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;
}
}
}
void operator () ( const adcontrols::MassSpectrum& data
, adportable::counting::counting_result& result
, std::vector< double >& processed ) {
assert ( method.algo_ == adcontrols::threshold_method::Differential );
assert ( findPositive == ( method.slope == adcontrols::threshold_method::CrossUp ) );
double level = method.threshold_level;
adportable::counting::peak_finder< findPositive > finder;
finder( data.getIntensityArray(), data.getIntensityArray() + data.size(), result.indices2(), level );
}
//virtual
bool
datafile::getSpectrum( int fcn, size_t pos, adcontrols::MassSpectrum& ms, uint32_t objId ) const
{
(void)fcn;
try {
EDAL::IMSSpectrumCollectionPtr pSpectra = pAnalysis_->GetMSSpectrumCollection();
EDAL::IMSSpectrumPtr pSpectrum = pSpectra->GetItem( long(pos) + 1 ); // 1-origin
if ( pSpectrum->Polarity == EDAL::SpectrumPolarity::IonPolarity_Negative )
ms.setPolarity( adcontrols::MS_POLARITY::PolarityNegative );
else if ( pSpectrum->Polarity == EDAL::SpectrumPolarity::IonPolarity_Positive )
ms.setPolarity( adcontrols::MS_POLARITY::PolarityPositive );
else
ms.setPolarity( adcontrols::MS_POLARITY::PolarityIndeterminate );
adcontrols::MSProperty prop = ms.getMSProperty();
prop.setTimeSinceInjection( static_cast< unsigned long >( pSpectrum->RetentionTime /* sec */ * 1.0e6 ) ); // usec
ms.setMSProperty( prop ); // <- end of prop set
_variant_t vMasses, vIntens;
if ( objId <= 1 ) {
pSpectrum->GetMassIntensityValues( EDAL::SpectrumType_Profile, &vMasses, &vIntens );
ms.setCentroid( adcontrols::CentroidNone ); // profile
} else { // objId should be 2
pSpectrum->GetMassIntensityValues( EDAL::SpectrumType_Line, &vMasses, &vIntens );
ms.setCentroid( adcontrols::CentroidNative );
}
SafeArray sa_masses( vMasses );
ms.resize( sa_masses.size() );
ms.setMassArray( reinterpret_cast< const double *>( sa_masses.p() ) );
SafeArray sa_intensities( vIntens );
ms.setIntensityArray( reinterpret_cast< const double *>( sa_intensities.p() ) );
ms.setAcquisitionMassRange( ms.getMass( 0 ), ms.getMass( ms.size() - 1 ) );
return true;
} catch(_com_error& ex ) {
ADERROR() << std::wstring( ex.ErrorMessage() );
return false;
}
return false;
}
adcontrols::translate_state
DataInterpreter::translate_profile( adcontrols::MassSpectrum& ms
, const char * data, size_t dsize
, const char * meta, size_t msize
, const adcontrols::MassSpectrometer& spectrometer
, size_t idData ) const
{
(void)idData;
adportable::debug(__FILE__, __LINE__) << "translate_profile( dsize=" << dsize << ", msize=" << msize << ")";
import_profile profile;
import_continuum_massarray ma;
const batchproc::MassSpectrometer* pSpectrometer = dynamic_cast< const batchproc::MassSpectrometer * >( &spectrometer );
if ( pSpectrometer == 0 )
return adcontrols::translate_error;
if ( adportable::bzip2::is_a( data, dsize ) ) {
std::string ar;
adportable::bzip2::decompress( ar, data, dsize );
adportable::debug(__FILE__, __LINE__) << "translate_profile deserialize import_profile w/ decompress";
if ( ! adportable::serializer< import_profile >::deserialize( profile, ar.data(), ar.size() ) )
return adcontrols::translate_error;
} else {
adportable::debug(__FILE__, __LINE__) << "translate_profile deserialize import_profile w/o decompress";
if ( ! adportable::serializer< import_profile >::deserialize( profile, data, dsize ) )
return adcontrols::translate_error;
}
if ( meta && msize ) {
if ( adportable::bzip2::is_a( meta, msize ) ) {
std::string ar;
adportable::bzip2::decompress( ar, meta, msize );
if ( ! adportable::serializer< import_continuum_massarray >::deserialize( ma, ar.data(), ar.size() ) )
return adcontrols::translate_error;
} else {
if ( ! adportable::serializer< import_continuum_massarray >::deserialize( ma, meta, msize ) )
return adcontrols::translate_error;
}
}
adportable::debug(__FILE__, __LINE__) << "translate_profile checkpoint 3";
const import_continuum_massarray& continuum_massarray = meta ? ma : pSpectrometer->continuum_massarray();
ms.setMSProperty( profile.prop_ );
ms.setPolarity( profile.polarity_ );
ms.resize( profile.intensities_.size() );
adportable::debug(__FILE__, __LINE__) << "translate_profile checkpoint 4";
ms.setMassArray( continuum_massarray.masses_.data() );
auto intens = profile.intensities_.data();
for ( size_t i = 0; i < ms.size(); ++i )
ms.setIntensity( i, *intens++ );
adportable::debug(__FILE__, __LINE__) << "translate_profile checkpoint 5";
ms.setAcquisitionMassRange( ms.getMass( 0 ), ms.getMass( ms.size() - 1 ) );
adportable::debug(__FILE__, __LINE__) << "translate_profile checkpoint 6";
return adcontrols::translate_complete;
}
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;
}