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 "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 "mediastinum" m "Input mediastinum mask filename" string yes
-option "trachea" t "Input trachea mask filename" string yes
-option "output" o "Output lungs mask filename" string yes
-
-option "carenaZposition" c "Sup-Inf position of the carena (in mm, with origin)" double no
-option "middleLobeBronchusZposition" b "Sup-Inf position of the middle lobe bronchus (in mm, with origin)" double no
-option "spacing" - "Intermediate resampling spacing" double no default="6"
-option "fuzzy1" - "Fuzzy relative position threshold" double no default="0.6"
-
-
-
+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