bool
waveform::fft::lowpass_filter( adcontrols::MassSpectrum& ms, double freq )
{
if ( ms.isCentroid() )
return false;
size_t totalSize = ms.size();
(void)totalSize;
size_t N = 32;
while ( N < ms.size() )
N *= 2;
const size_t NN = ms.size();
double sampInterval = ms.getMSProperty().getSamplingInfo().fSampInterval(); // seconds
if ( sampInterval == 0 )
sampInterval = ( ms.getTime( ms.size() - 1 ) - ms.getTime( 0 ) ) / ms.size();
const double T = N * sampInterval; // time full scale in seconds. Freq = n/T (Hz)
// power spectrum has N/2 points and is n/T Hz horizontal axis := data[N/2] = (N/2)/T Hz
size_t cutoff = size_t( T * freq );
adportable::array_wrapper<const double> pIntens( ms.getIntensityArray(), N );
std::vector< std::complex<double> > spc( N );
std::vector< std::complex<double> > fft( N );
size_t n;
for ( n = 0; n < N && n < NN; ++n )
spc[ n ] = std::complex<double>( pIntens[ n ] );
while ( n < N )
spc[ n++ ] = pIntens[ NN - 1 ];
adportable::fft::fourier_transform( fft, spc, false );
// appodization
for ( size_t i = cutoff; i < N - cutoff; ++i )
fft[ i ] = 0;
//adportable::fft::apodization( N/2 - N/16, N / 16, fft );
adportable::fft::fourier_transform( spc, fft, true );
std::vector<double> data( N );
for ( size_t i = 0; i < NN; ++i )
data[ i ] = spc[i].real();
ms.setIntensityArray( &data[0] );
return true;
}
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
MSChromatogramExtractor::impl::doMSLock( adcontrols::lockmass::mslock& mslock
, const adcontrols::MassSpectrum& centroid
, const adcontrols::MSLockMethod& m )
{
// TODO: consider how to handle segmented spectrum -- current impl is always process first
adcontrols::MSFinder find( m.tolerance( m.toleranceMethod() ), m.algorithm(), m.toleranceMethod() );
for ( auto& msref : msrefs_ ) {
size_t idx = find( centroid, msref.second );
if ( idx != adcontrols::MSFinder::npos )
mslock << adcontrols::lockmass::reference( msref.first, msref.second, centroid.getMass( idx ), centroid.getTime( idx ) );
}
if ( mslock.fit() ) {
// mslock( centroid, true );
return true;
}
return false;
}
bool
assign_masses::operator()( adcontrols::MSAssignedMasses& assignedMasses
, const adcontrols::MassSpectrum& centroid
, const adcontrols::MSReferences& references
, int mode
, int fcn )
{
using adportable::array_wrapper;
using adcontrols::MSReferences;
array_wrapper<const double> masses( centroid.getMassArray(), centroid.size() );
array_wrapper<const double> intens( centroid.getIntensityArray(), centroid.size() );
for ( MSReferences::vector_type::const_iterator it = references.begin(); it != references.end(); ++it ) {
double exactMass = it->exact_mass();
array_wrapper<const double>::const_iterator lBound = std::lower_bound( masses.begin(), masses.end(), exactMass - tolerance_ );
array_wrapper<const double>::const_iterator uBound = std::lower_bound( masses.begin(), masses.end(), exactMass + tolerance_ );
if ( lBound != masses.end() ) {
size_t lIdx = std::distance( masses.begin(), lBound );
size_t uIdx = std::distance( masses.begin(), uBound );
// find closest
size_t cIdx = lIdx;
for ( size_t i = lIdx + 1; i < uIdx; ++i ) {
double d0 = std::abs( masses[ cIdx ] - exactMass );
double d1 = std::abs( masses[ i ] - exactMass );
if ( d1 < d0 )
cIdx = i;
}
// find highest
array_wrapper<const double>::const_iterator hIt = std::max_element( intens.begin() + lIdx, intens.begin() + uIdx );
if ( *hIt < threshold_ )
continue;
size_t idx = std::distance( intens.begin(), hIt );
adcontrols::MSAssignedMass assigned( uint32_t( std::distance( references.begin(), it ) )
, fcn
, uint32_t(idx) // idMassSpectrum (index on centroid peak)
, it->display_formula()
, it->exact_mass()
, centroid.getTime( idx )
, masses[ idx ]
, it->enable()
, false // flags
, mode );
// duplicate assign check
adcontrols::MSAssignedMasses::vector_type::iterator assignIt =
std::find_if( assignedMasses.begin(), assignedMasses.end(), [&]( const adcontrols::MSAssignedMass& a ){
return a.idPeak() == idx && a.idMassSpectrum() == unsigned(fcn);
});
if ( assignIt != assignedMasses.end() ) {
// already assined to another refernce
if ( std::fabs( assignIt->exactMass() - assignIt->mass() ) >
std::fabs( assigned.exactMass() - assigned.mass() ) ) {
*assignIt = assigned; // replace
}
} else
assignedMasses << assigned;
}
}
return true;
}
bool
QuanSampleProcessor::doMSLock( adcontrols::MSPeakInfo& pkInfo // will override
, adcontrols::MassSpectrum& centroid // will override
, const adcontrols::MSLockMethod& m
, const adcontrols::QuanCompounds& compounds )
{
// find reference peak by mass window
adcontrols::lockmass::mslock mslock;
// TODO: consider how to handle segmented spectrum -- current impl is always process first
adcontrols::MSFinder find( m.tolerance( m.toleranceMethod() ), m.algorithm(), m.toleranceMethod() );
for ( auto& compound : compounds ) {
if ( compound.isLKMSRef() ) {
double exactMass = cformula_->getMonoIsotopicMass( compound.formula() );
size_t idx = find( centroid, exactMass );
if ( idx != adcontrols::MSFinder::npos ) {
// add found peaks into mslock
mslock << adcontrols::lockmass::reference( compound.formula(), exactMass, centroid.getMass( idx ), centroid.getTime( idx ) );
}
}
}
if ( mslock.fit() ) {
mslock( centroid, true );
mslock( pkInfo, true );
return true;
}
return false;
}
