MSChromatogram<> toChromatogram(const MSSpectrum<>& in)
{
MSChromatogram<> out;
for (Size ic = 0; ic < in.size(); ++ic)
{
ChromatogramPeak peak;
peak.setMZ(in[ic].getMZ());
peak.setIntensity(in[ic].getIntensity());
out.push_back(peak);
}
out.setChromatogramType(ChromatogramSettings::SELECTED_ION_CURRENT_CHROMATOGRAM);
return out;
}
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]);
IndexedMzMLFileLoader imzml;
// load data from an indexed MzML file
OnDiscMSExperiment<> map;
imzml.load(tutorial_data_path + "/data/Tutorial_FileIO_indexed.mzML", map);
// Get the first spectrum in memory, do some constant (non-changing) data processing
MSSpectrum<> s = map.getSpectrum(0);
std::cout << "There are " << map.getNrSpectra() << " spectra in the input file." << std::endl;
std::cout << "The first spectrum has " << s.size() << " peaks." << std::endl;
// store the (unmodified) data in a different file
imzml.store("Tutorial_FileIO_output.mzML", map);
return 0;
} //end of main
ExitCodes main_(int, const char**)
{
//----------------------------------------------------------------
// load data
//----------------------------------------------------------------
StringList in_list = getStringList_("in");
String out = getStringOption_("out");
String out_csv = getStringOption_("out_csv");
String format = getStringOption_("out_type");
if (out.empty() && out_csv.empty())
{
LOG_ERROR << "Neither 'out' nor 'out_csv' were provided. Please assign at least one of them." << std::endl;
return ILLEGAL_PARAMETERS;
}
if (!out.empty() && format == "") // get from filename
{
try
{
format = out.suffix('.');
}
catch (Exception::ElementNotFound& /*e*/)
{
format = "nosuffix";
}
// check if format is valid:
if (!ListUtils::contains(out_formats_, format.toLower()))
{
LOG_ERROR << "No explicit image output format was provided via 'out_type', and the suffix ('" << format << "') does not resemble a valid type. Please fix one of them." << std::endl;
return ILLEGAL_PARAMETERS;
}
}
double q_min = getDoubleOption_("q_min");
double q_max = getDoubleOption_("q_max");
if (q_min >= q_max)
{
LOG_ERROR << "The parameter 'q_min' must be smaller than 'q_max'. Quitting..." << std::endl;
return ILLEGAL_PARAMETERS;
}
IDEvaluationBase* mw = new IDEvaluationBase();
Param alg_param = mw->getParameters();
alg_param.insert("", getParam_().copy("algorithm:", true));
mw->setParameters(alg_param);
if (!mw->loadFiles(in_list))
{
LOG_ERROR << "Tool failed. See above." << std::endl;
return INCOMPATIBLE_INPUT_DATA;
}
mw->setVisibleArea(q_min, q_max);
if (!out.empty()) // save as image and exit
{
String error;
bool r = mw->exportAsImage(out.toQString(), error, format.toQString());
if (r) return EXECUTION_OK;
else
{
LOG_ERROR << error << std::endl;
return ILLEGAL_PARAMETERS;
}
}
if (!out_csv.empty())
{
TextFile tf;
for (Size i = 0; i < mw->getPoints().size(); ++i)
{
MSSpectrum s = mw->getPoints()[i];
StringList sl1;
StringList sl2;
for (Size j = 0; j < s.size(); ++j)
{
sl1.push_back(s[j].getMZ());
sl2.push_back(s[j].getIntensity());
}
tf.addLine(String("# ") + String(s.getMetaValue("search_engine")));
tf.addLine(ListUtils::concatenate(sl1, ","));
tf.addLine(ListUtils::concatenate(sl2, ","));
}
tf.store(out_csv);
}
delete(mw);
return EXECUTION_OK;
}
