From: David Sarrut <david.sarrut@creatis.insa-lyon.fr>
Date: Fri, 5 Sep 2014 14:12:14 +0000 (+0200)
Subject: Merge branch 'master' of git.creatis.insa-lyon.fr:clitk
X-Git-Tag: v1.4.0~16^2~10^2
X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=e06bbd15e271bf0a4092b673399d040a5cb25efe;hp=1eb88e752e0985548fc83742ed92ab395f9c77fc;p=clitk.git

Merge branch 'master' of git.creatis.insa-lyon.fr:clitk
---

diff --git a/common/clitkCommon.h b/common/clitkCommon.h
index 2f5b26f..b58974a 100644
--- a/common/clitkCommon.h
+++ b/common/clitkCommon.h
@@ -1,7 +1,7 @@
 /*=========================================================================
   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
 
-  Authors belong to: 
+  Authors belong to:
   - University of LYON              http://www.universite-lyon.fr/
   - Léon Bérard cancer center       http://www.centreleonberard.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
@@ -34,7 +34,7 @@
 #include <fstream>
 
 // Include for "rusage"
-#include <ctime> 
+#include <ctime>
 #if defined(unix) || defined(__APPLE__)
 #  include <sys/time.h>
 #  include <sys/resource.h>
@@ -51,7 +51,7 @@ namespace clitk {
   typedef unsigned char uchar;
   typedef unsigned short ushort;
   typedef unsigned int uint;
-  
+
 #define CLITK_TRY_CATCH_EXIT(func) \
   try { \
     func; \
@@ -68,13 +68,13 @@ namespace clitk {
     std::cout << "Unknown excpetion" << std::endl; \
     exit(-3); \
   }
-    
+
 
   //--------------------------------------------------------------------
   // when everything goes wrong
 #define WHEREAMI "[ " << __FILE__  << " ] line " << __LINE__
-#define FATAL(a) std::cerr << "ERROR in " << WHEREAMI << ": " << a; exit(0);
-  
+#define FATAL(a) { std::cerr << "ERROR in " << WHEREAMI << ": " << a; exit(0); }
+
   //--------------------------------------------------------------------
   // GGO with modified struct name
 #define GGO(ggo_filename, args_info)                                    \
@@ -82,7 +82,7 @@ namespace clitk {
   cmdline_parser_##ggo_filename##2(argc, argv, &args_info, 1, 1, 0);			\
   if (args_info.config_given)						\
     cmdline_parser_##ggo_filename##_configfile (args_info.config_arg, &args_info, 0, 0, 1); \
-  else cmdline_parser_##ggo_filename(argc, argv, &args_info);  
+  else cmdline_parser_##ggo_filename(argc, argv, &args_info);
 
   //--------------------------------------------------------------------
   // skip line with #
@@ -95,15 +95,15 @@ namespace clitk {
   //--------------------------------------------------------------------
   // Return filename extension
   std::string GetExtension(const std::string& filename);
-  
+
   //--------------------------------------------------------------------
   // Convert float, double ... to string
   template<class T> std::string toString(const T & t);
   template<class T> std::string toStringVector(const T * t, const int n);
   template<class T> std::string toStringVector(const T & t, const int n);
   template<class T> std::string toStringVector(const std::vector<T> & t);
-  template <class T> bool fromString(T& t, 
-                                     const std::string& s, 
+  template <class T> bool fromString(T& t,
+                                     const std::string& s,
                                      std::ios_base& (*f)(std::ios_base&)=std::dec);
 
   //--------------------------------------------------------------------
@@ -129,7 +129,7 @@ namespace clitk {
   // Return the name of a type as a string
   template<class TPixel>
   std::string GetTypeAsString();
-  
+
   //--------------------------------------------------------------------
   // Convert radian / degree
   double rad2deg(double anglerad);
@@ -152,13 +152,13 @@ namespace clitk {
   std::string CreateListOfTypes(bool last=true) {
     return GetTypeAsString<T1>();
   }
-  
+
   template<class T1, class T2>
   std::string CreateListOfTypes(bool last=true) {
     if (last) return CreateListOfTypes<T1>()+" and "+CreateListOfTypes<T2>();
     else return CreateListOfTypes<T1>()+", "+CreateListOfTypes<T2>();
   }
-  
+
   template<class T1, class T2, class T3>
   std::string CreateListOfTypes(bool last=true) {
     if (last) return CreateListOfTypes<T1,T2>(false)+" and "+CreateListOfTypes<T3>();
@@ -195,7 +195,7 @@ namespace clitk {
     else return CreateListOfTypes<T1,T2,T3,T4,T5,T6,T7>(false)+", "+CreateListOfTypes<T8>();
   }
   //--------------------------------------------------------------------
-  
+
   //--------------------------------------------------------------------
   void FindAndReplace(std::string & line, const std::string & tofind, const std::string & replacement);
   void FindAndReplace(std::string & line, const std::vector<std::string> & tofind, const std::vector<std::string> & toreplace);
@@ -203,8 +203,8 @@ namespace clitk {
   //--------------------------------------------------------------------
 
