#File clitkExtractLymphStations.ggo
package "clitkExtractLymphStations"
version "1.0"
purpose "Extract LymphStations with help of TODO"

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 "afdb"          a	"Input Anatomical Feature DB"     string  	no
option "input"         i	"Input filename"                  string  	no
option "output"        o 	"Output lungs mask filename"      string 	no
option "station"       - 	"Force to compute station even if already exist in the DB"      string 	no multiple

section "Options for Station 8"
option "S8_esophagusDilatationForAnt"   - "Dilatation of esophagus, in mm, for 'anterior' limits (default=15,2,1)" double no multiple
option "S8_esophagusDilatationForRight" - "Dilatation of esophagus, in mm, for 'right' limits (default=5,10,1)" double no multiple
option "S8_ft_Esophagus"                - "Fuzzy Threshold for 'Post' to dilated Esophagus" double default="0.5" no 

section "Options for Station 7"
option "S7_ft_Bronchi"                    - "Fuzzy Threshold for Left/Right bronchi" double default="0.1" no 
option "S7_ft_LeftSuperiorPulmonaryVein"  - "Fuzzy Threshold for LeftSuperiorPulmonaryVein" double default="0.3" no 
option "S7_ft_RightSuperiorPulmonaryVein" - "Fuzzy Threshold for RightSuperiorPulmonaryVein" double default="0.2" no 
option "S7_ft_RightPulmonaryArtery"       - "Fuzzy Threshold for RightPulmonaryArtery" double default="0.3" no 
option "S7_ft_LeftPulmonaryArtery"        - "Fuzzy Threshold for LeftPulmonaryArtery (NOT USEFUL YET)" double default="0.5" no 
option "S7_ft_SVC"                        - "Fuzzy Threshold for SVC" double default="0.2" no 
option "S7_UseMostInferiorPartOnly"    - "Inferior separation with S8."  flag off

section "Options for Station 3A"
option "S3A_ft_Sternum"          - "Fuzzy Threshold for Post to Sternum" double default="0.5" no 
option "S3A_ft_SubclavianArtery" - "Fuzzy Threshold for Ant to SubclavianArtery" double default="0.2" no 

section "Options for Station 2RL"
option "S2RL_ft_CommonCarotidArtery"   - "Threshold for NotAntTo to CommonCarotidArtery"   double default="0.7" no 
option "S2RL_ft_BrachioCephalicTrunk"  - "Threshold for NotAntTo to BrachioCephalicTrunk"  double default="0.7" no 
option "S2RL_ft_BrachioCephalicVein"   - "Threshold for NotAntTo to BrachioCephalicVein"   double default="0.3" no 
option "S2RL_ft_Aorta"                 - "Threshold for RightTo  to Aorta"                 double default="0.7" no 
option "S2RL_ft_SubclavianArteryRight" - "Threshold for NotLeft  to SubclavianArteryRight" double default="0.5" no 
option "S2RL_ft_SubclavianArteryLeft"  - "Threshold for NotRight to SubclavianArteryLeft"  double default="0.8" no