Debug RTStruct conversion with empty struc

[clitk.git] / tools / clitkWriteDicomSeriesGenericFilter.txx

diff --git a/tools/clitkWriteDicomSeriesGenericFilter.txx b/tools/clitkWriteDicomSeriesGenericFilter.txx
index 70123e6bac6c1721c04d4433b530349a5cafa999..a2bccc4aa0daa52fbef3b8a34cb115b3eb9cc20c 100644 (file)
--- a/tools/clitkWriteDicomSeriesGenericFilter.txx
+++ b/tools/clitkWriteDicomSeriesGenericFilter.txx
@@ -139,7 +139,7 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
   namesGenerator->SetInputDirectory( m_ArgsInfo.inputDir_arg );
   namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg  );
   typename   ReaderType::FileNamesContainer filenames_in = namesGenerator->GetInputFileNames();
-  typename   ReaderType::FileNamesContainer filenames_out;
+  typename   ReaderType::FileNamesContainer filenames_out = namesGenerator->GetOutputFileNames();
 
   // Output the dicom files
   unsigned int numberOfFilenames =  filenames_in.size();
@@ -153,6 +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 {
@@ -267,12 +273,12 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
     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);
+    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
@@ -308,13 +314,12 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
   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
-  }
-  else {
     namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg  );
-    filenames_out = namesGenerator->GetOutputFileNames();
   }
   
   filenames_out.resize(numberOfFilenames);
@@ -356,9 +361,9 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
     // study description
     if (studyUIDGiven || m_ArgsInfo.newStudyUID_flag) {
       if (!studyIDGiven)
-        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyIDKey, m_ArgsInfo.outputDir_arg );
+        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyIDKey,itksys::SystemTools::GetFilenameName( m_ArgsInfo.outputDir_arg ));
       if (!studyDescriptionGiven)
-        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyDescriptionKey, m_ArgsInfo.outputDir_arg );
+        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() );
@@ -367,9 +372,9 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
     // series description/number
     if (seriesUIDGiven || m_ArgsInfo.newSeriesUID_flag) {
       if (!seriesDescriptionGiven)
-        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesDescriptionKey, m_ArgsInfo.outputDir_arg );
+        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesDescriptionKey, itksys::SystemTools::GetFilenameName(m_ArgsInfo.outputDir_arg) );
       if (!seriesNumberGiven)
-        itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesNumberKey, m_ArgsInfo.outputDir_arg );
+        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() );
@@ -378,6 +383,9 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
     // 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;
@@ -405,6 +413,8 @@ WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
 
   // Write
   try {
+    if (m_ArgsInfo.verbose_flag)
+      std::cout << seriesWriter << std::endl;
     seriesWriter->Update();
   } catch( itk::ExceptionObject & excp ) {
     std::cerr << "Error: Exception thrown while writing the series!!" << std::endl;