X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=segmentation%2FclitkExtractPatientFilter.txx;h=97f79c5e9050bdcf1b5b4d2275ad0a32e73c60f8;hb=aa424793243b9b210a0d009f5cb8031db985549a;hp=00e31653afce00e5ea32c5a91a1218fbe39251fa;hpb=5d07c6f09eee2f55347c6722c16c1f81de28e747;p=clitk.git

diff --git a/segmentation/clitkExtractPatientFilter.txx b/segmentation/clitkExtractPatientFilter.txx
index 00e3165..97f79c5 100644
--- a/segmentation/clitkExtractPatientFilter.txx
+++ b/segmentation/clitkExtractPatientFilter.txx
@@ -48,6 +48,7 @@ ExtractPatientFilter():
   this->SetNumberOfRequiredInputs(1);
   SetBackgroundValue(0); // Must be zero
   SetForegroundValue(1);
+  SetPrimaryOpeningRadius(0);
 
   // Step 1: Threshold + CC + sort (Find low density areas)
   SetUpperThreshold(-300);
@@ -116,6 +117,7 @@ GenerateOutputInformation() {
   StartNewStep("Find low densities areas");
 
   // Pad images with air to prevent patient touching the image border
+  // But the lungs can touch the outside air. In such case, use primaryOpeningRadius with 1 kernel
   typedef itk::ConstantPadImageFilter<InputImageType, InputImageType> PadFilterType;
   typename PadFilterType::Pointer padFilter = PadFilterType::New();
   padFilter->SetInput(input);
@@ -126,7 +128,8 @@ GenerateOutputInformation() {
   bounds[Dim - 1] = 0;
   padFilter->SetPadLowerBound(bounds);
   padFilter->SetPadUpperBound(bounds);
-
+  padFilter->Update();
+  
   typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> BinarizeFilterType;
   typename BinarizeFilterType::Pointer binarizeFilter=BinarizeFilterType::New();
   binarizeFilter->SetInput(padFilter->GetOutput());
@@ -134,20 +137,47 @@ GenerateOutputInformation() {
   binarizeFilter->SetUpperThreshold(GetUpperThreshold());
   binarizeFilter ->SetInsideValue(this->GetForegroundValue());
   binarizeFilter ->SetOutsideValue(this->GetBackgroundValue());
+  padFilter->GetOutput()->ReleaseData();
+  working_image = binarizeFilter->GetOutput();
+
+  typedef itk::BinaryBallStructuringElement<InternalPixelType,Dim> KernelType;
+  unsigned int radius = this->GetPrimaryOpeningRadius();
+  if (radius > 0)
+  {
+    if (this->GetVerboseOptionFlag()) std::cout << ("Opening after threshold; R = ") << radius << std::endl;
+    KernelType kernel;
+    kernel.SetRadius(radius);
+    
+    typedef itk::BinaryMorphologicalOpeningImageFilter<InternalImageType, InternalImageType , KernelType> OpenFilterType2;
+    typename OpenFilterType2::Pointer openFilter2 = OpenFilterType2::New();
+    openFilter2->SetInput(working_image);
+    openFilter2->SetBackgroundValue(0);
+    openFilter2->SetForegroundValue(1);
+    openFilter2->SetKernel(kernel);
+    openFilter2->Update();
+    working_image->ReleaseData();
+    working_image = openFilter2->GetOutput();
+  }
 
+  if (this->GetVerboseOptionFlag()) std::cout << ("Labelling") << std::endl;
   // Connected component labeling
   typedef itk::ConnectedComponentImageFilter<InternalImageType, InternalImageType> ConnectFilterType;
   typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
-  connectFilter->SetInput(binarizeFilter->GetOutput());
+  connectFilter->SetInput(working_image);
   connectFilter->SetBackgroundValue(this->GetBackgroundValue());
   connectFilter->SetFullyConnected(false);
+  connectFilter->Update();
+  working_image->ReleaseData();
+  working_image = connectFilter->GetOutput();
 
+  if (this->GetVerboseOptionFlag()) std::cout << ("RelabelComponentImageFilter") << std::endl;
   // Sort labels according to size
   typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelFilterType;
   typename RelabelFilterType::Pointer relabelFilter=RelabelFilterType::New();
   relabelFilter->InPlaceOn();
   relabelFilter->SetInput(connectFilter->GetOutput());
   relabelFilter->Update();
+  working_image->ReleaseData();
   working_image = relabelFilter->GetOutput();
 
