Name

sxheader - Perform operations on headers of hdf or bdb file

Usage

Usage in command lines:

sxheader.py stack.hdf --params="parm1 parm2 ..." --zero --one --randomize -- rand_alpha --import=filename --export=filename --print --backup --restore --suffix --delete

Usage in python programming:

header(stack, params, zero, one, randomize, rand_alpha, fimport, fexport, fprint, backup, suffix, restore, delete)

Input

stack

image stack file (can be bdb or hdf)

Options

params

list of parameters to perform operations on.

If operating on 2D alignment parameters, use "xform.align2d", which automatically includes the parameters "alpha", "sx", "sy", "mirror" and "scale".

If operating on projection alignment parameters, use "xform.projection", which automatically includes the parameters "phi", "theta", "psi", "s2x" and "s2y".

If operating on 3D alignment parameters, use "xform.align3d", which automatically includes the parameters "phi", "theta", "psi", "s3x", "s3y", "s3z", "mirror" and "scale".

Contrast Transfer Function is accessible as object "ctf" and involves six parameters: defocus [microns], cs [mm], voltage [kV], apix [A], bfactor [A^2], ampcont [%], astigmatism amplitude, astigmatism angle.

See description of parameters http://sparx-em.org/sparxwiki/I_O

zero

set all parameters to zero.

one

set all parameters to one (not applicable to xform.align2d, xform.proj or xform.align3d, since it doesn't make sense).

randomize

set all parameters to randomized value (only works for xform.align2d, xform.proj and xform.align3d, there is little need to randomize other parameters, and it is also difficult to guess the random range beforehand.)

rand_alpha

set all angles to randomized value

import

import parameters from file.

export

export parameters to file.

print

whether print parameters to screen.

backup

backup all parameters

restore

restore all parameters

suffix

suffix which will be added to the name of a parameter or removed during restore.

delete

delete all parameters

Typical usage

Print parameterrs:

• sxheader.py bdb:file --print --params=xform.projection

Export ctf values to a text file:

• sxheader.py bdb:file --export=ctf.txt --params=ctf

Import ctf values from a text file and set them to headers:

• sxheader.py bdb:file --import=ctf.txt --params=ctf

Backup current alignment parameters:

• sxheader.py bdb:file --backup --suffix=_original --params=xform.projection

Restore original alignment parameters:

• sxheader.py bdb:file --restore --params=xform.projection_original

• Note: command will recognize the valid name of a parameters and truncate the suffix, thus in this case the restored parameter will be xform_projection.

Delete parameters:

• sxheader.py bdb:file --delete --params=xform.projection_original

• Note: the parameters will be permanently deleted and cannot be recovered.

Description

This program now works for both hdf and bdb files.

Author / Maintainer

Wei Zhang, Zhengfan Yang

Keywords

category 1

APPLICATIONS

Files

applications.py

Maturity

stable

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

Bugs

None. It is perfect.