systole

… image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3607912.svg :target: https://doi.org/10.5281/zenodo.3607912

… image:: https://img.shields.io/badge/License-Apache 2.0-blue.svg :target: https://github.com/embodied-computation-group/systole/blob/master/LICENSE

… image:: https://img.shields.io/pypi/v/systole-core :target: https://pypi.org/project/systole-core/

… image:: https://github.com/embodied-computation-group/systole/actions/workflows/test.yml/badge.svg :target: https://github.com/embodied-computation-group/systole/actions/workflows/test.yml

… image:: https://joss.theoj.org/papers/10.21105/joss.03832/status.svg :target: https://doi.org/10.21105/joss.03832

… image:: https://codecov.io/gh/embodied-computation-group/systole/branch/master/graph/badge.svg :target: https://codecov.io/gh/embodied-computation-group/systole

… image:: https://img.shields.io/badge/code style-black-000000.svg :target: https://github.com/psf/black

… image:: https://img.shields.io/badge/ imports-isort-%231674b1?style=flat&labelColor=ef8336 :target: https://pycqa.github.io/isort/

… image:: https://img.shields.io/badge/mypy-checked-blue.svg :target: https://mypy-lang.org/

… image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white :target: https://github.com/pre-commit/pre-commit

================

… image:: https://raw.githubusercontent.com/embodied-computation-group/systole/master/docs/source/images/logo.png :align: center

================

Systole is an open-source Python package implementing simple tools for working with cardiac signals for psychophysiology research. In particular, the package provides tools to pre-process, visualize, and analyze cardiac data. This includes tools for data epoching, artefact detection, artefact correction, evoked heart rate analyses, heart rate variability analyses, circular statistical approaches to analysing cardiac cycles, and synchronising stimulus presentation with different cardiac phases via Psychopy.

The documentation can be found under the following link <https://www.the-ecg.org/systole/>_.

If you have questions, please open an issue on the issue tracker <https://github.com/embodied-computation-group/systole/issues>_.

… note::

This repository is the official version of Systole, maintained by the Embodied Computation Group, and is the version used by Cardioception <https://github.com/embodied-computation-group/Cardioception>_.

How to cite? ++++++++++++

If you are using Systole in a publication we ask you to cite the following paper::

Legrand, N. & Allen, M., (2022). Systole: A python package for cardiac signal synchrony and analysis. Journal of Open Source Software, 7(69), 3832, https://doi.org/10.21105/joss.03832

Installation ++++++++++++

Systole can be installed using pip:

… code-block:: shell

pip install systole-core

… note::

The distribution is named systole-core on PyPI, but the package is still imported as systole::

 import systole

The following packages are required to use Systole:

• Numpy <https://numpy.org/>_ (>=1.21)
• SciPy <https://www.scipy.org/>_ (>=1.3.0)
• Pandas <https://pandas.pydata.org/>_ (>=0.24)
• Numba <http://numba.pydata.org/>_ (>=0.58.0)
• Seaborn <https://seaborn.pydata.org/>_ (>=0.9.0)
• Matplotlib <https://matplotlib.org/>_ (>=3.0.2)
• Bokeh <https://docs.bokeh.org/en/latest/index.html#>_ (>=3.0.0)
• Jinja2 <https://jinja.palletsprojects.com/>_ (>=3.0)
• pyserial <https://pyserial.readthedocs.io/en/latest/pyserial.html>_ (>=3.4)
• setuptools <https://setuptools.pypa.io/en/latest/>_ (>=38.4)
• requests <https://docs.python-requests.org/en/latest/>_ (>=2.26.0)
• tabulate <https://github.com/astanin/python-tabulate/>_ (>=0.8.9)
• sleepecg <https://github.com/cbrnr/sleepecg>_ (>=0.5.1)
• joblib <https://joblib.readthedocs.io/>_ (>=1.3.2)
• tqdm <https://tqdm.github.io/>_
• packaging <https://packaging.pypa.io/>_

The Python version should be 3.7 or higher.

Tutorials

For an introduction to Systole and cardiac signal analysis, you can refer to the following tutorial:

… list-table:: :widths: 60 40 :header-rows: 0 :align: center

• • Cardiac signal analysis
  • |Colab badge 1|
• • Detecting cardiac cycles
  • |Colab badge 2|
• • Detecting and correcting artefats
  • |Colab badge 3|
• • Heart rate variability
  • |Colab badge 4|
• • Instantaneous and evoked heart rate
  • |Colab badge 5|
• • Working with BIDS folders
  • |Colab badge 6|

… |Colab badge 1| image:: https://colab.research.google.com/assets/colab-badge.svg :target: https://colab.research.google.com/github/embodied-computation-group/systole/blob/master/docs/source/notebooks/1-PhysiologicalSignals.ipynb

… |Colab badge 2| image:: https://colab.research.google.com/assets/colab-badge.svg :target: https://colab.research.google.com/github/embodied-computation-group/systole/blob/master/docs/source/notebooks/2-DetectingCycles.ipynb

… |Colab badge 3| image:: https://colab.research.google.com/assets/colab-badge.svg :target: https://colab.research.google.com/github/embodied-computation-group/systole/blob/master/docs/source/notebooks/3-DetectingAndCorrectingArtefacts.ipynb

