Merge branch 'master' of tux.creatis.insa-lyon.fr:clitk

[clitk.git] / segmentation / clitkExtractPatient.ggo

diff --git a/segmentation/clitkExtractPatient.ggo b/segmentation/clitkExtractPatient.ggo
index 3a239e7df6a7f4a14a827cb8669be86832718ef2..f4944409a1b10e6286a9930b1046b659a2301ece 100644 (file)
--- a/segmentation/clitkExtractPatient.ggo
+++ b/segmentation/clitkExtractPatient.ggo
@@ -1,7 +1,7 @@
 #File clitkExtractPatient.ggo
 package "clitkExtractPatient"
 version "1.0"
-purpose "Prefer high resolution input and resample (NN) output at the end (like). 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 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."
 
 option "config"                -  "Config file"                  string        no
 option "imagetypes"     -  "Display allowed image types"  flag          off
@@ -10,16 +10,19 @@ 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 image filename"            string        yes
-option "output"        o       "Output image filename"           string        yes
+option "input"   i     "Input image filename"               string  yes
+option "afdb"    a     "Output Anatomical Feature in a DB"  string  no
+option "output"  o     "Output image filename"              string  yes
 
 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)"
 
@@ -47,7 +50,7 @@ option  "remove"      -               "Labels to remove"                      int     no      multiple
 
 section "Clean-up"
 
-option "openClose"     -       "Perform morphological opening and closing with unit radius"    flag    on
-option "autoCrop"      -       "Crop final mask to BoundingBox"                                flag    off
+option "openClose"     -       "Perform morphological opening and closing with unit radius"    flag    off
+option "noAutoCrop"    -       "If set : do no crop final mask to BoundingBox"                         flag    off