void SimplePairFinder::run(const std::vector<ConsensusMap> & input_maps, ConsensusMap & result_map)
{
if (input_maps.size() != 2)
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "exactly two input maps required");
checkIds_(input_maps);
// progress dots
Int progress_dots = 0;
if (this->param_.exists("debug::progress_dots"))
{
progress_dots = (Int) this->param_.getValue("debug:progress_dots");
}
Int number_of_considered_element_pairs = 0;
// For each element in map 0, find its best friend in map 1
std::vector<UInt> best_companion_index_0(input_maps[0].size(), UInt(-1));
std::vector<double> best_companion_quality_0(input_maps[0].size(), 0);
for (UInt fi0 = 0; fi0 < input_maps[0].size(); ++fi0)
{
double best_quality = -std::numeric_limits<double>::max();
for (UInt fi1 = 0; fi1 < input_maps[1].size(); ++fi1)
{
double quality = similarity_(input_maps[0][fi0], input_maps[1][fi1]);
if (quality > best_quality)
{
best_quality = quality;
best_companion_index_0[fi0] = fi1;
}
++number_of_considered_element_pairs;
if (progress_dots && !(number_of_considered_element_pairs % progress_dots))
{
std::cout << '-' << std::flush;
}
}
best_companion_quality_0[fi0] = best_quality;
}
// For each element in map 1, find its best friend in map 0
std::vector<UInt> best_companion_index_1(input_maps[1].size(), UInt(-1));
std::vector<double> best_companion_quality_1(input_maps[1].size(), 0);
for (UInt fi1 = 0; fi1 < input_maps[1].size(); ++fi1)
{
double best_quality = -std::numeric_limits<double>::max();
for (UInt fi0 = 0; fi0 < input_maps[0].size(); ++fi0)
{
double quality = similarity_(input_maps[0][fi0], input_maps[1][fi1]);
if (quality > best_quality)
{
best_quality = quality;
best_companion_index_1[fi1] = fi0;
}
++number_of_considered_element_pairs;
if (progress_dots && !(number_of_considered_element_pairs % progress_dots))
{
std::cout << '+' << std::flush;
}
}
best_companion_quality_1[fi1] = best_quality;
}
// And if both like each other, they become a pair.
// element_pairs_->clear();
for (UInt fi0 = 0; fi0 < input_maps[0].size(); ++fi0)
{
// fi0 likes someone ...
if (best_companion_quality_0[fi0] > pair_min_quality_)
{
// ... who likes him too ...
UInt best_companion_of_fi0 = best_companion_index_0[fi0];
if (best_companion_index_1[best_companion_of_fi0] == fi0 &&
best_companion_quality_1[best_companion_of_fi0] > pair_min_quality_
)
{
ConsensusFeature f;
f.insert(input_maps[0][fi0]);
f.insert(input_maps[1][best_companion_of_fi0]);
f.computeConsensus();
f.setQuality(best_companion_quality_0[fi0] + best_companion_quality_1[best_companion_of_fi0]);
result_map.push_back(f);
}
}
}
return;
}
ExitCodes main_(int, const char**) override
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
String in = getStringOption_("in");
String out = getStringOption_("out");
FileTypes::Type out_type = FileTypes::nameToType(getStringOption_("out_type"));
if (out_type == FileTypes::UNKNOWN)
{
out_type = FileHandler().getTypeByFileName(out);
}
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
MzMLFile mz_data_file;
mz_data_file.setLogType(log_type_);
PeakMap ms_peakmap;
std::vector<Int> ms_level(1, 1);
(mz_data_file.getOptions()).setMSLevels(ms_level);
mz_data_file.load(in, ms_peakmap);
if (ms_peakmap.size() == 0)
{
LOG_WARN << "The given file does not contain any conventional peak data, but might"
" contain chromatograms. This tool currently cannot handle them, sorry.";
return INCOMPATIBLE_INPUT_DATA;
}
// make sure that the spectra are sorted by m/z
ms_peakmap.sortSpectra(true);
//-------------------------------------------------------------
// get params for MTD and EPD algorithms
//-------------------------------------------------------------
Param com_param = getParam_().copy("algorithm:common:", true);
writeDebug_("Common parameters passed to both sub-algorithms (mtd and epd)", com_param, 3);
Param mtd_param = getParam_().copy("algorithm:mtd:", true);
writeDebug_("Parameters passed to MassTraceDetection", mtd_param, 3);
Param epd_param = getParam_().copy("algorithm:epd:", true);
writeDebug_("Parameters passed to ElutionPeakDetection", epd_param, 3);
//-------------------------------------------------------------
// configure and run MTD
//-------------------------------------------------------------
MassTraceDetection mt_ext;
mtd_param.insert("", com_param);
mtd_param.remove("chrom_fwhm");
mt_ext.setParameters(mtd_param);
vector<MassTrace> m_traces;
mt_ext.run(ms_peakmap, m_traces);
vector<MassTrace> m_traces_final;
bool use_epd = epd_param.getValue("enabled").toBool();
if (!use_epd)
{
swap(m_traces_final, m_traces);
}
else
{
ElutionPeakDetection ep_det;
epd_param.remove("enabled"); // artificially added above
epd_param.insert("", com_param);
ep_det.setParameters(epd_param);
std::vector<MassTrace> split_mtraces;
// note: this step will destroy any meta data annotation (e.g. FWHM_mz_avg)
ep_det.detectPeaks(m_traces, split_mtraces);
if (ep_det.getParameters().getValue("width_filtering") == "auto")
{
m_traces_final.clear();
ep_det.filterByPeakWidth(split_mtraces, m_traces_final);
LOG_INFO << "Notice: " << split_mtraces.size() - m_traces_final.size()
<< " of total " << split_mtraces.size()
<< " were dropped because of too low peak width." << std::endl;
}
else
{
swap(m_traces_final, split_mtraces);
}
}
//-------------------------------------------------------------
// writing consensus map output
//-------------------------------------------------------------
if (out_type == FileTypes::CONSENSUSXML)
{
ConsensusMap consensus_map;
StringList ms_runs;
ms_peakmap.getPrimaryMSRunPath(ms_runs);
consensus_map.setPrimaryMSRunPath(ms_runs);
for (Size i = 0; i < m_traces_final.size(); ++i)
{
if (m_traces_final[i].getSize() == 0) continue;
ConsensusFeature fcons;
int k = 0;
for (MassTrace::const_iterator it = m_traces_final[i].begin(); it != m_traces_final[i].end(); ++it)
{
FeatureHandle fhandle;
fhandle.setRT(it->getRT());
fhandle.setMZ(it->getMZ());
fhandle.setIntensity(it->getIntensity());
fhandle.setUniqueId(++k);
fcons.insert(fhandle);
}
fcons.setMetaValue(3, m_traces_final[i].getLabel());
fcons.setCharge(0);
fcons.setWidth(m_traces_final[i].estimateFWHM(use_epd));
fcons.setQuality(1 - (1.0 / m_traces_final[i].getSize()));
fcons.setRT(m_traces_final[i].getCentroidRT());
fcons.setMZ(m_traces_final[i].getCentroidMZ());
fcons.setIntensity(m_traces_final[i].getIntensity(false));
consensus_map.push_back(fcons);
}
consensus_map.applyMemberFunction(&UniqueIdInterface::setUniqueId);
addDataProcessing_(consensus_map, getProcessingInfo_(DataProcessing::QUANTITATION));
consensus_map.setUniqueId();
ConsensusXMLFile().store(out, consensus_map);
}
else //(out_type == FileTypes::FEATUREXML)
{
//-----------------------------------------------------------
// convert mass traces to features
//-----------------------------------------------------------
std::vector<double> stats_sd;
FeatureMap ms_feat_map;
StringList ms_runs;
ms_peakmap.getPrimaryMSRunPath(ms_runs);
ms_feat_map.setPrimaryMSRunPath(ms_runs);
for (Size i = 0; i < m_traces_final.size(); ++i)
{
if (m_traces_final[i].getSize() == 0) continue;
m_traces_final[i].updateMeanMZ();
m_traces_final[i].updateWeightedMZsd();
Feature f;
f.setMetaValue(3, m_traces_final[i].getLabel());
f.setCharge(0);
f.setMZ(m_traces_final[i].getCentroidMZ());
f.setIntensity(m_traces_final[i].getIntensity(false));
f.setRT(m_traces_final[i].getCentroidRT());
f.setWidth(m_traces_final[i].estimateFWHM(use_epd));
f.setOverallQuality(1 - (1.0 / m_traces_final[i].getSize()));
f.getConvexHulls().push_back(m_traces_final[i].getConvexhull());
double sd = m_traces_final[i].getCentroidSD();
f.setMetaValue("SD", sd);
f.setMetaValue("SD_ppm", sd / f.getMZ() * 1e6);
if (m_traces_final[i].fwhm_mz_avg > 0) f.setMetaValue("FWHM_mz_avg", m_traces_final[i].fwhm_mz_avg);
stats_sd.push_back(m_traces_final[i].getCentroidSD());
ms_feat_map.push_back(f);
}
// print some stats about standard deviation of mass traces
if (stats_sd.size() > 0)
{
std::sort(stats_sd.begin(), stats_sd.end());
LOG_INFO << "Mass trace m/z s.d.\n"
<< " low quartile: " << stats_sd[stats_sd.size() * 1 / 4] << "\n"
<< " median: " << stats_sd[stats_sd.size() * 1 / 2] << "\n"
<< " upp quartile: " << stats_sd[stats_sd.size() * 3 / 4] << std::endl;
}
ms_feat_map.applyMemberFunction(&UniqueIdInterface::setUniqueId);
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
// annotate output with data processing info TODO
addDataProcessing_(ms_feat_map, getProcessingInfo_(DataProcessing::QUANTITATION));
//ms_feat_map.setUniqueId();
FeatureXMLFile().store(out, ms_feat_map);
}
return EXECUTION_OK;
}
void QTClusterFinder::makeConsensusFeature_(list<QTCluster> & clustering,
ConsensusFeature & feature, OpenMSBoost::unordered_map<GridFeature *,
std::vector< QTCluster * > > & element_mapping)
{
// find the best cluster (a valid cluster with the highest score)
list<QTCluster>::iterator best = clustering.begin();
while (best != clustering.end() && best->isInvalid()) {++best;}
for (list<QTCluster>::iterator it = best;
it != clustering.end(); ++it)
{
if (!it->isInvalid())
{
if (it->getQuality() > best->getQuality())
{
best = it;
}
}
}
// no more clusters to process -> clear clustering and return
if (best == clustering.end())
{
clustering.clear();
return;
}
OpenMSBoost::unordered_map<Size, GridFeature *> elements;
best->getElements(elements);
// cout << "Elements: " << elements.size() << " with best " << best->getQuality() << " invalid " << best->isInvalid() << endl;
// create consensus feature from best cluster:
feature.setQuality(best->getQuality());
for (OpenMSBoost::unordered_map<Size, GridFeature *>::const_iterator it = elements.begin();
it != elements.end(); ++it)
{
feature.insert(it->first, it->second->getFeature());
}
feature.computeConsensus();
// update the clustering:
// 1. remove current "best" cluster
// 2. update all clusters accordingly and invalidate elements whose central
// element is removed
best->setInvalid();
for (OpenMSBoost::unordered_map<Size, GridFeature *>::const_iterator it = elements.begin();
it != elements.end(); ++it)
{
for (std::vector< QTCluster* >::iterator
cluster = element_mapping[&(*it->second)].begin();
cluster != element_mapping[&(*it->second)].end(); ++cluster)
{
// we do not want to update invalid features (saves time and does not
// recompute the quality)
if (!(*cluster)->isInvalid())
{
if (!(*cluster)->update(elements)) // cluster is invalid (center point removed):
{
(*cluster)->setInvalid();
}
}
}
}
}
