New way to extract support

[clitk.git] / segmentation / clitkExtractLymphStations.ggo

diff --git a/segmentation/clitkExtractLymphStations.ggo b/segmentation/clitkExtractLymphStations.ggo
index 96ac9940799a7ed377e47cdced452bca33e571b4..457f64e933d19174c37db836b435de6be1a99dc0 100644 (file)
--- a/segmentation/clitkExtractLymphStations.ggo
+++ b/segmentation/clitkExtractLymphStations.ggo
@@ -3,44 +3,46 @@ 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
+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
+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_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 
+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_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 
+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
+