Input Data Options
	tomographic data (1)
	segmented data (2)
	burn data (3)
	medial axis data (4)
	throat data (5)
	pore-throat network data (6)
	fluid data (7)
	Lattice Boltzmann simulation (8)
Enter choice: 4

Data Processing Options
	plot MA (1)
	plot MA with MS (2)
	convert MS files to segmented file type (3)
	histogram and fit pore MA burn data (4)
	embed search tree(s) (5)
	shortest paths (6)
	min cut/max flow (7)
	convert data to/from ascii format (8)
	convert MA list to/from node/path formats (9)
	modify MA (10)
	histogram MA info (11)
	throat calculation (12)
	convert to graph format (13)
	reconstruct burn layers (14)
Enter choice: 10

    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 Medial structure file(s): ../ma/sw
Are file(s) compressed? [y,n]: y

Enter basename for burn file(s): ../burn/sw
Are file(s) compressed? [y,n]: y


Resize information selection.
NOTE, row and column numbers begin from 0

For each slice,
   enter first and last column of data to use (x-dir): 0 255
   enter first and last row of data to use (y-dir): 0 255

enter first and last slice of data to use (z-dir): 1 256

Trim medial structure voxels on volume edges? (y,n(dflt)): y

Medial axis clean up control menu

	Maximum burn number on medial axis is 13

    Remove isolated voxels (y,n(dflt)): y
	Remove isolated voxels having burn number less than: 30

    Remove isolated paths (y,n(dflt)): y
	Remove isolated paths having length less than: 1000

    Remove branch-leaf paths (y,n(dflt)): y
    Retain branch-leaf paths exiting through boundary? (y,n(dflt): y
    branch-leaf path removal criteria
	Remove path if length less than
		maximum cluster burn number (auto)
		user specified tolerance    (user)
	Enter choice (a(dflt),u): u
	Enter tolerance length: 1000

    Remove needle-eye paths (y,n(dflt)): y
    needle-eye path removal criteria
	Remove path if length less than
		maximum cluster burn number (auto)
		user specified tolerance    (user)
	Enter choice (a(dflt),u): u
	Enter tolerance length: 1000

    Surface Remnant clean up
	Reduce surface remant structure where possible(y,n(dflt)): y

Enter voxel length in physical units: 4.93

Specify output medial axis data format
	voxel location list only (v)
	cluster/path format      (cp)
	graph node/path format   (g)
Enter format (v,cp,g): cp


Merge close clusters? (y,n(dflt)): n


Enter basename for singlet loc/burn file(s): ../ma_t/cp_sngl
Enter basename for cluster/path loc/burn file(s): ../ma_t/cp_loc
Enter basename for cluster/path structure file(s): ../ma_t/cp_struct
Are file(s) to be compressed? [y,n]: y