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pipeline:movie:sxunblur [2018/02/16 10:11]
127.0.0.1 external edit 		pipeline:movie:sxunblur [2018/02/27 13:58]
moriya
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 ~~NOTOC~~ ~~NOTOC~~
  
-====== sxunblur ====== +===== sxunblur ===== 
-Micrograph movie alignment: align micrograph movies with Unblur. [[http://grigoriefflab.janelia.org/unblur]]+Micrograph Movie Alignment: Align frames of micrograph movies with [[http://grigoriefflab.janelia.org/unblur|Unblur & Summovie]].
  
 \\ \\
-====== Usage ======+===== Usage ===== 
 Usage in command line Usage in command line
  
-  sxunblur.py  --input_micrograph_list_file unblur  input_mrc_micrograph  output --nr_threads=NR_THREADS  --nr_frames=nr_frames  --pixel_size=pixel_size  --skip_dose_filter  --exposure_per_frame=exposure_per_frame  --voltage=voltage  --pre_exposure=pre_exposure  --save_frames  --expert_mode  --shift_initial=shift_initial  --shift_radius=shift_radius  --b_factor=b_factor  --fourier_vertical=fourier_vertical  --fourier_horizontal=fourier_horizontal  --shift_threshold=shift_threshold  --iterations=iterations  --dont_restore_noise --verbose+  sxunblur.py  unblur_path  input_micrograph_pattern  output_directory  --summovie_path=SUMMOVIE_PATH  --selection_list=SELECTION_LIST  --nr_frames=NUM_OF_FRAMES  --pixel_size=PIXEL_SIZE  --voltage=VOLTAGE  --exposure_per_frame=EXPOSURE  --pre_exposure=EXPOSURE  --nr_threads=NUM_OF_THREADS  --save_frames  --skip_dose_filter  --expert_mode  --shift_initial=SHIFT  --shift_radius=SHIFT_RADISU  --b_factor=B_FACTOR  --fourier_vertical=VERTICAL_MASK  --fourier_horizontal=HORIZONTAL_MASK  --shift_threshold=SHIFT_THRESHOLD  --iterations=ITERATIONS  --dont_restore_noise  --verbose
  
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-====== Typical usage ====== +===== Typical usage =====
-Just shift data with dose filter.+
  
-  sxunblur.py directory_to_unblur directory/prefix*suffix.mrc output_directory --nr_frames=25 --pixel_size=1.19 --exposure_per_frame=1.0 --voltage=300.0 --pre_exposure=0.0+sxunblur exists only in non-MPI version.
  
-Shift data with aligned sum files, and aligned frames without dose filter.+Run Unblur with dose-filtering, and then run Summovie without dose-filtering.
  
-  sxunblur.py directory_to_unblur directory/prefix*suffix.mrc output_directory --nr_frames=25 --pixel_size=1.19 --skip_dose_filter --save_frames --nr_threads=2+  sxunblur.py ~/my_app/unblur 'movies/micrograph_*_frames.mrc' outdir_unblur --summovie_path=~/my_app/summovie --nr_frames=25 --pixel_size=1.19 --exposure_per_frame=1.0 --voltage=300.0 --pre_exposure=0.0 --nr_threads=1
  
-Dose filter and Expert Options and aligned frames+Run Unblur with dose-filtering, and then run Summovie without dose-filtering with selection list.
  
