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Comment: Zhong's name rule, function end with verbs

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get_defocus  Estimate defocus from 1D rotationally averaged power spectrum. This function is semiautomated, and requires the user to give correct cut_off frequency to determine the area of power spectrum for defocus estimation.  defocus_get  Estimate defocus from 1D rotationally averaged power spectrum. This function is semiautomated, and requires the user to give correct cut_off frequency to determine the area of power spectrum for defocus estimation. 
Name
defocus_get  Estimate defocus from 1D rotationally averaged power spectrum. This function is semiautomated, and requires the user to give correct cut_off frequency to determine the area of power spectrum for defocus estimation.
Usage
defocus = get_defocus((fnam_roo, volt=300,ps=1,cs=2,amplitude_contrast=.1,f_start=30,f_stop=8,docf="a",skip="#",round_off=100,nr1=3,nr2=6)
Input
 fnam_roo
 document file name of 1D rotational average of power spectrum
 volt
 voltage
 ps
 pixel size of the micrograph
 cs
 Sherical abberation constant
 amplitude_constrast
 amplitude constrast ratio
 f_start
 low frequency limit (in Ansgtrom) of selecting power spectrum containing strong CTF for defocus estimation. The default value is 30 Angstrom.
 f_stop
 high frequency limit (in Angstrom) of selecting power spectrum containing strong CTF for defocus estimation. The default value is 8 Angstrom.
 docf
 1D power spectrum document file format, either standard spider one "s" or arbitrary format "a"
 skip
 the mark of comments in the document file, such as ";", or "#"
 round_off
 round_off error,by default it is set as 100 Angstrom. By adjusting this number( set as 0.1), the estimated defocus can be accurate to 0.01 Angstrom.
 nr1
 the highest rank of polynomials used to fit envelop function
 nr2
 the highest rank of polynomials used to fit background noise
Output
 defocus
 the estimated defocus in Angstrom.
Options
Description
 The function requires the user to define the area in the 1D rotationally averaged power spectrum for defocus estimation.
 Empirically power spectrum from 1/30 Ansgtrom to 1/8 Angstrom contains discernable CTF traces, and tends to give estimation which is close to the true defocus setting.
 The starting frequency is supposed to exclude the protein peak, and other spurious peaks caused by artifacts.
 The stopping freqeuncy is supposed to exclude too flat area of the power spectrum in high frequency area, which tends to underestimate the defocus.
 This function won't estimate astigmatsim.
Method
 Constrained simplex method.
Reference
.1. 1. Barrodale and F.D.K. Roberts L1 solution to linear equations subject to linear equality and inequality constraints ACM TOMS 6 (1980), 231235.
.2. Z. Huang, P. R. Baldwin, S.Mullapudi, and P .A. Penczek, Automated determination of parameters describing power spectra of micrograph images in electron microscopy. J. Struct. Biol. 144 (2003), pp. 79–94.
Author / Maintainer
Zhong Huang
Keywords
 category 1
 UTILITIES
Files
utilities.py
See also
["guess defocus"],["pw extract"]
Maturity
 stable
 works for most people, has been tested; test cases/examples available.
Bugs
None. It is perfect.