agcounts

A python package for extracting actigraphy counts from accelerometer data.

Install

pip install agcounts

Test

Download test data:

curl -L https://github.com/actigraph/agcounts/files/8247896/GT3XPLUS-AccelerationCalibrated-1x8x0.NEO1G75911139.2000-01-06-13-00-00-000-P0000.sensor.csv.gz --output data.csv.gz

Run a simple test

import pandas as pd
import numpy as np
from agcounts.extract import get_counts


def get_counts_csv(
    file,
    freq: int,
    epoch: int,
    fast: bool = True,
    verbose: bool = False,
    time_column: str = None,
):
    if verbose:
        print("Reading in CSV", flush=True)
    raw = pd.read_csv(file, skiprows=0)
    if time_column is not None:
        ts = raw[time_column]
        ts = pd.to_datetime(ts)
        time_freq = str(epoch) + "S"
        ts = ts.dt.round(time_freq)
        ts = ts.unique()
        ts = pd.DataFrame(ts, columns=[time_column])
    raw = raw[["X", "Y", "Z"]]
    if verbose:
        print("Converting to array", flush=True)
    raw = np.array(raw)
    if verbose:
        print("Getting Counts", flush=True)
    counts = get_counts(raw, freq=freq, epoch=epoch, fast=fast, verbose=verbose)
    del raw
    counts = pd.DataFrame(counts, columns=["Axis1", "Axis2", "Axis3"])
    counts["AC"] = (
        counts["Axis1"] ** 2 + counts["Axis2"] ** 2 + counts["Axis3"] ** 2
    ) ** 0.5
    ts = ts[0 : counts.shape[0]]
    if time_column is not None:
        counts = pd.concat([ts, counts], axis=1)
    return counts


def convert_counts_csv(
    file,
    outfile,
    freq: int,
    epoch: int,
    fast: bool = True,
    verbose: bool = False,
    time_column: str = None,
):
    counts = get_counts_csv(
        file, freq=80, epoch=60, verbose=True, time_column=time_column
    )
    counts.to_csv(outfile, index=False)
    return counts


counts = get_counts_csv("data.csv.gz", freq=80, epoch=60)
counts = convert_counts_csv(
    "data.csv.gz",
    outfile="counts.csv.gz",
    freq=80,
    epoch=60,
    verbose=True,
    time_column="HEADER_TIMESTAMP",
)