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So, I did some testing and adding the scale augmentation improved all the models that include images from different sources (where the animals have different sizes).
I will post a more quantitative analysis when everything is done, but visually things are better and the switches are gone!
I implemented two options. Scaling + DLC and scaling + DLC + horizontal/vertical flips.
It is getting a bit wild with all the options. I wondered if it makes sense to let the user pass multiple augmentation building blocks and then build the logic around that. So the user passes a list like so: [dlc, topdown, lr, scale].
I also noticed that currently the exact settings of the augmentation can't be changed in the config. Maybe it's a bit overkill for now, but I could imagine augmentations being its own part of the config in the future.