I'm not very familiar with how tkinter does things, but kivy requires a slightly different mental model here. You don't want to stop and start the eventloop in between bits of python code, but instead probably want to start the popup, pass any state you need into it or store it somewhere else, then bind the result of the popup (e.g. when the user presses a 'done' button) to some new function that does the rest of your calculation.
I can provide an example if you like, especially if you give more information about what you're trying to do.