Plot raw physiological signal

# Author: Nicolas Legrand <nicolas.legrand@cfin.au.dk>
# Licence: GPL v3


from bokeh.io import output_notebook
from bokeh.plotting import show
from systole.plots import plot_raw

from systole import import_dataset1, import_ppg

Plot raw ECG signal

# Import PPG recording as pandas data frame
physio_df = import_dataset1(modalities=['ECG', 'Respiration'])

# Only use the first 60 seconds for demonstration
ecg = physio_df[physio_df.time.between(60, 90)].ecg
plot_raw(ecg, modality='ecg', sfreq=1000, detector='sleepecg')

  0%|          | 0/2 [00:00<?, ?it/s]
Downloading ECG channel:   0%|          | 0/2 [00:00<?, ?it/s]
Downloading ECG channel:  50%|█████     | 1/2 [00:00<00:00,  4.10it/s]
Downloading Respiration channel:  50%|█████     | 1/2 [00:00<00:00,  4.10it/s]
Downloading Respiration channel: 100%|██████████| 2/2 [00:00<00:00,  2.88it/s]
Downloading Respiration channel: 100%|██████████| 2/2 [00:00<00:00,  3.01it/s]

<Axes: title={'center': 'ECG recording'}, ylabel='ECG (mV)'>

Plot raw PPG signal

Import Respiration recording as pandas data frame

rsp = import_dataset1(modalities=['Respiration'])

# Only use the first 90 seconds for demonstration
rsp = physio_df[physio_df.time.between(500, 600)].respiration
plot_raw(rsp, sfreq=1000, modality="respiration")

  0%|          | 0/1 [00:00<?, ?it/s]
Downloading Respiration channel:   0%|          | 0/1 [00:00<?, ?it/s]
Downloading Respiration channel: 100%|██████████| 1/1 [00:00<00:00,  4.33it/s]
Downloading Respiration channel: 100%|██████████| 1/1 [00:00<00:00,  4.32it/s]

<Axes: title={'center': 'Respiration'}, ylabel='Respiratory signal'>

Plot raw respiratory signal

# Import PPG recording as pandas data frame
ppg = import_ppg()

# Only use the first 60 seconds for demonstration
plot_raw(ppg[ppg.time<60], sfreq=75)

<Axes: title={'center': 'PPG recording'}, ylabel='PPG level (a.u.)'>

Using Bokeh as plotting backend

output_notebook()

show(
    plot_raw(ppg, backend="bokeh", show_heart_rate=True, show_artefacts=True)
 )

BokehDeprecationWarning: CDSView.source is no longer needed, and is now ignored. In a future release, passing source will result an error.
BokehDeprecationWarning: CDSView.filters was deprecated in bokeh 3.0. Use CDSView.filter instead.
BokehDeprecationWarning: CDSView.source is no longer needed, and is now ignored. In a future release, passing source will result an error.
BokehDeprecationWarning: CDSView.filters was deprecated in bokeh 3.0. Use CDSView.filter instead.