MSSpectrum* nullPointer = 0; START_SECTION((MSSpectrum())) ptr = new MSSpectrum(); TEST_NOT_EQUAL(ptr, nullPointer) END_SECTION START_SECTION((~MSSpectrum())) delete ptr; END_SECTION START_SECTION(([EXTRA] MSSpectrum())) MSSpectrum tmp; Peak1D peak; peak.getPosition()[0] = 47.11; tmp.push_back(peak); TEST_EQUAL(tmp.size(),1); TEST_REAL_SIMILAR(tmp[0].getMZ(),47.11); END_SECTION ///////////////////////////////////////////////////////////// // Member accessors START_SECTION((UInt getMSLevel() const)) MSSpectrum spec; TEST_EQUAL(spec.getMSLevel(),1) END_SECTION START_SECTION((void setMSLevel(UInt ms_level))) MSSpectrum spec; spec.setMSLevel(17); TEST_EQUAL(spec.getMSLevel(),17)
void PeakPickerHiRes::pick(const MSSpectrum& input, MSSpectrum& output, std::vector<PeakBoundary>& boundaries, bool check_spacings) const
{
// copy meta data of the input spectrum
output.clear(true);
output.SpectrumSettings::operator=(input);
output.MetaInfoInterface::operator=(input);
output.setRT(input.getRT());
output.setMSLevel(input.getMSLevel());
output.setName(input.getName());
output.setType(SpectrumSettings::CENTROID);
if (report_FWHM_)
{
output.getFloatDataArrays().resize(1);
output.getFloatDataArrays()[0].setName( report_FWHM_as_ppm_ ? "FWHM_ppm" : "FWHM");
}
// don't pick a spectrum with less than 5 data points
if (input.size() < 5) return;
// if both spacing constraints are disabled, don't check spacings at all:
if ((spacing_difference_ == std::numeric_limits<double>::infinity()) &&
(spacing_difference_gap_ == std::numeric_limits<double>::infinity()))
{
check_spacings = false;
}
// signal-to-noise estimation
SignalToNoiseEstimatorMedian<MSSpectrum > snt;
snt.setParameters(param_.copy("SignalToNoise:", true));
if (signal_to_noise_ > 0.0)
{
snt.init(input);
}
// find local maxima in profile data
for (Size i = 2; i < input.size() - 2; ++i)
{
double central_peak_mz = input[i].getMZ(), central_peak_int = input[i].getIntensity();
double left_neighbor_mz = input[i - 1].getMZ(), left_neighbor_int = input[i - 1].getIntensity();
double right_neighbor_mz = input[i + 1].getMZ(), right_neighbor_int = input[i + 1].getIntensity();
// do not interpolate when the left or right support is a zero-data-point
if (std::fabs(left_neighbor_int) < std::numeric_limits<double>::epsilon()) continue;
if (std::fabs(right_neighbor_int) < std::numeric_limits<double>::epsilon()) continue;
// MZ spacing sanity checks
double left_to_central = 0.0, central_to_right = 0.0, min_spacing = 0.0;
if (check_spacings)
{
left_to_central = central_peak_mz - left_neighbor_mz;
central_to_right = right_neighbor_mz - central_peak_mz;
min_spacing = (left_to_central < central_to_right) ? left_to_central : central_to_right;
}
double act_snt = 0.0, act_snt_l1 = 0.0, act_snt_r1 = 0.0;
if (signal_to_noise_ > 0.0)
{
act_snt = snt.getSignalToNoise(input[i]);
act_snt_l1 = snt.getSignalToNoise(input[i - 1]);
act_snt_r1 = snt.getSignalToNoise(input[i + 1]);
}
// look for peak cores meeting MZ and intensity/SNT criteria
if ((central_peak_int > left_neighbor_int) &&
(central_peak_int > right_neighbor_int) &&
(act_snt >= signal_to_noise_) &&
(act_snt_l1 >= signal_to_noise_) &&
(act_snt_r1 >= signal_to_noise_) &&
(!check_spacings ||
((left_to_central < spacing_difference_ * min_spacing) &&
(central_to_right < spacing_difference_ * min_spacing))))
{
// special case: if a peak core is surrounded by more intense
// satellite peaks (indicates oscillation rather than
// real peaks) -> remove
double act_snt_l2 = 0.0, act_snt_r2 = 0.0;
if (signal_to_noise_ > 0.0)
{
act_snt_l2 = snt.getSignalToNoise(input[i - 2]);
act_snt_r2 = snt.getSignalToNoise(input[i + 2]);
}
// checking signal-to-noise?
