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);
}
ExitCodes main_(int, const char **)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
in = getStringOption_("in");
out = getStringOption_("out");
String process_option = getStringOption_("processOption");
Param filter_param = getParam_().copy("algorithm:", true);
writeDebug_("Parameters passed to filter", filter_param, 3);
SavitzkyGolayFilter sgolay;
sgolay.setLogType(log_type_);
sgolay.setParameters(filter_param);
if (process_option == "lowmemory")
{
return doLowMemAlgorithm(sgolay);
}
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
MzMLFile mz_data_file;
mz_data_file.setLogType(log_type_);
PeakMap exp;
mz_data_file.load(in, exp);
if (exp.empty() && exp.getChromatograms().size() == 0)
{
LOG_WARN << "The given file does not contain any conventional peak data, but might"
" contain chromatograms. This tool currently cannot handle them, sorry.";
return INCOMPATIBLE_INPUT_DATA;
}
//check for peak type (profile data required)
if (!exp.empty() && PeakTypeEstimator().estimateType(exp[0].begin(), exp[0].end()) == SpectrumSettings::PEAKS)
{
writeLog_("Warning: OpenMS peak type estimation indicates that this is not profile data!");
}
//check if spectra are sorted
for (Size i = 0; i < exp.size(); ++i)
{
if (!exp[i].isSorted())
{
writeLog_("Error: Not all spectra are sorted according to peak m/z positions. Use FileFilter to sort the input!");
return INCOMPATIBLE_INPUT_DATA;
}
}
//check if chromatograms are sorted
for (Size i = 0; i < exp.getChromatograms().size(); ++i)
{
if (!exp.getChromatogram(i).isSorted())
{
writeLog_("Error: Not all chromatograms are sorted according to peak m/z positions. Use FileFilter to sort the input!");
return INCOMPATIBLE_INPUT_DATA;
}
}
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
sgolay.filterExperiment(exp);
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(exp, getProcessingInfo_(DataProcessing::SMOOTHING));
mz_data_file.store(out, exp);
return EXECUTION_OK;
}
