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
  -k,--keepInputDomain                  Keep the resulting image domain equal to the input image (instead using the resulting bouding box set).
  -O,--exportOBJ TEXT                   Export the resulting set of points in an OBJ file.
  -I,--exportInputOBJ TEXT              Export the input set of points in an OBJ file.

Example:

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

You should obtain such a result:

Resulting visualization.

See also

criticalKernelsThinning3D.cpp