X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLung.ggo;h=186508602e980191bb4b9db2e59578f06e7e5ae6;hb=7d7668046785090bc4ded5d15da5f94586af8a4d;hp=ddc1fe71bb1c9a1b33b5c3cfa26651193bf837b0;hpb=5668d4a49a5a6b68dc80fa28f0f82b54187cb70c;p=clitk.git

diff --git a/segmentation/clitkExtractLung.ggo b/segmentation/clitkExtractLung.ggo
index ddc1fe7..1865086 100644
--- a/segmentation/clitkExtractLung.ggo
+++ b/segmentation/clitkExtractLung.ggo
@@ -10,6 +10,7 @@ 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"
 
@@ -20,12 +21,12 @@ 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"
 
@@ -34,20 +35,22 @@ 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