bool
rawdata::applyCalibration( const std::wstring& dataInterpreterClsid, const adcontrols::MSCalibrateResult& calibResult )
{
#if 0
boost::uuids::uuid objid;
auto it = std::find_if( conf_.begin(), conf_.end(), [=](const adutils::AcquiredConf::data& c){
return c.dataInterpreterClsid == dataInterpreterClsid;
});
if ( it != conf_.end() )
objid = it->objid;
else {
if ( conf_.empty() )
adutils::v3::AcquiredConf::create_table_v3( dbf_.db() );
adutils::v3::AcquiredConf::data d;
d.objid = objid;
d.dataInterpreterClsid.resize( dataInterpreterClsid.size() );
std::copy( dataInterpreterClsid.begin(), dataInterpreterClsid.end(), d.dataInterpreterClsid.begin() );
if ( !adutils::v3::AcquiredConf::insert( dbf_.db(), objid, d ) )
return false;
}
const std::wstring calibId = calibResult.calibration().calibId();
std::string device;
if ( adportable::binary::serialize<>()(calibResult, device) ) {
adutils::mscalibio::writeCalibration( dbf_.db(), uint32_t( objid ), calibId.c_str(), calibResult.dataClass(), device.data(), device.size() );
loadAcquiredConf();
loadCalibrations();
return true;
}
#endif
return false;
}
static void
calibresult_validation( const adcontrols::MSCalibrateResult& res
, const adcontrols::MassSpectrum& centroid
, double threshold )
{
const adcontrols::MSReferences& ref = res.references();
const adcontrols::MSAssignedMasses& assigned = res.assignedMasses();
std::ofstream of( "massassign.txt" );
of << "#\tm/z(observed)\ttof(us)\tintensity\t\tformula,\tm/z(exact)\tm/z(calibrated)\terror(mDa)" << std::endl;
adcontrols::MSReferences::vector_type::const_iterator refIt = ref.begin();
for ( adcontrols::MSAssignedMasses::vector_type::const_iterator it = assigned.begin(); it != assigned.end(); ++it, ++refIt ) {
const adcontrols::MSAssignedMass& a = *it;
std::string formula = adportable::string::convert( a.formula() );
of << std::setprecision(8)
<< std::setw(4) << a.idMassSpectrum() << "\t" // id
<< std::setw(15) << std::fixed << centroid.getMass( a.idMassSpectrum() ) << "\t" // m/z(observed)
<< std::scientific << centroid.getTime( a.idMassSpectrum() ) << "\t" // tof
<< std::fixed << std::setprecision( 0 ) << centroid.getIntensity( a.idMassSpectrum() ) << "\t" // intensity
<< formula << "\t"
<< std::setprecision(8) << std::fixed << it->exactMass() << "\t" // mass(exact)
<< std::fixed << a.mass() << "\t" // m/z(calibrated)
<< std::setprecision(1) << ( a.mass() - it->exactMass() ) * 1000 << "\t" // error(mDa)
<< ( it->enable() ? "used" : "not used" )
<< std::endl;
}
const std::vector<double>& coeffs = res.calibration().coeffs();
of << "#--------------------------- Calibration coefficients: " << std::endl;
for ( size_t i = 0; i < coeffs.size(); ++i )
of << std::scientific << std::setprecision(14) << coeffs[i] << std::endl;
of << "#--------------------------- centroid peak list (#,mass,intensity)--------------------------" << std::endl;
adcontrols::MSReferences::vector_type::const_iterator it = res.references().begin();
for ( size_t i = 0; i < centroid.size(); ++i ) {
if ( centroid.getIntensity( i ) > threshold ) {
double mq = adcontrols::MSCalibration::compute( res.calibration().coeffs(), centroid.getTime( i ) );
double mass = mq * mq;
double error = 0;
if ( it != res.references().end() && std::abs( it->exactMass() - mass ) < 0.2 ) {
error = ( it->exactMass() - mass ) * 1000; // mDa
++it;
}
of << i << "\t"
<< std::setprecision(8) << std::fixed << centroid.getMass( i ) << "\t"
<< std::setprecision(8) << mass << "\t"
<< std::setprecision(1) << centroid.getIntensityArray()[i] << std::endl;