   //--------------------------------------------------------------------
-  double ComputeEuclideanDistanceFromPointToPlane(const itk::ContinuousIndex<double, 3> point, 
-						  const itk::ContinuousIndex<double, 3> pointInPlane, 
+  double ComputeEuclideanDistanceFromPointToPlane(const itk::ContinuousIndex<double, 3> point,
+						  const itk::ContinuousIndex<double, 3> pointInPlane,
 						  const itk::ContinuousIndex<double, 3> normalPlane);
 
   //--------------------------------------------------------------------
@@ -232,9 +232,9 @@ namespace clitk {
 
   //--------------------------------------------------------------------
   // Convert a map to a vector
-  template <typename M, typename V> 
+  template <typename M, typename V>
   void MapToVecFirst(const M & m, V & v);
-  template <typename M, typename V> 
+  template <typename M, typename V>
   void MapToVecSecond(const M & m, V & v);
 
   //--------------------------------------------------------------------
@@ -247,4 +247,3 @@ namespace clitk {
 } // end namespace
 
 #endif /* end #define CLITKCOMMON_H */
-
diff --git a/common/clitkDD.h b/common/clitkDD.h
index 97ba443..c5a9996 100644
--- a/common/clitkDD.h
+++ b/common/clitkDD.h
@@ -38,6 +38,6 @@
   template<class T>
     void _print_container(T const& a)
     { for(typename T::const_iterator i=a.begin();i!=a.end();++i) { std::cout << *i << " "; };}
-#define DDS(a) { std::cout << #a " = [ "; _print_container(a) ; std::cout << " ]" << std::endl;std::cout.flush():}
+#define DDS(a) { std::cout << #a " = [ "; _print_container(a) ; std::cout << " ]" << std::endl;std::cout.flush();}
 
 #endif
diff --git a/common/clitkTimer.cxx b/common/clitkTimer.cxx
index cd74428..329ca13 100644
--- a/common/clitkTimer.cxx
+++ b/common/clitkTimer.cxx
@@ -64,13 +64,15 @@ void clitk::Timer::Stop(bool accumulate)
     mElapsed += (mEnd.ru_utime.tv_usec - mBegin.ru_utime.tv_usec)+
                 (mEnd.ru_utime.tv_sec - mBegin.ru_utime.tv_sec)*1000000;
   }
+  else
 #elif defined(_WIN32)
   QueryPerformanceCounter((LARGE_INTEGER*)&mEnd);
   if (accumulate) {
     mElapsed += ((mEnd-mBegin)*1000000)/(long double)mFrequency;
   }
+  else
 #endif
-  else {
+  {
     mNumberOfCall--;
   }
 }
@@ -114,4 +116,3 @@ void clitk::Timer::Reset()
 
 // #endif // If UNIX
 #endif /* end #define CLITKTIMER_CXX */
-
diff --git a/itk/clitkInvertVFFilter.txx b/itk/clitkInvertVFFilter.txx
index 34500a3..e26fed7 100644
--- a/itk/clitkInvertVFFilter.txx
+++ b/itk/clitkInvertVFFilter.txx
@@ -145,7 +145,7 @@ void HelperClass1<InputImageType, OutputImageType>::ThreadedGenerateData(const O
   typedef typename OutputImageType::PixelType DisplacementType;
   DisplacementType displacement;
   inputIt.GoToBegin();
-  
+
   typename OutputImageType::SizeType size = outputPtr->GetLargestPossibleRegion().GetSize();
 