if ((i > 1) &&
(i + 2 < input.size()) &&
(left_neighbor_int < input[i - 2].getIntensity()) &&
(right_neighbor_int < input[i + 2].getIntensity()) &&
(act_snt_l2 >= signal_to_noise_) &&
(act_snt_r2 >= signal_to_noise_) &&
(!check_spacings ||
((left_neighbor_mz - input[i - 2].getMZ() < spacing_difference_ * min_spacing) &&
(input[i + 2].getMZ() - right_neighbor_mz < spacing_difference_ * min_spacing))))
{
++i;
continue;
}
std::map<double, double> peak_raw_data;
peak_raw_data[central_peak_mz] = central_peak_int;
peak_raw_data[left_neighbor_mz] = left_neighbor_int;
peak_raw_data[right_neighbor_mz] = right_neighbor_int;
// peak core found, now extend it
// to the left
Size k = 2;
bool previous_zero_left(false); // no need to extend peak if previous intensity was zero
Size missing_left(0);
Size left_boundary(i - 1); // index of the left boundary for the spline interpolation
while ((k <= i) && // prevent underflow
(i - k + 1 > 0) &&
!previous_zero_left &&
(missing_left <= missing_) &&
(input[i - k].getIntensity() <= peak_raw_data.begin()->second) &&
(!check_spacings ||
(peak_raw_data.begin()->first - input[i - k].getMZ() < spacing_difference_gap_ * min_spacing)))
{
double act_snt_lk = 0.0;
if (signal_to_noise_ > 0.0)
{
act_snt_lk = snt.getSignalToNoise(input[i - k]);
}
if ((act_snt_lk >= signal_to_noise_) &&
(!check_spacings ||
(peak_raw_data.begin()->first - input[i - k].getMZ() < spacing_difference_ * min_spacing)))
{
peak_raw_data[input[i - k].getMZ()] = input[i - k].getIntensity();
}
else
{
++missing_left;
if (missing_left <= missing_)
{
peak_raw_data[input[i - k].getMZ()] = input[i - k].getIntensity();
}
}
previous_zero_left = (input[i - k].getIntensity() == 0);
left_boundary = i - k;
++k;
}
// to the right
k = 2;
bool previous_zero_right(false); // no need to extend peak if previous intensity was zero
Size missing_right(0);
Size right_boundary(i+1); // index of the right boundary for the spline interpolation
while ((i + k < input.size()) &&
!previous_zero_right &&
(missing_right <= missing_) &&
(input[i + k].getIntensity() <= peak_raw_data.rbegin()->second) &&
(!check_spacings ||
(input[i + k].getMZ() - peak_raw_data.rbegin()->first < spacing_difference_gap_ * min_spacing)))
{
double act_snt_rk = 0.0;
if (signal_to_noise_ > 0.0)
{
act_snt_rk = snt.getSignalToNoise(input[i + k]);
}
if ((act_snt_rk >= signal_to_noise_) &&
(!check_spacings ||
(input[i + k].getMZ() - peak_raw_data.rbegin()->first < spacing_difference_ * min_spacing)))
{
peak_raw_data[input[i + k].getMZ()] = input[i + k].getIntensity();
}
else
{
++missing_right;
if (missing_right <= missing_)
{
peak_raw_data[input[i + k].getMZ()] = input[i + k].getIntensity();
}
}
previous_zero_right = (input[i + k].getIntensity() == 0);
right_boundary = i + k;
++k;
}
// skip if the minimal number of 3 points for fitting is not reached
if (peak_raw_data.size() < 3) continue;
CubicSpline2d peak_spline (peak_raw_data);
// calculate maximum by evaluating the spline's 1st derivative
// (bisection method)
double max_peak_mz = central_peak_mz;
double max_peak_int = central_peak_int;
double threshold = 1e-6;
OpenMS::Math::spline_bisection(peak_spline, left_neighbor_mz, right_neighbor_mz, max_peak_mz, max_peak_int, threshold);
//
// compute FWHM
//
if (report_FWHM_)
{
double fwhm_int = max_peak_int / 2.0;
threshold = 0.01 * fwhm_int;
double mz_mid, int_mid;
// left:
double mz_left = peak_raw_data.begin()->first;
double mz_center = max_peak_mz;
if (peak_spline.eval(mz_left) > fwhm_int)
{ // the spline ends before half max is reached -- take the leftmost point (probably an underestimation)
mz_mid = mz_left;
}
else
{
do
{
mz_mid = mz_left / 2 + mz_center / 2;
int_mid = peak_spline.eval(mz_mid);
if (int_mid < fwhm_int)
{
mz_left = mz_mid;
}
else
{
mz_center = mz_mid;
}
} while (fabs(int_mid - fwhm_int) > threshold);
}
const double fwhm_left_mz = mz_mid;
// right ...
double mz_right = peak_raw_data.rbegin()->first;
mz_center = max_peak_mz;
if (peak_spline.eval(mz_right) > fwhm_int)
{ // the spline ends before half max is reached -- take the rightmost point (probably an underestimation)
mz_mid = mz_right;
}
else
{
do
{
mz_mid = mz_right / 2 + mz_center / 2;
int_mid = peak_spline.eval(mz_mid);
if (int_mid < fwhm_int)
{
mz_right = mz_mid;
}
else
{
mz_center = mz_mid;
}
} while (fabs(int_mid - fwhm_int) > threshold);
}
const double fwhm_right_mz = mz_mid;
const double fwhm_absolute = fwhm_right_mz - fwhm_left_mz;
output.getFloatDataArrays()[0].push_back( report_FWHM_as_ppm_ ? fwhm_absolute / max_peak_mz * 1e6 : fwhm_absolute);
} // FWHM
// save picked peak into output spectrum
Peak1D peak;
PeakBoundary peak_boundary;
peak.setMZ(max_peak_mz);
peak.setIntensity(max_peak_int);
peak_boundary.mz_min = input[left_boundary].getMZ();
peak_boundary.mz_max = input[right_boundary].getMZ();
output.push_back(peak);
boundaries.push_back(peak_boundary);
// jump over profile data points that have been considered already
i = i + k - 1;
}
}
return;
}