X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractBonesGenericFilter.txx;h=47734300ea11185ba25dbcbb2509a8179a268944;hb=HEAD;hp=5c72672b17249abe3793152276312a1f6300e056;hpb=e008d74b0ecdc4ca2eaae8c429901a78f9ef5c31;p=clitk.git

diff --git a/segmentation/clitkExtractBonesGenericFilter.txx b/segmentation/clitkExtractBonesGenericFilter.txx
index 5c72672..4773430 100644
--- a/segmentation/clitkExtractBonesGenericFilter.txx
+++ b/segmentation/clitkExtractBonesGenericFilter.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 CLITKEXTRACTBONESSGENERICFILTER_TXX
 #define CLITKEXTRACTBONESSGENERICFILTER_TXX
@@ -38,9 +38,9 @@ template<class ArgsInfoType>
 template<unsigned int Dim>
 void clitk::ExtractBonesGenericFilter<ArgsInfoType>::InitializeImageType() 
 {  
-  ADD_IMAGE_TYPE(Dim, short);
+  //ADD_IMAGE_TYPE(Dim, short);
   // ADD_IMAGE_TYPE(Dim, int);
-  // ADD_IMAGE_TYPE(Dim, float);
+  ADD_IMAGE_TYPE(Dim, float);
 }
 //--------------------------------------------------------------------
   
@@ -50,10 +50,54 @@ template<class ArgsInfoType>
 void clitk::ExtractBonesGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a) 
 {
   mArgsInfo=a;
-  SetIOVerbose(mArgsInfo.verbose_flag);
+  this->SetIOVerbose(mArgsInfo.verbose_flag);
   if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
-  if (mArgsInfo.input_given)   AddInputFilename(mArgsInfo.input_arg);
-  if (mArgsInfo.output_given)  AddOutputFilename(mArgsInfo.output_arg);
+  if (mArgsInfo.input_given)   this->AddInputFilename(mArgsInfo.input_arg);
+  if (mArgsInfo.output_given)  this->AddOutputFilename(mArgsInfo.output_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class FilterType>
+void clitk::ExtractBonesGenericFilter<ArgsInfoType>::
+SetOptionsFromArgsInfoToFilter(FilterType * f) 
+{
+  f->SetVerboseOptionFlag(mArgsInfo.verboseOption_flag);
+  f->SetVerboseStepFlag(mArgsInfo.verboseStep_flag);
+  f->SetWriteStepFlag(mArgsInfo.writeStep_flag);
+  f->SetVerboseWarningFlag(!mArgsInfo.verboseWarningOff_flag);
+  f->SetVerboseMemoryFlag(mArgsInfo.verboseMemory_flag);
+
+  if (mArgsInfo.afdb_given)
+    f->SetAFDBFilename(mArgsInfo.afdb_arg);
+
+  f->SetOutputBonesFilename(mArgsInfo.output_arg);
+
+  f->SetInitialSmoothing(mArgsInfo.smooth_flag);
+  f->SetSmoothingConductanceParameter(mArgsInfo.cond_arg);
+  f->SetSmoothingNumberOfIterations(mArgsInfo.iter_arg);
+  f->SetSmoothingTimeStep(mArgsInfo.time_arg);
+  f->SetSmoothingUseImageSpacing(mArgsInfo.spacing_flag);
+
+  f->SetMinimalComponentSize(mArgsInfo.minSize_arg);
+  f->SetUpperThreshold1(mArgsInfo.upper1_arg);
+  f->SetLowerThreshold1(mArgsInfo.lower1_arg);
+  f->SetFullConnectivity(mArgsInfo.full_flag);
+
+  f->SetUpperThreshold2(mArgsInfo.upper2_arg);
+  f->SetLowerThreshold2(mArgsInfo.lower2_arg);
+
+  typename FilterType::InputImageSizeType s;
+  if (mArgsInfo.radius2_given) {
+    ConvertOptionMacro(mArgsInfo.radius2, s, 3, false);
+    f->SetRadius2(s);
+  }
+
+  f->SetSampleRate2(mArgsInfo.sampleRate2_arg);
+  f->SetAutoCrop(!mArgsInfo.noAutoCrop_flag);
+  f->SetFillHoles(!mArgsInfo.doNotFillHoles_flag);
 }
 //--------------------------------------------------------------------
 
@@ -66,32 +110,25 @@ template<class ImageType>
 void clitk::ExtractBonesGenericFilter<ArgsInfoType>::UpdateWithInputImageType() 
 { 
   // Mask & output image type
-  typedef itk::Image<uchar, ImageType::ImageDimension> OutputImageType;
+  typedef itk::Image<uchar, ImageType::ImageDimension> MaskImageType;
 
   // Reading input
   typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
 
   // Create filter
-  typedef clitk::ExtractBonesFilter<ImageType, OutputImageType> FilterType;
+  typedef clitk::ExtractBonesFilter<ImageType> FilterType;
   typename FilterType::Pointer filter = FilterType::New();
     
   // Set global Options 
-  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 OutputImageType::Pointer output = filter->GetOutput();
-  this->template SetNextOutput<OutputImageType>(output); 
+  typename MaskImageType::Pointer output = filter->GetOutput();
+  this->template SetNextOutput<MaskImageType>(output); 
 }
 //--------------------------------------------------------------------