# mrcImageMultiCTFCompensation

## Usage

    Usage: mrcImageMultiCTFCompensation
    Options:
        [-i[nput]            In                  (stdin     ).as(inFileList          ) ] :Essential :Input: filename ...
        [-info2              CTF                 (stdin     ).as(inFileList          ) ] :Optional  :InputFileList: the same order as the input: ctfinfo from Display2/ctfDisplay
        [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Essential :OutputDataFile(average file)
        [-f[ft]              fftOut              (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile(averaged fft file)
        [-W[hiteNoise]       WhiteNoise          (1.0       ).as(Real                ) ] :Optional  :
        [-W[hiteNoise]R[aising]WhiteNoiseRaising   (1.0       ).as(Real                ) ] :Optional  :Weight:W*exp(WR*R)
        [-maxW[hiteNoise]R[aising]MaxWhiteNoise       (1.0       ).as(Real                ) ] :Optional  :max(W*exp(WR*R),maxWhiteNoise)
        [-Ndep[endent]W[hiteNoise]R[aising]NdependentWhiteNoise(1         ).as(Integer             ) ] :Optional  :W*exp(WR*R)/sqrt(N)
        [-SinWin             SinWinRmin          (0.1       ).as(Real                )
                             SinWinRmax          (1.0       ).as(Real                ) ] :Optional  :Windowing by sine function from Rmin[/A] to Rmax[/A]
        [-MaxIter[ation]     MaxIter             (10        ).as(Integer             ) ] :Optional  :Max Iteration
        [-ctfMode            CTFMode             (1         ).as(Integer             ) ] :Optional  :CTFMode: refer to mrcImageCTFObservation
        [-solventMode        solventMode         (0         ).as(Real                ) ] :Optional  :If solvent flatterning is used, NEED
        [-solventSTD         solventSTD          (-1.0      ).as(Real                ) ] :Optional  :If solvent flatterning is used as mode=1, NEED
        [-log[file]          Log                 (stderr    ).as(outFile             ) ] :Optional  :Log File Name
        [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
        [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
    ----- InputFileFormat -----
    filename0 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
    filename1 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
    .................

    ----- Input: ctfinfo, with the same order as the input; from Display2/ctfDisplay -----
    filename0.ctfinfo
    filename1.ctfinfo
    .................

    mode: 0  : CTF-weighted compensation, CTF/(SQR(CTF) + (NS)^2)
    mode: +1 : Adding solvent-flattening process
    mode: +16: Without phase flipping, in case of images after phase only correction.