-#!/usr/bin/env bash -x
+#! /usr/local/bin/bash -lx
#
# MACRODIR
# MACROFILE
|| error "gate failed"
fi
+date
echo "Copying data back"
ssh -i ${HOME}/.ssh/ccin2p3 linux1.dg.creatis.insa-lyon.fr "mkdir cc/$(basename ${OUTPUTDIR})/output.${JOB_ID%%.*}"
rsync -av --remove-source-files -e "ssh -i ${HOME}/.ssh/ccin2p3" output/ "linux1.dg.creatis.insa-lyon.fr:./cc/$(basename ${OUTPUTDIR})/output.${JOB_ID%%.*}"
echo "Cleanup"
rm -r ${LOCALMACRODIR}
+date
echo "Success!!!"
-#!/usr/bin/env bash
+#! /usr/local/bin/bash -lx
set -u
SCRIPTNAME="$(basename "${0}")"
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
keys = merge_keys(ikeys,jkeys)
output = format_keys(keys)
open(sys.argv[6],"w").write(output)
-
/*=========================================================================
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
#include <fstream>
// Include for "rusage"
-#include <ctime>
+#include <ctime>
#if defined(unix) || defined(__APPLE__)
# include <sys/time.h>
# include <sys/resource.h>
typedef unsigned char uchar;
typedef unsigned short ushort;
typedef unsigned int uint;
-
+
#define CLITK_TRY_CATCH_EXIT(func) \
try { \
func; \
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) \
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 #
//--------------------------------------------------------------------
// 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);
//--------------------------------------------------------------------
// Return the name of a type as a string
template<class TPixel>
std::string GetTypeAsString();
-
+
//--------------------------------------------------------------------
// Convert radian / degree
double rad2deg(double anglerad);
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>();
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);
//--------------------------------------------------------------------
//--------------------------------------------------------------------
- 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);
//--------------------------------------------------------------------
//--------------------------------------------------------------------
// 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);
//--------------------------------------------------------------------
} // end namespace
#endif /* end #define CLITKCOMMON_H */
-
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
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--;
}
}
// #endif // If UNIX
#endif /* end #define CLITKTIMER_CXX */
-
if(pixelType=="Type_float")
SetComponentType(itk::ImageIOBase::FLOAT);
- if(dic["dimensions"].GetPointer()==NULL)
+ if( dic["dimensions"].GetPointer() == NULL )
SetNumberOfDimensions(3);
else
SetNumberOfDimensions( ( dynamic_cast<MetaDataIntType *>(dic["dimensions"].GetPointer() )->GetMetaDataObjectValue() ) );
{
SetDimensions(2, dynamic_cast<MetaDataIntType *>(dic["z"].GetPointer() )->GetMetaDataObjectValue() );
SetSpacing(2, dynamic_cast<MetaDataDoubleType *>(dic["spacing_z"].GetPointer() )->GetMetaDataObjectValue() );
+ if(GetSpacing(2) == 0)
+ SetSpacing(2, 1);
}
- std::istringstream iss(
- dynamic_cast<MetaDataStringType*>(dic["matrixTransform"].GetPointer() )->GetMetaDataObjectValue() );
itk::Matrix<double, 4, 4> matrix;
- for(unsigned int j=0; j<4; j++)
- for(unsigned int i=0; i<4; i++)
- iss >> matrix[j][i];
- matrix /= matrix[3][3];
+ if(dic["matrixTransform"].GetPointer() == NULL)
+ matrix.SetIdentity();
+ else
+ {
+ std::istringstream iss(
+ dynamic_cast<MetaDataStringType*>(dic["matrixTransform"].GetPointer() )->GetMetaDataObjectValue() );
+ for(unsigned int j=0; j<4; j++)
