# mrcImageAutoRotationAverage

## Usage

    Usage: mrcImageAutoRotationAverage
    Options:
        [-i[nput]            In                  (stdin     ).as(inFileList::mrcImage) ] :Essential :Input: Ins
        [-r[eferenc]         Ref                 (NULL      ).as(inFile::mrcImage    ) ] :Optional  :Input: Ref
        [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output:Average
        [-range              Min                 (0.0       ).as(Real                )
                             Max                 (360.0     ).as(Real                )
                             Delta               (5.0       ).as(Real                )
                             Iter                (2         ).as(Integer             ) ] :Optional  :Mode
        [-iter               iter                (2         ).as(Integer             ) ] :Optional  :iteration for rotation
        [-M[odeCorrelation]  CorMode             (16        ).as(Integer             ) ] :Optional  :Mode: Correlation
        [-Method[Correlation]Method              (0         ).as(Integer             ) ] :Optional  :Method: Correlation
        [-Periodic                                                                     ] :Optional  :Periodic
        [-maxIter[aration]   maxIter             (10        ).as(Integer             ) ] :Optional  :MaxIteration
        [-rmsd               rmsd                (1e-2      ).as(Real                ) ] :Optional  :rmsd
        [-log                Log                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :logFile
        [-thres[hold]        Thres               (0.2       ).as(Real                ) ] :Optional  :threshold: Linear Correlation
        [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
        [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
    ----- Additional Usage -----
    ----- -Mode -----
    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|  )