int NoiseAdjustGadget::process_config(ACE_Message_Block* mb)
{
if ( !workingDirectory.value().empty() ) {
noise_dependency_folder_ = workingDirectory.value();
}
else {
#ifdef _WIN32
noise_dependency_folder_ = std::string("c:\\temp\\gadgetron\\");
#else
noise_dependency_folder_ = std::string("/tmp/gadgetron/");
#endif // _WIN32
}
GDEBUG("Folder to store noise dependencies is %s\n", noise_dependency_folder_.c_str());
if ( !noise_dependency_prefix.value().empty() ) noise_dependency_prefix_ = noise_dependency_prefix.value();
perform_noise_adjust_ = perform_noise_adjust.value();
GDEBUG("NoiseAdjustGadget::perform_noise_adjust_ is %d\n", perform_noise_adjust_);
pass_nonconformant_data_ = pass_nonconformant_data.value();
GDEBUG("NoiseAdjustGadget::pass_nonconformant_data_ is %d\n", pass_nonconformant_data_);
noise_dwell_time_us_preset_ = noise_dwell_time_us_preset.value();
ISMRMRD::deserialize(mb->rd_ptr(),current_ismrmrd_header_);
if ( current_ismrmrd_header_.acquisitionSystemInformation ) {
receiver_noise_bandwidth_ = (float)(current_ismrmrd_header_.acquisitionSystemInformation->relativeReceiverNoiseBandwidth ?
*current_ismrmrd_header_.acquisitionSystemInformation->relativeReceiverNoiseBandwidth : 0.793f);
GDEBUG("receiver_noise_bandwidth_ is %f\n", receiver_noise_bandwidth_);
}
// find the measurementID of this scan
if ( current_ismrmrd_header_.measurementInformation )
{
if ( current_ismrmrd_header_.measurementInformation->measurementID )
{
measurement_id_ = *current_ismrmrd_header_.measurementInformation->measurementID;
GDEBUG("Measurement ID is %s\n", measurement_id_.c_str());
}
// find the noise depencies if any
if ( current_ismrmrd_header_.measurementInformation->measurementDependency.size() > 0 )
{
measurement_id_of_noise_dependency_.clear();
std::vector<ISMRMRD::MeasurementDependency>::const_iterator iter = current_ismrmrd_header_.measurementInformation->measurementDependency.begin();
for ( ; iter!= current_ismrmrd_header_.measurementInformation->measurementDependency.end(); iter++ )
{
std::string dependencyType = iter->dependencyType;
std::string dependencyID = iter->measurementID;
GDEBUG("Found dependency measurement : %s with ID %s\n", dependencyType.c_str(), dependencyID.c_str());
if ( dependencyType=="Noise" || dependencyType=="noise" ) {
measurement_id_of_noise_dependency_ = dependencyID;
}
}
if ( !measurement_id_of_noise_dependency_.empty() ) {
GDEBUG("Measurement ID of noise dependency is %s\n", measurement_id_of_noise_dependency_.c_str());
full_name_stored_noise_dependency_ = this->generateNoiseDependencyFilename(generateMeasurementIdOfNoiseDependency(measurement_id_of_noise_dependency_));
GDEBUG("Stored noise dependency is %s\n", full_name_stored_noise_dependency_.c_str());
// try to load the precomputed noise prewhitener
if ( !this->loadNoiseCovariance() ) {
GDEBUG("Stored noise dependency is NOT found : %s\n", full_name_stored_noise_dependency_.c_str());
noiseCovarianceLoaded_ = false;
noise_dwell_time_us_ = -1;
noise_covariance_matrixf_.clear();
} else {
GDEBUG("Stored noise dependency is found : %s\n", full_name_stored_noise_dependency_.c_str());
GDEBUG("Stored noise dwell time in us is %f\n", noise_dwell_time_us_);
GDEBUG("Stored noise channel number is %d\n", noise_covariance_matrixf_.get_size(0));
if (noise_ismrmrd_header_.acquisitionSystemInformation) {
if (noise_ismrmrd_header_.acquisitionSystemInformation->coilLabel.size() !=
current_ismrmrd_header_.acquisitionSystemInformation->coilLabel.size()) {
GDEBUG("Length of coil label arrays do not match");
return GADGET_FAIL;
}
bool labels_match = true;
for (size_t l = 0; l < noise_ismrmrd_header_.acquisitionSystemInformation->coilLabel.size(); l++) {
if (noise_ismrmrd_header_.acquisitionSystemInformation->coilLabel[l].coilNumber !=
current_ismrmrd_header_.acquisitionSystemInformation->coilLabel[l].coilNumber) {
labels_match = false; break;
}
if (noise_ismrmrd_header_.acquisitionSystemInformation->coilLabel[l].coilName !=
current_ismrmrd_header_.acquisitionSystemInformation->coilLabel[l].coilName) {
labels_match = false; break;
}
}
if (!labels_match) {
GDEBUG("Noise and measurement coil labels don't match\n");
return GADGET_FAIL;
}
} else if (current_ismrmrd_header_.acquisitionSystemInformation) {
GDEBUG("Noise ismrmrd header does not have acquisition system information but current header does\n");
return GADGET_FAIL;
}
noiseCovarianceLoaded_ = true;
number_of_noise_samples_ = 1; //When we load the matrix, it is already scaled.
