Manpage of calcSSNR
Section: User Commands (1)
Return to Main Contents
calcSSNR - calculate the spectral signal-to-noise ratio of an alignment
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
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'.
PEET(1), plotSSNR(1), prmParser(1), prepareEM(1), prepareRef(1), mergeEM(1),
averageAll(1), alignSubset(1), and calcFSC(1)
- SEE ALSO
This document was created by
using the manual pages.
Time: 16:44:59 GMT, March 05, 2018