# file clitkDicomRTStruct2BinaryImage.ggo
package "clitk"
version "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

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

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 "roi"		 r "ROI to print (ID)"		 int		no
#option "contour"	 c "contour to print (ID)"	 int            no
#option "offset"		 o "to display points as image offsets" flag	off