X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStationsGenericFilter.txx;h=9dfa850f67eb7e20683f6f38521b78ef2e5231d9;hb=dad240d633996ba10087d96ece317415086f5a59;hp=2644c1fc99153a50c7694150e8c91dabcc39de35;hpb=e008d74b0ecdc4ca2eaae8c429901a78f9ef5c31;p=clitk.git

diff --git a/segmentation/clitkExtractLymphStationsGenericFilter.txx b/segmentation/clitkExtractLymphStationsGenericFilter.txx
index 2644c1f..9dfa850 100644
--- a/segmentation/clitkExtractLymphStationsGenericFilter.txx
+++ b/segmentation/clitkExtractLymphStationsGenericFilter.txx
@@ -28,7 +28,7 @@ clitk::ExtractLymphStationsGenericFilter<ArgsInfoType>::ExtractLymphStationsGene
 {
   // Default values
   cmdline_parser_clitkExtractLymphStations_init(&mArgsInfo);
-  InitializeImageType<3>();
+  InitializeImageType<3>(); // Only for 3D images
 }
 //--------------------------------------------------------------------
 
@@ -38,10 +38,7 @@ template<class ArgsInfoType>
 template<unsigned int Dim>
 void clitk::ExtractLymphStationsGenericFilter<ArgsInfoType>::InitializeImageType() 
 {  
-  ADD_IMAGE_TYPE(Dim, uchar);
-  // ADD_IMAGE_TYPE(Dim, short);
-  // ADD_IMAGE_TYPE(Dim, int);
-  // ADD_IMAGE_TYPE(Dim, float);
+  ADD_IMAGE_TYPE(Dim, short); // Can add float later
 }
 //--------------------------------------------------------------------
   
@@ -53,9 +50,23 @@ void clitk::ExtractLymphStationsGenericFilter<ArgsInfoType>::SetArgsInfo(const A
   mArgsInfo=a;
   SetIOVerbose(mArgsInfo.verbose_flag);
   if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
-  if (mArgsInfo.mediastinum_given) AddInputFilename(mArgsInfo.mediastinum_arg);
-  if (mArgsInfo.trachea_given) AddInputFilename(mArgsInfo.trachea_arg);
-  if (mArgsInfo.output_given)  AddOutputFilename(mArgsInfo.output_arg);
+  if (mArgsInfo.input_given) AddInputFilename(mArgsInfo.input_arg);
+  if (mArgsInfo.output_given) AddOutputFilename(mArgsInfo.output_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class FilterType>
+void 
+clitk::ExtractLymphStationsGenericFilter<ArgsInfoType>::
+SetOptionsFromArgsInfoToFilter(FilterType * f)
+{
+  f->SetVerboseOption(mArgsInfo.verbose_flag);
+  f->SetVerboseStep(mArgsInfo.verboseStep_flag);
+  f->SetWriteStep(mArgsInfo.writeStep_flag);
+  f->SetAFDBFilename(mArgsInfo.afdb_arg);  
 }
 //--------------------------------------------------------------------
 
@@ -68,31 +79,24 @@ template<class ImageType>
 void clitk::ExtractLymphStationsGenericFilter<ArgsInfoType>::UpdateWithInputImageType() 
 { 
   // Reading input
-  typename ImageType::Pointer mediastinum = this->template GetInput<ImageType>(0);
-  typename ImageType::Pointer trachea = this->template GetInput<ImageType>(1);
+  typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
 
   // Create filter
   typedef clitk::ExtractLymphStationsFilter<ImageType> FilterType;
   typename FilterType::Pointer filter = FilterType::New();
     
   // Set global Options 
-  filter->SetInputMediastinumLabelImage(mediastinum, 0); // change 0 with BG 
-  filter->SetInputTracheaLabelImage(trachea, 0); // change 0 with BG 
-  filter->SetArgsInfo(mArgsInfo);
+  filter->SetInput(input);
+  SetOptionsFromArgsInfoToFilter<FilterType>(filter);
 
   // Go !
   filter->Update();
-  
-  // Check if error
-  if (filter->HasError()) {
-    SetLastError(filter->GetLastError());
-    // No output
-    return;
-  }
 
   // Write/Save results
-  typename ImageType::Pointer output = filter->GetOutput();
-  this->template SetNextOutput<ImageType>(output); 
+  typedef uchar MaskImagePixelType;
+  typedef itk::Image<MaskImagePixelType, 3> OutputImageType;
+  typename OutputImageType::Pointer output = filter->GetOutput();
+  this->template SetNextOutput<OutputImageType>(output); 
 }
 //--------------------------------------------------------------------