}
}
}
bool
DataprocHandler::doMSCalibration( adcontrols::MSCalibrateResult& res
, adcontrols::MassSpectrum& centroid
, const adcontrols::MSCalibrateMethod& m )
{
using adcontrols::MSProperty;
res.calibration( centroid.calibration() );
res.references( m.references() );
double tolerance = m.massToleranceDa();
double threshold = adcontrols::segments_helper::max_intensity( centroid ) * m.minimumRAPercent() / 100;
res.tolerance( tolerance );
res.threshold( threshold );
assign_masses assigner( tolerance, threshold );
adcontrols::MSAssignedMasses assignedMasses;
adcontrols::segment_wrapper< adcontrols::MassSpectrum > segments( centroid );
int n = 0;
for ( auto seg: segments )
assigner( assignedMasses, seg, res.references(), seg.mode(), n++ );
res.assignedMasses( assignedMasses ); // set peak assign result
// annotate each peak on spectrum
doAnnotateAssignedPeaks( centroid, assignedMasses );
mass_calibrator calibrator( assignedMasses, centroid.getMSProperty() );
adcontrols::MSCalibration calib;
if ( calibrator.polfit( calib, m.polynomialDegree() + 1 ) ) {
for ( auto it: assignedMasses ) {
double mass = calibrator.compute_mass( it.time(), it.mode(), calib );
it.mass( mass );
}
res.calibration( calib );
// res.assignedMasses( assignedMasses );
#if defined _DEBUG && 0
calibresult_validation( res, centroid, threshold );
#endif
return true;
}
return false;
}
bool
DataprocHandler::doMSCalibration( adcontrols::MSCalibrateResult& res
, adcontrols::MassSpectrum& centroid
, const adcontrols::MSCalibrateMethod& m
, const adcontrols::MSAssignedMasses& assigned )
{
using adcontrols::MSProperty;
const double tolerance = m.massToleranceDa();
const double threshold = centroid.getMaxIntensity() * m.minimumRAPercent() / 100;
res.tolerance( tolerance ); // set tolerance in result
res.threshold( threshold ); // set threshold in result
std::map< size_t, size_t > mode_map;
for ( adcontrols::MSAssignedMasses::vector_type::const_iterator it = assigned.begin(); it != assigned.end(); ++it )
mode_map[ it->mode() ]++;
// std::map<size_t, size_t>::iterator itMax = std::max_element( mode_map.begin(), mode_map.end() );
// int mode = static_cast<int>(itMax->first);
mass_calibrator calibrator( assigned, centroid.getMSProperty() );
adcontrols::MSCalibration calib;
if ( ! calibrator.polfit( calib, m.polynomialDegree() + 1 ) )
return false;
res.references( m.references() );
res.calibration( calib );
centroid.setCalibration( calib, true ); // m/z assign based on manually determined peaks
// continue auto-assign
assign_masses assign( tolerance, threshold );
adcontrols::MSAssignedMasses assignedMasses;
adcontrols::segment_wrapper< adcontrols::MassSpectrum > segments( centroid );
for ( size_t n = 0; n < segments.size(); ++n ) {
assign( assignedMasses, segments[n], m.references(), 0, static_cast<int>(n) );
}
mass_calibrator calibrator2( assignedMasses, centroid.getMSProperty() );
if ( calibrator2.polfit( calib, m.polynomialDegree() + 1 ) ) {
for ( auto it: assignedMasses )
it.mass( calibrator2.compute_mass( it.time(), it.mode(), calib ) );
centroid.setCalibration( calib, true );
res.calibration( calib );
res.assignedMasses( assignedMasses );
return true;
}
return false;
}
bool
fsio::load_mscalibfile( adfs::filesystem& fs, adcontrols::MSCalibrateResult& d )
{
return load( fs, d, d.dataClass(), L"/MSCalibration" );
}
bool
fsio::save_mscalibfile( adfs::filesystem& fs, const adcontrols::MSCalibrateResult& d )
{
return save( fs, d, d.dataClass(), L"/MSCalibration" );
}
