#File clitkRegionGrowing.ggo
package "clitkRegionGrowing"
version "1.0"
purpose "Region growing from a seed point using various types of conditions to control the growing"

option "config"     - "Config file"                                                                                                                                         string  no
option "verbose"    v "Verbose"                                                                                                                                             flag    off

section "I/O"

option "input"      i "Input image filename"                                                                                                                                string  yes
option "output"     o "Output image filename"                                                                                                                               string  yes


section "Parameters"

option "type"       t "Region growing filter type: 0=threshold , 1=neighborhood-threshold , 2=confidence , 3=locally-adaptive-threshold, 4=explosion-controlled-threshold"  int     no  default="0"
option "lower"      l "Lower threshold value"                                                                                                                               double  no  default="310"
option "upper"      u "Upper threshold value"                                                                                                                               double  no  default="4000"
option "seed"       s "Seed index postion (in voxels)"                                                                                                                      int     no  default="0" multiple
option "seedRadius" - "Radius used for seed dilatation(in voxel)"                                                                                                           int     no  default="0" multiple
option "pad"        p "The replace padding value"                                                                                                                           double  no  default="1.0"
option "radius"     r "1-3: The radius of the neighborhood"                                                                                                                 int     no  default="1" multiple
option "iter"       - "2: Iterations"                                                                                                                                       int     no  default="5"
option "multiplier" m "2-4: (2-3) accept if within mean+-mutiplier*SD, (4) explosion if size increases multiplier times"                                                    double  no  default="2.0"
option "maxSD"      - "3: Limit to SD"                                                                                                                                      double  no
option "adaptLower" - "3,4: (locally) adapt lower thresholding"                                                                                                             flag    off
option "adaptUpper" - "3,4: (locally) adapt upper thresholding"                                                                                                             flag    off
option "maxUpper"   - "4: Maximum upper threshold value"                                                                                                                    double  no  default="2000"
option "minLower"   - "4: Minimum lower threshold value"                                                                                                                    double  no  default="-1000"
option "step"       - "4: Threshold step size"                                                                                                                              double  no  default="64.0"
option "minStep"    - "4: Minimum threshold step size"                                                                                                                      double  no  default="1"
option "full"       - "4: use full connectivity (not implemented yet)"                                                                                                      flag    off