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[PeejAvery]

Keep a hidden button in the parent which calls a function on click.
Click this button from the popup.

Nice one. I tried the code below and it works nicely.

<input id="execbutton" type="button" value="Click Here" onclick="alert('It Worked!')" style="display:none">

<script language="JavaScript">
document.getElementById('execbutton').click();
</script>

One other thing, newer browsers even accept function calls between windows. I just found it and I never knew about it even though it seemed dumb to not work this way.

All you have to do is call the window's name and then the function.

windowname.window.function();

Sorry gilly914 for making that one hard on you.