### Sidebar

#### Release history

This version is outdated by a newer approved version.This version (2021/10/11 17:07) is a draft.
Approvals: 0/1

This is an old revision of the document!

Generate and Apply Mask : Make a soft mask of the region to be excluded.

## Usage

Usage in command line

    sp_signalsubtract.py sp_mask --map2mask=map_to_make_mask_from --fullmap=full_map --outdir=output_subtraction_directory --mapthresh=threshold --verbosity=verbosity_level


## Typical usage

sp_signalsubtract comprises the steps needed to subtract masked regions from a map in order to focus on the remaining features from that map. There are six steps for this process (five within SPHIRE):

2. Locate regions to be subtracted

3. Mask a soft mask of the region to be excluded :

sp_signalsubtract.py sp_mask --map2mask=map_to_make_mask_from --outdir=output_subtraction_directory --fullmap=full_map --mapthresh=threshold


The map to make a mask from (–map2mask) corresponds to the region that you want to subtract.

!!!IMPORTANT!!! The full map which is to be multiplied by the mask (–fullmap) must NOT have been postprocessed (e.g., sharpened). Otherwise, re-projections will not be optimally comparable to the experimental images.

Grouped segments

## Input

#### Main Parameters

; ; --map2mask : : Map from which a mask will be generated. (default required string) ; ; --fullmap : : Map which will be multiplied by the mask. (default None) ; ; --outdir : : Directory where outputs will be written. (default required string) ; ; --mapthresh : : Full map will be initially binarized at this threshold. (default None)

; ; --verbosity : : Verbosity level : : Controls how much information will be written to the screen. (default 2)

## Output

; ; mask_final.hdf : : Final mask ; ; vol_masked.hdf : : Diagnostic masked input map ; ; ctf_params.txt : : CTF parameter file

## Description

Tapu Shaikh

### Keywords

Category 1:: APPLICATIONS

### Files

sphire/bin/sp_signalsubtract.py