Name

sxshiftali - Determines shift parameters for aligning a 2D image series. The computed shift parameters are always integers.

Usage

Usage in command lines:

sxshiftali.py stack outdir <maskfile> --search_rng --ou=outer_radius --maxit=max_iteration --CTF --snr=SNR --Fourvar=Fourier_variance --oneDx --MPI

Usage in python programming:

shiftali_MPI(stack, outdir, maskfile=None, ou=-1, maxit=100, CTF=False, snr=1.0, Fourvar=False, search_rng=-1, oneDx=False')

Currently, there is only the MPI version.

Typical usage

1. Compute shift alignment parameters for images in input stack and save to header in attribute 'xform.align2d'

mpirun -np 2 sxshftali.py input_stack output_directory --outstack='aligned_stack.hdf'

2. Compute shift alignment parameters for images in input stack, apply the computed parameters to the images, and save results to an output stack. The input images are not changed.

mpirun -np 2 sxshftali.py input_stack output_directory --Applyparams --outstack='aligned_stack.hdf'

Input

stack
set of 2-D images in a stack file (format hdf or bdb), images need not be square.
maskfile
optional mask file to be used internally during alignment. Default is a circle mask with radius min(nx, ny)//2 - 2, where nx and ny are the x and y dimensions respectively of the input data. outdir::output directory, cannot already exist.
  • The parameters preceded with -- are optional and default values are given in parenthesis.

  • search_rng
    Used to compute the dimension of a nwx by nwy section of the 2D ccf which is windowed out for peak search: nwx=2*search_rng+1. Default is -1, in which case nwx=nx.
    search_rng_y
    Used to compute the dimension of a nwx by nwy section of the 2D ccf which is windowed out for peak search: nwy=2*search_rng_y+1. Default is -1, in which case nwy=ny. This is ignored when oneDx flag is activated for x-shift only search.
    outer_radius
    radius of the particle - used for constructing the default mask. Default is -1, in which case the mask is a circle with radius nx/2 - 2
    max_iteration
    maximum number of iterations program will perform. Default is 100.
    CTF

    if this flag is set, the program will use 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)
    Fourvar
    compute Fourier variance (recommended default False)
    oneDx
    Window out central line of 2D cross correlation for peak search, default is false.
    MPI
    if this flag is set, use MPI version

    Output

    header
    the alignment parameters are stored in the headers of input files as 'xform.align2d'.

    Description

    Method

    Reference

    Author / Maintainer

    Jia Fang

    Keywords

    category 1
    APPLICATIONS

    Files

    sparx/bin/sxshiftali.py

    See also

    Maturity

    beta
    works for author, often works for others.

    Bugs

    sxshiftali (last edited 2013-07-01 13:12:37 by localhost)