N,S,LOC);
auto new_traj=hoNDArray<float>(3,E0,E1/R_E1,E2/R_E2);
auto new_dcw=hoNDArray<float>(E0,E1/R_E1,E2/R_E2);
std::vector<uint16_t> E1_to_copy;
std::vector<uint16_t> E2_to_copy;
for (uint16_t loc = 0; loc < LOC; loc++)
{
for (uint16_t s = 0; s < S; s++)
{
for (uint16_t n = 0; n < N; n++)
{
for (uint16_t e2 = 0; e2 < E2; e2++)
{
for (uint16_t e1 = 0; e1 < E1; e1++)
{
auto & nsamp=h(e1,e2,n,s,loc).number_of_samples;
if(nsamp>0)
{
E1_to_copy.push_back(h(e1,e2,n,s,loc).idx.kspace_encode_step_1);
E2_to_copy.push_back(h(e1,e2,n,s,loc).idx.kspace_encode_step_2);
//CAIPI _SHIFT will fail
new_headers(e1/R_E1,e2/R_E2,n,s,loc)=h(e1,e2,n,s,loc);
for (uint16_t cha=0; cha<CHA;cha++)
{
complex_float_t* FromPtr= &data(0,e1,e2,cha,n,s,loc);
complex_float_t* ToPtr= &new_data(0,e1/R_E1,e2/R_E2,cha,n,s,loc);
std::copy(FromPtr,FromPtr+E0,ToPtr);
}
}
}
}
}
}
}
auto traj_dim=traj.get_size(0);
float* ToPtr_traj= &new_traj[0];
float* ToPtr_dcw= &new_dcw[0];
for (uint16_t idx = 0; idx <E1_to_copy.size() ; idx++)
{
//traj
float* FromPtr_traj= &traj(0,0,E1_to_copy[idx],E2_to_copy[idx]);
std::copy(FromPtr_traj,FromPtr_traj+(E0*traj_dim),ToPtr_traj);
//dcw
float* FromPtr= &dcw(0,E1_to_copy[idx],E2_to_copy[idx]);
std::copy(FromPtr,FromPtr+E0,ToPtr_dcw);
ToPtr_traj+=(E0*traj_dim);
ToPtr_dcw+=(E0);
}
dbuff.data_=new_data;
dbuff.density_=new_dcw;
dbuff.headers_=new_headers;
dbuff.trajectory_=new_traj;
GDEBUG("Sucssfully modified recon buff\n");
return true;
}
bool AddTrajInfoGadget::CalcTrajectory3D(IsmrmrdDataBuffered &dbuff)
{
// make the first dim 2 to 3
auto & kTraj2D=dbuff.trajectory_.value();
auto & dcw2D=dbuff.density_.value();
auto mat_sz = MeasHeader.encoding[0].encodedSpace.matrixSize;
auto ktraj3D = Gadgetron::hoNDArray<float>(3, kTraj2D.get_size(1), kTraj2D.get_size(2), mat_sz.z);
auto dcw3D = Gadgetron::hoNDArray<float>(dcw2D.get_size(0), dcw2D.get_size(1), mat_sz.z);
auto nPts_2D = kTraj2D.get_size(1) * kTraj2D.get_size(2);
float kz = 0.0f;
for (size_t z = 0; z < mat_sz.z; z++)
{
auto startPtr = &ktraj3D(0, 0, 0, z);
if (mat_sz.z > 1)
kz = static_cast<float>(z) / static_cast<float>(mat_sz.z) - 0.5f;
for (size_t elem = 0; elem < nPts_2D; elem++)
{
startPtr[elem * 3] = kTraj2D[elem * 2];
startPtr[elem * 3 + 1] = kTraj2D[elem * 2 + 1];
startPtr[elem * 3 + 2] = kz;
}
auto startPtr_dcw=&dcw3D(0,0,z);
std::copy(&dcw2D[0],&dcw2D[0]+dcw2D.get_number_of_elements(),startPtr_dcw);
}
dbuff.trajectory_=ktraj3D;
dbuff.density_=dcw3D;
return true;
}
GADGET_FACTORY_DECLARE(AddTrajInfoGadget)
}