Type->Enum // added .as_ref() // adjust ITK git tag

ANTsX · Feb 4, 2020 · 31f18fe · 31f18fe
1 parent f028a73
commit 31f18fe
Show file tree

Hide file tree

Showing 40 changed files with 74 additions and 74 deletions.
diff --git a/Examples/ANTS.cxx b/Examples/ANTS.cxx
@@ -190,14 +190,14 @@ int ANTS( std::vector<std::string> args, std::ostream* /*out_stream = nullptr*/
   if( argc == 3 && ( std::stoi( argv[1] ) != '-' || std::stoi( argv[1] ) != 2 || std::stoi( argv[1] ) != 3 ) )
     {
     itk::ImageIOBase::Pointer fixedImageIO
-      = itk::ImageIOFactory::CreateImageIO( argv[1], itk::ImageIOFactory::FileModeType::ReadMode );
+      = itk::ImageIOFactory::CreateImageIO( argv[1], itk::ImageIOFactory::FileModeEnum::ReadMode );
     if( fixedImageIO.IsNull() )
       {
       std::cerr << "Invalid fixed image: " << argv[1] << std::endl;
       return EXIT_FAILURE;
       }
     itk::ImageIOBase::Pointer movingImageIO
-      = itk::ImageIOFactory::CreateImageIO( argv[2], itk::ImageIOFactory::FileModeType::ReadMode );
+      = itk::ImageIOFactory::CreateImageIO( argv[2], itk::ImageIOFactory::FileModeEnum::ReadMode );
     if( movingImageIO.IsNull() )
       {
       std::cerr << "Invalid moving image: " << argv[2] << std::endl;

diff --git a/Examples/ANTSIntegrateVectorField.cxx b/Examples/ANTSIntegrateVectorField.cxx
@@ -464,7 +464,7 @@ int ANTSIntegrateVectorField( std::vector<std::string> args, std::ostream* /*out
 
   std::string               ifn = std::string(argv[1]);
   itk::ImageIOBase::Pointer imageIO =
-    itk::ImageIOFactory::CreateImageIO(ifn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+    itk::ImageIOFactory::CreateImageIO(ifn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(ifn.c_str() );
   imageIO->ReadImageInformation();
   unsigned int dim =  imageIO->GetNumberOfDimensions();

diff --git a/Examples/ANTSIntegrateVelocityField.cxx b/Examples/ANTSIntegrateVelocityField.cxx
@@ -169,7 +169,7 @@ int ANTSIntegrateVelocityField( std::vector<std::string> args, std::ostream* /*o
   std::cout << " start " << std::endl;
   std::string               ifn = std::string(argv[1]);
   itk::ImageIOBase::Pointer imageIO =
-    itk::ImageIOFactory::CreateImageIO(ifn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+    itk::ImageIOFactory::CreateImageIO(ifn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(ifn.c_str() );
   imageIO->ReadImageInformation();
   unsigned int dim =  imageIO->GetNumberOfDimensions();

diff --git a/Examples/ANTSUseLandmarkImagesToGetAffineTransform.cxx b/Examples/ANTSUseLandmarkImagesToGetAffineTransform.cxx
@@ -436,7 +436,7 @@ int ANTSUseLandmarkImagesToGetAffineTransform( std::vector<std::string> args, st
   // Get the image dimension
   std::string               fn = std::string(argv[1]);
   itk::ImageIOBase::Pointer imageIO =
-    itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+    itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(fn.c_str() );
   imageIO->ReadImageInformation();
 

diff --git a/Examples/ANTSUseLandmarkImagesToGetBSplineDisplacementField.cxx b/Examples/ANTSUseLandmarkImagesToGetBSplineDisplacementField.cxx
@@ -541,7 +541,7 @@ int ANTSUseLandmarkImagesToGetBSplineDisplacementField( std::vector<std::string>
   // Get the image dimension
   std::string               fn = std::string(argv[1]);
   itk::ImageIOBase::Pointer imageIO =
-    itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+    itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(fn.c_str() );
   imageIO->ReadImageInformation();
 

diff --git a/Examples/Atropos.cxx b/Examples/Atropos.cxx
@@ -1778,7 +1778,7 @@ int Atropos( std::vector<std::string> args, std::ostream* /*out_stream = nullptr
       return EXIT_FAILURE;
       }
     itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(
-        filename.c_str(), itk::ImageIOFactory::FileModeType::ReadMode );
+        filename.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode );
     dimension = imageIO->GetNumberOfDimensions();
     }
 

diff --git a/Examples/AverageImages.cxx b/Examples/AverageImages.cxx
@@ -72,7 +72,7 @@ int AverageImages1(unsigned int argc, char *argv[])
     // Get the image dimension
     const std::string fn = std::string(argv[j]);
     typename itk::ImageIOBase::Pointer imageIO =
-      itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+      itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
     imageIO->SetFileName(fn.c_str() );
     imageIO->ReadImageInformation();
 
