bool MappedSpectrum::transform( adcontrols::MassSpectrum& ms ) const { auto& prop = ms.getMSProperty(); int32_t nDelay = int32_t( ( delay_ / sampInterval_ ) + 0.5 ); auto si = SamplingInfo( sampInterval_, delay_, nDelay, nSamples_, num_average_, 0 /* mode */ ); si.fSampInterval( sampInterval_ ); prop.setSamplingInfo( si ); prop.setNumAverage( num_average_ ); prop.setTrigNumber( trig_number_, trig_number_origin_ ); prop.setTimeSinceEpoch( timeSinceEpoch_.second ); ms.resize( data_.size() ); ms.setCentroid( adcontrols::CentroidNative ); //auto scanlaw = prop.scanLaw(); for ( size_t idx = 0; idx < data_.size(); ++idx ) { double tof = this->time( idx ); ms.setTime( idx, tof ); //if ( scanlaw ) // ms.setMass( idx, ms.compute_mass( data_[ idx ].first ) ); ms.setIntensity( idx, data_[ idx ].second ); } return true; }
//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; }
bool TimeDigitalHistogram::translate( adcontrols::MassSpectrum& sp , const TimeDigitalHistogram& hgrm ) { sp.setCentroid( adcontrols::CentroidNative ); using namespace adcontrols::metric; // ext_trig_delay should be managed before came here. (ex. histogram::move()) double ext_trig_delay = hgrm.this_protocol_.delay_pulses().at( adcontrols::TofProtocol::EXT_ADC_TRIG ).first; adcontrols::MSProperty prop; adcontrols::SamplingInfo info( hgrm.xIncrement() , hgrm.initialXOffset() + ext_trig_delay , int32_t( ( hgrm.initialXOffset() + ext_trig_delay ) / hgrm.xIncrement() ) // delay , uint32_t( hgrm.actualPoints() ) // this is for acq. time range calculation , uint32_t( hgrm.trigger_count() ) , hgrm.this_protocol_.mode() /* mode */); prop.setAcceleratorVoltage( 0 ); // empty prop.setSamplingInfo( info ); prop.setTimeSinceInjection( hgrm.initialXTimeSeconds() ); prop.setTimeSinceEpoch( hgrm.timeSinceEpoch().first ); prop.setNumAverage( uint32_t( hgrm.trigger_count() ) ); prop.setTrigNumber( uint32_t( hgrm.serialnumber().first ) ); prop.setDataInterpreterClsid( "adcontrols::TimeDigitalHistogram" ); TimeDigitalHistogram::device_data data( hgrm.this_protocol_ ); std::string ar; adportable::binary::serialize<>()( data, ar ); prop.setDeviceData( ar.data(), ar.size() ); sp.setMSProperty( prop ); size_t size = hgrm.size(); sp.resize( size ); size_t idx = 0; for ( auto it = hgrm.begin(); it != hgrm.end(); ++it, ++idx ) { sp.setTime( idx, it->first ); sp.setIntensity( idx, it->second ); } return true; }