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; }
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 idx, adcontrols::MassSpectrum& ms, uint32_t /* objid */) const { if ( unsigned( idx ) < spcfile_->number_of_subfiles() ) { const galactic::spchdr& hdr = *spcfile_->spchdr(); const galactic::subhdr& sub = *spcfile_->subhdr( idx ); std::pair< double, double > range = std::make_pair( hdr.ffirst(), hdr.flast() ); const size_t npts = hdr.fnpts(); ms.resize( npts ); ms.setAcquisitionMassRange( range.first, range.second ); for ( size_t i = 0; i < npts; ++i ) { ms.setMass( int(i), i * double(( range.second - range.first )) / ( npts - 1 ) + range.first ); ms.setIntensity( int(i), sub[i] ); } return true; } 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; }