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pipeline:movie:sxunblur [2018/06/20 13:12] 127.0.0.1 external edit |
pipeline:movie:sxunblur [2019/04/02 10:55] lusnig [See also] |
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~~NOTOC~~ | ~~NOTOC~~ | ||
- | ===== sxunblur | + | ===== sp_unblur |
- | Micrograph Movie Alignment: Align frames of micrograph movies with [[http://grigoriefflab.janelia.org/unblur|Unblur | + | Unblur cisTEM: Align frames of micrograph movies with [[https://cistem.org/ |
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Usage in command line | Usage in command line | ||
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===== Typical usage ===== | ===== Typical usage ===== | ||
- | sxunblur | + | sp_unblur |
- | Run Unblur | + | Run unblur |
- | sxunblur.py ~/my_app/unblur 'movies/micrograph_*_frames.mrc' | + | mpirun -np 12 sp_unblur.py path/to/ |
- | Run Unblur with dose-filtering, | ||
- | sxunblur.py ~/my_app/unblur | + | Run unblur |
- | Run Unblur without dose-filtering. | + | mpirun |
- | sxunblur.py ~/ | ||
- | Run Unblur | + | Run unblur |
- | sxunblur.py ~/my_app/unblur 'movies/micrograph_*_frames.mrc' | + | mpirun -np 12 sp_unblur.py path/to/ |
- | Run Unblur with dose-filtering, | + | Run unblur without |
- | sxunblur.py ~/my_app/unblur 'movies/micrograph_*_frames.mrc' | + | mpirun -np 12 sp_unblur.py path/to/ |
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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 (*). 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: | + | ; 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: |
- | ; 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_directory : Output directory: The results will be written here. It cannot |
+ | |||
+ | ; %%--%%selection_file : Movie selection file: Specify a name of micrograph movie selection list text file. The file extension must be ' | ||
+ | |||
+ | ; %%--%%pixel_size : Pixel size [A]: The pixel size of input micrographs. (default 1.0) | ||
+ | ; %%--%%bin_factor : Bin factor : Output bin factor. (default 1.0) | ||
+ | |||
+ | ; %%--%%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) | ||
- | ; %%--%%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_list : Movie selection file: Specify a name of micrograph movie selection list text file. The file extension must be ' | ||
- | ; %%--%%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 required float) | ||
- | ; %%--%%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) | ||
- | ; %%--%%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) | ||
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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 |
- | ; %%--%%skip_dose_filter | + | |
- | ; %%--%%expert_mode : Use expert mode: Requires %%--%%initial_shift, | + | ; %%--%%min_shift_initial |
- | ; %%--%%shift_initial | + | ; %%--%%outer_radius |
- | ; %%--%%shift_radius | + | |
; %%--%%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 | + | ; %%--%%half_width_vert |
- | ; %%--%%fourier_horizontal | + | ; %%--%%half_width_hor |
- | ; %%--%%shift_threshold | + | ; %%--%%termination |
- | ; %%--%%iterations : Maximum iterations: Effective only when %%--%%expert_mode option is used. (default | + | ; %%--%%max_iterations : Maximum |
- | ; %%--%%dont_restore_noise | + | ; %%--%%dont_restore_noise_power |
- | ; %%--%%verbose | + | ; %%--%%first_frame : First frame: First frame to use for sum. (default |
+ | ; %%--%%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 | ||
+ | ; %%--%%minor_scale : Minor scale: Minor scale. (default | ||
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==== Files ==== | ==== Files ==== | ||
- | sparx/bin/sxunblur.py | + | sparx/bin/sp_unblur.py |
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==== See also ==== | ==== See also ==== | ||
- | [[pipeline: | + | [[pipeline: |
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