   //define some temp variables
@@ -199,7 +199,7 @@ void HelperClass1<InputImageType, OutputImageType>::ThreadedGenerateData(const O
             overlap *= 1.0 - distance[dim];
           }
           upper >>= 1;
-          
+
           if (neighIndex[dim] >= size[dim])
             neighIndex[dim] = size[dim] - 1;
         }
@@ -320,7 +320,10 @@ protected:
 //Empty constructor
 template<class InputImageType, class OutputImageType > HelperClass2<InputImageType, OutputImageType>::HelperClass2()
 {
-  m_EdgePaddingValue=itk::NumericTraits<PixelType>::Zero;
+  PixelType zero;
+  for(unsigned int i=0;i <PixelType::Dimension; i++) zero[i] = 0.0;
+  m_EdgePaddingValue=zero;
+  //m_EdgePaddingValue=itk::NumericTraits<PixelType>::Zero;
 }
 
 
@@ -333,7 +336,7 @@ template<class InputImageType, class OutputImageType > void HelperClass2<InputIm
 #endif
 {
 //   std::cout << "HelperClass2::ThreadedGenerateData - IN " << threadId << std::endl;
-  
+
   //Get pointer to the input
   typename InputImageType::ConstPointer inputPtr = this->GetInput();
 
@@ -383,9 +386,9 @@ template<class InputImageType, class OutputImageType > void HelperClass2<InputIm
     ++inputIt;
 
   }//end while
-  
+
 //   std::cout << "HelperClass2::ThreadedGenerateData - OUT " << threadId << std::endl;
-  
+
 }//end member
 
 
@@ -405,7 +408,12 @@ namespace clitk
 template <class InputImageType, class OutputImageType>
 InvertVFFilter<InputImageType, OutputImageType>::InvertVFFilter()
 {
-  m_EdgePaddingValue=itk::NumericTraits<PixelType>::Zero; //no other reasonable value?
+
+  //m_EdgePaddingValue=itk::NumericTraits<PixelType>::Zero; //no other reasonable value?
+  PixelType zero;
+  for(unsigned int i=0;i <PixelType::Dimension; i++) zero[i] = 0.0;
+  m_EdgePaddingValue=zero; //no other reasonable value?
+
   m_ThreadSafe=false;
   m_Verbose=false;
 }
@@ -487,7 +495,7 @@ template <class InputImageType, class OutputImageType> void InvertVFFilter<Input
 
   //Set the output
   this->SetNthOutput(0, helper2->GetOutput());
-  
+
   //std::cout << "InvertVFFilter::GenerateData - OUT" << std::endl;
 }
 
diff --git a/tools/clitkImageConvert.cxx b/tools/clitkImageConvert.cxx
index 3a9beaf..8138682 100644
--- a/tools/clitkImageConvert.cxx
+++ b/tools/clitkImageConvert.cxx
@@ -68,6 +68,7 @@ int main(int argc, char * argv[])
   filter->SetIOVerbose(args_info.verbose_flag);
   filter->SetOutputFilename(output);
   filter->SetVV(args_info.vv_flag);
+  filter->SetCorrectNegativeSpacingFlag(args_info.correct_flag);
   filter->EnableWriteCompression(args_info.compression_flag);
   if (args_info.type_given) filter->SetOutputPixelType(args_info.type_arg);
 
@@ -80,4 +81,3 @@ int main(int argc, char * argv[])
 //-------------------------------------------------------------------=
 
 #endif /* end #define CLITKIMAGECONVERT_CXX */
-
diff --git a/tools/clitkImageConvert.ggo b/tools/clitkImageConvert.ggo
index b6f003c..6d74318 100644
--- a/tools/clitkImageConvert.ggo
+++ b/tools/clitkImageConvert.ggo
@@ -10,3 +10,4 @@ option "type"        t "Output type (float, ushort ...)"
 option "verbose"     v "Verbose"                                                    flag   off
 option "compression" c "Compress output"                                            flag   off
 option "vv"          - "Read image as in vv and save transform in meta information" flag   off
+option "correct"     - "Correct dicom with negative Z spacing"                      flag   off
diff --git a/tools/clitkImageConvertGenericFilter.cxx b/tools/clitkImageConvertGenericFilter.cxx
index 2783053..a603385 100644
--- a/tools/clitkImageConvertGenericFilter.cxx
+++ b/tools/clitkImageConvertGenericFilter.cxx
@@ -15,12 +15,21 @@
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
   ===========================================================================**/
+
 #ifndef CLITKIMAGECONVERTGENERICFILTER_CXX
 #define CLITKIMAGECONVERTGENERICFILTER_CXX
 
 #include "clitkImageConvertGenericFilter.h"
 #include "vvImageReader.h"
 #include "vvImageWriter.h"
+#include "itkFlipImageFilter.h"
+#include "itkGDCMImageIO.h"
+
+#include "gdcmReader.h"
+#include "gdcmAttribute.h"
+#include "gdcmPrinter.h"
+#include "gdcmDict.h"
+#include "gdcmStringFilter.h"
 
