#File clitkExtractPatient.ggo
package "clitkExtractPatient"
version "1.0"
purpose "Input is binarized using initial thresholds, connected components are labeled (firstLabel). The air label (1) is removed. The remaining is binarized and relabeled, patient should now be the principal label (secondLabel). Two mechanismes are provided to influence the label images. Crop to reduce connectivity (image is restored to original size), eg for SBF. Decomposition through ersion and reconstruction through dilation (slow), eg for Pulmo bellows. Choose which labels to keep from second Label image. Final mask is cleaned by opening and closing."

option "config"	        -  "Config file"		  string  	no
option "imagetypes"     -  "Display allowed image types"  flag          off
option "verbose"        v  "Verbose"			  flag		off
option "verboseStep"    -  "Verbose each step"		  flag		off
option "writeStep"      w  "Write image at each step"	  flag		off
option "verboseOption"  -  "Display options values"       flag          off
option "verboseWarningOff" -  "Do not display warning"    flag          off
option "verboseMemory"  -  "Display memory usage"         flag          off

section "I/O"

option "input"   i	"Input image filename"		     string  yes
option "afdb"    a	"Output Anatomical Feature in a DB"  string  no
option "output"  o  	"Output image filename"		     string  yes

section "Binarize"

option "lower"		-	"Initial lower threshold"	double		no  	
option "upper"		-	"Initial upper threshold"	double		no  	default="-300"
option "openingRadius"    - "Radius for opening after threshold"  int no  default="0"

section "First Label Image (air=1)"

option "erode1"		 -	"Decompose through erosion" 		flag		off	
option "radius1"	 -	"Radius for erosion and dilation" 	int		multiple 	no 	default="1"
option "new1"		 -	"Number of new labels" 			int		no 	default="1"	
option "max1"		 -	"Max number of labels to consider" 	int		no 	default="2"	

section "Second Label Image (air=1)"

option "erode2"		 -	"Decompose through erosion" 		flag		off	
option "radius2"	 -	"Radius for erosion and dilation" 	int		multiple 	no 	default="1"
option "new2"		 -	"Number of new labels" 			int		no 	default="1"	
option "max2"		 -	"Max number of labels to consider" 	int		no 	default="2"	
# option "crop"		-	"Crop the first label image"	  	flag 	off	
# option "boundingBox"   	b   	"Bounding box of the crop region (minX,maxX,...)" int 	no  multiple
# option "lowerS"    	-   	"Size of the lower crop region"	  int 	no  multiple
# option "upperS"    	-   	"Size of the upper crop region"	  int 	no  multiple

section "Labels to keep (air=1)"

option	"firstKeep"  	-		"First label to keep"			int 	no	default="1"
option  "lastKeep" 	-		"Last label to keep"			int 	no	default="1"	
option  "remove"  	-		"Labels to remove"			int 	no	multiple	

section "Clean-up"

option "openClose"	- 	"Perform morphological opening and closing with unit radius"	flag 	off
option "noAutoCrop"	- 	"If set : do no crop final mask to BoundingBox"	                        flag 	off