Hi,

the best solution I have found for the moment is to 
 - slice the video on picture (I use premiere but you can have a lot of 
method to do that)
 - create one template .pto with all the modification you want to do
 - copy the template the time you have of picture (3600 times for you...)
 - change the name of the picture inside the pto
 - use the batch tool on hugin to import all the pto and process them

I have made a little tool with processing to copy the pto and change the 
picture name inside
you can take a look and modify the code to make what you want

If you don't know how to play with processing let me know and if I have 
time I do a special version for you
https://fablabwgtn.github.io/Mobile-360/post/tutorial-stitch.html

Zoilo

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