pipeline:utilities:sxpipe_organize_micrographs

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Last revision Both sides next revision
pipeline:utilities:sxpipe_organize_micrographs [2018/06/20 13:12]
127.0.0.1 external edit
pipeline:utilities:sxpipe_organize_micrographs [2019/04/02 09:18]
lusnig
Line 1: Line 1:
 ~~NOTOC~~ ~~NOTOC~~
  
-===== sxpipe ​organize_micrographs ===== +===== sp_pipe ​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.+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.
  
 \\ \\
Line 9: Line 9:
 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
  
 \\ \\
 ===== 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 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 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
  
 \\ \\
 ===== 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 (*). 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)+  ; 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. ​This directory will be created automatically if it does not exist. (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. Please use this option to restore the previously-moved micrographs/​movies. (default False)+  ; %%--%%reverse : Reverse operation: Move back micrographs/​movies from the destination directory to the source directory. (default False)
  
 \\ \\
Line 62: Line 62:
 \\ \\
 ==== Files ==== ==== Files ====
-sparx/bin/sxpipe.py+sparx/bin/sp_pipe.py
  
 \\ \\
 ==== See also ==== ==== See also ====
-[[pipeline:​cter:​sxgui_cter|sxgui_cter]] and [[pipeline:​movie:​sxgui_unblur|sxgui_unblur]]+[[pipeline:​cter:​sp_gui_cter|sp_gui_cter]] and [[pipeline:​movie:​sp_gui_unblur|sp_gui_unblur]]
  
 \\ \\
  • pipeline/utilities/sxpipe_organize_micrographs.txt
  • Last modified: 2019/04/02 10:24
  • by lusnig