tools/clitkWriteDicomSeriesGenericFilter.txx

   1 #ifndef clitkWriteDicomSeriesGenericFilter_txx
   2 #define clitkWriteDicomSeriesGenericFilter_txx
   3
   4 /* =================================================
   5  * @file   clitkWriteDicomSeriesGenericFilter.txx
   6  * @author
   7  * @date
   8  *
   9  * @brief
  10  *
  11  ===================================================*/
  12
  13
  14 namespace clitk
  15 {
  16
  17
  18   //-----------------------------------------------------------
  19   // Constructor
  20   //-----------------------------------------------------------
  21   template<class args_info_type>
  22   WriteDicomSeriesGenericFilter<args_info_type>::WriteDicomSeriesGenericFilter()
  23   {
  24     m_Verbose=false;
  25     m_InputFileName="";
  26   }
  27
  28
  29   //-----------------------------------------------------------
  30   // Update
  31   //-----------------------------------------------------------
  32   template<class args_info_type>
  33   void WriteDicomSeriesGenericFilter<args_info_type>::Update()
  34   {
  35     // Read the Dimension and PixelType
  36     int Dimension;
  37     std::string PixelType;
  38     ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType);
  39
  40
  41     // Call UpdateWithDim
  42     if(Dimension==2) UpdateWithDim<2>(PixelType);
  43     else if(Dimension==3) UpdateWithDim<3>(PixelType);
  44     // else if (Dimension==4)UpdateWithDim<4>(PixelType);
  45     else
  46       {
  47         std::cout<<"Error, Only for 2 or 3  Dimensions!!!"<<std::endl ;
  48         return;
  49       }
  50   }
  51
  52   //-------------------------------------------------------------------
  53   // Update with the number of dimensions
  54   //-------------------------------------------------------------------
  55   template<class args_info_type>
  56   template<unsigned int Dimension>
  57   void
  58   WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType)
  59   {
  60     if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
  61
  62     if(PixelType == "short"){
  63       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
  64       UpdateWithDimAndPixelType<Dimension, signed short>();
  65     }
  66     //    else if(PixelType == "unsigned_short"){
  67     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
  68     //       UpdateWithDimAndPixelType<Dimension, unsigned short>();
  69     //     }
  70
  71     else if (PixelType == "unsigned_char"){
  72       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
  73       UpdateWithDimAndPixelType<Dimension, unsigned char>();
  74     }
  75
  76     //     else if (PixelType == "char"){
  77     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
  78     //       UpdateWithDimAndPixelType<Dimension, signed char>();
  79     //     }
  80     else {
  81       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  82       UpdateWithDimAndPixelType<Dimension, float>();
  83     }
  84   }
  85
  86
  87   //-------------------------------------------------------------------
  88   // Update with the number of dimensions and the pixeltype
  89   //-------------------------------------------------------------------
  90   template<class args_info_type>
  91   template <unsigned int Dimension, class  PixelType>
  92   void
  93   WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
  94   {
  95
  96     // ImageTypes
  97     typedef itk::Image<PixelType, Dimension> InputImageType;
  98     typedef itk::Image<PixelType, 2> OutputImageType;
  99
 100     // Read the input (volumetric)
 101     typedef itk::ImageFileReader<InputImageType> InputReaderType;
 102     typename InputReaderType::Pointer volumeReader = InputReaderType::New();
 103     volumeReader->SetFileName( m_InputFileName);
 104     volumeReader->Update();
 105     typename InputImageType::Pointer input= volumeReader->GetOutput();
 106
 107     // Read the dicom directory
 108     typedef itk::ImageSeriesReader< InputImageType >     ReaderType;
 109     typedef itk::GDCMImageIO ImageIOType;
 110     typedef itk::GDCMSeriesFileNames NamesGeneratorType;
 111
 112     ImageIOType::Pointer gdcmIO = ImageIOType::New();
 113     NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
 114     namesGenerator->SetInputDirectory( m_ArgsInfo.inputDir_arg );
 115     typename   ReaderType::FileNamesContainer filenames = namesGenerator->GetInputFileNames();
 116
 117     // Output the dicom files
 118     unsigned int numberOfFilenames =  filenames.size();
 119     if (m_Verbose)
 120       {
 121         std::cout << numberOfFilenames <<" were read in the directory "<<m_ArgsInfo.inputDir_arg<<"..."<<std::endl<<std::endl;
 122         for(unsigned int fni = 0; fni<numberOfFilenames; fni++)
 123           {
 124             std::cout << "filename # " << fni << " = ";
 125             std::cout << filenames[fni] << std::endl;
 126           }
 127       }
 128
 129     // Read the series
 130     typename ReaderType::Pointer reader = ReaderType::New();
 131     reader->SetImageIO( gdcmIO );
 132     reader->SetFileNames( filenames );
 133     try
 134       {
 135         reader->Update();
 136       }
 137     catch (itk::ExceptionObject &excp)
 138       {
 139         std::cerr << "Error: Exception thrown while writing the DICOM series!!" << std::endl;
 140         std::cerr << excp << std::endl;
 141       }
 142
 143
 144     // Modify the meta dictionary
 145     typedef itk::MetaDataDictionary   DictionaryType;
 146     const std::vector<DictionaryType*>* dictionary = reader->GetMetaDataDictionaryArray();
 147
 148     // Get keys
 149     unsigned int numberOfKeysGiven=0;
 150     if(m_ArgsInfo.midP_flag && m_ArgsInfo.key_given)
 151         std::cerr<<"Error: both keys and midP option are given"<<std::endl;
 152     else if (m_ArgsInfo.midP_flag)
 153         numberOfKeysGiven=1;
 154     else
 155       numberOfKeysGiven=m_ArgsInfo.key_given;
 156
 157     for (unsigned int i = 0; i < numberOfKeysGiven; i++)
 158       {
 159         std::string entryId(m_ArgsInfo.key_arg[i]  );
 160         std::string value( m_ArgsInfo.tag_arg[i] );
 161         for(unsigned int fni = 0; fni<numberOfFilenames; fni++)
 162           itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), entryId, value );
 163       }
 164
 165     // Output directory and filenames
 166     itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputDir_arg ); // create if it doesn't exist
 167     typedef itk::ImageSeriesWriter<InputImageType, OutputImageType >  SeriesWriterType;
 168     typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
 169
 170     seriesWriter->SetInput( volumeReader->GetOutput() );
 171     seriesWriter->SetImageIO( gdcmIO );
 172     namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg  );
 173     seriesWriter->SetFileNames( namesGenerator->GetOutputFileNames() );
 174     //seriesWriter->SetMetaDataDictionaryArray( dictionary );
 175     seriesWriter->SetMetaDataDictionaryArray( dictionary );
 176
 177     // Write
 178     try
 179       {
 180         seriesWriter->Update();
 181       }
 182     catch( itk::ExceptionObject & excp )
 183       {
 184         std::cerr << "Error: Exception thrown while writing the series!!" << std::endl;
 185         std::cerr << excp << std::endl;
 186       }
 187
 188   }
 189
 190
 191 }//end clitk
 192
 193 #endif //#define clitkWriteDicomSeriesGenericFilter_txx