pipeline:utilities:sxpipe_organize_micrographs

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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]
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
  • Last modified: 2019/04/02 10:24
  • by lusnig