X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkWriteDicomSeriesGenericFilter.txx;h=d49c51e567b9ac836ddd6cb817df51195b4dbf79;hb=d24dbd466ba6aac0ed3e85f590ee1b933eb141d4;hp=113eaab8523a62e4508252a418f0e8b0a5994a46;hpb=1e034c70105f0926939acaaa27ddb46e904ae8bf;p=clitk.git

diff --git a/tools/clitkWriteDicomSeriesGenericFilter.txx b/tools/clitkWriteDicomSeriesGenericFilter.txx
index 113eaab..d49c51e 100644
--- a/tools/clitkWriteDicomSeriesGenericFilter.txx
+++ b/tools/clitkWriteDicomSeriesGenericFilter.txx
@@ -3,7 +3,7 @@
 
   Authors belong to:
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
 
   This software is distributed WITHOUT ANY WARRANTY; without even
@@ -14,7 +14,7 @@
 
   - 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
 
@@ -27,6 +27,9 @@
  *
  ===================================================*/
 
+// clitk
+#include "clitkResampleImageWithOptionsFilter.h"
+
 
 namespace clitk
 {
@@ -99,7 +102,163 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDim(std::string PixelTy
   }
 }
 
+//-------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype read from
+// the dicom files. The MHD files may be resampled to match the
+// dicom spacing (and number of slices). Rounding errors in resampling
+// are handled by removing files when generating the output dicom
+// series.
+//-------------------------------------------------------------------
+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 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;
+    }
+  }
+
+  // Read the series
+  typename ReaderType::Pointer reader = ReaderType::New();
+  reader->SetImageIO( gdcmIO );
+  reader->SetFileNames( filenames_in );
+  try {
+    reader->Update();
+  } catch (itk::ExceptionObject &excp) {
+    std::cerr << "Error: Exception thrown while reading the DICOM series!!" << std::endl;
+    std::cerr << excp << std::endl;
+  }
+
+  // Read the input (MHD file)
+  typedef typename InputImageType::RegionType RegionType;
+  typedef typename RegionType::SizeType SizeType;
+  typedef itk::ImageFileReader<InputImageType> InputReaderType;
+  typename InputReaderType::Pointer volumeReader = InputReaderType::New();
+  volumeReader->SetFileName( m_InputFileName);
+  volumeReader->Update();
+  
+  typename InputImageType::Pointer input = volumeReader->GetOutput();
+  if ((!m_ArgsInfo.useSizeAsReference_flag && (input->GetSpacing() != reader->GetOutput()->GetSpacing())) || 
+      (m_ArgsInfo.useSizeAsReference_flag && (input->GetLargestPossibleRegion().GetSize() != reader->GetOutput()->GetLargestPossibleRegion().GetSize()))) {
+        
+    // resampling is carried out on the fly if resolution or size between 
+    // the input mhd and input dicom series is different
+    
+    // Filter
+    typedef clitk::ResampleImageWithOptionsFilter<InputImageType, InputImageType> ResampleImageFilterType;
+    typename ResampleImageFilterType::Pointer filter = ResampleImageFilterType::New();
+    filter->SetInput(input);
+    filter->SetVerboseOptions(m_Verbose);
+    filter->SetGaussianFilteringEnabled(false);
+    filter->SetDefaultPixelValue(0);
+    
+    if (!m_ArgsInfo.useSizeAsReference_flag) {
+      filter->SetOutputSpacing(reader->GetOutput()->GetSpacing());
+      if (m_Verbose) {
+        std::cout << "Warning: The image spacing differs between the MHD file and the input dicom series. Performing resampling with default options using spacing as reference (for advanced options, use clitkResampleImage)." << std::endl;
+        std::cout << "MHD -> " << input->GetSpacing() << std::endl;
+        std::cout << "dicom -> " << reader->GetOutput()->GetSpacing() << std::endl;
+      }
+    }
+    else {
+      const SizeType& dicom_size = reader->GetOutput()->GetLargestPossibleRegion().GetSize();
+      SizeType output_size;
+      for (unsigned int i = 0; i < Dimension; i++)
+        output_size[i] = dicom_size[i];
+      filter->SetOutputSize(output_size);
+      if (m_Verbose) {
+          std::cout << "Warning: The image size differs between the MHD file and the input dicom series. Performing resampling with default options using size as reference (for advanced options, use clitkResampleImage)." << std::endl;
+          std::cout << "MHD -> " << input->GetLargestPossibleRegion().GetSize() << std::endl;
+          std::cout << "dicom -> " << reader->GetOutput()->GetLargestPossibleRegion().GetSize() << std::endl;
+      }
+    }
+
+    filter->Update();
+    input = filter->GetOutput();
+  }
+
+  //	In some cases, due to resampling approximation issues, 
+  //	the number of slices in the MHD file may be different (smaller)
+  //	from the number of files in the template dicom directory. 
+  //	To avoid ITK generating an exception, we reduce the number 
+  //	of DCM files to be considered, and a warning is printed
+  //	in verbose mode
+  const RegionType volumeRegion = input->GetLargestPossibleRegion();
+  const SizeType& volumeSize = volumeRegion.GetSize();
+  if (Dimension == 3 && volumeSize[2] < numberOfFilenames) {
+    if (m_Verbose)
+      std::cout << "Warning: The number of files in " << m_ArgsInfo.inputDir_arg << " (" << filenames_in.size() << " files) is greater than the number of slices in MHD (" << volumeSize[2] << " slices). Using only " << volumeSize[2] << " files." << std::endl;
+    
+    filenames_in.resize(volumeSize[2]);
+    filenames_out.resize(filenames_in.size());
+    numberOfFilenames =  filenames_in.size();
+  }
+
+  // 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( 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
 //-------------------------------------------------------------------
@@ -128,26 +287,47 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
   ImageIOType::Pointer gdcmIO = ImageIOType::New();
   NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
   namesGenerator->SetInputDirectory( m_ArgsInfo.inputDir_arg );
-  typename   ReaderType::FileNamesContainer filenames = namesGenerator->GetInputFileNames();
+  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.size();
+  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[fni] << std::endl;
+      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)
+  {
+    std::cout << "Warning: Number of files in " << m_ArgsInfo.inputDir_arg << " is greater than the number of slices in MHD. Using only " << volumeSize[2] << " files." << std::endl;
+    filenames_in.resize(volumeSize[2]);
+    filenames_out.resize(filenames_in.size());
+    numberOfFilenames =  filenames_in.size();
+  }
 
   // Read the series
   typename ReaderType::Pointer reader = ReaderType::New();
   reader->SetImageIO( gdcmIO );
-  reader->SetFileNames( filenames );
+  reader->SetFileNames( filenames_in );
   try {
     reader->Update();
   } catch (itk::ExceptionObject &excp) {
-    std::cerr << "Error: Exception thrown while writing the DICOM series!!" << std::endl;
+    std::cerr << "Error: Exception thrown while reading the DICOM series!!" << std::endl;
     std::cerr << excp << std::endl;
   }
 
@@ -179,9 +359,8 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
 
   seriesWriter->SetInput( volumeReader->GetOutput() );
   seriesWriter->SetImageIO( gdcmIO );
-  namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg  );
-  seriesWriter->SetFileNames( namesGenerator->GetOutputFileNames() );
-  //seriesWriter->SetMetaDataDictionaryArray( dictionary );
+  
+  seriesWriter->SetFileNames( filenames_out );
   seriesWriter->SetMetaDataDictionaryArray( dictionary );
 
   // Write
@@ -193,7 +372,7 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
   }
 
 }
-
+*/
 
 }//end clitk