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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 in command line

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

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/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)
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: The micrographs/movies in selecting list will be moved to this directory. It cannot be an existing one. (default required string)
Reverse operation: Move back micrographs/movies from the destination directory to the source directory. (default False)

Advanced Parameters

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)

Toshio Moriya



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

There are no known bugs so far.

  • pipeline/utilities/sxpipe_organize_micrographs.1554189493.txt.gz
  • Last modified: 2019/04/02 09:18
  • by lusnig