+ for(unsigned int i=0; i<4; i++)
+ iss >> matrix[j][i];
+ matrix /= matrix[3][3];
+ }
std::vector<double> direction;
for(unsigned int i=0; i<GetNumberOfDimensions(); i++)
//--------------------------------------------------------------------
// Write Image Information
-void rtk::ImagXImageIO::WriteImageInformation(bool keepOfStream)
+void rtk::ImagXImageIO::WriteImageInformation( bool itkNotUsed(keepOfStream) )
{
}
//--------------------------------------------------------------------
// Write Image Information
-bool rtk::ImagXImageIO::CanWriteFile(const char* FileNameToWrite)
+bool rtk::ImagXImageIO::CanWriteFile( const char* itkNotUsed(FileNameToWrite) )
{
return false;
}
//--------------------------------------------------------------------
// Write Image
-void rtk::ImagXImageIO::Write(const void * buffer)
+void rtk::ImagXImageIO::Write( const void * itkNotUsed(buffer) )
{
} ////
-
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
version "1.0"
purpose "Resample with or without affine transform of 2D, 3D, 4D images or vector fields"
-option "config" - "Config file" string no
-option "verbose" v "Verbose" flag off
+option "config" - "Config file" string no
+option "verbose" v "Verbose" flag off
section "I/O"
-option "input" i "Input image filename" string yes
-option "output" o "Output image filename" string yes
-option "like" l "Resample output this image (size, spacing,origin)" string no
-option "transform_grid" - "Apply affine transform to input grid for output's" flag off
+option "input" i "Input image filename" string yes
+option "output" o "Output image filename" string yes
+option "like" l "Resample output this image (size, spacing, origin, direction)" string no
+option "transform_grid" - "Apply affine transform to input grid for output's" flag off
section "Options"
-option "size" - "New output size if different from input" int no multiple
-option "spacing" - "New output spacing if different from input" double no multiple
-option "spacinglike" - "New output spacing like this image" string no
-option "origin" - "New output origin if different from input" double no multiple
-option "matrix" m "Affine matrix (homogene) filename" string no
-option "elastix" e "Read EulerTransform from elastix output file (combine if multiple)" string no
-option "rotate" r "Rotation to apply (radians)" double no multiple
-option "translate" t "Translation to apply (mm)" double no multiple
-option "pad" - "Edge padding value" double no default="0.0"
+option "size" - "New output size if different from input" int no multiple
+option "spacing" - "New output spacing if different from input" double no multiple
+option "spacinglike" - "New output spacing like this image" string no
+option "origin" - "New output origin if different from input" double no multiple
+option "matrix" m "Affine matrix (homogene) filename" string no
+option "elastix" e "Read EulerTransform from elastix output file (combine if multiple)" string no
+option "rotate" r "Rotation to apply (radians)" double no multiple
+option "translate" t "Translation to apply (mm)" double no multiple
+option "pad" - "Edge padding value" double no default="0.0"
section "Interpolation"
-option "interp" - "Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT" int no default="1"
-option "interpOrder" - "Order if BLUT or BSpline (0-5)" int no default="3"
-option "interpSF" - "Sampling factor if BLUT" int no default="20"
-option "interpVF" - "Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT" int no default="1"
-option "interpVFOrder" - "Order if BLUT or BSpline (0-5)" int no default="3"
