void LowessSmoothing::smoothData(const DoubleVector& input_x, const DoubleVector& input_y, DoubleVector& smoothed_output)
{
if (input_x.size() != input_y.size())
{
throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
"Sizes of x and y values not equal! Aborting... ", String(input_x.size()));
}
// unable to smooth over 2 or less data points (we need at least 3)
if (input_x.size() <= 2)
{
smoothed_output = input_y;
return;
}
Size input_size = input_y.size();
// const Size q = floor( input_size * alpha );
const Size q = (window_size_ < input_size) ? static_cast<Size>(window_size_) : input_size - 1;
DoubleVector distances(input_size, 0.0);
DoubleVector sortedDistances(input_size, 0.0);
for (Size outer_idx = 0; outer_idx < input_size; ++outer_idx)
{
// Compute distances.
// Size inner_idx = 0;
for (Size inner_idx = 0; inner_idx < input_size; ++inner_idx)
{
distances[inner_idx] = std::fabs(input_x[outer_idx] - input_x[inner_idx]);
sortedDistances[inner_idx] = distances[inner_idx];
}
// Sort distances in order from smallest to largest.
std::sort(sortedDistances.begin(), sortedDistances.end());
// Compute weigths.
std::vector<double> weigths(input_size, 0);
for (Size inner_idx = 0; inner_idx < input_size; ++inner_idx)
{
weigths.at(inner_idx) = tricube_(distances[inner_idx], sortedDistances[q]);
}
//calculate regression
Math::QuadraticRegression qr;
std::vector<double>::const_iterator w_begin = weigths.begin();
qr.computeRegressionWeighted(input_x.begin(), input_x.end(), input_y.begin(), w_begin);
//smooth y-values
double rt = input_x[outer_idx];
smoothed_output.push_back(qr.eval(rt));
}
return;
}
void TOFCalibration::calculateCalibCoeffs_(MSExperiment<> & calib_spectra)
{
// flight times are needed later
calib_peaks_ft_ = calib_spectra;
// convert flight times of peaks into m/z values
applyTOFConversion_(calib_spectra);
std::vector<std::vector<unsigned int> > monoiso_peaks;
getMonoisotopicPeaks_(calib_spectra, monoiso_peaks);
startProgress(0, calib_spectra.size(), "quadratic fitting of calibrant spectra");
// do the quadratic fitting for each calibration spectra separately
for (unsigned int spec = 0; spec < calib_spectra.size(); ++spec)
{
std::vector<unsigned int> monoiso_peaks_scan;
std::vector<double> exp_masses;
// match the m/z-values to the expected masses
matchMasses_(calib_spectra, monoiso_peaks, monoiso_peaks_scan, exp_masses, spec);
// the actual quadratic fitting part
Size n = exp_masses.size();
if (n < 3)
{
continue;
}
// matrix containing the observations
std::vector<double> x;
// vector containing the expected masses
std::vector<double> y;
for (Size i = 0; i < n; i++)
{
// get the flight time
double xi = ((calib_peaks_ft_.begin() + spec)->begin() + monoiso_peaks_scan[i])->getMZ();
x.push_back(xi);
y.push_back(exp_masses[i]);
}
Math::QuadraticRegression qr;
qr.computeRegression(x.begin(), x.end(), y.begin());
#ifdef DEBUG_CALIBRATION
std::cout << "chi^2: " << qr.getChiSquared() << std::endl;//DEBUG
std::cout << "a: " << qr.getA() << "b: " << qr.getB()
<< "c: " << qr.getC() << std::endl;//DEBUG
#endif
// store the coefficients
coeff_quad_fit_.push_back(qr.getA());
coeff_quad_fit_.push_back(qr.getB());
coeff_quad_fit_.push_back(qr.getC());
// determine the errors in ppm
for (Size p = 0; p < n; ++p)
{
#ifdef DEBUG_CALIBRATION
std::cout << exp_masses[p]
<< "\t" << mQ_(calib_peaks_ft_[spec][monoiso_peaks_scan[p]].getMZ(), spec) - exp_masses[p] << std::endl;
#endif
errors_[exp_masses[p]].push_back((mQ_(calib_peaks_ft_[spec][monoiso_peaks_scan[p]].getMZ(), spec) - exp_masses[p]));
}
setProgress(spec);
}
endProgress();
if (coeff_quad_fit_.empty())
{
String mess = String("Data can't be calibrated, not enough reference masses found: ") + coeff_quad_fit_.size() / 3;
throw Exception::UnableToCalibrate(__FILE__, __LINE__, __PRETTY_FUNCTION__, "UnableToCalibrate", mess.c_str());
}
averageErrors_();
averageCoefficients_();
}
bool MZTrafoModel::train( std::vector<double> obs_mz, std::vector<double> theo_mz, std::vector<double> weights, MODELTYPE md, bool use_RANSAC )
{
coeff_.clear();
if (obs_mz.empty())
{
//LOG_ERROR << "Input to calibration model is empty!" << std::endl;
