+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ 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
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
#ifndef clitkAverageTemporalDimensionGenericFilter_txx
#define clitkAverageTemporalDimensionGenericFilter_txx
/* =================================================
* @file clitkAverageTemporalDimensionGenericFilter.txx
- * @author
- * @date
- *
- * @brief
- *
+ * @author
+ * @date
+ *
+ * @brief
+ *
===================================================*/
namespace clitk
{
- //-----------------------------------------------------------
- // Constructor
- //-----------------------------------------------------------
- template<class args_info_type>
- AverageTemporalDimensionGenericFilter<args_info_type>::AverageTemporalDimensionGenericFilter()
- {
- m_Verbose=false;
- m_InputFileName="";
+//-----------------------------------------------------------
+// Constructor
+//-----------------------------------------------------------
+template<class args_info_type>
+AverageTemporalDimensionGenericFilter<args_info_type>::AverageTemporalDimensionGenericFilter()
+{
+ m_Verbose=false;
+ m_InputFileName="";
+}
+
+
+//-----------------------------------------------------------
+// Update
+//-----------------------------------------------------------
+template<class args_info_type>
+void AverageTemporalDimensionGenericFilter<args_info_type>::Update()
+{
+ // Read the Dimension and PixelType
+ int Dimension, Components;
+ std::string PixelType;
+ ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
+
+
+ // Call UpdateWithDim
+ if (m_ArgsInfo.input_given>1) Dimension+=1;
+ if(Dimension==2) UpdateWithDim<2>(PixelType, Components);
+ else if(Dimension==3)UpdateWithDim<3>(PixelType, Components);
+ else if (Dimension==4)UpdateWithDim<4>(PixelType, Components);
+ else {
+ std::cout<<"Error, Only for 2, 3 or 4D!!!"<<std::endl ;
+ return;
+ }
+}
+
+//-------------------------------------------------------------------
+// Update with the number of dimensions
+//-------------------------------------------------------------------
+template<class args_info_type>
+template<unsigned int Dimension>
+void
+AverageTemporalDimensionGenericFilter<args_info_type>::UpdateWithDim(const std::string PixelType, const int Components)
+{
+ if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D with "<<Components<<" component(s) of "<< PixelType<<"..."<<std::endl;
+
+ if (Components==1) {
+ if(PixelType == "short") {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, signed short>();
+ }
+ // else if(PixelType == "unsigned_short"){
+ // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
+ // UpdateWithDimAndPixelType<Dimension, unsigned short>();
+ // }
+
+ else if (PixelType == "unsigned_char") {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, unsigned char>();
+ }
+
+ // else if (PixelType == "char"){
+ // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
+ // UpdateWithDimAndPixelType<Dimension, signed char>();
+ // }
+ else {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, float>();
+ }
}
+ // else if (Components==2)
+ // {
+ // if (m_Verbose) std::cout << "Launching transform in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
+ // UpdateWithDimAndPixelType<Dimension, itk::Vector<float, 2> >();
+ // }
- //-----------------------------------------------------------
- // Update
- //-----------------------------------------------------------
- template<class args_info_type>
- void AverageTemporalDimensionGenericFilter<args_info_type>::Update()
- {
- // Read the Dimension and PixelType
- int Dimension, Components;
- std::string PixelType;
- ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
-
-
- // Call UpdateWithDim
- if (m_ArgsInfo.input_given>1) Dimension+=1;
- if(Dimension==2) UpdateWithDim<2>(PixelType, Components);
- else if(Dimension==3)UpdateWithDim<3>(PixelType, Components);
- else if (Dimension==4)UpdateWithDim<4>(PixelType, Components);
- else
- {
- std::cout<<"Error, Only for 2, 3 or 4D!!!"<<std::endl ;
- return;
- }
+ else if (Components==3) {
+ if (m_Verbose) std::cout << "Launching transform in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
+ UpdateWithDimAndPixelType<Dimension, itk::Vector<float, 3> >();
}
- //-------------------------------------------------------------------
- // Update with the number of dimensions
- //-------------------------------------------------------------------
- template<class args_info_type>
- template<unsigned int Dimension>
- void
- AverageTemporalDimensionGenericFilter<args_info_type>::UpdateWithDim(const std::string PixelType, const int Components)
- {
