DGtalTools  1.2.0
criticalKernelsThinning3D

Applies an criticalKernels thinning algorithm of a 3d image file (vol,longvol,pgm3d...) with 3D viewer.

Usage: criticalKernelsThinning3D [options] –input <3dImageFileName> {vol,longvol,pgm3d...}

Allowed options are :

Positionals:
1 TEXT:FILE REQUIRED Input vol file.
Options:
-h,--help Print this help message and exit
-i,--input TEXT:FILE REQUIRED Input vol file.
-s,--skel TEXT:{ulti,end,isthmus,1isthmus}=1isthmus
Type of skeletonization. Options: 1isthmus, isthmus, end, ulti.
Options: ulti,end, 1isthmus, isthmusulti: delete all voxels except those that change topology.
end: keep voxels with only one neighbor.
1isthmus: keep voxels that are one-isthmus (using LookUpTables) [faster]
isthmus: keep voxels that are one-isthmus or two-isthmus (using LookUpTables) [faster]
-c,--select TEXT:{random,dmax,first}=dmax
Select the ordering for skeletonization. Options: dmax, random, first
Options: dmax, first, random
dmax: Use distance map, selecting voxel with max value.
first: Select first pixel (lexicographical order)
random: Select voxel at random.
-f,--foreground TEXT:{white,black}=black
Foreground color in binary image
-m,--thresholdMin INT=0 Threshold min (excluded) to define binary shape
-M,--thresholdMax INT=255 Threshold max (included) to define binary shape
-p,--persistence INT:POSITIVE=0 Persistence value, implies use of persistence algorithm if p>=1
--profile Profile algorithm
-v,--verbose Verbose output
-o,--exportImage TEXT Export the resulting set of points to a image compatible with GenericWriter.
-e,--exportSDP TEXT Export the resulting set of points in a simple (sequence of discrete point (sdp)).
-t,--visualize Visualize result in viewer

Example:

$ criticalKernelsThinning3D --input ${DGtal}/examples/samples/Al.100.vol --select dmax --skel 1isthmus --persistence 1 -t
Definition: ATu0v1.h:57

You should obtain such a result:

Resulting visualization.
See also
criticalKernelsThinning3D.cpp