[Python] How do I implement a stop button with Tkinter for a stepper motor system?

I have a question regarding the use of a stop button in Tkinter.

For an experiment, I have to set up and X/Y stage that works by using two stepper motors. The arduino program works perfectly. The only problem is that when I activate the start function, which drives the stage to various coordinates, it freezes. Now the problem is that it has to run for weeks on end and it needs a stop button for emergencies and stopping the stepper motor in general. The stop button has to do two things: it has to stop the stepper driver motors, and it has to break the tkinter.after loop. However, due to the freezing, it is impossible to click on the button.

Here is my code:

import tkinter as tk
import serial

ser = serial.Serial('COM5', 115200)

running = False

def quit():
"""Function that closes the serial port and destroys the root of the GUI"""
global root
ser.close()
root.destroy()

def route():
"""Writes coordinates to the arduino, which in return drives the stepper motors"""
if running == True:
# The g line stands for go to!
ser.write(b'g115000\r\n')
root.after(50)
ser.write(b'g225000\r\n')
root.after(30000)
ser.write(b'g1400\r\n')
root.after(50)
ser.write(b'g2500\r\n')

root.after(12000,route())


def zeroing():
"""Zeros the program, this is necessary for the stage to
calibrate it's boundary conditions"""
#zeros the stage so that it is ready to use!
varLabel.set("zeroing, please move away from the stage")
#the z command zeros the motors for boundary business
ser.write(b'z\r\n')

def run_program():
"""Runs the function Route and sets running to True (not a good start/stop system)"""
#starts the program, but only after you zero the stage
global running
running = True
varLabel.set("Program running")
route()

def stop_program():
"""Sets the running flag to False and sends a stop command to the arduino"""
#stops the program immediately
global running
running = False
varLabel.set("Program stopped,please zero before continuing")
#the s byte is a command that stops the stepper motors
ser.write(b's\r\n')


if __name__== "__main__":
root = tk.Tk()

canvas1 = tk.Canvas(root, width=800, height=400)
canvas1.pack()

root.title('XY-stage controller')

#instructions
instructions = tk.Label(root,text='Enter the amount of hours you want your measurements to last in the text box.'
'\n Click on run program to start a measurement session.'
'\n Click on stop incase of an emergency or if it is wanted to stop the program.',
font = "Raleway")

instructions.pack(side='bottom')

# initialize active labels
varLabel = tk.IntVar()
tkLabel = tk.Label(textvariable=varLabel,)
tkLabel.pack(side='top')


# Buttons for initializing a bunch of good functions

zerobutton = tk.IntVar()
tkrunprogram= tk.Button(
root,
text='Zero',
command = zeroing,
height = 4,
fg = "black",
width = 10,
bg = 'gray',
bd = 5,
activebackground = 'green'
)
tkrunprogram.pack(side='top')

runprogbutton = tk.IntVar()
tkrunprogram= tk.Button(
root,
text='Run Program',
command = run_program,
height = 4,
fg = "black",
width = 10,
bg = 'gray',
bd = 5,
activebackground = 'green'
)
tkrunprogram.pack(side='top')

stopbutton = tk.IntVar()
tkstopprog= tk.Button(
root,
text='Stop Program',
command = stop_program,
height = 4,
fg = "black",
width = 10,
bg = 'gray',
bd = 5,
activebackground = 'red'
)
tkstopprog.pack(side='top')

Buttonquit = tk.IntVar()
tkButtonQuit = tk.Button(
root,
text='Quit',
command = quit,
height = 4,
fg = "black",
width = 10,
bg = 'yellow',
bd = 5
)

# initialize an entry box
entry1 = tk.Entry(root)
durbox = canvas1.create_window(400, 200, window=entry1)
tkButtonQuit.pack(side='top')

root.mainloop()


The after commands in the end will introduce pauses of 60 minutes, which would make the program freeze for 60 minutes. Hopefully there is an easy solution to interrupting the function!

Thank you in advance!

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