em_map_utils.filled_sphere

filled_sphere.py

Author:

Ardan Patwardhan

Affiliation:

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

Date:

28/07/2025

Description:

Generate a 3D volume of filled sphere.

Attributes

parser

Functions

filled_sphere([diameter, box_size, inside_value, ...])

Generate a 3D volume containing a filled sphere.

Module Contents

em_map_utils.filled_sphere.filled_sphere(diameter=50, box_size=(100, 100, 100), inside_value=1.0, outside_value=0.0, cent_coos=None, dtype=np.float32)

Generate a 3D volume containing a filled sphere.

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

varying axis.

Parameters:

  • diameter – Diameter of the filled sphere in voxels.

  • box_size – Lengths of the sides of the 3D volume along the (i,j,k) axes.

  • inside_value – Map value inside and on the filled sphere.

  • outside_value – Map value outside the filled sphere.

  • cent_coos – Centre (i,j,k) coordinates of the filled sphere. If none are specified, 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 filled sphere.

em_map_utils.filled_sphere.parser