X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLungFilter.txx;h=3a098e9aad5c84bbbe965995ef7200ee974368ab;hb=615a1af31ba4649c58c684b006b696536e7d8ef5;hp=32d480c3395bc3f7cf36cf2c83eb175e1d63d353;hpb=a339bdc482ea9752ec53195bc9a47e8b05dba582;p=clitk.git

diff --git a/segmentation/clitkExtractLungFilter.txx b/segmentation/clitkExtractLungFilter.txx
index 32d480c..3a098e9 100644
--- a/segmentation/clitkExtractLungFilter.txx
+++ b/segmentation/clitkExtractLungFilter.txx
@@ -3,7 +3,7 @@
 
   Authors belong to: 
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
 
   This software is distributed WITHOUT ANY WARRANTY; without even
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ======================================================================-====*/
+  ===========================================================================**/
 
 #ifndef CLITKEXTRACTLUNGSFILTER_TXX
 #define CLITKEXTRACTLUNGSFILTER_TXX
@@ -96,6 +96,7 @@ ExtractLungFilter():
   
   // Step 6
   FillHolesFlagOn();
+  AutoCropOn();
 }
 //--------------------------------------------------------------------
 
@@ -311,7 +312,8 @@ GenerateOutputInformation()
   //--------------------------------------------------------------------
   PrintMemory(GetVerboseMemoryFlag(), "before autocropfilter");
   if (m_Seeds.size() != 0) { // if ==0 ->no trachea found
-    trachea = clitk::AutoCrop<MaskImageType>(trachea, GetBackgroundValue());
+    if (GetAutoCrop())
+      trachea = clitk::AutoCrop<MaskImageType>(trachea, GetBackgroundValue());
     StopCurrentStep<MaskImageType>(trachea);  
     PrintMemory(GetVerboseMemoryFlag(), "after delete trachea");
   }
@@ -321,7 +323,8 @@ GenerateOutputInformation()
   //--------------------------------------------------------------------
   StartNewStep("Cropping lung");
   PrintMemory(GetVerboseMemoryFlag(), "Before Autocropfilter");
-  working_mask = clitk::AutoCrop<MaskImageType>(working_mask, GetBackgroundValue());
+  if (GetAutoCrop())
+    working_mask = clitk::AutoCrop<MaskImageType>(working_mask, GetBackgroundValue());
   StopCurrentStep<MaskImageType>(working_mask);
 
   //--------------------------------------------------------------------
@@ -588,7 +591,7 @@ ComputeTracheaVolume()
 
 //--------------------------------------------------------------------
 template <class ImageType>
-void 
+void
 clitk::ExtractLungFilter<ImageType>::
 SearchForTrachea()
 {
@@ -603,8 +606,8 @@ SearchForTrachea()
   double volume = 0.0;
   int skip = GetNumberOfSlicesToSkipBeforeSearchingSeed();
   while (!stop) {
-    stop = SearchForTracheaSeed(skip);
-    if (stop) {
+    stop = true;
+    if (SearchForTracheaSeed(skip)) {
       TracheaRegionGrowing();
       volume = ComputeTracheaVolume()/1000; // assume mm3, so divide by 1000 to get cc
       if (GetWriteStepFlag()) {
@@ -616,7 +619,6 @@ SearchForTrachea()
           if (GetVerboseStepFlag()) {
             std::cout << "\t Found trachea with volume " << volume << " cc." << std::endl;
           }
-          stop = true; 
         }
         else {
           if (GetVerboseStepFlag()) {
@@ -629,6 +631,11 @@ SearchForTrachea()
           // empty the list of seed
           m_Seeds.clear();
         }
+        if (skip > 0.5 * working_input->GetLargestPossibleRegion().GetSize()[2]) {
+          // we want to skip more than a half of the image, it is probably a bug
+          std::cerr << "2 : Number of slices to skip to find trachea too high = " << skip << std::endl;
+          stop = true;
+        }
       }
       else {
         stop = true;