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pipeline:movie:sxunblur [2018/08/22 11:47]
fmerino 		pipeline:movie:sxunblur [2019/04/02 10:13]
lusnig
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 ~~NOTOC~~ ~~NOTOC~~
  
-===== sxunblur ===== +===== sp_unblur ===== 
-Micrograph Movie Alignment: Align frames of micrograph movies with [[http://grigoriefflab.janelia.org/unblur|Unblur & Summovie]].+Unblur cisTEM: Align frames of micrograph movies with [[https://cistem.org/|Unblur]].
  
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 Usage in command line Usage in command line
  
-  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+  sp_unblur.py  unblur_path  input_micrograph_pattern  output_directory   --selection_file=SELECTION_FILE  --pixel_size=PIXEL_SIZE   --bin_factor=BIN_FACTOR  --skip_dose_adjustment --additional_dose_unadjusted  --voltage=VOLTAGE  --exposure_per_frame=EXPOSURE  --pre_exposure=EXPOSURE   --min_shift_initial=MIN_SHIFT_INITIAL  --outer_radius=OUTER_RADIUS  --b_factor=B_FACTOR  --half_width_vert=HALF_WIDTH_VERT  --half_width_hor=HALF_WIDTH_HOR  --termination=TERMINATION  --max_iterations=MAX_ITERATIONS  --dont_restore_noise_power  --gain_file=GAIN_FILE  --first_frame=FIRST_FRAME  --last_frame=LAST_FRAME  --distortion_angle=DISTORTION_ANGLE  --major_scale=MAJOR_SCALE  --minor_scale=MINOR_SCALE
  
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 ===== Typical usage ===== ===== Typical usage =====
  
-sxunblur exists only in non-MPI version.+sp_unblur exists in both MPI and non-MPI versions (Running MPI version does not require --MPI flag). 
  
-Run Unblur with dose-filtering, and then run Summovie without dose-filtering.+Run unblur with dose adjustment
  
-  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+mpirun -np 12 sp_unblur.py  path/to/unblur  'Movies/*' unblur_out_dir  --pixel_size=1.14  --voltage=300  --exposure_per_frame=1.3
  
-Run Unblur with dose-filtering, and then run Summovie without dose-filtering with selection list. 
  
-  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 with dose adjustment and gain reference file
  
-Run Unblur without dose-filtering.+mpirun -np 12 sp_unblur.py  path/to/unblur  'Movies/*' unblur_out_dir  --pixel_size=1.14  --voltage=300  --exposure_per_frame=1.3  --gain_file=/path/to/gain.mrc
  
-  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.+Run unblur without dose adjustment
  
-  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+mpirun -np 12 sp_unblur.py  path/to/unblur  'Movies/*' unblur_out_dir  --pixel_size=1.14  --skip_dose_adjustment
  
-Run Unblur with dose-filtering, and then run Summovie without dose-filtering with all options.+Run unblur without dose adjustment and in addition with dose adjustment
  
-  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+mpirun -np 12 sp_unblur.py  path/to/unblur  'Movies/*' unblur_out_dir  --pixel_size=1.14  --voltage=300  --exposure_per_frame=1.3  --additional_dose_unadjusted
  
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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 (*).. 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)+  ; 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 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)   ; 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) +  ; %%--%%selection_file : 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) 
-  ; %%--%%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) + 
-  ; %%--%%nr_frames : Number of movie frames: The number of movie frames in each input micrograph. (default 3) +  ; %%--%%pixel_size : Pixel size [A]: The pixel size of input micrographs. (default 1.0) 
-  ; %%--%%pixel_size : Pixel size [A]: The pixel size of input micrographs. (default required float) +  ; %%--%%bin_factor : Bin factor : Output bin factor. (default 1.0) 
-  ; %%--%%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) + 
-  ; %%--%%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) +  ; %%--%%voltage : Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. (default 300.0) : %%--%%skip_dose_adjustment==True 
-  ; %%--%%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) +  ; %%--%%exposure_per_frame : Per frame exposure [e/A^2]: The electron dose per frame in e/A^2. (default 1.0) : %%--%%skip_dose_adjustment==True 
-  ; %%--%%nr_threads : Number of threads: The number of threads Unblur can use. The higher the faster, but it requires larger memory. (default 1)+  ; %%--%%pre_exposure : Pre-exposure [e/A^2]: The electron does in e/A^2 used for exposure prior to imaging. (default 0.0) : %%--%%skip_dose_adjustment==True 
 +  ; %%--%%additional_dose_unadjusted : Create unadjusted sums in addition: Run unblur twice to also create dose unadjusted sums. (default False) : %%--%%skip_dose_adjustment==True 
 +  ; %%--%%gain_file : Gain file : Gain file in case of gain uncorrected movies. (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) +  ; %%--%%skip_dose_adjustment : Apply dose filter: Indicate if dose filter should be applied or not. 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) +  ; %%--%%min_shift_initial : Minimum shift for initial search [A]: 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) +  ; %%--%%outer_radius : Outer radius shift limit [A]: Outer radius shift limit (default 20.0)
-  ; %%--%%shift_radius : Outer radius shift limit [A]: Effective only when %%--%%expert_mode option is used. (default 200.0)+
   ; %%--%%b_factor : Apply B-factor to images [A^2]: Effective only when %%--%%expert_mode option is used. (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 : 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) +  ; %%--%%half_width_vert : Vertical Fourier central mask size: The half-width of central vertical 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) +  ; %%--%%half_width_hor : Horizontal Fourier central mask size: The half-width of central horizontal line of Fourier mask. (default 1) 
-  ; %%--%%shift_threshold : Termination shift threshold: Effective only when %%--%%expert_mode option is used. (default 0.1) +  ; %%--%%termination : Termination shift threshold: Termination shift threshold. (default 1) 
-  ; %%--%%iterations : Maximum iterations: Effective only when %%--%%expert_mode option is used. (default 10) +  ; %%--%%max_iterations : Maximum iterations: Maximum iterations. (default 20) 
-  ; %%--%%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) +  ; %%--%%dont_restore_noise_power : Restore noise power: Indicate if noise power should be restored after dose adjustment or not. By default, restore noise power. (default False question reversed in GUI) 
-  ; %%--%%verbose : Verbose: Effective only when %%--%%expert_mode option is used. (default False)+  ; %%--%%first_frame : First frame: First frame to use for sum. (default 1) 
 +  ; %%--%%last_frame : Last frame: Last frame to use for sum. (default 0) 
 +  ; %%--%%distortion_angle : Distortion Angle [deg]: Distortion Angle in degrees. (default 0.0) 
 +  ; %%--%%major_scale : Major scale : Major scale. (default 1.0) 
 +  ; %%--%%minor_scale : Minor scale: Minor scale. (default 1.0)
  
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 ==== Files ==== ==== Files ====
-sparx/bin/sxunblur.py+sparx/bin/sp_unblur.py
  
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 ==== See also ==== ==== See also ====
-[[pipeline:movie:sxgui_unblur|sxgui_unblur]]+[[pipeline:movie:sp_gui_unblur|sp_gui_unblur]]
  
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pipeline/movie/sxunblur.txt · Last modified: 2019/04/02 10:55 by lusnig

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