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 ===========================================================================**/
19 #ifndef CLITKREGIONGROWINGGENERICFILTER_TXX
20 #define CLITKREGIONGROWINGGENERICFILTER_TXX
22 #include <itkBinaryBallStructuringElement.h>
23 #include <itkConstShapedNeighborhoodIterator.h>
26 //--------------------------------------------------------------------
27 template<class ArgsInfoType>
28 clitk::RegionGrowingGenericFilter<ArgsInfoType>::RegionGrowingGenericFilter():
29 ImageToImageGenericFilter<Self>("RegionGrowing")
31 InitializeImageType<2>();
32 InitializeImageType<3>();
33 //InitializeImageType<4>();
35 //--------------------------------------------------------------------
38 //--------------------------------------------------------------------
39 template<class ArgsInfoType>
40 template<unsigned int Dim>
41 void clitk::RegionGrowingGenericFilter<ArgsInfoType>::InitializeImageType()
43 ADD_IMAGE_TYPE(Dim, uchar);
44 ADD_IMAGE_TYPE(Dim, short);
45 // ADD_IMAGE_TYPE(Dim, int);
46 ADD_IMAGE_TYPE(Dim, float);
48 //--------------------------------------------------------------------
51 //--------------------------------------------------------------------
52 template<class ArgsInfoType>
53 void clitk::RegionGrowingGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a)
56 this->SetIOVerbose(mArgsInfo.verbose_flag);
57 if (mArgsInfo.input_given) this->AddInputFilename(mArgsInfo.input_arg);
58 if (mArgsInfo.output_given) this->SetOutputFilename(mArgsInfo.output_arg);
60 //--------------------------------------------------------------------
63 //--------------------------------------------------------------------
64 // Update with the number of dimensions and the pixeltype
65 //--------------------------------------------------------------------
66 template<class ArgsInfoType>
67 template<class ImageType>
68 void clitk::RegionGrowingGenericFilter<ArgsInfoType>::UpdateWithInputImageType()
70 DD("UpdateWithInputImageType");
71 const int Dimension = ImageType::ImageDimension;
74 typedef ImageType InputImageType;
75 typedef ImageType OutputImageType;
76 typedef typename ImageType::PixelType PixelType;
79 typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
82 typedef typename std::vector<typename InputImageType::IndexType> SeedsType;
84 if (mArgsInfo.seed_given==Dimension)
85 for (unsigned int i=0; i<Dimension;i++)
86 seeds[0][i]=mArgsInfo.seed_arg[i];
88 else if ( mArgsInfo.seed_given==1)
89 seeds[0].Fill(mArgsInfo.seed_arg[0]);
91 else seeds[0].Fill(mArgsInfo.seed_arg[0]);
92 if (mArgsInfo.verbose_flag) std::cout<<"Setting seed seeds to "<<seeds[0]<<"..."<<std::endl;
94 if (mArgsInfo.seedRadius_given)
96 typedef itk::BinaryBallStructuringElement<PixelType, Dimension> BallType;
97 typename BallType::RadiusType r;
99 if (mArgsInfo.seedRadius_given == Dimension)
100 for (unsigned i = 0; i < Dimension; i++)
101 r[i] = mArgsInfo.seedRadius_arg[i];
103 r.Fill(mArgsInfo.seedRadius_arg[0]);
107 ball.CreateStructuringElement();
109 typedef itk::ConstShapedNeighborhoodIterator<InputImageType> IteratorType;
110 IteratorType it(ball.GetRadius(),
112 input->GetLargestPossibleRegion());
113 it.CreateActiveListFromNeighborhood(ball);
114 it.NeedToUseBoundaryConditionOff();
116 it.SetLocation(seeds[0]);
117 for (typename IteratorType::ConstIterator i = it.Begin(); !i.IsAtEnd(); ++i)
119 typename InputImageType::IndexType id = seeds[0] + i.GetNeighborhoodOffset();
120 if (id != seeds[0] && input->GetLargestPossibleRegion().IsInside(id))
126 typedef itk::ImageToImageFilter<InputImageType, OutputImageType> ImageToImageFilterType;
127 typename ImageToImageFilterType::Pointer filter;
129 switch (mArgsInfo.type_arg)
133 typedef itk::ConnectedThresholdImageFilter<InputImageType, OutputImageType> ImageFilterType;
134 typename ImageFilterType::Pointer f= ImageFilterType::New();
136 f->SetLower(mArgsInfo.lower_arg);
137 f->SetUpper(mArgsInfo.upper_arg);
138 f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
139 for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
142 if (mArgsInfo.verbose_flag) std::cout<<"Using the connected threshold image filter..."<<std::endl;
149 typedef itk::NeighborhoodConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