-  sxunblur.py directory_to_unblur directory/prefix*suffix.mrc output_directory --nr_frames=25 --pixel_size=1.19 --exposure_per_frame=1.0 --voltage=300.0 --pre_exposure=0.0 --save_frames --expert_mode --shift_initial=2.0 --shift_radius=200.0 --b_factor=1500.0 --fourier_vertical=1 --fourier_horizontal=1 --shift_threshold=0.1 --iterations=10 --verbose --nr_threads=1+  sxunblur.py ~/my_app/unblur 'movies/micrograph_*_frames.mrc' outdir_unblur --summovie_path=~/my_app/summovie --selection_list=selected_micrograph_file --nr_frames=25 --pixel_size=1.19 --exposure_per_frame=1.0 --voltage=300.0 --pre_exposure=0.0 --nr_threads=1 
 + 
 +Run Unblur without dose-filtering. 
 + 
 +  sxunblur.py ~/my_app/unblur 'movies/micrograph_*_frames.mrc' outdir_unblur --nr_frames=25 --pixel_size=1.19 --skip_dose_filter --nr_threads=1 
 + 
 +Run Unblur without dose-filtering, and save the frames. 
 + 
 +  sxunblur.py ~/my_app/unblur 'movies/micrograph_*_frames.mrc' outdir_unblur --nr_frames=25 --pixel_size=1.19 --skip_dose_filter --save_frames --nr_threads=1 
 + 
 +Run Unblur with dose-filtering, and then run Summovie without dose-filtering with all options. 
 + 
 +  sxunblur.py ~/my_app/unblur 'movies/micrograph_*_frames.mrc' outdir_unblur --summovie_path=~/my_app/summovie --nr_frames=25 --pixel_size=1.19 --exposure_per_frame=1.0 --voltage=300.0 --pre_exposure=0.0 --save_frames --expert_mode --shift_initial=2.0 --shift_radius=200.0 --b_factor=1500.0 --fourier_vertical=1 --fourier_horizontal=1 --shift_threshold=0.1 --iterations=10 --verbose --nr_threads=1
  
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-====== Input ======+===== Input =====
 === Main Parameters === === Main Parameters ===
-  ; input_micrograph_list_file : Input micrograph list file: Not an unblur option, extension of input micrograph list file must be '.txt'. If this is not provided, all files matched with the micrograph name pattern will be processed. (default none) +  ; 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 to unblur 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 Unblur and Summovie executables.) (default required string) 
-  ; input_mrc_micrograph : Input micrographs: You can use the wild cards (e.g. *) to specify a list of micrographs. (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 : Output directory: The results will be written here. This directory will be created automatically and it must not exist previously. (default required string) + 
-  ; nr_threads : Number of threads: Not an unblur option, number of threads unblur is allowed to use. The higher the faster, but it also needs a higher amount of memory. (default 1) +  ; %%--%%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) 
-  ; nr_frames :  Number of frames: (default 3) +  ; %%--%%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 Unblur and Summovie executables.) (default none) 
-  ; pixel_size : Pixel size [A]: (default  required -1.0) +  ; %%--%%nr_frames : Number of movie frames: The number of movie frames in each input micrograph. (default 3) 
-  ; exposure_per_frame : Per frame exposure [e/A^2]: (default 1.0) +  ; %%--%%pixel_size : Pixel size [A]: The pixel size of input micrographs. (default required float) 
-  ; voltage : Microscope voltage [kV]: (default 300.0) +  ; %%--%%voltage : Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. Will be ignored when %%--%%skip_dose_filter option is used. (default 300.0) 
-  ; pre_exposure : Pre exposure [e/A^2]: (default 0.0)+  ; %%--%%exposure_per_frame : Per frame exposure [e/A^2]: The electron dose per frame in e/A^2. Will be ignored when %%--%%skip_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. Will be ignored when %%--%%skip_dose_filter option is used. (default 0.0) 
 +  ; %%--%%nr_threads : Number of threads: The number of threads Unblur can use. The higher the faster, but it requires larger memory. (default 1)
  
