/* Cause us to be subscribed to the given publisher (if any) and not to
any other publisher. */
void reset(publisher_t *pub = NULL) {
if (publisher) {
mutex_assertion_t::acq_t acq(&publisher->mutex);
publisher->subscriptions.remove(this);
}
publisher = pub;
if (publisher) {
mutex_assertion_t::acq_t acq(&publisher->mutex);
publisher->subscriptions.push_back(this);
}
}
ZRef<Callable_PullSuggested> Searcher_DatonSet::GetCallable_PullSuggested()
{
ZAcqMtxR acq(fMtxR);
if (not fCallable_PullSuggested_Self)
fCallable_PullSuggested_Self = sCallable(sWeakRef(this), &Searcher_DatonSet::pPullSuggested);
return fCallable_PullSuggested_Self;
}
void push(const T &value) {
write_message_t wm;
// Despite that we are serializing this *to disk*, disk backed queues are not
// intended to persist across restarts, so using
// `cluster_version_t::LATEST_OVERALL` is safe.
serialize<cluster_version_t::LATEST_OVERALL>(&wm, value);
mutex_t::acq_t acq(&push_mutex);
items_in_queue++;
if (disk_queue.has()) {
disk_queue->push(wm);
// Check if we need to restart the copy coroutine that may have exited while we pushed
if (restart_copy_coro) {
restart_copy_coro = false;
coro_t::spawn_sometime(std::bind(
&disk_backed_queue_wrapper_t<T>::copy_from_disk_queue_to_memory_queue,
this, auto_drainer_t::lock_t(&drainer)));
}
} else {
if (memory_queue_free_space <= 0) {
disk_queue.init(new internal_disk_backed_queue_t(
io_backender, filename, stats_parent));
disk_queue->push(wm);
coro_t::spawn_sometime(std::bind(
&disk_backed_queue_wrapper_t<T>::copy_from_disk_queue_to_memory_queue,
this, auto_drainer_t::lock_t(&drainer)));
} else {
memory_queue.emplace_back(std::move(wm));
available_control.set_available(true);
}
}
}
void Searcher::SetCallable_SearcherResultsAvailable(
ZRef<Callable_SearcherResultsAvailable> iCallable)
{
ZAcqMtx acq(fMtx);
fCalled_SearcherResultsAvailable.Reset();
fCallable_SearcherResultsAvailable = iCallable;
}
void Relater_Asyncify::ModifyRegistrations(
const AddedQuery* iAdded, size_t iAddedCount,
const int64* iRemoved, size_t iRemovedCount)
{
ZAcqMtxR acq(fMtxR);
while (iAddedCount--)
{
if (ZLOGPF(s, eDebug + 1))
s << "Add: " << iAdded->GetRefcon();
sInsertMust(fPendingAdds, iAdded->GetRefcon(), iAdded->GetRel());
++iAdded;
}
while (iRemovedCount--)
{
const int64 theRefcon = *iRemoved++;
if (ZLOGPF(s, eDebug + 1))
s << "Remove: " << theRefcon;
if (not sQErase(fPendingAdds, theRefcon))
sInsertMust(fPendingRemoves, theRefcon);
if (sQErase(fPendingResults, theRefcon))
{
// Not sure if this is actually an issue.
ZLOGTRACE(eDebug);
}
}
this->pTrigger_Update();
}
void ZServer::Start(ZRef<ZCaller> iCaller,
ZRef<ZStreamerRWFactory> iFactory,
ZRef<Callable_Connection> iCallable_Connection)
{
ZAssert(iCaller);
ZAssert(iFactory);
// Declared before the acq, so it goes out of scope after it, and any
// callable on the roster is invoked with our mutex released.
