<input> | Input images to classify |
<ref set> | Reference data set |
<basis set> | A set of orthogonal basis images as generated by svdcmp |
[mask=<rad>] | Mask radius |
[frac=<num>/<denom>] | Operate only on a fraction of the raw images |
[nbasis=<n>] | Number of basis images to use from the basis set. Defaults to all. |
[saveali=<aligned out>] | File to write aligned images to |
[logit=<label>] | This specifies a label to use in the particle.log file. This records particle number classification throughout a refinement. |
[groups=<ngrp>] | This will classify into multiple sets. Used by svdmultirefine.py |
[maxshift=<dxy>] | Maximum radial translation |
[verbose[=<n>]] | More verbose output |
[lcmptoo] | This will also generate an lcmp quality factor for each classification |
[clsbylcmp[=<filt rad>]] | This will classify based on lcmp comparison of the aligned images |
[quiet] | No logging |
[noisecomp] | Noise compensation |
[skip1] | Skips the first basis vector |
[shrink=<n>] | Scales the images down for initial orientation search, may be risky but gives a big speedup |
[svweight] | Weight each basis vector by its singular value (rarely a good idea) |