edf-reader 0.1.3

Lightweight EDF file reader, which can handle discontinuities.

EDF Reader

A lightweight EDF (European Data Format) file reader for Python that can handle discontinuities in EDF+D files.

Description

EDF Reader is a Python package for reading EDF (European Data Format) files, which are commonly used for storing medical/biological signals like EEG data. This implementation is optimized for performance, especially when reading files over network drives, and can handle discontinuities in EDF+D format files.

Key features:

• Read EDF and EDF+D files
• Parse file headers and signal information
• Read signal data with time-based filtering
• Handle annotations and discontinuities in EDF+D files
• Optimized for performance with network drives

Installation

You can install the package using pip:

pip install edf-reader

For development installation:

git clone https://gitlab.com/bbeer_group/development/epycom/edf_reader.git
cd edf_reader
pip install -e .

Usage

Basic usage example:

from edf_reader import EdfWrapper

# Open an EDF file
reader = EdfWrapper('/path/to/your/file.edf')

# Get basic information about the channels
channel_info = reader.read_ts_channel_basic_info()
print(channel_info)

# Read data from specific channels
# The time range is specified in microseconds UTC (uutc)
# [None, None] means the entire recording
data = reader.read_ts_channels_uutc(['Channel1', 'Channel2'], [None, None])

# Check for discontinuities in the recording
discontinuities = reader.get_discontinuities()
print(f"Found {len(discontinuities)} discontinuities")

# Close the file when done
reader.close()

Testing

The package includes a comprehensive test suite using pytest. To run the tests, first install the development dependencies:

pip install -e .[dev]

Then run the tests using pytest:

pytest

Or use the provided test runner script:

./run_tests.py

The tests use mocks to avoid requiring actual EDF files, making them fast and reliable to run in any environment.

License

This project is licensed under the BSD 3.0 License - see the LICENSE file for details.

Authors

• Vojtech Travnicek - [e-mail], [e-mail]