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pipeline:utilities:sxpipe_organize_micrographs [2018/08/22 11:34]
fmerino 		pipeline:utilities:sxpipe_organize_micrographs [2019/04/02 10:24] (current)
lusnig
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 ~~NOTOC~~ ~~NOTOC~~
  
-===== sxpipe organize_micrographs =====+===== 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. 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.
  
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 Usage in command line Usage in command line
  
-  sxpipe.py  organize_micrographs  source_micrograph_pattern  selection_list  destination_directory  --reverse  --check_consistency+  sp_pipe.py  organize_micrographs  source_micrograph_pattern  selection_list  destination_directory  --reverse  --check_consistency
  
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 ===== Typical usage ===== ===== Typical usage =====
  
-sxpipe organize_micrographs does not support MPI. +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. 1. Normal Operation Mode: The program moves micrographs/movies listed 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'+  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. 2. Reverse Operation Mode: The program moves micrographs/movies listed 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+  sp_pipe.py organize_micrographs 'CorrectedSums/corrsum/TcdA1-*_frames_sum.mrc' 'CTFest/Tutorial_micrographs_discard.txt' 'CorrectedSums/MRK_DISCARDED'  --reverse
  
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 ===== Input ===== ===== Input =====
 === Main Parameters === === 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: 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 cannot be selected as source micrographs/movies. (default required string)+  ; 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)   ; 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)   ; 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)
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 ==== Files ==== ==== Files ====
-sparx/bin/sxpipe.py+sparx/bin/sp_pipe.py
  
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 ==== See also ==== ==== See also ====
-[[pipeline:cter:sxgui_cter|sxgui_cter]] and [[pipeline:movie:sxgui_unblur|sxgui_unblur]]+[[pipeline:cter:sxgui_cter|sp_gui_cter]] and [[pipeline:movie:sxgui_unblur|sp_gui_unblur]]
  
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pipeline/utilities/sxpipe_organize_micrographs.txt ยท Last modified: 2019/04/02 10:24 by lusnig

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