ZRef<ZRoster> priorRoster;
ZAcqMtx acq(fMtx);
ZAssert(not fWorker);
ZAssert(not fFactory);
ZAssert(not fCallable_Connection);
priorRoster = fRoster;
fRoster = new ZRoster;
fFactory = iFactory;
fCallable_Connection = iCallable_Connection;
fWorker = new ZWorker(
sCallable(sWeakRef(this), &ZServer::pWork),
sCallable(sWeakRef(this), &ZServer::pWorkDetached));
fWorker->Attach(iCaller);
fWorker->Wake();
}
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
if(nrhs < 1)
mexErrMsgTxt("At least one input argument is required.");
if (nlhs > 1)
mexErrMsgTxt("Too many output arguments.");
btk::MergeAcquisitionFilter::Pointer merger = btk::MergeAcquisitionFilter::New();
std::vector<btk::Acquisition::Pointer> acq(nrhs);
for (int i = 0 ; i < nrhs ; ++i)
merger->SetInput(i, btk_MOH_get_object<btk::Acquisition>(prhs[i]));
// Redirection of the btk::Logger::Warning stream.
btk::MEXWarnLogToWarnMsgTxt warnRedir = btk::MEXWarnLogToWarnMsgTxt("btk:MergeAcquisitions");
merger->Update();
plhs[0] = btk_MOH_create_handle(merger->GetOutput());
#if defined(__APPLE__) || (defined(BTK_BUILD_SHARED_LIBS) && defined(__unix__))
// It seems to be related only to Linux with shared libraries
// This fix was only tested with Matlab r2009a (7.8)
// FIXME: This solution clear all the acquisitions and not only the ones
// created from this function
mexAtExit(btk::MEXHandleCollector<btk::Acquisition>::ManualClear);
#endif
};
void push(const T &value) {
mutex_t::acq_t acq(&push_mutex);
items_in_queue++;
if (disk_queue.has()) {
disk_queue->push(value);
// Check if we need to restart the copy coroutine that may have exited while we pushed
if (restart_copy_coro) {
restart_copy_coro = false;
coro_t::spawn_sometime(std::bind(
&disk_backed_queue_wrapper_t<T>::copy_from_disk_queue_to_memory_queue,
this, auto_drainer_t::lock_t(&drainer)));
}
} else {
if (memory_queue.full()) {
disk_queue.init(new disk_backed_queue_t<T>(io_backender, filename, stats_parent));
disk_queue->push(value);
coro_t::spawn_sometime(std::bind(
&disk_backed_queue_wrapper_t<T>::copy_from_disk_queue_to_memory_queue,
this, auto_drainer_t::lock_t(&drainer)));
} else {
memory_queue.push_back(value);
available_control.set_available(true);
}
}
}
~StartOnNewThreadHandler()
{
ZAcqMtx acq(fMtx);
fKeepRunning = false;
fCnd.Broadcast();
while (fActiveThreads)
fCnd.WaitFor(fMtx, 7);
}
void publish(const callable_t &callable) {
mutex_assertion_t::acq_t acq(&publisher.mutex);
for (typename publisher_t<subscriber_t>::subscription_t *sub = publisher.subscriptions.head();
sub;
sub = publisher.subscriptions.next(sub)) {
/* `callable()` should not block */
ASSERT_FINITE_CORO_WAITING;
callable(sub->subscriber);
}
}
void ZServer::Stop()
{
ZAcqMtx acq(fMtx);
if (ZRef<ZStreamerRWFactory> theFactory = fFactory)
{
fFactory.Clear();
theFactory->Cancel();
}
fCallable_Connection.Clear();
fCnd.Broadcast();
}
void Relater_Asyncify::CollectResults(vector<QueryResult>& oChanged)
{
ZAcqMtxR acq(fMtxR);
Relater::pCalled_RelaterCollectResults();
oChanged.reserve(fPendingResults.size());
foreachi (iter, fPendingResults)
{
// May need to filter entries on our fPendingRemoves list.
oChanged.push_back(iter->second);
}
void reset(signal_t *s = nullptr) {
if (s) {
mutex_assertion_t::acq_t acq(&s->lock);
if (s->is_pulsed()) {
subs.subscriber->run();
} else {
subs.reset(s->publisher_controller.get_publisher());
}
} else {
subs.reset(nullptr);
}
}
ZQ<void> Worker::QCall()
{
ZAcqMtx acq(fMtx);
for (;;)
{
fWorking = ZThread::sID();
fNextWake = kDistantFuture;
ZRelMtx rel(fMtx);
ZQ<bool> result;
try { result = fCallable_Work->QCall(this); }
catch (...) {}
ZAcqMtx acq(fMtx);
fWorking = 0;
if (result && *result)
{
if (fNextWake < kDistantFuture)
{
if (fNextWake <= Time::sSystem())
continue;
sNextStartAt(fNextWake, Job(fStarter, this));
}
return notnull;
}
fStarter.Clear();
fCnd.Broadcast();
ZRelMtx rel2(fMtx);
try { sCall(fCallable_Detached, this); }
catch (...) {}
return null;
}
}
void RunLoop()
{
ZAcqMtx acq(fMtx);
double expires = Time::sSystem() + 10;
for (;;)
{
if (fQueue.empty())
{
ZThread::sSetName("SONT idle");
if (not fKeepRunning)
{
fCnd.Broadcast();
break;
}
else if (Time::sSystem() > expires)
{
break;
}
++fIdleThreads;
fCnd.WaitFor(fMtx, 5);
--fIdleThreads;
}
else
{
ZThread::sSetName("SONT call");
ZRef<Callable<void()>> theCallable = fQueue.front();
fQueue.pop_front();
try
{
ZRelMtx acq(fMtx);
theCallable->QCall();
}
catch (...)
{}
}
}
--fActiveThreads;
}
void Worker::pWakeAt(double iSystemTime)
{
ZAcqMtx acq(fMtx);
if (fStarter)
{
if (fWorking)
{
if (fNextWake > iSystemTime)
fNextWake = iSystemTime;
}
else
{
sNextStartAt(iSystemTime, Job(fStarter, this));
}
}
}
void ZServer::StopWait()
{
ZAcqMtx acq(fMtx);
if (ZRef<ZStreamerRWFactory> theFactory = fFactory)
{
fFactory.Clear();
theFactory->Cancel();
}
if (fWorker)
{
fWorker->Wake();
while (fWorker)
fCnd.Wait(fMtx);
}
}
void Start(const ZRef<Callable<void()>>& iCallable)
{
ZAcqMtx acq(fMtx);
fQueue.push_back(iCallable);
if (fIdleThreads < fQueue.size())
{
++fActiveThreads;
for (int xx = 0; /*no test*/; ++xx)
{
try
{
ZThread::sStartRaw(0, (ZThread::ProcRaw_t)spRunLoop, this);
if (xx != 0)
{
if (ZLOGF(w, eErr))
w << "ZThread::sStartRaw succeeded after " << xx << " additional tries.";
}
break;
}
catch (std::exception& ex)
{
if (xx == 0)
{
if (ZLOGF(w, eErr))
{
w << "Exception: " << ex.what() << "\n";
Util_Debug::sWriteBacktrace(w);
}
}
else
{
ZThread::sSleep(0.01);
}
}
}
}
else
{
fCnd.Broadcast();
}
}
void ZStreamRWCon_SSL_Win::Imp_SendDisconnect()
{
ZAcqMtx acq(fMtx_W);
if (not fSendOpen)
return;
fSendOpen = false;
SecBuffer outSB[1];
outSB[0].cbBuffer = 0;
outSB[0].pvBuffer = nullptr;
outSB[0].BufferType= SECBUFFER_TOKEN;
SecBufferDesc outSBD;
outSBD.cBuffers = 1;
outSBD.pBuffers = outSB;
outSBD.ulVersion = SECBUFFER_VERSION;
DWORD attributes;
SECURITY_STATUS scRet = spPSFT->InitializeSecurityContextA(
&fCredHandle,
&fCtxtHandle,
nullptr,
spRequirements,
0, // Reserved1
SECURITY_NATIVE_DREP,
nullptr,
0, // Reserved2
nullptr,
&outSBD,
&attributes,
nullptr);
if (FAILED(scRet))
return;
spWriteFreeFlush(outSB[0], fStreamW);
}
bool Worker::Attach(ZRef<Starter> iStarter)
{
