actfast 0.1.9

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[!NOTE]
actfast is currently in early development and is not yet ready for production use. Please open an issue if you encounter any problems or have any feature requests.

actfast Fast actigraphy data reader

actfast is a minimal Python package for reading raw actigraphy data from various devices. It is written in Rust and Python, and is designed with performance and memory safety in mind.

In preliminary benchmarks, actfast showed around 40x speedup compared to pygt3x for reading ActiGraph GT3X files.

Installation

Install from PyPI via:

pip install actfast

Or, install the latest development version from GitHub via:

pip install git+https://github.com/childmindresearch/actfast.git

Hardware support

This package has been tested with data captured by the following devices:

Device	Firmware	API
ActiGraph wGT3X-BT	1.9.2	actfast.read_actigraph_gt3x(file)
GENEActiv 1.2	Ver06.17 15June23	actfast.read_geneactiv_bin(file)

Similar devices might work, but have not been tested. Please open an issue and attach a sample file if you have a device that is not supported yet. We will do our best to add support for it.

Usage

import actfast

subject1 = actfast.read_actigraph_gt3x("data/subject1.gt3x")

If you are using Pandas and want a similar dataframe to what pygt3x offers, you can convert the data to a dataframe using the following code snippet:

import pandas as pd

accel = subject1["timeseries"]["acceleration"]

df = pd.DataFrame.from_dict({
    "Timestamp": accel["datetime"],
    "X": accel["acceleration"][:, 0],
    "Y": accel["acceleration"][:, 1],
    "Z": accel["acceleration"][:, 2]
})

df["Timestamp"] = pd.to_datetime(df["Timestamp"], unit='ns')
df = df.set_index("Timestamp")