Calculating features

Usage

• Install the library with:

  pip install build
  python -m build
  

  Alternative:

  pip install pep517
  python -m pep517.build .
  

• Basic usage is:

from cr_features.helper_functions import empatica1d_to_array, convert_to2d, frequency_features, hrv_features, gsr_features
from cr_features.calculate_features import calculate_features
import pandas as pd

pathToHrvCsv = "example_data/S2_E4_Data/BVP.csv"
windowLength = 500

# get an array of values from HRV empatica file
hrv_data, startTimeStamp, sampleRate = empatica1d_to_array(pathToHrvCsv)

# Convert the HRV data into 2D array
hrv_data_2D = convert_to2d(hrv_data, windowLength)

# Create a list with feature names
featureNames = []
featureNames.extend(hrv_features)
featureNames.extend(frequency_features)

pd.set_option('display.max_columns', None)
 
# Calculate features
calculatedFeatures = calculate_features(hrv_data_2D, fs=int(sampleRate), feature_names=featureNames)

• More usage examples are located in usage_examples.ipynb file

Features

• Features are returned (from calculateFeatures() function) in a Pandas DataFrame object.
• In the case if a feature couldn't be calculated (for example, if input signal is invalid), NaN value is returned.
• Further in this section, the list with descriptions of all possible features is presented.

GSR features:

These features are useful for 1D GSR(EDA) signals

• mean: mean of the signal
• std: standard deviation of signal
• q25: 0.25 quantile
• q75: 0.75 quantile
• qd: q75 - q25
• deriv: sum of gradients of the signal
• power: power of the signal (mean of squared signal)
• numPeaks: number of EDA peaks
• ratePeaks: average number of peaks per second
• powerPeaks: power of peaks (mean of signal at indexes of peaks)
• sumPosDeriv: sum of positive derivatives divided by number of all derivatives
• propPosDeriv: proportion of positive derivatives per all derivatives
• derivTonic: sum of gradients of the tonic
• sigTonicDifference: mean of tonic subtracted from signal
• freqFeats:
• maxPeakAmplitudeChangeBefore: maximum peak amplitude change before peak
• maxPeakAmplitudeChangeAfter: maximum peak amplitude change after peak
• avgPeakAmplitudeChangeBefore: average peak amplitude change before peak
• avgPeakAmplitudeChangeAfter: average peak amplitude change after peak
• avgPeakChangeRatio: avg_peak_increase_time / avg_peak_decrease_time
• maxPeakIncreaseTime: maximum peak increase time
• maxPeakDecreaseTime: maximum peak decrease time
• maxPeakDuration: maximum peak duration
• maxPeakChangeRatio: max_peak_increase_time / max_peak_decrease_time
• avgPeakIncreaseTime: average peak increase time
• avgPeakDecreaseTime: average peak decreade time
• avgPeakDuration: average peak duration
• maxPeakResponseSlopeBefore: maximum peak response slope before peak
• maxPeakResponseSlopeAfter: maximum peak response slope after peak
• signalOverallChange: maximum difference between samples (max(sig)-min(sig))
• changeDuration: duration between maximum and minimum values
• changeRate: change_duration / signal_overall_change
• significantIncrease:
• significantDecrease:

HRV features:

These features are useful for 1D HRV(BVP) signals.

If number of RR intervals (numRR) is less than length of sample / (2 * sampling rate) (30 BPM) or greater than length of sample / (sampling rate / 4) (240 BPM), BPM value is incorrect and thus, all other HRV features are set to NaN.

• meanHr: mean heart rate
• ibi: mean interbeat interval
• sdnn: standard deviation of the ibi
• sdsd: standard deviation of the differences between all subsequent R-R intervals
• rmssd: root of the mean of the list of squared differences
• pnn20: the proportion of NN20 intervals to all intervals
• pnn50: the proportion of NN50 intervals to all intervals
• sd:
• sd2:
• sd1/sd2: sd / sd2 ratio
• numRR: number of RR intervals

Accelerometer features:

These features are useful for 3D signals from accelerometer

• meanLow: mean of low-pass filtered signal
• areaLow: area under the low-pass filtered signal
• totalAbsoluteAreaBand: sum of absolute areas under the band-pass filtered x, y and z signal
• totalMagnitudeBand: square root of sum of squared band-pass filtered x, y and z components
• entropyBand: entropy of band-pass filtered signal
• skewnessBand: skewness of band-pass filtered signal
• kurtosisBand: kurtosis of band-pass filtered signal
• postureDistanceLow: calculates difference between mean values for a given sensor (low-pass filtered)
• absoluteMeanBand: mean of band-pass filtered signal
• absoluteAreaBand: area under the band-pass filtered signal
• quartilesBand: quartiles of band-pass filtered signal
• interQuartileRangeBand: inter quartile range of band-pass filtered signal
• varianceBand: variance of band-pass filtered signal
• coefficientOfVariationBand: dispersion of band-pass filtered signal
• amplitudeBand: difference between maximum and minimum sample of band-pass filtered signal
• totalEnergyBand: total magnitude of band-pass filtered signal
• dominantFrequencyEnergyBand: ratio of energy in dominant frequency
• meanCrossingRateBand: the number of signal crossings with mean of band-pass filtered signal
• correlationBand: Pearson's correlation between band-pass filtered axis
• quartilesMagnitudesBand: quartiles at 25%, 50% and 75% per band-pass filtered signal
• interQuartileRangeMagnitudesBand: interquartile range of band-pass filtered signal
• areaUnderAccelerationMagnitude: area under acceleration magnitude
• peaksDataLow: number of peaks, sum of peak values, peak avg, amplitude avg
• sumPerComponentBand: sum per component of band-pass filtered signal
• velocityBand: velocity of the band-pass filtered signal
• meanKineticEnergyBand: mean kinetic energy 1/2*mV^2 of band-pass filtered signal
• totalKineticEnergyBand: total kinetic energy 1/2*mV^2 for all axes (band-pass filtered)
• squareSumOfComponent: squared sum of component
• sumOfSquareComponents: sum of squared components
• averageVectorLength: mean of magnitude vector
• averageVectorLengthPower: square mean of magnitude vector
• rollAvgLow: maximum difference of low-pass filtered roll samples
• pitchAvgLow: maximum difference of low-pass filtered pitch samples
• rollStdDevLow: standard deviation of roll (calculated from low-pass filtered signal)
• pitchStdDevLow: standard deviation of pitch (calculated from low-pass filtered signal)
• rollMotionAmountLow: amount of wrist roll (from low-pass filtered signal) motion
• rollMotionRegularityLow: regularity of wrist roll motion
• manipulationLow: manipulation of low-pass filtered signals
• rollPeaks: number of roll peaks, sum of roll peak values, roll peak avg, roll amplitude avg
• pitchPeaks: number of pitch peaks, sum of pitch peak values, pitch peak avg, pitch amplitude avg
• rollPitchCorrelation: correlation between roll and peak (obtained from low-pass filtered signal)

