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 clitkRegionGrowingGenericFilter_txx
19 #define clitkRegionGrowingGenericFilter_txx
21 /* =================================================
22 * @file clitkRegionGrowingGenericFilter.txx
28 ===================================================*/
34 //-------------------------------------------------------------------
35 // Update with the number of dimensions
36 //-------------------------------------------------------------------
37 template<unsigned int Dimension>
39 RegionGrowingGenericFilter::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 RegionGrowingGenericFilter::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::IndexType index;
89 if(m_ArgsInfo.seed_given==Dimension)
90 for (unsigned int i=0; i<Dimension;i++)
91 index[i]=m_ArgsInfo.seed_arg[i];
93 else if ( m_ArgsInfo.seed_given==1)
94 index.Fill(m_ArgsInfo.seed_arg[0]);
96 else index.Fill(m_ArgsInfo.seed_arg[0]);
97 if(m_Verbose)std::cout<<"Setting seed index to "<<index<<"..."<<std::endl;
101 typedef itk::ImageToImageFilter<InputImageType, OutputImageType> ImageToImageFilterType;
102 typename ImageToImageFilterType::Pointer filter;
104 switch (m_ArgsInfo.type_arg)
108 typedef itk::ConnectedThresholdImageFilter<InputImageType, OutputImageType> ImageFilterType;
109 typename ImageFilterType::Pointer f= ImageFilterType::New();
111 f->SetLower(m_ArgsInfo.lower_arg);
112 f->SetUpper(m_ArgsInfo.upper_arg);
113 f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
116 if(m_Verbose)std::cout<<"Using the connected threshold image filter..."<<std::endl;
123 typedef itk::NeighborhoodConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
124 typename ImageFilterType::Pointer f= ImageFilterType::New();
127 typename InputImageType::SizeType size;
128 if(m_ArgsInfo.radius_given==Dimension)
129 for (unsigned int i=0; i<Dimension;i++)
130 size[i]=m_ArgsInfo.radius_arg[i];
132 else if ( m_ArgsInfo.radius_given==1)
133 size.Fill(m_ArgsInfo.radius_arg[0]);
135 else size.Fill(m_ArgsInfo.radius_arg[0]);
136 if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
138 f->SetLower(m_ArgsInfo.lower_arg);
139 f->SetUpper(m_ArgsInfo.upper_arg);
140 f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
144 if(m_Verbose)std::cout<<"Using the neighborhood threshold connected image filter..."<<std::endl;
151 typedef itk::ConfidenceConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
152 typename ImageFilterType::Pointer f= ImageFilterType::New();
155 typename InputImageType::SizeType size;
156 if(m_ArgsInfo.radius_given==Dimension)
157 for (unsigned int i=0; i<Dimension;i++)
158 size[i]=m_ArgsInfo.radius_arg[i];
160 else if ( m_ArgsInfo.radius_given==1)
161 size.Fill(m_ArgsInfo.radius_arg[0]);
163 else size.Fill(m_ArgsInfo.radius_arg[0]);
164 if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
166 f->SetMultiplier( m_ArgsInfo.multiplier_arg );
167 f->SetNumberOfIterations( m_ArgsInfo.multiplier_arg );
169 f->SetNumberOfIterations( m_ArgsInfo.iter_arg);
170 f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
171 f->SetInitialNeighborhoodRadius(size[0]);
173 if(m_Verbose)std::cout<<"Using the confidence threshold connected image filter..."<<std::endl;
180 typedef clitk::LocallyAdaptiveThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
181 typename ImageFilterType::Pointer f= ImageFilterType::New();
184 typename InputImageType::SizeType size;
185 if(m_ArgsInfo.radius_given==Dimension)
186 for (unsigned int i=0; i<Dimension;i++)
187 size[i]=m_ArgsInfo.radius_arg[i];
188 else size.Fill(m_ArgsInfo.radius_arg[0]);
189 if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
192 f->SetLower(m_ArgsInfo.lower_arg);
193 f->SetUpper(m_ArgsInfo.upper_arg);
194 f->SetLowerBorderIsGiven(m_ArgsInfo.adaptLower_flag);
195 f->SetLowerBorderIsGiven(m_ArgsInfo.adaptUpper_flag);
196 f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
197 f->SetMultiplier(m_ArgsInfo.multiplier_arg);
198 f->SetMaximumSDIsGiven(m_ArgsInfo.maxSD_given);
199 if (m_ArgsInfo.maxSD_given) f->SetMaximumSD(m_ArgsInfo.maxSD_arg);
203 if(m_Verbose)std::cout<<"Using the locally adaptive threshold connected image filter..."<<std::endl;
210 typedef clitk::ExplosionControlledThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
211 typename ImageFilterType::Pointer f= ImageFilterType::New();
214 // typename InputImageType::SizeType size;
215 // if(m_ArgsInfo.radius_given==Dimension)
216 // for (unsigned int i=0; i<Dimension;i++)
217 // size[i]=m_ArgsInfo.radius_arg[i];
218 // else size.Fill(m_ArgsInfo.radius_arg[0]);
219 // if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
222 f->SetVerbose(m_ArgsInfo.verbose_flag);
223 f->SetLower(m_ArgsInfo.lower_arg);
224 f->SetUpper(m_ArgsInfo.upper_arg);
225 f->SetMinimumLowerThreshold(m_ArgsInfo.minLower_arg);
226 f->SetMaximumUpperThreshold(m_ArgsInfo.maxUpper_arg);
227 f->SetAdaptLowerBorder(m_ArgsInfo.adaptLower_flag);
228 f->SetAdaptUpperBorder(m_ArgsInfo.adaptUpper_flag);
229 f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
230 f->SetMultiplier(m_ArgsInfo.multiplier_arg);
231 f->SetThresholdStepSize(m_ArgsInfo.step_arg);
232 f->SetMinimumThresholdStepSize(m_ArgsInfo.minStep_arg);
233 f->SetFullyConnected(m_ArgsInfo.full_flag);
236 if(m_Verbose)std::cout<<"Using the explosion controlled threshold connected image filter..."<<std::endl;
244 filter->SetInput(input);
246 typename OutputImageType::Pointer output=filter->GetOutput();
249 typedef itk::ImageFileWriter<OutputImageType> WriterType;
250 typename WriterType::Pointer writer = WriterType::New();
251 writer->SetFileName(m_ArgsInfo.output_arg);
252 writer->SetInput(output);
258 #endif //#define clitkRegionGrowingGenericFilter_txx