/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
/* =================================================
* @file clitkWriteDicomSeriesGenericFilter.txx
- * @author
- * @date
- *
- * @brief
- *
+ * @author
+ * @date
+ *
+ * @brief
+ *
===================================================*/
{
- //-----------------------------------------------------------
- // Constructor
- //-----------------------------------------------------------
- template<class args_info_type>
- WriteDicomSeriesGenericFilter<args_info_type>::WriteDicomSeriesGenericFilter()
- {
- m_Verbose=false;
- m_InputFileName="";
+//-----------------------------------------------------------
+// Constructor
+//-----------------------------------------------------------
+template<class args_info_type>
+WriteDicomSeriesGenericFilter<args_info_type>::WriteDicomSeriesGenericFilter()
+{
+ m_Verbose=false;
+ m_InputFileName="";
+}
+
+
+//-----------------------------------------------------------
+// Update
+//-----------------------------------------------------------
+template<class args_info_type>
+void WriteDicomSeriesGenericFilter<args_info_type>::Update()
+{
+ // Read the Dimension and PixelType
+ int Dimension;
+ std::string PixelType;
+ ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType);
+
+
+ // Call UpdateWithDim
+ if(Dimension==2) UpdateWithDim<2>(PixelType);
+ else if(Dimension==3) UpdateWithDim<3>(PixelType);
+ // else if (Dimension==4)UpdateWithDim<4>(PixelType);
+ else {
+ std::cout<<"Error, Only for 2 or 3 Dimensions!!!"<<std::endl ;
+ return;
}
+}
+
+//-------------------------------------------------------------------
+// Update with the number of dimensions
+//-------------------------------------------------------------------
+template<class args_info_type>
+template<unsigned int Dimension>
+void
+WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType)
+{
+ if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
+ if(PixelType == "short") {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, signed short>();
+ }
+ // else if(PixelType == "unsigned_short"){
+ // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
+ // UpdateWithDimAndPixelType<Dimension, unsigned short>();
+ // }
+
+ else if (PixelType == "unsigned_char") {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, unsigned char>();
+ }
- //-----------------------------------------------------------
- // Update
- //-----------------------------------------------------------
- template<class args_info_type>
- void WriteDicomSeriesGenericFilter<args_info_type>::Update()
- {
- // Read the Dimension and PixelType
- int Dimension;
- std::string PixelType;
- ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType);
-
-
- // Call UpdateWithDim
- if(Dimension==2) UpdateWithDim<2>(PixelType);
- else if(Dimension==3) UpdateWithDim<3>(PixelType);
- // else if (Dimension==4)UpdateWithDim<4>(PixelType);
- else
- {
- std::cout<<"Error, Only for 2 or 3 Dimensions!!!"<<std::endl ;
- return;
- }
+ // else if (PixelType == "char"){
+ // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
+ // UpdateWithDimAndPixelType<Dimension, signed char>();
+ // }
+ else {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, float>();
}
+}
- //-------------------------------------------------------------------
- // Update with the number of dimensions
- //-------------------------------------------------------------------
- template<class args_info_type>
- template<unsigned int Dimension>
- void
- WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType)
- {
- if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
-
- if(PixelType == "short"){
- if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, signed short>();
- }
- // else if(PixelType == "unsigned_short"){
- // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
- // UpdateWithDimAndPixelType<Dimension, unsigned short>();
- // }
-
- else if (PixelType == "unsigned_char"){
- if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, unsigned char>();
- }
-
- // else if (PixelType == "char"){
- // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
- // UpdateWithDimAndPixelType<Dimension, signed char>();
- // }
- else {
- if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, float>();
+
+//-------------------------------------------------------------------
+// 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 );
+ typename ReaderType::FileNamesContainer filenames = namesGenerator->GetInputFileNames();
+
+ // Output the dicom files
+ unsigned int numberOfFilenames = filenames.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[fni] << std::endl;
}
}
+ // Read the series
+ typename ReaderType::Pointer reader = ReaderType::New();
+ reader->SetImageIO( gdcmIO );
+ reader->SetFileNames( filenames );
+ try {
+ reader->Update();
+ } catch (itk::ExceptionObject &excp) {
+ std::cerr << "Error: Exception thrown while writing the DICOM 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 );
- typename ReaderType::FileNamesContainer filenames = namesGenerator->GetInputFileNames();
-
- // Output the dicom files
- unsigned int numberOfFilenames = filenames.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[fni] << std::endl;
- }
- }
-
- // Read the series
- typename ReaderType::Pointer reader = ReaderType::New();
- reader->SetImageIO( gdcmIO );
- reader->SetFileNames( filenames );
- try
- {
- reader->Update();
- }
- catch (itk::ExceptionObject &excp)
- {
- std::cerr << "Error: Exception thrown while writing the DICOM series!!" << std::endl;
- std::cerr << excp << std::endl;
- }
-
-
- // Modify the meta dictionary
- typedef itk::MetaDataDictionary DictionaryType;
- const std::vector<DictionaryType*>* dictionary = reader->GetMetaDataDictionaryArray();
-
- // 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( volumeReader->GetOutput() );
- seriesWriter->SetImageIO( gdcmIO );
- namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg );
- seriesWriter->SetFileNames( namesGenerator->GetOutputFileNames() );
- //seriesWriter->SetMetaDataDictionaryArray( dictionary );
- 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;
- }
+ // Modify the meta dictionary
+ typedef itk::MetaDataDictionary DictionaryType;
+ const std::vector<DictionaryType*>* dictionary = reader->GetMetaDataDictionaryArray();
+
+ // 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( volumeReader->GetOutput() );
+ seriesWriter->SetImageIO( gdcmIO );
+ namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg );
+ seriesWriter->SetFileNames( namesGenerator->GetOutputFileNames() );
+ //seriesWriter->SetMetaDataDictionaryArray( dictionary );
+ 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;
}
+}
+
}//end clitk
-
+
#endif //#define clitkWriteDicomSeriesGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff