Tkinter button executing script throws NameError

If you need to run code from another python script, then you should use an import to get the other script and run a function in the other script. This will be a problem with your code since you have the core of your program outside of a function, so it would run as soon as it's imported. For the reason (and others) you should have all of your code in functions. You can detect if the code was imported or not by checking the __main__ attribute.

I restructured your code to move all the code into functions, then import it and call the appropriate function from the GUI buttons.

This is what your GUI code should look like:

import tkinter

import motionindexthreshold
import motionindexgenerator
import stepthrough

def main():
    top=tkinter.Tk()
    top.geometry("300x350")
    top.config(background='black')
    top.title('Test')
    top.resizable(height=False, width=False)

    M = tkinter.Message(top, text='Test', width=280, background='black', foreground='white', font=('Courier', 28))
    B = tkinter.Button(top,text="Define Motion Index Threshold",command=motionindexthreshold.main)
    C = tkinter.Button(top,text="Autoremove Nonmovement Video Segments",command=motionindexgenerator.main)
    D = tkinter.Button(top,text="Tag Video Frames",command=stepthrough.main)
    E = tkinter.Button(top,text="Quit", command=top.destroy)
    B.config(height=5, width=80, background='red')
    C.config(height=5, width=80, background='blue', foreground='white')
    D.config(height=5, width=80, background='yellow')
    E.config(height=5, width=80, background='green')
    M.pack()
    B.pack()
    C.pack()
    D.pack()
    E.pack()
    top.mainloop()

if __name__ == '__main__':
    main()

And this is what your module code should look like:

import cv2
import tkinter as tk
from tkinter.filedialog import askopenfilename

def stanceTag(cap, framevalues):    
    framevalues.append('0' + ' ' + '|' + ' ' + str(int(cap.get(1))))
    print (str(int(cap.get(1))), '/', length) 
    print(framevalues)

def swingTag(cap, framevalues):
    framevalues.append('1' + ' ' + '|' + ' ' + str(int(cap.get(1))))
    print (str(int(cap.get(1))), '/', length)
    print(framevalues) 

def unsureTag(cap, framevalues):
    framevalues.append('-1' + ' ' + '|' + ' ' + str(int(cap.get(1))))
    print (str(int(cap.get(1))), '/', length) 
    print(framevalues)

def rewindFrames(cap, framevalues):
    cap.set(1,((int(cap.get(1)) - 2)))
    print (int(cap.get(1)), '/', length) 
    framevalues.pop()
    print(framevalues)  


def main():
    framevalues = []
    count = 1

    selectedvideo = askopenfilename()
    selectedvideostring = str(selectedvideo)
    cap = cv2.VideoCapture(selectedvideo)
    length = int(cap.get(cv2.CAP_PROP_FRAME_COUNT))

    while (cap.isOpened()): 
        ret, frame = cap.read()

        # check if read frame was successful
        if ret == False:
                break
        # show frame first
        cv2.imshow('frame',frame)

        # then waitKey
        frameclick = cv2.waitKey(0) & 0xFF

        if frameclick == ord('a'):
            swingTag(cap, framevalues)

        elif frameclick == ord('r'):
            rewindFrames(cap, framevalues)

        elif frameclick == ord('s'):
            stanceTag(cap, framevalues)

        elif frameclick == ord('d'):
            unsureTag(cap, framevalues)

        elif frameclick == ord('q'):
            with open((selectedvideostring + '.txt'), 'w') as textfile:
                for item in framevalues:
                    textfile.write("{}\n".format(item))
            break

        else:
            continue

    cap.release()
    cv2.destroyAllWindows()

if __name__ == '__main__':
    # this is called if this code was not imported ... ie it was directly run
    # if this is called, that means there is no GUI already running, so we need to create a root
    root = tk.Tk()
    root.withdraw()
    main()

Obviously this is a guess; I have no way to test if this solves your issue, but I think it will.