int main(int argc, const char** argv)
{
if (argc < 2) return 1;
// the path to the data should be given on the command line
String tutorial_data_path(argv[1]);
PeakSpectrum spectrum;
DTAFile dta_file;
dta_file.load(tutorial_data_path + "/data/Tutorial_SavitzkyGolayFilter.dta", spectrum);
LinearResampler lr;
Param param_lr;
param_lr.setValue("spacing", 0.01);
lr.setParameters(param_lr);
lr.raster(spectrum);
SavitzkyGolayFilter sg;
Param param_sg;
param_sg.setValue("frame_length", 21);
param_sg.setValue("polynomial_order", 3);
sg.setParameters(param_sg);
sg.filter(spectrum);
return 0;
} //end of main
void ElutionPeakDetection::smoothData(MassTrace& mt, int win_size) const
{
// alternative smoothing using SavitzkyGolay
// looking at the unit test, this method gives better fits than lowess smoothing
// reference paper uses lowess smoothing
MSSpectrum<PeakType> spectrum;
spectrum.insert(spectrum.begin(), mt.begin(), mt.end());
SavitzkyGolayFilter sg;
Param param;
param.setValue("polynomial_order", 2);
param.setValue("frame_length", std::max(3, win_size)); // frame length must be at least polynomial_order+1, otherwise SG will fail
sg.setParameters(param);
sg.filter(spectrum);
MSSpectrum<PeakType>::iterator iter = spectrum.begin();
std::vector<double> smoothed_intensities;
for (; iter != spectrum.end(); ++iter)
{
smoothed_intensities.push_back(iter->getIntensity());
}
mt.setSmoothedIntensities(smoothed_intensities);
//alternative end
// std::cout << "win_size elution: " << scan_time << " " << win_size << std::endl;
// if there is no previous FWHM estimation... do it now
// if (win_size == 0)
// {
// mt.estimateFWHM(false); // estimate FWHM
// win_size = mt.getFWHMScansNum();
// }
// use one global window size for all mass traces to smooth
// std::vector<double> rts, ints;
//
// for (MassTrace::const_iterator c_it = mt.begin(); c_it != mt.end(); ++c_it)
// {
// rts.push_back(c_it->getRT());
// ints.push_back(c_it->getIntensity());
// }
// LowessSmoothing lowess_smooth;
// Param lowess_params;
// lowess_params.setValue("window_size", win_size);
// lowess_smooth.setParameters(lowess_params);
// std::vector<double> smoothed_data;
// lowess_smooth.smoothData(rts, ints, smoothed_data);
// mt.setSmoothedIntensities(smoothed_data);
}