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# mrcImageCorrelation

## Usage

    Usage: mrcImageCorrelation
    Options:
        [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
        [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile: Correlation Map
        [-O[utput]           Out2                (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile: Correlation Map for Refinement
        [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Essential :ReferenceDataFile
        [-cor[relation]Info  OutCor              (stdout    ).as(outFile             ) ] :Optional  :Output: Correlation Info
        [-a[verage]          Avg                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile: Averaged File
        [-s[hit]             Shift               (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile: Shifted InputFile
        [-refine             RefineStep          (0.25      ).as(Real                )
                             RefineRange         (3.0       ).as(Real                )
                             RefineMode          (2         ).as(Integer             ) ] :Optional  :Refinemnet: Step Range[pixelUnit]
        [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
        [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
        [-M[ode2]            mode2               (0         ).as(Integer             ) ] :Optional  :Mode2
    ----- Mode:  -m -----
    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|  )
    ----- Mode2: -M -----
    mode 0: Correlation by FFT.  Output is a mrcImage to file.
                -a : Averaged image after Shift Transform [pixel unit] and Averaging
                -s : Shifted  image after Shift Transform [pixel unit]
                -o : Correation Map
    mode 1: Correlation by multiplying in normal space.  Output is a real value
                Normalized correlation value
                No shift transform
                No Correlation Map
    ----- Refinement:  -refine -----
                refineStep[PixelUnit]  : refinement step size
                refineRange[PixelUnit] : refinement range
                refineMode             : refinement mode
                --- search area -----
                the position of max correlation +- refineRange / refineStep
                Attention: If this option is set, the meaning of -o option is changed to a residual map