First, thanks to everyone for their suggestions and tips!! I'm going to 
describe my procedure and test results in detail for the benefit of people 
reading this post in the future. 

Here's my current setup:

*Computer: *
Macbook PRO 2.3 GHz i7
OS X 10.9.5

*Test Video:*
clip0076.mov
- 1080p 59.94fps
- movie is approx. 1 min 52 sec, 6,711 total frames
- file size is 419.9 MB


I'm using Hugin 2014.0.0 installed in /Applications/Hugin

I created a file named "hugin" in my paths.d folder with these paths:
/Applications/Hugin/Hugin.app/Contents/MacOS
/Applications/Hugin/Hugin.app/Contents/Resources
/Applications/Hugin/Hugin.app/Contents/Resources/HuginStitchProject.app/Contents/MacOS

This lets me run nona from the command line without having to type the full 
path

I installed FFmpeg using Homebrew:
https://trac.ffmpeg.org/wiki/CompilationGuide/MacOSX



*TEST RESULTS:*

1. Use FFmpeg to split the movie into a folder of numbered images:


METHOD 1 - lossless PNG

ffmpeg -i clip0076.mov frame-%05d.png

- 21 minutes to create 6,711 PNG files totaling 29.81 GB (70X the original 
file size!) 


METHOD 2 - high quality JPG

ffmpeg -i GOPR0076clip.mov -qscale:v 2 frame-%05d.jpg

- LESS THAN 2 minutes to create 6,711 JPG files totaling 3.88 GB (more 
reasonable)


2. Use Hugin to convert all of the images to Equirectangular Panini:

Here's the bash script (slightly modified from Carlos Cartola's suggestion):

# loop on the frames
for number in $(seq 1 $total); do
  n=$(printf %05d $number)
  echo $n
  nona -o out-$n /Users/design215/Video/_hugin/test.0001.pto frame-$n.jpg
done


test.0001.pto is a Hugin .pto file that I edited. I'm using this single 
.pto file to modify all of my images because the loop feeds each filename 
to the .pto file. 

- 1 HOUR, 4 minutes to create 6,711 corrected JPG images
- Images are all 2250x1362. I prefer to crop in Premiere, not Hugin


3. Use FFmpeg to combine the corrected images back into a movie:

ffmpeg -framerate 59.94 -i out-%05d.jpg -pix_fmt yuv420p -c:v libx264 -crf 
16 output.mp4

- 8 minutes to create output.mp4
- These settings give me the original framerate, and high quality output

output.mp4:
- 2250x1362p 59.94fps
- file size is 703.6 MB
- quality looks good!




*CONCLUSION:*The total time to do the conversion with my 2 minute clip = 1 
hour, 33 minutes using PNG images, or 1 hour, 14 minutes using JPG images.

Hugin gives me complete control over the projection and I can do exactly 
what I want.

The downsides to method are:
- My test clip was less than 2 minutes. Imagine the space you need for a 10 
minute clip.
- The images are re-compressed multiple times. Even if you start with PNG 
images, they are compressed once by Hugin, and again by FFmpeg when merging 
the images back to video. I know I could have Hugin output PNGs but then I 
would need at least 60 GB just to process 2 minutes of footage!

Don't get me wrong, the final video quality is VERY GOOD!

But, I can do almost the same thing in Photoshop CS6 with fewer steps and 
no folders with thousands of files.

The downsides to using Photoshop are:
- It takes just over 2 hours to process the same 2 minute clip.
- I have much less control than I have with Hugin. I can get close but not 
exactly what I want. 

My feeling is- There HAS to be a better, more efficient way to do this. 



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