heartpy
Python Heart Rate Analysis Package, for both PPG and ECG signals
Science Score: 33.0%
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Keywords
Repository
Python Heart Rate Analysis Package, for both PPG and ECG signals
Basic Info
Statistics
- Stars: 1,038
- Watchers: 25
- Forks: 337
- Open Issues: 22
- Releases: 3
Topics
Metadata Files
README.md
HeartPy - Python Heart Rate Analysis Toolkit
Like HeartPy? Don't forget to leave a star!
Structural update
HeartPy 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, see this notebook in the examples folder
Installation
python setup.py install
Alternatively, we're also on PIP:
python -m pip install heartpy
That's it! Note that Github always has the newest version.
Documentation
The official documentation is online! You can find the official documentation here
Python 2.7
The module compiles and and runs fine on Python 2.7, but the 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 like nbviewer.
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 Styles
More information
HeartPy, the Python Heart Rate Analysis Toolkit is 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, BPM * interbeat interval, IBI * standard deviation if intervals between adjacent beats, SDNN * standard deviation of successive differences between adjacent R-R intervals, SDSD * root mean square of successive differences between adjacend R-R intervals, RMSSD * proportion of differences between R-R intervals greater than 20ms, 50ms, pNN20, pNN50 * median absolute deviation, MAD * Poincare analysis (SD1, SD2, S, SD1/SD2) * Poincare plotting
Frequency domain (ranges per Shaffer and Ginsberg: https://doi.org/10.3389/fpubh.2017.00258) * very low frequency component (0.0033–0.04 Hz), VLF * low frequency component (0.04–0.15 Hz), LF * high frequency component (0.15–0.4 Hz), HF * lf/hf ratio, LF/HF
When 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.241
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, 368–378. https://doi.org/10.1016/j.trf.2019.09.015
Documentation
You can find the official documentation here
The module is also to some extent described in my tutorial series:
- Analyzing a Discrete Heart Rate Signal Using Python - Part 1
- Analyzing a Discrete Heart Rate Signal Using Python - Part 2
- Analyzing a Discrete Heart Rate Signal Using Python - Part 3
- Analyzing a Discrete Heart Rate Signal Using Python - Part 4: in development
License
The module is licensed under the MIT License
Validation
Initial 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. 173–178).
[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, 368–378. https://doi.org/10.1016/j.trf.2019.09.015
To-do
The module is still in active development. See the changelog for past changes. The to-do for the coming months is:
to do before V1.3 - [X] Same but for PPG - morphology too variable, method unstable - [ ] Add 'strictness parameter' to affect how HeartPy evaluates peaks for acceptance/rejection - [ ] Add method to handle NaN data automatically - [ ] clean_rr method now removes incorrect values, update to allow for replacement by median of surrounding data points - [ ] add method that can fill in missing R-peaks, settable to search for either local optimum OR mean imputation. - [ ] Report validation performance on repo (published paper + key-points document once published) - [ ] Change backend structure in anticipation of GUI development - [ ] Develop GUI for HeartPy
Owner
- Name: Paul van Gent
- Login: paulvangentcom
- Kind: user
- Company: Delft University of Technology
- Repositories: 8
- Profile: https://github.com/paulvangentcom
GitHub Events
Total
- Issues event: 1
- Watch event: 102
- Fork event: 19
Last Year
- Issues event: 1
- Watch event: 102
- Fork event: 19
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Paul van Gent | p****9@g****m | 284 |
| Constantino Álvarez | A****c | 14 |
| Andrew Davis | s****p@g****m | 14 |
| Arritmic | a****c@g****m | 12 |
| Jonathan | j****s@g****m | 3 |
| Igor | i****g | 3 |
| Manuel Meier | m****r@i****h | 3 |
| Alex Page | a****e@g****m | 2 |
| Manuel Meier | m****l@m****h | 2 |
| Kris | b****0@s****e | 1 |
| Glenn Fernandes | 1****f | 1 |
| Eeshan Gupta | e****5@g****m | 1 |
| Michael Gathara | m****m@g****m | 1 |
| Andrew Davis | A****s | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 88
- Total pull requests: 20
- Average time to close issues: about 2 months
- Average time to close pull requests: 3 months
- Total issue authors: 61
- Total pull request authors: 12
- Average comments per issue: 2.34
- Average comments per pull request: 1.0
- Merged pull requests: 15
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: about 1 hour
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 0.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- paulvangentcom (9)
- FrancoisCosta (6)
- sedurCode (3)
- meierman1 (3)
- mshafieluru (2)
- sakluk (2)
- PartyTrix (2)
- talhaanwarch (2)
- yurasmol (2)
- saranzeb (2)
- christianschneebeli (2)
- kmf909 (2)
- abdulkhaliq7 (2)
- renatosc (2)
- vishakha18tiwari (1)
Pull Request Authors
- AndrewDDavis (5)
- meierman1 (3)
- Arritmic (3)
- IgorWounds (2)
- atpage (1)
- KrisITB (1)
- J535D165 (1)
- eeshan9815 (1)
- Michaelgathara (1)
- igrowing (1)
- glenn124f (1)
- koenraijer (1)
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Packages
- Total packages: 1
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Total downloads:
- pypi 5,314 last-month
- Total docker downloads: 37
- Total dependent packages: 12
- Total dependent repositories: 42
- Total versions: 11
- Total maintainers: 1
pypi.org: heartpy
Heart Rate Analysis Toolkit
- Homepage: https://github.com/paulvangentcom/heartrate_analysis_python
- Documentation: https://heartpy.readthedocs.io/
- License: GNU General Public License (GPL)
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Latest release: 1.2.7
published almost 5 years ago
Rankings
Maintainers (1)
Dependencies
- cycler ==0.10.0
- kiwisolver ==1.1.0
- matplotlib <=3.1.2
- matplotlib <=3.0.0
- matplotlib <=2.2.3
- matplotlib *
- matplotlib <=3.3.4
- matplotlib ==2.2.3
- numpy >=1.17
- numpy <=1.15
- numpy <=1.17
- pyparsing ==2.4.7
- scipy <=1.1.0
- scipy *
- scipy <=1.2.0
- scipy <=1.4.1