Name

sxlocal_ali2d - Perform local refinement of 2-D alignment of an image series

Usage

Usage in command line:

sxlocal_ali2d.py stack output_directory <maskfile> --ou=outer_radius --br=brackets --center=center_type --eps=epsilon --maxit=max_iter --CTF --snr=SNR --function=user_function_name

Usage in Python programming:

local_ali2d(stack, outdir, maskfile = None, ou = -1, br = 1.75, center = 1, eps = 0.001, maxit = 10, CTF = False, snr = 1.0, user_func_name="ref_ali2d")

Typical usage

Input

stack

set of 2-D images in a stack file (format hdf), images have to be squares (nx=ny)

maskfile
optional mask file to use internally during alignment
  • The parameters preceded with -- are optional and default values are given in paranthesis.

    outer_radius

    outer radius for rotational correlation < int(nx/2)-1 (set to int(nx/2)-2, should be set to the radius of the particle)

    br
    brackets for the search of orientation parameters (each parameter will be checked +/- bracket) (set to 1.75)
    center_type
    0 - if you do not want the average to be centered, 1 - center the average (default=1)
    epsilon
    stopping criterion, program will terminate when the relative increase of the criterion is less than epsilon (set to 0.001)
    max_iter
    maximum number of iterations the program will perform (set to 10)
    CTF

    if this flag is set, the program will use during the alignment CTF information provided in file headers (for details see I_O). (default no CTF)

    snr
    Signal-to-Noise Ratio of the data (default SNR=1.0)
    function

    name of the user-supplied function that prepares reference image for each iteration (default ref_ali2d)

  • Output

    output_directory
    directory name into which the output files will be written. If it does not exist, the directory will be created. If it does exist, the program will crash and an error message will come up. Please change the name of directory and restart the program . The program will write two kind of files: the average of the aligned image series (aqe***.spi) and the Fourier Resolution Criterion curve (dre***). Both files are numbered by the iteration number.
    header
    the alignment parameters are stored in the headers of input files as 'alpha', 'sx', 'sy', 'mirror'

    Description

    Method

    Program uses simplex optimization method to refine for each image three orientation parameters (psi, sx, sy) such that the inner product between the image and the average of remaining images is maximized.

    Reference

    Author / Maintainer

    Pawel A. Penczek

    Keywords

    category 1
    APPLICATIONS
    category 3
    GRIDDING

    Files

    sparx/bin/sxali2d_e.py

    See also

    sxtransform2d

    Maturity

    beta
    works for author, often works for others.

    Bugs

    The centering may fail. It will also fail if the images are not very similar to each other, say circles and rectangles.

    sxlocal_ali2d (last edited 2013-07-01 13:12:38 by localhost)