em_map_utils.map_threshold¶

map_threshold.py

Author:: Ardan Patwardhan
Affiliation:: EMBL-EBI, Wellcome Genome Campus, CB10 1SD, UK
Date:: 05/08/2025
Description:: Threshold map.

Attributes¶

`logger`
`parser`

Classes¶

Classes¶
`MapHistogram`	Class to represent the map histogram, the related cumulative

Functions¶

`count_voxels_matching_criteria`(map, threshold, cuboid_dims)	Count the number of voxels in the map that are within the dimensions
`threshold_map`(map_grid)	Determine a threshold level for the map which is suitable for

Module Contents¶

em_map_utils.map_threshold.logger¶

class em_map_utils.map_threshold.MapHistogram(map_grid, histogram_bins=5000, sigma_factor=3.0, log_histogram=False)¶

Class to represent the map histogram, the related cumulative distribution function and histogram of the background (noise) in a map.

plot_map_histogram(log_y=True)¶

Plot the map histogram.

Parameters:: log_y – If True, log scale the y-axis of the map histogram.
Returns:: A tuple with the figure and axes objects.

plot_map_cdf()¶

Plot the map cumulative distribution function.

Returns:: A tuple with the figure and axes objects.

plot_bg_histogram(log_y=True)¶

Plots the background histogram.

Parameters:: log_y – If True, log scale the y-axis of the map histogram.
Returns:: A tuple with the figure and axes objects.

sigma_factor = 3.0¶

bin_width¶

cum_dist_func¶

map_hist_peak_idx¶

map_hist_peak_val¶

map_mean¶

map_var¶

map_sigma¶

bg_hist_sum¶

bg_frac¶

bg_mean_idx¶

bg_var_idx¶

bg_mean¶

bg_var¶

bg_sigma¶

bg_threshold¶

em_map_utils.map_threshold.count_voxels_matching_criteria(map, threshold, cuboid_dims)¶

Count the number of voxels in the map that are within the dimensions of a centred cuboid and with map values above a threshold.

Parameters:

map – Input map.
threshold – Threshold to count voxels with.
cuboid_dims – Only count voxels within a centred cuboid with these dimensions.

Returns:

Count of voxels within the cuboid and with map values above a threshold.

em_map_utils.map_threshold.threshold_map(map_grid)¶

Determine a threshold level for the map which is suitable for visualisation. A two-step procedure is used. First the background sigma in the map is estimated and a threshold is calculated based on this. The map is thresholded and then orthogonal line projection profiles are calculated. A second threshold is calculated based on the width of these profiles. These two values are averaged to a final value. Note: This algorithm exploits the characteristics of cryoEM maps

and may not work on synthetic maps.

Parameters:: map_grid – Input map.
Returns:: A tuple with the thresholded map, the threshold level, the histogram object and the line profile object.

em_map_utils.map_threshold.parser¶