Local motion correction distances

Motion Correction
1

Hello
How can I get a list of all the particles motion distances in a local motion correction job?
Thanks for your help
Ran

2

Hi @zalkr, if you’re familiar with Python programming, you could go into the local motion job directory, and then open the files localmotioncorrected/*_particles_traj.npy using numpy.load. There’s one such file per source micrograph, each containing a numpy array of shape [P,Z,2] where P is the number of particles in that micrograph, Z is the number of frames that were used for motion correction, and the last dimension stores the x and y components of the displacement for that particle, at that frame number. From there, you can do whatever you want. Note that the trajectories include rigid motion (that is, stage drift).
–Harris

3

Thanks! ChatGPT is a close friend for those not familiar with python programming :^)
Ran

1 Like
4

Hi @hsnyder , where does one find information on the array shapes for the different types of motioncor jobs, other than asking here? E.g. bending_traj gives (2,4,3,3), what is what in that array shape? In the end I want to make fluence plots.
Wim