tools/clitkInvertVFGenericFilter.txx

   1 #ifndef clitkInvertVFGenericFilter_txx
   2 #define clitkInvertVFGenericFilter_txx
   3
   4 /* =================================================
   5  * @file   clitkInvertVFGenericFilter.txx
   6  * @author
   7  * @date
   8  *
   9  * @brief
  10  *
  11  ===================================================*/
  12
  13
  14 namespace clitk
  15 {
  16
  17   //-----------------------------------------------------------
  18   // Constructor
  19   //-----------------------------------------------------------
  20   template<class args_info_type>
  21   InvertVFGenericFilter<args_info_type>::InvertVFGenericFilter()
  22   {
  23     m_Verbose=false;
  24     m_InputFileName="";
  25   }
  26
  27
  28   //-----------------------------------------------------------
  29   // Update
  30   //-----------------------------------------------------------
  31   template<class args_info_type>
  32   void InvertVFGenericFilter<args_info_type>::Update()
  33   {
  34     // Read the Dimension and PixelType
  35     int Dimension;
  36     std::string PixelType;
  37     ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType);
  38
  39
  40     // Call UpdateWithDim
  41     if(Dimension==2) UpdateWithDim<2>(PixelType);
  42     else if(Dimension==3) UpdateWithDim<3>(PixelType);
  43     // else if (Dimension==4)UpdateWithDim<4>(PixelType);
  44     else
  45       {
  46         std::cout<<"Error, Only for 2 or 3  Dimensions!!!"<<std::endl ;
  47         return;
  48       }
  49   }
  50
  51   //-------------------------------------------------------------------
  52   // Update with the number of dimensions
  53   //-------------------------------------------------------------------
  54   template<class args_info_type>
  55   template<unsigned int Dimension>
  56   void
  57   InvertVFGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType)
  58   {
  59     if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
  60
  61     //    if(PixelType == "short"){
  62     //       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
  63     //       UpdateWithDimAndPixelType<Dimension, signed short>();
  64     //     }
  65     //    else if(PixelType == "unsigned_short"){
  66     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
  67     //       UpdateWithDimAndPixelType<Dimension, unsigned short>();
  68     //     }
  69
  70     //     else if (PixelType == "unsigned_char"){
  71     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
  72     //       UpdateWithDimAndPixelType<Dimension, unsigned char>();
  73     //     }
  74
  75     //     else if (PixelType == "char"){
  76     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
  77     //       UpdateWithDimAndPixelType<Dimension, signed char>();
  78     //     }
  79     //  else {
  80       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  81       UpdateWithDimAndPixelType<Dimension, itk::Vector<float, Dimension> >();
  82       // }
  83   }
  84
  85
  86   //-------------------------------------------------------------------
  87   // Update with the number of dimensions and the pixeltype
  88   //-------------------------------------------------------------------
  89   template<class args_info_type>
  90   template <unsigned int Dimension, class  PixelType>
  91   void
  92   InvertVFGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
  93   {
  94
  95     // ImageTypes
  96     typedef itk::Image<PixelType, Dimension> InputImageType;
  97     typedef itk::Image<PixelType, Dimension> OutputImageType;
  98
  99     // Read the input
 100     typedef itk::ImageFileReader<InputImageType> InputReaderType;
 101     typename InputReaderType::Pointer reader = InputReaderType::New();
 102     reader->SetFileName( m_InputFileName);
 103     reader->Update();
 104     typename InputImageType::Pointer input= reader->GetOutput();
 105
 106     // Filter
 107     typename OutputImageType::Pointer output;
 108     switch (m_ArgsInfo.type_arg)
 109       {
 110
 111         // clitk filter
 112       case 0:
 113         {
 114           // Create the InvertVFFilter
 115           typedef clitk::InvertVFFilter<InputImageType,OutputImageType> FilterType;
 116           typename FilterType::Pointer filter =FilterType::New();
 117           filter->SetInput(input);
 118           filter->SetVerbose(m_Verbose);
 119           if (m_ArgsInfo.threads_given) filter->SetNumberOfThreads(m_ArgsInfo.threads_arg);
 120           if (m_ArgsInfo.pad_given)
 121             {
 122               PixelType pad;
 123               if (m_ArgsInfo.pad_given !=  (pad.GetNumberOfComponents()) )
 124                 pad.Fill(m_ArgsInfo.pad_arg[0]);
 125               else
 126                 for(unsigned int i=0; i<Dimension; i++)
 127                   pad[i]=m_ArgsInfo.pad_arg[i];
 128             }
 129           filter->SetThreadSafe(m_ArgsInfo.threadSafe_flag);
 130           filter->Update();
 131           output=filter->GetOutput();
 132
 133           break;
 134         }
 135
 136       case 1:
 137         {
 138           // Create the InverseDeformationFieldFilter
 139           typedef itk::InverseDeformationFieldImageFilter<InputImageType,OutputImageType> FilterType;
 140           typename FilterType::Pointer filter =FilterType::New();
 141           filter->SetInput(input);
 142           filter->SetOutputOrigin(input->GetOrigin());
 143           filter->SetOutputSpacing(input->GetSpacing());
 144           filter->SetSize(input->GetLargestPossibleRegion().GetSize());
 145           filter->SetSubsamplingFactor(m_ArgsInfo.sampling_arg);
 146           filter->Update();
 147           output=filter->GetOutput();
 148
 149           break;
 150         }
 151
 152       }
 153
 154     // Output
 155     typedef itk::ImageFileWriter<OutputImageType> WriterType;
 156     typename WriterType::Pointer writer = WriterType::New();
 157     writer->SetFileName(m_ArgsInfo.output_arg);
 158     writer->SetInput(output);
 159     writer->Update();
 160
 161   }
 162
 163
 164 }//end clitk
 165
 166 #endif //#define clitkInvertVFGenericFilter_txx