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pipeline:utilities:sxpipe_restacking

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pipeline:utilities:sxpipe_restacking [2018/03/05 15:47]
moriya created 		pipeline:utilities:sxpipe_restacking [2018/08/22 11:39]
fmerino
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 ===== sxpipe restacking ===== ===== sxpipe restacking =====
-Restacking: Generate all necessary information to restack the input stack (i.e. particle image ID list and projection parameters list) while appling micrograph selection list. Optinally, the command can directly output the virtual stack.  Also, this command can be used to generate all parameters files for reboxing (i.e. original/centered particle coordinates list files, CTF parameters list, original/centered projection parameters list as well as micrograph selection file). Optionally, user can provided a 3D shift to recenter the projection parameters and so the particle coordinates.+Restacking: Generate all necessary information to restack the input stack (i.e., particle image ID list, CTF parameters list, projection parameters list) while appling micrograph selection list. Optionally, the command can directly output the virtual stack.  In addition, this command can be used to generate all parameters files for reboxing (i.e. original/centered particle coordinates list files, CTF parameters list, original/centered projection parameters list as well as micrograph selection file). Optionally, user can provided a 3D shift to recenter the projection parameters and so the particle coordinates.
  
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 ===== Input ===== ===== Input =====
 === Main Parameters === === Main Parameters ===
-  ; input_bdb_stack_path : Input BDB image stack: Specify the input BDB image stack. (default required string) +  ; input_bdb_stack_path : Input bdb image stack: Specify the input bdb image stack. (default required string) 
-  ; output_directory : Output directory: The results will be written here. This directory will be created automatically and it must not exist previously. (default required string)+  ; output_directory : Output directory: The results will be written here. It cannot be an existing one. (default required string)
  
   ; %%--%%selection_list : Micrograph/Movie selection file: Specify path to text file containing a list of selected micrograph/movie names or paths. The particles associated with the micrographs/movies in this list will be processed. The file extension must be //.txt//. The directory path of each entry will be ignored if there are any. (default none)   ; %%--%%selection_list : Micrograph/Movie selection file: Specify path to text file containing a list of selected micrograph/movie names or paths. The particles associated with the micrographs/movies in this list will be processed. The file extension must be //.txt//. The directory path of each entry will be ignored if there are any. (default none)
-  ; %%--%%shift3d_x : 3D x-shift [Pixels]: Provide 3D x-shift corresponding to shifting the 3D volume along x-axis. (default 0) +  ; %%--%%shift3d_x : 3D x-shift [Pixels]: 3D x-shift value. (default 0) 
-  ; %%--%%shift3d_y : 3D y-shift [Pixels]: Provide 3D y-shift corresponding to shifting the 3D volume along y-axis. (default 0) +  ; %%--%%shift3d_y : 3D y-shift [Pixels]: 3D y-shift value. (default 0) 
-  ; %%--%%shift3d_z : 3D z-shift [Pixels]: Provide 3D z-shift corresponding to shifting the 3D volume along z-axis. (default 0)+  ; %%--%%shift3d_z : 3D z-shift [Pixels]: 3D z-shift value. (default 0)
   ; %%--%%save_vstack : Save virtual stack: Use this option to save the virtual stack. By default, the virtual stack will not be generated. (default False)   ; %%--%%save_vstack : Save virtual stack: Use this option to save the virtual stack. By default, the virtual stack will not be generated. (default False)
   ; %%--%%sv_vstack_basename : Virtual stack basename: For %%--%%save_vstack, specify the basename of output virtual stack file. It cannot be empty string or only white spaces. (default vstack)   ; %%--%%sv_vstack_basename : Virtual stack basename: For %%--%%save_vstack, specify the basename of output virtual stack file. It cannot be empty string or only white spaces. (default vstack)
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pipeline/utilities/sxpipe_restacking.txt · Last modified: 2019/04/02 10:59 by lusnig

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