//Load a trained Svm and Prob. models
void SvmTheoreticalSpectrumGeneratorSet::load(String filename)
{
if (!File::readable(filename)) // look in OPENMS_DATA_PATH
{
filename = File::find(filename);
}
Param sim_param = SvmTheoreticalSpectrumGenerator().getDefaults();
TextFile file(filename);
TextFile::ConstIterator it = file.begin();
if (it == file.end()) return; // no data to load
// skip header line
++it;
// process content
for (; it != file.end(); ++it)
{
std::vector<String> spl;
it->split(":", spl);
Int precursor_charge = spl[0].toInt();
if (spl.size() != 2 || precursor_charge < 1)
{
throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, *it, " Invalid entry in SVM model File");
}
//load the model into the map
sim_param.setValue("model_file_name", File::path(filename) + "/" + spl[1]);
simulators_[precursor_charge].setParameters(sim_param);
simulators_[precursor_charge].load();
}
}
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]);
TOFCalibration ec;
PeakMap exp_raw, calib_exp;
MzMLFile mzml_file;
mzml_file.load(tutorial_data_path + "/data/Tutorial_TOFCalibration_peak.mzML", calib_exp);
mzml_file.load(tutorial_data_path + "/data/Tutorial_TOFCalibration_raw.mzML", exp_raw);
vector<double> ref_masses;
TextFile ref_file;
ref_file.load(tutorial_data_path + "/data/Tutorial_TOFCalibration_masses.txt", true);
for (TextFile::ConstIterator iter = ref_file.begin(); iter != ref_file.end(); ++iter)
{
ref_masses.push_back(String(iter->c_str()).toDouble());
}
std::vector<double> ml1;
ml1.push_back(418327.924993827);
std::vector<double> ml2;
ml2.push_back(253.645187196031);
std::vector<double> ml3;
ml3.push_back(-0.0414243465397252);
ec.setML1s(ml1);
ec.setML2s(ml2);
ec.setML3s(ml3);
Param param;
param.setValue("PeakPicker:peak_width", 0.1);
ec.setParameters(param);
ec.pickAndCalibrate(calib_exp, exp_raw, ref_masses);
return 0;
} //end of main
ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
String in = getStringOption_("in");
String out = getStringOption_("out");
String in_calib = getStringOption_("ext_calibrants");
String ref = getStringOption_("ref_masses");
String conv = getStringOption_("tof_const");
//-------------------------------------------------------------
// init TOFCalibration
//-------------------------------------------------------------
TOFCalibration calib;
calib.setLogType(log_type_);
Param param = getParam_().copy("algorithm:", true);
calib.setParameters(param);
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
MSExperiment<Peak1D> ms_exp_calib, ms_exp_raw;
MzMLFile mz_data_file;
mz_data_file.setLogType(log_type_);
mz_data_file.load(in_calib, ms_exp_calib);
mz_data_file.load(in, ms_exp_raw);
vector<double> ref_masses;
TextFile ref_file;
ref_file.load(ref, true);
for (TextFile::ConstIterator iter = ref_file.begin(); iter != ref_file.end(); ++iter)
{
ref_masses.push_back(String(iter->c_str()).toDouble());
}
TextFile const_file;
const_file.load(conv, true);
std::vector<String> vec;
TextFile::ConstIterator iter = const_file.begin();
iter->split('\t', vec);
std::vector<double> ml1, ml2, ml3;
ml1.push_back(String(vec[0].c_str()).toDouble());
ml2.push_back(String(vec[1].c_str()).toDouble());
if (vec.size() == 3)
{
ml3.push_back(String(vec[2].c_str()).toDouble());
}
++iter;
for (; iter != const_file.end(); ++iter)
{
iter->split('\t', vec);
ml1.push_back(String(vec[0].c_str()).toDouble());
ml2.push_back(String(vec[1].c_str()).toDouble());
if (vec.size() == 3)
{
ml3.push_back(String(vec[2].c_str()).toDouble());
}
}
if (ml1.size() != 1 && ml1.size() != ms_exp_calib.size())
{
writeLog_("Incorrect number of calibration constants given. Aborting!");
return INPUT_FILE_CORRUPT;
}
calib.setML1s(ml1);
calib.setML2s(ml2);
if (!ml3.empty()) calib.setML3s(ml3);
//-------------------------------------------------------------
// perform calibration
//-------------------------------------------------------------
if (getFlag_("peak_data"))
{
calib.calibrate(ms_exp_calib, ms_exp_raw, ref_masses);
}
else
{
calib.pickAndCalibrate(ms_exp_calib, ms_exp_raw, ref_masses);
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(ms_exp_raw, getProcessingInfo_(DataProcessing::CALIBRATION));
mz_data_file.store(out, ms_exp_raw);
return EXECUTION_OK;
}
