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===== sp_bestsmear =====

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

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===== 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 

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===== 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
[{{ :pipeline:meridien:smear_nocutoff.png?200|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
[{{ :pipeline:meridien:smear_cutoff999.png?200|Distribution before (top) and after (bottom) cutoff}}]

If no input stack is provided, then only the plots, selection files, etc., will be written.
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===== 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)
  
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=== 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)
  
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===== Output =====
  ; plot_smear.png : Plot of smear distribution(s)
  ; bdb:bestsmear : Stack of selected particles
 
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===== Description =====

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==== Method ====

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==== Reference ====
 
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==== Developer Notes ====

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==== Author / Maintainer ====
Tapu Shaikh

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==== Keywords ====
Category 1:: APPLICATIONS

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==== Files ====
sphire/bin/sp_bestsmear.py

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==== See also ====

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

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==== Bugs ====

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