sp_pipe organize_micrographs
Organize Micrographs/Movies: Organize micrographs/movies by moving micrographs/movies listed in a selecting file from a source directory (specified by source micrographs/movies pattern) to a destination directory.
Usage
Usage in command line
sp_pipe.py organize_micrographs source_micrograph_pattern selection_list destination_directory --reverse --check_consistency
Typical usage
sp_pipe organize_micrographs does not support MPI.
1. Normal Operation Mode: The program moves micrographs/movies listed in selecting list from the source directory to the destination directory.
sp_pipe.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 listed in selecting list from the destination directory to the source directory.
sp_pipe.py organize_micrographs 'CorrectedSums/corrsum/TcdA1-*_frames_sum.mrc' 'CTFest/Tutorial_micrographs_discard.txt' 'CorrectedSums/MRK_DISCARDED' --reverse
Main Parameters
- source_micrograph_pattern
- Source micrograph/movies path pattern: Specify path pattern of source micrographs/movies with a wild card (*). The path pattern must be enclosed by single quotes (\') or double quotes (\“). (Note: sp_gui.py automatically adds single quotes (\')). The substring at the variable part must be same between each associated pair of micrograph/movie names. bdb files cannot 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. It cannot be an existing one. (default required string)
- --reverse
- Reverse operation: Move back micrographs/movies from the destination directory to the source directory. (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
Keywords
Category 1:: APPLICATIONS
Files
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.