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Revision 3 as of 2016-05-04 11:18:55
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Editor: penczek
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Revision 4 as of 2016-05-04 11:20:05
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Editor: penczek
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Deletions are marked like this. Additions are marked like this.
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sxgui_cter - CTF Assessment: GUI tool to assess micrographs based on CTF estimation produced by CTER.
sxunblur - Micrograph Alignment: Performs 2D Micrograph alignment with Unblur.
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sxgui_cter.py cter_ctf_file
sxunblur.py unblur input_mrc_micrograph output --nr_frames=nr_frames --pixel_size=pixel_size --dose_filter --exposure_per_frame=exposure_per_frame --voltage=voltage --pre_exposure=pre_exposure --save_frames --expert_mode --shift_initial=shift_initial --shift_radius=shift_radius --b_factor=b_factor --fourier_vertical=fourier_vertical --fourier_horizontal=fourier_horizontal --shift_threshold=shift_threshold --iterations=iterations --restore_noise --verbose --filter_sum --lowpass=lowpass --highpass=highpass --remove_sum
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sxgui_cter GUI tool can be run as a stand-alone program or run from sxgui.py. sxunblur exists in non-MPI version.
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''' sxgui_cter.py outdir_cter/partres.txt'''     Just shift data.
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    sxunblur.py directory_to_unblur directory/prefix*suffix.mrc output_directory--nr_frames=25 --pixel_size=1.19 --remove_sum

    Shift data with aligned sum files, filtered sum files and aligned frames.

    sxunblur.py directory_to_unblur directory/prefix*suffix.mrc output_directory --nr_frames=25 --pixel_size=1.19 --save_frames --filter_sum --lowpass=0.033 --highpass=0.00033

    Dose filter and Expert Options

    sxunblur.py directory_to_unblur directory/prefix*suffix.mrc output_directory --nr_frames=25 --pixel_size=1.19 --dose_filter --exposure_per_frame=1.0 --voltage=300.0 --pre_exposure=0.0 --save_frames --expert_mode --shift_initial=2.0 --shift_radius=200.0 --b_factor=1500.0 --fourier_vertical=1 --fourier_horizontal=1 --shift_threshold=0.1 --iterations=10 --restore_noise --verbose --filter_sum --lowpass=0.033 --highpass=0.00033
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    cter_ctf_file:: CTF parameters file in cter format: (default none)
    unblur:: path to unblur executable: (default required string)
    input_mrc_micrograph:: name pattern of input micrographs (mrc): use the wild card (*) to specify the place of micrograph id (e.g. serial number, time stamp, or etc). (default required string)
    output:: output directory: (default required string)

    nr_frames:: number of frames in the set of micrographs: (default 3)
    pixel_size:: pixel size [A]: (default required -1.0)
    save_frames:: save aligned frames: (default False)
    filter_sum:: filter the output images: (default False)
    lowpass:: apply a lowpass filter: abolute frequency. (default 0.033)
    highpass:: apply a highpass filter: abolute frequency. (default 0.00033)
    remove_sum:: remove the calculated sum files: (default False)

    * The remaining parameters are optional.
    dose_filter:: apply dose filter options: exposure_per_frame, voltage, pre_exposure. (default False)
    exposure_per_frame:: exposure per frame [e/A^2]: (default 1.0)
    voltage:: accelerate voltage [kV]: (default 300.0)
    pre_exposure:: pre exposure amount [e/A^2]: (default 0.0)
    expert_mode:: set expert mode settings: shift_initial, shift_radius, b_factor, fourier_vertical, fourier_horizontal, shift_threshold, iterations, restore_noise, verbose. (default False)
    shift_initial:: minimum shift for inital search [A]: (default 2.0)
    shift_radius:: outer radius shift limit [A]: (default 200.0)
    b_factor:: b-factor to appy to image [A^2]: (default 1500.0)
    fourier_vertical:: half-width of central vertical line of fourier mask: (default 1)
    fourier_horizontal:: half-width of central horizontal line of fourier mask: (default 1)
    shift_threshold:: termination shift threshold: (default 0.1)
    iterations:: maximum number of iterations: (default 10)
    restore_noise:: restore noise power: (default False)
    verbose:: verbose output: (default False)
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The program creates the directory automatically in the current directory. (default required string)

Sum files will be written to the "Micrographs" Folder.
Filtered sum files will be written to the "Filtered" Folder.
Aligned frames will be written to the "Micrographs" Folder.
Shift files will be written to the "Shift" folder.
FRC files will be written to the "FRC" folder.
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== Description == = Description =
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''''This is in progress 03/04/2016'''' = Author / Maintainer =
Markus Stabrin
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= Method =

= Reference =

== Author / Maintainer ==
Toshio Moriya

=== Attachments ===

== Keywords ==
= Keywords =
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== Files ==
sparx/bin/sxgui_cter.py
= Files =
sxunblur.py
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=== See also ===
[[http://sparx-em.org/sparxwiki/sxcter|sxcter]], [[http://sparx-em.org/sparxwiki/sxwindow|sxwindow]]
= See also =
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=== Maturity ===
 alpha:: in development
= Maturity =
No Bugs known so far.

