pipeline:utilities:sxsummovie

This version (2018/02/27 16:58) is a draft.
Approvals: 0/1

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Micrograph Movie Summation: Sum micrograph movies with Summovie.


Usage in command line

sxsummovie.py  summovie_path  input_micrograph_pattern  input_shift_pattern  output_directory  --selection_list=SELECTION_LIST  --nr_frames=NUM_OF_FRAMES  --first=FIRST_FRAME  --last=LAST_FRAME  --pixel_size=PIXEL_SIZE  --nr_threads=NUM_OF_THREADS  --apply_dose_filter  --voltage=VOLTAGE  --exposure_per_frame=EXPOSURE  --pre_exposure=EXPOSURE  --dont_restore_noise


sxsummovie exists only in non-MPI version.

Run Summovie without dose filtering:

sxsummovie.py ~/my_app/summovie 'outdir_unblur/corrsum/micrograph_*_frames_sum.mrc' 'outdir_unblur/shift/micrograph_*_frames_shift.txt' outdir_summovie --nr_frames=24 --pixel_size=1.19 --nr_threads=1


Run Summovie without dose filtering and with less frames:

sxsummovie.py ~/my_app/summovie 'outdir_unblur/corrsum/micrograph_*_frames_sum.mrc' 'outdir_unblur/shift/micrograph_*_frames_shift.txt' outdir_summovie --nr_frames=24 --first=3 --last=15 --pixel_size=1.19 --nr_threads=1


Run Summovie with dose filtering and with less frames:

sxsummovie.py ~/my_app/summovie 'outdir_unblur/corrsum/micrograph_*_frames_sum.mrc' 'outdir_unblur/shift/micrograph_*_frames_shift.txt' outdir_summovie --nr_frames=24 --first=3 --last=15 --pixel_size=1.19 --nr_threads=1 --apply_dose_filter --voltage=300 --exposure_per_frame=2 --pre_exposure=0


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)
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: sxgui.py automatically adds single quotes (')). bdb files can not be selected as input micrograph movies. (This argument is specific to SPHIRE, and not directly used by Summovie executable.) (default required string)
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: 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 executable.) (default required string)
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)
--selection_list
Movie selection file: Specify a name of micrograph movie selection list text file. The file extension must be '.txt'. If this is not provided, all files matched with the micrograph movie name pattern will be processed. (This option is specific to SPHIRE, and not directly used by Summovie executable.) (default none)
--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)
--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)
--nr_threads
Number of threads: The number of threads Summovie can use. The higher the faster, but it requires larger memory. (default 1)


Advanced Parameters

--apply_dose_filter
Apply dose filter: Requires --voltage, --exposure_per_frame, and --pre_exposure options. (default False)
--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)
--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
Restore noise power: Indicate if noise power should be restored or not. By default, restore noise power. (default False question reversed in GUI)


The program automatically creates the following subdirectories in the specified output directory.


Without dose-filtering:

  • Sum files will be written to the corrsum directory.
  • Log files will be written to the logfiles directory.
  • FRC files will be written to the frc directory.


With dose-filtering:

  • Dose filtered sum files will be written to the corrsum_dose_filtered directory.
  • Log files will be written to the logfiles directory
  • FRC files will be written to the frc directory.





Markus Stabrin


Category 1:: APPLICATIONS


sparx/bin/sxsummovie.py


Alpha:: Under development. Please let us know if there are any bugs.


There are no known bugs so far.


  • pipeline/utilities/sxsummovie.1519747104.txt.gz
  • Last modified: 2018/06/20 13:12
  • (external edit)