def test_oximeter(self):
serial = serialSim()
oxi = Oximeter(serial=serial, add_channels=1)
oxi.setup()
serial.ppg = serial.ppg[-2:] # To the end of recording
oxi.read(10)
oxi.find_peaks()
# Simulate events in recording
for idx in np.random.choice(len(oxi.recording), 5):
oxi.channels['Channel_0'][idx] = 1
ax = oxi.plot_events()
assert isinstance(ax, matplotlib.axes.Axes)
ax = oxi.plot_hr()
assert isinstance(ax, matplotlib.axes.Axes)
ax = oxi.plot_recording()
assert isinstance(ax, matplotlib.axes.Axes)
oxi.serial.ppg = [1000] # Insert error in recording
with self.assertRaises(ValueError):
oxi.readInWaiting(stop=True)
serial = serialSim()
oxi.serial.ppg = [1000, -1, 1000, -1, -1] # Insert error in recording
oxi.readInWaiting(stop=False)
oxi.serial.ppg = [1000, -1, 1000, -1, -1] # Insert error in recording
oxi.waitBeat()
oxi.find_peaks()
oxi.peaks = []
oxi.instant_rr = []
oxi.times = []
oxi.threshold = []
oxi.save('test')
assert os.path.exists("test.npy")
os.remove("test.npy")
oxi = Oximeter(serial=serial)
#%%
# If you want to allow online data acquisition, you should uncomment the
# following lines and provide the reference of the COM port where the pulse
# oximeter is plugged in.
###############################################################################
# .. code-block:: python
#
# import serial
# ser = serial.Serial('COM4') # Change this value according to your setup
#%%
# Create an Oximeter instance, initialize recording and record for 10 seconds
oxi = Oximeter(serial=ser, sfreq=75, add_channels=4).setup()
#%%
# Create an Oxymeter instance, initialize recording and record for 10 seconds
beat = Sound("C", secs=0.1)
diastole1 = Sound("E", secs=0.1)
diastole2 = Sound("G", secs=0.1)
diastole3 = Sound("Bfl", secs=0.1)
systoleTime1, systoleTime2, systoleTime3 = None, None, None
tstart = time.time()
while time.time() - tstart < 30:
# Check if there are new data to read
while oxi.serial.inWaiting() >= 5:
#%%
# Reading
# -------
# Recording and plotting your first time-series will only require 5 lines
# of code:
import time
import serial
from systole.recording import Oximeter
ser = serial.Serial("COM4") # Add your USB port here
# Open serial port, initialize and plot recording for Oximeter
oxi = Oximeter(serial=ser).setup().read(duration=10)
# The signal can be directly plotted using built-in functions.
oxi.plot_oximeter()
##############################################################################
# .. figure:: https://github.com/embodied-computation-group/systole/raw/master/Images/recording.png
# :align: center
##############################################################################
#%%
# Interfacing with PsychoPy
# -------------------------
# * The ``read()`` method will record for a predefined amount of time
# (specified by the ``duration`` parameter, in seconds). This 'serial mode'
# Author: Nicolas Legrand <*****@*****.**>
import numpy as np
import pandas as pd
import unittest
import matplotlib
from unittest import TestCase
from systole.plotting import plot_hr, plot_events, plot_oximeter,\
plot_subspaces, circular, plot_circular, plot_psd
from systole import import_ppg, import_rr, serialSim
from systole.recording import Oximeter
from systole.detection import hrv_subspaces
serial = serialSim()
oxi = Oximeter(serial=serial, add_channels=1).setup().read(10)
oxi.channels['Channel_0'][100] = 1
# Simulate oximeter instance from recorded signal
ppg = import_ppg()
oxi = Oximeter(serial=None, add_channels=1)
oxi.threshold = [0] * 75
oxi.peaks = [0] * 75
oxi.instant_rr = [0] * 75
oxi.recording = list(ppg[0, :75])
for i in range(len(ppg[0, 75:750])):
oxi.add_paquet(ppg[0, 75 + i])
oxi.channels['Channel_0'] = np.zeros(750, dtype=int)
oxi.channels['Channel_0'][np.random.choice(np.arange(0, 750), 5)] = 1
oxi.times = list(np.arange(0, 10, 1 / 75))
def test_oximeter(self):
serial = serialSim()
oxi = Oximeter(serial=serial, add_channels=1)
oxi.setup()
oxi.read(10)
oxi.find_peaks()
# Simulate events in recording
for idx in np.random.choice(len(oxi.recording), 5):
oxi.channels['Channel_0'][idx] = 1
ax = oxi.plot_events()
assert isinstance(ax, matplotlib.axes.Axes)
ax = oxi.plot_hr()
assert isinstance(ax, matplotlib.axes.Axes)
ax = oxi.plot_recording()
assert isinstance(ax, matplotlib.axes.Axes)
oxi.readInWaiting()
oxi.waitBeat()
oxi.find_peaks()
oxi.peaks = []
oxi.instant_rr = []
oxi.times = []
oxi.threshold = []
oxi.save('test')
assert os.path.exists("test.npy")
os.remove("test.npy")
ser = serialSim()
#%%
# If you want to enable online data acquisition, you should uncomment the
# following lines and provide the reference of the COM port where the pulse
# oximeter is plugged in.
###############################################################################
# .. code-block:: python
#
# import serial
# ser = serial.Serial('COM4') # Change this value according to your setup
# Create an Oxymeter instance, initialize recording and record for 10 seconds
oxi = Oximeter(serial=ser, sfreq=75).setup()
oxi.read(30)
#%%
# Plotting
# --------
fig, ax = plt.subplots(3, 1, figsize=(13, 8), sharex=True)
oxi.plot_recording(ax=ax[0])
ax[1].plot(oxi.times, oxi.peaks, 'k')
ax[1].set_title('Peaks vector', fontweight='bold')
ax[1].set_xlabel('Time (s)')
ax[1].set_ylabel('Peak\n detection')
hr, time = heart_rate(oxi.peaks, sfreq=75, unit='rr', kind='cubic')
# It can easily interface with `PsychoPy <https://www.psychopy.org/>`_ to
# record PPG signal during psychological experiments, and to synchronize
# stimulus deliver to e.g., systole or diastole.
# For example, you can record and plot data in less than 6 lines of code:
#%%
# Event related cardiac deceleration
# ----------------------------------
import serial
from systole.recording import Oximeter
ser = serial.Serial('COM4') # Add your USB port here
# Open serial port, initialize and plot recording for Oximeter
oxi = Oximeter(serial=ser).setup().read(duration=10)
Interfacing with PsychoPy
-------------------------
The ``Oximeter`` class can be used together with a stimulus presentation software to record cardiac activity during psychological experiments.
* The ``read()`` method
will record for a predefined amount of time (specified by the ``duration`` parameter, in seconds). This 'serial mode' is the easiest and most robust method, but it does not allow the execution of other instructions in the meantime.
.. code-block:: python
# Code 1 {}
oximeter.read(duration=10)