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; }
//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; }