Change paradigm to find files

[clitk.git] / segmentation / clitkExtractPatient.ggo

diff --git a/segmentation/clitkExtractPatient.ggo b/segmentation/clitkExtractPatient.ggo
index 6b15a6af14e7e167e2687bea3556f124a52b4906..5b695aef4e7b3449eb1095fec2e47cfa81d4e40c 100644 (file)
--- a/segmentation/clitkExtractPatient.ggo
+++ b/segmentation/clitkExtractPatient.ggo
@@ -1,7 +1,8 @@
 #File clitkExtractPatient.ggo
 package "clitkExtractPatient"
 version "1.0"
-purpose "Input is binarized using initial thresholds, connected components are labeled (firstLabel). The air label (1) is removed. The remaining is binarized and relabeled, patient should now be the principal label (secondLabel). Two mechanismes are provided to influence the label images. Crop to reduce connectivity (image is restored to original size), eg for SBF. Decomposition through ersion and reconstruction through dilation (slow), eg for Pulmo bellows. Choose which labels to keep from second Label image. Final mask is cleaned by opening and closing."
+purpose "Input is binarized using initial thresholds, connected components are labeled (firstLabel). The air label (1) is removed. The remaining is binarized and relabeled, patient should now be the principal label (secondLabel). Two mechanismes are provided to influence the label images. Crop to reduce connectivity (image is restored to original size), eg for SBF. Decomposition through erosion and reconstruction through dilation (slow), eg for Pulmo bellows. Choose which labels to keep from second Label image. Final mask is cleaned by opening and closing.
+The image is padded first with air. If lungs are touching the border (so the air), set openingRadius to 1 in order to have lungs segmented inside the patient"
 
 option "config"                -  "Config file"                  string        no
 option "imagetypes"     -  "Display allowed image types"  flag          off
@@ -10,6 +11,7 @@ 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"
 
@@ -21,6 +23,7 @@ section "Binarize"
 
 option "lower"         -       "Initial lower threshold"       double          no      
 option "upper"         -       "Initial upper threshold"       double          no      default="-300"
+option "openingRadius"    - "Radius for opening after threshold"  int no  default="0"
 
 section "First Label Image (air=1)"
 
@@ -49,6 +52,6 @@ option  "remove"      -               "Labels to remove"                      int     no      multiple
 section "Clean-up"
 
 option "openClose"     -       "Perform morphological opening and closing with unit radius"    flag    off
-option "noAutoCrop"    -       "If set : do no crop final mask to BoundingBox"                         flag    on
+option "noAutoCrop"    -       "If set : do no crop final mask to BoundingBox"                         flag    off