X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkWriteDicomSeriesGenericFilter.txx;h=113eaab8523a62e4508252a418f0e8b0a5994a46;hb=91dc23d0440db7c36cabdb46271bebe30a28819c;hp=2cabb04887873672c5986789fbd5cc77e280e7d0;hpb=931a42358442f4ee4f314613c991c838d4b4e3b7;p=clitk.git

diff --git a/tools/clitkWriteDicomSeriesGenericFilter.txx b/tools/clitkWriteDicomSeriesGenericFilter.txx
index 2cabb04..113eaab 100644
--- a/tools/clitkWriteDicomSeriesGenericFilter.txx
+++ b/tools/clitkWriteDicomSeriesGenericFilter.txx
@@ -1,13 +1,30 @@
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  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
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - BSD        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+======================================================================-====*/
 #ifndef clitkWriteDicomSeriesGenericFilter_txx
 #define clitkWriteDicomSeriesGenericFilter_txx
 
 /* =================================================
  * @file   clitkWriteDicomSeriesGenericFilter.txx
- * @author 
- * @date   
- * 
- * @brief 
- * 
+ * @author
+ * @date
+ *
+ * @brief
+ *
  ===================================================*/
 
 
@@ -15,179 +32,169 @@ namespace clitk
 {
 
 
-  //-----------------------------------------------------------
-  // 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