   // End
@@ -169,12 +199,14 @@ GenerateOutputInformation() {
     f->SetFullyConnected(true);
     f->SetNumberOfNewLabels(GetNumberOfNewLabels1());
     f->Update();
+    working_image->ReleaseData();
     working_image = f->GetOutput();
     StopCurrentStep<InternalImageType>(working_image);
   }
 
   //--------------------------------------------------------------------
   //--------------------------------------------------------------------
+  if (this->GetVerboseOptionFlag()) std::cout << ("Remove the air (largest area)") << std::endl;
   StartNewStep("Remove the air (largest area)");
   typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> iBinarizeFilterType;
   typename iBinarizeFilterType::Pointer binarizeFilter2 = iBinarizeFilterType::New();
@@ -183,16 +215,22 @@ GenerateOutputInformation() {
   binarizeFilter2->SetUpperThreshold(GetLastKeep());
   binarizeFilter2 ->SetInsideValue(0);
   binarizeFilter2 ->SetOutsideValue(1);
-  //  binarizeFilter2 ->Update(); // NEEDED ?
+  binarizeFilter2 ->Update();
+  working_image->ReleaseData();
+  working_image = binarizeFilter2->GetOutput();
 
   typename ConnectFilterType::Pointer connectFilter2 = ConnectFilterType::New();
-  connectFilter2->SetInput(binarizeFilter2->GetOutput());
+  connectFilter2->SetInput(working_image);
   connectFilter2->SetBackgroundValue(this->GetBackgroundValue());
   connectFilter2->SetFullyConnected(false);
+  connectFilter2->Update();
+  working_image->ReleaseData();
+  working_image = connectFilter2->GetOutput();
 
   typename RelabelFilterType::Pointer relabelFilter2 = RelabelFilterType::New();
-  relabelFilter2->SetInput(connectFilter2->GetOutput());
+  relabelFilter2->SetInput(working_image);
   relabelFilter2->Update();
+  working_image->ReleaseData();
   working_image = relabelFilter2->GetOutput();
 
   // Keep main label
@@ -216,6 +254,7 @@ GenerateOutputInformation() {
     f->SetFullyConnected(true);
     f->SetNumberOfNewLabels(GetNumberOfNewLabels2());
     f->Update();
+    working_image->ReleaseData();
     working_image = f->GetOutput();
     StopCurrentStep<InternalImageType>(working_image);
   }
@@ -226,7 +265,6 @@ GenerateOutputInformation() {
   if (GetFinalOpenClose()) {
     StartNewStep("Final OpenClose");
     // Open
-    typedef itk::BinaryBallStructuringElement<InternalPixelType,Dim> KernelType;
     KernelType structuringElement;
     structuringElement.SetRadius(1);
     structuringElement.CreateStructuringElement();
@@ -245,6 +283,7 @@ GenerateOutputInformation() {
     //  closeFilter->SetBackgroundValue(SetBackgroundValue());
     closeFilter->SetKernel(structuringElement);
     closeFilter->Update();
+    working_image->ReleaseData();
     working_image = closeFilter->GetOutput();
     StopCurrentStep<InternalImageType>(working_image);
   }
@@ -256,6 +295,7 @@ GenerateOutputInformation() {
   typename CastImageFilterType::Pointer caster= CastImageFilterType::New();
   caster->SetInput(working_image);
   caster->Update();
+  working_image->ReleaseData();
   output = caster->GetOutput();
 
   //--------------------------------------------------------------------
@@ -268,6 +308,7 @@ GenerateOutputInformation() {
     cropFilter->SetInput(output);
     cropFilter->SetBackgroundValue(GetBackgroundValue());
     cropFilter->Update();
+    output->ReleaseData();
     output = cropFilter->GetOutput();
     StopCurrentStep<MaskImageType>(output);
   }
@@ -280,6 +321,7 @@ GenerateOutputInformation() {
     cropFilter->SetLowerBoundaryCropSize(bounds);
     cropFilter->SetUpperBoundaryCropSize(bounds);
     cropFilter->Update();
+    output->ReleaseData();
     output = cropFilter->GetOutput();
   }
 }