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.

• To use MPI version:
• mpirun -np 2 sxshftali.py
• The above example is for mympi.

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

• For the program to work, attribute 'xform.align2d' has to be set in the header of each file. If their values are not known, all should be set to zero, please refer to sxheader.

• The program will not change the input images. It will store the alignment parameters in the image headers. To apply the alignment parameters to the images in input stack itself, use program sxtransform2d.

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