Python Delays on Raspberry Pi

Question

I am trying to model the complex action potential for calibrating research tools. The goal is to provide a signal with a frequency of 10 μV at 250 Hz. Low voltage will be considered later, the main problem for me is the frequency. The figure below shows an overview of the system I'm trying to make.

By collecting data from a live animal and processing the data in MATLAB, I made a low-noise signal with 789 values ​​in 12-bit format. Then I cloned the repository where I saved this in csv format for Raspberry Pi using Git. Below is the Python script I wrote in RPi. You can skip the main section in the script to see the functionality.

#!/usr/bin/python

import spidev
from time import sleep
import RPi.GPIO as GPIO
import csv
import sys
import math

DEBUG = False
spi_max_speed = 20 * 1000000
V_Ref = 5000
Resolution = 2**12
CE = 0

spi = spidev.SpiDev()
spi.open(0,CE)
spi.max_speed_hz = spi_max_speed

LDAQ = 22
GPIO.setmode(GPIO.BOARD)
GPIO.setup(LDAQ, GPIO.OUT)
GPIO.output(LDAQ,GPIO.LOW)

def setOutput(val):
    lowByte = val & 0b11111111 #Make bytes using MCP4921 data sheet info
    highByte = ((val >> 8) & 0xff) | 0b0 << 7 | 0b0 << 6 | 0b1 << 5 | 0b1 << 4
    if DEBUG :
        print("Highbyte = {0:8b}".format(highByte))
        print("Lowbyte =  {0:8b}".format(lowByte))
    spi.xfer2([highByte, lowByte])

def main():
    with open('signal12bit.csv') as signal:
        signal_length = float(raw_input("Please input signal length in ms: "))
        delay = float(raw_input("Please input delay after signal in ms: "))
        amplitude = float(raw_input("Please input signal amplitude in mV: "))
        print "Starting Simulant with signal length %.1f ms, delay %.1f ms and amplitude %.1f mV." % (signal_length, delay, amplitude)
        if not DEBUG : print "Press ctrl+c to close."
        sleep (1) #Wait a sec before starting
        read = csv.reader(signal, delimiter=' ', quotechar='|')
        try:
            while(True):
                signal.seek(0)
                for row in read: #Loop csv file rows
                    if DEBUG : print ', '.join(row)
                    setOutput(int(row)/int((V_Ref/amplitude))) #Adjust amplitude, not super necessary to do in software
                    sleep (signal_length/(data_points*1000) #Divide by 1000 to make into ms, divide by length of data
                sleep (delay/1000)
        except (KeyboardInterrupt, Exception) as e:
            print(e)
            print "Closing SPI channel"
            setOutput(0)
            GPIO.cleanup()
            spi.close()

if __name__ == '__main__':
    main()

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Answer 1

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#!/usr/bin/python

import spidev
from time import sleep
import RPi.GPIO as GPIO
import sys
import csv
import ast

spi_max_speed = 16 * 1000000 # 16 MHz
V_Ref = 5000 # 5V in mV
Resolution = 2**12 # 12 bits for the MCP 4921
CE = 0 # CE0 or CE1, select SPI device on bus
total_data_points = 9600 #CSV file length

spi = spidev.SpiDev()
spi.open(0,CE)
spi.max_speed_hz = spi_max_speed

LDAQ=22
GPIO.setmode(GPIO.BOARD)
GPIO.setup(LDAQ, GPIO.OUT)
GPIO.output(LDAQ,GPIO.LOW)

def main():

    #User inputs and checking for digits
    signalLengthU = raw_input("Input signal length in ms, minimum 4: ")
    if signalLengthU.isdigit():
        signalLength = signalLengthU
    else:
        signalLength = 4

    delayU = raw_input("Input delay after signal in ms: ")
    if delayU.isdigit():
        delay = delayU
    else:
        delay = 0

    amplitudeU = raw_input("Input signal amplitude in mV, between 1 and 5000: ")
    if amplitudeU.isdigit():
        amplitude = amplitudeU
    else:
        amplitude = 5000

    #Calculate data points, delay, and amplitude
    data_points = int((1000*float(signalLength)-24.6418)/12.3291)
    signalDelay = float(delay)/1000
    setAmplitude = V_Ref/float(amplitude)

    #Load and save CSV file
    datain = open('signal12bit.csv')
    read = csv.reader(datain, delimiter=' ', quotechar='|')
    signal = []
    for row in read:
        signal.append(ast.literal_eval(row[0]))

    #Downsampling to achieve desired signal length
    downsampling = int(round(total_data_points/data_points))
    signalSpeed = signal[0::downsampling]
    listlen = len(signalSpeed)

    #Construction of SPI bytes, to avoid calling functions in critical loop
    lowByte = []
    highByte = []
    for i in signalSpeed:
        lowByte.append(int(i/setAmplitude) & 0b11111111)
        highByte.append(((int(i/setAmplitude) >> 8) & 0xff) | 0b0 << 7 | 0b0 << 6 | 0b1 << 5 | 0b1 << 4)

    print "Starting Simulant with signal length %s ms, delay %s ms and amplitude %s mV." % (signalLength, delay, amplitude)
    print "Press ctrl+c to stop."
    sleep (1)

    try:
        while(True): #Main loop
            for i in range(listlen):
                spi.xfer2([highByte[i],lowByte[i]]) #Critical loop, no delay!
            sleep (signalDelay)
    except (KeyboardInterrupt, Exception) as e:
        print e
        print "Closing SPI channel"
        lowByte = 0 & 0b11111111
        highByte = ((0 >> 8) & 0xff) | 0b0 << 7 | 0b0 << 6 | 0b1 << 5 | 0b1 << 4
        spi.xfer2([highByte, lowByte])
        GPIO.cleanup()
        spi.close()

if __name__ == '__main__':
    main()

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