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pipeline:movie:sxsummovie [2018/08/22 11:48] fmerino |
pipeline:movie:sxsummovie [2019/04/02 10:57] (current) lusnig [See also] |
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~~NOTOC~~ | ~~NOTOC~~ | ||
- | ===== sxsummovie | + | ===== sp_summovie |
Micrograph Movie Summation: Sum micrograph movies with [[http:// | Micrograph Movie Summation: Sum micrograph movies with [[http:// | ||
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Usage in command line | Usage in command line | ||
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===== Typical usage ===== | ===== Typical usage ===== | ||
- | sxsummovie | + | sp_summovie |
__Run Summovie without dose filtering__: | __Run Summovie without dose filtering__: | ||
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__Run Summovie without dose filtering and with less frames__: | __Run Summovie without dose filtering and with less frames__: | ||
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__Run Summovie with dose filtering and with less frames__: | __Run Summovie with dose filtering and with less frames__: | ||
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=== Main Parameters === | === Main Parameters === | ||
; summovie_path : Summovie executable path: Specify the file path of Summovie executable. (This argument is specific to SPHIRE, and not directly used by Summovie executable.) (default required string) | ; summovie_path : Summovie executable path: Specify the file path of Summovie executable. (This argument is specific to SPHIRE, and not directly used by Summovie 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: | + | ; 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_shift_pattern : Input drift shift path pattern: Specify path pattern of input drift shift parameters files with a wild card (*).. The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: | + | ; input_shift_pattern : Input drift shift path pattern: Specify path pattern of input drift shift parameters files 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 Summovie executable.) (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 Summovie executable.) (default required string) | ||
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=== Advanced Parameters === | === Advanced Parameters === | ||
; %%--%%apply_dose_filter : Apply dose filter: Requires %%--%%voltage, | ; %%--%%apply_dose_filter : Apply dose filter: Requires %%--%%voltage, | ||
- | ; %%--%%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) : %%--%%apply_dose_filter==True |
- | ; %%--%%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) : %%--%%apply_dose_filter==True |
; %%--%%dont_restore_noise : Restore noise power: Indicate if noise power should be restored or not. By default, restore noise power. (default False question reversed in GUI) | ; %%--%%dont_restore_noise : Restore noise power: Indicate if noise power should be restored or not. By default, restore noise power. (default False question reversed in GUI) | ||
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==== Files ==== | ==== Files ==== | ||
- | sparx/bin/sxsummovie.py | + | sparx/bin/sp_summovie.py |
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==== See also ==== | ==== See also ==== | ||
- | [[pipeline: | + | [[pipeline: |
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