Name

sxmref_ali2d - Perform 2-D multi-reference alignment of an image series

Usage

Usage in command line:

sxmref_ali2d.py data_stack reference_stack outdir <maskfile> --ir=inner_radius --ou=outer_radius --rs=ring_step --xr=x_range --yr=y_range --ts=translation_step --center=center_type --maxit=max_iteration --CTF --snr=SNR --function=user_function_name --rand_seed=random_seed --MPI

Usage in Python programming:

mref_ali2d((stack, refim, outdir, maskfile=None, ir=1, ou=-1, rs=1, xrng=0, yrng=0, step=1, center=1, maxit=0, CTF=False, snr=1.0, user_func_name="ref_ali2d", rand_seed=1000, MPI=False)

Typical usage

  1. Prepare stack file with initial averages. Normally, they would result from running the 2-D alignment sxali2d and K-means classification sxk_means. Set the particle radius, and x-y range for translational search:

    • sxmref_ali2d.py input_stack.hdf ref_stack.hdf output_directory --ou=27 --xr=3 --yr=3 --maxit=6
  2. Continue the alignment from the previous result by replacing the ref_stack by the result of the previous run and using the same input_stack which has in the header previously obtained orientation paramters:
    • sxmref_ali2d.py input_stack.hdf output_directory/aqm005.hdf next_output_directory --ou=27 --xr=3 --yr=3 --maxit=6
  3. The above command is written in python program as:
    • mref_ali2d(input_stack.hdf, output_directory/aqm005.hdf, next_out_directory, ou=27, xr=3, yr=3, maxit=6)

Input

stack

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

refim
set of initial reference 2-D images in a stack file (format hdf or bdb)
maskfile
optional maskfile to be used in the alignment
  • The parameters preceded with -- are optional and default values are given in parenthesis.

    inner_radius

    inner radius for rotational correlation > 0 (set to 1)

    outer_radius

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

    ring_step

    step between rings in rotational correlation >0 (set to 1)

    x_range
    range for translation search in x direction, search is +/xr (set to zero, which corresponds to rotational alignment only)
    y_range
    range for translation search in y direction, search is +/yr (set to zero, which corresponds to rotational alignment only)
    translation_step
    step of translation search in both directions (set to 1, larger value increase the speed, but decrease the accuracy)
    center
    0 - if you do not want the average to be centered, 1 - center the average (default=1)
    maxit
    maximum number of iterations the program will perform (set to 10)
    CTF

    if this flag is set, the program will use CTF information provided in file headers (for details see I_O).

    snr
    signal-to-noise ratio of the data (default SNR=1.0)
    user_function_name
    name of the reference preparation function
    rand_seed
    the seed used for generating random numbers (set to 1000)
    MPI
    whether to use MPI version
  • 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 kinds of files: averages of the aligned image series (aqm***.hdf, numbered by the iteration number) and the Fourier Resolution Criterion curve (drm*******, first three digits indicate iteration number, last four indicate the reference image number).
    header
    the alignment parameters are stored in the headers of input files as 'xform.align2d'. In addition, attribute 'assign' indicates which reference the image was assigned to.

    Description

    Method

    Will describe one of these days....

    Reference

    Penczek 1992

    Author / Maintainer

    Pawel A. Penczek

    Keywords

    category 1
    APPLICATIONS
    category 2
    FOURIER

    Files

    sparx/bin/sxali2d_m.py, applications.py

    See also

    sxlocal_ali2d, sxali2d, sxtransform2d, sxk_means, sxk_means_groups

    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.

    sxmref_ali2d (last edited 2013-07-01 13:12:24 by localhost)