From: Brent Huisman Date: Tue, 8 Sep 2015 14:48:23 +0000 (+0200) Subject: Merge branch 'master' of git://git.creatis.insa-lyon.fr/clitk X-Git-Tag: v1.4.0~97 X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=27b0594e2e1fb1fb2b11265a1bfc5db439cc7d3f;hp=3b6b49593e7293aa8f10e7f8951742c73b31ab38;p=clitk.git Merge branch 'master' of git://git.creatis.insa-lyon.fr/clitk --- diff --git a/cluster_tools/mergeStatFile.py b/cluster_tools/mergeStatFile.py index a1cd573..ab50289 100755 --- 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 113bdfb..94d1c60 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 // Include for "rusage" -#include +#include #if defined(unix) || defined(__APPLE__) # include # include @@ -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 std::string toString(const T & t); template std::string toStringVector(const T * t, const int n); template std::string toStringVector(const T & t, const int n); template std::string toStringVector(const std::vector & t); - template bool fromString(T& t, - const std::string& s, + template 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 std::string GetTypeAsString(); - + //-------------------------------------------------------------------- // Convert radian / degree double rad2deg(double anglerad); @@ -154,13 +154,13 @@ namespace clitk { std::string CreateListOfTypes(bool last=true) { return GetTypeAsString(); } - + template std::string CreateListOfTypes(bool last=true) { if (last) return CreateListOfTypes()+" and "+CreateListOfTypes(); else return CreateListOfTypes()+", "+CreateListOfTypes(); } - + template std::string CreateListOfTypes(bool last=true) { if (last) return CreateListOfTypes(false)+" and "+CreateListOfTypes(); @@ -197,7 +197,7 @@ namespace clitk { else return CreateListOfTypes(false)+", "+CreateListOfTypes(); } //-------------------------------------------------------------------- - + //-------------------------------------------------------------------- void FindAndReplace(std::string & line, const std::string & tofind, const std::string & replacement); void FindAndReplace(std::string & line, const std::vector & tofind, const std::vector & toreplace); @@ -205,8 +205,8 @@ namespace clitk { //-------------------------------------------------------------------- //-------------------------------------------------------------------- - double ComputeEuclideanDistanceFromPointToPlane(const itk::ContinuousIndex point, - const itk::ContinuousIndex pointInPlane, + double ComputeEuclideanDistanceFromPointToPlane(const itk::ContinuousIndex point, + const itk::ContinuousIndex pointInPlane, const itk::ContinuousIndex normalPlane); //-------------------------------------------------------------------- @@ -234,9 +234,9 @@ namespace clitk { //-------------------------------------------------------------------- // Convert a map to a vector - template + template void MapToVecFirst(const M & m, V & v); - template + template 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 97ba443..c5a9996 100644 --- a/common/clitkDD.h +++ b/common/clitkDD.h @@ -38,6 +38,6 @@ template 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/registration/clitkBSplineDeformableTransform.h b/registration/clitkBSplineDeformableTransform.h index f5b2698..392247f 100644 --- 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 d864900..a1241b5 100644 --- 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 5b2ee9e..1b7909a 100644 --- 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 c9fb588..b192458 100644 --- 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 7e5a92e..1f5fd03 100644 --- 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 +#include +#include + #include #include #include @@ -24,15 +33,7 @@ #include #include #include -#include -#include -#include -using std::endl; -using std::cout; -#include "clitkGammaIndex_ggo.h" - -#include #include #include #include @@ -42,6 +43,9 @@ using std::cout; typedef itk::Image OutputImageType; typedef itk::ImageRegionIterator 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 49d4075..8477a35 100644 --- 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 3aa9318..429d203 100644 --- 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 }; //--------------------------------------------------------------------