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prmParser

Section: User Commands (1)
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NAME

prmParser - parse parameter file and create command files for parallel processing  

SYNOPSIS

prmParser file.prm  

DESCRIPTION

prmParser parses file.prm and outputs a complete set of .com command files for parallel processing. The first file, -start.com, runs prepareEM and prepareRef. Subsequent results vary, depending on the number of volumes and particles to be processed. When multiple volumes are to be processed (indicated by multiple lines in the eTomo Volume Table, or, equivalently, by multiple entries in the parameter file fnVolume array), when the total number of particles present is more than 100, and when at least one volume contains more than 10 particles, parallel averaging is used; if not, serial averaging is used. Multiple references to the same volume are treated as multiple volumes. This provides a way to force parallel averaging when a single volume containing many particles is to be processed. Conversely, parallel averaging may be disabled by setting flgAllowParallelAveraging = 0 in the parameter file.

For serial averaging, numbered files run alignSubset on a specified subset of the particles. A numbered -sync.com file is used at the end of each iteration, or an unnumbered -finish.com file after the final iteration, to run checkAlignmentLogs, mergeEM , optionally removeDuplicates, and averageAll.

For parallel averaging, two groups of numbered files, each followed by a -sync.com or a -finish.com, are written for each iteration. A first groups of numbered files runs alignSubset, as in serial averaging. This is followed by a -sync.com which runs checkAlignmentLogs, mergeEM, and, optionally, removeDuplicates. Next a second series of numbered files, one per volume, runs averageAll in parallel mode. Finally, a numbered -sync.com, or unnumbered finish.com for the final iteration, invokes averageAll again to collect results from the parallel computations and to write the resulting volume(s).

The parameter file is a MATLAB readable text file that specifies the parameter values in MATLAB syntax. See PEET(1) man page for a description of the parameter file options and syntax.

file.prm
The file name of the parameter file.
 

FILES

Sample parameter files are available in $PARTICLE_DIR/templates.  

AUTHORS

Quanren Xiong
John Heumann  

SEE ALSO

PEET(1), prepareEM(1), prepareRef(1), alignSubset(1), averageAll(1), mergeEM(1), removeDuplicates(1), calcFSC(1), and calcSSNR(1)


 

Index

NAME
SYNOPSIS
DESCRIPTION
FILES
AUTHORS
SEE ALSO

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Time: 21:10:06 GMT, March 20, 2017