usleep-api 0.1.3

Python bindings to the U-Sleep web API.

U-Sleep API Python Bindings

Python bindings to the U-Sleep Webserver API (https://sleep.ai.ku.dk).

Purpose and Usage

The U-Sleep Webserver provides a free and highly accurate sleep staging algorithm for Polysomnography data. It is publicly available for anyone interested in clinical sleep research. For details, see https://www.nature.com/articles/s41746-021-00440-5.

This repository stores Python bindings to the U-Sleep Webserver API. The Python bindings may be used to easily upload PSG files for scoring to the U-Sleep webservice and fetch the results without the need for installing anything except Python and this package (see Installation).

The API bindings may be called from a Python script by importing the USleepAPI class (see Python Example or Detailed Python Example below) or by calling the usleep-api console script (see Quick Start) below.

Installation

Via PIP:

pip install usleep-api

Alternatively, you may pull and install the latest version from GitHub:

git clone https://github.com/perslev/U-Sleep-API-Python-Bindings
pip install ./U-Sleep-API-Python-Bindings

API Overview

A brief overview of the API is provided at https://sleep.ai.ku.dk/docs/api/overview.

The API is documented at https://sleep.ai.ku.dk/docs/api/documentation.

Access to the API must be requested at https://sleep.ai.ku.dk/docs/api/access.

Authentication

Requests to any API endpoint must include an API authentication token. To obtain a token:

1. Log in to your account at https://sleep.ai.ku.dk/login.
2. Select "Account" and "Generate API Token" from the drop-down menu.
3. Paste the API token into your script or create an environment variable to store the token (see details below).

At the time of writing the obtained token is valid for 12 hours. Once expired, a new token must be generated following the above procedure. Keep your token(s) private as they represent your identity to the server and allow others to authenticate on your behalf.

API Token Environment Variable

It is recommended to store your API tokens using an environment variable named USLEEP_API_TOKEN. For instance, with a token ABCDEF123456:

>> export USLEEP_API_TOKEN=ABCDEF123456

Calls may now be made to the U-Sleep API using the console script (see Quick Start), the USleepAPI Python class (see Python Example) or directly, e.g. with:

curl -s -X GET -H "Authorization: Bearer $USLEEP_API_TOKEN" https://sleep.ai.ku.dk/api/v1/info/model_names
>> {"models":["U-Sleep v1.0"]}

Quick Start

When installing the usleep-api package via PIP, the console script usleep-api is made available. Calling this script will allow to score files without the need to create and run a Python script. For instance:

>> usleep-api ./my_psg.edf ./hypnogram.tsv --anonymize

This will upload an anonymized version of the file ./my_psg.edf to the U-Sleep webservice, then download the scored hypnogram and save it to ./hypnogram.tsv. Per default, the script scores the PSG at 1/30 Hz using the U-Sleep v1.0 model and all (automatically inferred) combinations of valid input channels. However, the script accepts several parameters to configure its use. Call usleep-api --help to see a list of available options.

Confidence Scores

To download a raw hypnogram numpy array with confidence scores:

>> usleep-api ./my_psg.edf ./hypnogram.npy --anonymize --with-confidence-scores

Python Bindings

The USleepAPI class provides bindings for most of the API endpoints.

Python Example

A PSG file may be anonymized, uploaded, scored and the resulting hypnogram downloaded to a file by calling the USleepAPI.quick_predict convenience method:

import os
from usleep_api import USleepAPI

# Create an API object with API token stored in environment variable 
api = USleepAPI(api_token=os.environ['USLEEP_API_TOKEN'])

# Predict on anonymized PSG and save hypnogram to file
hypnogram, log = api.quick_predict(
    input_file_path="./psg_001.edf",
    output_file_path="./psg_001_hypnogram.tsv",
    anonymize_before_upload=True
)

Detailed Python Example

For more fine-grained control, you may call the relevant lower-level API bindings e.g. as follows:

import logging
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger("api_example")

from usleep_api import USleepAPI

# Create an API token at https://sleep.ai.ku.dk.
# api_token = "eyJ0eXAiOiJKV1Q..."  # Alternatively, insert token here
api_token = os.environ['USLEEP_API_TOKEN']

# Create an API object and (optionally) a new session.
api = USleepAPI(api_token=api_token)
session = api.new_session(session_name="my_session")

# See a list of valid models and set which model to use
logger.info(f"Available models: {session.get_model_names()}")
session.set_model("U-Sleep v1.0")

# Upload a local file (usually .edf format)
session.upload_file("./my_psg.edf", anonymize_before_upload=True)

# Start the prediction on two channel groups:
#   1: EEG Fpz-Cz + EOG horizontal
#   2: EEG Pz-Oz + EOG horizontal
# Using 30 second windows (note: U-Slep v1.0 uses 128 Hz re-sampled signals)
session.predict(data_per_prediction=128*30,
                channel_groups=[["EEG Fpz-Cz", "EOG horizontal"],
                                ["EEG Pz-Oz", "EOG horizontal"]])

# Wait for the job to finish or stream to the log output
# session.stream_prediction_log()
success = session.wait_for_completion()

if success:
    # Fetch hypnogram
    hyp = session.get_hypnogram()
    logger.info(hyp["hypnogram"])

    # Download hypnogram file
    session.download_hypnogram(out_path="./hypnogram", file_type="tsv")
else:
    logger.error("Prediction failed.")

# Delete session (i.e., uploaded file, prediction and logs)
session.delete_session()