Appion

Neil, looks like you are clipping non-square images and throwing away the excess pixels. Are there any consequences of this that people should be aware of? Image off center, any possibility of throwing out relevant info?

It is just clipping the square because our cross_correlation algorithm does not work with rectangles. The clipping is not saved it only used for this function.

When we get the new camera, Jim will probably fix the cross_correlation algorithm to work with rectangular images, but I don't want to do that for fear of breaking Leginon.

Neil, What's the best way to test this before the release? Could you provide some procedures?

You can test it on any dataset with defocal pairs. Just pick on ef and make a stack from en.