I have a quick question. I am trying to analyze the *rigid_traj.npy files from the patch motion correction, but the units of the numbers in the array is not clear. I believe it should be pixel or angstrom, but which one is correct? Thank you!
The units of the trajectories are in pixels, in terms of the dimensions of the raw movie data. So a trajectory with 1.0 pixel motion corresponds to 1.0 * psize where psize is the pixel size of the input movie data, before any Fourier-cropping.
This pixel size is also recorded in the .cs file that is outputted in patch motion, the field is rigid_motion/psize_A (pixel size in units of Å per pix).