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pipeline:meridien:sp_bestsmear
This version (2021/02/19 17:00) was approved by shaikh.

sp_bestsmear

Best Smear : Shows distribution of particle smear and obtain subset.


Usage

Usage in command line

	sp_bestsmear.py meridien_params output_directory --max_smear=maximum_smear --stack=input_stack --verbosity=verbosity --iter=iteration_num --threads=num_threads 


Typical usage

The “smear” is the number of reference images to which Meridien has found a correlation. The assumption behind this utility is that a lower smear corresponds to higher certainty.

The purpose of sp_bestsmear.py is to:

: show the distribution of smear number for an iteration of Meridien
: select a subset of the particles with the lowest smear number
Distribution with no cutoff


1. Show the distribution of smear number:

sp_bestsmear.py meridien_params output_directory  

The main output is a distribution of the smear over the particle set.


2. Select a subset of the particles with the lowest smear:

sp_bestsmear.py meridien_params output_directory --max_smear=999 --stack=bdb:input_stack
Distribution before (top) and after (bottom) cutoff

If no input stack is provided, then only the plots, selection files, etc., will be written.

Input

Main Parameters

meridien_params
Parameter file from Meridien. (default required string)
output_directory
Toplevel directory where outputs will be written. (default required string)
--max_smear
Maximum smear number to allow. (default None)
--stack
Particle stack from which subset will be selected. (default None)
--verbosity
Controls how much information will be written to the screen. (default 3)


Advanced Parameters

--iter
Iteration number from Meridien
Only necessary if the Meridien parameter filename can't be parsed. (default None)
--threads
Number of parallel threads used during Meridien
Will be determined automatically if not specified. (default None)


Output

plot_smear.png
Plot of smear distribution(s)
bdb:bestsmear
Stack of selected particles


Description


Method


Reference


Developer Notes


Author / Maintainer

Tapu Shaikh


Keywords

Category 1:: APPLICATIONS


Files

sphire/bin/sp_bestsmear.py


See also


Maturity

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


Bugs


pipeline/meridien/sp_bestsmear.txt · Last modified: 2021/02/19 17:00 by shaikh