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pipeline:subtract:avgfilt
The most recent version of this page is a draft.This version (2021/02/02 13:56) was approved by twagner.

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## sp_signalsubtract avgfilt

Average and Filter : Average and low-pass filter a map for segmentation.

## Usage

Usage in command line

	sp_signalsubtract.py avgfilt --avol1=map_to_average_1 --avol2=map_to_average_2 --outdir=output_subtraction_directory --apix=pixel_size --filtrad=filter_radius --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):

1. Average and low-pass filter a map for segmentation :

sp_signalsubtract.py avgfilt --avol1=map_to_average_1 --avol2=map_to_average_2 --outdir=output_subtraction_directory --apix=pixel_size --filtrad=filter_radius

Generate a denoised map for segmentation. The input map(s) can be postprocessed (i.e., sharpened, masked, etc.), but it is important that the final map that is masked below (in Step 4) is not postprocessed.

Choose a low-pass filter radius so that a permissive (i.e., low) surface threshold can be used in Chimera. If too high a threshold is used during segmentation, then the resulting mask may not encapsulate the entire region of interest. If a low threshold is used on a not-post-processed high-resolution map, then disconnected “moon” densities will be included in the segmentation.

Segmented map after low-pass filtration
Segmented map without low-pass filtration

Note 1: If you already have an averaged map, or don't have two maps to average, skip the '–avol2' flag.

Note 2: Low-pass filter radius should be in units of Angstroms if pixel size (–apix) is provided. If pixel size is not provided, then the program expects the filter radius in units of absolute frequency (px^-1)

2. Locate regions to be subtracted

## Input

#### Main Parameters

--avol1
First map to average. (default required string)
--avol2
Second map to average. If not provided, first map will be used. (default None)
--outdir
Directory where outputs will be written. (default required string)
--filtrad
Low-pass filter radius. (default None)
--apix
Pixel size in Angstroms. (default None)

#### Advanced Parameters

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

## Output

vol_avg_unfil.hdf
Average of input half-set maps, unfiltered.
vol_avg_fil.hdf
Low-pass filtered average of input half-set maps.
input_filtered.hdf
Low-pass filtered input map.
Unfiltered map (yellow), low-pass filtered map (transparent cyan)

## Description

Tapu Shaikh

### Keywords

Category 1:: APPLICATIONS

### Files

sphire/bin/sp_signalsubtract.py

### Maturity

Beta:: Under evaluation and testing. Please let us know if there are any bugs.

### Bugs

/web/sphire/www/sphire/wiki/data/pages/pipeline/subtract/avgfilt.txt · Last modified: 2021/02/12 11:32 by shaikh