odm2.py

import sys, datetime, time, platform, pickle

try:
    import serial
    from serial.tools.list_ports import comports
except ImportError as err:
    sys.exit("❌ Can't find pyserial module - install it by running 'pip install pyserial'")

class run():
    def __init__(self):
        if len(sys.argv) == 2:
            self.comments = sys.argv[1].replace(' ', '_')
        else:
            self.comments = input("Sample?  ").replace(' ', '_')
        self.basefilename = datetime.datetime.now().strftime("%Y%m%dT%H%M%S") + "_" + self.comments

        ports = 0
        port = ""
        for p in comports():
            print(str(p))
            if "USB" in str(p) or "usb" in str(p):
                port = p.name
                ports += 1
        if ports == 0:
            sys.exit("❌ No port found - is the Arduino plugged in?")
        if ports >= 2:
            sys.exit("❌ Too many ports found - unplug everything but the Arduino and try again")
        if platform.system() == "Darwin":  # if MacOS...
            port = "/dev/" + port   # ...prepend /dev/
        print("✅ Found an Arduino at " + port)

        self.data = []
        ser = serial.Serial(port, 115200, timeout=5)

        start_time = time.time()
        self.start_time = str(start_time)

        t1 = 300  # 5 minutes  300
        t2 = 30*60 + t1  # 30 minutes of dissolution

        ser.flush()
        ser.read_all()
        while True:
            try:
                et = time.time() - start_time
                if 0 <= et < t1-5:  # baseline phase
                    print(f"{str(datetime.timedelta(seconds=t1-et))}", end="\t")
                elif t1-5 <= et < t1:  # alarm phase
                    print(f"{str(datetime.timedelta(seconds=t1-et))}\a", end="\t")
                elif t1 <= et < t2:  # dissolution phase
                    print(f"{str(datetime.timedelta(seconds=t2-et))}", end="\t")
                elif et >= t2:  # experiment over
                    break
                s = ser.readline().decode("utf-8", "ignore")
                print(f"{ser.inWaiting()}\t{s}", end="")
                self.data.append(int(s))
            except:
                break
        self.stop_time = str(time.time())
        print("\n\aDONE")

if __name__ == "__main__":
    r = run()
    pickle.dump(r, open("out.pickle", "wb"))