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