X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLungFilter.txx;h=a0acdd5ad2ab48aa3669d58f8d9d22171b74d329;hb=3b072585d9fc4e6b21940531196cec798ee74796;hp=f537fc1d2f5d483e33d3b9dfe7f6f33de4525c69;hpb=1c3642221e8bddabf9995271e41d36bd9c6772ab;p=clitk.git

diff --git a/segmentation/clitkExtractLungFilter.txx b/segmentation/clitkExtractLungFilter.txx
index f537fc1..a0acdd5 100644
--- a/segmentation/clitkExtractLungFilter.txx
+++ b/segmentation/clitkExtractLungFilter.txx
@@ -47,6 +47,8 @@
 #include "itkOrientImageFilter.h"
 #include "itkSpatialOrientationAdapter.h"
 #include "itkImageDuplicator.h"
+#include "itkRelabelComponentImageFilter.h"
+
 #include <fcntl.h>
 
 //--------------------------------------------------------------------
@@ -67,6 +69,7 @@ ExtractLungFilter():
   SetForegroundValue(1);
   SetMinimalComponentSize(100);
   VerboseRegionGrowingFlagOff();
+  RemoveSmallLabelBeforeSeparationFlagOn();
 
   // Step 1 default values
   SetUpperThreshold(-300);
@@ -259,6 +262,9 @@ GenerateOutputInformation()
   StartNewStep("Search for the trachea");
   SearchForTrachea();
   PrintMemory(GetVerboseMemoryFlag(), "After SearchForTrachea");
+  if (m_Seeds.empty()) {
+    clitkExceptionMacro("No seeds for trachea... Aborting.");
+  }
 
   //--------------------------------------------------------------------
   //--------------------------------------------------------------------
@@ -433,7 +439,7 @@ GenerateOutputInformation()
     //--------------------------------------------------------------------
     //--------------------------------------------------------------------
     StartNewStep("Separate Left/Right lungs");
-      PrintMemory(GetVerboseMemoryFlag(), "Before Separate");
+    PrintMemory(GetVerboseMemoryFlag(), "Before Separate");
     // Initial label
     working_mask = Labelize<MaskImageType>(working_mask, 
                                           GetBackgroundValue(), 
@@ -448,9 +454,33 @@ GenerateOutputInformation()
     statisticsImageFilter->SetInput(working_mask);
     statisticsImageFilter->Update();
     unsigned int initialNumberOfLabels = statisticsImageFilter->GetMaximum();
-    working_mask = statisticsImageFilter->GetOutput();	
-    
+    working_mask = statisticsImageFilter->GetOutput();	    
     PrintMemory(GetVerboseMemoryFlag(), "After count label");
+
+    // If already 2 labels, but a too big differences, remove the
+    // 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);
+        relabelFilter->SetMinimumObjectSize(10);
+        relabelFilter->Update();
+        const std::vector<float> & a = relabelFilter->GetSizeOfObjectsInPhysicalUnits();
+        std::vector<MaskImagePixelType> remove_label;
+        for(unsigned int i=1; i<a.size(); i++) {
+          if (a[i] < 0.5*a[0]) { // more than 0.5 difference
+            remove_label.push_back(i+1); // label zero is BG
+          }
+        }
+        working_mask = 
+          clitk::RemoveLabels<MaskImageType>(working_mask, GetBackgroundValue(), remove_label);
+        statisticsImageFilter->SetInput(working_mask);
+        statisticsImageFilter->Update();
+        initialNumberOfLabels = statisticsImageFilter->GetMaximum();
+      }
+    }
   
     // Decompose the first label
     if (initialNumberOfLabels<2) {
@@ -628,6 +658,9 @@ SearchForTracheaSeed2(int numberOfSlices)
     opening->Update();
     
     typename SlicerFilterType::Pointer slicer = SlicerFilterType::New();
+#if ITK_VERSION_MAJOR >= 4
+    slicer->SetDirectionCollapseToIdentity();
+#endif
     slicer->SetInput(opening->GetOutput());
     
     // label result
@@ -700,17 +733,20 @@ SearchForTracheaSeed2(int numberOfSlices)
         writer->Update();
       }
 
-      typename LabelImageType::LabelObjectContainerType shapes_map = label_map->GetLabelObjectContainer();
-      typename LabelImageType::LabelObjectContainerType::const_iterator s;
       typename ShapeLabelType::Pointer shape, max_e_shape;
       double max_elongation = GetMaxElongation();
       double max_size = size[0]*size[1]/128;
       double max_e = 0;
       int nshapes = 0;
-      for (s = shapes_map.begin(); s != shapes_map.end(); s++) {
-        shape = s->second;
-        if (shape->GetSize() > 150 && shape->GetSize() <= max_size) {
+      unsigned int nlables = label_map->GetNumberOfLabelObjects();
+      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++;
@@ -763,6 +799,11 @@ SearchForTracheaSeed2(int numberOfSlices)
         
         prev_e_centre= max_e_centre;
       }
+      else {
+        if (GetVerboseRegionGrowingFlag()) {
+          cout << "No shapes found at slice " << index[2] << std::endl;
+        }
+      }
     }
     
     size_t longest = 0;
@@ -775,9 +816,11 @@ SearchForTracheaSeed2(int numberOfSlices)
       }
     }
     
-    if (GetVerboseRegionGrowingFlag()) 
-      std::cout << "seed at: " << trachea_centre << std::endl;
-    m_Seeds.push_back(trachea_centre);
+    if (longest > 0) {
+      if (GetVerboseRegionGrowingFlag()) 
+        std::cout << "seed at: " << trachea_centre << std::endl;
+      m_Seeds.push_back(trachea_centre);
+    }
   }
   
   return (m_Seeds.size() != 0);
@@ -799,7 +842,7 @@ TracheaRegionGrowing()
   f->SetUpper(GetUpperThresholdForTrachea());
   f->SetMinimumLowerThreshold(-2000);
   //  f->SetMaximumUpperThreshold(0); // MAYBE TO CHANGE ???
-  f->SetMaximumUpperThreshold(-700); // MAYBE TO CHANGE ???
+  f->SetMaximumUpperThreshold(-300); // MAYBE TO CHANGE ???
   f->SetAdaptLowerBorder(false);
   f->SetAdaptUpperBorder(true);
   f->SetMinimumSize(5000); 
@@ -889,16 +932,17 @@ SearchForTrachea()
             std::cout << "\t Found trachea with volume " << volume << " cc." << std::endl;
           }
         }
-        else {
-          if (GetVerboseStepFlag()) {
-            std::cout << "\t The volume of the trachea (" << volume 
-                      << " cc) seems not correct. I skip some slices (" << skip << ") and restart to find seeds." 
-                      << std::endl;
-          }
-          skip += 5;
-          stop = false;
-          // empty the list of seed
-          m_Seeds.clear();
+        else 
+          if (GetTracheaSeedAlgorithm() == 0) {
+            if (GetVerboseStepFlag()) {
+              std::cout << "\t The volume of the trachea (" << volume 
+                        << " cc) seems not correct. I skip some slices (" << skip << ") and restart to find seeds." 
+                        << std::endl;
+            }
+            skip += 5;
+            stop = false;
+            // 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