FrequencyDataTest.cpp File Reference

#include "FrequencyData.hpp"
#include "FrequencyDataTestData.hpp"
#include "pwiz/data/misc/CalibrationParameters.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Filesystem.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include <boost/filesystem/operations.hpp>

Go to the source code of this file.

Functions
void	diff (const string &filename1, const string &filename2)
void	test ()
void	testFind ()
void	testAddition ()
void	testNoiseFloor ()
void	cleanTests ()
void	testNoiseFloorVarianceCalculation ()
int	main (int argc, char *argv[])

Variables
ostream *	os_
string	filename1 = "FrequencyDataTest.output1.txt"

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Function Documentation

void diff	(	const string &	filename1,
		const string &	filename2
	)

Definition at line 40 of file FrequencyDataTest.cpp.

References os_, and unit_assert.

Referenced by pwiz::data::Diff< object_type, config_type, object_result_type >::Diff(), pwiz::data::Diff< object_type, config_type, object_result_type >::operator()(), pwiz::data::operator<<(), test(), testAmbiguousResidue(), testAnalysisData(), testAnalysisSoftware(), testBinaryDataArray(), testChromatogram(), testChromatogramList(), testComponent(), testComponentList(), testCompound(), testConfiguration(), testContact(), testContactRole(), testCV(), testCVParam(), testDatabaseTranslation(), testDataCollection(), testDataProcessing(), testEnzyme(), testEnzymes(), testEvidence(), testFileContent(), testFileDescription(), testFilter(), testFragmentArray(), testIdentData(), testIdentifiable(), testInputs(), testInstrument(), testInstrumentConfiguration(), testIonType(), testMassTable(), testMaxPrecisionDiff(), testMeasure(), testModification(), testMSData(), testObject(), testObject_ChromatogramList(), testObject_SpectrumList(), testObjectWithMSData(), testParamContainer(), testParamGroup(), testPeptide(), testPeptideEvidence(), testPeptideHypothesis(), testPerson(), testPrecursor(), testPrediction(), testProcessingMethod(), testProduct(), testProtein(), testProteinAmbiguityGroup(), testProteinDetectionHypothesis(), testProteinDetectionList(), testProteinDetectionProtocol(), testProteinList(), testProteomeData(), testQR(), testRectangularQR(), testResidue(), testRetentionTime(), testRun(), testSample(), testScan(), testScanList(), testScanSettings(), testSearchDatabase(), testSearchModification(), testSerialize(), testSerializeReally(), testSnapModifications(), testSoftware(), testSource(), testSourceFile(), testSpectraData(), testSpectrum(), testSpectrumIdentificationList(), testSpectrumIdentificationProtocol(), testSpectrumList(), testTarget(), testTraData(), testTransition(), testUserParam(), testValidation(), testWriteRead(), testWriteReadBMS1(), testWriteReadBMS2(), testWriteReadCMS1(), testWriteReadCMS2(), testWriteReadMS1(), testWriteReadMS2(), and validateWriteRead().

{
        ifstream file1(filename1.c_str()), file2(filename2.c_str());
        string line1, line2;
        while (getline(file1, line1) && getline(file2, line2))
            unit_assert(line1 == line2);
    if (os_) *os_ << "diff " << filename1 << " " << filename2 << ": success\n";
}

void test

(

)

Definition at line 53 of file FrequencyDataTest.cpp.

References pwiz::data::CalibrationParameters::A, pwiz::data::FrequencyData::analyze(), pwiz::data::CalibrationParameters::B, pwiz::data::FrequencyData::calibrationParameters(), pwiz::data::FrequencyData::data(), diff(), e(), filename1, pwiz::data::FrequencyData::max(), max(), pwiz::data::FrequencyData::mean(), pwiz::data::FrequencyData::meanSquare(), pwiz::data::FrequencyData::noiseFloor(), pwiz::data::FrequencyData::normalize(), pwiz::data::FrequencyData::observationDuration(), pwiz::data::FrequencyData::observationDurationEstimatedFromData(), os_, pwiz::data::FrequencyData::retentionTime(), pwiz::data::FrequencyData::scale(), pwiz::data::FrequencyData::scanNumber(), pwiz::data::FrequencyData::shift(), pwiz::data::FrequencyData::sumSquares(), Text, pwiz::data::FrequencyData::transform(), unit_assert, unit_assert_equal, pwiz::data::FrequencyData::variance(), and pwiz::data::FrequencyData::write().

{
    // 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);
}

void testFind

(

)

Definition at line 151 of file FrequencyDataTest.cpp.

References pwiz::data::FrequencyData::data(), filename1, pwiz::data::FrequencyData::findNearest(), and unit_assert.

