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JohnDoenut committed Mar 6, 2020
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38 changes: 30 additions & 8 deletions README.md
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It processes these biosignals semi-automatically with sensible defaults and features the following
functionality:

* processing of the open biosignal formats [EDF](https://en.wikipedia.org/wiki/European_Data_Format)
* works with files in the open biosignal formats [EDF](https://en.wikipedia.org/wiki/European_Data_Format)
as well as [OpenSignals](https://bitalino.com/en/software)
* biosignal visualization
* interactive biosignal visualization
* biosignal segmentation
* extrema detection (R-peaks in ECG, exhalation troughs and inhalation
* automatic extrema detection (R-peaks in ECG, exhalation troughs and inhalation
peaks in breathing signals)
* state-of-the-art [automatic artifact correction](https://www.tandfonline.com/doi/full/10.1080/03091902.2019.1640306)
* automatic state-of-the-art [artifact correction](https://www.tandfonline.com/doi/full/10.1080/03091902.2019.1640306)
for ECG extrema
* manual editing of extrema (useful in case of poor biosignal quality)
* calculation of instantaneous (heart- or breathing-) rate and period, as well as
breathing amplitude
* fully automated batch processing
* batch processing


# Citation
Click on the badge below to cite `biopeaks` in a format of your choice.


[![DOI](https://www.zenodo.org/badge/172897525.svg)](https://www.zenodo.org/badge/latestdoi/172897525)

You can cite `biopeaks` as
> Jan C. Brammer. (2020, March 6). JanCBrammer/biopeaks: Version 1.1.5 (Version v1.1.5). Zenodo. http://doi.org/10.5281/zenodo.3698562

# User Guide

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controller).

# Tests
The test data have been recorded with\

## Frontend
The OpenSignals test data have been recorded with\
software: opensignals v2.0.0, 20190805\
hardware: BITalino (r)evolution (firmware 1281)

The EDF test data have been downloaded from https://www.teuniz.net/edf_bdf_testfiles/

The tests can be run from a Python console:
```
from biopeaks.test import frontend_test
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This will open an application, run a few tests on it and print the results to
the Python console.

## Backend
In order to validate the performance of the ECG peak detector `ecg.ecg_peaks()`,
please download the [Glasgow University Database (GUDB)](http://researchdata.gla.ac.uk/716/).
In addition you need to install the [wfdb](https://github.com/MIT-LCP/wfdb-python) package either with conda
```
conda install -c conda-forge wfdb
```
or pip.

```
pip install wfdb
```

You can then run the `benchmark_GUBD` script in the test folder.

# Changelog

### Version 1.1.6 (March 06, 2020)
+ enhancement: some small improvements of the statistics panel in **datadisplay**.

### Version 1.1.5 (March 01, 2020)
+ enhancement: added support for [EDF files](https://en.wikipedia.org/wiki/European_Data_Format).
+ enhancement: `ecg.ecg_peaks()` now filters out power-line noise at 50Hz. This
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setup(
name="biopeaks",
version="1.1.5",
description="A graphical user interface for the analysis of electrocardiogram and breathing biosignals",
version="1.1.6",
description="A graphical user interface for feature extraction from heart- and breathing biosignals.",
url="https://github.com/JanCBrammer/biopeaks",
author="Jan C. Brammer",
author_email="j.brammer@psych.ru.nl",
keywords="ECG Breathing Biosignals Bitalino OpenSignals EDF GUI",
packages=find_namespace_packages(exclude=["misc"]),
packages=find_namespace_packages(exclude=["misc", "paper"]),
python_requires=">=3.7",
license="GPL-3.0",
include_package_data=True,
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