void initializeWithTestData(FrequencyData& fd)
{
for (TestDatum* datum=testData_; datum<testData_+testDataSize_; datum++)
fd.data().push_back(FrequencyDatum(datum->frequency,
complex<double>(datum->real, datum->imaginary)));
fd.observationDuration(testDataObservationDuration_);
fd.calibrationParameters(CalibrationParameters(testDataCalibrationA_, testDataCalibrationB_));
fd.analyze();
}
int calibrate(const FrequencyData& fd, const peakdata::Scan& scan,
const Configuration& config, const string& outputDirectory)
{
try
{
const string& pdbFilename = config.calibrate_database_filename;
cout << "Using database " << pdbFilename << endl;
auto_ptr<MassDatabase> mdb = MassDatabase::createFromPeptideDatabase(pdbFilename);
vector<Calibrator::Measurement> measurements = createMeasurements(scan);
if (measurements.empty())
throw runtime_error("No measurements read.");
CalibrationParameters cp = fd.calibrationParameters();
bfs::create_directories(outputDirectory);
cerr << "Running calibrator..." << flush;
auto_ptr<Calibrator> calibrator = Calibrator::create(*mdb,
measurements,
cp,
config.calibrate_initial_error_estimate,
config.calibrate_error_estimator_iteration_count,
outputDirectory);
for (unsigned int i=0; i<config.calibrate_calibrator_iteration_count; i++)
calibrator->iterate();
cerr << "done.\n";
cout << "A: " << calibrator->parameters().A << " B: " << calibrator->parameters().B << endl;
}
catch (exception& e)
{
cerr << e.what() << endl;
}
return 0;
}
void PeakDetectorNaiveImpl::findPeaks(const FrequencyData& fd, peakdata::Scan& result) const
{
result.scanNumber = fd.scanNumber();
result.retentionTime = fd.retentionTime();
result.observationDuration = fd.observationDuration();
result.calibrationParameters = fd.calibrationParameters();
result.peakFamilies.clear();
const double noiseLevel = sqrt(fd.variance());
const double threshold = noiseLevel * noiseFactor_;
for (FrequencyData::const_iterator it=fd.data().begin(); it!=fd.data().end(); ++it)
if (isPeak(it, fd.data(), threshold, detectionRadius_))
{
result.peakFamilies.push_back(PeakFamily());
PeakFamily& peakFamily = result.peakFamilies.back();
peakFamily.peaks.push_back(Peak());
Peak& peak = peakFamily.peaks.back();
peak.frequency = it->x;
peak.intensity = it->y.real();
peak.phase = it->y.imag();
}
}
void test()
{
// create some data, f(x) = abs(5-(x-2))
FrequencyData fd;
FrequencyData::container& data = fd.data();
for (int i=-5; i<=5; i++)
data.push_back(FrequencyDatum(i+2, 5-abs(i)));
fd.analyze(); // recache after changing data
// verify peak()
FrequencyData::const_iterator max = fd.max();
unit_assert(max->x == 2);
unit_assert(max->y == 5.);
// verify stats
unit_assert(fd.mean() == 25./11);
unit_assert(fd.meanSquare() == 85./11);
unit_assert(fd.sumSquares() == 85.);
unit_assert_equal(fd.variance(), 85./11 - 25.*25/11/11, 1e-12);
// write out data
if (os_) *os_ << "Writing " << filename1 << endl;
fd.write(filename1, FrequencyData::Text);
// read into const FrequencyData
string filename2 = "FrequencyDataTest.output2.txt";
FrequencyData fd2(filename1, FrequencyData::Text);
// verify normalize()
fd2.normalize();
unit_assert(fd2.shift() == -2);
unit_assert(fd2.scale() == 1./5);
max = fd2.max();
unit_assert(max->x == 0);
unit_assert(max->y == 1.);
// verify transform(shift, scale)
fd2.transform(-fd2.shift(), 1./fd2.scale());
// verify read/write
if (os_) *os_ << "Writing " << filename2 << endl;
fd2.write(filename2, FrequencyData::Text);
diff(filename1, filename2);
// test subrange
string filename3 = "FrequencyDataTest.output3.txt";
FrequencyData fd3(fd2, fd2.data().begin(), fd2.max()); // copy first half
if (os_) *os_ << "Writing " << filename3 << endl;
fd3.write(filename3, FrequencyData::Text);
FrequencyData fd4(fd2, fd2.max(), fd2.data().end()); // copy second half
ofstream os(filename3.c_str(), ios::app);
fd4.write(os, FrequencyData::Text);
os.close();
diff(filename1, filename3);
// read/write binary, and metadata
fd.scanNumber(555);
fd.retentionTime(444);
fd.calibrationParameters(CalibrationParameters(1,1));
fd.observationDuration(666);
fd.noiseFloor(777);
string filename4a = "FrequencyDataTest.output4a.txt";
if (os_) *os_ << "Writing " << filename4a << endl;
fd.write(filename4a, FrequencyData::Text);
string filenameBinary1 = "FrequencyDataTest.output1.cfd";
if (os_) *os_ << "Writing " << filenameBinary1 << endl;
fd.write(filenameBinary1);
FrequencyData fd5(filenameBinary1);
unit_assert(fd5.observationDuration() == 666);
fd5.observationDuration(fd.observationDurationEstimatedFromData());
unit_assert(fd5.scanNumber() == 555);
unit_assert(fd5.retentionTime() == 444);
unit_assert(fd5.observationDuration() == 1);
unit_assert(fd5.noiseFloor() == 777);
if (os_) *os_ << "Calibration: " << fd5.calibrationParameters().A << " " << fd5.calibrationParameters().B << endl;
string filename4b = "FrequencyDataTest.output4b.txt";
if (os_) *os_ << "Writing " << filename4b << endl;
fd5.write(filename4b, FrequencyData::Text);
diff(filename4a, filename4b);
fd.calibrationParameters(CalibrationParameters());
// test window
FrequencyData window1(fd, data.begin()+1, 2);
FrequencyData window2(fd, fd.max(), 1);
FrequencyData window3(fd, data.end()-2, 2);
string filename5 = "FrequencyDataTest.output5.txt";
if (os_) *os_ << "Writing " << filename5 << endl;
ofstream os5(filename5.c_str());
window1.write(os5, FrequencyData::Text);
window2.write(os5, FrequencyData::Text);
window3.write(os5, FrequencyData::Text);
os5.close();
diff(filename1, filename5);
}