150 typename ImageFilterType::Pointer f= ImageFilterType::New();
153 typename InputImageType::SizeType size;
154 if (mArgsInfo.radius_given==Dimension)
155 for (unsigned int i=0; i<Dimension;i++)
156 size[i]=mArgsInfo.radius_arg[i];
158 else if ( mArgsInfo.radius_given==1)
159 size.Fill(mArgsInfo.radius_arg[0]);
161 else size.Fill(mArgsInfo.radius_arg[0]);
162 if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
164 f->SetLower(mArgsInfo.lower_arg);
165 f->SetUpper(mArgsInfo.upper_arg);
166 f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
167 for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
171 if (mArgsInfo.verbose_flag) std::cout<<"Using the neighborhood threshold connected image filter..."<<std::endl;
178 typedef itk::ConfidenceConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
179 typename ImageFilterType::Pointer f= ImageFilterType::New();
182 typename InputImageType::SizeType size;
183 if (mArgsInfo.radius_given==Dimension)
184 for (unsigned int i=0; i<Dimension;i++)
185 size[i]=mArgsInfo.radius_arg[i];
187 else if ( mArgsInfo.radius_given==1)
188 size.Fill(mArgsInfo.radius_arg[0]);
190 else size.Fill(mArgsInfo.radius_arg[0]);
191 if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
193 f->SetMultiplier( mArgsInfo.multiplier_arg );
194 f->SetNumberOfIterations( mArgsInfo.multiplier_arg );
195 for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
197 f->SetNumberOfIterations( mArgsInfo.iter_arg);
198 f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
199 f->SetInitialNeighborhoodRadius(size[0]);
201 if (mArgsInfo.verbose_flag) std::cout<<"Using the confidence threshold connected image filter..."<<std::endl;
208 typedef clitk::LocallyAdaptiveThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
209 typename ImageFilterType::Pointer f= ImageFilterType::New();
212 typename InputImageType::SizeType size;
213 if (mArgsInfo.radius_given==Dimension)
214 for (unsigned int i=0; i<Dimension;i++)
215 size[i]=mArgsInfo.radius_arg[i];
216 else size.Fill(mArgsInfo.radius_arg[0]);
217 if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
220 f->SetLower(mArgsInfo.lower_arg);
221 f->SetUpper(mArgsInfo.upper_arg);
222 f->SetLowerBorderIsGiven(mArgsInfo.adaptLower_flag);
223 f->SetLowerBorderIsGiven(mArgsInfo.adaptUpper_flag);
224 f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
225 f->SetMultiplier(mArgsInfo.multiplier_arg);
226 f->SetMaximumSDIsGiven(mArgsInfo.maxSD_given);
227 if (mArgsInfo.maxSD_given) f->SetMaximumSD(mArgsInfo.maxSD_arg);
228 for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
232 if (mArgsInfo.verbose_flag) std::cout<<"Using the locally adaptive threshold connected image filter..."<<std::endl;
239 typedef clitk::ExplosionControlledThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
240 typename ImageFilterType::Pointer f= ImageFilterType::New();
243 // typename InputImageType::SizeType size;
244 // if (mArgsInfo.radius_given==Dimension)
245 // for (unsigned int i=0; i<Dimension;i++)
246 // size[i]=mArgsInfo.radius_arg[i];
247 // else size.Fill(mArgsInfo.radius_arg[0]);
248 // if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
251 f->SetVerbose(mArgsInfo.verbose_flag);
252 f->SetLower(mArgsInfo.lower_arg);
253 f->SetUpper(mArgsInfo.upper_arg);
254 f->SetMinimumLowerThreshold(mArgsInfo.minLower_arg);
255 f->SetMaximumUpperThreshold(mArgsInfo.maxUpper_arg);
256 f->SetAdaptLowerBorder(mArgsInfo.adaptLower_flag);
257 f->SetAdaptUpperBorder(mArgsInfo.adaptUpper_flag);
258 f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
259 f->SetMultiplier(mArgsInfo.multiplier_arg);
260 f->SetThresholdStepSize(mArgsInfo.step_arg);
261 f->SetMinimumThresholdStepSize(mArgsInfo.minStep_arg);
262 f->SetFullyConnected(mArgsInfo.full_flag);
263 for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
266 if (mArgsInfo.verbose_flag) std::cout<<"Using the explosion controlled threshold connected image filter..."<<std::endl;
274 filter->SetInput(input);
276 typename OutputImageType::Pointer output=filter->GetOutput();
278 // Write/Save results
279 this->template SetNextOutput<OutputImageType>(output);
281 //--------------------------------------------------------------------
284 #endif //#define CLITKREGIONGROWINGGENERICFILTER_TXX