 //--------------------------------------------------------------------
 clitk::ImageConvertGenericFilter::ImageConvertGenericFilter():
@@ -30,7 +39,8 @@ clitk::ImageConvertGenericFilter::ImageConvertGenericFilter():
   mDisplayWarning = true;
   mWarning = "";
   mWarningOccur = false;
-  
+  SetCorrectNegativeSpacingFlag(false);
+
   InitializeImageType<2>();
   InitializeImageType<3>();
   InitializeImageType<4>();
@@ -90,12 +100,85 @@ void clitk::ImageConvertGenericFilter::UpdateWithInputImageType()
     return;
   }
   else if ((m_PixelTypeName == mOutputPixelTypeName) || (mOutputPixelTypeName == "NotSpecified")) {
+
+    // Get input image
     typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
-    this->SetNextOutput<InputImageType>(input);
+
+    if (mCorrectNegativeSpacingFlag) {
+      // Read dicom
+      gdcm::Reader reader;
+      reader.SetFileName(m_InputFilenames[0].c_str());
+      // if (!reader.CanReadFile(m_InputFilenames[0])) {
+      //   std::cout << "Error: " << m_InputFilenames[0] << " is not a dicom file. Abort." << std::endl;
+      //   exit(0);
+      // }
+      reader.Read();
+
+      // the dataset is the the set of element we are interested in:
+      gdcm::DataSet & ds = reader.GetFile().GetDataSet();
+
+      // Read the attribute SpacingBetweenSlices, check if negative and replace
+      gdcm::Attribute<0x0018,0x0088> SpacingBetweenSlices;
+      SpacingBetweenSlices.SetFromDataSet(ds);
+      double s = SpacingBetweenSlices.GetValue();
+      if (s >=0) {
+        std::cout << "Error: no negative spacing found SpacingBetweenSlices = " << s << " Abort. " << std::endl;
+        exit(0);
+      }
+      s = -s;
+
+      // Set spacing
+      typename InputImageType::SpacingType spacing = input->GetSpacing();
+      spacing[2] = s;
+      input->SetSpacing(spacing);
+
+      // Flip
+      typedef itk::FlipImageFilter< InputImageType >  FilterType;
+      typename FilterType::Pointer filter = FilterType::New();
+      typedef typename FilterType::FlipAxesArrayType     FlipAxesArrayType;
+      FlipAxesArrayType flipArray;
+      flipArray[0] = false;
+      flipArray[1] = false;
+      flipArray[2] = true;
+      filter->SetFlipAxes(flipArray);
+      filter->SetInput(input);
+      filter->Update();
+
+      // Read the attribute  Image Position (Patient)
+      gdcm::Tag  DetectorInformationSequenceTag(0x0054,0x0022);
+      const gdcm::DataElement & DIS = ds.GetDataElement(DetectorInformationSequenceTag);
+      gdcm::SmartPointer<gdcm::SequenceOfItems> sqf = DIS.GetValueAsSQ();
+      gdcm::Item & item = sqf->GetItem(1);
+      gdcm::DataSet & ds_position = item.GetNestedDataSet();
+      gdcm::Attribute<0x0020,0x0032> ImagePositionPatient;
+      ImagePositionPatient.SetFromDataSet(ds_position);
+      double x = ImagePositionPatient.GetValue(0);
+      double y = ImagePositionPatient.GetValue(1);
+      double z = ImagePositionPatient.GetValue(2);
+
+      // Set offset
+      typename InputImageType::PointType origin = input->GetOrigin();
+      origin[0] = x;
+      origin[1] = y;
+      origin[2] = z;
+      input->SetOrigin(origin);
+
+      // Orientation
+      typename InputImageType::DirectionType direction = input->GetDirection();
+      direction[2][2] = -1;
+      input->SetDirection(direction);
+
+      // Empty meta info
+      itk::MetaDataDictionary dict;// = new itk::MetaDataDictionary;
+      input->SetMetaDataDictionary(dict);
+
+      this->SetNextOutput<InputImageType>(input);
+    }
+
   } else {
-    // "trick" to call independent versions of update according to the 
+    // "trick" to call independent versions of update according to the
     // pixel type (vector or scalar), using partial specializations
-    if (!UpdateWithSelectiveOutputType<InputImageType, ImageConvertTraits<typename InputImageType::PixelType>::IS_VECTOR>::Run(*this, mOutputPixelTypeName))    
+    if (!UpdateWithSelectiveOutputType<InputImageType, ImageConvertTraits<typename InputImageType::PixelType>::IS_VECTOR>::Run(*this, mOutputPixelTypeName))
       exit(-1);
   }
 }
@@ -143,4 +226,3 @@ void clitk::ImageConvertGenericFilter::CheckTypes(
 
