# defocusDeterminationFromThonRing

## Usage

    Usage: defocusDeterminationFromThonRing
    Options:
        [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Optional  :InputDataFile
        [-i[nput] N[ame]     InN                 (stdin     ).as(String              ) ] :Optional  :InputNameInInformationFile
        [-i[nput] R[eference]InR                 (stdin     ).as(String              ) ] :Optional  :InputReferenceForLength
        [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
        [-o[utput] I[nformation]OutI                (stdout    ).as(outFile             ) ] :Optional  :OutputInformationFile
        [-o[utput] I[nformation]OutI2               (stdout    ).as(outFile             ) ] :Optional  :OutputInformationFile
        [-o[utput] I[nformation]OutI3               (stdout    ).as(outFile             ) ] :Optional  :OutputInformationFile
        [-kV                 kV                  (200       ).as(Real                ) ] :Optional  :kV
        [-Cs                 Cs                  (2.1       ).as(Real                ) ] :Optional  :Cs[mm]
        [-A[mplitude contrast]AoverP              (0.05      ).as(Real                ) ] :Optional  :The ratio of amplitude contrast to phase contrast
        [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
        [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
        [-ctfMode            ctfMode             (0         ).as(Integer             ) ] :Optional  :CTFMode
        [-truePitch          truePitch           (430       ).as(Real                ) ] :Optional  :True Pitch
        [-PixelSize          PixelSize           (5         ).as(Real                ) ] :Optional  :Pixel Size [A]
        [-deltadY            deltadY             (0.5       ).as(Real                ) ] :Optional  :A range of deltadY to determine dY.
        [-R[/A]              R                   (NULL      ).as(Real                ) ... ] :Variable  :ThonRing[/A]
    ----- Additional Usage -----
    >>>> o[uput] I[nformation] <<<<
    This file is used for [mrcImageMultiCTFCompensation and mrcImageCTFCompensation]
    >>>> o[uput] I[nformation] 2<<<<
    This file is used for [llDataCTFCompensate -I2]
    >>>> o[uput] I[nformation] 3<<<<
    This file is used for [llExtractWithLayerSeparation]
    Options: -truePitch, -PixelSize, -deltadY and -ctfMode
    >>>> ctfMode <<<<
     0: Phase CTF
     1: PhaseCTF + ratio*AmpCTF
    >>>> mode <<<<
    No action