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pipeline:subtract:sp_mask
This version (2021/10/11 17:13) was approved by shaikh.

sp_signalsubtract sp_mask

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):


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


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
Final mask


4. Compute re-projections of map to be subtracted, and subtract them from the original images


5. Compute reconstruction of density remaining after signal-subtraction


6. Center map of the remaining density

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)

Advanced Parameters

--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

Method

Reference

Developer Notes

Author / Maintainer

Tapu Shaikh

Keywords

Category 1:: APPLICATIONS

Files

sphire/bin/sp_signalsubtract.py

See also

Maturity

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

Bugs

pipeline/subtract/sp_mask.txt · Last modified: 2021/10/11 17:13 by shaikh