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pipeline:movie:sxsummovie [2018/08/22 11:48]
fmerino 		pipeline:movie:sxsummovie [2019/04/02 10:15]
lusnig
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 ~~NOTOC~~ ~~NOTOC~~
  
-===== sxsummovie =====+===== sp_summovie =====
 Micrograph Movie Summation: Sum micrograph movies with [[http://grigoriefflab.janelia.org/unblur|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=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+  sp_summovie.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
  
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 ===== Typical usage ===== ===== Typical usage =====
  
-sxsummovie exists only in non-MPI version.+sp_summovie exists only in non-MPI version.
  
 __Run 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+  sp_summovie.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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 __Run 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+  sp_summovie.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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 __Run 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+  sp_summovie.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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 === 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 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 Summovie executable.) (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: sp_gui.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 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 (*).. 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 (*).. 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 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. It cannot be an existing one. (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. It cannot be an existing one. (This argument is specific to SPHIRE, and not directly used by Summovie executable.) (default required string)
  
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 === Advanced Parameters === === Advanced Parameters ===
   ; %%--%%apply_dose_filter : Apply dose filter: 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) : %%--%%apply_dose_filter==True 
-  ; %%--%%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) : %%--%%apply_dose_filter==True 
-  ; %%--%%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) : %%--%%apply_dose_filter==True
   ; %%--%%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)   ; %%--%%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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 ==== Files ==== ==== Files ====
-sparx/bin/sxsummovie.py+sparx/bin/sp_summovie.py
  
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 ==== See also ==== ==== See also ====
-[[pipeline:movie:sxunblur|sxunblur]] and [[http://grigoriefflab.janelia.org/unblur|Unblur & Summovie]].+[[pipeline:movie:sp_unblur|sp_unblur]] and [[http://grigoriefflab.janelia.org/unblur|Unblur & Summovie]].
  
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pipeline/movie/sxsummovie.txt · Last modified: 2019/04/02 10:57 by lusnig

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