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

diff --git a/cluster_tools/mergeStatFile.py b/cluster_tools/mergeStatFile.py
index a1cd573cdb21e5f23488992c401d029a74d6b17a..ab5028954ce62feeab9953d0baf3af6dc0eb4f49 100755 (executable)
--- a/cluster_tools/mergeStatFile.py
+++ b/cluster_tools/mergeStatFile.py
@@ -27,7 +27,9 @@ def parse_stat_file(filename):
     keys = {}
     for line in open(filename,"r").readlines():
         match = linere.match(line)
-        assert(match is not None)
+        #assert(match is not None)
+        if match is None:
+            continue
         groups = match.groups()
         if groups[0] not in mergedlines:
             continue
@@ -88,4 +90,3 @@ jkeys = parse_stat_file(sys.argv[4])
 keys  = merge_keys(ikeys,jkeys)
 output = format_keys(keys)
 open(sys.argv[6],"w").write(output)
-

diff --git a/common/clitkCommon.h b/common/clitkCommon.h
index 113bdfb3299657eefdd1c942b64cf3a2fca1aa7c..94d1c607b6049e7d353e1209a4e31b6ba39b5d77 100644 (file)
--- 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);
 
   //--------------------------------------------------------------------
@@ -131,7 +131,7 @@ namespace clitk {
   // Return the name of a type as a string
   template<class TPixel>
   std::string GetTypeAsString();
-  
+
   //--------------------------------------------------------------------
   // Convert radian / degree
   double rad2deg(double anglerad);
@@ -154,13 +154,13 @@ 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>();
@@ -197,7 +197,7 @@ 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);
@@ -205,8 +205,8 @@ 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);
 
   //--------------------------------------------------------------------
@@ -234,9 +234,9 @@ 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);
 
   //--------------------------------------------------------------------
@@ -249,4 +249,3 @@ namespace clitk {
 } // end namespace
 
 #endif /* end #define CLITKCOMMON_H */
-

diff --git a/common/clitkDD.h b/common/clitkDD.h
index 97ba4437b07e5f5207faf55bfee180ac63f1cd2b..c5a999629358e06be28d4f6232f047d8dc4f909c 100644 (file)
--- 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 cd74428832f4505df7edd11028b359030ab064c5..329ca13f04272d44104a3f0926e54e3b0e5b0aa8 100644 (file)
--- 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/registration/clitkBSplineDeformableTransform.h b/registration/clitkBSplineDeformableTransform.h
index f5b269828fffb20b5759ae061d8390e3f8698908..392247f25717e80e6dede00e6e8167414af11b4a 100644 (file)
--- a/registration/clitkBSplineDeformableTransform.h
+++ b/registration/clitkBSplineDeformableTransform.h
@@ -387,7 +387,7 @@ namespace clitk
 
 }  // namespace itk
 
-#if ITK_TEMPLATE_TXX
+#ifndef ITK_MANUAL_INSTANTIATION
 # include "clitkBSplineDeformableTransform.txx"
 #endif
 

diff --git a/registration/clitkMatrixTransformToVFGenericFilter.txx b/registration/clitkMatrixTransformToVFGenericFilter.txx
index d864900c0cc0d37a6d299d000634300fe818717c..a1241b5358cc06a0ab63065be57a2f41134c0bfe 100644 (file)
--- a/registration/clitkMatrixTransformToVFGenericFilter.txx
+++ b/registration/clitkMatrixTransformToVFGenericFilter.txx
@@ -101,6 +101,7 @@ namespace clitk
        typename OutputImageType::Pointer image=reader2->GetOutput();
 #if ITK_VERSION_MAJOR > 4 || (ITK_VERSION_MAJOR == 4 && ITK_VERSION_MINOR >= 6)
     filter->SetReferenceImage(image);
+    filter->UseReferenceImageOn();
 #else
     filter->SetOutputParametersFromImage(image);
 #endif

diff --git a/registration/clitkMultipleBSplineDeformableTransform.h b/registration/clitkMultipleBSplineDeformableTransform.h
index 5b2ee9eb35686933603bb10b4f22796e1be100b7..1b7909ab6f35146deac97d95cc1ed689bf45d81b 100644 (file)
--- a/registration/clitkMultipleBSplineDeformableTransform.h
+++ b/registration/clitkMultipleBSplineDeformableTransform.h
@@ -289,7 +289,7 @@ namespace clitk
 
 }  // namespace clitk
 
-#if ITK_TEMPLATE_TXX
+#ifndef ITK_MANUAL_INSTANTIATION
 # include "clitkMultipleBSplineDeformableTransform.txx"
 #endif
 

diff --git a/registration/clitkShapedBLUTSpatioTemporalDeformableTransform.h b/registration/clitkShapedBLUTSpatioTemporalDeformableTransform.h
index c9fb588e30f83641260459a16e9d57e0cd684a66..b1924580c503d9ff9f62f58cdc29cb004a66bfa7 100644 (file)
--- a/registration/clitkShapedBLUTSpatioTemporalDeformableTransform.h
+++ b/registration/clitkShapedBLUTSpatioTemporalDeformableTransform.h
@@ -454,7 +454,7 @@ namespace clitk
 
