Package: heartpy
HeartPy - Python Heart Rate Analysis ToolkitLike HeartPy? Don't forget to leave a star!Structural updateHeartPy V1.2 has landed! The structure of the package has been reworked to be in separate modules now in preparation of the next big update, which will feature many analysis expansions and the first steps towards a GUI for HeartPy. HeartPy has been growing steadily and had reached the point where it became cluttered and unwieldy to keep in a single file. The API remains unchanged.An 'Examples' folder has been added to the repo which will be expanded soon. Now there's two notebooks explaining how to analyse ppg signals from smartwatches and smart rings.Colorblind support has been added, seethis notebook in the examples folderInstallationpython setup.py installAlternatively, we're also on PIP:python -m pip install heartpyThat's it! Note that Github always has the newest version.DocumentationThe official documentation is online!You can find the official documentation herePython 2.7The module compiles and and runs fine on Python 2.7,butthe some unit tests fail.Tutorial notebooks are now available in Examples/These show how to handle various analysis tasks with HeartPy, from smartwatch data, smart ring data, regular PPG, and regular (and very noisy) ECG. The notebooks sometimes don't render through the github engine, so either open them locally, or use an online viewer likenbviewer.We recommend you follow the notebooks in order:1. Analysing a PPG signal, a notebook for starting out with HeartPy using built-in examples.2. Analysing an ECG signal, a notebook for working with HeartPy and typical ECG data.3. Analysing smartwatch data, a notebook on analysing low resolution PPG data from a smartwatch.4. Analysing smart ring data, a notebook on analysing smart ring PPG data.5. Analysing noisy ECG data, an advanced notebook on working with very noisy ECG data, using data from the MIT-BIH noise stress test dataset.6. Colorblind mode - How To and StylesMore informationHeartPy, thePython Heart Rate Analysis Toolkitis a module for heart rate analysis in Python. It started as pure-python implementation to analyse physiological data taken in naturalistic driving and cycling experiments.The module takes a discrete heart rate signal and outputs time-domain and frequency-domain measures often found in scientific literature:Time domain:beats per minute, BPMinterbeat interval, IBIstandard deviation  if intervals between adjacent beats, SDNNstandard deviation of successive differences between adjacent R-R intervals, SDSDroot mean square of successive differences between adjacend R-R intervals, RMSSDproportion of differences between R-R intervals greater than 20ms, 50ms, pNN20, pNN50median absolute deviation, MADPoincare analysis (SD1, SD2, S, SD1/SD2)Poincare plottingFrequency domain (ranges per Shaffer and Ginsberg:https://doi.org/10.3389/fpubh.2017.00258)very low frequency component (0.0033â€“0.04â€‰Hz), VLFlow frequency component (0.04â€“0.15â€‰Hz), LFhigh frequency component (0.15â€“0.4â€‰Hz), HFlf/hf ratio, LF/HFWhen using the package in your research, please cite:van Gent, P., Farah, H., van Nes, N., & van Arem, B. (2019). Analysing Noisy Driver Physiology Real-Time Using Off-the-Shelf Sensors: Heart Rate Analysis Software from the Taking the Fast Lane Project. Journal of Open Research Software, 7(1), 32. DOI:http://doi.org/10.5334/jors.241van Gent, P., Farah, H., van Nes, N., & van Arem, B. (2019). HeartPy: A novel heart rate algorithm for the analysis of noisy signals. Transportation Research Part F: Traffic Psychology and Behaviour, 66, 368â€“378.https://doi.org/10.1016/j.trf.2019.09.015DocumentationYou can find the official documentation hereThe module is also to some extent described in my tutorial series:Analyzing a Discrete Heart Rate Signal Using Python - Part 1Analyzing a Discrete Heart Rate Signal Using Python - Part 2Analyzing a Discrete Heart Rate Signal Using Python - Part 3Analyzing a Discrete Heart Rate Signal Using Python - Part 4: in developmentLicenseThe module is licensed under theGNU General Public License Version3, GPL-v3ValidationInitial results of the validation have been reported in [1, 2].[1]van Gent, P., Farah, H., van Nes, N., & van Arem, B. (2018). Heart Rate Analysis for Human Factors: Development and Validation of an Open Source Toolkit for Noisy Naturalistic Heart Rate Data. In Proceedings of the 6th HUMANIST Conference (pp. 173â€“178).[2] van Gent, P., Farah, H., van Nes, N., & van Arem, B. (2019). HeartPy: A novel heart rate algorithm for the analysis of noisy signals. Transportation Research Part F: Traffic Psychology and Behaviour, 66, 368â€“378.https://doi.org/10.1016/j.trf.2019.09.015To-doThe module is still in active development. See the changelog for past changes. The to-do for the coming months is:to do before V1.3Same but for PPG - morphology too variable, method unstableAdd 'strictness parameter' to affect how HeartPy evaluates peaks for acceptance/rejectionAutoscale data during process() methodexpand enhance_peaks to only include those above a thresholdAdd method to handle NaN data automaticallyclean_rr method now removes incorrect values, update to allow for replacement by median of surrounding data pointsReport validation performance on repo (published paper + key-points document once published)Change backend structure in anticipation of GUI developmentDevelop GUI for HeartPy