~~NOTOC~~

===== 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.

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===== Usage =====

Usage in command line

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

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===== 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

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===== Input =====
=== 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)

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=== 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)

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===== Output =====

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===== Description =====

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==== Method ====

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==== Reference ====

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==== Developer Notes ====

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==== Author / Maintainer ====
Toshio Moriya

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==== Keywords ====
Category 1:: APPLICATIONS

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==== Files ====
sparx/bin/sp_pipe.py

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==== See also ====
[[pipeline:cter:sxgui_cter|sp_gui_cter]] and [[pipeline:movie:sxgui_unblur|sp_gui_unblur]]

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

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==== Bugs ====
There are no known bugs so far.

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