pipeline:utilities:sxsummovie

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pipeline:utilities:sxsummovie [2018/02/16 10:11]
127.0.0.1 external edit
pipeline:utilities:sxsummovie [2018/06/20 13:12] (current)
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 ~~NOTOC~~ ~~NOTOC~~
  
-===== sxsummovie ​===== +===== sxgui_unblur ​===== 
-Micrograph ​movie summation: Sum micrograph movies with SumMovie.+Micrograph ​Movie Summation: Sum micrograph movies with [[http://​grigoriefflab.janelia.org/​unblur|Summovie]].
  
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 Usage in command line Usage in command line
  
-  sxsummovie.py ​ summovie_path ​ input_micrograph_pattern ​ input_shift_pattern ​ output_directory ​ --selection_list=SELECTION_LIST ​ --nr_frames=nr_frames ​ ​--first=FIRST  ​--last=LAST  ​--pixel_size=pixel_size ​ ​--nr_threads=NR_THREADS ​ ​--apply_dose_filter ​ --voltage=voltage ​ ​--exposure_per_frame=exposure_per_frame ​ ​--pre_exposure=pre_exposure ​ ​--dont_restore_noise+  sxsummovie.py ​ summovie_path ​ input_micrograph_pattern ​ input_shift_pattern ​ output_directory ​ --selection_list=SELECTION_LIST ​ --nr_frames=NUM_OF_FRAMES ​ ​--first=FIRST_FRAME ​ ​--last=LAST_FRAME ​ ​--pixel_size=PIXEL_SIZE ​ ​--nr_threads=NUM_OF_THREADS ​ ​--apply_dose_filter ​ --voltage=VOLTAGE ​ ​--exposure_per_frame=EXPOSURE ​ ​--pre_exposure=EXPOSURE ​ ​--dont_restore_noise
  
- +\\ 
-=== Typical usage ===+===== Typical usage =====
  
 sxsummovie exists only in non-MPI version. sxsummovie exists only in non-MPI version.
  
-__Perform summovie ​without dose filtering__:​+__Run Summovie ​without dose filtering__:​
  
   sxsummovie.py ~/​my_app/​summovie '​outdir_unblur/​corrsum/​micrograph_*_frames_sum.mrc'​ '​outdir_unblur/​shift/​micrograph_*_frames_shift.txt'​ outdir_summovie --nr_frames=24 --pixel_size=1.19 --nr_threads=1   sxsummovie.py ~/​my_app/​summovie '​outdir_unblur/​corrsum/​micrograph_*_frames_sum.mrc'​ '​outdir_unblur/​shift/​micrograph_*_frames_shift.txt'​ outdir_summovie --nr_frames=24 --pixel_size=1.19 --nr_threads=1
  
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-__Perform summovie ​without dose filtering and with less frames__:+__Run Summovie ​without dose filtering and with less frames__:
  
   sxsummovie.py ~/​my_app/​summovie '​outdir_unblur/​corrsum/​micrograph_*_frames_sum.mrc'​ '​outdir_unblur/​shift/​micrograph_*_frames_shift.txt'​ outdir_summovie --nr_frames=24 --first=3 --last=15 --pixel_size=1.19 --nr_threads=1   sxsummovie.py ~/​my_app/​summovie '​outdir_unblur/​corrsum/​micrograph_*_frames_sum.mrc'​ '​outdir_unblur/​shift/​micrograph_*_frames_shift.txt'​ outdir_summovie --nr_frames=24 --first=3 --last=15 --pixel_size=1.19 --nr_threads=1
  
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-__Perform summovie ​with dose filtering and with less frames__:+__Run Summovie ​with dose filtering and with less frames__:
  
   sxsummovie.py ~/​my_app/​summovie '​outdir_unblur/​corrsum/​micrograph_*_frames_sum.mrc'​ '​outdir_unblur/​shift/​micrograph_*_frames_shift.txt'​ outdir_summovie --nr_frames=24 --first=3 --last=15 --pixel_size=1.19 --nr_threads=1 --apply_dose_filter --voltage=300 --exposure_per_frame=2 --pre_exposure=0   sxsummovie.py ~/​my_app/​summovie '​outdir_unblur/​corrsum/​micrograph_*_frames_sum.mrc'​ '​outdir_unblur/​shift/​micrograph_*_frames_shift.txt'​ outdir_summovie --nr_frames=24 --first=3 --last=15 --pixel_size=1.19 --nr_threads=1 --apply_dose_filter --voltage=300 --exposure_per_frame=2 --pre_exposure=0
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 ===== Input ===== ===== Input =====
 === Main Parameters === === Main Parameters ===
-  ; summovie_path : summovie ​executable path: Specify the file path of summovie ​executable. (This argument is specific to SPHIRE, and not directly used by summovie ​executable.) (default required string) +  ; summovie_path : Summovie ​executable path: Specify the file path of Summovie ​executable. (This argument is specific to SPHIRE, and not directly used by Summovie ​executable.) (default required string) 
-  ; input_micrograph_pattern : Input micrograph ​path pattern: Specify path pattern of input micrographs ​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 micrographs. (This argument is specific to SPHIRE, and not directly used by summovie ​executable.) (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 Summovie ​executable.) (default required string) 
-  ; input_shift_pattern : Input shift path pattern: Specify path pattern of input shift files 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 the associated pair of input micrograph and shift file. (This argument is specific to SPHIRE, and not directly used by summovie ​executable.) (default required string)+  ; input_shift_pattern : Input drift shift path pattern: Specify path pattern of input drift shift parameters ​files 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 the associated pair of input micrograph and shift file. (This argument is specific to SPHIRE, and not directly used by Summovie executable.) (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 Summovie ​executable.) (default required string)
  
