1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
5 - University of LYON http://www.universite-lyon.fr/
6 - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
7 - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
9 This software is distributed WITHOUT ANY WARRANTY; without even
10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
11 PURPOSE. See the copyright notices for more information.
13 It is distributed under dual licence
15 - BSD See included LICENSE.txt file
16 - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
17 ======================================================================-====*/
18 #ifndef clitkAverageTemporalDimensionGenericFilter_txx
19 #define clitkAverageTemporalDimensionGenericFilter_txx
21 /* =================================================
22 * @file clitkAverageTemporalDimensionGenericFilter.txx
28 ===================================================*/
34 //-----------------------------------------------------------
36 //-----------------------------------------------------------
37 template<class args_info_type>
38 AverageTemporalDimensionGenericFilter<args_info_type>::AverageTemporalDimensionGenericFilter()
45 //-----------------------------------------------------------
47 //-----------------------------------------------------------
48 template<class args_info_type>
49 void AverageTemporalDimensionGenericFilter<args_info_type>::Update()
51 // Read the Dimension and PixelType
52 int Dimension, Components;
53 std::string PixelType;
54 ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
58 if (m_ArgsInfo.input_given>1) Dimension+=1;
59 if(Dimension==2) UpdateWithDim<2>(PixelType, Components);
60 else if(Dimension==3)UpdateWithDim<3>(PixelType, Components);
61 else if (Dimension==4)UpdateWithDim<4>(PixelType, Components);
64 std::cout<<"Error, Only for 2, 3 or 4D!!!"<<std::endl ;
69 //-------------------------------------------------------------------
70 // Update with the number of dimensions
71 //-------------------------------------------------------------------
72 template<class args_info_type>
73 template<unsigned int Dimension>
75 AverageTemporalDimensionGenericFilter<args_info_type>::UpdateWithDim(const std::string PixelType, const int Components)
77 if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D with "<<Components<<" component(s) of "<< PixelType<<"..."<<std::endl;
81 if(PixelType == "short"){
82 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
83 UpdateWithDimAndPixelType<Dimension, signed short>();
85 // else if(PixelType == "unsigned_short"){
86 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
87 // UpdateWithDimAndPixelType<Dimension, unsigned short>();
90 else if (PixelType == "unsigned_char"){
91 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
92 UpdateWithDimAndPixelType<Dimension, unsigned char>();
95 // else if (PixelType == "char"){
96 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
97 // UpdateWithDimAndPixelType<Dimension, signed char>();
100 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
101 UpdateWithDimAndPixelType<Dimension, float>();
105 // else if (Components==2)
107 // if (m_Verbose) std::cout << "Launching transform in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
108 // UpdateWithDimAndPixelType<Dimension, itk::Vector<float, 2> >();
111 else if (Components==3)
113 if (m_Verbose) std::cout << "Launching transform in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
114 UpdateWithDimAndPixelType<Dimension, itk::Vector<float, 3> >();
117 // else if (Components==4)
119 // if (m_Verbose) std::cout << "Launching transform in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
120 // UpdateWithDimAndPixelType<Dimension, itk::Vector<float, 3> >();
122 else std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
126 //-------------------------------------------------------------------
127 // Update with the number of dimensions and the pixeltype
128 //-------------------------------------------------------------------
129 template<class args_info_type>
130 template <unsigned int Dimension, class PixelType>
132 AverageTemporalDimensionGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
136 typedef itk::Image<PixelType, Dimension> InputImageType;
137 typedef itk::Image<PixelType, Dimension-1> OutputImageType;
138 typename InputImageType::Pointer input;
140 if (m_ArgsInfo.input_given ==1 )
143 typedef itk::ImageFileReader<InputImageType> InputReaderType;
144 typename InputReaderType::Pointer reader = InputReaderType::New();
145 reader->SetFileName( m_InputFileName);
147 input= reader->GetOutput();
152 // Read and join multiple inputs
153 if (m_Verbose) std::cout<<m_ArgsInfo.input_given<<" inputs given..."<<std::endl;
154 std::vector<std::string> filenames;
155 for(unsigned int i=0; i<m_ArgsInfo.input_given;i++)
157 if (m_Verbose) std::cout<<m_ArgsInfo.input_arg[i]<<std::endl;
158 filenames.push_back(m_ArgsInfo.input_arg[i]);
161 typedef itk::ImageSeriesReader<InputImageType> ImageReaderType;
162 typename ImageReaderType::Pointer reader= ImageReaderType::New();
163 reader->SetFileNames(filenames);
165 input =reader->GetOutput();
170 typename OutputImageType::RegionType region;
171 typename OutputImageType::RegionType::SizeType size;
172 typename OutputImageType::IndexType index;
173 typename OutputImageType::SpacingType spacing;
174 typename OutputImageType::PointType origin;
175 typename InputImageType::RegionType region4D=input->GetLargestPossibleRegion();
176 typename InputImageType::RegionType::SizeType size4D=region4D.GetSize();
177 typename InputImageType::IndexType index4D=region4D.GetIndex();
178 typename InputImageType::SpacingType spacing4D=input->GetSpacing();
179 typename InputImageType::PointType origin4D=input->GetOrigin();
181 for (unsigned int i=0; i< Dimension-1; i++)
185 spacing[i]=spacing4D[i];
186 origin[i]=origin4D[i];
188 region.SetSize(size);
189 region.SetIndex(index);
190 typename OutputImageType::Pointer output= OutputImageType::New();
191 output->SetRegions(region);
192 output->SetSpacing(spacing);
193 output->SetOrigin(origin);
198 typedef itk::ImageRegionIterator<InputImageType> IteratorType;
199 std::vector<IteratorType> iterators(size4D[Dimension-1]);
200 for (unsigned int i=0; i< size4D[Dimension-1]; i++)
202 typename InputImageType::RegionType regionIt=region4D;
203 typename InputImageType::RegionType::SizeType sizeIt=regionIt.GetSize();
204 sizeIt[Dimension-1]=1;
205 regionIt.SetSize(sizeIt);
206 typename InputImageType::IndexType indexIt=regionIt.GetIndex();
207 indexIt[Dimension-1]=i;
208 regionIt.SetIndex(indexIt);
209 iterators[i]=IteratorType(input, regionIt);
212 typedef itk::ImageRegionIterator<OutputImageType> OutputIteratorType;
213 OutputIteratorType avIt(output, output->GetLargestPossibleRegion());
217 PixelType zeroVector=itk::NumericTraits<PixelType>::Zero;
218 //zeroVector.Fill(0.0);
219 while (!(iterators[0]).IsAtEnd())
222 for (unsigned int i=0; i<size4D[Dimension-1]; i++)
224 vector+=iterators[i].Get();
227 vector/=size4D[Dimension-1];
233 typedef itk::ImageFileWriter<OutputImageType> WriterType;
234 typename WriterType::Pointer writer = WriterType::New();
235 writer->SetFileName(m_ArgsInfo.output_arg);
236 writer->SetInput(output);
244 #endif //#define clitkAverageTemporalDimensionGenericFilter_txx