pipeline:window:e2boxer_old

This version (2019/04/02 09:12) is a draft.
Approvals: 0/1

Particle Coordinates: Generate files containing particle coordinates for all input micrographs by picking particles manual and/or automatically.


Usage in command line

e2boxer_old.py  input_micrograph_list  --boxsize=BOXSIZE  --write_dbbox  --write_ptcls  --exclude_edges  --force  --format=FORMAT  --norm=NORM  --invert  --suffix=SUFFIX  --dbls=DBLS  --autoboxer=AUTOBOXER  --ppid=PPID  --gui  --verbose=n  --gauss_autoboxer=GAUSS_AUTOBOXER  --do_ctf=DO_CTF  --cter  --indir=INDIR  --nameroot=NAMEROOT  --micsuffix=MICSUFFIX  --wn=WN  --Cs=CS  --voltage=VOLTAGE  --ac=AC  --kboot=KBOOT  --debug  --apix=APIX


e2boxer_old exists in non-MPI version.


Start the e2boxer_old GUI with a list of micrographs:

e2boxer_old.py micrographs_number*


Main Parameters

input_micrograph_list
Input micrographs: Wild cards (e.g. *) can be used to specify a list of micrographs. Not recommended if their number is very large. (default required string)
--boxsize
Box size [Pixels]: Box size for extraction of particle images. (default -1)


Advanced Parameters

--write_dbbox
Write coordinate files: Write coordinate files. (default False)
--write_ptcls
Write particle images: Write particle images. (default False)
--exclude_edges
Exclude edge images: Exclude particles extending outside the micrograph. (default False)
--force
Force overwrite: Force overwrite. (default False)
--format
Particle image format: Format of the output particles images. (default hdf)
--norm
Particle normalization: Normalization processor applied to the final particle images. (default normalize.edgemean)
--invert
Invert contrast: Invert contrast of micrographs. (default False)
--suffix
Particle name suffix: Suffix used for the name of the output images and coordinates. (default _ptcls)
--dbls
Data base list storage: Data base list storage, used by the workflow. (default none)
--autoboxer
Swarm_boxers dict key: A key of the swarm_boxers dict in the local directory, used by the workflow. (default none)
--ppid
Set PPID: Sets the PPID of the process. (default -1)
--gui
Dummy option: Dummy option used in even older version of e2boxer_old. (default True)
--verbose
Verbose: Verbose level. Accepted values 0-9. (default 0)
--gauss_autoboxer
Sample autoboxed image: Gets the parameters used for autoboxing from the EMANDB. It requires the name of a micrograph used for automatic boxing previously. (default none)
--do_ctf
CTF parameters file: Specify name of file whose CTF estimation parameters should be used for automatic CTF estimation. (default none)
--cter
Use CTER CTF estimation: CTF estimation using CTER. (default False)
--indir
Input directory: Directory containing micrographs to be processed. (default current directory)
--nameroot
Micrograph rootname: Rootname of micrographs to be processed. (default none)
--micsuffix
Micrograph type: A string denoting micrograph type. (default none)
--wn
Window size: size of window to use. (default 256)
--Cs
Spherical aberration [mm]: Spherical aberration [mm] used to acquire the input micrographs. (default 2.0)
--voltage
Microscope voltage [kV]: Microscope voltage [kV] used to acquire the input micrographs. (default 300.0)
--ac
Amplitude contrast: Expected amplitude contrast of this dataset. (default 10.0)
--kboot
kboot: The number of boot-strap trials. (default 16)
--debug
Debug mode: Use debug mode. (default False)
--apix
Pixel size [A]: Pixel size of the input micrographs. (default -1.0)


The program creates the directory automatically in the micrograph directory.






EMAN2 Group


Category 1:: APPLICATIONS


programs/e2boxer_old.py


There are no known bugs so far.


  • pipeline/window/e2boxer_old.txt
  • Last modified: 2019/04/02 09:12
  • by lusnig