segmentation/clitkFillImageRegionGenericFilter.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 #ifndef clitkFillImageRegionGenericFilter_txx
  19 #define clitkFillImageRegionGenericFilter_txx
  20
  21 /* =================================================
  22  * @file   clitkFillImageRegionGenericFilter.txx
  23  * @author
  24  * @date
  25  *
  26  * @brief
  27  *
  28  ===================================================*/
  29
  30
  31 namespace clitk
  32 {
  33
  34   //-------------------------------------------------------------------
  35   // Update with the number of dimensions
  36   //-------------------------------------------------------------------
  37   template<unsigned int Dimension>
  38   void
  39   FillImageRegionGenericFilter::UpdateWithDim(std::string PixelType)
  40   {
  41     if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
  42
  43     if(PixelType == "short"){
  44       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
  45       UpdateWithDimAndPixelType<Dimension, signed short>();
  46     }
  47     //    else if(PixelType == "unsigned_short"){
  48     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
  49     //       UpdateWithDimAndPixelType<Dimension, unsigned short>();
  50     //     }
  51
  52     else if (PixelType == "unsigned_char"){
  53       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
  54       UpdateWithDimAndPixelType<Dimension, unsigned char>();
  55     }
  56
  57     //     else if (PixelType == "char"){
  58     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
  59     //       UpdateWithDimAndPixelType<Dimension, signed char>();
  60     //     }
  61     else {
  62       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  63       UpdateWithDimAndPixelType<Dimension, float>();
  64     }
  65   }
  66
  67
  68   //-------------------------------------------------------------------
  69   // Update with the number of dimensions and the pixeltype
  70   //-------------------------------------------------------------------
  71   template <unsigned int Dimension, class  PixelType>
  72   void
  73   FillImageRegionGenericFilter::UpdateWithDimAndPixelType()
  74   {
  75
  76     // ImageTypes
  77     typedef itk::Image<PixelType, Dimension> InputImageType;
  78     typedef itk::Image<PixelType, Dimension> OutputImageType;
  79
  80     // Read the input
  81     typedef itk::ImageFileReader<InputImageType> InputReaderType;
  82     typename InputReaderType::Pointer reader = InputReaderType::New();
  83     reader->SetFileName( m_InputFileName);
  84     reader->Update();
  85     typename InputImageType::Pointer input= reader->GetOutput();
  86
  87     // Processing
  88     switch(m_ArgsInfo.shape_arg)
  89       {
  90         //rectangular
  91       case 0:
  92         {
  93           // Get Size  and index of the region
  94           typename InputImageType::SizeType size;
  95           if (m_ArgsInfo.size_given)
  96             for(unsigned int i=0; i<Dimension; i++)
  97               size[i]=m_ArgsInfo.size_arg[i];
  98           else
  99             size.Fill(m_ArgsInfo.size_arg[0]);
 100
 101           // Get Index of the region
 102           typename InputImageType::IndexType index;
 103           if (m_ArgsInfo.index_given)
 104             for(unsigned int i=0; i<Dimension; i++)
 105               index[i]=m_ArgsInfo.index_arg[i];
 106           else
 107             index.Fill(m_ArgsInfo.index_arg[0]);
 108
 109           // Set the region
 110           typename InputImageType::RegionType region;
 111           region.SetIndex(index);
 112           region.SetSize(size);
 113
 114           // Iterator
 115           typedef itk::ImageRegionIterator<InputImageType> IteratorType;
 116           IteratorType it(input, region);
 117           it.GoToBegin();
 118           while (!it.IsAtEnd()) {
 119             it.Set(m_ArgsInfo.value_arg);
 120             ++it;
 121           }
 122
 123           break;
 124         }
 125
 126         //ellipsoide
 127       case 1:
 128         {
 129
 130           //Get the center
 131           typename InputImageType::PointType center;
 132           if (m_ArgsInfo.center_given)
 133             for(unsigned int i=0; i<Dimension; i++)
 134               center[i]=m_ArgsInfo.center_arg[i];
 135           else
 136             {
 137               typename InputImageType::SizeType size= input->GetLargestPossibleRegion().GetSize();
 138               typename InputImageType::SpacingType spacing= input->GetSpacing();
 139               typename InputImageType::PointType origin= input->GetOrigin();
 140               for (unsigned int i=0; i<Dimension; i++)
 141                 center[i]=origin[i]+(double)size[i]/2*spacing[i];
 142             }
 143           if (m_ArgsInfo.offset_given)
 144             {
 145               typename itk::Vector<double, Dimension> offset;
 146               for (unsigned int i=0; i<Dimension; i++)
 147                   center[i]+=m_ArgsInfo.offset_arg[i];
 148             }
 149
 150
 151           // Get the half axes size
 152           typename itk::Vector<double, Dimension> axes;
 153           if (m_ArgsInfo.axes_given)
 154             for(unsigned int i=0; i<Dimension; i++)
 155               axes[i]=m_ArgsInfo.axes_arg[i];
 156           else
 157             axes.Fill(m_ArgsInfo.axes_arg[0]);
 158
 159
 160           // Build iterator
 161           typedef itk::ImageRegionIteratorWithIndex<InputImageType> IteratorType;
 162           IteratorType it(input, input->GetLargestPossibleRegion());
 163           it.GoToBegin();
 164
 165           typename InputImageType::PointType point;
 166           typename InputImageType::IndexType index;
 167           double distance;
 168
 169           while (!it.IsAtEnd())
 170             {
 171               index=it.GetIndex();
 172               input->TransformIndexToPhysicalPoint(index, point);
 173               distance=0.0;
 174               for(unsigned int i=0; i<Dimension; i++)
 175                 distance+=powf( ( (center[i]-point[i])/axes[i] ), 2);
 176
 177               if (distance<1)
 178                 it.Set(m_ArgsInfo.value_arg);
 179               ++it;
 180             }
 181           break;
 182         }
 183       }
 184
 185     // Output
 186     typedef itk::ImageFileWriter<OutputImageType> WriterType;
 187     typename WriterType::Pointer writer = WriterType::New();
 188     writer->SetFileName(m_ArgsInfo.output_arg);
 189     writer->SetInput(input);
 190     writer->Update();
 191
 192   }
 193
 194
 195 }//end clitk
 196
 197 #endif //#define clitkFillImageRegionGenericFilter_txx