 
 #endif /* end #define CLITKIMAGECONVERTGENERICFILTER_CXX */
-
diff --git a/tools/clitkImageConvertGenericFilter.h b/tools/clitkImageConvertGenericFilter.h
index 8ffb360..aa8b2ba 100644
--- a/tools/clitkImageConvertGenericFilter.h
+++ b/tools/clitkImageConvertGenericFilter.h
@@ -1,7 +1,7 @@
 /*=========================================================================
   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
 
-  Authors belong to: 
+  Authors belong to:
   - University of LYON              http://www.universite-lyon.fr/
   - Léon Bérard cancer center       http://www.centreleonberard.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
@@ -23,7 +23,7 @@
  * @author David Sarrut <David.Sarrut@creatis.insa-lyon.fr>
  * @date   05 May 2008 10:40:24
 
- * @brief  
+ * @brief
 
  ===================================================================*/
 
@@ -36,7 +36,7 @@
 
 
 namespace clitk {
-  
+
   template <class TPixel>
   class ImageConvertTraits
   {
@@ -47,17 +47,17 @@ namespace clitk {
     }
   };
 
-  template < class TPixel, unsigned int Comp > 
-  class ImageConvertTraits< itk::Vector<TPixel, Comp> > 
-  { 
-  public: 
-    enum { IS_VECTOR = true }; 
+  template < class TPixel, unsigned int Comp >
+  class ImageConvertTraits< itk::Vector<TPixel, Comp> >
+  {
+  public:
+    enum { IS_VECTOR = true };
   };
 
-  class ImageConvertGenericFilter: 
+  class ImageConvertGenericFilter:
     public clitk::ImageToImageGenericFilter<ImageConvertGenericFilter> {
-    
-  public: 
+
+  public:
     // constructor - destructor
     ImageConvertGenericFilter();
 
@@ -68,7 +68,7 @@ namespace clitk {
 
     // New
     itkNewMacro(Self);
-    
+
     // Members functions
     std::string GetInputPixelTypeName() { return m_PixelTypeName; }
     std::string GetOutputPixelTypeName() { return mOutputPixelTypeName; }
@@ -77,15 +77,16 @@ namespace clitk {
     bool IsWarningOccur() { return mWarningOccur; }
     std::string & GetWarning() { return mWarning; }
     void EnableDisplayWarning(bool b) { mDisplayWarning = b; }
+    void SetCorrectNegativeSpacingFlag(bool b) { mCorrectNegativeSpacingFlag = b; }
 
     //--------------------------------------------------------------------
     // Main function called each time the filter is updated
-    template<class InputImageType>  
+    template<class InputImageType>
     void UpdateWithInputImageType();
 
     template<class PixelType, class OutputPixelType>
     void CheckTypes(std::string inType, std::string outType);
-    
+
   protected:
 
     template<unsigned int Dim> void InitializeImageType();
@@ -94,6 +95,7 @@ namespace clitk {
     bool mWarningOccur;
     bool mDisplayWarning;
     bool mVV;
+    bool mCorrectNegativeSpacingFlag;
 
   private:
     template <class InputImageType, bool isVector>
@@ -119,17 +121,17 @@ namespace clitk {
           else
           {
             std::string list = CreateListOfTypes<float, double>();
-            std::cerr << "Error, I don't know the vector output type '" << outputPixelType 
+            std::cerr << "Error, I don't know the vector output type '" << outputPixelType
                       << "'. " << std::endl << "Known types are " << list << "." << std::endl;
             return false;
           }
-          
+
           return true;
       }
 
