COMMENTS ARE IN RED.
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: 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)
set fiducial polygon exterior to grain phase (10)
overlay segmented and tomographic images (11)
pore erosion connectivity analysis (12)
directional erosion connectivity analysis (13)
seal image volume (14)
convert to/from segmented slice/volume file formats (15)
image magnification (16)
create hexagonal sphere pack segmented image (17)
L2 distance based burn (18)
estimate shifted overlay of seg images (19)
estimate rotated overlay of seg images (20)
segmented file intersection (21)
Enter choice: 4
Enter basename for input segmented volume file(s): ../seg/sw
Are file(s) compressed? [y,n]: y
Enter first and last slice of data to use: 1 256
Whether or not you want to invert depends on the tomographic data. By
default, the 3DMA-Rock algorithms operate on phase 0 in the segmented images.
In the data for these examples, the water (i.e. the void) phase is the lower
attenuating phase and is segmented as phase 0 while the higher attenuating
phase, the sandstone grain, is segmented as phase 1. Thus, for this data set,
there is no need to invert. There are data sets where the pore space is
filled with highly attenuating fluid and/or the "grain" phase has lower
attenuation than the pore filling fluid. In such cases the void phase will
be segmented as phase 1 (while the grain is designated as phase 0). In such
cases the segmented data should be inverted so that the 3DMA-Rock algorithms
operate on the void phase.
If the intention is to utilize 3DMA-Rock to analyze the grain phase, then
the segmented data may also have to be inverted.
Input data can be inverted to compute burn/medial axis of
grain space rather than void space.
Invert data (y,n(dflt))?: n
If the interest is ultimately in the generation of a pore/throat network,
we strongly advise either the application of the closure operation (next menu
item) or the choice of void/grain interface smoothing option 2) further below.
The closure operation is stronger, in the sense that it reduces the porosity
more than the interface smoothing operation.
The point behind either choice is to eliminate the possibility of "single
voxel thick channels" running between grains. These can occur purely due to
digitization artifacts, especially in artificial porous medium images such as
digitized sphere packs.
Apply morphological closure operation to grain space? (y,n(dflt)): n
Fiducial polygon generation methods
NONE (N)
MANUAL (M)
AUTOMATIC (A)
Enter method: N
Ring artifacts show up from time to time in microtomography images and are
an imaging artifact. The presence of strong rings will result in radial "pores"
in the segmented image. This correction attempts to reconstruct affected areas
of the segmented image using neighboring voxels on either side of a ring.
Correct for ring artifacts? (y,n(dflt)): n
See the comment above related to the decision whether to apply the
morphological closure operation.
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): 2
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.
3DMA-Rock provides the capability to "remove" (convert to the opposite phase)
isolated clusters of voxels of each phase.
As examples:
Unless they are touching the boundary, isolated grains that "float" in
void space may be unphysical. They may result from segmentation errors the
"break" thin neck connections.
Isolated void spaces ("air bubbles") may be physical or unphysical;
of interest or not of interest.
The minimum allowed size of an isolated, disconnected component of either phase
that is to be retained by the code for inclusion in the analysis,
(maximum size allowed for conversion to the other phase),
is up to the user and the data analysis needs.
The output from case 2.3 can be a useful guide for making a decision on the
conversion/retention size threshold.
Convert isolated grain clusters? (y,n): y
Enter maximum allowed size (number of voxels)
for convertible isolated grain cluster: 1000
Convert isolated pore clusters? (y,n): y
Enter maximum allowed size (number of voxels)
for convertible isolated pore cluster: 1000
Enter basename for output segmented file(s): ../c_seg/sw
Are file(s) to be compressed? [y,n]: y
Prepare raster files of corrected segmented image (y,n(dflt)): n