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://www.centreleonberard.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 clitkMorphoReconstructionGenericFilter_txx
19 #define clitkMorphoReconstructionGenericFilter_txx
21 /* =================================================
22 * @file clitkMorphoReconstructionGenericFilter.txx
28 ===================================================*/
34 //-------------------------------------------------------------------
35 // Update with the number of dimensions
36 //-------------------------------------------------------------------
37 template<unsigned int Dimension>
39 MorphoReconstructionGenericFilter::UpdateWithDim(std::string PixelType)
41 if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
43 if(PixelType == "short"){
44 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
45 UpdateWithDimAndPixelType<Dimension, signed short>();
47 // else if(PixelType == "unsigned_short"){
48 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
49 // UpdateWithDimAndPixelType<Dimension, unsigned short>();
52 else if (PixelType == "unsigned_char"){
53 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
54 UpdateWithDimAndPixelType<Dimension, unsigned char>();
57 // else if (PixelType == "char"){
58 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
59 // UpdateWithDimAndPixelType<Dimension, signed char>();
62 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
63 UpdateWithDimAndPixelType<Dimension, float>();
68 //-------------------------------------------------------------------
69 // Update with the number of dimensions and the pixeltype
70 //-------------------------------------------------------------------
71 template <unsigned int Dimension, class PixelType>
73 MorphoReconstructionGenericFilter::UpdateWithDimAndPixelType()
77 typedef itk::Image<PixelType, Dimension> InputImageType;
78 typedef itk::Image<PixelType, Dimension> OutputImageType;
81 typedef itk::ImageFileReader<InputImageType> InputReaderType;
82 typename InputReaderType::Pointer reader = InputReaderType::New();
83 reader->SetFileName( m_InputFileName);
85 typename InputImageType::Pointer input= reader->GetOutput();
88 typename InputImageType::Pointer mask;
89 if (m_ArgsInfo.mask_given)
91 typename InputReaderType::Pointer maskReader=InputReaderType::New();
92 maskReader->SetFileName(m_ArgsInfo.mask_arg);
94 mask=maskReader->GetOutput();
98 //---------------------------------
99 // Find the type of action
100 //---------------------------------
101 typedef itk::ImageToImageFilter<InputImageType, InputImageType> ImageFilterType;
102 typename ImageFilterType::Pointer filter;
104 typedef itk::BinaryBallStructuringElement<PixelType, Dimension > KernelType;
105 KernelType structuringElement;
106 structuringElement.SetRadius(m_ArgsInfo.radius_arg);
107 structuringElement.CreateStructuringElement();
110 switch(m_ArgsInfo.type_arg)
115 typedef itk::ReconstructionByErosionImageFilter<InputImageType, OutputImageType> FilterType;
116 typename FilterType::Pointer m = FilterType::New();
117 m->SetMarkerImage(input);
118 m->SetMaskImage(mask);
121 if(m_Verbose) std::cout<<"Using the reconstruction by erosion filter..."<<std::endl;
127 typedef itk::ReconstructionByDilationImageFilter<InputImageType, OutputImageType> FilterType;
128 typename FilterType::Pointer m = FilterType::New();
129 m->SetMarkerImage(input);
130 m->SetMaskImage(mask);
133 if(m_Verbose) std::cout<<"Using the reconstruction by dilation filter..."<<std::endl;
140 typedef itk::ClosingByReconstructionImageFilter<InputImageType, OutputImageType, KernelType> FilterType;
141 typename FilterType::Pointer m = FilterType::New();
143 m->SetKernel(structuringElement);
144 m->SetFullyConnected(m_ArgsInfo.full_flag);
145 m->SetPreserveIntensities(m_ArgsInfo.int_flag);
148 if(m_Verbose) std::cout<<"Using the closing by reconstruction filter..."<<std::endl;
155 typedef itk::OpeningByReconstructionImageFilter<InputImageType, OutputImageType, KernelType> FilterType;
156 typename FilterType::Pointer m = FilterType::New();
158 m->SetKernel(structuringElement);
159 m->SetFullyConnected(m_ArgsInfo.full_flag);
160 m->SetPreserveIntensities(m_ArgsInfo.int_flag);
163 if(m_Verbose) std::cout<<"Using the opening by reconstruction filter..."<<std::endl;
169 //---------------------------------
170 // Execute the filter
171 //---------------------------------
172 filter->SetInput(input);
177 catch( itk::ExceptionObject & err )
179 std::cerr << "ExceptionObject caught executing the filter!" << std::endl;
180 std::cerr << err << std::endl;
183 typename OutputImageType::Pointer output=filter->GetOutput();
188 typedef itk::ImageFileWriter<OutputImageType> WriterType;
189 typename WriterType::Pointer writer = WriterType::New();
190 writer->SetFileName(m_ArgsInfo.output_arg);
191 writer->SetInput(output);
199 #endif //#define clitkMorphoReconstructionGenericFilter_txx