sxlocal_ali3d - Perform local refinement of 3-D projection alignment of image series using highy accurate gridding method.
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)
- 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.
set of 2-D images in a stack file, images have to be squares (nx=ny)
- name of the output directory where the results and debug information will be placed
- filename used to create the mask
The parameters preceded with -- are optional and default values are given in parenthesis.
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)
- angular bracket for the search of orientation parameters (each parameter will be checked +/- delta) (set to 2.0)
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 of data after which the 3D will be updated 0<chunk<=1.0 (default 1.0)
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)
- Signal-to-Noise Ratio of the data (default SNR=1.0)
- symmetry of the volume under reconstruction (set to c1)
user-supplied-function that prepares the reference volume during each iteration (default: ref_ali3d)
- run program in MPI mode
- padding size for 3D reconstruction, default is 2.
- 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).
- 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
- 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.
- 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.
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.
Yang and Penczek, Ultramicroscopy 2008.
Author / Maintainer
Pawel A. Penczek
- category 1
- category 3
- works for author, often works for others.
The centering may fail.