You only need to use that

You only need to use that method if you want to manually override the default rotation of an image at some part in the processing pipeline.

Instead, you want to use the outputImageOrientation property of the camera input to set the rotation of the input image to match your interface. You use code like the following to do that:

videoCamera.outputImageOrientation = UIInterfaceOrientationPortrait

with the orientation being replaced by whatever your actual interface orientation is at that moment. You change this value in response to changes in the rotation of your interface.

As far as what's meant by the index in the method you're referring to, you can see that defined in GPUImageFilter. The index is the location of the particular input you're trying to rotate. This primarily comes into play for two-input blends and filters like that.

Sunset Lake Software - Comments for "setInputRotation:atIndex:"

You only need to use that