C++ MassSpectrum::resize方法代码示例

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 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;
}

//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;
}

//virtual
bool
datafile::getSpectrum( int /* fcn*/, size_t idx, adcontrols::MassSpectrum& ms, uint32_t /* objid */) const
{
    if ( lrpfile_ && unsigned( idx ) < lrpfile_->number_of_spectra() ) {

        if ( auto msdata = (*lrpfile_)[ idx ] ) {

            std::vector< double > time, intens;
            if ( lrpfile_->getMS( *msdata, time, intens ) ) {

                ms.resize( time.size() );
                ms.setMassArray( time.data() );
                ms.setIntensityArray( intens.data() );

                ms.setAcquisitionMassRange( time.front(), time.back() );

                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;
}