# mrcImageAutoRotationCorrelation3D

## Usage

    Usage: mrcImageAutoRotationCorrelation3D
    Options:
        [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrc[test]
        [-r[ef]              Ref                 (NULL      ).as(inFile              ) ] :Essential :Input: mrc[ref]
        [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: Parameter
        [-cor                Cor                 (NULL      ).as(outFile             ) ] :Optional  :Output: CorMap
        [-fit                Fit                 (stdout    ).as(outFile             ) ] :Optional  :Output: Best Fit
        [-E[uler]A[ngle]     EulerAngle          (YOYS      ).as(String              ) ] :Optional  :Input: EulerAngle
        [-Rot1               Rot1Min             (0.0       ).as(Real                )
                             Rot1Max             (360.0     ).as(Real                )
                             Rot1Delta           (5.0       ).as(Real                ) ] :Optional  :Rot1
        [-Rot2               Rot2Min             (0.0       ).as(Real                )
                             Rot2Max             (180.0     ).as(Real                )
                             Rot2Delta           (5.0       ).as(Real                ) ] :Optional  :Rot2
        [-Rot3               Rot3Min             (0.0       ).as(Real                )
                             Rot3Max             (360.0     ).as(Real                )
                             Rot3Delta           (5.0       ).as(Real                ) ] :Optional  :Rot3
        [-Xrange             XrangeMin           (0         ).as(Real                )
                             XrangeMax           (0         ).as(Real                ) ] :Optional  :Xrange[pixel]: Not set, all space search
        [-Yrange             YrangeMin           (0         ).as(Real                )
                             YrangeMax           (0         ).as(Real                ) ] :Optional  :Yrange[pixel]: Not set, all space search
        [-Zrange             ZrangeMin           (0         ).as(Real                )
                             ZrangeMax           (0         ).as(Real                ) ] :Optional  :Zrange[pixel]: Not set, all space search
        [-M[ode]             Mode                (0         ).as(Integer             ) ] :Optional  :Mode: Correlation Mode
        [-M[ode]R[otation]   ModeRotation        (0         ).as(Integer             ) ] :Optional  :Mode: Rotation3D Mode
        [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
        [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode: InterpolationMode
    ----- Additional Usage -----
    ----- -M  CorrelationMode -----
    0: Normal Correlation FxG*
    1: Phase  Correlation FxG*/     |FxG*|
    2: Phase  Correlation FxG*/sqrt(|FxG*|)
    3: Normalized Normal Correlation FxG*/|F||G|)
    16: (0,0) = 0
    Refinement Correlation Map
    0: sqrt(Sum |Fi-Gi|^2                 / Sum |Gi|^2)
    1:      Sum |Gi||phaseFi - phaseGi|   / Sum |Gi|
    2: sqrt(Sum |Gi||phaseFi - phaseGi|^2 / Sum |Gi|  )
    ----- -MR RotationMode -----
     0: padding 0
     1: padding average
     +0:  within ellipsoidal area.
     +16: within square area.