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)
fluid data (6)
Enter choice: 2
Data Processing Options
plot image (1)
resize data (2)
disconnected volume distribution (3)
clean up segmented files (4)
burn and compute LKC medial axis/surface (5)
moment of inertia of disconnected components (6)
convert data to/from ascii format (7)
2-point covariance function (8)
tomographic/segmented data covariance comparison (9)
compress data in z direction (10)
count voxels in spherical/cylindrical shells (11)
set fiducial polygon exterior to grain phase (12)
overlay segmented and tomographic images (13)
pore erosion disconnectivity analysis (14)
Enter choice: 4
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 input segmented
files: ../seg/oil
Are files compressed? [y,n]: y
Enter first and last slice of data to use: 1 100
Input data can be inverted to compute
burn/medial axis of
grain space rather than void space.
Invert data (y,n(dflt))?: y
Medial axis analysis operates by default on phase 0 in the segmented files.
Phase 0 is the phase having lower X-ray attenuation coefficients. In this
example, the "rock" phase, the polyethylene core" has the lower X-ray
attenuation coefficient. We therefore have to INVERT the two phases to have
0 designate pore space and 1 designate grain space.
Whether or not you need to invert depends on your data.
Fiducial polygon generation methods
NONE (N)
MANUAL (M)
AUTOMATIC (A)
Enter method: N
Correct for ring artifacts? (y,n(dflt)): n
Ring artifacts show up from time to time in microtomography images. Saying yes here turns on an algorithm that attempts to locate and correct such artifacts in the segmented image. It contains hard-coded parameters that may have to be adjusted for your data; it has been used with limited success. If you have ring artifacts: a) you have our sympathy; b) you can try this algorithm - it requires you to type in the x-y coordinates of the center of rotation of the sample; c) we don't guarantee success.
The material/void boundary can be lightly
smoothed.
Available options are
0) no conversion
or convert those boundary voxels having
1) exactly one neighbor of the same type
2) less than a majority of neighbors of the same type
Enter choice (0(dflt),1,2): 0
Medial axis algorithms are susceptible to noise on the material-void interface. The ability to lightly smooth the boundary my result in lessening of extraneous dead end medial axis paths. There is however a later opportunity to trim such paths directly.
Isolated clusters of grain and/or pore
voxels up to a specifed size
can be assumed to be misidentified
and converted to the opposite material type.
Convert isolated grain clusters? (y,n):
y
Enter maximum allowed size (number
of voxels)
for convertible isolated grain cluster: 50
Unless they touch the boundary of the imaged region, isolated grains that "float" in void space are unphysical.
Convert isolated pore clusters?
(y,n): y
Enter maximum allowed size (number
of voxels)
for convertible isolated pore cluster: 50
The choice of minimum size for retention of an isolated phase blob is decided by the user and data analysis needs. Case 2.3 is provided to produce the observed blob size distribution and aid the user in making a choice.
Enter basename for output segmented
files: ../c_seg/oil
Are files to be compressed? [y,n]:
y
Prepare raster files of corrected segmented
image (y,n(dflt)): y
Enter basename for raster files: ../c_seg/oil
Merge raster files of segmented image (y,n(dflt)): n