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 /* =================================================
  22  * @file   clitkRegionGrowingGenericFilter.txx
  23  * @author
  24  * @date
  25  *
  26  * @brief
  27  *
  28  ===================================================*/
  29
  30
  31 namespace clitk
  32 {
  33
  34   //-------------------------------------------------------------------
  35   // Update with the number of dimensions
  36   //-------------------------------------------------------------------
  37   template<unsigned int Dimension>
  38   void
  39   RegionGrowingGenericFilter::UpdateWithDim(std::string PixelType)
  40   {
  41     if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
  42
  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>();
  46     }
  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>();
  50     //     }
  51
  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>();
  55     }
  56
  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>();
  60     //     }
  61     else {
  62       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  63       UpdateWithDimAndPixelType<Dimension, float>();
  64     }
  65   }
  66
  67
  68   //-------------------------------------------------------------------
  69   // Update with the number of dimensions and the pixeltype
  70   //-------------------------------------------------------------------
  71   template <unsigned int Dimension, class  PixelType>
  72   void
  73   RegionGrowingGenericFilter::UpdateWithDimAndPixelType()
  74   {
  75
  76     // ImageTypes
  77     typedef itk::Image<PixelType, Dimension> InputImageType;
  78     typedef itk::Image<PixelType, Dimension> OutputImageType;
  79
  80     // Read the input
  81     typedef itk::ImageFileReader<InputImageType> InputReaderType;
  82     typename InputReaderType::Pointer reader = InputReaderType::New();
  83     reader->SetFileName( m_InputFileName);
  84     reader->Update();
  85     typename InputImageType::Pointer input= reader->GetOutput();
  86
  87     // Seed
  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];
  92
  93     else if ( m_ArgsInfo.seed_given==1)
  94       index.Fill(m_ArgsInfo.seed_arg[0]);
  95
  96     else index.Fill(m_ArgsInfo.seed_arg[0]);
  97     if(m_Verbose)std::cout<<"Setting seed index to "<<index<<"..."<<std::endl;
  98
  99
 100     // Filter
 101     typedef itk::ImageToImageFilter<InputImageType, OutputImageType> ImageToImageFilterType;
 102     typename ImageToImageFilterType::Pointer filter;
 103
 104     switch (m_ArgsInfo.type_arg)
 105       {
 106       case 0: {
 107
 108         typedef itk::ConnectedThresholdImageFilter<InputImageType, OutputImageType> ImageFilterType;
 109         typename ImageFilterType::Pointer f= ImageFilterType::New();
 110
 111         f->SetLower(m_ArgsInfo.lower_arg);
 112         f->SetUpper(m_ArgsInfo.upper_arg);
 113         f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
 114         f->SetSeed(index);
 115         filter=f;
 116         if(m_Verbose)std::cout<<"Using the connected threshold image filter..."<<std::endl;
 117
 118         break;
 119       }
 120
 121       case 1: {
 122
 123         typedef itk::NeighborhoodConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 124         typename ImageFilterType::Pointer f= ImageFilterType::New();
 125
 126         // Radius
 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];
 131
 132         else if ( m_ArgsInfo.radius_given==1)
 133           size.Fill(m_ArgsInfo.radius_arg[0]);
 134
 135         else size.Fill(m_ArgsInfo.radius_arg[0]);
 136         if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
 137
 138         f->SetLower(m_ArgsInfo.lower_arg);
 139         f->SetUpper(m_ArgsInfo.upper_arg);
 140         f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
 141         f->AddSeed(index);
 142         f->SetRadius(size);
 143         filter=f;
 144         if(m_Verbose)std::cout<<"Using the neighborhood threshold connected image filter..."<<std::endl;
 145
 146         break;
 147       }
 148
 149       case 2: {
 150
 151         typedef itk::ConfidenceConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 152         typename ImageFilterType::Pointer f= ImageFilterType::New();
 153
 154         // Radius
 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];
 159
 160         else if ( m_ArgsInfo.radius_given==1)
 161           size.Fill(m_ArgsInfo.radius_arg[0]);
 162
 163         else size.Fill(m_ArgsInfo.radius_arg[0]);
 164         if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
 165
 166         f->SetMultiplier( m_ArgsInfo.multiplier_arg );
 167         f->SetNumberOfIterations( m_ArgsInfo.multiplier_arg );
 168         f->AddSeed( index );
 169         f->SetNumberOfIterations( m_ArgsInfo.iter_arg);
 170         f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
 171         f->SetInitialNeighborhoodRadius(size[0]);
 172         filter=f;
 173         if(m_Verbose)std::cout<<"Using the confidence threshold connected image filter..."<<std::endl;
 174
 175         break;
 176       }
 177
 178       case 3: {
 179
 180         typedef clitk::LocallyAdaptiveThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 181         typename ImageFilterType::Pointer f= ImageFilterType::New();
 182
 183         // Radius
 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;
 190
 191         // params
 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);
 200         f->AddSeed(index);
 201         f->SetRadius(size);
 202         filter=f;
 203         if(m_Verbose)std::cout<<"Using the locally adaptive threshold connected image filter..."<<std::endl;
 204
 205         break;
 206       }
 207
 208       case 4: {
 209
 210         typedef clitk::ExplosionControlledThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 211         typename ImageFilterType::Pointer f= ImageFilterType::New();
 212
 213         //      // Radius
 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;
 220
 221         // params
 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);
 234         f->AddSeed(index);
 235         filter=f;
 236         if(m_Verbose)std::cout<<"Using the explosion controlled threshold connected image filter..."<<std::endl;
 237
 238         break;
 239       }
 240
 241     }
 242
 243
 244     filter->SetInput(input);
 245     filter->Update();
 246     typename OutputImageType::Pointer output=filter->GetOutput();
 247
 248     // Output
 249     typedef itk::ImageFileWriter<OutputImageType> WriterType;
 250     typename WriterType::Pointer writer = WriterType::New();
 251     writer->SetFileName(m_ArgsInfo.output_arg);
 252     writer->SetInput(output);
 253     writer->Update();
 254   }
 255
 256 }//end clitk
 257
 258 #endif //#define clitkRegionGrowingGenericFilter_txx