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#include <cppunit/extensions/HelperMacros.h>
#include "cppUnitHelper.hxx"
#include "similarityHelper.hxx"
#include "Spectrum.hxx"
#include "SpectralAnalysisExampleHelper.hxx"
#include "SpectralPeakDetectExampleHelper.hxx"
#include "SpectralPeakArray.hxx"
#include "SpectralPeakDetect.hxx"
#include "XMLStorage.hxx"
#include <fstream>
namespace CLAMTest
{
class SpectralPeakDetectFunctionalTest;
CPPUNIT_TEST_SUITE_REGISTRATION( SpectralPeakDetectFunctionalTest );
class SpectralPeakDetectFunctionalTest
: public CppUnit::TestFixture
{
CPPUNIT_TEST_SUITE( SpectralPeakDetectFunctionalTest );
CPPUNIT_TEST( test_ProofOfConcept );
CPPUNIT_TEST( test_DetectsSamePeaksFromNoiseSignal );
CPPUNIT_TEST_SUITE_END();
protected:
static double smSimilarityThreshold;
static bool smBack2BackDataLoaded;
static CLAM::SpectralPeakArray smReferenceSpectralPeakArray;
static CLAM::Spectrum smReferenceSpectrum;
static CLAMExamples::SpectralPeaksSet smReferenceSpectralPeaksSet;
std::string mPathToTestData;
protected: // Auxiliary methods
static void loadBack2BackDataset( const std::string& pathToTestData )
{
if ( !smBack2BackDataLoaded )
{
CLAM::XMLStorage::Restore( smReferenceSpectralPeakArray,
pathToTestData + "OneSineSpectrum_RectWindow_P2_Peaks.xml" );
CLAM::XMLStorage::Restore( smReferenceSpectrum,
pathToTestData + "OneSineSpectrum_RectWindow_P2.xml" );
CLAM::XMLStorage::Restore( smReferenceSpectralPeaksSet,
pathToTestData + "DetectedPeaks_0001.xml" );
smBack2BackDataLoaded = true;
}
}
public:
void setUp()
{
mPathToTestData = GetTestDataDirectory("spectralData/");
loadBack2BackDataset( mPathToTestData );
}
void tearDown()
{
}
private:
void test_ProofOfConcept()
{
CLAM::SpectralPeakArray detectedPeaks;
detectedPeaks.SetScale( CLAM::EScale::eLog );
CLAM::SpectralPeakDetectConfig processingConfig; // default
CLAM::SpectralPeakDetect processing;
smReferenceSpectrum.ToDB();
processing.Configure( processingConfig );
// (*processing.GetInPorts().Begin())->Attach( smReferenceSpectrum );
// (*processing.GetOutPorts().Begin())->Attach( detectedPeaks );
processing.Start();
processing.Do( smReferenceSpectrum, detectedPeaks );
processing.Stop();
CLAM::DataArray flattenedReference;
CLAM::DataArray flattenedResult;
flattenSpectralPeakArray( smReferenceSpectralPeakArray,
flattenedReference );
flattenSpectralPeakArray( detectedPeaks,
flattenedResult );
double similarity = evaluateSimilarity( flattenedReference,
flattenedResult );
// We dump the detected peaks if the similitude between
// the reference dataset and the detected peaks is outside
// our confidence interval
if ( smSimilarityThreshold > similarity )
{
/*
CLAMVM::SpectrumAndPeaksPlot refDataPlot( "plot_1" );
refDataPlot.SetPosition( 0, 100 );
refDataPlot.SetSize( 300, 300 );
refDataPlot.SetYRange( -80, 500 );
refDataPlot.SetLabel( "Reference dataset results" );
refDataPlot.SetData( smReferenceSpectrum,
smReferenceSpectralPeakArray );
CLAMVM::SpectrumAndPeaksPlot actualDataPlot( "plot_2" );
actualDataPlot.SetPosition( 320, 100 );
actualDataPlot.SetSize( 300, 300 );
actualDataPlot.SetYRange( -80, 500 );
actualDataPlot.SetLabel( "Obtained peaks" );
