def calc_crystal_frame_vectors(reflection_table, experiments):
"""Calculate the diffraction vectors in the crystal frame."""
reflection_table["s0"] = flex.vec3_double([experiments.beam.get_s0()] *
len(reflection_table))
rot_axis = flex.vec3_double([experiments.goniometer.get_rotation_axis()])
angles = reflection_table[
"phi"] * -1.0 * pi / 180 # want to do an inverse rot.
reflection_table["s1c"] = rotate_vectors_about_axis(
rot_axis, reflection_table["s1"], angles)
reflection_table["s0c"] = rotate_vectors_about_axis(
rot_axis, reflection_table["s0"], angles)
reflection_table["s1c"] = align_rotation_axis_along_z(
rot_axis, reflection_table["s1c"])
reflection_table["s0c"] = align_rotation_axis_along_z(
rot_axis, reflection_table["s0c"])
return reflection_table
def align_rotation_axis_along_z(exp_rot_axis, vectors):
"""Rotate the coordinate system such that the exp_rot_axis is along z."""
if list(exp_rot_axis) == [(0.0, 0.0, 1.0)]:
return vectors
(ux, uy, uz) = exp_rot_axis[0][0], exp_rot_axis[0][1], exp_rot_axis[0][2]
cross_prod_uz = flex.vec3_double([(uy, -1.0 * ux, 0.0)])
angle_between_u_z = +1.0 * acos(uz / ((ux**2 + uy**2 + uz**2)**0.5))
phi = flex.double(vectors.size(), angle_between_u_z)
new_vectors = rotate_vectors_about_axis(cross_prod_uz, vectors, phi)
return flex.vec3_double(new_vectors)
