sxpipe organize_micrographs

Organize Micrographs/Movies: Organize micrographs/movies by moving micrographs/movies in a selecting file from a source directory (specified by source micrographs/movies pattern) to a destination directory.


Usage

Usage in command line

sxpipe.py  organize_micrographs  source_micrograph_pattern  selection_list  destination_directory  --reverse  --check_consistency


Typical usage

sxpipe organize_micrographs does not support MPI.

1. Normal Operation Mode: The program moves micrographs/movies in selecting list from the source directory to the destination directory.

sxpipe.py organize_micrographs 'CorrectedSums/corrsum/TcdA1-*_frames_sum.mrc' 'CTFest/Tutorial_micrographs_discard.txt' 'CorrectedSums/DISCARDED'

2. Reverse Operation Mode: The program moves micrographs/movies in selecting list from the destination directory to the source directory.

sxpipe.py organize_micrographs 'CorrectedSums/corrsum/TcdA1-*_frames_sum.mrc' 'CTFest/Tutorial_micrographs_discard.txt' 'CorrectedSums/MRK_DISCARDED'  --reverse


Input

Main Parameters

source_micrograph_pattern
Source micrograph/movies path pattern: Specify path pattern of source micrographs/movies with a wild card (*). Use the wild card to indicate the place of variable part of the file names (e.g. serial number, time stamp, and etc). The path pattern must be enclosed by single quotes (') or double quotes (“). (Note: sxgui.py automatically adds single quotes (')). The substring at the variable part must be same between each associated pair of micrograph/movie names. bdb files can not be selected as source micrographs/movies. (default required string)
selection_list
Micrograph/Movie selection file: Specify a path of text file containing a list of selected micrograph/movie names or paths. The file extension must be '.txt'. The directory path of each entry will be ignored if there are any. (default required string)
destination_directory
Destination directory: The micrographs/movies in selecting list will be moved to this directory. This directory will be created automatically if it does not exist. (default required string)
--reverse
Reverse operation: Move back micrographs/movies from the destination directory to the source directory. Please use this option to restore the previously-moved micrographs/movies. (default False)


Advanced Parameters

--check_consistency
Check consistency of dataset: Create a text file containing the list of micrograph/movie ID entries might have inconsitency among the provided dataset. (i.e. mic_consistency_check_info.txt). (default False)


Output


Description


Method


Reference


Developer Notes


Author / Maintainer

Toshio Moriya


Keywords

Category 1:: APPLICATIONS


Files

sparx/bin/sxpipe.py


See also

Maturity

Beta:: Under evaluation and testing. Please let us know if there are any bugs.


Bugs

There are no known bugs so far.