return false;
}
if (use_RANSAC)
{
if (ransac_params_ == nullptr)
{
throw Exception::Precondition(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "TrafoModel::train(): no RANSAC parameters were set before calling train(). Internal error!");
}
if (!(md == LINEAR || md == QUADRATIC))
{
LOG_ERROR << "RANSAC is implemented for LINEAR and QUADRATIC models only! Please disable RANSAC or choose the LINEAR or QUADRATIC model." << std::endl;
throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
}
}
try
{
if (md == LINEAR)
{
if (obs_mz.size() < 2) return false;
if (use_RANSAC &&
(obs_mz.size() > ransac_params_->n)) // with fewer points, RANSAC will fail
{
std::vector<std::pair<double, double> > r, pairs;
for (Size i = 0; i < obs_mz.size(); ++i)
{
pairs.push_back(std::make_pair(theo_mz[i], obs_mz[i]));
}
r = Math::RANSAC<Math::RansacModelLinear>().ransac(pairs, *ransac_params_);
if (r.size() < 2)
{
return false; // RANSAC failed
}
obs_mz.clear();
theo_mz.clear();
for (Size i = 0; i < r.size(); ++i)
{
theo_mz.push_back(r[i].first);
obs_mz.push_back(r[i].second);
}
}
double confidence_interval_P(0.0);
Math::LinearRegression lr;
lr.computeRegression(confidence_interval_P, theo_mz.begin(), theo_mz.end(), obs_mz.begin(), false);
coeff_.push_back(lr.getIntercept());
coeff_.push_back(lr.getSlope());
coeff_.push_back(0.0);
}
else if (md == LINEAR_WEIGHTED)
{
if (obs_mz.size() < 2) return false;
double confidence_interval_P(0.0);
Math::LinearRegression lr;
lr.computeRegressionWeighted(confidence_interval_P, theo_mz.begin(), theo_mz.end(), obs_mz.begin(), weights.begin(), false);
coeff_.push_back(lr.getIntercept());
coeff_.push_back(lr.getSlope());
coeff_.push_back(0.0);
}
else if (md == QUADRATIC)
{
if (obs_mz.size() < 3) return false;
if (use_RANSAC &&
(obs_mz.size() > ransac_params_->n)) // with fewer points, RANSAC will fail
{
std::vector<std::pair<double, double> > r, pairs;
for (Size i = 0; i < obs_mz.size(); ++i)
{
pairs.push_back(std::make_pair(theo_mz[i], obs_mz[i]));
}
r = Math::RANSAC<Math::RansacModelQuadratic>().ransac(pairs, *ransac_params_);
obs_mz.clear();
theo_mz.clear();
for (Size i = 0; i < r.size(); ++i)
{
theo_mz.push_back(r[i].first);
obs_mz.push_back(r[i].second);
}
}
// Quadratic fit
Math::QuadraticRegression qr;
qr.computeRegression(theo_mz.begin(), theo_mz.end(), obs_mz.begin());
coeff_.push_back(qr.getA());
coeff_.push_back(qr.getB());
coeff_.push_back(qr.getC());
}
else if (md == QUADRATIC_WEIGHTED)
{
if (obs_mz.size() < 3) return false;
// Quadratic fit (weighted)
Math::QuadraticRegression qr;
qr.computeRegressionWeighted(theo_mz.begin(), theo_mz.end(), obs_mz.begin(), weights.begin());
coeff_.push_back(qr.getA());
coeff_.push_back(qr.getB());
coeff_.push_back(qr.getC());
}
#ifdef DEBUG_TRAFOMODEL
printf("# mz regression parameters: Y = %3.10f + %3.10f X + %3.10f X^2\n",
coeff_[0],
coeff_[1],
coeff_[2]);
// print results
std::cout << "Calibration details:\n\n";
std::cout << "m/z(theo) m/z(obs) ppm(before) | ppm(after)\n";
std::vector<double> st_ppm_before, st_ppm_after;
for (Size i = 0; i < obs_mz.size(); i++)
{
if (use_ppm_) st_ppm_before.push_back(obs_mz[i]);
else st_ppm_before.push_back(Math::getPPM(theo_mz[i], obs_mz[i]));
double obs_mz_v = obs_mz[i];
if (use_ppm_) obs_mz_v = Math::ppmToMass(obs_mz_v, theo_mz[i]) + theo_mz[i]; //
st_ppm_after.push_back(Math::getPPM(theo_mz[i], predict(obs_mz_v))); // predict() is ppm-aware itself
printf("%4.5f %4.5f %2.1f | %2.1f\n", theo_mz[i], obs_mz_v, st_ppm_before.back(), st_ppm_after.back());
}
// use median and MAD to ignore outliers
double m = Math::median(st_ppm_before.begin(), st_ppm_before.end());
std::cout << "ppm before: median = " << m << " MAD = " << Math::MAD(st_ppm_before.begin(), st_ppm_before.end(), m) << "\n";
m = Math::median(st_ppm_after.begin(), st_ppm_after.end());
std::cout << "ppm after : median = " << m << " MAD = " << Math::MAD(st_ppm_after.begin(), st_ppm_after.end(), m) << "\n";
#endif
return true;
}
catch (Exception::BaseException& /*e*/)
{
//LOG_ERROR << "Exception during model fitting: " << e.getMessage() << std::endl;
return false;
}
}