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Next: case1.5smpl: Segment Data Using Up: Main Menu 1: Operations Previous: case1.5mh/case1.5mh.in: Mardia-Hainsworth Segmentation on

case1.5mh/case1.5mh.in: Mardia-Hainsworth Segmentation on 3D Data Set


  

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: 250 253 Slice size of data, (nx,ny): 250 250

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: n Number of vertices on fiducial polygon 1: 4 Enter 4 vertex coordinates ix,iy (integers >= 1) one pair per line The points should be ordered counterclockwise in a right handed coordinate system, clockwise in a left handed system. : 61 61 : 120 61 : 120 120 : 61 120

Select segmentation stencil segment in 3d (v) segment by slice (s) Enter choice (v,s(dflt)): v Enter basename for segmented files: mh3d/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 Enter choice (e,m,u): g

Merge histogram files of variogram image (y,n(dflt)): y 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: \

Prepare raster files of segmented image (y,n(dflt)): y

Merge raster files of segmented image (y,n(dflt)): y Number of segmented files to be merged per page: 4 Are files compressed? [y,n]: y Enter basename for merged_segmented files: mh3d/seg_mer Specify layout of 9 merged segmented files Regular matrix arrangment (r) user specified arrangment (u) Enter choice (r(dflt),u): r segmented files arranged nrows by ncols on a page Enter nrows and ncols: 2 2

Delete single slice rasterfiles after merging? (y,n(dflt)): y

Enter voxel length in physical units: 7



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Next: case1.5smpl: Segment Data Using Up: Main Menu 1: Operations Previous: case1.5mh/case1.5mh.in: Mardia-Hainsworth Segmentation on

Brent Lindquist
Thu Sep 30 12:33:54 EDT 1999