actualDataPlot.SetData( smReferenceSpectrum,
detectedPeaks );
CLAMVM::SystemPlots::DisplayAll();
*/
CLAM::XMLStorage::Dump( detectedPeaks,
"PeaksFailedToPassTest",
"detectedPeaks_ProofOfConcept.xml" );
}
CPPUNIT_ASSERT( smSimilarityThreshold <= similarity );
}
void test_DetectsSamePeaksFromNoiseSignal()
{
// Load spectral analysis needed for repeating the peak detection
// process
CLAMExamples::SpectralAnalysis specAnalysis;
CLAM::XMLStorage::Restore( specAnalysis,
mPathToTestData+smReferenceSpectralPeaksSet.GetSpectralAnalysis() );
CLAM::SpectralPeakDetect peakDetector;
peakDetector.Configure( smReferenceSpectralPeaksSet.GetPeakDetectionSettings() );
CLAMExamples::SpectralPeaksSet detectedPeaks;
CLAM::SpectralPeakArray tmpPeakArray;
tmpPeakArray.SetScale( CLAM::EScale::eLog );
peakDetector.Start();
CLAMExamples::SpectralAnalysis::FramesContainer::iterator i =
specAnalysis.GetResultingFrames().begin();
while( i!= specAnalysis.GetResultingFrames().end() )
{
i->ToDB();
peakDetector.Do( *i, tmpPeakArray );
detectedPeaks.GetDetectedPeaks().push_back( tmpPeakArray );
i++;
}
peakDetector.Stop();
// Let's check that the detected peaks resemble the reference peaks
std::ofstream log;
log.open( "TestSpectralPeakDetect_DetectsSamePeaksFromNoiseSignal.log" );
CLAMExamples::SpectralPeaksSet::SpectralPeaksList::iterator k =
smReferenceSpectralPeaksSet.GetDetectedPeaks().begin();
CLAMExamples::SpectralPeaksSet::SpectralPeaksList::iterator l =
detectedPeaks.GetDetectedPeaks().begin();
bool everythingWentOK = true;
int frameCounter = 0;
while ( k != smReferenceSpectralPeaksSet.GetDetectedPeaks().end()
&& l != detectedPeaks.GetDetectedPeaks().end() )
{
CLAM::DataArray flattenedReference;
CLAM::DataArray flattenedResult;
flattenSpectralPeakArray( *k,
flattenedReference );
flattenSpectralPeakArray( *l,
flattenedResult );
try
{
double similarity = evaluateSimilarity( flattenedReference,
flattenedResult );
if ( smSimilarityThreshold > similarity )
{
log << "Frame #" << frameCounter << ": Was dissimilar ";
log << "similarity index was " << similarity*100. << "%" << std::endl;
everythingWentOK = false;
}
}
catch( CLAMTest::DataSizeMismatch& error )
{
log << "Frame #" << frameCounter << ": Could not be compared ";
log << "revise spectral peak arrays visually" << std::endl;
everythingWentOK = false;
}
frameCounter++;
k++;
l++;
}
if ( frameCounter != smReferenceSpectralPeaksSet.GetDetectedPeaks().size() )
{
log << "there was a difference of ";
log << smReferenceSpectralPeaksSet.GetDetectedPeaks().size() - frameCounter;
log << " between reference peaks in frame list and the actual" << std::endl;
}
log.close();
CPPUNIT_ASSERT_EQUAL( true, everythingWentOK );
}
};
double SpectralPeakDetectFunctionalTest::smSimilarityThreshold = 0.9999;
bool SpectralPeakDetectFunctionalTest::smBack2BackDataLoaded = false;
CLAM::Spectrum SpectralPeakDetectFunctionalTest::smReferenceSpectrum;
CLAM::SpectralPeakArray SpectralPeakDetectFunctionalTest::smReferenceSpectralPeakArray;
CLAMExamples::SpectralPeaksSet SpectralPeakDetectFunctionalTest::smReferenceSpectralPeaksSet;
}
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