# ctfDetermine

## Usage

    Usage: ctfDetermine
    Options:
        [-i[nput]            In                  (NULL      )] :Essential :InputDataFile:  mrcImage
        [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile: Parameters
        [-D[efocus]          Defocus             (0.0       )] :Optional  :InitialDefocus[A]
        [-Cs                 Cs                  (1.7       )] :Optional  :InitialCs[mm]
        [-Cc                 Cc                  (1.2       )] :Optional  :InitialCs[mm]
        [-dE                 dE                  (0.2       )] :Optional  :InitialCs[mm]
        [-Ac[cerratedVoltage]Ac                  (200       )] :Optional  :Ac[kV]
        [-CutLow             CutLow              (0.05      )] :Optional  :CutOffLowFrequncy[/A]
        [-CutHigh            CutHigh             (0.5       )] :Optional  :CutOffHighFrequncy[/A]
        [-I0                 I0                  (1.0       )] :Optional  :I0
        [-ratio              ratioOfAmpToPhase   (0.1       )] :Optional  :ratioOfAmpToPhase
        [-Ai                 Ai                  (0.03      )] :Optional  :IlluminationAngle[mrad]
        [-BofMTF             BofMTF              (15.0      )] :Optional  :B of MTF [A]
        [-BofV[ibration]     BofVibration        (3.0       )] :Optional  :B of Vibration [A]
        [-Mag[nification]    Magnification       (1.0       )] :Optional  :Magnification
        [-[White]Noise       WhiteNoise          (0.0       )] :Optional  :Signal/Noise Ratio
        [-[White]Noise2      WhiteNoise2         (0.0       )] :Optional  :Signal/Noise Ratio
        [-MolcEnv            MolcEnv             (0.0       )] :Optional  :Gaussian: Molcular Envelop [A]
        [-MolcEnv2           MolcEnvTable        (NULL      )] :Optional  :Table: Molcular Envelop
        [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
        [-m[ode]             mode                (0         )] :Optional  :Mode
        [-min                min                 (-10       )] :Optional  :min of coefficient area
        [-max                max                 (10        )] :Optional  :max of coefficient area
        [-s[tep]             step                (0.01      )] :Optional  :step of coefficient
        [-d[egree]           degree              (6         )] :Optional  :agree of function
        [-S[ection]          section             (4         )] :Optional  :section number of fft
    >>> Mode <<<
    	  0 : MinMax Methods (Henderson-like CTF determination)
    	  16: Fitting Methods
    	  32: Differential Methods
    	  64: Covariance Methods
    	  96: Differential & covariance  Methods
    	 128: MinSquare Methods
    	 160: Differential+MinSquare Methods by Imamura
    	 161: Differential+MinSquare Methods+NoiseRemoval(+1)
    	 163: Differential+MinSquare Methods+NoiseRemoval(+1)+EnvelopeFromLocalMaxima(+2)