ECGController::ECGController (void) :
ecg_baseline_module(new BaselineRemoval()),
rpeaks_module(new RPeaksDetector()),
hrv1_module(new HRV1Analyzer())
{
TRI_LOG_STR("ECGController created, 20:51 17-12-2012");
//TODO: create modules objects
}
void ECGController::setWavesNotRun()
{
TRI_LOG_STR(__FUNCTION__);
waves_module->run_ = false;
setQRSClassNotRun();
setSTIntervalNotRun();
setTwaveAltNotRun();
setHRTNotRun();
LOG_END
}
void ECGController::setRPeaksNotRun()
{
TRI_LOG_STR(__FUNCTION__);
rpeaks_module->run_ = false;
setHRTNotRun();
setWavesNotRun();
setHRV1NotRun();
setHRV2NotRun();
setHRVDFANotRun();
LOG_END
}
void ECGController::runHRVDFA ()
{
TRI_LOG_STR(__FUNCTION__);
if (!rpeaks_module->run_)
{
runRPeaks();
}
hrv_dfa_module->runModule(r_peaks_data, hrv_dfa_data);
hrv_dfa_module->run_ = true;
LOG_END
}
void ECGController::runRPeaks ()
{
TRI_LOG_STR(__FUNCTION__);
if (!ecg_baseline_module->run_)
{
runECGBaseline();
}
rpeaks_module->runModule(filtered_signal, ecg_info, r_peaks_data);
rpeaks_module->run_ = true;
LOG_END
}
void ECGController::setECGBaselineNotRun()
{
TRI_LOG_STR(__FUNCTION__);
ecg_baseline_module->run_ = false;
setRPeaksNotRun();
setQRSClassNotRun();
setSTIntervalNotRun();
setTwaveAltNotRun();
setHRTNotRun();
setWavesNotRun();
LOG_END
}
bool ECGController::readFile(std::string filename)
{
TRI_LOG_STR(__FUNCTION__);
//check filename to be correct with WFDB
int pos;
if ((pos = filename.find('.')) != std::string::npos)
{
filename = filename.substr(0, pos);
}
int nr_samples;
size_t i;
WFDB_Sample v[2];
WFDB_Siginfo s[2];
if (isigopen(const_cast<char*> (filename.c_str()), s, 2) < 2)
{
TRI_LOG_STR("File");
TRI_LOG(filename);
TRI_LOG_STR("Not loaded");
LOG_END
return false;
}
void ECGController::runTwaveAlt ()
{
TRI_LOG_STR(__FUNCTION__);
if (!ecg_baseline_module->run_)
{
runECGBaseline();
}
if (!waves_module->run_)
{
runWaves();
}
t_wave_alt_module->runModule(waves_data, filtered_signal, ecg_info, twave_data);
t_wave_alt_module->run_ = true;
LOG_END
}
void ECGController::runSTInterval ()
{
TRI_LOG_STR(__FUNCTION__);
if (!ecg_baseline_module->run_)
{
runECGBaseline();
}
if (!waves_module->run_)
{
runWaves();
}
st_interval_module->runModule(waves_data, filtered_signal, ecg_info, st_data);
st_interval_module->run_ = true;
LOG_END
}
void ECGController::runQRSClass ()
{
TRI_LOG_STR(__FUNCTION__);
if (!ecg_baseline_module->run_)
{
runECGBaseline();
}
if (!waves_module->run_)
{
runWaves();
}
qrs_class_module->runModule(waves_data, filtered_signal, ecg_info, classes_data);
qrs_class_module->run_ = true;
LOG_END
}
b2Fixture* BodyWrapper::LookUpFixture( const std::string& fixtureName ) const
{
FixtureMap::const_iterator iter = _fixtureMap.find( fixtureName );
if( iter != _fixtureMap.end() )
{
return iter->second.fixture;
}
else
{
TRI_LOG_STR("Unable to find fixture.");
TRI_LOG(fixtureName);
}
return nullptr;
}
ECGController::~ECGController (void)
{
TRI_LOG_STR("ECGController destroyed");
}
void ECGController::setHRTNotRun()
{
TRI_LOG_STR(__FUNCTION__);
hrt_module->run_ = false;
LOG_END
}
void ECGController::setTwaveAltNotRun()
{
TRI_LOG_STR(__FUNCTION__);
t_wave_alt_module->run_ = false;
LOG_END
}
void ECGController::setSTIntervalNotRun()
{
TRI_LOG_STR(__FUNCTION__);
st_interval_module->run_ = false;
LOG_END
}
void RPeaksDetector::setParams(ParametersTypes ¶meterTypes)
{
TRI_LOG_STR(__FUNCTION__);
if(parameterTypes.find("detection_method") != parameterTypes.end())
{
int method = (int)parameterTypes["detection_method"];
if(method == 0)
{
this->detectionMethod = HILBERT;
}
else if(method == 1)
{
