#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 "afdb_path"  p "Input path for image in AFDB" string default="./" no
option "input"      i "Input filename"               string no
option "support_limits" - "Filename to read the support limits"                           string yes
option "check_support_limits" - "Display stat on the support limits" flag off
option "output"     o "Output lungs mask filename"   string no

section "Options for all stations"
option "force_support"  - "Force to compute all supports even if already available"       flag   off
option "station"        - "Force to compute this station even if already exist in the DB" string no multiple
option "relpos"         - "List of filenames for relativeposition operations"             string no multiple



# section "Options for Station 3A"
# section "Options for Station 2RL"
# section "Options for Station 1RL"

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