# file clitkDicomRTStruct2BinaryImage.ggo
package "clitk"
version "1.0"
description "Convert DICOM RT Structure Set (contours) to binary image"

option "config"       - "Config file"                                                           string  no
option "verbose"      v "Verbose"                                                               flag    off
option "verboseFile"  - "Verbose file content"                                                  flag    off
option "input"        i "Input Dicom file"                                                      string  yes
option "image"        j "Used to read image info (spacing, origin)"                             string  yes
option "output"       o "Output image base filename (roi number and extension will be append)"  string  yes
option "tolerance"    t "Tolerance for slice position"                                          double  no  default="0"

text "\nOutput options - the default output format is mhd"
option "crop"         c "Crop binary mask"                                                      flag off
option "mha"          - "Write the RTStruct as a mha image to avoid special character problems" flag off
option "nii"          - "Write the RTStruct as a nii image"                                     flag off
option "niigz"        - "Write the RTStruct as a gzipped nii image"                             flag off
option "vtk"          - "Write the vtk Mesh as a vtk file"                                      flag off

defgroup "ROI option" groupdesc="an option of this group is required"
groupoption "roi"           r "ROI number to binarize (if -1 = all roi)"                                                      int     no default="-1" group="ROI option"
groupoption "roiName"       n "ROI name to binarize (be wary of spaces in ROI names; if blank, use given 'roi' value)"        string  no default=""   group="ROI option"
groupoption "roiNameSubstr" s "Substring of ROI name to binarize (returns all matches; if blank, use given 'roiName' value)"  string  no default=""   group="ROI option"