{
    const FrequencyData fd(filename1);

    FrequencyData::const_iterator it = fd.findNearest(-.2);
    unit_assert(it!=fd.data().end() && it->x==0);

    it = fd.findNearest(.2);
    unit_assert(it!=fd.data().end() && it->x==0);

    it = fd.findNearest(6.1);
    unit_assert(it!=fd.data().end() && it->x==6);

    it = fd.findNearest(7.1);
    unit_assert(it!=fd.data().end() && it->x==7);
    
    it = fd.findNearest(666);
    unit_assert(it!=fd.data().end() && it->x==7);

    it = fd.findNearest(-666);
    unit_assert(it==fd.data().begin());
}

void testAddition

(

)

Definition at line 175 of file FrequencyDataTest.cpp.

References pwiz::data::FrequencyData::data(), filename1, pwiz::data::FrequencyData::transform(), and unit_assert.

Referenced by main().

{
    FrequencyData fd(filename1);
    FrequencyData fd2(filename1);

    fd += fd;

    for (FrequencyData::const_iterator it=fd.data().begin(), jt=fd2.data().begin(); 
         it!=fd.data().end(); 
         ++it, ++jt)
        unit_assert(it->y == 2.*jt->y);

    fd2.transform(0, -2.);
    fd += fd2;

    for (FrequencyData::const_iterator it=fd.data().begin(); it!=fd.data().end(); ++it)
        unit_assert(it->y == 0.);
}

void testNoiseFloor

(

)

Definition at line 195 of file FrequencyDataTest.cpp.

References filename1, pwiz::data::FrequencyData::noiseFloor(), os_, and pwiz::data::FrequencyData::variance().

Referenced by main().

{
    FrequencyData fd(filename1);
    if (os_) *os_ << "variance: " << fd.variance() << endl;
    if (os_) *os_ << "noiseFloor: " << fd.noiseFloor() << endl;
}

void cleanTests

(

)

Definition at line 203 of file FrequencyDataTest.cpp.

References pwiz::util::expand_pathmask(), and os_.

Referenced by main().

{
    if (os_) *os_ << "Deleting FrequencyDataTest.output*.txt\n";
    vector<bfs::path> filepaths;
    expand_pathmask("FrequencyDataTest.output*.*", filepaths);
    for (size_t i=0; i < filepaths.size(); ++i)
        boost::filesystem::remove(filepaths[i]);
}

void testNoiseFloorVarianceCalculation

(

)

Definition at line 213 of file FrequencyDataTest.cpp.

References pwiz::data::FrequencyData::analyze(), pwiz::data::FrequencyData::cutoffNoiseFloor(), pwiz::data::FrequencyData::data(), pwiz::data::CalibrationParameters::frequency(), os_, sampleFrequencyData_, sampleMassData_, sampleMassDataSize_, and unit_assert_equal.

Referenced by main().

{
    if (os_) *os_ << "testNoiseFloorVarianceCalculation()\n";
    if (os_) *os_ << setprecision(10);

    // test noise floor calculation on sample frequency data 

    string filename = "FrequencyDataTest.cfd.temp.txt";
    ofstream temp(filename.c_str());
    temp << sampleFrequencyData_;
    temp.close();

    FrequencyData fd(filename);
    boost::filesystem::remove(filename);

    double result = fd.cutoffNoiseFloor();
    if (os_) *os_ << "result: " << result << endl;
    unit_assert_equal(result, 29000, 1000);

    // test noise floor calculation on sample mass data 

    FrequencyData fdMasses;
    CalibrationParameters cp = CalibrationParameters::thermo_FT();

    for (RawMassDatum* p=sampleMassData_; p!=sampleMassData_+sampleMassDataSize_; ++p)
        fdMasses.data().push_back(FrequencyDatum(cp.frequency(p->mz), p->intensity));
    fdMasses.analyze();

    double result2 = fdMasses.cutoffNoiseFloor();
    if (os_) *os_ << "result2: " << result2 << endl;
    unit_assert_equal(result2, 6000, 1000);
}

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

Definition at line 247 of file FrequencyDataTest.cpp.

References cleanTests(), e(), os_, test(), TEST_EPILOG, TEST_FAILED, TEST_PROLOG, testAddition(), testFind(), testNoiseFloor(), and testNoiseFloorVarianceCalculation().

{
    TEST_PROLOG(argc, argv)

    try
    {
        if (argc>1 && !strcmp(argv[1],"-v")) // verbose
            os_ = &cout;

        if (os_) *os_ << "FrequencyDataTest\n";

        test();
        testFind();
        testAddition();
        testNoiseFloor();
        cleanTests();
        testNoiseFloorVarianceCalculation();

        if (os_) *os_ << "success\n";
    }
    catch (exception& e)
    {
        TEST_FAILED(e.what())
    }
    catch (...)
    {
        TEST_FAILED("Caught unknown exception.")
    }

    TEST_EPILOG
}

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Variable Documentation

ostream* os_

Definition at line 37 of file FrequencyDataTest.cpp.

string filename1 = "FrequencyDataTest.output1.txt"

Definition at line 50 of file FrequencyDataTest.cpp.

Referenced by test(), testAddition(), testFind(), testNoiseFloor(), and validateWriteRead().