- if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D with "<<Components<<" component(s) of "<< PixelType<<"..."<<std::endl;
-
- if (Components==1)
- {
- if(PixelType == "short"){
- if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, signed short>();
- }
- // else if(PixelType == "unsigned_short"){
- // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
- // UpdateWithDimAndPixelType<Dimension, unsigned short>();
- // }
-
- else if (PixelType == "unsigned_char"){
- if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, unsigned char>();
- }
-
- // else if (PixelType == "char"){
- // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
- // UpdateWithDimAndPixelType<Dimension, signed char>();
- // }
- else {
- if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, float>();
- }
- }
-
- // else if (Components==2)
- // {
- // if (m_Verbose) std::cout << "Launching transform in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
- // UpdateWithDimAndPixelType<Dimension, itk::Vector<float, 2> >();
- // }
-
- else if (Components==3)
- {
- if (m_Verbose) std::cout << "Launching transform in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
- UpdateWithDimAndPixelType<Dimension, itk::Vector<float, 3> >();
- }
-
- // else if (Components==4)
- // {
- // if (m_Verbose) std::cout << "Launching transform in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
- // UpdateWithDimAndPixelType<Dimension, itk::Vector<float, 3> >();
- // }
- else std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
+ // else if (Components==4)
+ // {
+ // if (m_Verbose) std::cout << "Launching transform in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
+ // UpdateWithDimAndPixelType<Dimension, itk::Vector<float, 3> >();
+ // }
+ else std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
+}
+
+
+//-------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//-------------------------------------------------------------------
+template<class args_info_type>
+template <unsigned int Dimension, class PixelType>
+void
+AverageTemporalDimensionGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
+{
+
+ // ImageTypes
+ typedef itk::Image<PixelType, Dimension> InputImageType;
+ typedef itk::Image<PixelType, Dimension-1> OutputImageType;
+ typename InputImageType::Pointer input;
+
+ if (m_ArgsInfo.input_given ==1 ) {
+ // Read the input
+ typedef itk::ImageFileReader<InputImageType> InputReaderType;
+ typename InputReaderType::Pointer reader = InputReaderType::New();
+ reader->SetFileName( m_InputFileName);
+ reader->Update();
+ input= reader->GetOutput();
}
+ else {
+ // Read and join multiple inputs
+ if (m_Verbose) std::cout<<m_ArgsInfo.input_given<<" inputs given..."<<std::endl;
+ std::vector<std::string> filenames;
+ for(unsigned int i=0; i<m_ArgsInfo.input_given; i++) {
+ if (m_Verbose) std::cout<<m_ArgsInfo.input_arg[i]<<std::endl;
+ filenames.push_back(m_ArgsInfo.input_arg[i]);
+ }
+
+ typedef itk::ImageSeriesReader<InputImageType> ImageReaderType;
+ typename ImageReaderType::Pointer reader= ImageReaderType::New();
+ reader->SetFileNames(filenames);
+ reader->Update();
+ input =reader->GetOutput();
+ }
- //-------------------------------------------------------------------
- // Update with the number of dimensions and the pixeltype
- //-------------------------------------------------------------------
- template<class args_info_type>
- template <unsigned int Dimension, class PixelType>
- void
- AverageTemporalDimensionGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
- {
-
- // ImageTypes
- typedef itk::Image<PixelType, Dimension> InputImageType;
- typedef itk::Image<PixelType, Dimension-1> OutputImageType;
- typename InputImageType::Pointer input;
-
- if (m_ArgsInfo.input_given ==1 )
- {
- // Read the input
- typedef itk::ImageFileReader<InputImageType> InputReaderType;
- typename InputReaderType::Pointer reader = InputReaderType::New();
- reader->SetFileName( m_InputFileName);
- reader->Update();
- input= reader->GetOutput();
- }
-
- else
- {
- // Read and join multiple inputs
- if (m_Verbose) std::cout<<m_ArgsInfo.input_given<<" inputs given..."<<std::endl;
- std::vector<std::string> filenames;
- for(unsigned int i=0; i<m_ArgsInfo.input_given;i++)
- {
- if (m_Verbose) std::cout<<m_ArgsInfo.input_arg[i]<<std::endl;
- filenames.push_back(m_ArgsInfo.input_arg[i]);
- }
-
- typedef itk::ImageSeriesReader<InputImageType> ImageReaderType;
- typename ImageReaderType::Pointer reader= ImageReaderType::New();
- reader->SetFileNames(filenames);
- reader->Update();
- input =reader->GetOutput();
- }
-
-
- // Output properties
- typename OutputImageType::RegionType region;
