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;
}