em_map_utils.demos.demo_map_covariance

demo_map_covariance.py

Author:

Ardan Patwardhan

Affiliation:

EMBL-EBI, Wellcome Genome Campus, CB10 1SD, UK

Date:

04/08/2025

Description:

Demonstrate the use of estimating map principal axes. A cuboid is first rotated by a known angle. The principal axes of the rotated map are used to estimate the back rotation of the map which is then applied to the map. Orthogonal surface views of the initial cuboid and the back-rotated cuboid are plotted and can be compared. They should be the same unless something has gone wrong with either the map rotation or the principal axes determination.

Attributes

logger

parser

Functions

plot_back_rotated_cuboid(in_file, lengths, box_size, ...)

A cuboid (or an optionally specified input map) is first rotated

Module Contents

em_map_utils.demos.demo_map_covariance.logger
em_map_utils.demos.demo_map_covariance.plot_back_rotated_cuboid(in_file, lengths, box_size, rotation, cubify, out_file)

A cuboid (or an optionally specified input map) is first rotated by a known angle. The principal axes of the rotated map are used to estimate the back rotation of the map which is then applied to the map. Orthogonal surface views of the initial map and the back-rotated map are plotted and can be compared.

Parameters:

  • in_file – Path to the optional input map or None.

  • lengths – Lengths of the cuboid.

  • box_size – Size of the 3D volume box.

  • rotation – Euler angle of rotation in an intrinsic frame following Z-Y’-Z” convention.

  • cubify – If the map is not cubic, pad it to the largest dimension before rotation operations.

  • out_file – Optional file to save the figure to.

Returns:

No return value.

em_map_utils.demos.demo_map_covariance.parser