Name

sxlocal_ali3d - Perform local refinement of 3-D projection alignment of image series using highy accurate gridding method.

Usage

usage in command line

sxlocal_ali3d.py stack outdir <maskfile> --ou=outer_radius --delta=angular_bracket --ts=shift_bracket --debug=Debug_printout --Fourvar=Fourier_variance --maxit=max_iter --chunk=data_chunk_for_update --center --CTF --snr=SNR --sym=symmetry --function=user_function --MPI

usage in python programming

local_ali3d(input_stack, output_directory, maskfile, ou = radius, delta = angular_bracket, maxit = max_iter, CTF = False, snr = SNR, sym = symmetry, chunk = data_chunk_for_update, user_function, debug)

Typical usage

• sxlocal_ali3d.py input_stack output_directory --ou=27
• The above command is written in python code as:
• local_ali3d(input_stack, output_directory, ou=27)

• To use MPI || version:

• 1. add --MPI in the command line
• 2. mpirun -np 32 sxali3d_d.py --MPI and the remaining parameters
• The above example is for mympi.

Input

input_stack

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

output_directory

name of the output directory where the results and debug information will be placed

maskfile

filename used to create the mask

The parameters preceded with -- are optional and default values are given in parenthesis.

ou

outer radius of a circular mask used to calculate correlation between 2-D data and projections of the structure< int(nx/2)-1 (set to int(nx/2)-2, should be set to the radius of the particle)

delta

angular bracket for the search of orientation parameters (each parameter will be checked +/- delta) (set to 2.0)

max_iter

maximum number of iterations the program will perform (set to 10). Within each iteration the 3-D reference structure will be updated after each chunk of 2-D dat.

chunk

chunk of data after which the 3D will be updated 0<chunk<=1.0 (default 1.0)

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)

sym

symmetry of the volume under reconstruction (set to c1)

function

user-supplied-function that prepares the reference volume during each iteration (default: ref_ali3d)

MPI

run program in MPI mode

npad

padding size for 3D reconstruction, default is 2.

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 three kinds of files: the "raw" 3D reconstruction (vol***_***.hdf), the 3D reconstruction processed by the user function, which will be used as a template in the next iteration (golf***_***.hdf), and the Fourier Shell Resolution curve (resolution***_***). The files are numbered by both the iteration number and the chunk number (the latter if specified).

header

the alignment parameters of each 2D projection (Euler angles and two in-plane translations) are stored in the headers of input files as xform.projection

Description

• For the program to work, attributes 'xform.projection' have to be set in the header of each file. Since the program performs only local searches, they have to be approximately correct.

• This program is meant to refine orientation parameters found by sxali3d and it should be used after sxali3d was run.

• The program prints the value of the alignment criterion (see the reference). If the program is started using results of the previous alignment, the initial value of the criterion may be slightly lower than that achieved at the end of the previous alignment - this is due to numerical accuracy and it is not a reason to be concerned. However, for the same reason, the alignment may slightly change during the second run.
• The program will not change the input images, only the alignment parameters in their header.

Method

Program uses simplex optimization method to refine for each image five orientation parameters such that the inner product between the image and the average of remaining images is maximized.

Reference

Yang and Penczek, Ultramicroscopy 2008.

Author / Maintainer

Pawel A. Penczek

Keywords

category 1

APPLICATIONS

category 3

GRIDDING

Files

sparx/bin/sxlocal_ali3d.py

See also

sxali3d

Maturity

beta

works for author, often works for others.

Bugs

The centering may fail.