# mrcImageCTFCompensation

## Usage

    Usage: mrcImageCTFCompensation
    Options:
        [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Essential :InputFile
        [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Essential :OutputDataFile
        [-info[mation]       Info                (NULL      ).as(inFile              ) ] :Optional  :InformationFile(Essense only)
        [-info[mation]2      Info2               (NULL      ).as(inFile              ) ] :Optional  :InformationFile2(Display2 ctfinfo format)
        [-kV                 kV                  (200       ).as(Real                ) ] :Optional  :AccVol[kV]
        [-Cs                 Cs                  (2.1       ).as(Real                ) ] :Optional  :Cs[mm]
        [-df                 Defocus             (27000     ).as(Real                ) ] :Optional  :Defocus[A]:under(+)
        [-white              WhiteNoise          (0.1       ).as(Real                ) ] :Optional  :WhiteNoise(N/S)
        [-SinWin             SinWinRmin          (0.1       ).as(Real                )
                             SinWinRmax          (1.0       ).as(Real                ) ] :Optional  :Windowing by sine function from Rmin[/A] to Rmax[/A].Default: No Window.
        [-A[mplitude contrast]Amp                 (0.1       ).as(Real                ) ] :Optional  :The ratio of amplitude contrast to phase contrast
        [-Astig[matism]      dfMin               (0         ).as(Real                )
                             dfMax               (0         ).as(Real                )
                             asAxis              (0         ).as(Real                ) ] :Optional  :With Astigmatism
        [-NoAstig[matism]                                                              ] :Optional  :Without Astigmatism
        [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
        [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
    ----- mode -----
    mode 0: No Correction
    mode 1: x ctf/|ctf|, phase flipping
    mode 2: x ctf,       phase flipping and ctf-multiplying
    mode 3: x 1/ctf    (0.1<|ctf|       phase flipping and ctf-divided
    mode 4: x ctf/(SQR(ctf)+SQR(NS))    phase-flipping + Winner Filtering
    mode 5: x SQR(ctf) x ctf/|ctf|      phase-flipping + ctf-Weighted
    mode 6: x 1/|ctf|  (0.1<|ctf|)      No phase-flipping + ctf-divided
    mode 7: x |ctf|/(SQR(ctf)+SQR(NS))  No phase flipping + Winner Filtering
    mode 8: x  ctf /(SQR(ctf)+SQR(NS*exp(a*R)))  phase flipping + Winner Filtering + NS-raising
    mode 9: x |ctf|/(SQR(ctf)+SQR(NS*exp(a*R)))  No phase flipping + Winner Filtering + NS-raising
    ----- Note -----
    You can enter information from -info
    Info file was made by llExtractWithLayerSeparationFilamentInfo -oI
    defocus Cs kV AmplitudeContrast
    ----- Note1 -----
    -NoStig is the highest priority and so -Astig and parameters in -info2 are ignored.