em_map_utils.filled_cuboid

filled_cuboid.py

Author:

Ardan Patwardhan

Affiliation:

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

Date:

28/07/2025

Description:

Generate a 3D volume containing a filled cuboid.

Attributes

parser

Functions

filled_cuboid([lengths, box_size, inside_value, ...])

Generate a cuboid of given lengths.

Module Contents

em_map_utils.filled_cuboid.filled_cuboid(lengths=(80, 50, 20), box_size=(100, 100, 100), inside_value=1.0, outside_value=0.0, cent_coos=None, dtype=np.float32)

Generate a cuboid of given lengths.

Note: Coordinate system is (i,j,k) going from the slowest to fastest

varying axis.

Parameters:

  • lengths – Tuple/list/array of cuboid lengths aligned to box axes.

  • box_size – Tuple/list/array of box dimensions.

  • inside_value – Voxel value inside and on cuboid.

  • outside_value – Voxel value outside cuboid.

  • cent_coos – Centre coordinates of cuboid as tuple/list or array. If None, the centre of the box is used.

  • dtype – Data type of 3D volume. Note: it cannot be float64 for the current MRC format.

Returns:

3D numpy grid with a cuboid.

em_map_utils.filled_cuboid.parser