OpenSwath::SpectrumPtr OpenSwathScoring::getAddedSpectra_(OpenSwath::SpectrumAccessPtr swath_map,
double RT, int nr_spectra_to_add)
{
std::vector<std::size_t> indices = swath_map->getSpectraByRT(RT, 0.0);
if (indices.empty() )
{
OpenSwath::SpectrumPtr sptr(new OpenSwath::Spectrum);
return sptr;
}
int closest_idx = boost::numeric_cast<int>(indices[0]);
if (indices[0] != 0 &&
std::fabs(swath_map->getSpectrumMetaById(boost::numeric_cast<int>(indices[0]) - 1).RT - RT) <
std::fabs(swath_map->getSpectrumMetaById(boost::numeric_cast<int>(indices[0])).RT - RT))
{
closest_idx--;
}
if (nr_spectra_to_add == 1)
{
OpenSwath::SpectrumPtr spectrum_ = swath_map->getSpectrumById(closest_idx);
return spectrum_;
}
else
{
std::vector<OpenSwath::SpectrumPtr> all_spectra;
// always add the spectrum 0, then add those right and left
all_spectra.push_back(swath_map->getSpectrumById(closest_idx));
for (int i = 1; i <= nr_spectra_to_add / 2; i++) // cast to int is intended!
{
if (closest_idx - i >= 0)
{
all_spectra.push_back(swath_map->getSpectrumById(closest_idx - i));
}
if (closest_idx + i < (int)swath_map->getNrSpectra())
{
all_spectra.push_back(swath_map->getSpectrumById(closest_idx + i));
}
}
OpenSwath::SpectrumPtr spectrum_ = SpectrumAddition::addUpSpectra(all_spectra, spacing_for_spectra_resampling_, true);
return spectrum_;
}
}
void ChromatogramExtractorAlgorithm::extractChromatograms(const OpenSwath::SpectrumAccessPtr input,
std::vector< OpenSwath::ChromatogramPtr >& output,
std::vector<ExtractionCoordinates> extraction_coordinates, double mz_extraction_window,
bool ppm, String filter)
{
Size input_size = input->getNrSpectra();
if (input_size < 1)
{
return;
}
if (output.size() != extraction_coordinates.size())
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
"Output and extraction coordinates need to have the same size");
}
int used_filter = getFilterNr_(filter);
// assert that they are sorted!
if (std::adjacent_find(extraction_coordinates.begin(), extraction_coordinates.end(),
ExtractionCoordinates::SortExtractionCoordinatesReverseByMZ) != extraction_coordinates.end())
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
"Input to extractChromatogram needs to be sorted by m/z");
}
//go through all spectra
startProgress(0, input_size, "Extracting chromatograms");
for (Size scan_idx = 0; scan_idx < input_size; ++scan_idx)
{
setProgress(scan_idx);
OpenSwath::SpectrumPtr sptr = input->getSpectrumById(scan_idx);
OpenSwath::SpectrumMeta s_meta = input->getSpectrumMetaById(scan_idx);
OpenSwath::BinaryDataArrayPtr mz_arr = sptr->getMZArray();
OpenSwath::BinaryDataArrayPtr int_arr = sptr->getIntensityArray();
std::vector<double>::const_iterator mz_start = mz_arr->data.begin();
std::vector<double>::const_iterator mz_end = mz_arr->data.end();
std::vector<double>::const_iterator mz_it = mz_arr->data.begin();
std::vector<double>::const_iterator int_it = int_arr->data.begin();
if (sptr->getMZArray()->data.size() == 0)
continue;
// go through all transitions / chromatograms which are sorted by
// ProductMZ. We can use this to step through the spectrum and at the
// same time step through the transitions. We increase the peak counter
// until we hit the next transition and then extract the signal.
for (Size k = 0; k < extraction_coordinates.size(); ++k)
{
double integrated_intensity = 0;
double current_rt = s_meta.RT;
if (extraction_coordinates[k].rt_end - extraction_coordinates[k].rt_start > 0 &&
(current_rt < extraction_coordinates[k].rt_start ||
current_rt > extraction_coordinates[k].rt_end) )
{
continue;
}
if (used_filter == 1)
{
extract_value_tophat( mz_start, mz_it, mz_end, int_it,
extraction_coordinates[k].mz, integrated_intensity, mz_extraction_window, ppm);
}
else if (used_filter == 2)
{
throw Exception::NotImplemented(__FILE__, __LINE__, __PRETTY_FUNCTION__);
}
// Time is first, intensity is second
output[k]->binaryDataArrayPtrs[0]->data.push_back(current_rt);
output[k]->binaryDataArrayPtrs[1]->data.push_back(integrated_intensity);
}
}
endProgress();
}