Extract particles poses from a RELION 3.1 STAR file

relion31_particle_pose.py

import starfile
from scipy.spatial.transform import Rotation as R

particle_star_file = 'hiv/01_10.00Apx_particles.star'

star = starfile.read(particle_star_file)

df = df = star['particles'].merge(star['optics'], on='rlnOpticsGroup')

# get necessary info from dataframes
xyz = df[['rlnCoordinateX', 'rlnCoordinateY', 'rlnCoordinateZ']].to_numpy()
shifts_ang = df[['rlnOriginXAngst', 'rlnOriginYAngst', 'rlnOriginZAngst']].to_numpy()
pixel_size = df['rlnImagePixelSize'].to_numpy()
euler_angles = df[['rlnAngleRot', 'rlnAngleTilt', 'rlnAnglePsi']].to_numpy()

# Get absolute position and orientations
particle_positions = xyz - (shifts_ang / pixel_size)
rotation_matrices = R.from_euler(
    seq='ZYZ', angles=euler_angles, degrees=True
).inv().as_matrix()