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 clitkRegionGrowingGenericFilter_txx
19 #define clitkRegionGrowingGenericFilter_txx
24 //-------------------------------------------------------------------
25 // Update with the number of dimensions
26 //-------------------------------------------------------------------
27 template<unsigned int Dimension>
29 RegionGrowingGenericFilter::UpdateWithDim(std::string PixelType)
31 if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
33 if(PixelType == "short"){
34 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
35 UpdateWithDimAndPixelType<Dimension, signed short>();
37 // else if(PixelType == "unsigned_short"){
38 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
39 // UpdateWithDimAndPixelType<Dimension, unsigned short>();
42 else if (PixelType == "unsigned_char"){
43 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
44 UpdateWithDimAndPixelType<Dimension, unsigned char>();
47 // else if (PixelType == "char"){
48 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
49 // UpdateWithDimAndPixelType<Dimension, signed char>();
52 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
53 UpdateWithDimAndPixelType<Dimension, float>();
58 //-------------------------------------------------------------------
59 // Update with the number of dimensions and the pixeltype
60 //-------------------------------------------------------------------
61 template <unsigned int Dimension, class PixelType>
63 RegionGrowingGenericFilter::UpdateWithDimAndPixelType()
67 typedef itk::Image<PixelType, Dimension> InputImageType;
68 typedef itk::Image<PixelType, Dimension> OutputImageType;
71 typedef itk::ImageFileReader<InputImageType> InputReaderType;
72 typename InputReaderType::Pointer reader = InputReaderType::New();
73 reader->SetFileName( m_InputFileName);
75 typename InputImageType::Pointer input= reader->GetOutput();
78 typename InputImageType::IndexType index;
79 if(m_ArgsInfo.seed_given==Dimension)
80 for (unsigned int i=0; i<Dimension;i++)
81 index[i]=m_ArgsInfo.seed_arg[i];
83 else if ( m_ArgsInfo.seed_given==1)
84 index.Fill(m_ArgsInfo.seed_arg[0]);
86 else index.Fill(m_ArgsInfo.seed_arg[0]);
87 if(m_Verbose)std::cout<<"Setting seed index to "<<index<<"..."<<std::endl;
91 typedef itk::ImageToImageFilter<InputImageType, OutputImageType> ImageToImageFilterType;
92 typename ImageToImageFilterType::Pointer filter;
94 switch (m_ArgsInfo.type_arg)
98 typedef itk::ConnectedThresholdImageFilter<InputImageType, OutputImageType> ImageFilterType;
99 typename ImageFilterType::Pointer f= ImageFilterType::New();
101 f->SetLower(m_ArgsInfo.lower_arg);
102 f->SetUpper(m_ArgsInfo.upper_arg);
103 f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
106 if(m_Verbose)std::cout<<"Using the connected threshold image filter..."<<std::endl;
113 typedef itk::NeighborhoodConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
114 typename ImageFilterType::Pointer f= ImageFilterType::New();
117 typename InputImageType::SizeType size;
118 if(m_ArgsInfo.radius_given==Dimension)
119 for (unsigned int i=0; i<Dimension;i++)
120 size[i]=m_ArgsInfo.radius_arg[i];
122 else if ( m_ArgsInfo.radius_given==1)
123 size.Fill(m_ArgsInfo.radius_arg[0]);
125 else size.Fill(m_ArgsInfo.radius_arg[0]);
126 if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
128 f->SetLower(m_ArgsInfo.lower_arg);
129 f->SetUpper(m_ArgsInfo.upper_arg);
130 f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
134 if(m_Verbose)std::cout<<"Using the neighborhood threshold connected image filter..."<<std::endl;
141 typedef itk::ConfidenceConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
142 typename ImageFilterType::Pointer f= ImageFilterType::New();
145 typename InputImageType::SizeType size;
146 if(m_ArgsInfo.radius_given==Dimension)
147 for (unsigned int i=0; i<Dimension;i++)
148 size[i]=m_ArgsInfo.radius_arg[i];
150 else if ( m_ArgsInfo.radius_given==1)
151 size.Fill(m_ArgsInfo.radius_arg[0]);
153 else size.Fill(m_ArgsInfo.radius_arg[0]);
154 if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
156 f->SetMultiplier( m_ArgsInfo.multiplier_arg );
157 f->SetNumberOfIterations( m_ArgsInfo.multiplier_arg );
159 f->SetNumberOfIterations( m_ArgsInfo.iter_arg);
160 f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
161 f->SetInitialNeighborhoodRadius(size[0]);
163 if(m_Verbose)std::cout<<"Using the confidence threshold connected image filter..."<<std::endl;
170 typedef clitk::LocallyAdaptiveThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
171 typename ImageFilterType::Pointer f= ImageFilterType::New();
174 typename InputImageType::SizeType size;
175 if(m_ArgsInfo.radius_given==Dimension)
176 for (unsigned int i=0; i<Dimension;i++)
177 size[i]=m_ArgsInfo.radius_arg[i];
178 else size.Fill(m_ArgsInfo.radius_arg[0]);
179 if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
182 f->SetLower(m_ArgsInfo.lower_arg);
183 f->SetUpper(m_ArgsInfo.upper_arg);
184 f->SetLowerBorderIsGiven(m_ArgsInfo.adaptLower_flag);
185 f->SetLowerBorderIsGiven(m_ArgsInfo.adaptUpper_flag);
186 f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
187 f->SetMultiplier(m_ArgsInfo.multiplier_arg);
188 f->SetMaximumSDIsGiven(m_ArgsInfo.maxSD_given);
189 if (m_ArgsInfo.maxSD_given) f->SetMaximumSD(m_ArgsInfo.maxSD_arg);
193 if(m_Verbose)std::cout<<"Using the locally adaptive threshold connected image filter..."<<std::endl;
200 typedef clitk::ExplosionControlledThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
201 typename ImageFilterType::Pointer f= ImageFilterType::New();
204 // typename InputImageType::SizeType size;
205 // if(m_ArgsInfo.radius_given==Dimension)
206 // for (unsigned int i=0; i<Dimension;i++)
207 // size[i]=m_ArgsInfo.radius_arg[i];
208 // else size.Fill(m_ArgsInfo.radius_arg[0]);
209 // if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
212 f->SetVerbose(m_ArgsInfo.verbose_flag);
213 f->SetLower(m_ArgsInfo.lower_arg);
214 f->SetUpper(m_ArgsInfo.upper_arg);
215 f->SetMinimumLowerThreshold(m_ArgsInfo.minLower_arg);
216 f->SetMaximumUpperThreshold(m_ArgsInfo.maxUpper_arg);
217 f->SetAdaptLowerBorder(m_ArgsInfo.adaptLower_flag);
218 f->SetAdaptUpperBorder(m_ArgsInfo.adaptUpper_flag);
219 f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
220 f->SetMultiplier(m_ArgsInfo.multiplier_arg);
221 f->SetThresholdStepSize(m_ArgsInfo.step_arg);
222 f->SetMinimumThresholdStepSize(m_ArgsInfo.minStep_arg);
223 f->SetFullyConnected(m_ArgsInfo.full_flag);
226 if(m_Verbose)std::cout<<"Using the explosion controlled threshold connected image filter..."<<std::endl;
234 filter->SetInput(input);
236 typename OutputImageType::Pointer output=filter->GetOutput();
239 typedef itk::ImageFileWriter<OutputImageType> WriterType;
240 typename WriterType::Pointer writer = WriterType::New();
241 writer->SetFileName(m_ArgsInfo.output_arg);
242 writer->SetInput(output);
248 #endif //#define clitkRegionGrowingGenericFilter_txx