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pipeline:movie:sxsummovie [2018/02/27 17:09] moriya |
pipeline:movie:sxsummovie [2019/04/02 10:15] lusnig |
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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 (*). 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: |
- | ; input_shift_pattern : Input drift shift path pattern: Specify path pattern of input drift shift parameters 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: | + | ; 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. 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) | + | ; output_directory : Output directory: The results will be written here. It cannot |
; %%--%%selection_list : Movie selection file: Specify a name of micrograph movie selection list text file. The file extension must be ' | ; %%--%%selection_list : Movie selection file: Specify a name of micrograph movie selection list text file. The file extension must be ' | ||
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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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