# mrcImageClusterAnalysis

## Usage

    Usage: mrcImageClusterAnalysis
    Options:
        [-I[nput array of file]In                  (NULL      ).as(inFileListNoOpen    ) ] :Essential :InputDataFiles
        [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
        [-O[utput]                                                                     ] :Optional  :Output: averaged images: filename is xxxx.avg: xxxx is input filename.
        [-N[umberOfClusters] N                   (1         ).as(Integer             ) ] :Optional  :Number of clusters
        [-Min[imumCorrelation]Min                 (0.0       ).as(Real                ) ] :Optional  :Minimum: Correlation: Conditions for ending
        [-Iter[ation]                                                                  ] :Optional  :IterationFlag
        [-A[uto]R[otation]   AutoRotation        (72        ).as(Integer             ) ] :Optional  :AutoRotation: rotation divided by this value
        [-A[utoRot]Range     ARMin               (0         ).as(Real                )
                             ARMax               (360       ).as(Real                ) ] :Optional  :AutoRotationRange
        [-A[uto]R[otation]iter[ation]AutoRotationIteration(2         ).as(Integer             ) ] :Optional  :AutoRotationIteration
        [-A[uto]R[otation]MethodAutoRotationMethod  (0         ).as(Integer             ) ] :Optional  :Method for Correlation for Auto Rotation
        [-M[odeForCorrelation]correlationMode     (19        ).as(Integer             ) ] :Optional  :Correlation Mode for AutoRotation
        [-Log                Log                 (stdout    ).as(appendFile          ) ] :Optional  :Log: Output
        [-Log2               Log2                (NULL      ).as(appendFile          ) ] :Optional  :Log2: Output: ClusterNode Only
        [-LogIn              LogIn               (NULL      ).as(inFile              ) ] :Optional  :previousLog: Input
        [-prevF[ileNum]      prevFileNum         (0         ).as(Integer             ) ] :Optional  :previousLogFileNum: Input
        [-pthread            pthread             (0         ).as(Integer             ) ] :Optional  :pthread: Input
        [-NoRecalc                                                                     ] :Optional  :No recalculation of distances
        [-pvm                                                                          ] :Optional  :Parallel Analysis by PVM
        [-pvmList            pvmList             (NULL      ).as(inFile              ) ] :Optional  :pvmList: Input
        [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
        [-m[ode]             mode                (2         ).as(Integer             ) ] :Optional  :Mode
    ----- Additional Usage -----
    Distance between clusters: mode
    	mode 0: By Correlation
    	mode 1: By Euclid Distance
    	mode 2: By Ward Method (default) : Euclid Length (no rotation) or its square (rotation)
    	mode 3: By Ward Method using Linear Correlation : (1 - Correlation)/(1 + Correlation)
    	mode 4: By Linear Correlation :                   (1 - Correlation)/(1 + Correlation)
    	mode 5: Not supported
    	mode 6: Not supported
    	mode 7: used for method masking
    	mode 8: Not supported.