segmentation/clitkFillMaskFilter.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 #ifndef CLITKFILLMASKFILTER_TXX
  20 #define CLITKFILLMASKFILTER_TXX
  21
  22 //--------------------------------------------------------------------
  23 template <class ImageType>
  24 clitk::FillMaskFilter<ImageType>::FillMaskFilter():
  25   itk::ImageToImageFilter<ImageType, ImageType>()
  26 {
  27   // Default global options
  28   this->SetNumberOfRequiredInputs(1);
  29   ResetDirections();
  30   AddDirection(2);
  31   AddDirection(1);
  32   AddDirection(0);
  33 }
  34 //--------------------------------------------------------------------
  35
  36
  37 //--------------------------------------------------------------------
  38 template <class ImageType>
  39 void
  40 clitk::FillMaskFilter<ImageType>::
  41 AddDirection(int dir)
  42 {
  43   m_Directions.push_back(dir);
  44 }
  45 //--------------------------------------------------------------------
  46
  47
  48 //--------------------------------------------------------------------
  49 template <class ImageType>
  50 void
  51 clitk::FillMaskFilter<ImageType>::
  52 ResetDirections()
  53 {
  54   m_Directions.clear();
  55 }
  56 //--------------------------------------------------------------------
  57
  58
  59 //--------------------------------------------------------------------
  60 template <class ImageType>
  61 template<class ArgsInfoType>
  62 void
  63 clitk::FillMaskFilter<ImageType>::
  64 SetOptionsFromArgsInfo(ArgsInfoType & mArgsInfo)
  65 {
  66   ResetDirections();
  67   for(uint i=0; i<mArgsInfo.dir_given; i++) {
  68     AddDirection(mArgsInfo.dir_arg[i]);
  69   }
  70 }
  71 //--------------------------------------------------------------------
  72
  73
  74 //--------------------------------------------------------------------
  75 template <class ImageType>
  76 template<class ArgsInfoType>
  77 void
  78 clitk::FillMaskFilter<ImageType>::
  79 SetOptionsToArgsInfo(ArgsInfoType & mArgsInfo)
  80 {
  81   mArgsInfo.dir_arg = new int[m_Directions.size()];
  82   mArgsInfo.dir_given = m_Directions.size();
  83   for(uint i=0; i<mArgsInfo.dir_given; i++) {
  84     mArgsInfo.dir_arg[i] = m_Directions[i];
  85   }
  86 }
  87 //--------------------------------------------------------------------
  88
  89
  90 //--------------------------------------------------------------------
  91 template <class ImageType>
  92 void
  93 clitk::FillMaskFilter<ImageType>::
  94 GenerateData()
  95 {
  96   InputImagePointer input  = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
  97
  98   // Cast
  99   typedef int InternalPixelType;
 100   typedef itk::Image<InternalPixelType, ImageType::ImageDimension> InternalImageType;
 101   typedef itk::CastImageFilter<ImageType,InternalImageType> InputCastImageFilterType;
 102   typename InputCastImageFilterType::Pointer inputCaster = InputCastImageFilterType::New();
 103   inputCaster->SetInput(input);
 104   inputCaster->Update();
 105
 106   //----------------------------------------
 107   // Loop over directions
 108   //----------------------------------------
 109   typename InternalImageType::Pointer output = inputCaster->GetOutput();
 110   for (unsigned int i=0; i<m_Directions.size();i++) {
 111     DD(i);
 112     //----------------------------------------
 113     // Fill the holes of a mask in 2D
 114     //----------------------------------------
 115
 116     // We define the region to be extracted.
 117     typedef  itk::Image<InternalPixelType, ImageType::ImageDimension-1> ImageSliceType;
 118     typedef  itk::Image<InternalPixelType, ImageType::ImageDimension-1> MaskSliceType;
 119     typename InternalImageType::RegionType region3D = input->GetLargestPossibleRegion();
 120     typename InternalImageType::RegionType::SizeType size3D = region3D.GetSize();
 121     typename InternalImageType::RegionType::SizeType size2D = size3D;
 122     size2D[m_Directions[i]]=0;
 123     typename InternalImageType::IndexType start2D;
 124     start2D.Fill(0);
 125     typename InternalImageType::RegionType desiredRegion;
 126     desiredRegion.SetSize( size2D );
 127     desiredRegion.SetIndex( start2D );
 128
 129     // Extract and Join
 130     typedef itk::ExtractImageFilter<InternalImageType, ImageSliceType> ExtractImageFilterType;
 131     typedef itk::JoinSeriesImageFilter<ImageSliceType, InternalImageType> JoinSeriesFilterType;
 132     typename JoinSeriesFilterType::Pointer joinFilter=JoinSeriesFilterType::New();
 133     joinFilter->SetSpacing(input->GetSpacing()[m_Directions[i]]);
 134
 135     //----------------------------------------
 136     // Run over the sliceIndexs
 137     // ----------------------------------------
 138     for(unsigned int sliceIndex=0; sliceIndex <size3D[m_Directions[i]]; sliceIndex++)
 139       {
 140         //----------------------------------------
 141         // Extract mask sliceIndex