… |Colab badge 4| image:: https://colab.research.google.com/assets/colab-badge.svg :target: https://colab.research.google.com/github/embodied-computation-group/systole/blob/master/docs/source/notebooks/4-HeartRateVariability.ipynb

… |Colab badge 5| image:: https://colab.research.google.com/assets/colab-badge.svg :target: https://colab.research.google.com/github/embodied-computation-group/systole/blob/master/docs/source/notebooks/5-InstantaneousHeartRate.ipynb

… |Colab badge 6| image:: https://colab.research.google.com/assets/colab-badge.svg :target: https://colab.research.google.com/github/embodied-computation-group/systole/blob/master/docs/source/notebooks/6-WorkingWithBIDSFolders.ipynb

Getting started +++++++++++++++

… code-block:: python

from systole import import_dataset1

Import ECg recording

signal = import_dataset1(modalities=[‘ECG’]).ecg.to_numpy()

Signal extraction and interactive plotting

The package integrates a set of functions for interactive or non interactive data visualization based on Matplotlib <https://matplotlib.org/>_ and Bokeh <https://docs.bokeh.org/en/latest/index.html#>_.

… code-block:: python

from systole.plots import plot_raw

plot_raw(signal[60000 : 120000], modality=“ecg”, backend=“bokeh”, show_heart_rate=True, show_artefacts=True, figsize=300)

… image:: https://raw.githubusercontent.com/embodied-computation-group/systole/master/docs/source/images/raw.png :align: center

Artefacts detection and rejection

Artefacts can be detected and corrected in the RR interval time series or the peaks vector using the method proposed by Lipponen & Tarvainen (2019).

… code-block:: python

from systole.detection import ecg_peaks from systole.plots import plot_subspaces

R peaks detection

signal, peaks = ecg_peaks(signal, method=‘pan-tompkins’, sfreq=1000)

plot_subspaces(peaks, input_type=“peaks”, backend=“bokeh”)

… image:: https://raw.githubusercontent.com/embodied-computation-group/systole/master/docs/source/images/subspaces.png :align: center

Heart rate variability analysis

Systole implements time-domain, frequency-domain and non-linear HRV indices, as well as tools for evoked heart rate analysis.

… code-block:: python

from bokeh.layouts import row from systole.plots import plot_frequency, plot_poincare

row( plot_frequency(peaks, input_type=“peaks”, backend=“bokeh”, figsize=(300, 200)), plot_poincare(peaks, input_type=“peaks”, backend=“bokeh”, figsize=(200, 200)), )

… image:: https://raw.githubusercontent.com/embodied-computation-group/systole/master/docs/source/images/hrv.png :align: center

Online systolic peak detection, cardiac-stimulus synchrony, and cardiac circular analysis

The package natively supports recording of physiological signals from the following setups:

• Nonin 3012LP Xpod USB pulse oximeter <https://www.nonin.com/products/xpod/>_ together with the Nonin 8000SM 'soft-clip' fingertip sensors <https://www.nonin.com/products/8000s/>_ (USB).
• Remote Data Access (RDA) via BrainVision Recorder together with Brain product ExG amplifier <https://www.brainproducts.com/>_ (Ethernet).

Interactive visualization of BIDS structured datasets

… code-block:: python

from systole.viewer import Viewer

view = Viewer( input_folder=“/BIDS/folder/path/”, pattern=“task-mytask”, modality=“beh”, signal_type=“ECG” )

… image:: https://raw.githubusercontent.com/embodied-computation-group/systole/master/docs/source/images/editor.gif :align: center

Inserting and removing peaks

… image:: https://raw.githubusercontent.com/embodied-computation-group/systole/master/docs/source/images/peaks.gif :align: center

Annotating bad segments

… image:: https://raw.githubusercontent.com/embodied-computation-group/systole/master/docs/source/images/segments.gif :align: center

Development +++++++++++

Written and maintained by Micah Allen and the Embodied Computation Group, Aarhus University. Contact: [email protected]

If you want to contribute, feel free to contact one of the developers, open an issue or submit a pull request.

This program is provided with NO WARRANTY OF ANY KIND.

Acknowledgements ++++++++++++++++

This software and the ECG are supported by a Lundbeckfonden Fellowship (R272-2017-4345), and the AIAS-COFUND II fellowship programme that is supported by the Marie Skłodowska-Curie actions under the European Union’s Horizon 2020 (Grant agreement no 754513), and the Aarhus University Research Foundation.

Systole was largely inspired by pre-existing toolboxes dedicated to heartrate variability and signal analysis.

• HeartPy: https://python-heart-rate-analysis-toolkit.readthedocs.io/en/latest/

• hrv: https://github.com/rhenanbartels/hrv

• pyHRV: https://pyhrv.readthedocs.io/en/latest/index.html

• ECG-detector: https://github.com/berndporr/py-ecg-detectors

• Pingouin: https://pingouin-stats.org/

• NeuroKit2: https://github.com/neuropsychology/NeuroKit

================

|AU| |lundbeck| |lab|

… |AU| image:: https://raw.githubusercontent.com/embodied-computation-group/systole/master/docs/source/images/au_clinisk_logo.png :width: 100%

… |lundbeck| image:: https://raw.githubusercontent.com/embodied-computation-group/systole/master/docs/source/images/lundbeckfonden_logo.png :width: 20%

… |lab| image:: https://raw.githubusercontent.com/embodied-computation-group/systole/master/docs/source/images/lablogo_2024.png :width: 20%