Name

sxunblur - Micrograph Alignment: Performs 2D Micrograph alignment with Unblur.

Usage

usage in command line

sxunblur.py unblur input_mrc_micrograph output --nr_frames=nr_frames --pixel_size=pixel_size --dose_filter --exposure_per_frame=exposure_per_frame --voltage=voltage --pre_exposure=pre_exposure --save_frames --expert_mode --shift_initial=shift_initial --shift_radius=shift_radius --b_factor=b_factor --fourier_vertical=fourier_vertical --fourier_horizontal=fourier_horizontal --shift_threshold=shift_threshold --iterations=iterations --restore_noise --verbose --filter_sum --lowpass=lowpass --highpass=highpass --remove_sum

Typical usage

sxunblur exists in non-MPI version.

  • Just shift data. sxunblur.py directory_to_unblur directory/prefix*suffix.mrc output_directory--nr_frames=25 --pixel_size=1.19 --remove_sum Shift data with aligned sum files, filtered sum files and aligned frames. sxunblur.py directory_to_unblur directory/prefix*suffix.mrc output_directory --nr_frames=25 --pixel_size=1.19 --save_frames --filter_sum --lowpass=0.033 --highpass=0.00033 Dose filter and Expert Options sxunblur.py directory_to_unblur directory/prefix*suffix.mrc output_directory --nr_frames=25 --pixel_size=1.19 --dose_filter --exposure_per_frame=1.0 --voltage=300.0 --pre_exposure=0.0 --save_frames --expert_mode --shift_initial=2.0 --shift_radius=200.0 --b_factor=1500.0 --fourier_vertical=1 --fourier_horizontal=1 --shift_threshold=0.1 --iterations=10 --restore_noise --verbose --filter_sum --lowpass=0.033 --highpass=0.00033

Input

unblur
path to unblur executable: (default required string)
input_mrc_micrograph
name pattern of input micrographs (mrc): use the wild card (*) to specify the place of micrograph id (e.g. serial number, time stamp, or etc). (default required string)
output
output directory: (default required string)
nr_frames
number of frames in the set of micrographs: (default 3)
pixel_size
pixel size [A]: (default required -1.0)
save_frames
save aligned frames: (default False)
filter_sum
filter the output images: (default False)
lowpass
apply a lowpass filter: abolute frequency. (default 0.033)
highpass
apply a highpass filter: abolute frequency. (default 0.00033)
remove_sum
remove the calculated sum files: (default False)
  • The remaining parameters are optional.
  • dose_filter
    apply dose filter options: exposure_per_frame, voltage, pre_exposure. (default False)
    exposure_per_frame
    exposure per frame [e/A^2]: (default 1.0)
    voltage
    accelerate voltage [kV]: (default 300.0)
    pre_exposure
    pre exposure amount [e/A^2]: (default 0.0)
    expert_mode
    set expert mode settings: shift_initial, shift_radius, b_factor, fourier_vertical, fourier_horizontal, shift_threshold, iterations, restore_noise, verbose. (default False)
    shift_initial
    minimum shift for inital search [A]: (default 2.0)
    shift_radius
    outer radius shift limit [A]: (default 200.0)
    b_factor
    b-factor to appy to image [A^2]: (default 1500.0)
    fourier_vertical
    half-width of central vertical line of fourier mask: (default 1)
    fourier_horizontal
    half-width of central horizontal line of fourier mask: (default 1)
    shift_threshold
    termination shift threshold: (default 0.1)
    iterations
    maximum number of iterations: (default 10)
    restore_noise
    restore noise power: (default False)
    verbose
    verbose output: (default False)

    Output

    The program creates the directory automatically in the current directory. (default required string)

    Sum files will be written to the "Micrographs" Folder. Filtered sum files will be written to the "Filtered" Folder. Aligned frames will be written to the "Micrographs" Folder. Shift files will be written to the "Shift" folder. FRC files will be written to the "FRC" folder.

    Description

    Author / Maintainer

    Markus Stabrin

    Keywords

    category 1
    APPLICATIONS

    Files

    sxunblur.py

    See also

    Maturity

    No Bugs known so far.

    sxunblur (last edited 2016-05-04 11:20:05 by penczek)