 142         //----------------------------------------
 143         typename ExtractImageFilterType::Pointer extractFilter=ExtractImageFilterType::New();
 144         extractFilter->SetInput(output);
 145         start2D[m_Directions[i]]=sliceIndex;
 146         desiredRegion.SetIndex( start2D );
 147         extractFilter->SetExtractionRegion( desiredRegion );
 148         extractFilter->Update( );
 149         typename ImageSliceType::Pointer slice= extractFilter->GetOutput();
 150
 151         // Binarize the image (Before: OBJECT!=0, rest=0, After: object=1, rest=0 )
 152         typedef itk::BinaryThresholdImageFilter<ImageSliceType,ImageSliceType> BinarizeFilterType;
 153         typename BinarizeFilterType::Pointer binarizeFilter=BinarizeFilterType::New();
 154         binarizeFilter->SetInput(slice);
 155         binarizeFilter->SetUpperThreshold(0);
 156         binarizeFilter->SetOutsideValue(0);
 157         binarizeFilter->SetInsideValue(1);
 158         // writeImage<ImageSliceType>(binarizeFilter->GetOutput(),"/home/jef/tmp/input.mhd");
 159
 160         // Perform connected labelling on the slice (body+air=0 )
 161         typedef itk::ConnectedComponentImageFilter<ImageSliceType, ImageSliceType> ConnectFilterType;
 162         typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
 163         connectFilter->SetInput(binarizeFilter->GetOutput());
 164         connectFilter->SetBackgroundValue(0);
 165         connectFilter->SetFullyConnected(false);
 166         //connectFilter->Update();
 167         //writeImage<ImageSliceType>(connectFilter->GetOutput(),"/home/jef/tmp/connect.mhd");
 168
 169         // Sort the labels
 170         typedef itk::RelabelComponentImageFilter<ImageSliceType, ImageSliceType> RelabelFilterType;
 171         typename RelabelFilterType::Pointer relabelFilter=RelabelFilterType::New();
 172         relabelFilter->SetInput(connectFilter->GetOutput());
 173         //relabelFilter->Update();
 174         //writeImage<ImageSliceType>(relabelFilter->GetOutput(),"/home/jef/tmp/label.mhd");
 175
 176         // Keep the first
 177         typedef itk::ThresholdImageFilter<ImageSliceType> ThresholdFilterType;
 178         typename ThresholdFilterType::Pointer thresholdFilter=ThresholdFilterType::New();
 179         thresholdFilter->SetInput(relabelFilter->GetOutput());
 180         thresholdFilter->SetUpper(1);
 181         thresholdFilter->SetOutsideValue(0);
 182         // thresholdFilter->Update();
 183         // writeImage<ImageSliceType>(thresholdFilter->GetOutput(),"/home/jef/tmp/bin.mhd");
 184
 185         // Invert the labels (lung 1, rest 0)
 186         typename BinarizeFilterType::Pointer switchFilter=BinarizeFilterType::New();
 187         switchFilter->SetInput(thresholdFilter->GetOutput());
 188         switchFilter->SetUpperThreshold(0);
 189         switchFilter->SetOutsideValue(0);
 190         switchFilter->SetInsideValue(1);
 191         switchFilter->Update();
 192         //writeImage<ImageSliceType>(switchFilter->GetOutput(),"/home/jef/tmp/inv_bin.mhd");
 193
 194         //Join
 195         joinFilter->SetInput( sliceIndex, switchFilter->GetOutput());
 196       }
 197
 198     // Join to a 3D image
 199     std::cout<<"Joining the slices..."<<std::endl;
 200     joinFilter->Update();
 201
 202     // Permute the axes to reset to orientation
 203     typedef itk::PermuteAxesImageFilter<InternalImageType> PermuteFilterType;
 204     typename PermuteFilterType::Pointer permuteFilter=PermuteFilterType::New();
 205     permuteFilter->SetInput(joinFilter->GetOutput());
 206     typename PermuteFilterType::PermuteOrderArrayType order;
 207     order[m_Directions[i]]=2;
 208     if( m_Directions[i]==2)
 209       {
 210         order[0]=0;
 211         order[1]=1;
 212       }
 213     else if ( m_Directions[i]==1)
 214       {
 215         order[0]=0;
 216         order[2]=1;
 217       }
 218     else if (m_Directions[i]==0)
 219       {
 220         order[1]=0;
 221         order[2]=1;
 222       }
 223     permuteFilter->SetOrder(order);
 224     permuteFilter->Update();
 225     output = permuteFilter->GetOutput();
 226
 227     // Set the image direction to the input one
 228     output->SetDirection(input->GetDirection());
 229     output->SetOrigin(input->GetOrigin());
 230   }
 231
 232   writeImage<InternalImageType>(output, "toto.mhd");
 233
 234   // Cast
 235   DD("cast");
 236   typedef itk::CastImageFilter<InternalImageType,ImageType> OutputCastImageFilterType;
 237   typename OutputCastImageFilterType::Pointer outputCaster =OutputCastImageFilterType::New();
 238   outputCaster->SetInput(output);
 239   outputCaster->Update();
 240
 241   // Output
 242   DD("Graft");
 243   this->GraftOutput(outputCaster->GetOutput());
 244 }
 245 //--------------------------------------------------------------------
 246
 247 #endif //#define CLITKFILLMASKFILTER_TXX