Debug RTStruct conversion with empty struc

[clitk.git] / segmentation / clitkExtractBonesFilter.txx

diff --git a/segmentation/clitkExtractBonesFilter.txx b/segmentation/clitkExtractBonesFilter.txx
index 00f72f21b204695e7b9e65ce7187868554d98afc..e00945e14fcc9cdcb98903b4cf988f191ebd06e3 100644 (file)
--- a/segmentation/clitkExtractBonesFilter.txx
+++ b/segmentation/clitkExtractBonesFilter.txx
@@ -3,7 +3,7 @@
 
   Authors belong to: 
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
 
   This software is distributed WITHOUT ANY WARRANTY; without even
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ======================================================================-====*/
+  ===========================================================================**/
 
 #ifndef CLITKEXTRACTBONESSFILTER_TXX
 #define CLITKEXTRACTBONESSFILTER_TXX
@@ -24,24 +24,33 @@
 #include "clitkSetBackgroundImageFilter.h"
 #include "clitkSegmentationUtils.h"
 #include "clitkAutoCropFilter.h"
+#include "clitkFillMaskFilter.h"
 
 // itk
 #include "itkBinaryThresholdImageFilter.h"
 #include "itkConnectedComponentImageFilter.h"
 #include "itkRelabelComponentImageFilter.h"
 #include "itkNeighborhoodConnectedImageFilter.h"
+#include "itkCurvatureAnisotropicDiffusionImageFilter.h"
 
 //--------------------------------------------------------------------
-template <class TInputImageType, class TOutputImageType>
-clitk::ExtractBonesFilter<TInputImageType, TOutputImageType>::
+template <class TInputImageType>
+clitk::ExtractBonesFilter<TInputImageType>::
 ExtractBonesFilter():
   clitk::FilterBase(),
-  itk::ImageToImageFilter<TInputImageType, TOutputImageType>()
+  clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
+  itk::ImageToImageFilter<TInputImageType, MaskImageType>()
 {
   // Default global options
   this->SetNumberOfRequiredInputs(1);
   SetBackgroundValue(0); // Must be zero
   SetForegroundValue(1);
+  SetInitialSmoothing(false);
+
+  SetSmoothingConductanceParameter(3.0);
+  SetSmoothingNumberOfIterations(5);
+  SetSmoothingTimeStep(0.0625);
+  SetSmoothingUseImageSpacing(false);
 
   SetMinimalComponentSize(100);
   SetUpperThreshold1(1500);
@@ -54,15 +63,16 @@ ExtractBonesFilter():
   s.Fill(1);
   SetRadius2(s);
   SetSampleRate2(0);
-  AutoCropOff();
+  AutoCropOn();
+  FillHolesOn();
 }
 //--------------------------------------------------------------------
 
 
 //--------------------------------------------------------------------
-template <class TInputImageType, class TOutputImageType>
+template <class TInputImageType>
 void 
-clitk::ExtractBonesFilter<TInputImageType, TOutputImageType>::
+clitk::ExtractBonesFilter<TInputImageType>::
 SetInput(const TInputImageType * image) 
 {
   this->SetNthInput(0, const_cast<TInputImageType *>(image));
@@ -70,64 +80,61 @@ SetInput(const TInputImageType * image)
 //--------------------------------------------------------------------
 
 
-//--------------------------------------------------------------------
-template <class TInputImageType, class TOutputImageType>
-template<class ArgsInfoType>
-void 
-clitk::ExtractBonesFilter<TInputImageType, TOutputImageType>::
-SetArgsInfo(ArgsInfoType mArgsInfo)
-{
-  SetVerboseOption_GGO(mArgsInfo);
-  SetVerboseStep_GGO(mArgsInfo);
-  SetWriteStep_GGO(mArgsInfo);
-  SetVerboseWarningOff_GGO(mArgsInfo);
-
-  SetMinimalComponentSize_GGO(mArgsInfo);
-  SetUpperThreshold1_GGO(mArgsInfo);
-  SetLowerThreshold1_GGO(mArgsInfo);
-  SetFullConnectivity_GGO(mArgsInfo);
-
-  SetUpperThreshold2_GGO(mArgsInfo);
-  SetLowerThreshold2_GGO(mArgsInfo);
-  SetRadius2_GGO(mArgsInfo);
-  SetSampleRate2_GGO(mArgsInfo);
-  SetAutoCrop_GGO(mArgsInfo);
-}
-//--------------------------------------------------------------------
-
 
 //--------------------------------------------------------------------
-template <class TInputImageType, class TOutputImageType>
+template <class TInputImageType>
 void 
-clitk::ExtractBonesFilter<TInputImageType, TOutputImageType>::
+clitk::ExtractBonesFilter<TInputImageType>::
 GenerateOutputInformation() { 
+
   // Get input pointers
   InputImagePointer input   = dynamic_cast<TInputImageType*>(itk::ProcessObject::GetInput(0));
-  //  InputImagePointer input = dynamic_cast<TInputImageType*>(itk::ProcessObject::GetInput(0));
   Superclass::GenerateOutputInformation();
-  OutputImagePointer outputImage = this->GetOutput(0);
+  MaskImagePointer outputImage = this->GetOutput(0);
   outputImage->SetRegions(input->GetLargestPossibleRegion());
 
