I ended up using jquery's replaceWith command and gave all the frames a class "frame" that i could select with $('.frame') which happened to only select visible frames.
<script type="text/javascript">
var animation = [];
var firstFrame = 1;
var lastFrame = 96;
var animationFrames = 16;
var loadedImageCount = 0;
$(function() {
$("button, input:submit",'#forecastForm').button();
$("#progressbar").progressbar({
value: 0
});
$('#id_Species').attr('onChange', 'loadAnimation($(\'#id_Species\').val(),$(\'#id_Layer\').val(),$(\'#id_StartTime\').val(),$(\'#id_EndTime\').val())' )
$('#id_Layer').attr('onChange', 'loadAnimation($(\'#id_Species\').val(),$(\'#id_Layer\').val(),$(\'#id_StartTime\').val(),$(\'#id_EndTime\').val())' )
$('#id_StartTime').attr('onChange', 'loadAnimation($(\'#id_Species\').val(),$(\'#id_Layer\').val(),$(\'#id_StartTime\').val(),$(\'#id_EndTime\').val())' )
$('#id_EndTime').attr('onChange', 'loadAnimation($(\'#id_Species\').val(),$(\'#id_Layer\').val(),$(\'#id_StartTime\').val(),$(\'#id_EndTime\').val())' )
});
if (document.images) { // Preloaded images
loadAnimation('Dry_GEM',1,1,96);
}
function rotate(animation, frame)
{
if (frame >= animation.length)
frame = 0;
$('.frame').replaceWith(animation[frame]);
window.setTimeout('rotate(animation,'+eval(frame+1)+')',150);
}
function loadAnimation(species, layer, startTime, endTime)
{
layer = Number(layer);
startTime = Number(startTime);
endTime = Number(endTime);
if (startTime > endTime)
{
swap = startTime;
startTime = endTime;
endTime = swap;
delete swap;
}
for (i=0;i<animation.length;i++)
delete animation[i];
delete animation;
animation = []
$('#progressbar').progressbar({value: 0});
loadedImgCount = 0;
animationFrames = endTime - startTime + 1;
for(i=0;i < animationFrames;i++)
{
animation[i] = new Image();
animation[i].height = 585;
animation[i].width = 780;
$(animation[i]).attr('class','frame');
animation[i].onload = function()
{
loadedImgCount += 1;
$('#progressbar').progressbar({value: eval(loadedImgCount / animationFrames * 100)});
};
animation[i].src = 'http://[[url]]/hemi_2d/' + species + '_' + layer + '_' + eval(i+startTime) + '.png';
}
}
</script>