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;
}
void
MSPropertyForm::render( std::ostream& o, const adcontrols::MassSpectrum& ms )
{
using adportable::utf;
using namespace adcontrols::metric;
static const char * const polarities [] = { "Indeterminant", "Positive", "Negative", "Mixed" };
adcontrols::segment_wrapper< const adcontrols::MassSpectrum > segments( ms );
std::vector< std::pair< std::string, std::string > > temp;
temp.push_back( std::make_pair( "Spectrum", ( ms.isCentroid() ? "Centroid" : "Profile" ) ) );
temp.push_back( std::make_pair( "Polarity", polarities[ ms.polarity() ] ) );
o << "<hr>";
o << "<table border=\"1\" cellpadding=\"1\">";
o << "<caption>Descriptions</caption>";
o << "<tr>";
o << "<th>key</th>"
<< "<th>description</th>"
<< "</tr>";
for ( auto it: temp ) {
o << "<tr>"
<< "<td>" << it.first << "</td>"
<< "<td>" << it.second << "</td>"
<< "</tr>";
}
for ( size_t i = 0; i < ms.getDescriptions().size(); ++i ) {
auto desc = ms.getDescriptions()[ i ];
o << "<tr>"
<< "<td>" << utf::to_utf8( desc.key() ) << "</td>"
<< "<td>" << utf::to_utf8( desc.text() ) << "</td>"
<< "</tr>";
}
o << "</table>";
std::pair< double, double > massrange = ms.getAcquisitionMassRange();
o << "Acquisition mass range: " << boost::format( "%.3lf -- %.3lf" ) % massrange.first % massrange.second;
o << "<table border=\"1\" cellpadding=\"4\">";
o << "<caption>Acquisition and calibration parameter(s)</caption>";
o << "<tr>";
o << "<th>#seg</th>"
<< "<th>samp. interval(ps)</th>"
<< "<th>sampling start (μs)</th>"
<< "<th>sampling end (μs)</th>"
<< "<th>num. samples</th>"
<< "<th>num. average</th>"
<< "<th>mode</th>"
<< "<th>classid</th>"
<< "</tr>";
int n = 0;
for ( auto& m: segments ) {
const adcontrols::MSCalibration& calib = m.calibration();
size_t nrowspan = calib.coeffs().empty() ? 1 : 2;
const adcontrols::MSProperty& prop = m.getMSProperty();
const adcontrols::MSProperty::SamplingInfo& info = prop.getSamplingInfo();
double start_delay = scale_to<double, micro>( info.sampInterval * info.nSamplingDelay, pico );
double time_end = scale_to<double, micro>( info.sampInterval * ( info.nSamplingDelay + info.nSamples ), pico );
o << "<tr>"
<< boost::format( "<td rowspan=\"%1%\">" ) % nrowspan << n++ << "</td>"
<< "<td>" << info.sampInterval << "</td>"
<< "<td>" << boost::format( "%.4lfμs" ) % start_delay << "</td>"
<< "<td>" << boost::format( "%.4lfμs" ) % time_end << "</td>"
<< "<td>" << info.nSamples << "</td>"
<< "<td>" << info.nAverage << "</td>"
<< "<td>" << info.mode << "</td>"
<< "<td>" << prop.dataInterpreterClsid() << "</td>"
<< "</tr>";
if ( ! calib.coeffs().empty() ) {
//-----------------------------
o << "<tr>";
o << "<td colspan=7><b>Calibration ID:</b><i>" << utf::to_utf8( calib.calibId() ) << "</i>"
<< " " << calib.date();
o << "<hr>";
o << "√<span style=\"text-decoration: overline\"> <i>m/z</i></span> = "
<< boost::format( "%.14lf" ) % calib.coeffs()[0] << " + ";
for ( size_t i = 1; i < calib.coeffs().size(); ++i )
o << boost::format( "\t%.14lf × t<sup>%d</sup>" ) % calib.coeffs()[i] % i;
if ( ! calib.t0_coeffs().empty() ) {
o << "<br>"
<< "T<sub>0</sub> = " << calib.t0_coeffs()[0];
for ( size_t i = 1; i < calib.t0_coeffs().size(); ++i )
o << boost::format( "\t%.14lf × √<span style=\"text-decoration: overline\"> <i>m/z</i></span><sup>%d</sup>" )
% calib.coeffs()[i] % i;
if ( calib.algorithm() == adcontrols::MSCalibration::MULTITURN_NORMALIZED )
o << "\t(MULTITURN_NORMAILZED algorithm)";
}
o << "</tr>";
//-----------------------------
}
}
o << "</table>";
o << "<hr>";
try {
// device (averager) dependent data (require data interpreter)
std::vector < std::pair< std::string, std::string > > textv;
auto& prop = ms.getMSProperty();
const char * ipClsid = prop.dataInterpreterClsid();
if ( ipClsid && (std::strlen( ipClsid )) > 0 ) {
auto& interpreter = prop.spectrometer().getDataInterpreter();
if ( interpreter.make_device_text( textv, ms.getMSProperty() ) ) {
o << "<table border=\"1\" cellpadding=\"4\">";
o << "<caption>Averager/digitizer dependent information</caption>";
o << "<tr>";
o << "<th>#seg</th>";
std::for_each( textv.begin(), textv.end(), [&] ( const std::pair< std::string, std::string>& text ) { o << "<th>" << text.first << "</th>"; } );
o << "</tr>";
int seg = 0;
for ( auto& m : segments ) {
if ( interpreter.make_device_text( textv, m.getMSProperty() ) ) {
o << "<tr>";
o << "<td>" << seg++ << "</td>";
std::for_each( textv.begin(), textv.end(), [&] ( const std::pair< std::string, std::string>& text ) { o << "<td>" << text.second << "</td>"; } );
o << "</tr>";
}
}
o << "</table>";
o << "<hr>";
}
}
else {
o << "<hr>No dataInterpreterClsid specifid.</hr>";
ADERROR() << "no dataInterpreterClisidSpecified.";
}
}
catch ( boost::exception& ex ) {
o << "<hr>data exception: " << boost::diagnostic_information( ex ) << "</hr>";
ADERROR() << boost::diagnostic_information( ex );
}
catch ( ... ) {
o << "<hr>data exception: " << boost::current_exception_diagnostic_information() << "</hr>";
ADERROR() << boost::current_exception_diagnostic_information();
}
}