+ // Get keys
+ unsigned int numberOfKeysGiven=0;
+ if(m_ArgsInfo.midP_flag && m_ArgsInfo.key_given)
+ std::cerr<<"Error: both keys and midP option are given"<<std::endl;
+ else if (m_ArgsInfo.midP_flag)
+ numberOfKeysGiven=1;
+ else
+ numberOfKeysGiven=m_ArgsInfo.key_given;
+
+ for (unsigned int i = 0; i < numberOfKeysGiven; i++) {
+ std::string entryId(m_ArgsInfo.key_arg[i] );
+ std::string value( m_ArgsInfo.tag_arg[i] );
+ for(unsigned int fni = 0; fni<numberOfFilenames; fni++)
+ itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), entryId, value );
+ }
+
+ // Output directory and filenames
+ itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputDir_arg ); // create if it doesn't exist
+ typedef itk::ImageSeriesWriter<InputImageType, OutputImageType > SeriesWriterType;
+ typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
+
+ seriesWriter->SetInput( input );
+ seriesWriter->SetImageIO( gdcmIO );
+
+ seriesWriter->SetFileNames( filenames_out );
+ seriesWriter->SetMetaDataDictionaryArray( dictionary );
+
+ // Write
+ try {
+ seriesWriter->Update();
+ } catch( itk::ExceptionObject & excp ) {
+ std::cerr << "Error: Exception thrown while writing the series!!" << std::endl;
+ std::cerr << excp << std::endl;
+ }
+
+}
+
+/*
+//-------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//-------------------------------------------------------------------
+template<class args_info_type>
+template <unsigned int Dimension, class PixelType>
+void
+WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
+{
+
+ // ImageTypes
+ typedef itk::Image<PixelType, Dimension> InputImageType;
+ typedef itk::Image<PixelType, 2> OutputImageType;
+
+ // Read the input (volumetric)
+ typedef itk::ImageFileReader<InputImageType> InputReaderType;
+ typename InputReaderType::Pointer volumeReader = InputReaderType::New();
+ volumeReader->SetFileName( m_InputFileName);
+ volumeReader->Update();
+ typename InputImageType::Pointer input= volumeReader->GetOutput();
+
+ // Read the dicom directory
+ typedef itk::ImageSeriesReader< InputImageType > ReaderType;
+ typedef itk::GDCMImageIO ImageIOType;
+ typedef itk::GDCMSeriesFileNames NamesGeneratorType;
+
+ ImageIOType::Pointer gdcmIO = ImageIOType::New();
+ NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
+ namesGenerator->SetInputDirectory( m_ArgsInfo.inputDir_arg );
+ namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg );
+ typename ReaderType::FileNamesContainer filenames_in = namesGenerator->GetInputFileNames();
+ typename ReaderType::FileNamesContainer filenames_out = namesGenerator->GetOutputFileNames();
+
+ // Output the dicom files
+ unsigned int numberOfFilenames = filenames_in.size();
+ if (m_Verbose) {
+ std::cout << numberOfFilenames <<" were read in the directory "<<m_ArgsInfo.inputDir_arg<<"..."<<std::endl<<std::endl;
+ for(unsigned int fni = 0; fni<numberOfFilenames; fni++) {
+ std::cout << "filename # " << fni << " = ";
+ std::cout << filenames_in[fni] << std::endl;
+ }
+ }
+
+ // RP: 16/03/2011
+ // In some cases, due to resampling approximation issues,
+ // the number of slices in the MHD file may be different
+ // from the number of slices in the template DCM directory.
+ // To avoid ITK generating an exception, we reduce the number
+ // of DCM files to be considered, provided the --force
+ // option is set.
+ typedef typename InputImageType::RegionType RegionType;
+ typedef typename RegionType::SizeType SizeType;
+ const RegionType volumeRegion = input->GetLargestPossibleRegion();
+ const SizeType& volumeSize = volumeRegion.GetSize();
+ if (m_ArgsInfo.force_given && Dimension == 3 && volumeSize[2] < numberOfFilenames)