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pipeline:movie:sxunblur

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pipeline:movie:sxunblur [2018/02/27 13:58]
moriya 		pipeline:movie:sxunblur [2018/08/22 11:47]
fmerino
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 === Main Parameters === === Main Parameters ===
   ; unblur_path : Unblur executable path: Specify the file path of Unblur executable. (This argument is specific to SPHIRE, and not directly used by Unblur and Summovie executables.) (default required string)   ; unblur_path : Unblur executable path: Specify the file path of Unblur executable. (This argument is specific to SPHIRE, and not directly used by Unblur and Summovie executables.) (default required string)
-  ; input_micrograph_pattern : Input movie path pattern: Specify path pattern of input micrograph 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 (')). bdb files can not be selected as input micrograph movies. (This argument is specific to SPHIRE, and not directly used by Unblur and Summovie executables.) (default required string) +  ; input_micrograph_pattern : Input movie path pattern: Specify path pattern of input micrograph movies with a wild card (*).. The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: sxgui.py automatically adds single quotes (')). bdb files cannot be selected as input micrograph movies. (This argument is specific to SPHIRE, and not directly used by Unblur and Summovie executables.) (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. (This argument is specific to SPHIRE, and not directly used by Unblur and Summovie executables.) (default required string)+  ; output_directory : Output directory: The results will be written here. It cannot be an existing one. (This argument is specific to SPHIRE, and not directly used by Unblur and Summovie executables.) (default required string)
  
   ; %%--%%summovie_path : Summovie executable path: Specify the file path of Summovie executable. (This option is specific to SPHIRE, and not directly used by Unblur and Summovie executables.) (default none)   ; %%--%%summovie_path : Summovie executable path: Specify the file path of Summovie executable. (This option is specific to SPHIRE, and not directly used by Unblur and Summovie executables.) (default none)
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 === Advanced Parameters === === Advanced Parameters ===
   ; %%--%%save_frames : Save aligned movie frames: Save aligned movie frames. This option slows down the process. (default False)   ; %%--%%save_frames : Save aligned movie frames: Save aligned movie frames. This option slows down the process. (default False)
-  ; %%--%%skip_dose_filter : Apply dose filter: Indicate if dose filter should be applied or not. With this option, voltage, exposure per frame, and pre exposure will be ignored. By default, apply dose filter. (default False question reversed in GUI)+  ; %%--%%skip_dose_filter : Apply dose filter: Indicate if dose filter should be applied or not. With this option, %%--%%voltage, %%--%%exposure_per_frame, and %%--%%pre_exposure will be ignored. By default, apply dose filter. (default False question reversed in GUI)
   ; %%--%%expert_mode : Use expert mode: Requires %%--%%initial_shift, %%--%%shift_radius, %%--%%b_factor, %%--%%fourier_vertical, %%--%%fourier_horizontal, %%--%%shift_threshold, %%--%%iterations, %%--%%dont_restore_noise, and %%--%%verbosity options. (default False)   ; %%--%%expert_mode : Use expert mode: Requires %%--%%initial_shift, %%--%%shift_radius, %%--%%b_factor, %%--%%fourier_vertical, %%--%%fourier_horizontal, %%--%%shift_threshold, %%--%%iterations, %%--%%dont_restore_noise, and %%--%%verbosity options. (default False)
   ; %%--%%shift_initial : Minimum shift for initial search [A]: Effective only when %%--%%expert_mode option is used. (default 2.0)   ; %%--%%shift_initial : Minimum shift for initial search [A]: Effective only when %%--%%expert_mode option is used. (default 2.0)
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 The program automatically creates the following subdirectories in the specified output directory. The program automatically creates the following subdirectories in the specified output directory.
  
-__Run without dose-filtering__: +\\ __Run without dose-filtering__: 
-  * Sum files will be written to the "corrsum" directory. +  * Sum files will be written to the ''corrsum'' directory. 
-  * Log files will be written to the "logfiles" directory. +  * Log files will be written to the ''logfiles'' directory. 
-  * Aligned frames will be written to the "corrsum" directory. +  * Aligned frames will be written to the ''corrsum'' directory. 
-  * Shift files  will be written to the "shift" directory. +  * Shift files  will be written to the ''shift'' directory. 
-  * FRC files will be written to the "frc" directory.+  * FRC files will be written to the ''frc'' directory.
  
-__Run with dose-filtering (as without dose-filtering plus)__: +\\ __Run with dose-filtering (as without dose-filtering plus)__: 
-  * Dose filtered sum files will be written to the "corrsum_dose_filtered" directory. +  * Dose filtered sum files will be written to the ''corrsum_dose_filtered'' directory. 
-  * Log files will be written to the "logfiles" directory. +  * Log files will be written to the ''logfiles'' directory. 
-  * Dose filtered aligned frames will be written to the "corrsum_dose_filtered" directory. +  * Dose filtered aligned frames will be written to the ''corrsum_dose_filtered'' directory. 
-  * Shift files  will be written to the "shift" directory. +  * Shift files  will be written to the ''shift'' directory. 
-  * FRC files will be written to the "frc" directory.+  * FRC files will be written to the ''frc'' directory.
  
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pipeline/movie/sxunblur.txt · Last modified: 2019/04/02 10:55 by lusnig

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