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://www.centreleonberard.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 #include <itkBinaryBallStructuringElement.h>
  21 #include <itkConstShapedNeighborhoodIterator.h>
  22
  23 namespace clitk
  24 {
  25
  26   //-------------------------------------------------------------------
  27   // Update with the number of dimensions
  28   //-------------------------------------------------------------------
  29   template<unsigned int Dimension>
  30   void
  31   RegionGrowingGenericFilter::UpdateWithDim(std::string PixelType)
  32   {
  33     if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
  34
  35     if(PixelType == "short"){
  36       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
  37       UpdateWithDimAndPixelType<Dimension, signed short>();
  38     }
  39     //    else if(PixelType == "unsigned_short"){
  40     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
  41     //       UpdateWithDimAndPixelType<Dimension, unsigned short>();
  42     //     }
  43
  44     else if (PixelType == "unsigned_char"){
  45       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
  46       UpdateWithDimAndPixelType<Dimension, unsigned char>();
  47     }
  48
  49     //     else if (PixelType == "char"){
  50     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
  51     //       UpdateWithDimAndPixelType<Dimension, signed char>();
  52     //     }
  53     else {
  54       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  55       UpdateWithDimAndPixelType<Dimension, float>();
  56     }
  57   }
  58
  59
  60   //-------------------------------------------------------------------
  61   // Update with the number of dimensions and the pixeltype
  62   //-------------------------------------------------------------------
  63   template <unsigned int Dimension, class  PixelType>
  64   void
  65   RegionGrowingGenericFilter::UpdateWithDimAndPixelType()
  66   {
  67
  68     // ImageTypes
  69     typedef itk::Image<PixelType, Dimension> InputImageType;
  70     typedef itk::Image<PixelType, Dimension> OutputImageType;
  71
  72     // Read the input
  73     typedef itk::ImageFileReader<InputImageType> InputReaderType;
  74     typename InputReaderType::Pointer reader = InputReaderType::New();
  75     reader->SetFileName( m_InputFileName);
  76     reader->Update();
  77     typename InputImageType::Pointer input= reader->GetOutput();
  78
  79     // Seed
  80     typedef typename  std::vector<typename InputImageType::IndexType> SeedsType;
  81     SeedsType seeds(1);
  82     if(m_ArgsInfo.seed_given==Dimension)
  83       for (unsigned int i=0; i<Dimension;i++)
  84         seeds[0][i]=m_ArgsInfo.seed_arg[i];
  85
  86     else if ( m_ArgsInfo.seed_given==1)
  87       seeds[0].Fill(m_ArgsInfo.seed_arg[0]);
  88
  89     else seeds[0].Fill(m_ArgsInfo.seed_arg[0]);
  90     if(m_Verbose)std::cout<<"Setting seed seeds to "<<seeds[0]<<"..."<<std::endl;
  91
  92     if (m_ArgsInfo.seedRadius_given)
  93     {
  94       typedef itk::BinaryBallStructuringElement<PixelType, Dimension> BallType;
  95       typename BallType::RadiusType r;
  96
  97       if (m_ArgsInfo.seedRadius_given == Dimension)
  98         for (unsigned i = 0; i < Dimension; i++)
  99           r[i] = m_ArgsInfo.seedRadius_arg[i];
 100       else
 101         r.Fill(m_ArgsInfo.seedRadius_arg[0]);
 102
 103       BallType ball;
 104       ball.SetRadius(r);
 105       ball.CreateStructuringElement();
 106
 107       typedef itk::ConstShapedNeighborhoodIterator<InputImageType> IteratorType;
 108       IteratorType it(ball.GetRadius(),
 109           input,
 110           input->GetLargestPossibleRegion());
 111 #if ITK_VERSION_MAJOR < 4
 112       typename BallType::ConstIterator nit;
 113       unsigned idx = 0;
