correct options scheme

[clitk.git] / segmentation / clitkExtractLung.ggo

diff --git a/segmentation/clitkExtractLung.ggo b/segmentation/clitkExtractLung.ggo
index e91a2eaed9c79344301337273ca49f55369acd47..186508602e980191bb4b9db2e59578f06e7e5ae6 100644 (file)
--- a/segmentation/clitkExtractLung.ggo
+++ b/segmentation/clitkExtractLung.ggo
@@ -10,24 +10,23 @@ 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 CT image filename"         string        yes
-option "patient"       p       "Input patient mask filename"     string        yes
-option "patientBG"   - "Patient Background"              int           default="0" no
-option "afdb"          a       "Output Anatomical Feature DB (Carina position)"    string      no
+option "afdb"          a       "Output Anatomical Feature DB (Carina position)"  string  no
 option "output"        o       "Output lungs mask filename"      string        yes
 option "outputTrachea" t       "Output trachea mask filename"    string        no
 
 section "Step 1 : Air remove"
 
-option "lower"      -  "Initial lower threshold"                 double        no      
-option "upper"      -  "Initial upper threshold"                 double        no      default="-300"
+option "lower"      -  "Initial lower threshold"                 int   no      
+option "upper"      -  "Initial upper threshold"                 int   no      default="-300"
 option "minSize"     - "Minimum component size in voxels"        int           no      default="100"
-option "remove1"     - "Labels not to keep in air mask (lungs)"  int           no      multiple        default="2"
-option "firstKeep1"  - "First label to keep"                     int           no      default="1"
-option "lastKeep1"   - "Last label to keep"                      int           no      
+#option "remove1"     -        "Labels not to keep in air mask (lungs)"  int           no      multiple        default="2"
+#option "firstKeep1"  -        "First label to keep"                     int           no      default="1"
+#option "lastKeep1"   -        "Last label to keep"                      int           no      
 
 section "Step 2 : find trachea"
 
@@ -36,18 +35,28 @@ option "upperThresholdForTrachea"    -      "Initial upper threshold for trachea"  do
 option "multiplierForTrachea"       -  "Multiplier for the region growing"    double   no  default="5"
 option "thresholdStepSizeForTrachea" - "Threshold step size"                  int      no  default="64"
 option "seed"                        - "Index of the trachea seed point"      int      no  multiple
+option "doNotCheckTracheaVolume"     -  "If set, do not check the trachea volume" flag off
+option "verboseRG"                   -  "Verbose RegionGrowing"   flag off
 
 section "Step 3 : auto extract lung"
 
 option "bins"       -  "Number of bins to use for the Otsu thresholding"       int             no      default="500"   
-option "remove2"     - "Labels not to keep in air mask (gas)"    int           no      multiple
-option "firstKeep2"  - "First label to keep"                     int           no      default="1"
-option "lastKeep2"   - "Last label to keep"                      int           no      
+# option "remove2"     -       "Labels not to keep in air mask (gas)"    int           no      multiple
+# option "firstKeep2"  -       "First label to keep"                     int           no      default="1"
+# option "lastKeep2"   -       "Last label to keep"                      int           no      
 
 section "Step 4 : remove trachea"
 
 option "radius"      -  "Radius for dilation"                     int           no      default="1"
-option "remove3"     - "Labels not to keep in lungs mask (trachea)"    int             no      multiple
-option "firstKeep3"  - "First label to keep"                     int           no      default="1"
-option "lastKeep3"   - "Last label to keep"                      int           no      default="2"
+# option "remove3"     -       "Labels not to keep in lungs mask (trachea)"    int             no      multiple
+# option "firstKeep3"  -       "First label to keep"                     int           no      default="1"
+# option "lastKeep3"   -       "Last label to keep"                      int           no      default="2"
+
+section "Step 5 : [optional] openclose"
+option "openclose"             -  "Perform an OpenClose operation"             flag off
+option "opencloseRadius"       -  "OpenClose radius"                           int no default="1"
+
+section "Step 6 : fill holes"
+option "doNotFillHoles"                -  "Do not fill holes if set"                 flag on
+option "dir"                   d  "Directions (axes) to perform filling (defaults to 2,1,0)"   int multiple no