segmentation/clitkRegionGrowingGenericFilter.txx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   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
   8
   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.
  12
  13   It is distributed under dual licence
  14
  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
  20
  21 namespace clitk
  22 {
  23
  24   //-------------------------------------------------------------------
  25   // Update with the number of dimensions
  26   //-------------------------------------------------------------------
  27   template<unsigned int Dimension>
  28   void
  29   RegionGrowingGenericFilter::UpdateWithDim(std::string PixelType)
  30   {
  31     if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
  32
  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>();
  36     }
  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>();
  40     //     }
  41
  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>();
  45     }
  46
  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>();
  50     //     }
  51     else {
  52       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  53       UpdateWithDimAndPixelType<Dimension, float>();
  54     }
  55   }
  56
  57
  58   //-------------------------------------------------------------------
  59   // Update with the number of dimensions and the pixeltype
  60   //-------------------------------------------------------------------
  61   template <unsigned int Dimension, class  PixelType>
  62   void
  63   RegionGrowingGenericFilter::UpdateWithDimAndPixelType()
  64   {
  65
  66     // ImageTypes
  67     typedef itk::Image<PixelType, Dimension> InputImageType;
  68     typedef itk::Image<PixelType, Dimension> OutputImageType;
  69
  70     // Read the input
  71     typedef itk::ImageFileReader<InputImageType> InputReaderType;
  72     typename InputReaderType::Pointer reader = InputReaderType::New();
  73     reader->SetFileName( m_InputFileName);
  74     reader->Update();
  75     typename InputImageType::Pointer input= reader->GetOutput();
  76
  77     // Seed
  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];
  82
  83     else if ( m_ArgsInfo.seed_given==1)
  84       index.Fill(m_ArgsInfo.seed_arg[0]);
  85
  86     else index.Fill(m_ArgsInfo.seed_arg[0]);
  87     if(m_Verbose)std::cout<<"Setting seed index to "<<index<<"..."<<std::endl;
  88
  89
  90     // Filter
  91     typedef itk::ImageToImageFilter<InputImageType, OutputImageType> ImageToImageFilterType;
  92     typename ImageToImageFilterType::Pointer filter;
  93
  94     switch (m_ArgsInfo.type_arg)
  95       {
  96       case 0: {
  97
  98         typedef itk::ConnectedThresholdImageFilter<InputImageType, OutputImageType> ImageFilterType;
  99         typename ImageFilterType::Pointer f= ImageFilterType::New();
 100
 101         f->SetLower(m_ArgsInfo.lower_arg);
 102         f->SetUpper(m_ArgsInfo.upper_arg);
 103         f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
 104         f->SetSeed(index);
 105         filter=f;
 106         if(m_Verbose)std::cout<<"Using the connected threshold image filter..."<<std::endl;
 107
 108         break;
 109       }
 110
 111       case 1: {
 112
 113         typedef itk::NeighborhoodConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 114         typename ImageFilterType::Pointer f= ImageFilterType::New();
 115
 116         // Radius
 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];
 121
 122         else if ( m_ArgsInfo.radius_given==1)
 123           size.Fill(m_ArgsInfo.radius_arg[0]);
 124
 125         else size.Fill(m_ArgsInfo.radius_arg[0]);
 126         if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
 127
 128         f->SetLower(m_ArgsInfo.lower_arg);
 129         f->SetUpper(m_ArgsInfo.upper_arg);
 130         f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
 131         f->AddSeed(index);
 132         f->SetRadius(size);
 133         filter=f;
 134         if(m_Verbose)std::cout<<"Using the neighborhood threshold connected image filter..."<<std::endl;
 135
 136         break;
 137       }
 138
 139       case 2: {
 140
 141         typedef itk::ConfidenceConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 142         typename ImageFilterType::Pointer f= ImageFilterType::New();
 143
 144         // Radius
 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];
 149
 150         else if ( m_ArgsInfo.radius_given==1)
 151           size.Fill(m_ArgsInfo.radius_arg[0]);
 152
 153         else size.Fill(m_ArgsInfo.radius_arg[0]);
 154         if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
 155
 156         f->SetMultiplier( m_ArgsInfo.multiplier_arg );
 157         f->SetNumberOfIterations( m_ArgsInfo.multiplier_arg );
 158         f->AddSeed( index );
 159         f->SetNumberOfIterations( m_ArgsInfo.iter_arg);
 160         f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
 161         f->SetInitialNeighborhoodRadius(size[0]);
 162         filter=f;
 163         if(m_Verbose)std::cout<<"Using the confidence threshold connected image filter..."<<std::endl;
 164
 165         break;
 166       }
 167
 168       case 3: {
 169
 170         typedef clitk::LocallyAdaptiveThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 171         typename ImageFilterType::Pointer f= ImageFilterType::New();
 172
 173         // Radius
 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;
 180
 181         // params
 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);
 190         f->AddSeed(index);
 191         f->SetRadius(size);
 192         filter=f;
 193         if(m_Verbose)std::cout<<"Using the locally adaptive threshold connected image filter..."<<std::endl;
 194
 195         break;
 196       }
 197
 198       case 4: {
 199
 200         typedef clitk::ExplosionControlledThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 201         typename ImageFilterType::Pointer f= ImageFilterType::New();
 202
 203         //      // Radius
 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;
 210
 211         // params
 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);
 224         f->AddSeed(index);
 225         filter=f;
 226         if(m_Verbose)std::cout<<"Using the explosion controlled threshold connected image filter..."<<std::endl;
 227
 228         break;
 229       }
 230
 231     }
 232
 233
 234     filter->SetInput(input);
 235     filter->Update();
 236     typename OutputImageType::Pointer output=filter->GetOutput();
 237
 238     // Output
 239     typedef itk::ImageFileWriter<OutputImageType> WriterType;
 240     typename WriterType::Pointer writer = WriterType::New();
 241     writer->SetFileName(m_ArgsInfo.output_arg);
 242     writer->SetInput(output);
 243     writer->Update();
 244   }
 245
 246 }//end clitk
 247
 248 #endif //#define clitkRegionGrowingGenericFilter_txx