- typename OutputImageType::RegionType::SizeType size;
- typename OutputImageType::IndexType index;
- typename OutputImageType::SpacingType spacing;
- typename OutputImageType::PointType origin;
- typename InputImageType::RegionType region4D=input->GetLargestPossibleRegion();
- typename InputImageType::RegionType::SizeType size4D=region4D.GetSize();
- typename InputImageType::IndexType index4D=region4D.GetIndex();
- typename InputImageType::SpacingType spacing4D=input->GetSpacing();
- typename InputImageType::PointType origin4D=input->GetOrigin();
-
- for (unsigned int i=0; i< Dimension-1; i++)
- {
- size[i]=size4D[i];
- index[i]=index4D[i];
- spacing[i]=spacing4D[i];
- origin[i]=origin4D[i];
- }
- region.SetSize(size);
- region.SetIndex(index);
- typename OutputImageType::Pointer output= OutputImageType::New();
- output->SetRegions(region);
- output->SetSpacing(spacing);
- output->SetOrigin(origin);
- output->Allocate();
-
-
- // Region iterators
- typedef itk::ImageRegionIterator<InputImageType> IteratorType;
- std::vector<IteratorType> iterators(size4D[Dimension-1]);
- for (unsigned int i=0; i< size4D[Dimension-1]; i++)
- {
- typename InputImageType::RegionType regionIt=region4D;
- typename InputImageType::RegionType::SizeType sizeIt=regionIt.GetSize();
- sizeIt[Dimension-1]=1;
- regionIt.SetSize(sizeIt);
- typename InputImageType::IndexType indexIt=regionIt.GetIndex();
- indexIt[Dimension-1]=i;
- regionIt.SetIndex(indexIt);
- iterators[i]=IteratorType(input, regionIt);
- }
-
- typedef itk::ImageRegionIterator<OutputImageType> OutputIteratorType;
- OutputIteratorType avIt(output, output->GetLargestPossibleRegion());
-
- // Average
- PixelType vector;
- PixelType zeroVector=itk::NumericTraits<PixelType>::Zero;
- //zeroVector.Fill(0.0);
- while (!(iterators[0]).IsAtEnd())
- {
- vector=zeroVector;
- for (unsigned int i=0; i<size4D[Dimension-1]; i++)
- {
- vector+=iterators[i].Get();
- ++(iterators[i]);
- }
- vector/=size4D[Dimension-1];
- avIt.Set(vector);
- ++avIt;
- }
-
- // Output
- typedef itk::ImageFileWriter<OutputImageType> WriterType;
- typename WriterType::Pointer writer = WriterType::New();
- writer->SetFileName(m_ArgsInfo.output_arg);
- writer->SetInput(output);
- writer->Update();
+ // Output properties
+ typename OutputImageType::RegionType region;
+ typename OutputImageType::RegionType::SizeType size;
+ typename OutputImageType::IndexType index;
+ typename OutputImageType::SpacingType spacing;
+ typename OutputImageType::PointType origin;
+ typename InputImageType::RegionType region4D=input->GetLargestPossibleRegion();
+ typename InputImageType::RegionType::SizeType size4D=region4D.GetSize();
+ typename InputImageType::IndexType index4D=region4D.GetIndex();
+ typename InputImageType::SpacingType spacing4D=input->GetSpacing();
+ typename InputImageType::PointType origin4D=input->GetOrigin();
+
+ for (unsigned int i=0; i< Dimension-1; i++) {
+ size[i]=size4D[i];
+ index[i]=index4D[i];
+ spacing[i]=spacing4D[i];
+ origin[i]=origin4D[i];
+ }
+ region.SetSize(size);
+ region.SetIndex(index);
+ typename OutputImageType::Pointer output= OutputImageType::New();
+ output->SetRegions(region);
+ output->SetSpacing(spacing);
+ output->SetOrigin(origin);
+ output->Allocate();
+
+
+ // Region iterators
+ typedef itk::ImageRegionIterator<InputImageType> IteratorType;
+ std::vector<IteratorType> iterators(size4D[Dimension-1]);
+ for (unsigned int i=0; i< size4D[Dimension-1]; i++) {
+ typename InputImageType::RegionType regionIt=region4D;
+ typename InputImageType::RegionType::SizeType sizeIt=regionIt.GetSize();
+ sizeIt[Dimension-1]=1;
+ regionIt.SetSize(sizeIt);
+ typename InputImageType::IndexType indexIt=regionIt.GetIndex();
+ indexIt[Dimension-1]=i;
+ regionIt.SetIndex(indexIt);
+ iterators[i]=IteratorType(input, regionIt);
}
+ typedef itk::ImageRegionIterator<OutputImageType> OutputIteratorType;
+ OutputIteratorType avIt(output, output->GetLargestPossibleRegion());
+
+ // Average
+ PixelType vector;
+ PixelType zeroVector=itk::NumericTraits<PixelType>::Zero;
+ //zeroVector.Fill(0.0);
+ while (!(iterators[0]).IsAtEnd()) {
+ vector=zeroVector;
+ for (unsigned int i=0; i<size4D[Dimension-1]; i++) {
+ vector+=iterators[i].Get();
+ ++(iterators[i]);
+ }
+ vector/=size4D[Dimension-1];
+ avIt.Set(vector);
+ ++avIt;
+ }
+
+ // Output
+ typedef itk::ImageFileWriter<OutputImageType> WriterType;
+ typename WriterType::Pointer writer = WriterType::New();
+ writer->SetFileName(m_ArgsInfo.output_arg);
+ writer->SetInput(output);
+ writer->Update();
+
+}
+
}//end clitk
-
+
#endif //#define clitkAverageTemporalDimensionGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff