void GaussTraceFitter::fit(FeatureFinderAlgorithmPickedHelperStructs::MassTraces& traces)
{
LOG_DEBUG << "Traces length: " << traces.size() << "\n";
setInitialParameters_(traces);
Eigen::VectorXd x_init(NUM_PARAMS_);
x_init(0) = height_;
x_init(1) = x0_;
x_init(2) = sigma_;
TraceFitter::ModelData data;
data.traces_ptr = &traces;
data.weighted = this->weighted_;
GaussTraceFunctor functor(NUM_PARAMS_, &data);
TraceFitter::optimize_(x_init, functor);
}
void EGHTraceFitter::setInitialParameters_(FeatureFinderAlgorithmPickedHelperStructs::MassTraces& traces)
{
LOG_DEBUG << "EGHTraceFitter->setInitialParameters(...)" << std::endl;
LOG_DEBUG << "Number of traces: " << traces.size() << std::endl;
// aggregate data; some peaks (where intensity is zero) can be missing!
// mapping: RT -> total intensity over all mass traces
std::list<std::pair<double, double> > total_intensities;
traces.computeIntensityProfile(total_intensities);
// compute moving average for smoothing:
const Size N = total_intensities.size();
const Size LEN = 2; // window size: 2 * LEN + 1
std::vector<double> totals(N + 2 * LEN); // pad with zeros at ends
Int index = LEN;
// LOG_DEBUG << "Summed intensities:\n";
for (std::list<std::pair<double, double> >::iterator it =
total_intensities.begin(); it != total_intensities.end(); ++it)
{
totals[index++] = it->second;
// LOG_DEBUG << it->second << std::endl;
}
std::vector<double> smoothed(N);
Size max_index = 0; // index of max. smoothed intensity
// LOG_DEBUG << "Smoothed intensities:\n";
double sum = std::accumulate(&totals[LEN], &totals[2 * LEN], 0.0);
for (Size i = 0; i < N; ++i)
{
sum += totals[i + 2 * LEN];
smoothed[i] = sum / (2 * LEN + 1);
sum -= totals[i];
if (smoothed[i] > smoothed[max_index]) max_index = i;
// LOG_DEBUG << smoothed[i] << std::endl;
}
LOG_DEBUG << "Maximum at index " << max_index << std::endl;
height_ = smoothed[max_index] - traces.baseline;
LOG_DEBUG << "height: " << height_ << std::endl;
std::list<std::pair<double, double> >::iterator it = total_intensities.begin();
std::advance(it, max_index);
apex_rt_ = it->first;
LOG_DEBUG << "apex_rt: " << apex_rt_ << std::endl;
region_rt_span_ = (total_intensities.rbegin()->first -
total_intensities.begin()->first);
LOG_DEBUG << "region_rt_span: " << region_rt_span_ << std::endl;
// find RT values where intensity is at half-maximum:
index = static_cast<Int>(max_index);
while ((index > 0) && (smoothed[index] > height_ * 0.5))
--index;
double left_height = smoothed[index];
it = total_intensities.begin();
std::advance(it, index);
double left_rt = it->first;
LOG_DEBUG << "Left half-maximum at index " << index << ", RT " << left_rt
<< std::endl;
index = static_cast<Int>(max_index);
while ((index < Int(N - 1)) && (smoothed[index] > height_ * 0.5))
++index;
double right_height = smoothed[index];
it = total_intensities.end();
std::advance(it, index - Int(N));
double right_rt = it->first;
LOG_DEBUG << "Right half-maximum at index " << index << ", RT "
<< right_rt << std::endl;
double A = apex_rt_ - left_rt;
double B = right_rt - apex_rt_;
//LOG_DEBUG << "A: " << A << std::endl;
//LOG_DEBUG << "B: " << B << std::endl;
// compute estimates for tau / sigma based on A and B:
double alpha = (left_height + right_height) * 0.5 / height_; // ~0.5
double log_alpha = log(alpha);
tau_ = -1 / log_alpha * (B - A);
//EGH function fails when tau==0
if (tau_ == 0) tau_ = std::numeric_limits<double>::epsilon();
LOG_DEBUG << "tau: " << tau_ << std::endl;
sigma_ = sqrt(-0.5 / log_alpha * B * A);
LOG_DEBUG << "sigma: " << sigma_ << std::endl;
}
void GaussTraceFitter::setInitialParameters_(FeatureFinderAlgorithmPickedHelperStructs::MassTraces& traces)
{
LOG_DEBUG << "GaussTraceFitter->setInitialParameters(...)" << std::endl;
LOG_DEBUG << "Number of traces: " << traces.size() << std::endl;
// aggregate data; some peaks (where intensity is zero) can be missing!
