I've been working with Pis since they came out, its a great little development board and I've done many projects with them, both successful and unsuccessful.
I wouldn't trust a Pi to control my drone, that and Android for Pi is not a success story. I would explore other avenues.
Neat, I wish I had area like that to explore close by.
Watch Expedition Overland on YT, they have some good video and you might pick up some ideas. And they're interesting to watch if you're into that kind of thing.
https://www.youtube.com/channel/UCiyiTqpss-ihtLHz-juFxIQ
I believe USA regs are 100m from whales, but not 100% sure. Researches are allowed to get closer, I believe 30m. I doubt a whale would even hear a drone at 30m.
Check out the whale photos by Stacy Garlington aka DroneDiva. She is involved in whale research so she does have an unfair advantage...
Thinking outside the bun here.... use mapping software (DroneDeploy, Maps Made Easy, Pix4D) and map the area, then get the ortho and you will be able to get GPS coords from the ortho.
Just a suggestion ;)
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