Header Operations: Perform operations on headers of hdf or bdb file.

Usage in command line

sp_header.py  stack  --params=PARAMS_NAME_LIST  --import=INPUT_PARAMS_PATH  --export==OUTPUT_PARAMS_FILE  --delete  --zero  --one  --set  --consecutive  --randomize  --rand_alpha  --print  --backup  --restore  --suffix=PARAMS_FILE_SUFFIX

sp_header does not support MPI.

Print parameterrs:

sp_header.py bdb:file --print --params=xform.projection

Export ctf values to a text file:

sp_header.py bdb:file --export=ctf.txt --params=ctf

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

sp_header.py bdb:file --import=ctf.txt --params=ctf

Backup current alignment parameters:

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

Restore original alignment parameters:

sp_header.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:

sp_header.py bdb:file --delete --params=xform.projection_original

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

stack

Input image stack: Path to input image stack. The stack can be either bdb or hdf. However, the GUI supports only bdb. (default required string)

--params

Target parameters: List of parameters names (i.e. image header entry keys) to perform operations on (e.g. “parm1 parm2 …”). (default required string)

--import

Import parameters: Import parameters from file. (default none)

--export

Export parameters: Export parameters to file. (default none)

--delete

Delete all: Delete all parameters. (default False)

--zero

Set to zero: Set all parameters to zero. (default False)

--one

Set to one: Set all parameters to one. This is not applicable to xform.align2d, xform.proj or xform.align3d, beccause they do not make sense. (default False)

--set

Set to constant: Set parameters to a specified constant value, other than 0.0. (default 0.0)

--consecutive

Set to consecutive: Set selected parameters to consecutive integers starting from 0. (default False)

--randomize

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

--rand_alpha

Set angles to random: Set all angles to random values. (default False)

--print

Print to screen: Print parameters to screen. (default False)

--backup

Backup all: Backup all parameters. (default False)

--restore

Restore all: Restore all parameters. (default False)

--suffix

Suffix for backup: Suffix for xform name in backup. This will be added to the name of a parameter or removed during restore. (default _backup)

This program now works for both hdf and bdb files.

See description of parameters Reading and writing the image files in SPARX/EMAN2.

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

Wei Zhang, Zhengfan Yang

Category 1:: APPLICATIONS

sparx/bin/sp_header.py

Reading and writing the image files in SPARX/EMAN2

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

There are no known bugs so far.