case1.2/case1.2a.in: Generate Attenuation Coefficient Histograms with Fiducial Polygon

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: 2

The tomographic data file is 
	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/berea/berea
Are files compressed? [y,n]: y

Enter first and last slice of data to use: 1 5
Slice size of data, (nx,ny): 541 541

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

	MANUAL fiducial boundary calculation

	The bounding curve for each fiducial polygon should be convex in
	the sense that at most 2 points on the bounding curve have the
	same y coordinate.
Enter number of polygons: 1

Are the coordinates of the fiducial polygon(s) stored in a file: y
	Filename of fiducial polygon 1: ../../Examples/data/polygon.541

Select method for determining MIN and MAX values for scaling data
	volume          (v)
	slice           (s)
	slice  adjusted (sa)
Enter choice: sa
Enter minimum counts to determine adjusted values
	 low: 100
	high: 100

Enter basename for histogram files: berea_a
Default histogram contains 128 bins. Change number of bins? (y,n(dflt)): n

Merge histogram files of tomographic image (y,n(dflt)): y
Number of histogram files to be merged per page: 5
histogram files arranged nrows by ncols on a page
Enter nrows and ncols: 2 3

Enter the title for histogram: Berea

Enter the data label for histogram: X-Ray attenuation coefficient