Debug RTStruct conversion with empty struc

[clitk.git] / segmentation / clitkExtractPatientGenericFilter.txx

diff --git a/segmentation/clitkExtractPatientGenericFilter.txx b/segmentation/clitkExtractPatientGenericFilter.txx
index 26252deb364edbe6d1a6600837779999ce156601..ae87cc8363afc36d6225d90cb36fef33505dec6b 100644 (file)
--- a/segmentation/clitkExtractPatientGenericFilter.txx
+++ b/segmentation/clitkExtractPatientGenericFilter.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
-  ======================================================================-====*/
+  ===========================================================================**/
 
 #include "clitkImageCommon.h"
 
@@ -36,6 +36,8 @@ template<unsigned int Dim>
 void clitk::ExtractPatientGenericFilter<ArgsInfoType>::InitializeImageType() 
 {  
   ADD_IMAGE_TYPE(Dim, short);
+  ADD_IMAGE_TYPE(Dim, unsigned short);
+  ADD_IMAGE_TYPE(Dim, float);
   // ADD_IMAGE_TYPE(Dim, int);
   // ADD_IMAGE_TYPE(Dim, float);
 }
@@ -47,10 +49,64 @@ template<class ArgsInfoType>
 void clitk::ExtractPatientGenericFilter<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)  SetInputFilename(mArgsInfo.input_arg);
-  if (mArgsInfo.output_given)  AddOutputFilename(mArgsInfo.output_arg);
+  if (mArgsInfo.input_given)  this->SetInputFilename(mArgsInfo.input_arg);
+  if (mArgsInfo.output_given)  this->AddOutputFilename(mArgsInfo.output_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class FilterType>
+void 
+clitk::ExtractPatientGenericFilter<ArgsInfoType>::
+SetOptionsFromArgsInfoToFilter(FilterType * f)
+{
+  f->SetVerboseOptionFlag(mArgsInfo.verbose_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->SetOutputPatientFilename(mArgsInfo.output_arg);
+
+  f->SetUpperThreshold(mArgsInfo.upper_arg);
+  f->SetLowerThreshold(mArgsInfo.lower_arg);
+  f->SetPrimaryOpeningRadius(mArgsInfo.openingRadius_arg);
+
+  f->SetDecomposeAndReconstructDuringFirstStep(mArgsInfo.erode1_flag);
+
+  // Convert to SizeType
+  typename FilterType::InputImageSizeType s;
+  if (mArgsInfo.radius1_given) {
+    ConvertOptionMacro(mArgsInfo.radius1, s, 3, false);
+    f->SetRadius1(s);
+  }
+
+  f->SetMaximumNumberOfLabels1(mArgsInfo.max1_arg);
+  f->SetNumberOfNewLabels1(mArgsInfo.new1_arg);
+
+  f->SetDecomposeAndReconstructDuringSecondStep(mArgsInfo.erode2_flag);
+
+  // Convert to SizeType
+  if (mArgsInfo.radius2_given) {
+    ConvertOptionMacro(mArgsInfo.radius2, s, 3, false);
+    f->SetRadius2(s);
+  }
+
+  f->SetMaximumNumberOfLabels2(mArgsInfo.max2_arg);
+  f->SetNumberOfNewLabels2(mArgsInfo.new2_arg);
+  
+  f->SetFirstKeep(mArgsInfo.firstKeep_arg);
+  f->SetLastKeep(mArgsInfo.lastKeep_arg);
+
+  f->SetFinalOpenClose(mArgsInfo.openClose_flag);
+  f->SetAutoCrop(!mArgsInfo.noAutoCrop_flag);
 }
 //--------------------------------------------------------------------
 
@@ -69,22 +125,18 @@ void clitk::ExtractPatientGenericFilter<ArgsInfoType>::UpdateWithInputImageType(
   typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
 
   // Create filter
-  typedef clitk::ExtractPatientFilter<ImageType, OutputImageType> FilterType;
+  typedef clitk::ExtractPatientFilter<ImageType> FilterType;
   typename FilterType::Pointer filter = FilterType::New();
     
+  // Set the filter (needed for example for threaded monitoring)
+  this->SetFilterBase(filter);
+    
   // 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();