X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLungFilter.txx;h=596604b61f44b1f6e1c8c39115f3888a4f069734;hb=ae015f09e2fa0ebc736d24b37c9ed6c1ca0cb5b2;hp=f84a0956fb61d1bc48cf202c5481267e132bf2cd;hpb=03fe0552e60847627ebbab852acf1d997379f1e9;p=clitk.git

diff --git a/segmentation/clitkExtractLungFilter.txx b/segmentation/clitkExtractLungFilter.txx
index f84a095..596604b 100644
--- a/segmentation/clitkExtractLungFilter.txx
+++ b/segmentation/clitkExtractLungFilter.txx
@@ -90,8 +90,7 @@ ExtractLungFilter():
   TracheaVolumeMustBeCheckedFlagOn();
   SetNumSlices(50);
   SetMaxElongation(0.5);
-  SetSeedPreProcessingThreshold(-400);
- 
+  SetSeedPreProcessingThreshold(-400); 
   
   // Step 3 default values
   SetNumberOfHistogramBins(500);
@@ -135,7 +134,19 @@ SetInput(const ImageType * image)
 template <class ImageType>
 void 
 clitk::ExtractLungFilter<ImageType>::
-AddSeed(InternalIndexType s) 
+//AddSeed(InternalIndexType s) 
+AddSeed(InputImagePointType s) 
+{ 
+  m_SeedsInMM.push_back(s);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractLungFilter<ImageType>::
+AddSeedInPixels(InternalIndexType s) 
 { 
   m_Seeds.push_back(s);
 }
@@ -461,7 +472,6 @@ GenerateOutputInformation()
     // smalest one (sometimes appends with the stomach
     if (initialNumberOfLabels >1) {
       if (GetRemoveSmallLabelBeforeSeparationFlag()) {
-        DD(GetRemoveSmallLabelBeforeSeparationFlag());
         typedef itk::RelabelComponentImageFilter<MaskImageType, MaskImageType> RelabelFilterType;
         typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
         relabelFilter->SetInput(working_mask);
@@ -577,7 +587,7 @@ SearchForTracheaSeed(int skip)
       it.GoToBegin();
       while (!it.IsAtEnd()) {
         if(it.Get() < GetUpperThresholdForTrachea() ) {
-          AddSeed(it.GetIndex());
+          AddSeedInPixels(it.GetIndex());
           // DD(it.GetIndex());
         }
         ++it;
@@ -658,6 +668,7 @@ SearchForTracheaSeed2(int numberOfSlices)
     opening->Update();
     
     typename SlicerFilterType::Pointer slicer = SlicerFilterType::New();
+    slicer->SetDirectionCollapseToIdentity();
     slicer->SetInput(opening->GetOutput());
     
     // label result
@@ -739,11 +750,7 @@ SearchForTracheaSeed2(int numberOfSlices)
       for (unsigned int j = 0; j < nlables; j++) {
         shape = label_map->GetNthLabelObject(j);
         if (shape->Size() > 150 && shape->Size() <= max_size) {
-#if ITK_VERSION_MAJOR < 4
-          double e = 1 - 1/shape->GetBinaryElongation();
-#else
           double e = 1 - 1/shape->GetElongation();
-#endif
           //double area = 1 - r->Area() ;
           if (e < max_elongation) {
             nshapes++;
@@ -850,7 +857,7 @@ TracheaRegionGrowing()
   f->SetVerbose(GetVerboseRegionGrowingFlag());
   for(unsigned int i=0; i<m_Seeds.size();i++) {
     f->AddSeed(m_Seeds[i]);
-    // DD(m_Seeds[i]);
+    //DD(m_Seeds[i]);
   }  
   f->Update();
   PrintMemory(GetVerboseMemoryFlag(), "After RG update");
@@ -904,6 +911,15 @@ SearchForTrachea()
   // compute trachea volume
   // if volume not plausible  -> skip more slices and restart 
 
+  // If initial seed, convert from mm to pixels
+  if (m_SeedsInMM.size() > 0) {
+    for(unsigned int i=0; i<m_SeedsInMM.size(); i++) {
+      InputImageIndexType index;
+      working_input->TransformPhysicalPointToIndex(m_SeedsInMM[i], index);
+      m_Seeds.push_back(index);
+    }
+  }
+
   bool has_seed;
   bool stop = false;
   double volume = 0.0;