X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkWriteDicomSeriesGenericFilter.txx;h=20e980ca603f86beb37fd4ea96ca08b4ab2e26f9;hb=a49ce6bf246efbaa348468bcb915493e0db17a9b;hp=d49c51e567b9ac836ddd6cb817df51195b4dbf79;hpb=573d80d0f7a17607d2ee883c21c940c0ba020282;p=clitk.git

diff --git a/tools/clitkWriteDicomSeriesGenericFilter.txx b/tools/clitkWriteDicomSeriesGenericFilter.txx
index d49c51e..20e980c 100644
--- a/tools/clitkWriteDicomSeriesGenericFilter.txx
+++ b/tools/clitkWriteDicomSeriesGenericFilter.txx
@@ -29,6 +29,12 @@
 
 // clitk
 #include "clitkResampleImageWithOptionsFilter.h"
+#if GDCM_MAJOR_VERSION >= 2
+#include "gdcmUIDGenerator.h"
+#else
+#include "gdcmFile.h"
+#include "gdcmUtil.h"
+#endif
 
 
 namespace clitk
@@ -82,10 +88,10 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDim(std::string PixelTy
     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_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;
@@ -96,6 +102,10 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDim(std::string PixelTy
   //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
   //       UpdateWithDimAndPixelType<Dimension, signed char>();
   //     }
+  else if (PixelType == "double") {
+    if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and double..." << std::endl;
+    UpdateWithDimAndPixelType<Dimension, double>();
+  }
   else {
     if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
     UpdateWithDimAndPixelType<Dimension, float>();
@@ -196,10 +206,15 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
       }
     }
 
-    filter->Update();
-    input = filter->GetOutput();
+    try {
+      filter->Update();
+      input = filter->GetOutput();
+    } catch( itk::ExceptionObject & excp ) {
+    std::cerr << "Error: Exception thrown while resampling!!" << std::endl;
+    std::cerr << excp << std::endl;
+    }
   }
-
+  
   //	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. 
@@ -208,6 +223,9 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
   //	in verbose mode
   const RegionType volumeRegion = input->GetLargestPossibleRegion();
   const SizeType& volumeSize = volumeRegion.GetSize();
+  if (m_Verbose) {
+    std::cout << volumeRegion << volumeSize << std::endl;
+  }
   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;
@@ -222,20 +240,74 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
   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;
+  unsigned int numberOfKeysGiven=m_ArgsInfo.key_given;
+
+  std::string seriesUID;
+  std::string frameOfReferenceUID;
+  if (m_ArgsInfo.newSeriesUID_flag) {
+#if GDCM_MAJOR_VERSION >= 2
+    gdcm::UIDGenerator suid;
+    seriesUID = suid.Generate();
+    gdcm::UIDGenerator fuid;
+    frameOfReferenceUID = fuid.Generate();
+#else
+    seriesUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
+    frameOfReferenceUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
+#endif
+    if (m_ArgsInfo.verbose_flag)
+    {
+      DD(seriesUID);
+      DD(frameOfReferenceUID);
+    }
+  }
+  
+
+  std::string studyUID;
+  if (m_ArgsInfo.newStudyUID_flag) {
+#if GDCM_MAJOR_VERSION >= 2
+    gdcm::UIDGenerator suid;
+    studyUID = suid.Generate();
+#else
+    studyUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
+#endif
+    if (m_ArgsInfo.verbose_flag)
+      DD(studyUID);
+  }
+#if GDCM_MAJOR_VERSION < 2
   else
-    numberOfKeysGiven=m_ArgsInfo.key_given;
+    gdcmIO->KeepOriginalUID();
+#endif
+  
+  std::string seriesUIDkey = "0020|000e";
+  std::string frameOfReferenceUIDKey = "0020|0052";
+  std::string studyUIDKey = "0020|000d";
+  for(unsigned int fni = 0; fni<numberOfFilenames; fni++) {
+    bool series_id_given = false;
+    bool study_id_given = false;
+    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 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 );
+      if (entryId ==  seriesUIDkey || entryId ==  frameOfReferenceUIDKey)
+        series_id_given = true;
+      if (entryId == studyUIDKey)
+        study_id_given = true;
+    }
+    
+    if (!series_id_given) {
+      if (m_ArgsInfo.newSeriesUID_flag) {
+        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesUIDkey, seriesUID );
+        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), frameOfReferenceUIDKey, frameOfReferenceUID );
+      }
+    }
+    
+    if (!study_id_given) {
+      if (m_ArgsInfo.newStudyUID_flag) 
+        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyUIDKey, studyUID );
+    }
   }
+  
 
   // Output directory and filenames
   itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputDir_arg ); // create if it doesn't exist