Content-type: text/html Manpage of calcSSNR

calcSSNR

Section: User Commands (1)
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NAME

calcSSNR - calculate the spectral signal-to-noise ratio of an alignment  

SYNOPSIS

calcSSNR file.prm  

DESCRIPTION

calcSSNR calculates spectral signal-to-noise ratios (SSNR) of a set of particle averages. Each average specified is compared to the individual particles used to construct the average, generating a SNR measurement as a function of frequency (or resolution). Results are written to text files and can be graphed using plotSSNR.

Parameter file 'file.prm' is a MATLAB readable text file that specifies parameter values in MATLAB syntax. Because calcSSNR uses averaged volumes written by averageAll, no parameters which can effect particle selection or averaging should be altered between running averageAll and calcSSNR, or the results may not be valid. (See the PEET and averageAll man page for descriptions of these parameters). Several additional, optional parameters effecting the SSNR calculation are listed below. These parameters, some of which are shared with calcFSC, all have reasonable defaults, and may be safely modified after running averageAll. Extra parameters used to control the other programs are ignored by calcSSNR and vice versa, so a single parameter file is often sufficient even when modifying some parameters. Sample parameter files describing the optional parameters are available in $PARTICLE_DIR/templates.

calcSSNR needs to be run in the same directory where alignSubset and averageAll were run.

freqShells = vector
The upper limit of each frequency shell. The default is [0.025:0.025:0.5].
windowName = string
The type of the mask window to apply to the data, 'gaussian', 'hamming', etc. The default is 'gaussian'. If windowName is 'file', windowParams must be a string with the name of an MRC file containing the mask.
windowParams = vector
The parameters to pass to the window generation function. For a gaussian window, the parameters are [radius sigma]; see gaussianMask in MATLAB help. The default is [0.35 0.05].
windowCenter = vector
The center of the mask window (default: [ ] = volume center). The default is floor(szVol/2)+1.
 

FILES

Sample parameter files are available in $PARTICLE_DIR/templates.

calcSSNR stores results in 4 text files in the current working directory. 'szVoxelSSNR.txt' contains the pixel size in Angstroms. 'nParticlesSSNR.txt' contains the number of particles in the various averages. 'freqShells.txt' has the value for parameter 'freqShells'. 'arrSSNR.txt' contains a 2 dimensional array of SSNR values. Each of its columns corresponds to a number of particles averaged, with rows corresponding to frequencies in 'freqShells'.  

AUTHORS

Rick Gaudette
Quanren Xiong
John Heumann  

SEE ALSO

PEET(1), plotSSNR(1), prmParser(1), prepareEM(1), prepareRef(1), mergeEM(1), averageAll(1), alignSubset(1), and calcFSC(1)


 

Index

NAME
SYNOPSIS
DESCRIPTION
FILES
AUTHORS
SEE ALSO

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Time: 21:10:05 GMT, March 20, 2017