// mapping: RT -> total intensity over all mass traces
std::list<std::pair<double, double> > total_intensities;
traces.computeIntensityProfile(total_intensities);
const Size N = total_intensities.size();
const Size LEN = 2; // window size: 2 * LEN + 1
std::vector<double> totals(N + 2 * LEN); // pad with zeros at ends
Int index = LEN;
// LOG_DEBUG << "Summed intensities:\n";
for (std::list<std::pair<double, double> >::iterator it =
total_intensities.begin(); it != total_intensities.end(); ++it)
{
totals[index++] = it->second;
// LOG_DEBUG << it->second << std::endl;
}
std::vector<double> smoothed(N);
Size max_index = 0; // index of max. smoothed intensity
if (N <= LEN + 1) // not enough distinct x values for smoothing
{
// throw Exception::UnableToFit(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "UnableToFit-MovingAverage", "Too few time points for smoothing with window size " + String(2 * LEN + 1));
for (Size i = 0; i < N; ++i)
{
smoothed[i] = totals[i + LEN];
if (smoothed[i] > smoothed[max_index]) max_index = i;
}
}
else // compute moving average for smoothing
{
// LOG_DEBUG << "Smoothed intensities:\n";
double sum = std::accumulate(&totals[LEN], &totals[2 * LEN], 0.0);
for (Size i = 0; i < N; ++i)
{
sum += totals[i + 2 * LEN];
smoothed[i] = sum / (2 * LEN + 1);
sum -= totals[i];
if (smoothed[i] > smoothed[max_index]) max_index = i;
// LOG_DEBUG << smoothed[i] << std::endl;
}
}
LOG_DEBUG << "Maximum at index " << max_index << std::endl;
height_ = smoothed[max_index] - traces.baseline;
LOG_DEBUG << "height: " << height_ << std::endl;
std::list<std::pair<double, double> >::iterator it = total_intensities.begin();
std::advance(it, max_index);
x0_ = it->first;
LOG_DEBUG << "x0: " << x0_ << std::endl;
region_rt_span_ = (total_intensities.rbegin()->first -
total_intensities.begin()->first);
LOG_DEBUG << "region_rt_span: " << region_rt_span_ << std::endl;
// find RT values where intensity is at half-maximum:
index = static_cast<Int>(max_index);
while ((index > 0) && (smoothed[index] > height_ * 0.5))
--index;
double left_height = smoothed[index];
it = total_intensities.begin();
std::advance(it, index);
double left_rt = it->first;
LOG_DEBUG << "Left half-maximum at index " << index << ", RT " << left_rt
<< std::endl;
index = static_cast<Int>(max_index);
while ((index < Int(N - 1)) && (smoothed[index] > height_ * 0.5))
++index;
double right_height = smoothed[index];
it = total_intensities.end();
std::advance(it, index - Int(N));
double right_rt = it->first;
LOG_DEBUG << "Right half-maximum at index " << index << ", RT "
<< right_rt << std::endl;
double delta_x = right_rt - left_rt;
double alpha = (left_height + right_height) * 0.5 / height_; // ~0.5
if (alpha >= 1) sigma_ = 1.0; // degenerate case, all values are the same
else sigma_ = delta_x * 0.5 / sqrt(-2.0 * log(alpha));
LOG_DEBUG << "sigma: " << sigma_ << std::endl;
}