 \\ \\
 === Advanced Parameters === === Advanced Parameters ===
-  ; save_frames : Save aligned frames: save aligned frames. This is only neccessary if one wants to perform movie refinement and will slow 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 : Skip the dose filter step: If yes, exposure per frame, voltage, and pre exposure will be ignored. (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) 
-  ; expert_mode : Set expert mode: Requires the options initial shift, shift radius, b-factor, fourier_vertical, fourier_horizontal, shift threshold, iterations, restore noise, and verbosity. (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 : *EXPERT* Minimum shift for initial search [A]: (default 2.0) +  ; %%--%%shift_initial : Minimum shift for initial search [A]: Effective only when %%--%%expert_mode option is used. (default 2.0) 
-  ; shift_radius : *EXPERT* Outer radius shift limit [A]: (default 200.0) +  ; %%--%%shift_radius : Outer radius shift limit [A]: Effective only when %%--%%expert_mode option is used. (default 200.0) 
-  ; b_factor : *EXPERT* Apply B-factor to images [A^2]: (default 1500.0) +  ; %%--%%b_factor : Apply B-factor to images [A^2]: Effective only when %%--%%expert_mode option is used. (default 1500.0) 
-  ; fourier_vertical : *EXPERT* Half-width of central vertical line of fourier mask: (default 1) +  ; %%--%%fourier_vertical : Vertical Fourier central mask size: The half-width of central vertical line of Fourier mask. Effective only when %%--%%expert_mode option is used. (default 1) 
-  ; fourier_horizontal : *EXPERT* Half-width of central horizontal line of fourier mask: (default 1) +  ; %%--%%fourier_horizontal : Horizontal Fourier central mask size: The half-width of central horizontal line of Fourier mask. Effective only when %%--%%expert_mode option is used. (default 1) 
-  ; shift_threshold : *EXPERT* Termination shift threshold: (default 0.1) +  ; %%--%%shift_threshold : Termination shift threshold: Effective only when %%--%%expert_mode option is used. (default 0.1) 
-  ; iterations : *EXPERT* Maximum iterations: (default 10) +  ; %%--%%iterations : Maximum iterations: Effective only when %%--%%expert_mode option is used. (default 10) 
-  ; dont_restore_noise : *EXPERT* 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. Effective only when %%--%%expert_mode option is used. (default False question reversed in GUI) 
-  ; verbose : *EXPERT* Verbose: (default False)+  ; %%--%%verbose : Verbose: Effective only when %%--%%expert_mode option is used. (default False)
  
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-====== Output ====== +===== Output ===== 
-The program creates the directory automatically in the chosen output directory. (default required string)+The program automatically creates the following subdirectories in the specified output directory.
  
-Without dosefilter: +__Run without dose-filtering__: 
-Sum files will be written to the "corrsum" folder. +  * Sum files will be written to the "corrsum" directory. 
-Log files will be written to the "logfiles" folder +  * Log files will be written to the "logfiles" directory. 
-Aligned frames will be written to the "corrsum" folder. +  * Aligned frames will be written to the "corrsum" directory. 
-Shift files  will be written to the "shift" folder. +  * Shift files  will be written to the "shift" directory. 
-FRC files will be written to the "frc" folder.+  * FRC files will be written to the "frc" directory.
  
-With dosefilter: As without dosefilter plus: +__Run with dose-filtering (as without dose-filtering plus)__: 
-Dose filtered sum files will be written to the "corrsum_dose_filtered" folder. +  * Dose filtered sum files will be written to the "corrsum_dose_filtered" directory. 
-Log files will be written to the "logfiles" folder +  * Log files will be written to the "logfiles" directory. 
-Dose filtered aligned frames will be written to the "corrsum_dose_filtered" folder. +  * Dose filtered aligned frames will be written to the "corrsum_dose_filtered" directory. 
-Shift files  will be written to the "shift" folder. +  * Shift files  will be written to the "shift" directory. 
-FRC files will be written to the "frc" folder.+  * FRC files will be written to the "frc" directory.
  
 \\ \\
-======= Description ======= +===== Description ===== 
----+ 
 +\\ 
 +==== Method ==== 
 + 
 +\\ 
 +==== Reference ==== 
 +[[http://grigoriefflab.janelia.org/unblur|Unblur & Summovie]] 
 + 
 +\\ 
 +==== Developer Notes ====
  
 \\ \\
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 ==== Files ==== ==== Files ====
-sxunblur.py+sparx/bin/sxunblur.py
  
 \\ \\
-==== See Also ==== +==== See also ==== 
-sxgui_unblur.py+[[pipeline:movie:sxgui_unblur|sxgui_unblur]]
  
 \\ \\
 ==== Maturity ==== ==== Maturity ====
-No bugs known so far.+Beta:: Under evaluation and testing. Please let us know if there are any bugs.
  
 \\ \\
 +==== Bugs ====
 +There are no known bugs so far.
 +
 +\\
 +
pipeline/movie/sxunblur.txt · Last modified: 2019/04/02 10:55 by lusnig

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