+  // Read DB
+  LoadAFDB();
+
   // typedefs
   typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> InputBinarizeFilterType;
   typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> BinarizeFilterType;
   typedef itk::ConnectedComponentImageFilter<InternalImageType, InternalImageType> ConnectFilterType;
   typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelFilterType;
   typedef clitk::SetBackgroundImageFilter<InternalImageType,InternalImageType, InternalImageType> SetBackgroundFilterType; 
-  typedef itk::CastImageFilter<InternalImageType,OutputImageType> CastImageFilterType; 
-  typedef itk::ImageFileWriter<OutputImageType> WriterType; 
+  typedef itk::CastImageFilter<InternalImageType,MaskImageType> CastImageFilterType; 
+  typedef itk::ImageFileWriter<MaskImageType> WriterType; 
+
+  //---------------------------------
+  // Smoothing [Optional]
+  //---------------------------------
+  if (GetInitialSmoothing()) {
+    StartNewStep("Initial Smoothing");
+    typedef itk::CurvatureAnisotropicDiffusionImageFilter<InputImageType, InputImageType> FilterType;
+    typename FilterType::Pointer df = FilterType::New(); 
+    df->SetConductanceParameter(GetSmoothingConductanceParameter());
+    df->SetNumberOfIterations(GetSmoothingNumberOfIterations());
+    df->SetTimeStep(GetSmoothingTimeStep());
+    df->SetUseImageSpacing(GetSmoothingUseImageSpacing());
+    df->SetInput(input);
+    df->Update();
+    filtered_input = df->GetOutput();
+    StopCurrentStep<InputImageType>(filtered_input);
+  }
+  else {
+    filtered_input = input;
+  }
 
   //--------------------------------------------------------------------
   //--------------------------------------------------------------------
   StartNewStep("Initial Labeling");
-
   typename InternalImageType::Pointer firstLabelImage;
     
   //---------------------------------
   // Binarize the image
   //---------------------------------
   typename InputBinarizeFilterType::Pointer binarizeFilter=InputBinarizeFilterType::New();
-  binarizeFilter->SetInput(input);
+  binarizeFilter->SetInput(filtered_input);
   binarizeFilter->SetLowerThreshold(GetLowerThreshold1());
   binarizeFilter->SetUpperThreshold(GetUpperThreshold1());
   binarizeFilter->SetInsideValue(this->GetForegroundValue());
@@ -160,6 +167,7 @@ GenerateOutputInformation() {
   binarizeFilter2->Update();
 
   firstLabelImage = binarizeFilter2->GetOutput();
+  StopCurrentStep<InternalImageType>(firstLabelImage);
 
   //--------------------------------------------------------------------
   //--------------------------------------------------------------------
@@ -179,7 +187,7 @@ GenerateOutputInformation() {
   neighborhoodConnectedImageFilter->SetUpper(GetUpperThreshold2());
   neighborhoodConnectedImageFilter->SetReplaceValue(this->GetForegroundValue());
   neighborhoodConnectedImageFilter->SetRadius(GetRadius2());
-  neighborhoodConnectedImageFilter->SetInput(input);
+  neighborhoodConnectedImageFilter->SetInput(filtered_input);
 
   // Seeds from label image
   typedef itk::ImageRegionIteratorWithIndex<InternalImageType> IteratorType;
@@ -209,7 +217,7 @@ GenerateOutputInformation() {
 
   //--------------------------------------------------------------------
   //--------------------------------------------------------------------
-  StartNewStep("Combine de images");
+  StartNewStep("Combine the images");
   typedef clitk::SetBackgroundImageFilter<InternalImageType, InternalImageType, InternalImageType> 
     SetBackgroundImageFilterType;
   typename SetBackgroundImageFilterType::Pointer setBackgroundFilter=SetBackgroundImageFilterType::New();
@@ -221,6 +229,20 @@ GenerateOutputInformation() {
 
   output = setBackgroundFilter->GetOutput();
 
+  //--------------------------------------------------------------------
+  //--------------------------------------------------------------------
+  // Fill Bones
+  if (GetFillHoles()) {
+    StartNewStep("Fill Holes");
+    typedef clitk::FillMaskFilter<InternalImageType> FillMaskFilterType;
+    typename FillMaskFilterType::Pointer fillMaskFilter = FillMaskFilterType::New();
+    fillMaskFilter->SetInput(output);
+    fillMaskFilter->AddDirection(2);
+    fillMaskFilter->Update();   
+    output = fillMaskFilter->GetOutput();
+    StopCurrentStep<InternalImageType>(output);
+  }
+
   //--------------------------------------------------------------------
   //--------------------------------------------------------------------
   // [Optional]
@@ -241,20 +263,23 @@ GenerateOutputInformation() {
 
 
 //--------------------------------------------------------------------
-template <class TInputImageType, class TOutputImageType>
+template <class TInputImageType>
 void 
-clitk::ExtractBonesFilter<TInputImageType, TOutputImageType>::
+clitk::ExtractBonesFilter<TInputImageType>::
 GenerateData() {
 
   //--------------------------------------------------------------------
   //--------------------------------------------------------------------
   // Final Cast 
-  typedef itk::CastImageFilter<InternalImageType, OutputImageType> CastImageFilterType;
+  typedef itk::CastImageFilter<InternalImageType, MaskImageType> CastImageFilterType;
   typename CastImageFilterType::Pointer caster= CastImageFilterType::New();
   caster->SetInput(output);
   caster->Update();
-  //this->SetNthOutput(0, caster->GetOutput());
   this->GraftOutput(caster->GetOutput());
+
+  // Store image filenames into AFDB 
+  GetAFDB()->SetImageFilename("Bones", this->GetOutputBonesFilename());  
+  WriteAFDB();
   return;
 }
 //--------------------------------------------------------------------