Gyroscope features:

These features are useful for 3D signals from gyroscope

• meanLow: mean of low-pass filtered signal
• areaLow: area under the low-pass filtered signal
• totalAbsoluteAreaLow: sum of absolute areas under the low-pass filtered x, y and z signal
• totalMagnitudeLow: square root of sum of squared band-pass filtered x, y and z components
• entropyLow: entropy of low-pass filtered signal
• skewnessLow: skewness of low-pass filtered signal
• kurtosisLow: kurtosis of low-pass filtered signal
• quartilesLow: quartiles of low-pass filtered signal
• interQuartileRangeLow: inter quartile range of low-pass filtered signal
• varianceLow: variance of low-pass filtered signal
• coefficientOfVariationLow: dispersion of low-pass filtered signal
• amplitudeLow: difference between maximum and minimum sample of low-pass filtered signal
• totalEnergyLow: total magnitude of low-pass filtered signal
• dominantFrequencyEnergyLow: ratio of energy in dominant frequency
• meanCrossingRateLow: the number of signal crossings with mean of low-pass filtered signal
• correlationLow: Pearson's correlation between low-pass filtered axis
• quartilesMagnitudeLow: quartiles at 25%, 50% and 75% per low-pass filtered signal
• interQuartileRangeMagnitudesLow: interquartile range of band-pass filtered signal
• areaUnderMagnitude: area under magnitude
• peaksCountLow: number of peaks in low-pass filtered signal
• averageVectorLengthLow: mean of low-pass filtered magnitude vector
• averageVectorLengthPowerLow: square mean of low-pass filtered magnitude vector

Generic features:

These are generic features, useful for many different types of signals

• autocorrelations: autocorrelations of the given signal with lags 5, 10, 20, 30, 50, 75 and 100
• countAboveMean: number of values in signal that are higher than the mean of signal
• countBelowMean: number of values in signal that are lower than the mean of signal
• maximum: maximum value of the signal
• minimum: minimum value of the signal
• meanAbsChange: the mean of absolute differences between subsequent time series values
• longestStrikeAboveMean: longest part of signal above mean
• longestStrikeBelowMean: longest part of signal below mean
• stdDev: standard deviation of the signal
• median: median of the signal
• meanChange: the mean over the differences between subsequent time series values
• numberOfZeroCrossings: number of crossings of signal on 0
• absEnergy: the absolute energy of the time series which is the sum over the squared values
• linearTrendSlope: a linear least-squares regression for the values of the time series versus the sequence from 0 to length of the time series minus one
• ratioBeyondRSigma: ratio of values that are more than r*std(x) (so r sigma) away from the mean of signal. r in this case is 2.5
• binnedEntropy: entropy of binned values
• numOfPeaksAutocorr: number of peaks of autocorrelations
• numberOfZeroCrossingsAutocorr: number of crossings of autocorrelations on 0
• areaAutocorr: area under autocorrelations
• calcMeanCrossingRateAutocorr: the number of autocorrelation crossings with mean
• countAboveMeanAutocorr: umber of values in signal that are higher than the mean of autocorrelation
• sumPer: sum per component
• sumSquared: squared sum per component
• squareSumOfComponent: square sum of component
• sumOfSquareComponents:sum of square components

Frequency features:

These are frequency features, useful for many different types of signals. The signal is converted to power spectral density signal and features are calculated on this signal

• fqHighestPeakFreqs: three frequencies corresponding to the largest peaks added to features
• fqHighestPeaks: three largest peaks added to features
• fqEnergyFeat: energy calculated as the sum of the squared FFT component magnitudes, and normalized
• fqEntropyFeat: entropy of the FFT of the signal
• fqHistogramBins: Binned distribution (histogram)
• fqAbsMean: absolute mean of the raw signal
• fqSkewness: skewness of the power spectrum of the data
• fqKurtosis: kurtosis of the power spectrum of the data
• fqInterquart: inter quartile range of the raw signal

Contributors

Several people contributed to making this library, both to its implemenetation and feature design: Vito Janko, Matjaž Bostič, Gašper Slapničar, Junoš Lukan, Nina Reščič, Simon Stankoski, Boža Cvetković, Mitja Luštrek