sxpipe reboxing
Reboxing: Generate coordinates files and micrograph selection text file based on information stored in the image headers of SPHIRE particle stack file, by extracting coordinates from the input stack, then center them according to projection parameters in the header and user-provided 3D shift.
Usage
Usage in command line
sxpipe.py reboxing input_stack_path output_directory --box_size=BOX_SIZE --shift3d_x=SHIFT3D_X --shift3d_y=SHIFT3D_Y --shift3d_z=SHIFT3D_Z
Typical usage
sxpipe reboxing does not support MPI.
sxpipe.py reboxing 'bdb:outdir_window#data' 'outdir_pipe_reboxing' --box_size=352 --shift3d_z=15
Main Parameters
- input_stack_path
- Input image stack: Specify path to input particle stack. (default required string)
- output_directory
- Output directory: The results will be written here. This directory will be created automatically and it must not exist previously. (default required string)
- --box_size
- Particle box size [Pixels]: The x and y dimensions of square area to be windowed. (default 0)
- --shift3d_x
- 3D x-shift [Pixels]: User-provided 3D x-shift corresponding to shifting the 3D volume along x-axis. (default 0)
- --shift3d_y
- 3D y-shift [Pixels]: User-provided 3D y-shift corresponding to shifting the 3D volume along y-axis. (default 0)
- --shift3d_z
- 3D z-shift [Pixels]: User-provided 3D z-shift corresponding to shifting the 3D volume along z-axis. (default 0)
Advanced Parameters
Output
List of output Files
| File Name | Discription |
| original/${MICROGRAPH_ROOTNAME}_original.box | The list of original coordinates stored in the headers of particle images in the stack. These files can be used as inputs of sxwindow |
| centered/${MICROGRAPH_ROOTNAME}_centered.box | The list of centered (or transformed) coordinates. . These files can be used as inputs of sxwindow |
| micrographs.txt | Micrograph selection text file containing the list of extracted micrograph basenames. This file can be used as micrograph selection text file for sxcter, sxgui_cter, sxwindow, sxpipe organize_micrographs, and e2bdb |
Description
This command executes the following processes:
Extract the following information stored in the header of each particle image.
Convert the center coordinates to EMAN1 box coordinates format, and then save the results to output files.
Transform the coordinates based on the projection parameters and user-provided 3D shift, and then save the results to output files.
Save the list of extracted micrograph names to an output file.
Method
Reference
Developer Notes
2018/02/21 Toshio Moriya
Wish list:
Add --proj_params to use the projection parameter files stored in a text file instead of image headers.
Setting --box_size to zero (default value) should save the coordinates file in SPHIRE format
Save adjusted shifts to files
Save projection parameters
Save CTF parameters
Author / Maintainer
Christos Gatsogiannis and Toshio Moriya
Keywords
Category 1:: APPLICATIONS
Files
See also
Maturity
Alpha:: Under development.
Bugs
There are no known bugs so far.