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pipeline:movie:sxunblur [2018/08/22 11:47] fmerino |
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 (*).. 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. 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 |
- | ; %%--%%selection_list | + | |
- | ; %%--%%nr_frames | + | ; %%--%%pixel_size |
- | ; %%--%%pixel_size | + | ; %%--%%bin_factor |
- | ; %%--%%voltage : Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. | + | |
- | ; %%--%%exposure_per_frame : Per frame exposure [e/A^2]: The electron dose per frame in e/ | + | ; %%--%%voltage : Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. |
- | ; %%--%%pre_exposure : Pre-exposure [e/A^2]: The electron does in e/A^2 used for exposure prior to imaging. | + | ; %%--%%exposure_per_frame : Per frame exposure [e/A^2]: The electron dose per frame in e/ |
- | ; %%--%%nr_threads | + | ; %%--%%pre_exposure : Pre-exposure [e/A^2]: The electron does in e/A^2 used for exposure prior to imaging. |
+ | ; %%--%%additional_dose_unadjusted : Create unadjusted sums in addition: Run unblur twice to also create dose unadjusted sums. (default | ||
+ | ; %%--%%gain_file | ||
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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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