ZAcqMtx acq(fMtx);
if (not fStarter)
{
fStarter = iStarter;
try
{
ZRelMtx rel(fMtx);
sCall(fCallable_Attached, this);
return true;
}
catch (...) {}
fStarter.Clear();
fCnd.Broadcast();
ZRelMtx rel(fMtx);
try { sCall(fCallable_Detached, this); }
catch (...) {}
}
return false;
}
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(...) ... ");
}
}
void Searcher::pCollectResultsCalled()
{
ZAcqMtx acq(fMtx);
fCalled_SearcherResultsAvailable.Reset();
}
// <@$M_{t2}$@> module
void foo () {
acq();
f(); g();
rel();
}
void ZServer::pWorkDetached(ZRef<ZWorker> iWorker)
{
ZAcqMtx acq(fMtx);
fWorker.Clear();
fCnd.Broadcast();
}
int main(void)
{
ArSerialConnection con;
ArRobot robot;
int ret;
std::string str;
ArActionLimiterForwards limiter("speed limiter near", 300, 600, 250);
ArActionLimiterForwards limiterFar("speed limiter far", 300, 1100, 400);
ArActionLimiterBackwards backwardsLimiter;
ArActionConstantVelocity stop("stop", 0);
ArActionConstantVelocity backup("backup", -200);
ArSonarDevice sonar;
ArACTS_1_2 acts;
ArSonyPTZ sony(&robot);
ArGripper gripper(&robot, ArGripper::GENIO);
Acquire acq(&acts, &gripper);
DriveTo driveTo(&acts, &gripper, &sony);
PickUp pickUp(&acts, &gripper, &sony);
TakeBlockToWall takeBlock(&robot, &gripper, &sony, &acq, &driveTo, &pickUp,
&backup);
Aria::init();
if (!acts.openPort(&robot))
{
printf("Could not connect to acts\n");
exit(1);
}
robot.addRangeDevice(&sonar);
//con.setBaud(38400);
if ((ret = con.open()) != 0)
{
str = con.getOpenMessage(ret);
printf("Open failed: %s\n", str.c_str());
Aria::shutdown();
return 1;
}
robot.setDeviceConnection(&con);
if (!robot.blockingConnect())
{
printf("Could not connect to robot... exiting\n");
Aria::shutdown();
return 1;
}
sony.init();
ArUtil::sleep(1000);
//robot.setAbsoluteMaxTransVel(400);
robot.setStateReflectionRefreshTime(250);
robot.comInt(ArCommands::ENABLE, 1);
robot.comInt(ArCommands::SOUNDTOG, 0);
ArUtil::sleep(200);
robot.addAction(&limiter, 100);
robot.addAction(&limiterFar, 99);
robot.addAction(&backwardsLimiter, 98);
robot.addAction(&acq, 77);
robot.addAction(&driveTo, 76);
robot.addAction(&pickUp, 75);
robot.addAction(&backup, 50);
robot.addAction(&stop, 30);
robot.run(true);
Aria::shutdown();
return 0;
}
ZRef<ZServer::Callable_Connection> ZServer::GetCallable_Connection()
{
ZAcqMtx acq(fMtx);
return fCallable_Connection;
}
ZRef<ZStreamerRWFactory> ZServer::GetFactory()
{
ZAcqMtx acq(fMtx);
return fFactory;
}
int main(void)
{
ArSerialConnection con;
ArRobot robot;
int ret;
std::string str;
ArActionLimiterForwards limiter("speed limiter near", 225, 600, 250);
ArActionLimiterForwards limiterFar("speed limiter far", 225, 1100, 400);
ArActionTableSensorLimiter tableLimiter;
ArActionLimiterBackwards backwardsLimiter;
ArActionConstantVelocity stop("stop", 0);
ArSonarDevice sonar;
ArACTS_1_2 acts;
ArPTZ *ptz;
ptz = new ArVCC4(&robot, true);
ArGripper gripper(&robot);
Acquire acq(&acts, &gripper);
DriveTo driveTo(&acts, &gripper, ptz);
DropOff dropOff(&acts, &gripper, ptz);
