case1.5mh/case1.5mh.in: Mardia-Hainsworth Segmentation on Data Slices

Input Data Options
	special purpose data requiring pre-processing (0)
	tomographic data (1)
	segmented data (2)
	burn data (3)
	medial axis data (4)
	throat data (5)
Enter choice: 1

Data Processing Options
	plot image (1)
	plot slice histograms (2)
	resize tomographic data (3)
	generate circular fiducial polygon (4)
	segment data (5)
	porosity/cut_off dependence (6)
	investigate dfn K values (7)
	investigate dfn threshold values (8)
	|grad image| histogram (9)
	compress data in z direction (10)
Enter choice: 5

Segment by
	simple threshold (smpl)
	anisotropic diffusion (dfn)
	indicator kriging (krig)
	Mardia-Hainsworth (mh)
	color values (hls)
Enter choice: mh

The tomographic data file is a
	raw data file (raw)
	partially diffused data file (dfn)
Enter choice: raw

Tomographic data slices are contained in
	separate files (slc)
	a single file  (vol)
Enter file type (slc,vol): slc

Recognized tomographic data file types are
	 ascii integer         array  (  ai)
	binary integer         array  (  bi)
	swapped binary integer array  ( sbi)
	binary short integer   array  (  bs)
	swapped binary short   array  ( sbs)
	binary unsigned char   array  ( ubc)
	netcdf files                  (  nc)
	netcdf ascii files            (  na)
	Kimberly Clark data           (  kc)
	punch ascii files             (  pa)
	sun rasterfile ( 8-bit color) ( sr8)
	sun rasterfile (24-bit color) (sr24)
Enter data type (ai,bi,sbi,bs,sbs,ubc,nc,na,kc,pa,sr8,sr24): bi

    Files assumed to be labelled  basename.ext,
    basename  is limited to 255 characters maximum,
    ext       is a numerical designator lying between 000 and 999
    It is assumed that the files have consecutively numbered extensions
        ie.  000 -> 056,  or   021 -> 049

Enter basename for tomographic files: ../../Examples/data/beads/beads
Are files compressed? [y,n]: y

Enter first and last slice of data to use: 250 250
Slice size of data, (nx,ny): 250 250

Fiducial polygon generation
	NONE         (N)
	MANUALLY set (M)
Enter method: N

Select segmentation stencil
	segment in 3d     (v)
	segment by slice  (s)
Enter choice (v,s(dflt)): s
Enter basename for segmented files: mh/seg

	covariance/semivariogram information

Available directions for estimating correlations
	vertical   (v)
	horizontal (h)
	isotropic  (i)
Enter choice (v,h,i): h

Available methods for thresholding data are by
	Entropy function (e)
	User specified   (u)
	Global mean	 (g)
Enter choice (e,u,g): g

Merge histogram files of variogram image (y,n(dflt)): n
Number of histogram files to be merged per page:4
histogram files arranged nrows by ncols on a page
Enter nrows and ncols:2 2

Enter the title for histogram: beads

Enter the data label for histogram:

Enter voxel length in physical units: 7