clitkExtractLung - new option

- doNotSeparateLungs

diff --git a/segmentation/clitkExtractLung.ggo b/segmentation/clitkExtractLung.ggo
index 12dd3e7040823c00e0676c005d95ec63d7522c94..98ddbd80d3dc29f1dcb53355d663a6dc7e1a4638 100644 (file)
--- a/segmentation/clitkExtractLung.ggo
+++ b/segmentation/clitkExtractLung.ggo
@@ -61,4 +61,7 @@ section "Step 6 : fill holes"
 option "doNotFillHoles"                -  "Do not fill holes if set"                 flag on
 option "dir"                   d  "Directions (axes) to perform filling (defaults to 2,1,0)"   int multiple no
 
+section "Step 7 : lung separation (labelling)"
+option "doNotSeparateLungs"   -  "Do not separate lungs if set"                 flag off
+
 option "noAutoCrop"    -       "If set : do no crop final mask to BoundingBox"                         flag    off

diff --git a/segmentation/clitkExtractLungFilter.h b/segmentation/clitkExtractLungFilter.h
index fa472ba711db3bff2c7ed8094380fc6b3505936c..23fbbc7a8fd427a8f5f749aaee81c69eae275064 100644 (file)
--- a/segmentation/clitkExtractLungFilter.h
+++ b/segmentation/clitkExtractLungFilter.h
@@ -191,6 +191,11 @@ namespace clitk {
     itkGetConstMacro(FillHolesFlag, bool);
     itkBooleanMacro(FillHolesFlag);
 
+    // Separate lungs
+    itkSetMacro(SeparateLungsFlag, bool);
+    itkGetConstMacro(SeparateLungsFlag, bool);
+    itkBooleanMacro(SeparateLungsFlag);
+
     // Step Auto Crop
     itkSetMacro(AutoCrop, bool);
     itkGetConstMacro(AutoCrop, bool);
@@ -250,6 +255,8 @@ namespace clitk {
     bool m_FillHolesFlag;    
     InputImageSizeType m_FillHolesDirections;
 
+    bool m_SeparateLungsFlag;
+    
     // Main functions
     virtual void GenerateOutputInformation();
     virtual void GenerateInputRequestedRegion();

diff --git a/segmentation/clitkExtractLungFilter.txx b/segmentation/clitkExtractLungFilter.txx
index 0954c2a3de46a11249c21237b9644e9a4a123404..d2bff5edd5962647512fd2d1070017b17a5dab34 100644 (file)
--- a/segmentation/clitkExtractLungFilter.txx
+++ b/segmentation/clitkExtractLungFilter.txx
@@ -414,49 +414,51 @@ GenerateOutputInformation()
     StopCurrentStep<MaskImageType>(working_mask);
   }
 
-  //--------------------------------------------------------------------
-  //--------------------------------------------------------------------
-  StartNewStep("Separate Left/Right lungs");
-    PrintMemory(GetVerboseMemoryFlag(), "Before Separate");
-  // Initial label
-  working_mask = Labelize<MaskImageType>(working_mask, 
-                                         GetBackgroundValue(), 
-                                         false, 
-                                         GetMinimalComponentSize());
-
-  PrintMemory(GetVerboseMemoryFlag(), "After Labelize");
-
-  // Count the labels
-  typedef itk::StatisticsImageFilter<MaskImageType> StatisticsImageFilterType;
-  typename StatisticsImageFilterType::Pointer statisticsImageFilter=StatisticsImageFilterType::New();
-  statisticsImageFilter->SetInput(working_mask);
-  statisticsImageFilter->Update();
-  unsigned int initialNumberOfLabels = statisticsImageFilter->GetMaximum();
-  working_mask = statisticsImageFilter->GetOutput();   
+  if (GetSeparateLungsFlag()) {
+    //--------------------------------------------------------------------
+    //--------------------------------------------------------------------
+    StartNewStep("Separate Left/Right lungs");
+      PrintMemory(GetVerboseMemoryFlag(), "Before Separate");
+    // Initial label
+    working_mask = Labelize<MaskImageType>(working_mask, 
+                                          GetBackgroundValue(), 
+                                          false, 
+                                          GetMinimalComponentSize());
+
+    PrintMemory(GetVerboseMemoryFlag(), "After Labelize");
+
+    // Count the labels
+    typedef itk::StatisticsImageFilter<MaskImageType> StatisticsImageFilterType;
+    typename StatisticsImageFilterType::Pointer statisticsImageFilter=StatisticsImageFilterType::New();
+    statisticsImageFilter->SetInput(working_mask);
+    statisticsImageFilter->Update();
+    unsigned int initialNumberOfLabels = statisticsImageFilter->GetMaximum();
+    working_mask = statisticsImageFilter->GetOutput(); 
+    
+    PrintMemory(GetVerboseMemoryFlag(), "After count label");
   
