PulseOx/collect_data.py at master · michaeljtang/PulseOx · GitHub

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from MAX30101 import *
from CMS50D import *
import csv
import time
from datetime import datetime

def real_time_plot():
    """
    Gives real-time plot of data from transmission and reflection pulseOx on the same graph
    """
    # plot waveform - adapted from stackoverflow.com/questions/45046239/python-realtime-plot-using-pyqtgraph
    app = QtGui.QApplication([])

    win = pg.GraphicsWindow(title='PulseOx Data')
    win.resize(1000,600)
    win.setWindowTitle('Waveform Data')

    p1 = win.addPlot(title='Waveform Data')
    transCurve = p1.plot()
    refRedCurve = p1.plot()
    refIrCurve = p1.plot()
    # p1.setRange(yRange=(0,100))
    windowWidth = 500
    transData = np.linspace(0,0,windowWidth)
    refRedData = np.linspace(0,0,windowWidth)
    refIrData = np.linspace(0,0,windowWidth)

    ptr = windowWidth - 1 # pointer to where data is added to our plot

    # enable antialiasing
    pg.setConfigOptions(antialias=True)

    # initialize data collection
    refPulseOx = MAX30101()
    transPulseOx = CMS50D('/dev/ttyUSB0')

    # realtime data plotting
    while True:
        # update data
        transData[ptr] = transPulseOx.get_waveform_data()

        # data from reflection PulseOx needs to be noramlized since it is so much larger than transmission data
        refRedDataPoint = 0
        refIrDataPoint = 0
        refDataPoint = refPulseOx.read_data()
        # 20600 is just filler value, change as needed
        refRedData[ptr] = max(0, refDataPoint[0] - 20600)
        refIrData[ptr] = max(0, refDataPoint[1] - 20600)
        # shift data windows one to the left
        transData[:-1] = transData[1:]
        refRedData[:-1] = refRedData[1:]
        refIrData[:-1] = refIrData[1:]

        # update plot
        transCurve.setData(transData)
        refRedCurve.setData(refRedData)
        refIrCurve.setData(refIrData)
        QtGui.QApplication.processEvents()

    # close Qt
    pg.QtGui.QApplication.exec_()

def collect_spo2_data(size):
    """
    Collects data from both pulseOx's while the reflection pulseOx is in SpO2 mode, and saves the data to a .csv file

    Inputs:
    size -- the number of data points we want to collect
    """
    transPulseOx = CMS50D('/dev/ttyUSB0')
    # 5 second delay is so that user has time to set up
    time.sleep(5)

    with open(f'data_{datetime.now()}.csv', 'w') as csvfile:
        fieldnames = ['time', 'bpm', 'spo2','Trans: Wave', 'Reflect: Red', 'Reflect: IR']
        writer = csv.DictWriter(csvfile, fieldnames)

        writer.writeheader()
        refPulseOx = MAX30101(mode='spo2',led=18 , adc_range=2 , sample_rate=1, pulse_width=3, sample_avg=2)
        start_time=time.time()

        # if we collect data for any longer than around 1700 times, the transmission pulseOx stops feeding data -- not sure why. The handshake may need to be sent periodically, easy fix
        for i in range(size):
            transData = transPulseOx.get_data()
            refData = refPulseOx.read_spo2_data()

            writer.writerow({fieldnames[0] : time.time() - start_time, fieldnames[1] : transData[0], fieldnames[2] : transData[1], fieldnames[3] : transData[2], fieldnames[4] : refData[0], fieldnames[5] : refData[1]})
        csvfile.close()
    refPulseOx.reset()

def collect_multi_data(size):
    """
    Collects data from both pulseOx's while the reflection pulseOx is in multi mode, and saves the data to a .csv file

    Inputs:
    size -- the number of data points we want to collect
    """
    transPulseOx = CMS50D('/dev/ttyUSB0')
    # 5 second delay is so that user has time to set up
    time.sleep(5)

    with open(f'data_{datetime.now()}.csv', 'w') as csvfile:
        fieldnames = ['time', 'bpm', 'spo2','Trans: Wave', 'Reflect: Red', 'Reflect: IR', 'Reflect: Green']
        writer = csv.DictWriter(csvfile, fieldnames)

        writer.writeheader()
        refPulseOx = MAX30101('multi')
        start_time=time.time()

        for i in range(size):
            transData = transPulseOx.get_data()
            refData = refPulseOx.read_multi_data()

            writer.writerow({fieldnames[0] : time.time() - start_time, fieldnames[1] : transData[0], fieldnames[2] : transData[1], fieldnames[3] : transData[2], fieldnames[4] : refData[0], fieldnames[5] : refData[1], fieldnames[6]: refData[2]})
        csvfile.close()
    refPulseOx.reset()

### EXAMPLE USE
# collect_spo2_data(1500)