biopsykit 0.2.2

A python package for the analysis of biopsychological data.

BioPsyKit

A Python package for the analysis of biopsychological data.

With this package you have everything you need for analyzing biopsychological data, including:

• Data processing pipelines for biosignals (ECG, EEG, ...)
• Methods for analyzing saliva samples (cortisol, amylase)
• Implementation of various psychological and HCI-related questionnaires

Additionally, there are modules to analyze and visualize data acquired from special measurement scenarios, such as:

• Montreal Imaging Stress Task (MIST)
• ... more to follow

Details

Biosignal Analysis

ECG Processing

BioPsyKit provides a whole ECG data processing pipeline, consisting of:

• Loading ECG data from:
  • generic .csv files
  • NilsPod binary (.bin) files (requires NilsPodLib: https://github.com/mad-lab-fau/NilsPodLib)
  • from other sensor types (coming soon)
• Splitting data into chunks (based on time intervals) that will be analyzed separately
• Perform ECG processing, including:
  • R peak detection (using Neurokit: https://github.com/neuropsychology/NeuroKit)
  • R peak outlier removal and interpolation
  • HRV feature computation
  • ECG-derived respiration (EDR) estimation for respiration rate and respiratory sinus arrhythmia (RSA) (experimental)
• Visualization of results

... more biosignals coming soon!

Biomarker Analysis

BioPsyKit provides several methods for the analysis of biomarkers, such as:

• Load saliva data (e.g. cortisol and amylase) from deepwell plate Excel exports
• Compute standard features (maximum increase, slope, AUC, ...)

Questionnaires

BioPsyKit implements various established psychological and HCI-related questionnaires, such as:

• Perceived Stress Scale (PSS)
• Positive Appraisal Negative Appraisal Scale (PANAS)
• Self-Compassion Scale (SCS)
• System Usability Scale (SUS)
• NASA Task Load Index (NASA-TLX)
• Short Stress State Questionnaire (SSSQ)
• ...

For more details, see the instructions in the questionnaire module.

Stress Protocols

BioPsyKit implements methods for analyzing data recorded with several established stress protocols, such as:

• Montreal Imaging Stress Task (MIST)
• Trier Social Stress Test (TSST) (coming soon...)

Installation

Install it via pip:

pip install biopsykit

For developer

git clone https://github.com/mad-lab-fau/BioPsyKit.git
cd biopsykit
poetry install

Install Python >3.8 and poetry. Then run the commands below to get the latest source and install the dependencies:

To run any of the tools required for the development workflow, use the doit commands:

$ poetry run doit list
docs                 Build the html docs using Sphinx.
format               Reformat all files using black.
format_check         Check, but not change, formatting using black.
lint                 Lint all files with Prospector.
test                 Run Pytest with coverage.
update_version       Bump the version in pyproject.toml and biopsykit.__init__ .

Examples

See Examples in the function documentations on how to use this library.