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);
}
START_SECTION([EXTRA](virtual void init(const PeakIterator& it_begin, const PeakIterator& it_end)))
MSSpectrum raw_data;
MSSpectrum::const_iterator it;
DTAFile dta_file;
dta_file.load(OPENMS_GET_TEST_DATA_PATH("SignalToNoiseEstimator_test.dta"), raw_data);
SignalToNoiseEstimatorMedian< MSSpectrum > sne;
Param p;
p.setValue("win_len", 40.0);
p.setValue("noise_for_empty_window", 2.0);
p.setValue("min_required_elements", 10);
sne.setParameters(p);
sne.init(raw_data.begin(),raw_data.end());
MSSpectrum stn_data;
dta_file.load(OPENMS_GET_TEST_DATA_PATH("SignalToNoiseEstimatorMedian_test.out"), stn_data);
int i = 0;
for (it=raw_data.begin();it!=raw_data.end(); ++it)
{
TEST_REAL_SIMILAR (stn_data[i].getIntensity(), sne.getSignalToNoise(it));
//Peak1D peak = (*it);
//peak.setIntensity(sne.getSignalToNoise(it));
//stn_data.push_back(peak);
++i;
}
GaussFilter* dgauss_nullPointer = nullptr;
START_SECTION((GaussFilter()))
dgauss_ptr = new GaussFilter;
TEST_NOT_EQUAL(dgauss_ptr, dgauss_nullPointer)
END_SECTION
START_SECTION((virtual ~GaussFilter()))
delete dgauss_ptr;
END_SECTION
START_SECTION((template <typename PeakType> void filter(MSSpectrum& spectrum)))
MSSpectrum spectrum;
spectrum.resize(5);
MSSpectrum::Iterator it = spectrum.begin();
for (Size i=0; i<5; ++i, ++it)
{
it->setIntensity(1.0f);
it->setMZ(500.0+0.2*i);
}
GaussFilter gauss;
Param param;
param.setValue( "gaussian_width", 1.0);
gauss.setParameters(param);
gauss.filter(spectrum);
it=spectrum.begin();
TEST_REAL_SIMILAR(it->getIntensity(),1.0)
++it;
TEST_REAL_SIMILAR(it->getIntensity(),1.0)
dsg_ptr = new SavitzkyGolayFilter;
TEST_NOT_EQUAL(dsg_ptr, dsg_nullPointer)
END_SECTION
START_SECTION((virtual ~SavitzkyGolayFilter()))
delete dsg_ptr;
END_SECTION
Param param;
param.setValue("polynomial_order",2);
param.setValue("frame_length",3);
START_SECTION((template < typename PeakType > void filter(MSSpectrum< PeakType > &spectrum)))
MSSpectrum<Peak1D> spectrum;
spectrum.resize(5);
MSSpectrum<Peak1D>::Iterator it = spectrum.begin();
for (int i=0; i<5; ++i, ++it)
{
it->setIntensity(0.0f);
if (i==2)
{
it->setIntensity(1.0f);
}
}
SavitzkyGolayFilter sgolay;
sgolay.setParameters(param);
sgolay.filter(spectrum);
it=spectrum.begin();
TEST_REAL_SIMILAR(it->getIntensity(),0.0)
START_SECTION(([EXTRA]PeakTypeEstimator()))
ptr = new PeakTypeEstimator();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION(([EXTRA] ~PeakTypeEstimator()))
delete ptr;
END_SECTION
START_SECTION((template<typename PeakConstIterator> SpectrumSettings::SpectrumType estimateType(const PeakConstIterator& begin, const PeakConstIterator& end) const))
DTAFile file;
MSSpectrum spec;
// raw data (with zeros)
file.load(OPENMS_GET_TEST_DATA_PATH("PeakTypeEstimator_raw.dta"), spec);
TEST_EQUAL(PeakTypeEstimator::estimateType(spec.begin(), spec.end()), SpectrumSettings::PROFILE);
// TOF raw data (without zeros)
file.load(OPENMS_GET_TEST_DATA_PATH("PeakTypeEstimator_rawTOF.dta"), spec);
TEST_EQUAL(PeakTypeEstimator::estimateType(spec.begin(), spec.end()), SpectrumSettings::PROFILE);
// peak data
file.load(OPENMS_GET_TEST_DATA_PATH("PeakTypeEstimator_peak.dta"), spec);
TEST_EQUAL(PeakTypeEstimator::estimateType(spec.begin(), spec.end()), SpectrumSettings::CENTROID);
// too few data points
spec.resize(4);
TEST_EQUAL(PeakTypeEstimator::estimateType(spec.begin(), spec.end()), SpectrumSettings::UNKNOWN);
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST