PWIZ_API_DECL ChromatogramPtr ChromatogramList_ABI::chromatogram(size_t index, bool getBinaryData) const
{
boost::call_once(indexInitialized_.flag, boost::bind(&ChromatogramList_ABI::createIndex, this));
if (index>size_)
throw runtime_error(("[ChromatogramList_ABI::chromatogram()] Bad index: "
+ lexical_cast<string>(index)).c_str());
// allocate a new Chromatogram
IndexEntry& ie = index_[index];
ChromatogramPtr result = ChromatogramPtr(new Chromatogram);
if (!result.get())
throw std::runtime_error("[ChromatogramList_Thermo::chromatogram()] Allocation error.");
result->index = index;
result->id = ie.id;
result->set(ie.chromatogramType);
switch (ie.chromatogramType)
{
case MS_TIC_chromatogram:
{
map<double, double> fullFileTIC;
int sampleCount = wifffile_->getSampleCount();
for (int i=1; i <= sampleCount; ++i)
{
try
{
int periodCount = wifffile_->getPeriodCount(i);
for (int ii=1; ii <= periodCount; ++ii)
{
//Console::WriteLine("Sample {0}, Period {1}", i, ii);
int experimentCount = wifffile_->getExperimentCount(i, ii);
for (int iii=1; iii <= experimentCount; ++iii)
{
ExperimentPtr msExperiment = (i == sample
? experimentsMap_.find(pair<int, int>(ii, iii))->second
: wifffile_->getExperiment(i, ii, iii));
// add current experiment TIC to full file TIC
vector<double> times, intensities;
msExperiment->getTIC(times, intensities);
for (int iiii = 0, end = intensities.size(); iiii < end; ++iiii)
fullFileTIC[times[iiii]] += intensities[iiii];
}
}
}
catch (exception&)
{
// TODO: log warning
}
}
result->setTimeIntensityArrays(std::vector<double>(), std::vector<double>(), UO_minute, MS_number_of_detector_counts);
if (getBinaryData)
{
BinaryDataArrayPtr timeArray = result->getTimeArray();
BinaryDataArrayPtr intensityArray = result->getIntensityArray();
timeArray->data.reserve(fullFileTIC.size());
intensityArray->data.reserve(fullFileTIC.size());
for (map<double, double>::iterator itr = fullFileTIC.begin();
itr != fullFileTIC.end();
++itr)
{
timeArray->data.push_back(itr->first);
intensityArray->data.push_back(itr->second);
}
}
result->defaultArrayLength = fullFileTIC.size();
}
break;
case MS_SRM_chromatogram:
{
ExperimentPtr experiment = ie.experiment;
pwiz::vendor_api::ABI::Target target;
experiment->getSRM(ie.transition, target);
// TODO: move to global scan settings or leave out entirely?
result->userParams.push_back(UserParam("MS_dwell_time", lexical_cast<string>(target.dwellTime /* milliseconds->seconds */ / 1000.0), "xs:float"));
result->precursor.isolationWindow.set(MS_isolation_window_target_m_z, ie.q1, MS_m_z);
//result->precursor.isolationWindow.set(MS_isolation_window_lower_offset, ie.q1, MS_m_z);
//result->precursor.isolationWindow.set(MS_isolation_window_upper_offset, ie.q1, MS_m_z);
result->precursor.activation.set(MS_CID);
result->precursor.activation.set(MS_collision_energy, target.collisionEnergy, UO_electronvolt);
result->precursor.activation.userParams.push_back(UserParam("MS_declustering_potential", lexical_cast<string>(target.declusteringPotential), "xs:float"));
result->product.isolationWindow.set(MS_isolation_window_target_m_z, ie.q3, MS_m_z);
//result->product.isolationWindow.set(MS_isolation_window_lower_offset, ie.q3, MS_m_z);
//result->product.isolationWindow.set(MS_isolation_window_upper_offset, ie.q3, MS_m_z);
result->setTimeIntensityArrays(std::vector<double>(), std::vector<double>(), UO_minute, MS_number_of_detector_counts);
vector<double> times, intensities;
experiment->getSIC(ie.transition, times, intensities);
result->defaultArrayLength = times.size();
if (getBinaryData)
{
BinaryDataArrayPtr timeArray = result->getTimeArray();
BinaryDataArrayPtr intensityArray = result->getIntensityArray();
std::swap(timeArray->data, times);
std::swap(intensityArray->data, intensities);
}
}
break;
}
return result;
}
void test()
{
{
MSData tiny;
examples::initializeTiny(tiny);
MSDataFile::WriteConfig writeConfig;
Serializer_mz5 serializer(writeConfig);
IterationListenerRegistry ilr;
serializer.write(testFilename, tiny, &ilr);
MSData dummy;
serializer.read(testFilename, dummy);
// so we don't have any dangling references
//dummy.instrumentPtrs.push_back(InstrumentPtr(new Instrument("LCQ_Deca")));
dummy.dataProcessingPtrs.push_back(DataProcessingPtr(new DataProcessing(
"pwiz_processing")));
dummy.dataProcessingPtrs.push_back(DataProcessingPtr(new DataProcessing(
"CompassXtract processing")));
ChromatogramListPtr sl = dummy.run.chromatogramListPtr;
// check easy functions
unit_assert(sl.get());
unit_assert(sl->size() == 2);
unit_assert(sl->find("tic") == 0);
unit_assert(sl->find("sic") == 1);
// check tic
ChromatogramPtr s = sl->chromatogram(0); // read without binary data
unit_assert(s.get());
unit_assert(s->id == "tic");
unit_assert(s->binaryDataArrayPtrs.empty());
unit_assert(sl->chromatogramIdentity(0).index == 0);
unit_assert(sl->chromatogramIdentity(0).id == "tic");
s = sl->chromatogram(0, true); // read with binary data
vector < TimeIntensityPair > pairs;
s->getTimeIntensityPairs(pairs);
unit_assert(pairs.size() == 15);
for (int i = 0; i < 15; i++)
unit_assert(pairs[i].time == i && pairs[i].intensity == 15 - i);
// check sic
s = sl->chromatogram(1, true);
unit_assert(s.get());
unit_assert(s->id == "sic");
unit_assert(sl->chromatogramIdentity(1).index == 1);
unit_assert(sl->chromatogramIdentity(1).id == "sic");
pairs.clear();
s->getTimeIntensityPairs(pairs);
unit_assert(pairs.size() == 10);
for (int i = 0; i < 10; i++)
unit_assert(pairs[i].time == i && pairs[i].intensity == (10 - i));
}
bfs::remove(testFilename);
}