waves-utilities 1.0.0

SURF WAVES physiological waveform dataset utilities

WAVES Utilities

This python package/repository contains useful scripts, dataloaders, and examples for working with the WAVES dataset of pediatric physiological waveforms.

What is WAVES?

WAVES is an open-access pediatric physiological waveform dataset containing ECG, respiratory, plethysmogram, arterial blood pressure, and a variety of other high-frequency waveforms extracted from bedside monitors for patients at the Lucile Packard Childrens Hospital. The WAVES dataset itself is hosted by Redivis at https://redivis.com/WAVES/datasets

WAVES is administrated by the SURF Stanford Medicine research group.

What is this repository for?

• Python utilities to load and plot physiological waveform data from the WAVES dataset

How do I get set up?

• Download/clone the repository
• Set up a python environment with the required dependencies: conda env create -f environment.yml
• Install the python package from pypi with pip install waves_utilities
  • (or run python setup.py develop for local development)

Usage Examples

Refer to the tests and API documentation for more information on API options/arguments.

Load data from .csv file

from waves_utilities import WavesUtilityAPI
util_api = WavesUtilityAPI()

# Load a single row
csv_row = next(util_api.csv_manager.read_csv("waveform_test_extract.csv", limit=1))

# Load all rows (keep memory usage in mind for large data extracts)
csv_rows = list(util_api.csv_manager.read_csv("waveform_test_extract.csv"))

Plot waveforms

# Plot 5 seconds from a single waveform
util_api.waveform_plotter.plot_waveform(
    csv_row, save_filepath="single_waveform.png", duration_seconds=5
)

# Plot the full duration of multiple waveforms in file
util_api.waveform_plotter.plot_waveforms(
    csv_rows, save_filepath="multi_waveforms.png", title="Test Waveform Data"
)

Contribution guidelines

• Writing tests
• Code review
• Other guidelines

Who do I talk to?

• Daniel Miller: Primary researcher/developer for the WAVES dataset and codebase
• David Scheinker: Head of the SURF Stanford Medicine research group