tools/clitkWriteDicomSeriesGenericFilter.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 clitkWriteDicomSeriesGenericFilter_txx
  19 #define clitkWriteDicomSeriesGenericFilter_txx
  20
  21 /* =================================================
  22  * @file   clitkWriteDicomSeriesGenericFilter.txx
  23  * @author
  24  * @date
  25  *
  26  * @brief
  27  *
  28  ===================================================*/
  29
  30
  31 namespace clitk
  32 {
  33
  34
  35   //-----------------------------------------------------------
  36   // Constructor
  37   //-----------------------------------------------------------
  38   template<class args_info_type>
  39   WriteDicomSeriesGenericFilter<args_info_type>::WriteDicomSeriesGenericFilter()
  40   {
  41     m_Verbose=false;
  42     m_InputFileName="";
  43   }
  44
  45
  46   //-----------------------------------------------------------
  47   // Update
  48   //-----------------------------------------------------------
  49   template<class args_info_type>
  50   void WriteDicomSeriesGenericFilter<args_info_type>::Update()
  51   {
  52     // Read the Dimension and PixelType
  53     int Dimension;
  54     std::string PixelType;
  55     ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType);
  56
  57
  58     // Call UpdateWithDim
  59     if(Dimension==2) UpdateWithDim<2>(PixelType);
  60     else if(Dimension==3) UpdateWithDim<3>(PixelType);
  61     // else if (Dimension==4)UpdateWithDim<4>(PixelType);
  62     else
  63       {
  64         std::cout<<"Error, Only for 2 or 3  Dimensions!!!"<<std::endl ;
  65         return;
  66       }
  67   }
  68
  69   //-------------------------------------------------------------------
  70   // Update with the number of dimensions
  71   //-------------------------------------------------------------------
  72   template<class args_info_type>
  73   template<unsigned int Dimension>
  74   void
  75   WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType)
  76   {
  77     if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
  78
  79     if(PixelType == "short"){
  80       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
  81       UpdateWithDimAndPixelType<Dimension, signed short>();
  82     }
  83     //    else if(PixelType == "unsigned_short"){
  84     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
  85     //       UpdateWithDimAndPixelType<Dimension, unsigned short>();
  86     //     }
  87
  88     else if (PixelType == "unsigned_char"){
  89       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
  90       UpdateWithDimAndPixelType<Dimension, unsigned char>();
  91     }
  92
  93     //     else if (PixelType == "char"){
  94     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
  95     //       UpdateWithDimAndPixelType<Dimension, signed char>();
  96     //     }
  97     else {
  98       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  99       UpdateWithDimAndPixelType<Dimension, float>();
 100     }
 101   }
 102
 103
 104   //-------------------------------------------------------------------
 105   // Update with the number of dimensions and the pixeltype
 106   //-------------------------------------------------------------------
 107   template<class args_info_type>
 108   template <unsigned int Dimension, class  PixelType>
 109   void
 110   WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
 111   {
 112
 113     // ImageTypes
 114     typedef itk::Image<PixelType, Dimension> InputImageType;
 115     typedef itk::Image<PixelType, 2> OutputImageType;
 116
 117     // Read the input (volumetric)
 118     typedef itk::ImageFileReader<InputImageType> InputReaderType;
 119     typename InputReaderType::Pointer volumeReader = InputReaderType::New();
 120     volumeReader->SetFileName( m_InputFileName);
 121     volumeReader->Update();
 122     typename InputImageType::Pointer input= volumeReader->GetOutput();
 123
 124     // Read the dicom directory
 125     typedef itk::ImageSeriesReader< InputImageType >     ReaderType;
 126     typedef itk::GDCMImageIO ImageIOType;
 127     typedef itk::GDCMSeriesFileNames NamesGeneratorType;
 128
 129     ImageIOType::Pointer gdcmIO = ImageIOType::New();
 130     NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
 131     namesGenerator->SetInputDirectory( m_ArgsInfo.inputDir_arg );
 132     typename   ReaderType::FileNamesContainer filenames = namesGenerator->GetInputFileNames();
 133
 134     // Output the dicom files
 135     unsigned int numberOfFilenames =  filenames.size();
 136     if (m_Verbose)
 137       {
 138         std::cout << numberOfFilenames <<" were read in the directory "<<m_ArgsInfo.inputDir_arg<<"..."<<std::endl<<std::endl;
 139         for(unsigned int fni = 0; fni<numberOfFilenames; fni++)
 140           {
 141             std::cout << "filename # " << fni << " = ";
 142             std::cout << filenames[fni] << std::endl;
 143           }
 144       }
 145
 146     // Read the series
 147     typename ReaderType::Pointer reader = ReaderType::New();
 148     reader->SetImageIO( gdcmIO );
 149     reader->SetFileNames( filenames );
 150     try
 151       {
 152         reader->Update();
 153       }
 154     catch (itk::ExceptionObject &excp)
 155       {
 156         std::cerr << "Error: Exception thrown while writing the DICOM series!!" << std::endl;
 157         std::cerr << excp << std::endl;
 158       }
 159
 160
 161     // Modify the meta dictionary
 162     typedef itk::MetaDataDictionary   DictionaryType;
 163     const std::vector<DictionaryType*>* dictionary = reader->GetMetaDataDictionaryArray();
 164
 165     // Get keys
 166     unsigned int numberOfKeysGiven=0;
 167     if(m_ArgsInfo.midP_flag && m_ArgsInfo.key_given)
 168         std::cerr<<"Error: both keys and midP option are given"<<std::endl;
 169     else if (m_ArgsInfo.midP_flag)
 170         numberOfKeysGiven=1;
 171     else
 172       numberOfKeysGiven=m_ArgsInfo.key_given;
 173
 174     for (unsigned int i = 0; i < numberOfKeysGiven; i++)
 175       {
 176         std::string entryId(m_ArgsInfo.key_arg[i]  );
 177         std::string value( m_ArgsInfo.tag_arg[i] );
 178         for(unsigned int fni = 0; fni<numberOfFilenames; fni++)
 179           itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), entryId, value );
 180       }
 181
 182     // Output directory and filenames
 183     itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputDir_arg ); // create if it doesn't exist
 184     typedef itk::ImageSeriesWriter<InputImageType, OutputImageType >  SeriesWriterType;
 185     typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
 186
 187     seriesWriter->SetInput( volumeReader->GetOutput() );
 188     seriesWriter->SetImageIO( gdcmIO );
 189     namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg  );
 190     seriesWriter->SetFileNames( namesGenerator->GetOutputFileNames() );
 191     //seriesWriter->SetMetaDataDictionaryArray( dictionary );
 192     seriesWriter->SetMetaDataDictionaryArray( dictionary );
 193
 194     // Write
 195     try
 196       {
 197         seriesWriter->Update();
 198       }
 199     catch( itk::ExceptionObject & excp )
 200       {
 201         std::cerr << "Error: Exception thrown while writing the series!!" << std::endl;
 202         std::cerr << excp << std::endl;
 203       }
 204
 205   }
 206
 207
 208 }//end clitk
 209
 210 #endif //#define clitkWriteDicomSeriesGenericFilter_txx