}
}
}
}
//Let's figure out if some channels are "scale_only"
std::string uncomb_str = scale_only_channels_by_name.value();
std::vector<std::string> uncomb;
if (uncomb_str.size()) {
GDEBUG("SCALE ONLY: %s\n", uncomb_str.c_str());
boost::split(uncomb, uncomb_str, boost::is_any_of(","));
for (unsigned int i = 0; i < uncomb.size(); i++) {
std::string ch = boost::algorithm::trim_copy(uncomb[i]);
if (current_ismrmrd_header_.acquisitionSystemInformation) {
for (size_t i = 0; i < current_ismrmrd_header_.acquisitionSystemInformation->coilLabel.size(); i++) {
if (ch == current_ismrmrd_header_.acquisitionSystemInformation->coilLabel[i].coilName) {
scale_only_channels_.push_back(i);//This assumes that the channels are sorted in the header
break;
}
}
}
}
}
#ifdef USE_OMP
omp_set_num_threads(1);
#endif // USE_OMP
return GADGET_OK;
}
int NoiseCovariancePlottingGadget::process_config(ACE_Message_Block* mb)
{
if (!workingDirectory.value().empty())
{
noise_dependency_folder_ = workingDirectory.value();
}
else
{
#ifdef _WIN32
noise_dependency_folder_ = std::string("c:\\temp\\gadgetron\\");
#else
noise_dependency_folder_ = std::string("/tmp/gadgetron/");
#endif // _WIN32
}
GDEBUG("Folder to store noise dependencies is %s\n", noise_dependency_folder_.c_str());
if (!noise_dependency_prefix.value().empty()) noise_dependency_prefix_ = noise_dependency_prefix.value();
ISMRMRD::deserialize(mb->rd_ptr(), current_ismrmrd_header_);
// find the measurementID of this scan
if (current_ismrmrd_header_.measurementInformation)
{
if (current_ismrmrd_header_.measurementInformation->measurementID)
{
measurement_id_ = *current_ismrmrd_header_.measurementInformation->measurementID;
GDEBUG("Measurement ID is %s\n", measurement_id_.c_str());
}
// find the noise depencies if any
if (current_ismrmrd_header_.measurementInformation->measurementDependency.size() > 0)
{
measurement_id_of_noise_dependency_.clear();
std::vector<ISMRMRD::MeasurementDependency>::const_iterator iter = current_ismrmrd_header_.measurementInformation->measurementDependency.begin();
for (; iter != current_ismrmrd_header_.measurementInformation->measurementDependency.end(); iter++)
{
std::string dependencyType = iter->dependencyType;
std::string dependencyID = iter->measurementID;
GDEBUG("Found dependency measurement : %s with ID %s\n", dependencyType.c_str(), dependencyID.c_str());
if (dependencyType == "Noise" || dependencyType == "noise") {
measurement_id_of_noise_dependency_ = dependencyID;
}
}
if (!measurement_id_of_noise_dependency_.empty())
{
GDEBUG("Measurement ID of noise dependency is %s\n", measurement_id_of_noise_dependency_.c_str());
full_name_stored_noise_dependency_ = this->generateNoiseDependencyFilename(generateMeasurementIdOfNoiseDependency(measurement_id_of_noise_dependency_));
GDEBUG("Stored noise dependency is %s\n", full_name_stored_noise_dependency_.c_str());
}
}
else
{
full_name_stored_noise_dependency_ = this->generateNoiseDependencyFilename(measurement_id_);
GDEBUG("Stored noise dependency is %s\n", full_name_stored_noise_dependency_.c_str());
}
}
return GADGET_OK;
}
