#File clitkMotionMask.ggo
package "clitkMotionMask"
version "1.0"
purpose "From an input CT image (HU), extract feature images (air, ribs and lungs) and calculate the motion mask using levelsets, Vandemeulebroucke2010, ICCR. More elaborate methods for extracting the feature images have been incude in clitkExtract*, with *=Lungs,Bones,Patient."

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
option "monitor"	m	"Monitoring image for levelsets"  string 	no
option "spacing"	-	"Low dimensional spacing to perform initial level set steps" double    no multiple	default="4"

section "Feature Images (feature=1,rest=0). Set them or extract them from the input"

option "featureAir"		-	"Input feature image"		string		no
option "lowerThresholdAir"	-	"Lower threshold for air feature image extraction"	double	no default="-10000" 
option "upperThresholdAir"	-	"Upper threshold for air feature image extraction"	double	no default="-800" 
option "pad"			-	"Make a border of air around the image (for cropped images)" flag	off 
option "featureBones"		-	"Input feature image"		string		no
option "lowerThresholdBones"	-	"Lower threshold for bones feature image extraction"	double	no default="100" 
option "upperThresholdBones"	-	"Upper threshold for bones feature image extraction"	double	no default="1000" 
option "featureLungs"		-	"Input feature image"		string		no
option "lowerThresholdLungs"	-	"Lower threshold for lungs feature image extraction"	double	no default="-950" 
option "upperThresholdLungs"	-	"Upper threshold for lungs feature image extraction"	double	no default="-600" 
option "writeFeature"		-	"Write the combined feature image"			string	no  


section "Ellipsoide initialization"

option	"ellips"	-	"Input ellipsoide image (=1, at half resolution)" 					   string	no
option  "writeEllips"	-	"Write the initial ellipsoide image"			string	no  
option "writeDistMap"   - "Write the distance map"      string  no  
#defgroup "EllipseParams" groupdesc="an option of this group is required" required
option  "ellipseAutoDetect"  - "Auto-detect offset and axes of initial ellipse"          flag  off  
option  "offset"  - "Offset for ellips center from body center of gravity (default= 0,-50,0 mm)"       double no  multiple
option  "axes"    - "Half axes of the ellips (default= 100,30,150)"            double   no  multiple


section "Ellipsoide growing"

option	"grownEllips"	-	"Input grown ellips image (=1, at half resolution)" 		   string	no
option	"offsetDetect"	-	"Offset of detection point from abdomen (default= 0,-10,0 mm)" 	   double	no	multiple
option	"detectionPairs" -	"Additional images to detect the abdomen (eg end-inhalation frame). The most anterior point will be retained." string no multiple
option	"detectionPoint"	-	"Physical coordinates of the detection point from abdomen (default= 0,-10,0 mm)" 	   double	no	multiple
option	"curve1"	-	"Curvature for this levelset" 					   double	no      default="35.0"	
option	"maxRMS1"	-	"Tolerance for this levelset"					   double	no      default="0.001"	
option	"iter1"		-	"Iterations performed between monitoring"  	 		   int		no      default="50"	
option  "writeGrownEllips"	-	"Write the grown ellipsoide image"			   string	no  


section "Filling the bones image"

option	"filledRibs"	-	"Input filled rib image (=1, at half resolution)" 	string	no
option	"fillingLevel"	-	"Minimum lung fill level: [0,100] %" 			double	no	default="98.0"
option	"curve2"	-	"Curvature for this levelset" 				double	no      default="30.0"	
option	"maxRMS2"	-	"Tolerance for this levelset"				double	no      default="0.001"	
option	"iter2"		-	"Iterations performed between monitoring"  	 	int	no      default="50"	
option  "writeFilledRibs"	-	"Write the filled ribs image image"		string	no  


section "Collapsing to the lung image"

option	"curve3"	-	"Curvature for this levelset" 		double	no      default="30.0"	
option	"prop3"		-	"Propagation for this levelset" 	double	no      default="0"
option	"maxRMS3"	-	"Tolerance for this levelset"		double	no      default="0.001"	
option	"iter3"		-	"Iterations performed between monitoring" int	no      default="20"	
option	"maxIter3"	-	"Iterations performed between monitoring" int	no      default="500"	
	

section "Clean-up"

option "openClose"	- 	"Perform morphological opening and closing with unit radius"	flag 	on