PickUp pickUp(&acts, &gripper, ptz);
TakeBlockToWall takeBlock(&robot, &gripper, ptz, &acq, &driveTo, &pickUp,
&dropOff, &tableLimiter);
if (!acts.openPort(&robot))
{
printf("Could not connect to acts, exiting\n");
exit(0);
}
Aria::init();
robot.addRangeDevice(&sonar);
//con.setBaud(38400);
if ((ret = con.open()) != 0)
{
str = con.getOpenMessage(ret);
printf("Open failed: %s\n", str.c_str());
Aria::shutdown();
return 1;
}
robot.setDeviceConnection(&con);
if (!robot.blockingConnect())
{
printf("Could not connect to robot... exiting\n");
Aria::shutdown();
return 1;
}
ptz->init();
ArUtil::sleep(8000);
printf("### 2222\n");
ptz->panTilt(0, -40);
printf("### whee\n");
ArUtil::sleep(8000);
robot.setAbsoluteMaxTransVel(400);
robot.setStateReflectionRefreshTime(250);
robot.comInt(ArCommands::ENABLE, 1);
robot.comInt(ArCommands::SOUNDTOG, 0);
ArUtil::sleep(200);
robot.addAction(&tableLimiter, 100);
robot.addAction(&limiter, 99);
robot.addAction(&limiterFar, 98);
robot.addAction(&backwardsLimiter, 97);
robot.addAction(&acq, 77);
robot.addAction(&driveTo, 76);
robot.addAction(&pickUp, 75);
robot.addAction(&dropOff, 74);
robot.addAction(&stop, 30);
robot.run(true);
Aria::shutdown();
return 0;
}
bool ZSocketWatcher::QErase(const Pair_t& iPair)
{
ZAcqMtx acq(fMtx);
return fSet.erase(iPair);
}
int _tmain(int argc, _TCHAR* argv[])
{
com_ptr<IDirectInput8> input(0);
com_ptr<IDirectInputDevice8> device(0);
HRESULT hr = 0;
{
IDirectInput8* ptr;
hr = ::DirectInput8Create(
::GetModuleHandleA(NULL),
DIRECTINPUT_VERSION,
IID_IDirectInput8,
reinterpret_cast<void**>(&ptr),
0);
if (FAILED(hr)) {
output("Failed to create DInput8 handle.\n");
return 0;
}
input = com_ptr<IDirectInput8>(ptr);
}
{
IDirectInputDevice8* ptr;
hr = input->CreateDevice(GUID_SysKeyboard, &ptr, 0);
if (FAILED(hr)) {
output("Failed to create keyboard device.\n");
return 0;
}
device = com_ptr<IDirectInputDevice8>(ptr);
}
hr = device->SetDataFormat(&c_dfDIKeyboard);
if (FAILED(hr)) {
output("Failed to set device data format.\n");
return 0;
}
hr = device->SetCooperativeLevel(GetConsoleHwnd(), DISCL_NONEXCLUSIVE | DISCL_FOREGROUND);
if (FAILED(hr)) {
output("Failed to set device cooperative level.\n");
return 0;
}
{
DIPROPDWORD dipdw = {0};
dipdw.diph.dwSize = sizeof(DIPROPDWORD);
dipdw.diph.dwHeaderSize = sizeof(DIPROPHEADER);
dipdw.diph.dwObj = 0;
dipdw.diph.dwHow = DIPH_DEVICE;
dipdw.dwData = 8; // バッファのサイズ
hr = device->SetProperty(DIPROP_BUFFERSIZE, &dipdw.diph);
if (FAILED(hr)) {
output("Failed to set device buffer size property.\n");
return 0;
}
}
acquire_device acq(device.get());
keyboard kbd;
while(!kbd.pressed(EscapeKey))
{
kbd.reset();
HRESULT hr = device->GetDeviceState(KeyboardSize, kbd.data());
if (FAILED(hr)) {
std::cout << "Failed to get keyboard device state\n";
break;
}
std::cout << std::hex;
//for(byte_t i = 0; i != KeyboardSize; ++i) {
byte_t i = 0;
do {
if (kbd.pressed(i))
std::cout << static_cast<size_t>(i) << " ";
} while(i != KeyboardSize-1);
//}
std::cout << std::endl;
::Sleep(100);
}
return 0;
}
