segmentation/clitkDecomposeAndReconstructGenericFilter.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 clitkDecomposeAndReconstructGenericFilter_txx
  19 #define clitkDecomposeAndReconstructGenericFilter_txx
  20
  21 namespace clitk
  22 {
  23
  24   //-------------------------------------------------------------------
  25   // Update with the number of dimensions
  26   //-------------------------------------------------------------------
  27   template<unsigned int Dimension>
  28   void
  29   DecomposeAndReconstructGenericFilter::UpdateWithDim(std::string PixelType)
  30   {
  31     if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
  32
  33     if(PixelType == "short"){
  34       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
  35       UpdateWithDimAndPixelType<Dimension, signed short>();
  36     }
  37     //    else if(PixelType == "unsigned_short"){
  38     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
  39     //       UpdateWithDimAndPixelType<Dimension, unsigned short>();
  40     //     }
  41
  42     else if (PixelType == "unsigned_char"){
  43       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
  44       std::cout  << "WARNING: Working in unsigned pixelType, remember to set the Erosion Padding Value to a suitable value!"<< std::endl;
  45       UpdateWithDimAndPixelType<Dimension, unsigned char>();
  46
  47     }
  48
  49     //     else if (PixelType == "char"){
  50     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
  51     //       UpdateWithDimAndPixelType<Dimension, signed char>();
  52     //     }
  53     else {
  54       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  55       UpdateWithDimAndPixelType<Dimension, float>();
  56     }
  57   }
  58
  59
  60   //-------------------------------------------------------------------
  61   // Update with the number of dimensions and the pixeltype
  62   //-------------------------------------------------------------------
  63   template <unsigned int Dimension, class  PixelType>
  64   void
  65   DecomposeAndReconstructGenericFilter::UpdateWithDimAndPixelType()
  66   {
  67
  68     // ImageTypes
  69     typedef itk::Image<PixelType, Dimension> InputImageType;
  70     typedef itk::Image<int, Dimension> InternalImageType;
  71     typedef itk::Image<PixelType, Dimension> OutputImageType;
  72
  73     // Read the input
  74     typedef itk::ImageFileReader<InputImageType> InputReaderType;
  75     typename InputReaderType::Pointer reader = InputReaderType::New();
  76     reader->SetFileName( m_InputFileName);
  77     reader->Update();
  78     typename InputImageType::Pointer input= reader->GetOutput();
  79
  80     // Structuring element radius
  81     typename InputImageType::SizeType radius;
  82     if (m_ArgsInfo.radius_given==Dimension)
  83       for (unsigned int i=0;i<Dimension;i++)
  84         {radius[i]=m_ArgsInfo.radius_arg[i];}
  85     else
  86       for (unsigned int i=0;i<Dimension;i++)
  87         radius[i]=m_ArgsInfo.radius_arg[0];
  88
  89     // Cast
  90     typedef itk::CastImageFilter<InputImageType, InternalImageType> InputCastImageFilterType;
  91     typename InputCastImageFilterType::Pointer inputCaster= InputCastImageFilterType::New();
  92     inputCaster->SetInput(input);
  93     inputCaster->Update();
  94
  95     // Filter
  96     typedef itk::ImageToImageFilter<InternalImageType, InternalImageType> ImageToImageFilterType;
  97     typename ImageToImageFilterType::Pointer filter;
  98
  99     switch (m_ArgsInfo.type_arg)
 100       {
 101       case 0:
 102         {
 103           typedef clitk::DecomposeThroughErosionImageFilter<InternalImageType,InternalImageType> FilterType;
 104           typename FilterType::Pointer f=FilterType::New();
 105           f->SetVerbose(m_Verbose);
 106           f->SetFullyConnected(m_ArgsInfo.full_flag);
 107           f->SetErosionPaddingValue(m_ArgsInfo.pad_arg);
 108           f->SetMinimumNumberOfIterations(m_ArgsInfo.min_arg);
 109           f->SetMinimumObjectSize(m_ArgsInfo.minSize_arg);
 110           f->SetRadius(radius);
 111           f->SetNumberOfNewLabels(m_ArgsInfo.new_arg);
 112           if(m_Verbose) std::cout<<"Using the DecomposeThroughErosionImageFilter..."<<std::endl;
 113           filter=f;
 114           break;
 115         }
 116
 117       case 1:
 118         {
 119           typedef clitk::ReconstructThroughDilationImageFilter<InternalImageType,InternalImageType> FilterType;
 120           typename FilterType::Pointer f=FilterType::New();
 121           f->SetVerbose(m_Verbose);
 122           f->SetErosionPaddingValue(m_ArgsInfo.pad_arg);
 123           f->SetRadius(radius);
 124           f->SetMaximumNumberOfLabels(m_ArgsInfo.max_arg);
 125           f->SetBackgroundValue(m_ArgsInfo.bg_arg);
 126           f->SetForegroundValue(m_ArgsInfo.fg_arg);
 127           if(m_Verbose) std::cout<<"Using the ReconstructThroughDilationImageFilter..."<<std::endl;
 128           filter=f;
 129           break;
 130         }
 131       case 2:
 132         {
 133           typedef clitk::DecomposeAndReconstructImageFilter<InternalImageType,InternalImageType> FilterType;
 134           typename FilterType::Pointer f=FilterType::New();
 135           f->SetVerbose(m_Verbose);
 136           f->SetRadius(radius);
 137           f->SetMaximumNumberOfLabels(m_ArgsInfo.max_arg);
 138           f->SetMinimumNumberOfIterations(m_ArgsInfo.min_arg);
 139           f->SetBackgroundValue(m_ArgsInfo.bg_arg);
 140           f->SetForegroundValue(m_ArgsInfo.fg_arg);
 141           f->SetFullyConnected(m_ArgsInfo.full_flag);
 142           f->SetNumberOfNewLabels(m_ArgsInfo.new_arg);
 143           f->SetMinimumObjectSize(m_ArgsInfo.minSize_arg);
 144           if(m_Verbose) std::cout<<"Using the DecomposeAndReconstructImageFilter..."<<std::endl;
 145           filter=f;
 146           break;
 147         }
 148       }
 149
 150     filter->SetInput(inputCaster->GetOutput());
 151     filter->Update();
 152     typename InternalImageType::Pointer output= filter->GetOutput();
 153
 154     // Cast
 155     typedef itk::CastImageFilter<InternalImageType, OutputImageType> OutputCastImageFilterType;
 156     typename OutputCastImageFilterType::Pointer outputCaster= OutputCastImageFilterType::New();
 157     outputCaster->SetInput(output);
 158     outputCaster->Update();
 159
 160     // Output
 161     typedef itk::ImageFileWriter<OutputImageType> WriterType;
 162     typename WriterType::Pointer writer = WriterType::New();
 163     writer->SetFileName(m_ArgsInfo.output_arg);
 164     writer->SetInput(outputCaster->GetOutput());
 165     writer->Update();
 166
 167   }
 168
 169
 170 }//end clitk
 171
 172 #endif //#define clitkDecomposeAndReconstructGenericFilter_txx