SURF WAVES physiological waveform dataset utilities
Project description
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)
- (or run
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
Project details
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