e2classaverage3d

--input

string

The name of the input volume stack. MUST be HDF or BDB, since volume stack support is required.

--output

string

The name of the output class-average stack. MUST be HDF or BDB, since volume stack support is required.

--oneclass

int

Create only a single class-average. Specify the class number.

--classmx

string

The name of the classification matrix specifying how particles in 'input' should be grouped. If omitted, all particles will be averaged.

--ref

string

Reference image(s). Used as an initial alignment reference and for final orientation adjustment if present. This is typically the projections that were used for classification.

--resultmx

string

Specify an output image to store the result matrix. This is in the same format as the classification matrix. http://blake.bcm.edu/emanwiki/EMAN2/ClassmxFiles

--iter

int

The number of iterations to perform. Default is 1.

--savesteps

bool

If set, will save the average after each iteration to class_#.hdf. Each class in a separate file. Appends to existing files.

--saveali

bool

If set, will save the aligned particle volumes in class_ptcl.hdf. Overwrites existing file.

--sym

string

Symmetry to impose - choices are: c<n>, d<n>, h<n>, tet, oct, icos

--mask

string

Mask processor applied to particles before alignment. Default is mask.sharp:outer_radius=-2

--normproc

string

Normalization processor applied to particles before alignment. Default is to use normalize.mask. If normalize.mask is used, results of the mask option will be passed in automatically. If you want to turn this option off specify 'None'

--preprocess

string

A processor (as in e2proc3d.py) to be applied to each volume prior to alignment. Not applied to aligned particles before averaging.

--npeakstorefine

int

The number of best coarse alignments to refine in search of the best final alignment. Default=4.

--align

string

This is the aligner used to align particles to the previous class average. Default is rotate_translate_3d:search=10:delta=15:dphi=15

--aligncmp

string

The comparator used for the --align aligner. Default is the internal tomographic ccc. Do not specify unless you need to use another specific aligner.

--ralign

string

This is the second stage aligner used to refine the first alignment. Default is refine.3d, specify 'None' to disable

--raligncmp

string

The comparator used by the second stage aligner. Default is the internal tomographic ccc

--averager

string

The type of averager used to produce the class average. Default=mean

--keep

float

The fraction of particles to keep in each class.

--keepsig

bool

Causes the keep argument to be interpreted in standard deviations.

--postprocess

string

A processor to be applied to the volume after averaging the raw volumes, before subsequent iterations begin.

--shrink

int

Optionally shrink the input volumes by an integer amount for coarse alignment.

--shrinkrefine

int

Optionally shrink the input volumes by an integer amount for refine alignment.

--parallel

string

Parallelism. See http://blake.bcm.edu/emanwiki/EMAN2/Parallel

-h

--help

bool

show this help message and exit

-v

--verbose

int

verbose level [0-9], higner number means higher level of verboseness