= Name =
sx3dvariability - 3D Variability Estimation: Calculate 3D variability using a set of aligned projection images as an input.

= Usage =


''usage in command line''

sx3dvariability.py  prj_stack  output_directory  --img_per_grp=img_per_grp  --sym=symmetry  --CTF  --fl=fl  --aa=aa  --force_symmetrize  --no_norm  --radius=radius  --npad=npad  --no_ave2D_save  --no_var2D_save  --VAR  --SND  --VERBOSE



=== Typical usage ===

sx3dvariability exists only in MPI version.


''' mpirun  -np  472  sx3dvariability.py  bdb:data  outdir_3dvariability  --img_per_grp=100  --sym=c2  --CTF  --fl=0.25  --aaf=0.1 ''' 


== Input ==
    prj_stack:: Input image stack: The images must containt the 3D orientation parameters in the header and optionally CTF information. (default required string)

    img_per_grp:: Number of projections: Images from the angular neighbourhood that will be used to estimate 2D variance for each projection data. The larger the number the less noisy the estimate, but the lower the resolution. Usage of large number also results in rotational artifacts in variances that will be visible in 3D variability volume. (default 10)
    sym:: Point-group symmetry: Only required if the structure has symmetry higher than c1. Notice this step can be run with only one CPU and there is no MPI version for it. (default c1)
    CTF:: Use CTF: If set to true, the a CTF correction will be applied using the parameters found in the image headers. (default False) 
    fl:: Low-pass filter frequency [1/Pixel]: Filter to be applied to the images prior to variability calculation. By default, no filtering. (default 0.0)
    aa:: Low-pass filter fall-off: Filter to be applied to the images prior to variability calculation. By default, no filtering. (default 0.0) 

    * The remaining parameters are optional.
    force_symmetrize:: Force symmetrising input stack: This preparation step is unnecessary if the structure is asymmetrical (i.e. c1), since it is required only when the structure has internal symmetry. (default False)
    no_norm:: Skip normalization: (default False)
    radius:: Radius for 3D variability [Pixels]: Normally, use the particle radius. (default -1)
    npad:: Image padding factor: The images are padded to achieve the original size times this option. (default 2)
    no_ave2D_save:: Do not save 2D averages: (default False)
    no_var2D_save:: Do not save 2D variances: (default False)
    VAR:: Stack on input consists of 2D variances: (default False)
    SND:: Squared normalized differences: If set to true, it computes the squared normalised differences. (default False)
    VERBOSE:: Verbose: Useful for debugging. (default False) 


== Output ==
    output_directory:: Output directory: The results will be written here. This directory will be created automatically and it must not exist previously. (default required string)


= Description =
The program calculates the variability observed in a collection of image projections. Structures with symmetry require preparing data before calculating the variability. The data preparation step would symmetrise the data and output a bdb:sdata for variability calculation. sx3dvariability.py can be slow.

= Method =

= Reference =

= Author / Maintainer =
Pawel Penczek

= Keywords =
 category 1:: APPLICATIONS

= Files =
sx3dvariability.py

= See also =

= Maturity =
 alpha::     it works.

= Bugs =
Did not discover any yet.
