Name

sx3dvariability.py - calculate 3D field using a set of aligned 2D projection images as an input

Usage

usage in command line - something like that:

mpirun -np 472 sx3dvariability.py bdb:./#post_all_new POST3dvar.hdf --CTF --img_per_grp=100 --freq=0.4 --fall_off=0.1 --ave2D=POSTave_stack.hdf --ave3D=POSTave_vol.hdf --var3D=POSTvar_vol.hdf --MPI --npad=2 --VERBOSE &

The REST TO BE WRITTEN 07/02/2023

usage in python programming

var(prefix, nfile, nprj, output, fl, fh, radccc, writelp, writestack)

Typical usage

mpirun -np 4 sxvar.py bootstrap/bsvol000*.hdf variance --fl=0.2 --aa=0.1 --radccc=24 --MPI

Input

prefix

the prefix of the set of volume stacks generated by sxbootstrap_bigdisk.py

fl,aa

the parameters of the low pass filtration using filt_tanl.

radccc
radius for calculating cross correlation coefficient and masking the 3D variance.
writelp
whether write the low-pass filtered volumes to the disk.
writestack
whether write the intermediate results (odd, even and all variance map for every 100 volumes).

Output

outputfile
the average and variance maps will be saved in current directory as avg.hdf and var.hdf.

Description

if FSC reaches 0.5 at frequency 0.3, fl and fh should be around 0.15, and the distance between them is suggested to be about 0.05.

Method

Reference

Author / Maintainer

Wei Zhang

Keywords

category 1
APPLICATIONS

Files

sparx/bin/sxnormal_prj.py

See also

sxali3d_e

Maturity

beta
works for author, often works for others.

Bugs

Did not discover any yet.

sx3dvariability (last edited 2023-07-02 15:37:05 by penczek)