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pipeline:movie:sxsummovie [2018/02/16 10:11] 127.0.0.1 external edit |
pipeline:movie:sxsummovie [2018/06/20 13:12] 127.0.0.1 external edit |
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===== sxsummovie ===== | ===== sxsummovie ===== | ||
- | Micrograph | + | Micrograph |
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Usage in command line | Usage in command line | ||
- | sxsummovie.py | + | sxsummovie.py |
- | + | \\ | |
- | === Typical usage === | + | ===== Typical usage ===== |
sxsummovie exists only in non-MPI version. | sxsummovie exists only in non-MPI version. | ||
- | __Perform summovie | + | __Run Summovie |
sxsummovie.py ~/ | sxsummovie.py ~/ | ||
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- | __Perform summovie | + | __Run Summovie |
sxsummovie.py ~/ | sxsummovie.py ~/ | ||
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- | __Perform summovie | + | __Run Summovie |
sxsummovie.py ~/ | sxsummovie.py ~/ | ||
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===== Input ===== | ===== Input ===== | ||
=== Main Parameters === | === Main Parameters === | ||
- | ; summovie_path : summovie | + | ; summovie_path : Summovie |
- | ; input_micrograph_pattern : Input micrograph | + | ; input_micrograph_pattern : Input movie path pattern: Specify path pattern of input micrograph movies |
- | ; input_shift_pattern : Input shift path pattern: Specify path pattern of input shift files 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: sxgui.py automatically adds single quotes (')). The substring at the variable part must be same between the associated pair of input micrograph and shift file. (This argument is specific to SPHIRE, and not directly used by summovie | + | ; input_shift_pattern : Input drift shift path pattern: Specify path pattern of input drift shift parameters |
+ | ; 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 Summovie | ||
- | ; selection_list : Micrograph selecting list: Specify a name of micrograph selection list text file. The file extension must be ' | + | ; %%--%%selection_list : Movie selection file: Specify a name of micrograph |
- | ; nr_frames : Number of movie frames: The number of movie frames in each input micrograph. (default 3) | + | ; %%--%%nr_frames : Number of movie frames: The number of movie frames in each input micrograph. (default 3) |
- | ; first : First movie frame: First movie frame for summing. (default 1) | + | ; %%--%%first : First movie frame: First movie frame for summing. (default 1) |
- | ; last : Last movie frame: Last movie frame for summing. (default -1) | + | ; %%--%%last : Last movie frame: Last movie frame for summing. (default -1) |
- | ; pixel_size : Pixel size [A]: The pixel size of input micrographs. (default required float) | + | ; %%--%%pixel_size : Pixel size [A]: The pixel size of input micrographs. (default required float) |
- | ; nr_threads : Number of threads: The number of threads | + | ; %%--%%nr_threads : Number of threads: The number of threads |
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=== Advanced Parameters === | === Advanced Parameters === | ||
- | ; apply_dose_filter : Apply dose filter | + | ; %%--%%apply_dose_filter : Apply dose filter: Requires |
- | ; voltage : Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. Effective only when apply_dose_filter option is used. (default 300.0) | + | ; %%--%%voltage : Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. Effective only when %%--%%apply_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. Effective only when apply_dose_filter option is used. (default 2.0) | + | ; %%--%%exposure_per_frame : Per frame exposure [e/A^2]: The electron dose per frame in e/A^2. Effective only when %%--%%apply_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. Effective only when apply_dose_filter option is used. (default 0.0) | + | ; %%--%%pre_exposure : Pre-exposure [e/A^2]: The electron does in e/A^2 used for exposure prior to imaging. Effective only when %%--%%apply_dose_filter option is used. (default 0.0) |
- | ; dont_restore_noise : Do not restore | + | ; %%--%%dont_restore_noise : Restore |
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===== Output ===== | ===== Output ===== | ||
- | ; 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 summovie executable.) (default required string) | ||
- | |||
- | \\ | ||
The program automatically creates the following subdirectories in the specified output directory. | The program automatically creates the following subdirectories in the specified output directory. | ||
\\ __Without dose-filtering__: | \\ __Without dose-filtering__: | ||
- | Sum files will be written to the "corrsum" | + | * Sum files will be written to the '' |
- | Log files will be written to the "logfiles" | + | |
- | FRC files will be written to the "frc" | + | |
\\ __With dose-filtering__: | \\ __With dose-filtering__: | ||
- | Dose filtered sum files will be written to the "corrsum_dose_filtered" | + | * Dose filtered sum files will be written to the '' |
- | Log files will be written to the "logfiles" | + | |
- | FRC files will be written to the "frc" | + | |
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===== Description ===== | ===== Description ===== | ||
+ | |||
+ | \\ | ||
+ | ==== Method ==== | ||
+ | |||
+ | \\ | ||
+ | ==== Reference ==== | ||
+ | [[http:// | ||
+ | |||
+ | \\ | ||
+ | ==== Developer Notes ==== | ||
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==== Files ==== | ==== Files ==== | ||
- | sxsummovie.py | + | sparx/bin/sxsummovie.py |
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==== See also ==== | ==== See also ==== | ||
+ | [[pipeline: | ||
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==== Maturity ==== | ==== Maturity ==== | ||
- | No bugs known so far. | + | Alpha:: Under development. Please let us know if there are any bugs. |
+ | |||
+ | \\ | ||
+ | ==== Bugs ==== | ||
+ | There are no known bugs so far. | ||
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