-  ; selection_list : Micrograph selecting list: Specify a name of micrograph selection list text file. The file extension must be '​.txt'​. If this is not provided, all files matched with the micrograph name pattern will be processed. (This option is specific to SPHIRE, and not directly used by summovie ​executable.) (default none) +  ; %%--%%selection_list : Movie selection file: Specify a name of micrograph ​movie selection list text file. The file extension must be '​.txt'​. If this is not provided, all files matched with the micrograph ​movie name pattern will be processed. (This option is specific to SPHIRE, and not directly used by Summovie ​executable.) (default none) 
-  ; nr_frames : Number of movie frames: The number of movie frames in each input micrograph. (default 3) +  ; %%--%%nr_frames : Number of movie frames: The number of movie frames in each input micrograph. (default 3) 
-  ; first : First movie frame: First movie frame for summing. (default 1) +  ; %%--%%first : First movie frame: First movie frame for summing. (default 1) 
-  ; last : Last movie frame: Last movie frame for summing. (default -1) +  ; %%--%%last : Last movie frame: Last movie frame for summing. (default -1) 
-  ; pixel_size : Pixel size [A]: The pixel size of input micrographs. (default required float) +  ; %%--%%pixel_size : Pixel size [A]: The pixel size of input micrographs. (default required float) 
-  ; nr_threads : Number of threads: The number of threads ​summovie ​can use. The higher the faster, but it requires larger memory. (default 1)+  ; %%--%%nr_threads : Number of threads: The number of threads ​Summovie ​can use. The higher the faster, but it requires larger memory. (default 1)
  
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 === Advanced Parameters === === Advanced Parameters ===
-  ; apply_dose_filter : Apply dose filter ​step: Requires voltage, ​exposure per frame, and pre exposure ​options. (default False) +  ; %%--%%apply_dose_filter : Apply dose filter: Requires ​%%--%%voltage, ​%%--%%exposure_per_frame, and %%--%%pre_exposure ​options. (default False) 
-  ; voltage : Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. Effective only when apply_dose_filter option is used. (default 300.0) +  ; %%--%%voltage : Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. Effective only when %%--%%apply_dose_filter option is used. (default 300.0) 
-  ; exposure_per_frame : Per frame exposure [e/A^2]: The electron dose per frame in e/A^2. Effective only when apply_dose_filter option is used. (default 2.0) +  ; %%--%%exposure_per_frame : Per frame exposure [e/A^2]: The electron dose per frame in e/A^2. Effective only when %%--%%apply_dose_filter option is used. (default 2.0) 
-  ; pre_exposure : Pre-exposure [e/A^2]: The electron does in e/A^2 used for exposure prior to imaging. Effective only when apply_dose_filter option is used. (default 0.0) +  ; %%--%%pre_exposure : Pre-exposure [e/A^2]: The electron does in e/A^2 used for exposure prior to imaging. Effective only when %%--%%apply_dose_filter option is used. (default 0.0) 
-  ; dont_restore_noise : Do not restore ​noise power: ​Do not restore noise power. (default False)+  ; %%--%%dont_restore_noise : Restore ​noise power: ​Indicate if noise power should be restored or not. By default, ​restore noise power. (default False question reversed in GUI)
  
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 ===== Output ===== ===== Output =====
-  ; 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 summovie executable.) (default required string) 
- 
-\\ 
 The program automatically creates the following subdirectories in the specified output directory. The program automatically creates the following subdirectories in the specified output directory.
  
 \\ __Without dose-filtering__:​ \\ __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. 
-FRC files will be written to the "frc" ​directory.+  ​* ​FRC files will be written to the ''​frc'' ​directory.
  
 \\ __With dose-filtering__:​ \\ __With dose-filtering__:​
-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 
-FRC files will be written to the "frc" ​directory.+  ​* ​FRC files will be written to the ''​frc'' ​directory.
  
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 ===== Description ===== ===== Description =====
 +
 +\\
 +==== Method ====
 +
 +\\
 +==== Reference ====
 +[[http://​grigoriefflab.janelia.org/​unblur|Unblur & Summovie]]
 +
 +\\
 +==== Developer Notes ====
  
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 ==== Files ==== ==== Files ====
-sxsummovie.py+sparx/bin/sxsummovie.py
  
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 ==== See also ==== ==== See also ====
 +[[pipeline:​movie:​sxunblur|sxunblur]] and [[http://​grigoriefflab.janelia.org/​unblur|Unblur & Summovie]].
  
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 ==== Maturity ==== ==== Maturity ====
-No bugs known so far.+Alpha:: Under development. Please let us know if there are any bugs
 + 
 +\\ 
 +==== Bugs ==== 
 +There are no known bugs so far.
  
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  • pipeline/utilities/sxsummovie.txt
  • Last modified: 2018/06/20 13:12
  • (external edit)