     private:
-      
-      template <class OutputPixelType> 
+
+      template <class OutputPixelType>
       static void UpdateWithOutputType(ImageConvertGenericFilter& filter)
       {
         // Read
@@ -152,7 +154,7 @@ namespace clitk {
         filter.SetNextOutput<OutputImageType>(cast_filter->GetOutput());
       }
     };
-    
+
     template <class InputImageType>
     class UpdateWithSelectiveOutputType<InputImageType, true>
     {
@@ -160,7 +162,7 @@ namespace clitk {
       static bool Run(ImageConvertGenericFilter& filter, std::string outputPixelType)
       {
         /*
-        // RP: future conversions? 
+        // RP: future conversions?
         if (IsSameType<char>(outputPixelType))
           UpdateWithOutputVectorType<char>();
         else if (IsSameType<uchar>(outputPixelType))
@@ -171,7 +173,7 @@ namespace clitk {
           UpdateWithOutputVectorType<ushort>();
         else if (IsSameType<int>(outputPixelType))
           UpdateWithOutputVectorType<int>();
-        else 
+        else
           */
         if (IsSameType<float>(outputPixelType))
           UpdateWithOutputVectorType<float>(filter);
@@ -180,17 +182,17 @@ namespace clitk {
         else
         {
           std::string list = CreateListOfTypes<float, double>();
-          std::cerr << "Error, I don't know the vector output type '" << outputPixelType  
+          std::cerr << "Error, I don't know the vector output type '" << outputPixelType
                     << "'. " << std::endl << "Known types are " << list << "." << std::endl;
           return false;
         }
-        
+
         return true;
       }
-      
+
     private:
-      
-      template <class OutputPixelType> 
+
+      template <class OutputPixelType>
       static void UpdateWithOutputVectorType(ImageConvertGenericFilter& filter)
       {
         // Read
@@ -201,7 +203,7 @@ namespace clitk {
 
         // Warning
         filter.CheckTypes<PixelType, OutputPixelType>(filter.GetInputPixelTypeName(), filter.GetOutputPixelTypeName());
-        
+
         // Cast
         typedef itk::Image<itk::Vector<OutputPixelType, InputImageType::PixelType::Dimension>, InputImageType::ImageDimension> OutputImageType;
         typedef itk::VectorCastImageFilter<InputImageType, OutputImageType> FilterType;
@@ -220,4 +222,3 @@ namespace clitk {
 } // end namespace
 
 #endif /* end #define CLITKIMAGECONVERTGENERICFILTER_H */
-
diff --git a/tools/clitkImageStatisticsGenericFilter.txx b/tools/clitkImageStatisticsGenericFilter.txx
index 5d46240..32b31bc 100644
--- a/tools/clitkImageStatisticsGenericFilter.txx
+++ b/tools/clitkImageStatisticsGenericFilter.txx
@@ -156,7 +156,7 @@ namespace clitk
 
           }
           else {
-            std::cerr << "Mask image has a different size/spacing than input. Abort" << std::endl;
+            std::cerr << "Mask image has a different size/spacing than input. Abort. (Use option to resize)" << std::endl;
             exit(-1);
           }
         }
@@ -169,6 +169,7 @@ namespace clitk
       labelImage->SetRegions(input->GetLargestPossibleRegion());
       labelImage->SetOrigin(input->GetOrigin());
       labelImage->SetSpacing(input->GetSpacing());
+      labelImage->SetDirection(input->GetDirection());
       labelImage->Allocate();
       labelImage->FillBuffer(m_ArgsInfo.label_arg[0]);
     }
@@ -212,7 +213,7 @@ namespace clitk
 
         std::cout<<std::endl;
         if (m_Verbose) std::cout<<"-------------"<<std::endl;
-        if (m_Verbose) std::cout<<"| Label: "<<label<<"  |"<<std::endl;
+        if (m_Verbose) std::cout<<"| Label: "<< (int) label<<"  |"<<std::endl;
         if (m_Verbose) std::cout<<"-------------"<<std::endl;
 
         // Histograms
diff --git a/vv/vvMidPosition.cxx b/vv/vvMidPosition.cxx
index b4582e2..f91422a 100644
--- a/vv/vvMidPosition.cxx
+++ b/vv/vvMidPosition.cxx
@@ -172,7 +172,8 @@ itk::Image<itk::Vector<float,3>,3>::Pointer AverageField(itk::Image<itk::Vector<
 
   // Average
   VFPixelType vector;
-  VFPixelType zeroVector=itk::NumericTraits<VFPixelType>::Zero;
+  VFPixelType zeroVector;//=itk::NumericTraits<VFPixelType>::Zero;
+  for(unsigned int i=0;i <VFPixelType::Dimension; i++) zeroVector[i] = 0.0;
 
   while (!(iterators[0]).IsAtEnd()) {
     vector=zeroVector;
@@ -194,4 +195,3 @@ void vvMidPosition::update_progress()
   p_bar.setValue(progress);
   p_bar.show();
 }
-