-option "interpVFSF" - "Sampling factor if BLUT" int no default="20"
+option "interp" - "Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT" int no default="1"
+option "interpOrder" - "Order if BLUT or BSpline (0-5)" int no default="3"
+option "interpSF" - "Sampling factor if BLUT" int no default="20"
+option "interpVF" - "Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT" int no default="1"
+option "interpVFOrder" - "Order if BLUT or BSpline (0-5)" int no default="3"
+option "interpVFSF" - "Sampling factor if BLUT" int no default="20"
likeReader->SetFileName(m_ArgsInfo.like_arg);
likeReader->Update();
resampler->SetOutputParametersFromImage(likeReader->GetOutput());
+ resampler->SetOutputDirection(likeReader->GetOutput()->GetDirection());
} else if(m_ArgsInfo.transform_grid_flag) {
typename itk::Matrix<double, Dimension+1, Dimension+1> invMatrix( matrix.GetInverse() );
typename itk::Matrix<double, Dimension, Dimension> invRotMatrix( clitk::GetRotationalPartMatrix(invMatrix) );
- 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>
#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>
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();
// 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
{
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);
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);
return 0;
}
-
if(m_ArgsInfo.dvhistogram_given)
{
typename StatisticsImageFilterType::HistogramPointer dvhistogram = statisticsFilter->GetHistogram(label);
+ double totalVolumeCC = ((statisticsFilter->GetCount(label))*spacing_cc);
+ double totalVolume = statisticsFilter->GetCount(label);
// Screen
std::cout<<"# Total volume : ";
- std::cout<<statisticsFilter->GetCount(label)<<" [No. of voxels]"<<std::endl;
+ std::cout<<totalVolume<<" [No. of voxels]"<<std::endl;
std::cout<<"# Total volume : ";
- std::cout<<((statisticsFilter->GetCount(label))*spacing_cc)<<" [cc]"<<std::endl;
+ std::cout<<totalVolumeCC<<" [cc]"<<std::endl;
std::cout<<"# Dose mean: ";
std::cout<<statisticsFilter->GetMean(label)<<" [Gy]"<<std::endl;
std::cout<<"# Dose min: ";
std::cout<<"# Dose max: ";
std::cout<<statisticsFilter->GetMaximum(label)<<" [Gy]"<<std::endl;
std::cout<<" "<<std::endl;
- std::cout<<"#Dose_diff[Gy] Volume_diff[No. of voxels] Volume_diff[%] Volume_diff[cc] #Dose_cumul[Gy] Volume_cumul[No. of voxels] Volume_cumul[%] Volume_cumul[cc]"<<std::endl;
+ std::cout<<"#Dose_diff[Gy] Volume_diff[No. of voxels] Volume_diff[%] Volume_diff[cc] Volume_cumul[No. of voxels] Volume_cumul[%] Volume_cumul[cc]"<<std::endl;
for( int i =0; i <m_ArgsInfo.bins_arg; i++)
{
double popCumulativeVolume = 0;
{
popCumulativeVolume+=(dvhistogram->GetFrequency(j));
}
- double cumulativeVolume = popCumulativeVolume + (dvhistogram->GetFrequency(i));
+ double cumulativeVolume = (totalVolume - (popCumulativeVolume + (dvhistogram->GetFrequency(i))));
double percentCumulativeVolume =(cumulativeVolume*100)/(statisticsFilter->GetCount(label)) ;
- double ccCumulativeVolume = (popCumulativeVolume + (dvhistogram->GetFrequency(i)))*spacing_cc;
+ double ccCumulativeVolume = (totalVolumeCC -((popCumulativeVolume + (dvhistogram->GetFrequency(i)))*spacing_cc));
double percentDiffVolume = dvhistogram->GetFrequency(i)*100/(statisticsFilter->GetCount(label));
- if(i == 0)
- {
- std::cout<<dvhistogram->GetBinMax(0,i)<<"\t "<<dvhistogram->GetFrequency(i)<<"\t "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<m_ArgsInfo.bins_arg<<"\t "<<cumulativeVolume<<"\t "<<percentCumulativeVolume<<"\t "<<ccCumulativeVolume<<"\t "<<std::endl;
- }else
- {
