PeakDetectorMatchedFilterTest.cpp File Reference

#include "PeakDetectorMatchedFilter.hpp"
#include "PeakDetectorMatchedFilterTestData.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Std.hpp"

Go to the source code of this file.

Functions
void	initializeWithTestData (FrequencyData &fd)
void	testCreation (const IsotopeEnvelopeEstimator &isotopeEnvelopeEstimator)
void	testFind (FrequencyData &fd, const IsotopeEnvelopeEstimator &isotopeEnvelopeEstimator)
auto_ptr < IsotopeEnvelopeEstimator >	createIsotopeEnvelopeEstimator ()
void	test ()
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0

---

Function Documentation

void initializeWithTestData

(

FrequencyData &

fd

)

Definition at line 41 of file PeakDetectorMatchedFilterTest.cpp.

References pwiz::data::FrequencyData::analyze(), pwiz::data::FrequencyData::calibrationParameters(), pwiz::data::FrequencyData::data(), pwiz::data::FrequencyData::observationDuration(), testData_, testDataCalibrationA_, testDataCalibrationB_, testDataObservationDuration_, and testDataSize_.

Referenced by test().

{
    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();
}

void testCreation

(

const IsotopeEnvelopeEstimator &

isotopeEnvelopeEstimator

)

Definition at line 53 of file PeakDetectorMatchedFilterTest.cpp.

References pwiz::frequency::PeakDetectorMatchedFilter::config(), pwiz::frequency::PeakDetectorMatchedFilter::Config::filterMatchRate, pwiz::frequency::PeakDetectorMatchedFilter::Config::filterSampleRadius, pwiz::frequency::PeakDetectorMatchedFilter::Config::isotopeEnvelopeEstimator, pwiz::frequency::PeakDetectorMatchedFilter::Config::isotopeThresholdFactor, pwiz::frequency::PeakDetectorMatchedFilter::Config::monoisotopicPeakThresholdFactor, os_, pwiz::frequency::PeakDetectorMatchedFilter::Config::peakMaxCorrelationAngle, pwiz::frequency::PeakDetectorMatchedFilter::Config::peakThresholdFactor, and unit_assert.

Referenced by test().

{
    if (os_) *os_ << "testCreation()\n";
    const int filterMatchRate = 4;
    const int filterSampleRadius = 2;
    const double peakThresholdFactor = 0;
    const double peakMaxCorrelationAngle = 5;
    const double isotopeThresholdFactor = 666;
    const double monoisotopicPeakThresholdFactor = 777;

    PeakDetectorMatchedFilter::Config config;
    config.isotopeEnvelopeEstimator = &isotopeEnvelopeEstimator; 
    config.filterMatchRate = filterMatchRate;
    config.filterSampleRadius = filterSampleRadius;
    config.peakThresholdFactor = peakThresholdFactor;
    config.peakMaxCorrelationAngle = peakMaxCorrelationAngle;
    config.isotopeThresholdFactor = isotopeThresholdFactor;
    config.monoisotopicPeakThresholdFactor = monoisotopicPeakThresholdFactor;

    auto_ptr<PeakDetectorMatchedFilter> pd = PeakDetectorMatchedFilter::create(config);

    unit_assert(pd->config().filterMatchRate == filterMatchRate); 
    unit_assert(pd->config().filterSampleRadius == filterSampleRadius); 
    unit_assert(pd->config().peakThresholdFactor == peakThresholdFactor); 
    unit_assert(pd->config().peakMaxCorrelationAngle == peakMaxCorrelationAngle); 
    unit_assert(pd->config().isotopeThresholdFactor == isotopeThresholdFactor); 
    unit_assert(pd->config().monoisotopicPeakThresholdFactor == monoisotopicPeakThresholdFactor); 
}

void testFind	(	FrequencyData &	fd,
		const IsotopeEnvelopeEstimator &	isotopeEnvelopeEstimator
	)

Definition at line 83 of file PeakDetectorMatchedFilterTest.cpp.

References pwiz::frequency::PeakDetectorMatchedFilter::Config::collapseRadius, e(), pwiz::frequency::PeakDetectorMatchedFilter::Config::filterMatchRate, pwiz::frequency::PeakDetectorMatchedFilter::Config::filterSampleRadius, pwiz::frequency::PeakDetectorMatchedFilter::findPeaks(), pwiz::frequency::PeakDetectorMatchedFilter::Config::isotopeEnvelopeEstimator, pwiz::frequency::PeakDetectorMatchedFilter::Config::isotopeMaxChargeState, pwiz::frequency::PeakDetectorMatchedFilter::Config::isotopeMaxNeutronCount, pwiz::frequency::PeakDetectorMatchedFilter::Config::isotopeThresholdFactor, pwiz::frequency::PeakDetectorMatchedFilter::Config::log, pwiz::frequency::PeakDetectorMatchedFilter::Config::logDetailLevel, pwiz::frequency::PeakDetectorMatchedFilter::Config::monoisotopicPeakThresholdFactor, norm(), os_, pwiz::frequency::PeakDetectorMatchedFilter::Config::peakMaxCorrelationAngle, pwiz::frequency::PeakDetectorMatchedFilter::Config::peakThresholdFactor, pwiz::data::peakdata::PeakData::scans, unit_assert, unit_assert_equal, and pwiz::frequency::PeakDetectorMatchedFilter::Config::useMagnitudeFilter.

