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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 | + | Micrograph |
\\ | \\ | ||
- | ====== Usage ====== | + | ===== Usage ===== |
Usage in command line | Usage in command line | ||
- | sxunblur.py | + | sxunblur.py |
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- | ====== Typical usage ====== | + | ===== Typical usage ===== |
- | Just shift data with dose filter. | + | |
- | | + | sxunblur |
- | Shift data with aligned sum files, and aligned frames | + | Run Unblur |
- | sxunblur.py | + | sxunblur.py |
- | Dose filter | + | Run Unblur with dose-filtering, |
- | sxunblur.py | + | sxunblur.py |
+ | |||
+ | Run Unblur without dose-filtering. | ||
+ | |||
+ | sxunblur.py ~/ | ||
+ | |||
+ | Run Unblur without dose-filtering, | ||
+ | |||
+ | sxunblur.py ~/ | ||
+ | |||
+ | Run Unblur with dose-filtering, | ||
+ | |||
+ | sxunblur.py ~/ | ||
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- | ====== Input ====== | + | ===== Input ===== |
=== Main Parameters === | === Main Parameters === | ||
- | ; input_micrograph_list_file | + | ; unblur_path |
- | ; unblur : Path to unblur executable: | + | ; input_micrograph_pattern |
- | ; input_mrc_micrograph | + | ; output_directory |
- | ; output | + | |
- | ; nr_threads | + | ; %%--%%summovie_path |
- | ; 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 ' |
- | ; pixel_size : Pixel size [A]: (default | + | ; %%--%%nr_frames : Number of movie frames: |
- | ; exposure_per_frame : Per frame exposure [e/ | + | ; %%--%%pixel_size : Pixel size [A]: The pixel size of input micrographs. |
- | ; voltage : Microscope voltage [kV]: (default | + | ; %%--%%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/ |
+ | ; %%--%%pre_exposure : Pre-exposure [e/ | ||
+ | ; %%--%%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_frames : Save aligned |
- | ; skip_dose_filter : Skip the dose filter | + | ; %%--%%skip_dose_filter : Apply dose filter: |
- | ; expert_mode : Set expert mode: Requires | + | ; %%--%%expert_mode : Use expert mode: Requires |
- | ; shift_initial : *EXPERT* | + | ; %%--%%shift_initial : Minimum shift for initial search [A]: Effective only when %%--%%expert_mode option is used. (default 2.0) |
- | ; shift_radius : *EXPERT* | + | ; %%--%%shift_radius : Outer radius shift limit [A]: Effective only when %%--%%expert_mode option is used. (default 200.0) |
- | ; b_factor : *EXPERT* | + | ; %%--%%b_factor : Apply B-factor to images [A^2]: |
- | ; fourier_vertical : *EXPERT* Half-width of central vertical line of fourier | + | ; %%--%%fourier_vertical : Vertical Fourier central mask size: The half-width of central vertical line of Fourier |
- | ; fourier_horizontal : *EXPERT* Half-width of central horizontal line of fourier | + | ; %%--%%fourier_horizontal : Horizontal Fourier central mask size: The half-width of central horizontal line of Fourier |
- | ; shift_threshold : *EXPERT* | + | ; %%--%%shift_threshold : Termination shift threshold: |
- | ; iterations : *EXPERT* | + | ; %%--%%iterations : Maximum iterations: |
- | ; 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, |
- | ; verbose : *EXPERT* | + | ; %%--%%verbose : Verbose: |
\\ | \\ | ||
- | ====== Output | + | ===== Output ===== |
- | The program creates the directory automatically | + | The program |
- | Without dosefilter: | + | __Run without dose-filtering__: |
- | Sum files will be written to the " | + | |
- | Log files will be written to the " | + | |
- | Aligned frames will be written to the " | + | |
- | Shift files will be written to the " | + | |
- | FRC files will be written to the " | + | |
- | With dosefilter: As without | + | __Run with dose-filtering (as without |
- | Dose filtered sum files will be written to the " | + | |
- | Log files will be written to the " | + | |
- | Dose filtered aligned frames will be written to the " | + | |
- | Shift files will be written to the " | + | |
- | FRC files will be written to the " | + | |
\\ | \\ | ||
- | ======= | + | ===== Description |
- | --- | + | |
+ | \\ | ||
+ | ==== Method | ||
+ | |||
+ | \\ | ||
+ | ==== Reference ==== | ||
+ | [[http:// | ||
+ | |||
+ | \\ | ||
+ | ==== Developer Notes ==== | ||
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==== Files ==== | ==== Files ==== | ||
- | sxunblur.py | + | sparx/bin/sxunblur.py |
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- | ==== See Also ==== | + | ==== See also ==== |
- | sxgui_unblur.py | + | [[pipeline: |
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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. |
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+ | ==== Bugs ==== | ||
+ | There are no known bugs so far. | ||
+ | |||
+ | \\ | ||
+ |