Name

sxrecons3d_n - 3D reconstruction

Usage

Usage in command lines:

[ mpirun -np 4 ] sxrecons3d_n.py prj_stack volume [begin end step] --CTF --npad=ntimes_padding --list=file --group=ID --snr=SNR --sym=symmetry --verbose=(0|1) --xysize=xysize --MPI

Usage in python programming:

recons3d_n(prj_stack, pid_list, volume, CTF=False, snr=1.0, sign=1, npad=4, sym="c1", listfile = "", group = -1, verbose=0, xysize=xysize, MPI=False)

Input

prj_stack: projection stack file

Output

volume: reconstructed volume file

Options

begin: first image for reconstruction
end: last image for reconstruction
step: step used for image list
list: list with projection numbers to be used in reconstruction
CTF: the data is CTF or not (default CTF=False)
npad: number of times padding (default npad=2)
snr: Singal-to-Noise Ratio of input data (default snr=1.0)
sym: symmetry of input data (default is "c1")
verbose: verbose level (0:no verbose, 1: verbose) default is 0
xysize: user expected size at xy direction. If user give xysize, rectangular construction will be performed. By default xysize=-1, do cubic reconstruction.

Description

Weighted nearest neighbour algorithm, works on data that contains CTF information in headers. Parameters of projections are read from the header's parameter called xform.projection.

Method

The memory requirement is 6*(npad*nx)**3, where nx is the linear size of projection in pixels. By default npad=2, so the memory is 48*nx**3.

(For nx=64, 13MB; for nx=128, 100MB).

Reference

Author / Maintainer

Wei Zhang

Keywords

category 1: APPLICATIONS

Files

sxrecons3d_n.py

Maturity

stable: works for most people, has been tested; test cases/examples available.

Bugs

None. It is perfect.