X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkWriteDicomSeriesGenericFilter.txx;h=a2bccc4aa0daa52fbef3b8a34cb115b3eb9cc20c;hb=d9c8c6e6c759655fc24d05d47b962d2ba574b95d;hp=9bc52dcfd8c2cd10c38b930cb0eada7033226691;hpb=6b3340701c3f6f4c87c1366b3090258c8df93deb;p=clitk.git

diff --git a/tools/clitkWriteDicomSeriesGenericFilter.txx b/tools/clitkWriteDicomSeriesGenericFilter.txx
index 9bc52dc..a2bccc4 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>();
@@ -143,6 +153,12 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
 
   // Read the series
   typename ReaderType::Pointer reader = ReaderType::New();
+  if (m_ArgsInfo.preserve_flag) {
+#if GDCM_MAJOR_VERSION >= 2
+    gdcmIO->LoadPrivateTagsOn();
+    gdcmIO->KeepOriginalUIDOn();
+#endif
+  }
   reader->SetImageIO( gdcmIO );
   reader->SetFileNames( filenames_in );
   try {
@@ -230,23 +246,160 @@ 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;
-  else
-    numberOfKeysGiven=m_ArgsInfo.key_given;
+  unsigned int numberOfKeysGiven=m_ArgsInfo.key_given;
+    if (m_ArgsInfo.verbose_flag) 
+      DD(numberOfKeysGiven);
 
+  std::string seriesUID;
+  std::string frameOfReferenceUID;
+  std::string studyUID;
+  
+  // one pass through the keys given on the cmd-line, to check what will be recreated
+  std::string seriesUIDkey = "0020|000e";
+  std::string seriesNumberKey = "0020|0011";
+  std::string seriesDescriptionKey = "0008|103e";
+  std::string frameOfReferenceUIDKey = "0020|0052";
+  std::string studyUIDKey = "0020|000d";
+  std::string studyIDKey = "0020|0010";
+  std::string studyDescriptionKey = "0008|1030";
+  bool seriesUIDGiven = false;
+  bool seriesNumberGiven = false;
+  bool seriesDescriptionGiven = false;
+  bool studyUIDGiven = false;
+  bool studyIDGiven = false;
+  bool studyDescriptionGiven = 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] );
-    std::cout << entryId << " " << value << std::endl;
-    for(unsigned int fni = 0; fni<numberOfFilenames; fni++)
-      itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), entryId, value );
+    std::string entryId( m_ArgsInfo.key_arg[i] );
+    if (m_ArgsInfo.verbose_flag) 
+      DD(entryId);
+    
+    seriesUIDGiven |= (entryId ==  seriesUIDkey || entryId ==  frameOfReferenceUIDKey);
+    seriesNumberGiven |= (entryId == seriesNumberKey);
+    seriesDescriptionGiven |= (entryId == seriesDescriptionKey);
+    studyUIDGiven |= (entryId == studyUIDKey);
+    studyIDGiven |= (entryId == studyIDKey);
+    studyDescriptionGiven |= (entryId == studyDescriptionKey);
+  }
+
+  // force the creation of a new series if a new study was specified
+  if (!studyUIDGiven && m_ArgsInfo.newStudyUID_flag) {
+    m_ArgsInfo.newSeriesUID_flag = true;
+#if GDCM_MAJOR_VERSION >= 2
+    gdcm::UIDGenerator suid;
+    studyUID = suid.Generate();
+#else
+    studyUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
+#endif
+  }
+    
+  if (!seriesUIDGiven && 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);
+    DD(studyUID);
+  }
+
+  // check if file UIDs will be be preserved
+  bool useInputFileUID = true;
+  if (m_ArgsInfo.newSeriesUID_flag || m_ArgsInfo.newStudyUID_flag || seriesUIDGiven || studyUIDGiven) {
+    useInputFileUID = false;
   }
+  else {
+#if GDCM_MAJOR_VERSION < 2
+    gdcmIO->SetKeepOriginalUID(true);
+#endif
+    namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg  );
+  }
+  
+  filenames_out.resize(numberOfFilenames);
   
