usage: prog <output> [options]

	This program produces iterative class-averages, one of the secrets to EMAN's rapid convergence.
	Normal usage is to provide a stack of particle images and a classification matrix file defining
	class membership. Members of each class are then iteratively aligned to each other and averaged
	together with (optional) CTF correction.  It is also possible to use this program on all of the
	images in a single stack.


Option Type Description
--version None show program's version number and exit
--input str The name of the input particle stack
--output str The name of the output class-average stack
--oneclass int Create only a single class-average. Specify the number.
--classmx str The name of the classification matrix specifying how particles in 'input' should be grouped. If omitted, all particles will be averaged.
--focused str Name of a reference projection file to read 1st iteration refine alignment references from.
--ref str Reference image(s). Used as an initial alignment reference and for final orientation adjustment if present. Also used to assign euler angles to the generated classes. This is typically the projections that were used for classification.
--storebad None Even if a class-average fails, write to the output. Forces 1->1 numbering in output
--compressbits int Bits to keep when writing class-averages with compression. 0->lossless floating point. Default 10 (3 significant figures)
--decayedge None Applies an edge decay to zero on the output class-averages. A very good idea if you plan on 3-D reconstruction.
--resultmx str Specify an output image to store the result matrix. This contains 5 images where row is particle number. Rows in the first image contain the class numbers and in the second image consist of 1s or 0s indicating whether or not the particle was included in the class. The corresponding rows in the third, fourth and fifth images are the refined x, y and angle (respectively) used in the final alignment, these are updated and accurate, even if the particle was excluded from the class.
--iter int The number of iterations to perform. Default is 1.
--prefilt None Filter each reference (c) to match the power spectrum of each particle (r) before alignment and comparison
--prectf None Apply particle CTF to each reference before alignment
--align str This is the aligner used to align particles to the previous class average. Default is None.
--aligncmp str The comparitor used for the --align aligner. Default is ccc.
--ralign str This is the second stage aligner used to refine the first alignment. This is usually the 'refine' aligner.
--raligncmp str The comparitor used by the second stage aligner.
--averager str The type of averager used to produce the class average.
--setsfref None This will impose the 1-D structure factor of the reference on the class-average (recommended when a reference is available)
--cmp str The comparitor used to generate quality scores for the purpose of particle exclusion in classes, strongly linked to the keep argument.
--keep float The fraction of particles to keep in each class.
--keepsig None Causes the keep argument to be interpreted in standard deviations.
--automask None Applies a 2-D automask before centering. Can help with negative stain data, and other cases where centering is poor.
--center str If the default centering algorithm (xform.center) doesn't work well, you can specify one of the others here (e2help.py processor center), or the word 'nocenter' for no centering
--bootstrap None Ignored. Present for historical reasons only.
--normproc str Normalization processor applied to particles before alignment. Default is normalize.edgemean. If you want to turn this option off specify 'None'
--usefilt None Specify a particle data file that has been low pass or Wiener filtered. Has a one to one correspondence with your particle data. If specified will be used to align particles to the running class average, however the original particle will be used to generate the actual final class average
--idxcache None Ignored. Present for historical reasons.
--dbpath None Ignored. Present for historical reasons.
--resample None If set, will perform bootstrap resampling on the particle data for use in making variance maps.
--odd None Used by EMAN2 when running eotests. Includes only odd numbered particles in class averages.
--even None Used by EMAN2 when running eotests. Includes only even numbered particles in class averages.
--parallel None parallelism argument
--saveali None Writes aligned particle images to aligned.hdf. Normally resultmx produces more useful information. This can be used for debugging.
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness
--debug, -d None Print debugging information while the program is running. Default is off.
--nofilecheck None Turns file checking off in the check functionality - used by e2refine.py.
--check, -c None Performs a command line argument check only.
--ppid int Set the PID of the parent process, used for cross platform PPID

For more information go to emanwiki/EMAN2/Programs/e2classaverage.