 114       for (nit = ball.Begin(); nit != ball.End(); ++nit, ++idx)
 115       {
 116         if (*nit)
 117         {
 118           it.ActivateOffset(it.GetOffset(idx));
 119         }
 120         else
 121         {
 122           it.DeactivateOffset(it.GetOffset(idx));
 123         }
 124       }
 125 #else
 126       it.CreateActiveListFromNeighborhood(ball);
 127       it.NeedToUseBoundaryConditionOff();
 128 #endif
 129
 130       it.SetLocation(seeds[0]);
 131       for (typename IteratorType::ConstIterator i = it.Begin(); !i.IsAtEnd(); ++i)
 132       {
 133         typename InputImageType::IndexType id = seeds[0] + i.GetNeighborhoodOffset();
 134         if (id != seeds[0] && input->GetLargestPossibleRegion().IsInside(id))
 135           seeds.push_back(id);
 136       }
 137     }
 138
 139     // Filter
 140     typedef itk::ImageToImageFilter<InputImageType, OutputImageType> ImageToImageFilterType;
 141     typename ImageToImageFilterType::Pointer filter;
 142
 143     switch (m_ArgsInfo.type_arg)
 144       {
 145       case 0: {
 146
 147         typedef itk::ConnectedThresholdImageFilter<InputImageType, OutputImageType> ImageFilterType;
 148         typename ImageFilterType::Pointer f= ImageFilterType::New();
 149
 150         f->SetLower(m_ArgsInfo.lower_arg);
 151         f->SetUpper(m_ArgsInfo.upper_arg);
 152         f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
 153         for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
 154           f->AddSeed(*it);
 155         filter=f;
 156         if(m_Verbose)std::cout<<"Using the connected threshold image filter..."<<std::endl;
 157
 158         break;
 159       }
 160
 161       case 1: {
 162
 163         typedef itk::NeighborhoodConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 164         typename ImageFilterType::Pointer f= ImageFilterType::New();
 165
 166         // Radius
 167         typename  InputImageType::SizeType size;
 168         if(m_ArgsInfo.radius_given==Dimension)
 169           for (unsigned int i=0; i<Dimension;i++)
 170             size[i]=m_ArgsInfo.radius_arg[i];
 171
 172         else if ( m_ArgsInfo.radius_given==1)
 173           size.Fill(m_ArgsInfo.radius_arg[0]);
 174
 175         else size.Fill(m_ArgsInfo.radius_arg[0]);
 176         if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
 177
 178         f->SetLower(m_ArgsInfo.lower_arg);
 179         f->SetUpper(m_ArgsInfo.upper_arg);
 180         f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
 181         for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
 182           f->AddSeed(*it);
 183         f->SetRadius(size);
 184         filter=f;
 185         if(m_Verbose)std::cout<<"Using the neighborhood threshold connected image filter..."<<std::endl;
 186
 187         break;
 188       }
 189
 190       case 2: {
 191
 192         typedef itk::ConfidenceConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 193         typename ImageFilterType::Pointer f= ImageFilterType::New();
 194
 195         // Radius
 196         typename  InputImageType::SizeType size;
 197         if(m_ArgsInfo.radius_given==Dimension)
 198           for (unsigned int i=0; i<Dimension;i++)
 199             size[i]=m_ArgsInfo.radius_arg[i];
 200
 201         else if ( m_ArgsInfo.radius_given==1)
 202           size.Fill(m_ArgsInfo.radius_arg[0]);
 203
 204         else size.Fill(m_ArgsInfo.radius_arg[0]);
 205         if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
 206
 207         f->SetMultiplier( m_ArgsInfo.multiplier_arg );
 208         f->SetNumberOfIterations( m_ArgsInfo.multiplier_arg );
 209         for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
 210           f->AddSeed(*it);
 211         f->SetNumberOfIterations( m_ArgsInfo.iter_arg);
 212         f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
