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pipeline:movie:sxunblur [2018/02/16 10:11]
127.0.0.1 external edit 		pipeline:movie:sxunblur [2019/04/02 10:13]
lusnig
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 ~~NOTOC~~ ~~NOTOC~~
  
-====== sxunblur ====== +===== sp_unblur ===== 
-Micrograph movie alignment: align micrograph movies with Unblur. [[http://grigoriefflab.janelia.org/unblur]]+Unblur cisTEM: Align frames of micrograph movies with [[https://cistem.org/|Unblur]].
  
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-====== 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+  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 =====
-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+sp_unblur exists in both MPI and non-MPI versions (Running MPI version does not require --MPI flag). 
  
-Shift data with aligned sum files, and aligned frames without dose filter.+Run unblur with dose adjustment
  
-  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+mpirun -np 12 sp_unblur.py  path/to/unblur  'Movies/*' unblur_out_dir  --pixel_size=1.14  --voltage=300  --exposure_per_frame=1.3
  
-Dose filter and Expert Options and aligned frames 
  
-  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+Run unblur with dose adjustment and gain reference file 
 + 
 +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 
 + 
 + 
 +Run unblur without dose adjustment 
 + 
 +mpirun -np 12 sp_unblur.py  path/to/unblur  'Movies/*' unblur_out_dir  --pixel_size=1.14  --skip_dose_adjustment 
 + 
 +Run unblur without dose adjustment and in addition with dose adjustment 
 + 
 +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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-====== 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 (*).. 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) 
-  ; 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. 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 : 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) +  ; %%--%%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) 
-  ; nr_frames :  Number of frames: (default 3) + 
-  ; pixel_size : Pixel size [A]: (default  required -1.0) +  ; %%--%%pixel_size : Pixel size [A]: The pixel size of input micrographs. (default 1.0) 
-  ; exposure_per_frame : Per frame exposure [e/A^2]: (default 1.0) +  ; %%--%%bin_factor : Bin factor : Output bin factor. (default 1.0) 
-  ; voltage : Microscope voltage [kV]: (default 300.0) + 
-  ; pre_exposure : Pre exposure [e/A^2]: (default 0.0)+  ; %%--%%voltage : Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. (default 300.0) : %%--%%skip_dose_adjustment==True 
 +  ; %%--%%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 
 +  ; %%--%%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 frames: save aligned frames. This is only neccessary if one wants to perform movie refinement and will slow 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 : Skip the dose filter step: If yes, exposure per frame, voltage, and pre exposure will be ignored. (default False) + 
-  ; 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) +  ; %%--%%min_shift_initial : Minimum shift for initial search [A]: Minimum shift for initial search [A] (default 2.0) 
-  ; shift_initial : *EXPERT* Minimum shift for initial search [A]: (default 2.0) +  ; %%--%%outer_radius : Outer radius shift limit [A]: Outer radius shift limit (default 20.0) 
-  ; shift_radius : *EXPERT* Outer radius shift limit [A]: (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 : *EXPERT* Apply B-factor to images [A^2]: (default 1500.0) +  ; %%--%%half_width_vert : Vertical Fourier central mask size: The half-width of central vertical line of Fourier mask. (default 1) 
-  ; fourier_vertical : *EXPERT* Half-width of central vertical line of fourier mask: (default 1) +  ; %%--%%half_width_hor : Horizontal Fourier central mask size: The half-width of central horizontal line of Fourier mask. (default 1) 
-  ; fourier_horizontal : *EXPERT* Half-width of central horizontal line of fourier mask: (default 1) +  ; %%--%%termination : Termination shift threshold: Termination shift threshold. (default 1) 
-  ; shift_threshold : *EXPERT* Termination shift threshold: (default 0.1) +  ; %%--%%max_iterations : Maximum iterations: Maximum iterations. (default 20) 
-  ; iterations : *EXPERT* Maximum iterations: (default 10) +  ; %%--%%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) 
-  ; dont_restore_noise : *EXPERT* Do not restore noise power: (default False) +  ; %%--%%first_frame : First frame: First frame to use for sum. (default 1) 
-  ; verbose : *EXPERT* Verbose: (default False)+  ; %%--%%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)
  
 \\ \\
-====== 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.
  
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-======= Description ======= +===== Description ===== 
----+ 
 +\\ 
 +==== Method ==== 
 + 
 +\\ 
 +==== Reference ==== 
 +[[http://grigoriefflab.janelia.org/unblur|Unblur & Summovie]] 
 + 
 +\\ 
 +==== Developer Notes ====
  
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 ==== Files ==== ==== Files ====
-sxunblur.py+sparx/bin/sp_unblur.py
  
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-==== See Also ==== +==== See also ==== 
-sxgui_unblur.py+[[pipeline:movie:sp_gui_unblur|sp_gui_unblur]]
  
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 ==== 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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