Referenced by main(), test(), and testThreadSafetyWorker().

{
    if (os_) *os_ << "testFind()\n";

    // fill in config structure
    PeakDetectorMatchedFilter::Config config;
    config.isotopeEnvelopeEstimator = &isotopeEnvelopeEstimator; 
    config.filterMatchRate = 4;
    config.filterSampleRadius = 2;
    config.peakThresholdFactor = 2;
    config.peakMaxCorrelationAngle = 30;
    config.isotopeThresholdFactor = 2;
    config.monoisotopicPeakThresholdFactor = 2;
    config.isotopeMaxChargeState = 6;
    config.isotopeMaxNeutronCount = 4;
    config.collapseRadius = 15;
    config.useMagnitudeFilter = false;
    config.logDetailLevel = 1;
    config.log = os_;

    // instantiate
    auto_ptr<PeakDetectorMatchedFilter> pd = PeakDetectorMatchedFilter::create(config);

    // find peaks
    PeakData data;
    data.scans.push_back(Scan());
    vector<PeakDetectorMatchedFilter::Score> scores;
    pd->findPeaks(fd, data.scans[0], scores);

    // report results
    if (os_) 
    {
        *os_ << "peaks found: " << data.scans[0].peakFamilies.size() << endl;
        *os_ << data.scans[0];
        *os_ << "scores: " << scores.size() << endl;
        copy(scores.begin(), scores.end(),
            ostream_iterator<PeakDetectorMatchedFilter::Score>(*os_, "\n"));
    }

    // assertions
    unit_assert(data.scans[0].peakFamilies.size() == 1);
    const PeakFamily& peakFamily = data.scans[0].peakFamilies.back(); 
    
    if (os_) *os_ << "peakFamily: " << peakFamily << endl;
    unit_assert(peakFamily.peaks.size() > 1);
    const Peak& peak = peakFamily.peaks[0];
    unit_assert_equal(peak.getAttribute(Peak::Attribute_Frequency), 159455, 1);
    unit_assert(peakFamily.charge == 2);
    
    unit_assert(scores.size() == 1);
    const PeakDetectorMatchedFilter::Score& score = scores.back();
    unit_assert(score.charge == peakFamily.charge);
    unit_assert(score.monoisotopicFrequency == peak.getAttribute(Peak::Attribute_Frequency));
    unit_assert_equal(norm(score.monoisotopicIntensity - 
                           polar(peak.intensity, peak.getAttribute(Peak::Attribute_Phase))),
                      0, 1e-14);
}

auto_ptr<IsotopeEnvelopeEstimator> createIsotopeEnvelopeEstimator

(

)

Definition at line 142 of file PeakDetectorMatchedFilterTest.cpp.

References pwiz::chemistry::IsotopeEnvelopeEstimator::Config::isotopeCalculator.

Referenced by test().

{
    const double abundanceCutoff = .01;
    const double massPrecision = .1; 
    IsotopeCalculator isotopeCalculator(abundanceCutoff, massPrecision);

    IsotopeEnvelopeEstimator::Config config;
    config.isotopeCalculator = &isotopeCalculator;

    return auto_ptr<IsotopeEnvelopeEstimator>(new IsotopeEnvelopeEstimator(config));
}

void test

(

)

Definition at line 155 of file PeakDetectorMatchedFilterTest.cpp.

References createIsotopeEnvelopeEstimator(), initializeWithTestData(), os_, testCreation(), and testFind().

{
    if (os_) *os_ << setprecision(12);

    auto_ptr<IsotopeEnvelopeEstimator> isotopeEnvelopeEstimator = createIsotopeEnvelopeEstimator();

    testCreation(*isotopeEnvelopeEstimator);

    FrequencyData fd;
    initializeWithTestData(fd);

    testFind(fd, *isotopeEnvelopeEstimator);
}

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 170 of file PeakDetectorMatchedFilterTest.cpp.

References e(), os_, test(), TEST_EPILOG, TEST_FAILED, and TEST_PROLOG.

{
    TEST_PROLOG(argc, argv)

    try
    {
        if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
        if (os_) *os_ << "PeakDetectorMatchedFilterTest\n";
        test();
    }
    catch (exception& e)
    {
        TEST_FAILED(e.what())
    }
    catch (...)
    {
        TEST_FAILED("Caught unknown exception.")
    }

    TEST_EPILOG
}

---

Variable Documentation

ostream* os_ = 0

Definition at line 38 of file PeakDetectorMatchedFilterTest.cpp.