# mrcImageAutoFilamentExtract

## Usage

    Usage: mrcImageAutoFilamentExtract
    Options:
        [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
        [-i[nput]S[ource]fileInS                 (NULL      ).as(inFile              ) ] :Essential :InputSourceFile
        [-o[utput]E[xtract]  OutE                (NULL      ).as(inFile              ) ] :Essential :OutputFileForExtraction
        [-o[utput]           Out                 (stdout    ).as(appendFile          ) ] :Optional  :Output Log File
        [-o[utput]F[inal]    OutF                (stdout    ).as(outFile             ) ] :Optional  :OutputFinalFile
        [-r[oi]ROI           blx                 (0.0       ).as(Real                )
                             bly                 (0.0       ).as(Real                )
                             brx                 (0.0       ).as(Real                )
                             bry                 (0.0       ).as(Real                )
                             trx                 (0.0       ).as(Real                )
                             try                 (0.0       ).as(Real                )
                             tlx                 (0.0       ).as(Real                )
                             tly                 (0.0       ).as(Real                ) ] :Optional  :Rectangle ROI
        [-r[oi]Unbent        roiLine             (0.0       ).as(Real                ) ... ] :Variable  :
        [-x                  x                   (120       ).as(Real                ) ] :Optional  :x range for ROI or Unbent
        [-d[elta]dYmax       ddYmax              (0.9       ).as(Real                ) ] :Optional  :delta dY max
        [-d[elta]dYmin       ddYmin              (0.2       ).as(Real                ) ] :Optional  :delta dY mim
        [-T[ransepose]       T                   (0         ).as(Integer             ) ] :Optional  :corresponding to mrcImageTransepose mode
        [-maxd[elta]Y        maxdY               (12        ).as(Integer             ) ] :Optional  :Maximum number of layer line
        [-H[eight] R[ange]   HeightRange         (0         ).as(Integer             ) ] :Optional  :Height Range [Pixel]
        [-RMaxX              RMaxX               (0.05      ).as(Real                ) ] :Optional  :RMaxX [1/A] (supported mode 1)
        [-mag                mag                 (1.1       ).as(Real                ) ] :Optional  :magnification ratio
        [-truePitch          truePitch           (430       ).as(Real                ) ] :Optional  :True Pitch [A]
        [-PixelSize          PixelSize           (5         ).as(Real                ) ] :Optional  :Pixel Size [A]
        [-finaly             finaly              (0         ).as(Integer             ) ] :Optional  :final y [pixel] for extraction
        [-Ignore             Ignore              (0         ).as(Integer             ) ] :Optional  :Ignore the final y
        [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
        [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
    ----- Additional Usage -----
    ----- mode -----
    0 : Meridian Reflection
    1 : All layer-lines
    ----- NOTE for Heigth Range-----
    HR option is stranger than caliculated HR
    ----- NOTE for ROI-----
    -rROI, -rUnbent, -iS, -ddYmax, -ddYmin and -T options are for ROI
    ----- NOTE for File for Extraction-----
    -oE file use as extraction file.
    ----- NOTE for FINAL-----
    -finaly and -oF is for final extraction
    -truePitch, -Ly and -dY are for magnification change
    -Ignore option ignore finaly
    This extract do with magnification and header change