The main question here is how your program is designed. If your acquisition is done via a UI timer, an asyncronous timer or a separate thread it will not be interrupted by a MessagePopup, unless it is issued in the exact function that is performing the acquisition (e.g. a MessagePopup called inside the async timer callback).
If this is your case, I suggest you use PostDeferredCall to call a callback outside the acquisition function (deferred callbacks are executed in the main thread, where normally runs the user interface). The callbackData parameter can be used to transmit informations to the deferred function.
On the other hand, if your acquisition is done within a control callback that runs a long loop... I suggest you to move to one of the structures I mentioned above!