 213         f->SetInitialNeighborhoodRadius(size[0]);
 214         filter=f;
 215         if(m_Verbose)std::cout<<"Using the confidence threshold connected image filter..."<<std::endl;
 216
 217         break;
 218       }
 219
 220       case 3: {
 221
 222         typedef clitk::LocallyAdaptiveThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 223         typename ImageFilterType::Pointer f= ImageFilterType::New();
 224
 225         // Radius
 226         typename  InputImageType::SizeType size;
 227         if(m_ArgsInfo.radius_given==Dimension)
 228           for (unsigned int i=0; i<Dimension;i++)
 229             size[i]=m_ArgsInfo.radius_arg[i];
 230         else size.Fill(m_ArgsInfo.radius_arg[0]);
 231         if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
 232
 233         // params
 234         f->SetLower(m_ArgsInfo.lower_arg);
 235         f->SetUpper(m_ArgsInfo.upper_arg);
 236         f->SetLowerBorderIsGiven(m_ArgsInfo.adaptLower_flag);
 237         f->SetLowerBorderIsGiven(m_ArgsInfo.adaptUpper_flag);
 238         f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
 239         f->SetMultiplier(m_ArgsInfo.multiplier_arg);
 240         f->SetMaximumSDIsGiven(m_ArgsInfo.maxSD_given);
 241         if (m_ArgsInfo.maxSD_given) f->SetMaximumSD(m_ArgsInfo.maxSD_arg);
 242         for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
 243           f->AddSeed(*it);
 244         f->SetRadius(size);
 245         filter=f;
 246         if(m_Verbose)std::cout<<"Using the locally adaptive threshold connected image filter..."<<std::endl;
 247
 248         break;
 249       }
 250
 251       case 4: {
 252
 253         typedef clitk::ExplosionControlledThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 254         typename ImageFilterType::Pointer f= ImageFilterType::New();
 255
 256         //      // Radius
 257         //      typename  InputImageType::SizeType size;
 258         //      if(m_ArgsInfo.radius_given==Dimension)
 259         //        for (unsigned int i=0; i<Dimension;i++)
 260         //          size[i]=m_ArgsInfo.radius_arg[i];
 261         //      else size.Fill(m_ArgsInfo.radius_arg[0]);
 262         //      if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
 263
 264         // params
 265         f->SetVerbose(m_ArgsInfo.verbose_flag);
 266         f->SetLower(m_ArgsInfo.lower_arg);
 267         f->SetUpper(m_ArgsInfo.upper_arg);
 268         f->SetMinimumLowerThreshold(m_ArgsInfo.minLower_arg);
 269         f->SetMaximumUpperThreshold(m_ArgsInfo.maxUpper_arg);
 270         f->SetAdaptLowerBorder(m_ArgsInfo.adaptLower_flag);
 271         f->SetAdaptUpperBorder(m_ArgsInfo.adaptUpper_flag);
 272         f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
 273         f->SetMultiplier(m_ArgsInfo.multiplier_arg);
 274         f->SetThresholdStepSize(m_ArgsInfo.step_arg);
 275         f->SetMinimumThresholdStepSize(m_ArgsInfo.minStep_arg);
 276         f->SetFullyConnected(m_ArgsInfo.full_flag);
 277         for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
 278           f->AddSeed(*it);
 279         filter=f;
 280         if(m_Verbose)std::cout<<"Using the explosion controlled threshold connected image filter..."<<std::endl;
 281
 282         break;
 283       }
 284
 285     }
 286
 287
 288     filter->SetInput(input);
 289     filter->Update();
 290     typename OutputImageType::Pointer output=filter->GetOutput();
 291
 292     // Output
 293     typedef itk::ImageFileWriter<OutputImageType> WriterType;
 294     typename WriterType::Pointer writer = WriterType::New();
 295     writer->SetFileName(m_ArgsInfo.output_arg);
 296     writer->SetInput(output);
 297     writer->Update();
 298   }
 299
 300 }//end clitk
 301
 302 #endif //#define clitkRegionGrowingGenericFilter_txx