this->detectionMethod = PAN_TOMPKINS;
}
else
{
#ifdef DEBUG
qDebug() << "Unknown detection method";
#endif
TRI_LOG_STR("Unknown detection method.");
throw new RPeaksDetectionException("Unknown detection method.");
}
}
else {
#ifdef DEBUG
qDebug() << "Parameter: detection method not found";
#endif
TRI_LOG_STR("Parameter: detection method not found");
throw new RPeaksDetectionException("Parameter: detection method not found");
}
if(parameterTypes.find("window_size") != parameterTypes.end())
{
this->panTompkinsMovinghWindowLenght = (int)parameterTypes["window_size"];
}
else {
#ifdef DEBUG
qDebug() << "Window size not found, use automatic calculated value";
#endif
}
if(parameterTypes.find("threshold_size") != parameterTypes.end())
{
panTompkinsThershold = parameterTypes["threshold_size"];
}
else {
#ifdef DEBUG
qDebug() << "Thersold size not found, use automatic calculated value";
#endif
}
this->customParameters = true;
#ifdef DEBUG
cout << "Input parameters for R peaks module:" << endl;
if(this->detectionMethod == PAN_TOMPKINS)
{
qDebug() << "Detection method: PanTompkins" << endl
<< "Moving window size: " << this->panTompkinsMovinghWindowLenght << endl
<< "Thersold size: " << panTompkinsThershold;
}
else if (this->detectionMethod == HILBERT)
{
qDebug() << "Detection method: Hilbert";
}
else
{
qDebug() << "Unknown detection method";
}
#endif
LOG_END;
}
bool RPeaksDetector::panTompkinsRPeaksDetection(ECGSignalChannel *signal)
{
TRI_LOG_STR(__FUNCTION__);
ECGSignalChannel sig;
sig = *signal;
int sigSize = 0;
if(sig->signal->size < 1)
{
#ifdef DEBUG
qDebug() << "Input signal size is 0";
#endif
TRI_LOG_STR("Input signal size is 0");
return false;
}
else
{
sigSize = sig->signal->size;
#ifdef DEBUG_SIGNAL
qDebug() << "Input signal";
for(int i = 0; i < sigSize; i++)
{
double inputValue = gsl_vector_get (sig->signal, i);
qDebug() << inputValue;
}
#endif
}
//Convolution [-0.125 -0.25 0.25 0.125] (Here we lose 4 signal samples)
#ifdef DEBUG
qDebug() << "Convolution [-0.125 -0.25 0.25 0.125]" << endl << "Orginal signal size: " << sigSize;
#endif
int newSigSize = 0;
ECGSignalChannel diffSig;
diffSig = ECGSignalChannel(new WrappedVector);
diffSig->signal = gsl_vector_alloc(sigSize);
double filter[] = {-0.125, -0.25, 0.25, 0.125};
int filterSize = 4;
for(int i = 0; i < sigSize - filterSize; i++)
{
double tmpSum = 0;
for(int j = 0; j < filterSize; j++)
{
double inputValue = gsl_vector_get (sig->signal, i + j);
tmpSum += inputValue * filter[j];
#ifdef DEBUG_SIGNAL_DETAILS
qDebug() << "Signal: " << inputValue << " Filter: " << filter[j] << " Sum: " << tmpSum;
#endif
}
#ifdef DEBUG_SIGNAL
qDebug() << "Final val: " << tmpSum << " at index: " << i;
#endif
gsl_vector_set(diffSig->signal, i, tmpSum);
newSigSize++;
}
//Exponentiation
sigSize = newSigSize;
#ifdef DEBUG
qDebug() << "Exponentiation ^2" << endl << "Signal size after convolution: " << sigSize;
#endif
ECGSignalChannel powSig;
powSig = ECGSignalChannel(new WrappedVector);
powSig->signal = gsl_vector_alloc(sigSize);
for(int i = 0; i < sigSize; i++)
{
double inputValue = gsl_vector_get (diffSig->signal, i);
double powVal = pow(inputValue, 2);
gsl_vector_set(powSig->signal, i, powVal);
#ifdef DEBUG_SIGNAL
qDebug() << " Pow: "<< powVal << " at index: " << i;
#endif
}
//Calculae moving window lenght or use custom value
// N=30 for f=200Hz - from literature
// N=24 for f=360Hz - from literature and tests
// Linear function for calculating window lenght
// wl = -0.0375 * fs + 37.5
if(panTompkinsMovinghWindowLenght == 0)
{
panTompkinsMovinghWindowLenght = -0.0375 * signalFrequency + 37.5;
}
//Moving window integration (Here we lose "movinghWindowLenght" signal samples)
#ifdef DEBUG
qDebug() << "Moving window integration" << endl << "Window size: " << panTompkinsMovinghWindowLenght << endl
<< "Signal size after exponentiation: " << sigSize;
#endif
ECGSignalChannel integrSig;
integrSig = ECGSignalChannel(new WrappedVector);
integrSig->signal = gsl_vector_alloc(sigSize);
newSigSize = 0;
int movinghWindowLenght = panTompkinsMovinghWindowLenght;
double tmpSum = 0;
for(int i = movinghWindowLenght; i < sigSize; i++)
{
for(int j = movinghWindowLenght - 1; j >= 0 ; j--)
{
double inputValue = gsl_vector_get (powSig->signal, i - j);
tmpSum += inputValue;
#ifdef DEBUG_SIGNAL_DETAILS
qDebug() << "Signal: " << inputValue << " Sum: " << tmpSum;
#endif
}
int index = i - movinghWindowLenght;
// TODO Why this is not working? (To small values and all are save as zero)
//double mwico = (1/movinghWindowLenght) * tmpSum;
double mwico = tmpSum;
#ifdef DEBUG_SIGNAL
qDebug() << "Final val: " << mwico << " at index: " << index;
#endif
gsl_vector_set(integrSig->signal, index, mwico);
tmpSum = 0;
newSigSize++;
}
//Calculating detection threshold
//TODO (Not important now) Try to find another way to calcutale threshold position, maybe dynamic threshold?
sigSize = newSigSize;
#ifdef DEBUG
qDebug() << "Calculating detection threshold" << endl << "After moving window integration signal size: " << sigSize;
#endif
double sigMaxVal = 0;
double meanVal = 0;
for(int i = 0; i < sigSize; i++)
{
double inputValue = gsl_vector_get (integrSig->signal, i);
if(inputValue > sigMaxVal)
{
sigMaxVal = inputValue;
#ifdef DEBUG_SIGNAL
qDebug() << "New max signal value: " << inputValue;
#endif
}
meanVal += inputValue;
}
meanVal = meanVal / sigSize;
#ifdef DEBUG
qDebug() << "Final max value for channel one: " << sigMaxVal << endl
<< "Final mean value: " << meanVal << endl;
#endif
// Select automatic or manual thersold
double threshold = 0;
if( this->panTompkinsThershold == 0)
{
threshold = meanVal + (sigMaxVal * 0.04);
}
else
{
threshold = this->panTompkinsThershold;
}
//Looking for points over thersold
#ifdef DEBUG
qDebug() << "Current thresold value: " << threshold << endl << "Looking for points over thersold";
#endif
ECGSignalChannel overThersold;
overThersold = ECGSignalChannel(new WrappedVector);
overThersold->signal = gsl_vector_alloc(sigSize);
for(int i = 0; i < sigSize; i++)
{
double inputValue = gsl_vector_get (integrSig->signal, i);
if(inputValue > threshold * sigMaxVal)
{
gsl_vector_set(overThersold->signal, i, 1);
#ifdef DEBUG_SIGNAL
qDebug() << "Value over thersold at index: " << i;
#endif
}
else
{
gsl_vector_set(overThersold->signal, i, 0);
}
}
#ifdef DEBUG_SIGNAL
qDebug() << "Signal with points over thersold";
for(int i = 0; i < sigSize; i++)
{
qDebug() << gsl_vector_get(overThersold->signal, i);
}
#endif
#ifdef DEBUG
qDebug() << "Detect begin and end of QRS complex";
#endif
ECGSignalChannel leftPoints;
ECGSignalChannel tmpRightPoints;
leftPoints = ECGSignalChannel(new WrappedVector);
tmpRightPoints = ECGSignalChannel(new WrappedVector);
leftPoints->signal = gsl_vector_alloc(sigSize);
tmpRightPoints->signal = gsl_vector_alloc(sigSize);
int leftPointsCount = 0;
int rightPointsCount = 0;
gsl_vector* copiedSig = gsl_vector_calloc(sigSize);
gsl_vector_memcpy(copiedSig, overThersold->signal);
// Boundary values
if(gsl_vector_get (copiedSig, 0) == 1)
{
gsl_vector_set(leftPoints->signal, leftPointsCount, 0);
leftPointsCount++;
#ifdef DEBUG_SIGNAL
qDebug() << "QRS complex left point at index: " << 0;
#endif
}
if(gsl_vector_get (copiedSig, sigSize - 1) == 1)
{
gsl_vector_set(tmpRightPoints->signal, rightPointsCount, sigSize - 1);
rightPointsCount++;
#ifdef DEBUG_SIGNAL
qDebug() << "QRS complex right point at index: " << sigSize - 1;
#endif
}
// Left points of QRS complex
for(int i = 0; i < sigSize - 1; i++)
{
double inputValue = gsl_vector_get (copiedSig, i);
double inputValueIndexPlus = gsl_vector_get (copiedSig, i + 1);
if((inputValueIndexPlus - inputValue) == 1)
{
gsl_vector_set(leftPoints->signal, leftPointsCount, i);
leftPointsCount++;
#ifdef DEBUG_SIGNAL
qDebug() << "QRS complex left point at index: " << i;
#endif
}
}
// Rights points of QRS complex
for(int i = sigSize - 1; i > 0; i--)
{
double reversedInput = gsl_vector_get(copiedSig, i);
double reversedInputIndexMinus = gsl_vector_get (copiedSig, i - 1);
if((reversedInputIndexMinus - reversedInput) == 1)
{
gsl_vector_set(tmpRightPoints->signal, rightPointsCount, i);
rightPointsCount++;
#ifdef DEBUG_SIGNAL
qDebug() << "QRS complex right at index: " << i;
#endif
}
}
#ifdef DEBUG_SIGNAL
cout << "Vector with left points:" << endl;
for(int i = 0; i < leftPointsCount; i++)
{
qDebug() << gsl_vector_get(leftPoints->signal, i);
}
qDebug() << endl << "Vector with right points:";
for(int i = 0; i < rightPointsCount; i++)
{
qDebug() << gsl_vector_get(tmpRightPoints->signal, i);
}
cout << endl;
#endif
// Invert vector with rightPoints
ECGSignalChannel rightPoints;
rightPoints = ECGSignalChannel(new WrappedVector);
rightPoints->signal = gsl_vector_alloc(sigSize);
for(int i = 0; i < rightPointsCount; i++)
{
double tmp = gsl_vector_get(tmpRightPoints->signal, rightPointsCount - i - 1);
gsl_vector_set(rightPoints->signal, i, tmp );
}
for(int i = 0; i < rightPointsCount; i++)
{
double tmp = gsl_vector_get(tmpRightPoints->signal, rightPointsCount - i - 1);
gsl_vector_set(rightPoints->signal, i, tmp );
}
#ifdef DEBUG_SIGNAL
qDebug() << "After vector invertion" << endl;
qDebug() << "Vector with left points:" << endl;
for(int i = 0; i < leftPointsCount; i++)
{
qDebug() << gsl_vector_get(leftPoints->signal, i);
}
qDebug() << endl << "Vector with right points:" << endl;
for(int i = 0; i < rightPointsCount; i++)
{
qDebug() << gsl_vector_get(rightPoints->signal, i);
}
#endif
#ifdef DEBUG
qDebug() << "Number of left points: " << leftPointsCount << endl
<< "Number of right points: " << rightPointsCount;
#endif
//Final R peaks detection
#ifdef DEBUG
qDebug() << "Final R peaks detection";
#endif
int partLength;
IntSignal rs;
int numberRs = 0;
if(leftPointsCount > 0 )
{
rs = IntSignal(new WrappedVectorInt);
rs->signal = gsl_vector_int_alloc(leftPointsCount);
for(int i = 0; i < leftPointsCount; i++)
{
partLength = gsl_vector_get (rightPoints->signal, i) - gsl_vector_get(leftPoints->signal, i);
double tmpMax = 0;
int tmpMaxIndex = 0;
for(int j = 0; j < partLength; j++)
{
int sigIndex = gsl_vector_get (leftPoints->signal, i) + j;
double sigVal = gsl_vector_get(sig->signal, sigIndex);
if(sigVal > tmpMax)
{
tmpMax = sigVal;
tmpMaxIndex = sigIndex;
}
}
gsl_vector_int_set(rs->signal, i, tmpMaxIndex);
numberRs++;
#ifdef DEBUG_SIGNAL
qDebug() << "R point at index: " << tmpMaxIndex
<< " signal value: " << gsl_vector_get(sig->signal, tmpMaxIndex);
#endif
}
rsPositions->setRs(rs);
#ifdef DEBUG
qDebug() << "Number of detected R-peaks:" << numberRs;
#endif
}
else
{
#ifdef DEBUG
qDebug() << "R peaks not detected. Check input signal.";
#endif
TRI_LOG_STR("R peaks not detected. Check input signal.");
return false;
}
gsl_vector_free(copiedSig);
rsDetected = true;
#ifdef DEBUG
qDebug() << "Done";
#endif
LOG_END;
return true;
}
