= Name =
sxlocres - Local Resolution: Compute local resolution of a map.

= Usage =


''Usage in command lines'':

sxlocres.py  firstvolume  secondvolume  maskfile  outputfile  --wn=window_size  --step=shell_step_size  --cutoff=res_cutoff --res_overall=overall_resolution --radius=radius  --fsc=output_file_name  --MPI

=== Typical usage ===

sxlocres exists in for both MPI and non-MPI versions.

''' mpirun -np 32  sxlocres.py refinementdir/main002/vol0.hdf  refinementdir/main002/vol2.hdf locres.hdf --cutoff=0.5 --radius=28 --res_overall=0.3  --fsc=fscvol.txt --MPI '''


== Input ==
    firstvolume:: First half-volume: (default required string)
    secondvolume:: Second half-volume: (default required string)
    maskfile:: 3D mask: Defines the region where the local filtering should be applied. (default none)
    
    wn:: FSC window size: Defines the size of window where the local real-space FSC is computed. (default 7)
    step:: Fourier shell step size [Pixels]: (default 1.0)
    cutoff:: Resolution cut-off [1/Pixel]: Cut-off for the FSC. By default it goes to the Nyquist frequencies. (default 0.5)
    radius:: Mask radius [Pixels]: In case no mask is provided, a hard sphere of this radius will be used. (default -1)
    res_overall:: Overall resolution [1/Pixel]: A value between 0 to 0.5 for calibration of the average local resolution. See Description section in the wiki page for details. (default -1.0)
    
    * The remaining parameters are optional.
    MPI:: Use MPI: (default False)


== Output ==
    outputfile:: Output volume: Each voxel contains the resolution for this area in [[absolute_frequency_units|absolute frequency]] units. (default required string)
    fsc:: FSC output file: Contains the overall FSC curve computed by rotational averaging of local resolution values. It is truncated to res_overall. (default no curve) 


= Description =
   Local resolution values are computed within small windowed areas (size wn^3). Due to small sample size the values are inaccurate and tend to underestimate resolution.
   Therefore, option res_overall allows to calibrate the average value of all local resolutions to the overall resolution, as estimated by the FSC between two full size volumes. I
   This value has to be independently obtained by the user - for example using sximgstat.py to compute (masked) FSC from half-volumes and reading the absolute frequency crresponding
   to 0.5 (or other) cut-off value.

= Method =

= Reference =

= Author / Maintainer =
Pawel Penczek

= Keywords =
    category 1:: APPLICATIONS

= Files =
sxlocres.py

= See also =

= Maturity =


    stable:: works for most people, has been tested; test cases/examples available.

= Bugs =
None.  It is perfect.
