Sleep Analyzer Example

This example illustrates how to import data (summary and raw data) from the Withings Sleep Analyzer, how to get sleep endpoints from the summary data and how to split the raw data (collected over several nights) into single nights.

Setup and Helper Functions

import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
from fau_colors import cmaps

import biopsykit as bp

%matplotlib inline
%load_ext autoreload
%autoreload 2

plt.close("all")

palette = sns.color_palette(cmaps.faculties)
sns.set_theme(context="notebook", style="ticks", font="sans-serif", palette=palette)

plt.rcParams["figure.figsize"] = (8, 4)
plt.rcParams["pdf.fonttype"] = 42
plt.rcParams["mathtext.default"] = "regular"

palette

def display_dict_structure(dict_to_display):
    _display_dict_recursive(dict_to_display)


def _display_dict_recursive(dict_to_display):
    if isinstance(dict_to_display, dict):
        display(dict_to_display.keys())
        _display_dict_recursive(next(iter(dict_to_display.values())))
    else:
        display(f"Dataframe shape: {dict_to_display.shape}")
        display(dict_to_display.head())

Sleep Analyzer Summary

sleep_summary = bp.example_data.get_sleep_analyzer_summary_example()
sleep_summary.head()

	sleep_onset	wake_onset	recording_start	recording_end	total_time_light_sleep	total_time_deep_sleep	total_time_rem_sleep	total_time_awake	number_wake_bouts	sleep_onset_latency	getup_latency	total_time_snoring	count_snoring_episodes	heart_rate_avg	heart_rate_min	heart_rate_max	total_duration	wake_after_sleep_onset	total_sleep_duration	net_sleep_duration
date
2020-10-10 00:00:00+02:00	2020-10-11 02:26:00+02:00	2020-10-11 09:47:00+02:00	2020-10-11 02:04:00+02:00	2020-10-11 09:59:00+02:00	263	89	82	41	1	22	12	19	1	68	55	82	28500	7	441	434
2020-10-11 00:00:00+02:00	2020-10-12 00:52:00+02:00	2020-10-12 07:15:00+02:00	2020-10-12 00:22:00+02:00	2020-10-12 07:15:00+02:00	120	165	96	30	1	30	0	0	0	72	58	87	24780	0	383	383
2020-10-12 00:00:00+02:00	2020-10-13 00:02:00+02:00	2020-10-13 07:21:00+02:00	2020-10-12 23:52:00+02:00	2020-10-13 07:21:00+02:00	272	108	59	10	0	10	0	0	0	51	43	72	26940	0	439	439
2020-10-15 00:00:00+02:00	2020-10-16 01:16:00+02:00	2020-10-16 07:56:00+02:00	2020-10-15 23:56:00+02:00	2020-10-16 07:56:00+02:00	254	97	43	86	1	80	0	0	0	66	55	75	28800	6	400	394
2020-10-17 00:00:00+02:00	2020-10-17 23:59:00+02:00	2020-10-18 10:29:00+02:00	2020-10-17 23:19:00+02:00	2020-10-18 10:29:00+02:00	397	72	91	83	8	40	0	0	0	65	47	82	40200	43	630	587

Sleep Analyzer Raw Data

sleep_data = bp.example_data.get_sleep_analyzer_raw_example()

/home/docs/checkouts/readthedocs.org/user_builds/biopsykit/envs/latest/lib/python3.10/site-packages/numpy/_core/fromnumeric.py:57: FutureWarning: 'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead.
  return bound(*args, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/biopsykit/envs/latest/lib/python3.10/site-packages/numpy/_core/fromnumeric.py:57: FutureWarning: 'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead.
  return bound(*args, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/biopsykit/envs/latest/lib/python3.10/site-packages/numpy/_core/fromnumeric.py:57: FutureWarning: 'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead.
  return bound(*args, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/biopsykit/envs/latest/lib/python3.10/site-packages/numpy/_core/fromnumeric.py:57: FutureWarning: 'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead.
  return bound(*args, **kwds)

display_dict_structure(sleep_data)

dict_keys([np.str_('2020-10-10'), np.str_('2020-10-11'), np.str_('2020-10-12'), np.str_('2020-10-15'), np.str_('2020-10-17'), np.str_('2020-10-19'), np.str_('2020-10-21'), np.str_('2020-10-23')])

'Dataframe shape: (486, 4)'

	heart_rate	respiration_rate	sleep_state	snoring
time
2020-10-11 02:04:00+02:00	52.0	15.0	0.0	0.0
2020-10-11 02:05:00+02:00	61.0	9.0	0.0	0.0
2020-10-11 02:06:00+02:00	65.0	16.0	0.0	0.0
2020-10-11 02:07:00+02:00	66.0	17.0	0.0	0.0
2020-10-11 02:08:00+02:00	65.0	11.0	0.0	0.0

for key in sleep_data:
    display(pd.concat([sleep_data[key].head(n=1), sleep_data[key].tail(n=1)]))

	heart_rate	respiration_rate	sleep_state	snoring
time
2020-10-11 02:04:00+02:00	52.0	15.0	0.0	0.0
2020-10-11 10:09:00+02:00	65.0	17.0	0.0	0.0

	heart_rate	respiration_rate	sleep_state	snoring
time
2020-10-12 00:22:00+02:00	68.0	13.0	0.0	0.0
2020-10-12 07:14:00+02:00	70.0	18.0	1.0	0.0

	heart_rate	respiration_rate	sleep_state	snoring
time
2020-10-12 20:47:00+02:00	65.0	11.0	0.0	0.0
2020-10-13 07:20:00+02:00	57.0	20.0	1.0	0.0

	heart_rate	respiration_rate	sleep_state	snoring
time
2020-10-15 23:53:00+02:00	70.0	14.0	0.0	0.0
2020-10-16 08:01:00+02:00	50.0	12.0	0.0	0.0

	heart_rate	respiration_rate	sleep_state	snoring
time
2020-10-17 23:14:00+02:00	64.0	12.0	0.0	0.0
2020-10-18 10:45:00+02:00	58.0	11.0	0.0	0.0

	heart_rate	respiration_rate	sleep_state	snoring
time
2020-10-20 00:36:00+02:00	69.0	15.0	0.0	0.0
2020-10-20 16:19:00+02:00	61.0	11.0	0.0	0.0

	heart_rate	respiration_rate	sleep_state	snoring
time
2020-10-21 23:36:00+02:00	69.0	13.0	0.0	0.0
2020-10-22 08:35:00+02:00	65.0	20.0	0.0	0.0

	heart_rate	respiration_rate	sleep_state	snoring
time
2020-10-23 22:03:00+02:00	66.0	11.0	0.0	0.0
2020-10-24 10:33:00+02:00	64.0	10.0	0.0	0.0

fig, ax = plt.subplots()
sleep_data["2020-10-17"].plot(ax=ax)
fig.tight_layout()

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Withings Sleep Analyzer Data Import Questionnaire Example