Adding in clipping to aligned images

I've clipped the bottom of the aligned images, so that each column is shifted down until the bottom pixel exceeds some threshold (a new option called "threshold" in the function "get_image_values_2").

The images are also clipped on the top, so that the edges are sharp, rather than fading away.

Finally, the images are downsampled by a factor of two (this is the "over-sampling" we discussed).

I've replaced the rotation by 90 degrees with a transposition. If you change this, you shouldn't do so in the function "get_image_values_2," but rather in the main function, once the output has been returned. This is because changing how "get_image_values_2" works might ruin the new image clipping feature.

When you actually run this code, you should remove the plotting code in "get_image_values_2" that I added for testing purposes.