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
  19 #ifndef CLITKREGIONGROWINGGENERICFILTER_TXX
  20 #define CLITKREGIONGROWINGGENERICFILTER_TXX
  21
  22 #include <itkBinaryBallStructuringElement.h>
  23 #include <itkConstShapedNeighborhoodIterator.h>
  24
  25
  26 //--------------------------------------------------------------------
  27 template<class ArgsInfoType>
  28 clitk::RegionGrowingGenericFilter<ArgsInfoType>::RegionGrowingGenericFilter():
  29   ImageToImageGenericFilter<Self>("RegionGrowing")
  30 {
  31   InitializeImageType<2>();
  32   InitializeImageType<3>();
  33   //InitializeImageType<4>();
  34 }
  35 //--------------------------------------------------------------------
  36
  37
  38 //--------------------------------------------------------------------
  39 template<class ArgsInfoType>
  40 template<unsigned int Dim>
  41 void clitk::RegionGrowingGenericFilter<ArgsInfoType>::InitializeImageType()
  42 {
  43   ADD_IMAGE_TYPE(Dim, uchar);
  44   ADD_IMAGE_TYPE(Dim, short);
  45   // ADD_IMAGE_TYPE(Dim, int);
  46   ADD_IMAGE_TYPE(Dim, float);
  47 }
  48 //--------------------------------------------------------------------
  49
  50
  51 //--------------------------------------------------------------------
  52 template<class ArgsInfoType>
  53 void clitk::RegionGrowingGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a)
  54 {
  55   mArgsInfo=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);
  59 }
  60 //--------------------------------------------------------------------
  61
  62
  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()
  69 {
  70   DD("UpdateWithInputImageType");
  71   const int Dimension = ImageType::ImageDimension;
  72
  73   // ImageTypes
  74   typedef ImageType InputImageType;
  75   typedef ImageType OutputImageType;
  76   typedef typename ImageType::PixelType PixelType;
  77
  78   // Reading input
  79   typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
  80
  81   // Seed
  82   typedef typename  std::vector<typename InputImageType::IndexType> SeedsType;
  83   SeedsType seeds(1);
  84   if (mArgsInfo.seed_given==Dimension)
  85     for (unsigned int i=0; i<Dimension;i++)
  86       seeds[0][i]=mArgsInfo.seed_arg[i];
  87
  88   else if ( mArgsInfo.seed_given==1)
  89     seeds[0].Fill(mArgsInfo.seed_arg[0]);
  90
  91   else seeds[0].Fill(mArgsInfo.seed_arg[0]);
  92   if (mArgsInfo.verbose_flag) std::cout<<"Setting seed seeds to "<<seeds[0]<<"..."<<std::endl;
  93
  94   if (mArgsInfo.seedRadius_given)
  95     {
  96       typedef itk::BinaryBallStructuringElement<PixelType, Dimension> BallType;
  97       typename BallType::RadiusType r;
  98
  99       if (mArgsInfo.seedRadius_given == Dimension)
 100         for (unsigned i = 0; i < Dimension; i++)
 101           r[i] = mArgsInfo.seedRadius_arg[i];
 102       else
 103         r.Fill(mArgsInfo.seedRadius_arg[0]);
 104
 105       BallType ball;
 106       ball.SetRadius(r);
 107       ball.CreateStructuringElement();
 108
 109       typedef itk::ConstShapedNeighborhoodIterator<InputImageType> IteratorType;
 110       IteratorType it(ball.GetRadius(),
 111                       input,
 112                       input->GetLargestPossibleRegion());
 113       it.CreateActiveListFromNeighborhood(ball);
 114       it.NeedToUseBoundaryConditionOff();
 115
 116       it.SetLocation(seeds[0]);
 117       for (typename IteratorType::ConstIterator i = it.Begin(); !i.IsAtEnd(); ++i)
 118         {
 119           typename InputImageType::IndexType id = seeds[0] + i.GetNeighborhoodOffset();
 120           if (id != seeds[0] && input->GetLargestPossibleRegion().IsInside(id))
 121             seeds.push_back(id);
 122         }
 123     }
 124
 125   // Filter
 126   typedef itk::ImageToImageFilter<InputImageType, OutputImageType> ImageToImageFilterType;
 127   typename ImageToImageFilterType::Pointer filter;
 128
 129   switch (mArgsInfo.type_arg)
 130     {
 131     case 0: {
 132
 133       typedef itk::ConnectedThresholdImageFilter<InputImageType, OutputImageType> ImageFilterType;
 134       typename ImageFilterType::Pointer f= ImageFilterType::New();
 135
 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)
 140         f->AddSeed(*it);
 141       filter=f;
 142       if (mArgsInfo.verbose_flag) std::cout<<"Using the connected threshold image filter..."<<std::endl;
 143
 144       break;
 145     }
 146
 147     case 1: {
 148
 149       typedef itk::NeighborhoodConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 150       typename ImageFilterType::Pointer f= ImageFilterType::New();
 151
 152       // Radius
 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];
 157
 158       else if ( mArgsInfo.radius_given==1)
 159         size.Fill(mArgsInfo.radius_arg[0]);
 160
 161       else size.Fill(mArgsInfo.radius_arg[0]);
 162       if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
 163
 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)
 168         f->AddSeed(*it);
 169       f->SetRadius(size);
 170       filter=f;
 171       if (mArgsInfo.verbose_flag) std::cout<<"Using the neighborhood threshold connected image filter..."<<std::endl;
 172
 173       break;
 174     }
 175
 176     case 2: {
 177
 178       typedef itk::ConfidenceConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 179       typename ImageFilterType::Pointer f= ImageFilterType::New();
 180
 181       // Radius
 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];
 186
 187       else if ( mArgsInfo.radius_given==1)
 188         size.Fill(mArgsInfo.radius_arg[0]);
 189
 190       else size.Fill(mArgsInfo.radius_arg[0]);
 191       if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
 192
 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)
 196         f->AddSeed(*it);
 197       f->SetNumberOfIterations( mArgsInfo.iter_arg);
 198       f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
 199       f->SetInitialNeighborhoodRadius(size[0]);
 200       filter=f;
 201       if (mArgsInfo.verbose_flag) std::cout<<"Using the confidence threshold connected image filter..."<<std::endl;
 202
 203       break;
 204     }
 205
 206     case 3: {
 207
 208       typedef clitk::LocallyAdaptiveThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 209       typename ImageFilterType::Pointer f= ImageFilterType::New();
 210
 211       // Radius
 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;
 218
 219       // params
 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)
 229         f->AddSeed(*it);
 230       f->SetRadius(size);
 231       filter=f;
 232       if (mArgsInfo.verbose_flag) std::cout<<"Using the locally adaptive threshold connected image filter..."<<std::endl;
 233
 234       break;
 235     }
 236
 237     case 4: {
 238
 239       typedef clitk::ExplosionControlledThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 240       typename ImageFilterType::Pointer f= ImageFilterType::New();
 241
 242       //        // Radius
 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;
 249
 250       // params
 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)
 264         f->AddSeed(*it);
 265       filter=f;
 266       if (mArgsInfo.verbose_flag) std::cout<<"Using the explosion controlled threshold connected image filter..."<<std::endl;
 267
 268       break;
 269     }
 270
 271     }
 272
 273
 274   filter->SetInput(input);
 275   filter->Update();
 276   typename OutputImageType::Pointer output=filter->GetOutput();
 277
 278   // Write/Save results
 279   this->template SetNextOutput<OutputImageType>(output);
 280 }
 281 //--------------------------------------------------------------------
 282
 283
 284 #endif //#define CLITKREGIONGROWINGGENERICFILTER_TXX