# mrcImageCTFDetermination

## Usage

    Usage: mrcImageCTFDetermination
    Options:
        [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
        [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Essential :ReferenceDataFile
        [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output Optimum [text]
        [-oP[utput]          Out2                (NULL      ).as(outFile             ) ] :Optional  :Output Distribution [mrc image]
        [-oC[utput]          OutC                (NULL      ).as(outFile             ) ] :Optional  :Output CTF Information file
        [-oF[utput]          OutF                (NULL      ).as(outFile             ) ] :Optional  :Output Result FFT[mrc image]
        [-kV                 kV                  (200       ).as(Real                ) ] :Optional  :AccVol[kV]
        [-Cs                 Cs                  (2.1       ).as(Real                ) ] :Optional  :Cs[mm]
        [-Ain                Ain                 (0.02      ).as(Real                ) ] :Optional  :IlluminationAperture[mrad]
        [-W[hiteNoise]       WhiteNoise          (1.0       ).as(Real                ) ] :Optional  :
        [-df                 mindf               (0.0       ).as(Real                )
                             maxdf               (200000    ).as(Real                )
                             deldf               (1000      ).as(Real                ) ] :Optional  :df[A] for in
        [-AoverP             minAoverP           (0.0       ).as(Real                )
                             maxAoverP           (1.0       ).as(Real                )
                             delAoverP           (0.01      ).as(Real                ) ] :Optional  :AoverP[A] for in
        [-Rmin               Rmin                (0.0       ).as(Real                ) ] :Optional  :Rmin[/A]
        [-Rmax               Rmax                (0.1       ).as(Real                ) ] :Optional  :Rmax[/A]
        [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
        [-m[ode]F[ilter type]mF                  (1         ).as(Integer             ) ] :Optional  :Filter Type
        [-m[ode]W[ight type] mW                  (0         ).as(Integer             ) ] :Optional  :Wight Type
        [-m[ode]S[um type]   mS                  (0         ).as(Integer             ) ] :Optional  :Sum Type
        [-m[ode]C[TF Info type]mC                  (0         ).as(Integer             ) ] :Optional  :CTF Information Type
        [-M[ode]             M                   (0         ).as(Integer             ) ] :Optional  :ref Type
        [-PixelSize          PixelSize           (5         ).as(Integer             ) ] :Optional  :Pixel Size [A]
        [-Width              Width               (120       ).as(Integer             ) ] :Optional  :Pad Width [pixel]
        [-truePitch          truePitch           (430       ).as(Real                ) ] :Optional  :True Pitch [A]
        [-dfRef              firstDf             (70000     ).as(Real                )
                             withinDf            (1000      ).as(Real                ) ] :Optional  :dfRef for ref
        [-AoverPRef          firstAoverP         (0.05      ).as(Real                )
                             withinAoverP        (0.01      ).as(Real                ) ] :Optional  :A over P Ref for ref
        [-MaxIter            maxiter             (10        ).as(Integer             ) ] :Optional  :MaxIteration for ref
        [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
    ----- Additional Usage -----
    ----- mrcFile -----
    in  <- Original Image
    ref <- CTF Compensated Image
    ----- in <- Fiter Type (-mF) -----
    		0: No CTF compensation
    		1: Phase only: W = CTF/|CTF|
    		2: Multiply  : W = CTF
    		3: Multiply  : W = 1/CTF
    		4: Wiener filter (constant noise): W = CTF/(|CTF|^2+N^2)
    		5: Multiply  : W = CTF^2
    ----- in <- Wight Type (-mW) -----
    		0: Weight = 1
    		1: Weight = (|in| + |ref|)/2
    ----- in <- Sum Type (-mS) -----
    		0: Sigma[Phase(i)]
    		1: Sigma[Phase(i)*Weight(i)] / Sigma[Weight(i)]
    ----- ref <- Type (-M) -----
    		0: CTF compensated single image
    		1: Three-dimentional reconstruction images that were made by
    		   nea and far Bessel separation.
    		   CTF compensatation were done between min defocus to max defocus.
    		   This mode is for myosin filaments.
    		   (Options) -PixelSize -Width -truePitch
    		             -dfRef -AoverPRef -MaxIter
    		2: Result FFT
    		   (Options) -oF, -dfRef, -AoverPRef
    ----- OutPut File-----
    		  -o : defocus and amlitude-contrast at minimum point
    		  -oP: mrc file
    		  -oC: ctf information file for ctf compensation
    		        Type (-mC)
    		        	0: lllExtractCtfinfFileCreate (mode 0)
    		        	1: lllExtractCtfinfFileCreate (mode 1)