+  time_t t;
+  t = time(&t);
+  struct tm* instanceDateTimeTm = localtime(&t);
+  char datetime[16];
+  strftime(datetime, 16, "%Y%m%d", instanceDateTimeTm);
+  std::ostringstream instanceDate;
+  instanceDate << datetime;
+  std::ostringstream instanceTime;
+  strftime(datetime, 16, "%H%M%S", instanceDateTimeTm);
+  instanceTime << datetime;
+  
+  // update output dicom keys/tags
+  for(unsigned int fni = 0; fni<numberOfFilenames; fni++) {
+    for (unsigned int i = 0; i < numberOfKeysGiven; i++) {
+      std::string entryId(m_ArgsInfo.key_arg[i]  );
+      std::string value( m_ArgsInfo.tag_arg[i] );
+
+      itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), entryId, value );
+    }
+
+    // series UID
+    if (!seriesUIDGiven) {
+      if (m_ArgsInfo.newSeriesUID_flag) {
+        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesUIDkey, seriesUID );
+        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), frameOfReferenceUIDKey, frameOfReferenceUID );
+      }
+    }
+    
+    // study UID
+    if (!studyUIDGiven) {
+      if (m_ArgsInfo.newStudyUID_flag) 
+        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyUIDKey, studyUID );
+    }
+    
+    // study description
+    if (studyUIDGiven || m_ArgsInfo.newStudyUID_flag) {
+      if (!studyIDGiven)
+        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyIDKey,itksys::SystemTools::GetFilenameName( m_ArgsInfo.outputDir_arg ));
+      if (!studyDescriptionGiven)
+        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyDescriptionKey,itksys::SystemTools::GetFilenameName( m_ArgsInfo.outputDir_arg ));
+      
+      itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0020", instanceDate.str() );
+      itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0030", instanceTime.str() );
+    }
+    
+    // series description/number
+    if (seriesUIDGiven || m_ArgsInfo.newSeriesUID_flag) {
+      if (!seriesDescriptionGiven)
+        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesDescriptionKey, itksys::SystemTools::GetFilenameName(m_ArgsInfo.outputDir_arg) );
+      if (!seriesNumberGiven)
+        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesNumberKey, itksys::SystemTools::GetFilenameName(m_ArgsInfo.outputDir_arg) );
+
+      itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0012", instanceDate.str() );
+      itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0013", instanceTime.str() );
+    }
 
+    // file UIDs are recreated for new studies or series
+    if (!useInputFileUID)
+    {
+      if (m_ArgsInfo.verbose_flag)
+        std::cout << "Recreating file UIDs" << std::endl;
+
+      std::string fileUID;
+#if GDCM_MAJOR_VERSION >= 2
+      gdcm::UIDGenerator fid;
+      fileUID = fid.Generate();
+#else
+      fileUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
+#endif
+      itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0018", fileUID );
+      itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0002|0003", fileUID );
+      
+      filenames_out[fni] = itksys::SystemTools::CollapseFullPath(fileUID.c_str(), m_ArgsInfo.outputDir_arg) + std::string(".dcm"); 
+    }
+  }
+  
   // Output directory and filenames
   itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputDir_arg ); // create if it doesn't exist
   typedef itk::ImageSeriesWriter<InputImageType, OutputImageType >  SeriesWriterType;
@@ -260,8 +413,9 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
 
   // Write
   try {
+    if (m_ArgsInfo.verbose_flag)
+      std::cout << seriesWriter << std::endl;
     seriesWriter->Update();
-    std::cerr << "filter update" << std::endl;
   } catch( itk::ExceptionObject & excp ) {
     std::cerr << "Error: Exception thrown while writing the series!!" << std::endl;
     std::cerr << excp << std::endl;