# mrcImageROI

## Usage

    Usage: mrcImageROI
    Options:
        [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input
        [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output
        [-r[oi]              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
        [-x                  WidthBeforeExpansion(1.0       ).as(Real                ) ] :Optional  :Width  before expansion: /* Default is set by -r */
        [-y                  HeightBeforeExpansion(1.0       ).as(Real                ) ] :Optional  :Height before expansion: /* Default is set by -r */
        [-a[ngle]            Angle               (0.0       ).as(Real                ) ] :Optional  :This value [degree] is added to angle of current source image.
        [-W                  WidthAfterExpansion (1.0       ).as(Real                ) ] :Optional  :Width  after expansion[Pixel]
        [-H                  HeightAfterExpansion(1.0       ).as(Real                ) ] :Optional  :Height after expansion[Pixel]:
    		ROI Size is (10,20):
    			If -W 30 -H 40, out (30,40)
    			If -W 30, out (30, 20*30/10)
    			If -H 40, out (10*40/20,40)
    				If omitted, out (10,20)
        [-Shift              ShiftX              (0.0       ).as(Real                )
                             ShiftY              (0.0       ).as(Real                ) ] :Optional  :ROI ARea Shift [Pixel]
        [-turePitch          truePitch           (430.0     ).as(Real                ) ] :Optional  :truePitch [A]
        [-dY                 dY                  (0.0       ).as(Real                ) ] :Optional  :Number of turePitch
        [-Ly                 Ly                  (5.0       ).as(Real                ) ] :Optional  :Header Length y [A/Pixel]
        [-S[hrink]           Shrink              (1         ).as(Integer             ) ] :Optional  :When inputfile is shrinked
        [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
        [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
    ---- mode ----
    	0: Nearest Neighbor Method
    	1: Bilinear method
    	2: Cubic Convolution method
    	3: Polynominal method
    ---- Note  (Magnification change for normalize)----
    -truePitch, -dY and -Ly options make
    H[pixel] = truePitch[A] / Ly[A/pixel] x dY