Inherits from ImageToImageGenericFilter

[clitk.git] / segmentation / clitkExtractLungFilter.txx

diff --git a/segmentation/clitkExtractLungFilter.txx b/segmentation/clitkExtractLungFilter.txx
index 2c7be4c3546fb80629a7b25af8667981582e27e5..e4aa902ee6cd2f81d91de731506a34b6dad6baab 100644 (file)
--- a/segmentation/clitkExtractLungFilter.txx
+++ b/segmentation/clitkExtractLungFilter.txx
@@ -22,7 +22,7 @@
 // clitk
 #include "clitkImageCommon.h"
 #include "clitkSetBackgroundImageFilter.h"
-#include "clitkSegmentationFunctions.h"
+#include "clitkSegmentationUtils.h"
 #include "clitkAutoCropFilter.h"
 
 // itk
@@ -38,6 +38,7 @@ ExtractLungFilter():
   clitk::FilterBase(),
   itk::ImageToImageFilter<TInputImageType, TMaskImageType>()
 {
+  SetNumberOfSteps(10);
   // Default global options
   this->SetNumberOfRequiredInputs(2);
   SetPatientMaskBackgroundValue(0);
@@ -154,18 +155,20 @@ GenerateOutputInformation()
 { 
   input   = dynamic_cast<const TInputImageType*>(itk::ProcessObject::GetInput(0));
   Superclass::GenerateOutputInformation();
-//   MaskImagePointer output = this->GetOutput(0);
 
   // Get input pointers
   input   = dynamic_cast<const TInputImageType*>(itk::ProcessObject::GetInput(0));
   patient = dynamic_cast<const TMaskImageType*>(itk::ProcessObject::GetInput(1));
 
   // Check image
-  if (!HasSameSizeAndSpacing<TInputImageType, TMaskImageType>(input, patient)) {
+  if (!HaveSameSizeAndSpacing<TInputImageType, TMaskImageType>(input, patient)) {
     this->SetLastError("* ERROR * the images (input and patient mask) must have the same size & spacing");
     return;
   }
   
+  // Set Number of steps
+  SetNumberOfSteps(9);
+  
   //--------------------------------------------------------------------
   //--------------------------------------------------------------------
   StartNewStep("Set background to initial image");
@@ -209,6 +212,7 @@ GenerateOutputInformation()
   //--------------------------------------------------------------------
   //--------------------------------------------------------------------
   StartNewStep("Find the trachea");
+  //DD(m_Seeds.size());
   if (m_Seeds.size() == 0) { // try to find seed
     // Search seed (parameters = UpperThresholdForTrachea)
     static const unsigned int Dim = InputImageType::ImageDimension;
@@ -219,18 +223,21 @@ GenerateOutputInformation()
     sliceRegionSize[Dim-1]=5;
     sliceRegion.SetSize(sliceRegionSize);
     sliceRegion.SetIndex(sliceRegionIndex);
-    
+    //DD(GetUpperThresholdForTrachea());
+    //DD(sliceRegion);
     typedef  itk::ImageRegionConstIterator<InputImageType> IteratorType;
     IteratorType it(working_input, sliceRegion);
     it.GoToBegin();
     while (!it.IsAtEnd()) {
       if(it.Get() < GetUpperThresholdForTrachea() ) {
         AddSeed(it.GetIndex());
+       //      DD(it.GetIndex());
       }
       ++it;
     }
   }
   
+  //DD(m_Seeds.size());
   if (m_Seeds.size() != 0) {
     // Explosion controlled region growing
     typedef clitk::ExplosionControlledThresholdConnectedImageFilter<InputImageType, InternalImageType> ImageFilterType;
@@ -360,10 +367,10 @@ GenerateOutputInformation()
   //--------------------------------------------------------------------
   //--------------------------------------------------------------------
   StartNewStep("Croping lung");
-  cropFilter = CropFilterType::New(); // Needed to reset pipeline
-  cropFilter->SetInput(working_image);
-  cropFilter->Update();   
-  working_image = cropFilter->GetOutput();
+  typename CropFilterType::Pointer cropFilter2 = CropFilterType::New(); // Needed to reset pipeline
+  cropFilter2->SetInput(working_image);
+  cropFilter2->Update();   
+  working_image = cropFilter2->GetOutput();
   StopCurrentStep<InternalImageType>(working_image);
 
   //--------------------------------------------------------------------