-  PrintMemory(GetVerboseMemoryFlag(), "After count label");
- 
-  // Decompose the first label
-  if (initialNumberOfLabels<2) {
-    // Structuring element radius
-    typename ImageType::SizeType radius;
-    for (unsigned int i=0;i<Dim;i++) radius[i]=1;
-    typedef clitk::DecomposeAndReconstructImageFilter<MaskImageType,MaskImageType> DecomposeAndReconstructFilterType;
-    typename DecomposeAndReconstructFilterType::Pointer decomposeAndReconstructFilter=DecomposeAndReconstructFilterType::New();
-    decomposeAndReconstructFilter->SetInput(working_mask);
-    decomposeAndReconstructFilter->SetVerbose(false);
-    decomposeAndReconstructFilter->SetRadius(radius);
-    decomposeAndReconstructFilter->SetMaximumNumberOfLabels(2);
-    decomposeAndReconstructFilter->SetMinimumObjectSize(this->GetMinimalComponentSize());
-    decomposeAndReconstructFilter->SetMinimumNumberOfIterations(1);
-    decomposeAndReconstructFilter->SetBackgroundValue(this->GetBackgroundValue());
-    decomposeAndReconstructFilter->SetForegroundValue(this->GetForegroundValue());
-    decomposeAndReconstructFilter->SetFullyConnected(true);
-    decomposeAndReconstructFilter->SetNumberOfNewLabels(1);
-    decomposeAndReconstructFilter->Update();
-    working_mask = decomposeAndReconstructFilter->GetOutput();      
+    // Decompose the first label
+    if (initialNumberOfLabels<2) {
+      // Structuring element radius
+      typename ImageType::SizeType radius;
+      for (unsigned int i=0;i<Dim;i++) radius[i]=1;
+      typedef clitk::DecomposeAndReconstructImageFilter<MaskImageType,MaskImageType> DecomposeAndReconstructFilterType;
+      typename DecomposeAndReconstructFilterType::Pointer decomposeAndReconstructFilter=DecomposeAndReconstructFilterType::New();
+      decomposeAndReconstructFilter->SetInput(working_mask);
+      decomposeAndReconstructFilter->SetVerbose(false);
+      decomposeAndReconstructFilter->SetRadius(radius);
+      decomposeAndReconstructFilter->SetMaximumNumberOfLabels(2);
+      decomposeAndReconstructFilter->SetMinimumObjectSize(this->GetMinimalComponentSize());
+      decomposeAndReconstructFilter->SetMinimumNumberOfIterations(1);
+      decomposeAndReconstructFilter->SetBackgroundValue(this->GetBackgroundValue());
+      decomposeAndReconstructFilter->SetForegroundValue(this->GetForegroundValue());
+      decomposeAndReconstructFilter->SetFullyConnected(true);
+      decomposeAndReconstructFilter->SetNumberOfNewLabels(1);
+      decomposeAndReconstructFilter->Update();
+      working_mask = decomposeAndReconstructFilter->GetOutput();      
+    }
+    PrintMemory(GetVerboseMemoryFlag(), "After decomposeAndReconstructFilter");
   }
-  PrintMemory(GetVerboseMemoryFlag(), "After decomposeAndReconstructFilter");
 
   // Retain labels ('1' is largset lung, so right. '2' is left)
   typedef itk::ThresholdImageFilter<MaskImageType> ThresholdImageFilterType;

diff --git a/segmentation/clitkExtractLungGenericFilter.txx b/segmentation/clitkExtractLungGenericFilter.txx
index 2dd396fb3a2498fb0a5ff15e3dc01a2bf6af6db8..b40dc28fc49de81bd0a4784fba74158b7dd333f6 100644 (file)
--- a/segmentation/clitkExtractLungGenericFilter.txx
+++ b/segmentation/clitkExtractLungGenericFilter.txx
@@ -108,6 +108,11 @@ SetOptionsFromArgsInfoToFilter(FilterType * f)
     f->SetFillHolesFlag(false);
   else
     f->SetFillHolesFlag(true);
+
+  if (mArgsInfo.doNotSeparateLungs_given)
+    f->SetSeparateLungsFlag(false);
+  else
+    f->SetSeparateLungsFlag(true);
 }
 //--------------------------------------------------------------------