Name

sxwindow.py - window out particles with known coordinates from a micrograph.

NOTE: This page is work in progress

Usage

For all micrographs in current directory:

sxwindow.py --coords_dir=info --coords_extension=box --coords_format=eman1 --importctf=ctfparams.txt --indir=./ --resample_ratio=0.5 --box_size=64 --nameroot=mic --micsuffix=hdf --outdir=particles --outsuffix=_ptcls --invert --defocuserror=10 --astigmatismerror=8

For mic0.hdf and mic2.hdf:

sxwindow.py mic0.hdf mic2.hdf --coords_dir=info --coords_extension=box --coords_format=eman1 --importctf=ctfparams.txt --indir=./ --resample_ratio=0.5 --box_size=64 --nameroot=mic --micsuffix=hdf --outdir=particles --outsuffix=_ptcls --invert --defocuserror=10 --astigmatismerror=8

NOTE: The script assumes that a coordinates file has the same name as the associated micrograph except the extension.

NOTE: Please remember to adjust box_size also when setting resample_ratio < 0.1.

Input

micrograph list

Input micrographs, if none is specified all files in option --indir are used

Output

• Stack of particle images

Options

--coords_dir

Directory containing files with particle coordinates.

--coords_suffix

Suffix of coordinate files. For example "_ptcls".

--coords_extension

File extension of coordinate files. e.g "box" for eman1, "json" for eman2, ...

--coords_format

Format of coordinates file: "sparx", "eman1", "eman2", or "spider". The coordinates of sparx, eman2, and spider format is particle center. The coordinates of eman1 format is particle box corner associated with the original box size.

--indir

Directory containing micrographs to be processed. (Default: current directory).

--importctf

File name with CTF parameters produced by sxcter.

--limitctf

Filter micrographs based on the CTF limit. It requires --importctf. (Default: no filter).

--resample_ratio

Ratio of new to old image size (or old to new pixel size) for resampling. Valid range is 0.0 < resample_ratio <= 1.0. (Default: 1.0).

--box_size

x and y dimension in pixels of square area to be windowed. Pixel size after resampling is assumed when resample_ratio < 1.0. Exclude the coordinates if the associated box is not entirely within micrograph. (Default 256).

--outdir

Output directory.

--outsuffix

Suffix for output stack, e.g. '_ptcls' etc. (Default '_ptcls').

--micsuffix

A string denoting micrograph type. (Default 'hdf').

--nameroot

Prefix of micrographs to be processed.

--invert

Invert image contrast (recommended for cryo data) (Default, no contrast inversion).

--defocuserror

Exclude micrographs whose relative defocus error as estimated by sxcter is larger than defocuserror percent. The error is computed as (std dev defocus)/defocus*100%. (Default: include all irrespective of error values).

--astigmatismerror

Set to zero astigmatism for micrographs whose astigmatism angular error as estimated by sxcter is larger than astigmatismerror degrees. (Default: include all irrespective of error values).

Description

1. Takes micrographs and coordinates as input and writes windowed out particle images to a stack.
2. Normalization is done by subtracting the average of the region outside of a circle with radius half of option --box_size.
3. Micrographs are applied a Gaussian high-pass Fourier filter with standard deviation of option --box_size.

Author / Maintainer

T. Durmaz and T.Moriya

Keywords

category 1

FUNDAMENTALS, UTILITIES, APPLICATIONS

Files

sxwindow.py

See also

window, windowallmic

Maturity

alpha

in development