- std::cout<<dvhistogram->GetBinMax(0,i)<<"\t "<<dvhistogram->GetFrequency(i)<<"\t "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<dvhistogram->GetBinMin(0,m_ArgsInfo.bins_arg-i)<<"\t "<<cumulativeVolume<<"\t "<<percentCumulativeVolume<<"\t "<<ccCumulativeVolume<<"\t "<<std::endl;
- }
+ std::cout<<dvhistogram->GetBinMax(0,i)<<"\t "<<dvhistogram->GetFrequency(i)<<"\t "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<"\t "<<cumulativeVolume<<"\t "<<percentCumulativeVolume<<"\t "<<ccCumulativeVolume<<"\t "<<std::endl;
}
// Add to the file
dvhistogramFile<<"# Total volume : ";
dvhistogramFile<<statisticsFilter->GetCount(label)<<" [No. of voxels]"<<std::endl;
dvhistogramFile<<"# Total volume : ";
- dvhistogramFile<<((statisticsFilter->GetCount(label))*spacing_cc)<<" [cc]"<<std::endl;
+ dvhistogramFile<<totalVolumeCC<<" [cc]"<<std::endl;
dvhistogramFile<<"# Dose mean: ";
dvhistogramFile<<statisticsFilter->GetMean(label)<<" [Gy]"<<std::endl;
dvhistogramFile<<"# Dose min: ";
dvhistogramFile<<"# Dose max: ";
dvhistogramFile<<statisticsFilter->GetMaximum(label)<<" [Gy]"<<std::endl;
dvhistogramFile<<" "<<std::endl;
- dvhistogramFile<<"#Dose_diff[Gy] Volume_diff[No. of voxels] Volume_diff[%] Volume_diff[cc] #Dose_cumulative[Gy] Volume_cumul[No. of voxels] Volume_cumul[%] Volume_cumul[cc]"<<std::endl;
+ dvhistogramFile<<"#Dose_diff[Gy] Volume_diff[No. of voxels] Volume_diff[%] Volume_diff[cc] Volume_cumul[No. of voxels] Volume_cumul[%] Volume_cumul[cc]"<<std::endl;
for( int i =0; i <m_ArgsInfo.bins_arg; i++)
{
double popCumulativeVolume = 0;
{
popCumulativeVolume+=(dvhistogram->GetFrequency(j));
}
- double cumulativeVolume = popCumulativeVolume + (dvhistogram->GetFrequency(i));
- double percentCumulativeVolume =(cumulativeVolume*100)/(statisticsFilter->GetCount(label)) ;
- double ccCumulativeVolume = (popCumulativeVolume + (dvhistogram->GetFrequency(i)))*spacing_cc;
+ double cumulativeVolume = (totalVolume - (popCumulativeVolume + (dvhistogram->GetFrequency(i))));
+ double percentCumulativeVolume =(cumulativeVolume*100)/(statisticsFilter->GetCount(label));
+ double ccCumulativeVolume = (totalVolumeCC -((popCumulativeVolume + (dvhistogram->GetFrequency(i)))*spacing_cc));
double percentDiffVolume = ((dvhistogram->GetFrequency(i))*100)/(statisticsFilter->GetCount(label));
- if(i == 0)
- {
- dvhistogramFile<<dvhistogram->GetBinMax(0,i)<<"\t "<<dvhistogram->GetFrequency(i)<<"\t "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<m_ArgsInfo.bins_arg<<"\t "<<cumulativeVolume<<"\t "<<percentCumulativeVolume<<"\t "<<ccCumulativeVolume<<std::endl;
- }else
- {
- dvhistogramFile<<dvhistogram->GetBinMax(0,i)<<"\t "<<dvhistogram->GetFrequency(i)<<"\t "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<dvhistogram->GetBinMin(0,m_ArgsInfo.bins_arg-i)<<"\t "<<cumulativeVolume<<"\t "<<percentCumulativeVolume<<"\t "<<ccCumulativeVolume<<std::endl;
- }
+ dvhistogramFile<<dvhistogram->GetBinMax(0,i)<<"\t "<<dvhistogram->GetFrequency(i)<<"\t "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<cumulativeVolume<<"\t "<<percentCumulativeVolume<<"\t "<<ccCumulativeVolume<<std::endl;
}
}
}
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();
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;
if (mArgsInfo.verbose_flag)
std::cout << "PadLike - OUT" << std::endl;
- return ERR_SUCCESS;
+ return PAD_ERR_SUCCESS;
}
} //end clitk
#include "clitkImageToImageGenericFilter.h"
#include "clitkPadImage_ggo.h"
-
//--------------------------------------------------------------------
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
};
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff