itk/clitkSegmentationUtils.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
  19 // clitk
  20 #include "clitkSetBackgroundImageFilter.h"
  21
  22 // itk
  23 #include <itkConnectedComponentImageFilter.h>
  24 #include <itkRelabelComponentImageFilter.h>
  25 #include <itkBinaryThresholdImageFilter.h>
  26 #include <itkPasteImageFilter.h>
  27
  28 //--------------------------------------------------------------------
  29 template<class ImageType>
  30 void clitk::ComputeBBFromImageRegion(typename ImageType::Pointer image,
  31                                      typename ImageType::RegionType region,
  32                                      typename itk::BoundingBox<unsigned long,
  33                                      ImageType::ImageDimension>::Pointer bb) {
  34   typedef typename ImageType::IndexType IndexType;
  35   IndexType firstIndex;
  36   IndexType lastIndex;
  37   for(unsigned int i=0; i<image->GetImageDimension(); i++) {
  38     firstIndex[i] = region.GetIndex()[i];
  39     lastIndex[i] = region.GetSize()[i];
  40   }
  41
  42   typedef itk::BoundingBox<unsigned long,
  43     ImageType::ImageDimension> BBType;
  44   typedef typename BBType::PointType PointType;
  45   PointType lastPoint;
  46   PointType firstPoint;
  47   image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
  48   image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
  49
  50   bb->SetMaximum(lastPoint);
  51   bb->SetMinimum(firstPoint);
  52 }
  53 //--------------------------------------------------------------------
  54
  55
  56 //--------------------------------------------------------------------
  57 template<int Dimension>
  58 void clitk::ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
  59                                   typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
  60                                   typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
  61
  62   typedef itk::BoundingBox<unsigned long, Dimension> BBType;
  63   typedef typename BBType::PointType PointType;
  64   PointType lastPoint;
  65   PointType firstPoint;
  66
  67   for(unsigned int i=0; i<Dimension; i++) {
  68     firstPoint[i] = std::max(bbi1->GetMinimum()[i],
  69                              bbi2->GetMinimum()[i]);
  70     lastPoint[i] = std::min(bbi1->GetMaximum()[i],
  71                             bbi2->GetMaximum()[i]);
  72   }
  73
  74   bbo->SetMaximum(lastPoint);
  75   bbo->SetMinimum(firstPoint);
  76 }
  77 //--------------------------------------------------------------------
  78
  79
  80 //--------------------------------------------------------------------
  81 template<class ImageType>
  82 void clitk::ComputeRegionFromBB(typename ImageType::Pointer image,
  83                                 const typename itk::BoundingBox<unsigned long,
  84                                 ImageType::ImageDimension>::Pointer bb,
  85                                 typename ImageType::RegionType & region) {
  86   // Types
  87   typedef typename ImageType::IndexType  IndexType;
  88   typedef typename ImageType::PointType  PointType;
  89   typedef typename ImageType::RegionType RegionType;
  90   typedef typename ImageType::SizeType   SizeType;
  91
  92   // Region starting point
  93   IndexType regionStart;
  94   PointType start = bb->GetMinimum();
  95   image->TransformPhysicalPointToIndex(start, regionStart);
  96
  97   // Region size
  98   SizeType regionSize;
  99   PointType maxs = bb->GetMaximum();
 100   PointType mins = bb->GetMinimum();
 101   for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
 102     regionSize[i] = floor((maxs[i] - mins[i])/image->GetSpacing()[i]);
 103   }
 104
 105   // Create region
 106   region.SetIndex(regionStart);
 107   region.SetSize(regionSize);
 108 }
 109 //--------------------------------------------------------------------
 110
 111 //--------------------------------------------------------------------
 112 template<class ImageType, class TMaskImageType>
 113 typename ImageType::Pointer
 114 clitk::SetBackground(typename ImageType::ConstPointer input,
 115                      typename TMaskImageType::ConstPointer mask,
 116                      typename TMaskImageType::PixelType maskBG,
 117                      typename ImageType::PixelType outValue) {
 118   typedef clitk::SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType> SetBackgroundImageFilterType;
 119   typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
 120   setBackgroundFilter->SetInput(input);
 121   setBackgroundFilter->SetInput2(mask);
 122   setBackgroundFilter->SetMaskValue(maskBG);
 123   setBackgroundFilter->SetOutsideValue(outValue);
 124   setBackgroundFilter->Update();
 125   return setBackgroundFilter->GetOutput();
 126 }
 127 //--------------------------------------------------------------------
 128
 129
 130 //--------------------------------------------------------------------
 131 template<class ImageType>
 132 int clitk::GetNumberOfConnectedComponentLabels(typename ImageType::Pointer input,
 133                                                typename ImageType::PixelType BG,
 134                                                bool isFullyConnected) {
 135   // Connected Component label
 136   typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
 137   typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 138   connectFilter->SetInput(input);
 139   connectFilter->SetBackgroundValue(BG);
 140   connectFilter->SetFullyConnected(isFullyConnected);
 141   connectFilter->Update();
 142
 143   // Return result
 144   return connectFilter->GetObjectCount();
 145 }
 146 //--------------------------------------------------------------------
 147
 148 //--------------------------------------------------------------------
 149 template<class ImageType>
 150 typename ImageType::Pointer
 151 clitk::Labelize(typename ImageType::Pointer input,
 152                 typename ImageType::PixelType BG,
 153                 bool isFullyConnected,
 154                 int minimalComponentSize) {
 155   // Connected Component label
 156   typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
 157   typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 158   connectFilter->SetInput(input);
 159   connectFilter->SetBackgroundValue(BG);
 160   connectFilter->SetFullyConnected(isFullyConnected);
 161
 162   // Sort by size and remove too small area.
 163   typedef itk::RelabelComponentImageFilter<ImageType, ImageType> RelabelFilterType;
 164   typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
 165   relabelFilter->InPlaceOn();
 166   relabelFilter->SetInput(connectFilter->GetOutput());
 167   relabelFilter->SetMinimumObjectSize(minimalComponentSize);
 168   relabelFilter->Update();
 169
 170   // Return result
 171   return relabelFilter->GetOutput();
 172 }
 173 //--------------------------------------------------------------------
 174
 175
 176 //--------------------------------------------------------------------
 177 template<class ImageType>
 178 typename ImageType::Pointer
 179 clitk::RemoveLabels(typename ImageType::Pointer input,
 180                     typename ImageType::PixelType BG,
 181                     std::vector<typename ImageType::PixelType> & labelsToRemove) {
 182   typename ImageType::Pointer working_image = input;
 183   for (unsigned int i=0; i <labelsToRemove.size(); i++) {
 184     typedef clitk::SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
 185     typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
 186     setBackgroundFilter->SetInput(input);
 187     setBackgroundFilter->SetInput2(input);
 188     setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
 189     setBackgroundFilter->SetOutsideValue(BG);
 190     setBackgroundFilter->Update();
 191     working_image = setBackgroundFilter->GetOutput();
 192   }
 193   return working_image;
 194 }
 195 //--------------------------------------------------------------------
 196
 197
 198 //--------------------------------------------------------------------
 199 template<class ImageType>
 200 typename ImageType::Pointer
 201 clitk::KeepLabels(typename ImageType::Pointer input,
 202                   typename ImageType::PixelType BG,
 203                   typename ImageType::PixelType FG,
 204                   typename ImageType::PixelType firstKeep,
 205                   typename ImageType::PixelType lastKeep,
 206                   bool useLastKeep) {
 207   typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType;
 208   typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
 209   binarizeFilter->SetInput(input);
 210   binarizeFilter->SetLowerThreshold(firstKeep);
 211   if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
 212   binarizeFilter->SetInsideValue(FG);
 213   binarizeFilter->SetOutsideValue(BG);
 214   binarizeFilter->Update();
 215   return binarizeFilter->GetOutput();
 216 }
 217 //--------------------------------------------------------------------
 218
 219
 220 //--------------------------------------------------------------------
 221 template<class ImageType>
 222 typename ImageType::Pointer
 223 clitk::LabelizeAndSelectLabels(typename ImageType::Pointer input,
 224                                typename ImageType::PixelType BG,
 225                                typename ImageType::PixelType FG,
 226                                bool isFullyConnected,
 227                                int minimalComponentSize,
 228                                LabelizeParameters<typename ImageType::PixelType> * param)
 229 {
 230   typename ImageType::Pointer working_image;
 231   working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
 232   working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
 233   working_image = KeepLabels<ImageType>(working_image,
 234                                         BG, FG,
 235                                         param->GetFirstKeep(),
 236                                         param->GetLastKeep(),
 237                                         param->GetUseLastKeep());
 238   return working_image;
 239 }
 240 //--------------------------------------------------------------------
 241
 242
 243 //--------------------------------------------------------------------
 244 template<class ImageType>
 245 typename ImageType::Pointer
 246 clitk::EnlargeImageLike(typename ImageType::Pointer input,
 247                         typename ImageType::Pointer like,
 248                         typename ImageType::PixelType backgroundValue)
 249 {
 250   if (!HaveSameSpacing<ImageType, ImageType>(input, like)) {
 251     FATAL("Images must have the same spacing");
 252   }
 253
 254   typename ImageType::Pointer output = ImageType::New();
 255   typename ImageType::SizeType size;
 256   for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
 257     size[i] = lrint((like->GetLargestPossibleRegion().GetSize()[i]*like->GetSpacing()[i])/
 258                     (double)like->GetSpacing()[i]);
 259   }
 260   // DD(size);
 261   typename ImageType::RegionType region;
 262   region.SetSize(size);
 263   output->SetRegions(region);
 264   output->SetSpacing(like->GetSpacing());
 265   output->SetOrigin(like->GetOrigin());
 266   output->Allocate();
 267   output->FillBuffer(backgroundValue);
 268   typedef itk::PasteImageFilter<ImageType,ImageType> PasteFilterType;
 269   typename PasteFilterType::Pointer pasteFilter = PasteFilterType::New();
 270   typename PasteFilterType::InputImageIndexType index;
 271   for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
 272     index[i] = lrint((input->GetOrigin()[i] - like->GetOrigin()[i])/(double)input->GetSpacing()[i]);
 273   }
 274   // DD(index);
 275   pasteFilter->SetSourceImage(input);
 276   pasteFilter->SetDestinationImage(output);
 277   pasteFilter->SetDestinationIndex(index);
 278   pasteFilter->SetSourceRegion(input->GetLargestPossibleRegion());
 279   pasteFilter->Update();
 280   return pasteFilter->GetOutput();
 281 }
 282 //--------------------------------------------------------------------