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 #if ITK_VERSION_MAJOR < 4
 114       typename BallType::ConstIterator nit;
 115       unsigned idx = 0;
 116       for (nit = ball.Begin(); nit != ball.End(); ++nit, ++idx)
 117         {
 118           if (*nit)
 119             {
 120               it.ActivateOffset(it.GetOffset(idx));
 121             }
 122           else
 123             {
 124               it.DeactivateOffset(it.GetOffset(idx));
 125             }
 126         }
 127 #else
 128       it.CreateActiveListFromNeighborhood(ball);
 129       it.NeedToUseBoundaryConditionOff();
 130 #endif
 131
 132       it.SetLocation(seeds[0]);
 133       for (typename IteratorType::ConstIterator i = it.Begin(); !i.IsAtEnd(); ++i)
 134         {
 135           typename InputImageType::IndexType id = seeds[0] + i.GetNeighborhoodOffset();
 136           if (id != seeds[0] && input->GetLargestPossibleRegion().IsInside(id))
 137             seeds.push_back(id);
 138         }
 139     }
 140
 141   // Filter
 142   typedef itk::ImageToImageFilter<InputImageType, OutputImageType> ImageToImageFilterType;
 143   typename ImageToImageFilterType::Pointer filter;
 144
 145   switch (mArgsInfo.type_arg)
 146     {
 147     case 0: {
 148
 149       typedef itk::ConnectedThresholdImageFilter<InputImageType, OutputImageType> ImageFilterType;
 150       typename ImageFilterType::Pointer f= ImageFilterType::New();
 151
 152       f->SetLower(mArgsInfo.lower_arg);
 153       f->SetUpper(mArgsInfo.upper_arg);
 154       f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
 155       for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
 156         f->AddSeed(*it);
 157       filter=f;
 158       if (mArgsInfo.verbose_flag) std::cout<<"Using the connected threshold image filter..."<<std::endl;
 159
 160       break;
 161     }
 162
 163     case 1: {
 164
 165       typedef itk::NeighborhoodConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 166       typename ImageFilterType::Pointer f= ImageFilterType::New();
 167
 168       // Radius
 169       typename  InputImageType::SizeType size;
 170       if (mArgsInfo.radius_given==Dimension)
 171         for (unsigned int i=0; i<Dimension;i++)
 172           size[i]=mArgsInfo.radius_arg[i];
 173
 174       else if ( mArgsInfo.radius_given==1)
 175         size.Fill(mArgsInfo.radius_arg[0]);
 176
 177       else size.Fill(mArgsInfo.radius_arg[0]);
 178       if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
 179
 180       f->SetLower(mArgsInfo.lower_arg);
 181       f->SetUpper(mArgsInfo.upper_arg);
 182       f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
 183       for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
 184         f->AddSeed(*it);
 185       f->SetRadius(size);
 186       filter=f;
 187       if (mArgsInfo.verbose_flag) std::cout<<"Using the neighborhood threshold connected image filter..."<<std::endl;
 188
 189       break;
 190     }
 191
 192     case 2: {
 193
 194       typedef itk::ConfidenceConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 195       typename ImageFilterType::Pointer f= ImageFilterType::New();
 196
 197       // Radius
 198       typename  InputImageType::SizeType size;
 199       if (mArgsInfo.radius_given==Dimension)
 200         for (unsigned int i=0; i<Dimension;i++)
 201           size[i]=mArgsInfo.radius_arg[i];
 202
 203       else if ( mArgsInfo.radius_given==1)
 204         size.Fill(mArgsInfo.radius_arg[0]);
 205
 206       else size.Fill(mArgsInfo.radius_arg[0]);
 207       if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
 208
 209       f->SetMultiplier( mArgsInfo.multiplier_arg );
 210       f->SetNumberOfIterations( mArgsInfo.multiplier_arg );
 211       for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
 212         f->AddSeed(*it);
 213       f->SetNumberOfIterations( mArgsInfo.iter_arg);
 214       f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
 215       f->SetInitialNeighborhoodRadius(size[0]);
 216       filter=f;
 217       if (mArgsInfo.verbose_flag) std::cout<<"Using the confidence threshold connected image filter..."<<std::endl;
 218
 219       break;
 220     }
 221
 222     case 3: {
 223
 224       typedef clitk::LocallyAdaptiveThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 225       typename ImageFilterType::Pointer f= ImageFilterType::New();
 226
 227       // Radius
 228       typename  InputImageType::SizeType size;
 229       if (mArgsInfo.radius_given==Dimension)
 230         for (unsigned int i=0; i<Dimension;i++)
 231           size[i]=mArgsInfo.radius_arg[i];
 232       else size.Fill(mArgsInfo.radius_arg[0]);
 233       if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
 234
 235       // params
 236       f->SetLower(mArgsInfo.lower_arg);
 237       f->SetUpper(mArgsInfo.upper_arg);
 238       f->SetLowerBorderIsGiven(mArgsInfo.adaptLower_flag);
 239       f->SetLowerBorderIsGiven(mArgsInfo.adaptUpper_flag);
 240       f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
 241       f->SetMultiplier(mArgsInfo.multiplier_arg);
 242       f->SetMaximumSDIsGiven(mArgsInfo.maxSD_given);
 243       if (mArgsInfo.maxSD_given) f->SetMaximumSD(mArgsInfo.maxSD_arg);
 244       for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
 245         f->AddSeed(*it);
 246       f->SetRadius(size);
 247       filter=f;
 248       if (mArgsInfo.verbose_flag) std::cout<<"Using the locally adaptive threshold connected image filter..."<<std::endl;
 249
 250       break;
 251     }
 252
 253     case 4: {
 254
 255       typedef clitk::ExplosionControlledThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
 256       typename ImageFilterType::Pointer f= ImageFilterType::New();
 257
 258       //        // Radius
 259       //        typename  InputImageType::SizeType size;
 260       //        if (mArgsInfo.radius_given==Dimension)
 261       //          for (unsigned int i=0; i<Dimension;i++)
 262       //            size[i]=mArgsInfo.radius_arg[i];
 263       //        else size.Fill(mArgsInfo.radius_arg[0]);
 264       //        if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
 265
 266       // params
 267       f->SetVerbose(mArgsInfo.verbose_flag);
 268       f->SetLower(mArgsInfo.lower_arg);
 269       f->SetUpper(mArgsInfo.upper_arg);
 270       f->SetMinimumLowerThreshold(mArgsInfo.minLower_arg);
 271       f->SetMaximumUpperThreshold(mArgsInfo.maxUpper_arg);
 272       f->SetAdaptLowerBorder(mArgsInfo.adaptLower_flag);
 273       f->SetAdaptUpperBorder(mArgsInfo.adaptUpper_flag);
 274       f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
 275       f->SetMultiplier(mArgsInfo.multiplier_arg);
 276       f->SetThresholdStepSize(mArgsInfo.step_arg);
 277       f->SetMinimumThresholdStepSize(mArgsInfo.minStep_arg);
 278       f->SetFullyConnected(mArgsInfo.full_flag);
 279       for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
 280         f->AddSeed(*it);
 281       filter=f;
 282       if (mArgsInfo.verbose_flag) std::cout<<"Using the explosion controlled threshold connected image filter..."<<std::endl;
 283
 284       break;
 285     }
 286
 287     }
 288
 289
 290   filter->SetInput(input);
 291   filter->Update();
 292   typename OutputImageType::Pointer output=filter->GetOutput();
 293
 294   // Write/Save results
 295   this->template SetNextOutput<OutputImageType>(output);
 296 }
 297 //--------------------------------------------------------------------
 298
 299
 300 #endif //#define CLITKREGIONGROWINGGENERICFILTER_TXX