 }  // namespace itk
 
-#if ITK_TEMPLATE_TXX
+#ifndef ITK_MANUAL_INSTANTIATION
 # include "clitkShapedBLUTSpatioTemporalDeformableTransform.txx"
 #endif
 

diff --git a/tools/clitkGammaIndex.cxx b/tools/clitkGammaIndex.cxx
index 7e5a92eba7cf32d67775e1910d596290c8f5eee9..1f5fd03f3a78c905ecd666dc2376569b674e9fa3 100644 (file)
--- a/tools/clitkGammaIndex.cxx
+++ b/tools/clitkGammaIndex.cxx
@@ -15,6 +15,15 @@
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
 ===========================================================================*/
+
+#include "clitkGammaIndex_ggo.h"
+#include "clitkIO.h"
+#include "clitkDD.h"
+
+#include <iostream>
+#include <cmath>
+#include <cassert>
+
 #include <vtkPoints.h>
 #include <vtkCellArray.h>
 #include <vtkPointData.h>
@@ -24,15 +33,7 @@
 #include <vtkPNGReader.h>
 #include <vtkPolyData.h>
 #include <vtkCellLocator.h>
-#include <iostream>
-#include <cmath>
-#include <cassert>
-using std::endl;
-using std::cout;
 
-#include "clitkGammaIndex_ggo.h"
-
-#include <clitkIO.h>
 #include <vvImage.h>
 #include <vvImageReader.h>
 #include <vvImageWriter.h>
@@ -42,6 +43,9 @@ using std::cout;
 typedef itk::Image<double> OutputImageType;
 typedef itk::ImageRegionIterator<OutputImageType> OutputImageIterator;
 
+using std::endl;
+using std::cout;
+
 vtkImageData* loadImage(const std::string& filename)
 {
     vvImageReader::Pointer reader = vvImageReader::New();
@@ -224,7 +228,7 @@ int main(int argc,char * argv[])
     // load reference
     vtkImageData* reference = loadImage(reference_filename);
     assert(reference);
- 
+
     // translate target with arguments values
     // reference is translated instead of target so that the output space stay the same as target
     {
@@ -248,10 +252,13 @@ int main(int argc,char * argv[])
 
     vtkAbstractCellLocator *locator = vtkCellLocator::New();
     locator->SetDataSet(data);
-    data->Delete();
+    DD("here");
+    //    data->Delete();
     locator->CacheCellBoundsOn();
     locator->AutomaticOn();
+    DD("BuildLocator");
     locator->BuildLocator();
+    DD("end BuildLocator");
 
     // load target
     vtkImageData* target = loadImage(target_filename);
@@ -277,6 +284,7 @@ int main(int argc,char * argv[])
     unsigned long over_one = 0;
     OutputImageIterator iter(output,output->GetLargestPossibleRegion());
     iter.GoToBegin();
+    DD("loop");
     while (!iter.IsAtEnd()) {
        double *point = target->GetPoint(kk);
        double value = target->GetPointData()->GetScalars()->GetTuple1(kk);
@@ -315,4 +323,3 @@ int main(int argc,char * argv[])
 
     return 0;
 }
-

diff --git a/tools/clitkPadImageGenericFilter.cxx b/tools/clitkPadImageGenericFilter.cxx
index 49d4075997b87e278216d2546a19e2faa393311d..8477a35d8c085574e7829a2b7dd1e2dfc8af2280 100644 (file)
--- a/tools/clitkPadImageGenericFilter.cxx
+++ b/tools/clitkPadImageGenericFilter.cxx
@@ -155,7 +155,7 @@ namespace clitk
     SpacingType spacing = input->GetSpacing(), like_spacing = like_image->GetSpacing(); 
     if (spacing != like_spacing) {
       std::cerr << "Like-image must have same spacing as input: " << spacing << " " << like_spacing << std::endl;
-      return ERR_NOT_SAME_SPACING;
+      return PAD_ERR_NOT_SAME_SPACING;
     }
     
     SizeType size = input->GetLargestPossibleRegion().GetSize(), like_size = like_image->GetLargestPossibleRegion().GetSize();
@@ -175,7 +175,7 @@ namespace clitk
 
       if (auxl < 0 || auxu < 0) {
         std::cerr << "Like-image's bounding box must be larger than input's" << std::endl;
-        return ERR_NOT_LIKE_LARGER;
+        return PAD_ERR_NOT_LIKE_LARGER;
       }
 
       padLower[i] = (PadBoundType)auxl;
@@ -184,7 +184,7 @@ namespace clitk
     
     if (mArgsInfo.verbose_flag)
       std::cout << "PadLike - OUT" << std::endl;
-    return ERR_SUCCESS;
+    return PAD_ERR_SUCCESS;
   }
 } //end clitk
 

diff --git a/tools/clitkPadImageGenericFilter.h b/tools/clitkPadImageGenericFilter.h
index 3aa9318057fa8ca850c2a29169dd058778f9807b..429d203d6588909abc7130d87ebf4e4b609a1679 100644 (file)
--- a/tools/clitkPadImageGenericFilter.h
+++ b/tools/clitkPadImageGenericFilter.h
@@ -24,7 +24,6 @@
 #include "clitkImageToImageGenericFilter.h"
 #include "clitkPadImage_ggo.h"
 
-
 //--------------------------------------------------------------------
 namespace clitk
 {
@@ -35,9 +34,9 @@ namespace clitk
   public:
     enum
     {
-      ERR_SUCCESS = 0,
-      ERR_NOT_SAME_SPACING = -1,
-      ERR_NOT_LIKE_LARGER = -2
+      PAD_ERR_SUCCESS = 0,
+      PAD_ERR_NOT_SAME_SPACING = -1,
+      PAD_ERR_NOT_LIKE_LARGER = -2
     };
 
     //--------------------------------------------------------------------