X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractBonesFilter.txx;h=7f59e92f947c25cc41b5d92b101cadcf8d1b0272;hb=df51e4850f784f8f2fbaead7bb82bd6897fb9fab;hp=ef3f9445ad171b4970d2aa8faf4cae1d87231daf;hpb=6e16222234a90c6079a8f4696c92de7349a496bb;p=clitk.git

diff --git a/segmentation/clitkExtractBonesFilter.txx b/segmentation/clitkExtractBonesFilter.txx
index ef3f944..7f59e92 100644
--- a/segmentation/clitkExtractBonesFilter.txx
+++ b/segmentation/clitkExtractBonesFilter.txx
@@ -24,6 +24,7 @@
 #include "clitkSetBackgroundImageFilter.h"
 #include "clitkSegmentationUtils.h"
 #include "clitkAutoCropFilter.h"
+#include "clitkFillMaskFilter.h"
 
 // itk
 #include "itkBinaryThresholdImageFilter.h"
@@ -33,11 +34,12 @@
 #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);
@@ -61,15 +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));
@@ -78,10 +81,10 @@ SetInput(const TInputImageType * image)
 
 
 //--------------------------------------------------------------------
-template <class TInputImageType, class TOutputImageType>
+template <class TInputImageType>
 template<class ArgsInfoType>
 void 
-clitk::ExtractBonesFilter<TInputImageType, TOutputImageType>::
+clitk::ExtractBonesFilter<TInputImageType>::
 SetArgsInfo(ArgsInfoType mArgsInfo)
 {
   SetVerboseOption_GGO(mArgsInfo);
@@ -89,6 +92,9 @@ SetArgsInfo(ArgsInfoType mArgsInfo)
   SetWriteStep_GGO(mArgsInfo);
   SetVerboseWarningOff_GGO(mArgsInfo);
   
+  SetAFDBFilename_GGO(mArgsInfo); 
+  SetOutputBonesFilename_GGO(mArgsInfo);
+
   SetInitialSmoothing_GGO(mArgsInfo);
   SetSmoothingConductanceParameter_GGO(mArgsInfo);
   SetSmoothingNumberOfIterations_GGO(mArgsInfo);
@@ -105,30 +111,34 @@ SetArgsInfo(ArgsInfoType mArgsInfo)
   SetRadius2_GGO(mArgsInfo);
   SetSampleRate2_GGO(mArgsInfo);
   SetAutoCrop_GGO(mArgsInfo);
+  SetFillHoles_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]
@@ -254,6 +264,20 @@ 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]
@@ -274,20 +298,23 @@ 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;
 }
 //--------------------------------------------------------------------