LightboxResources_Final/LBDataComm_NoFluorescence.py at main · GormleyLab/LightboxResources_Final · GitHub

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#THIS VERSION IS TO USE THE LIGHTBOX AS A STANDALONE MODULE

import pandas as pd
import numpy as np
import xml.etree.ElementTree as ET
import serial
import time
print ()
print ()


#Set COM port depending on current user setup
serPort = 'COM6'
baudRate = 9600
ser = serial.Serial(serPort, baudRate)
startMarker = 60
endMarker = 62

def sendToArduino(sendStr):
    ser.write(sendStr.encode('utf-8')) # change for Python3


#======================================

def recvFromArduino():
    global startMarker, endMarker

    ck = ""
    x = "z" # any value that is not an end- or startMarker
    byteCount = -1 # to allow for the fact that the last increment will be one too many

    # wait for the start character
    while  ord(x) != startMarker:
        x = ser.read()

    # save data until the end marker is found
    while ord(x) != endMarker:
        if ord(x) != startMarker:
            ck = ck + x.decode("utf-8") # change for Python3
            byteCount += 1
        x = ser.read()

    return(ck)


#============================

def waitForArduino():

    # wait until the Arduino sends 'Arduino Ready' - allows time for Arduino reset
    # it also ensures that any bytes left over from a previous message are discarded

    global startMarker, endMarker

    msg = ""
    while msg.find("Arduino is ready") == -1:

        while ser.inWaiting() == 0:
            pass

        msg = recvFromArduino()

        print (msg) # python3 requires parenthesis
        print ()

#======================================

def runTest(td):
    numLoops = len(td)
    waitingForReply = False

    n = 0
    while n < numLoops:
        teststr = td[n]

        if waitingForReply == False:
            sendToArduino(teststr)
            print ("Sent from PC -- LOOP NUM " + str(n) + " TEST STR " + teststr)
            waitingForReply = True

        if waitingForReply == True:

            while ser.inWaiting() == 0:
                pass

            dataRecvd = recvFromArduino()
            print ("Reply Received  " + dataRecvd)
            n += 1
            waitingForReply = False

            print ("===========")

        time.sleep(5)


#======================================


def blockshaped(arr, nrows, ncols):
    """
    Return an array of shape (n, nrows, ncols) where
    n * nrows * ncols = arr.size

    If arr is a 2D array, the returned array should look like n subblocks with
    each subblock preserving the "physical" layout of arr.
    """
    h, w = arr.shape
    assert h % nrows == 0, "{} rows is not evenly divisble by {}".format(h, nrows)
    assert w % ncols == 0, "{} cols is not evenly divisble by {}".format(w, ncols)
    return (arr.reshape(h//nrows, nrows, -1, ncols)
               .swapaxes(1,2)
               .reshape(-1, nrows, ncols))


print ("Serial port " + serPort + " opened  Baudrate " + str(baudRate))
waitForArduino()
#Data sent to the Arduino for Lighting
a = [4095, 4095,4095,4095,4095,4095,4095,4095]
b = '<'+ ','.join(map(str, a)) + '>'
testData = [b]

runTest(testData)


ser.close()