@@ -194,7 +194,7 @@ int AverageImages(unsigned int argc, char *argv[])
     std::string fn = std::string(argv[j]);
     std::cout << " fn " << fn << " " << ImageDimension << " " << NVectorComponents << std::endl;
     typename itk::ImageIOBase::Pointer imageIO =
-      itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+      itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
     imageIO->SetFileName( fn.c_str() );
     imageIO->ReadImageInformation();
 
@@ -326,7 +326,7 @@ int AverageImages( std::vector<std::string> args, std::ostream* /*out_stream = n
 
   const int                 dim = std::stoi( argv[1] );
   itk::ImageIOBase::Pointer imageIO =
-    itk::ImageIOFactory::CreateImageIO(argv[4], itk::ImageIOFactory::FileModeType::ReadMode);
+    itk::ImageIOFactory::CreateImageIO(argv[4], itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(argv[4]);
   imageIO->ReadImageInformation();
   unsigned int ncomponents = imageIO->GetNumberOfComponents();

diff --git a/Examples/AverageTensorImages.cxx b/Examples/AverageTensorImages.cxx
@@ -37,7 +37,7 @@ int AverageTensorImages(unsigned int argc, char *argv[])
     std::string fn = std::string(argv[j]);
     std::cout << " fn " << fn << std::endl;
     typename itk::ImageIOBase::Pointer imageIO =
-      itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+      itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
     imageIO->SetFileName(fn.c_str() );
     imageIO->ReadImageInformation();
     for( unsigned int i = 0; i < imageIO->GetNumberOfDimensions(); i++ )

diff --git a/Examples/ConvertImagePixelType.cxx b/Examples/ConvertImagePixelType.cxx
@@ -170,7 +170,7 @@ int ConvertImagePixelType( std::vector<std::string> args, std::ostream* /*out_st
   std::string               fn = std::string(argv[1]);
   itk::ImageIOBase::Pointer imageIO =
     itk::ImageIOFactory::CreateImageIO(
-      fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+      fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(fn.c_str() );
   imageIO->ReadImageInformation();
 

diff --git a/Examples/ConvertInputImagePixelTypeToFloat.cxx b/Examples/ConvertInputImagePixelTypeToFloat.cxx
@@ -150,7 +150,7 @@ int ConvertInputImagePixelTypeToFloat( std::vector<std::string> args, std::ostre
   std::string               fn = std::string(argv[1]);
   itk::ImageIOBase::Pointer imageIO =
     itk::ImageIOFactory::CreateImageIO(
-      fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+      fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(fn.c_str() );
   imageIO->ReadImageInformation();
 

diff --git a/Examples/ConvertToJpg.cxx b/Examples/ConvertToJpg.cxx
@@ -148,7 +148,7 @@ int ConvertToJpg( std::vector<std::string> args, std::ostream* /*out_stream = nu
     std::string               fn = std::string(argv[1]);
     itk::ImageIOBase::Pointer imageIO =
       itk::ImageIOFactory::CreateImageIO(
-        fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+        fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
     imageIO->SetFileName(fn.c_str() );
     imageIO->ReadImageInformation();
 

diff --git a/Examples/CopyImageHeaderInformation.cxx b/Examples/CopyImageHeaderInformation.cxx
@@ -184,7 +184,7 @@ int CopyImageHeaderInformation( std::vector<std::string> args, std::ostream* /*o
   std::string               fn = std::string(argv[1]);
   itk::ImageIOBase::Pointer imageIO =
     itk::ImageIOFactory::CreateImageIO(
-      fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+      fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(fn.c_str() );
   imageIO->ReadImageInformation();
   unsigned int dim = imageIO->GetNumberOfDimensions();

diff --git a/Examples/CreateDTICohort.cxx b/Examples/CreateDTICohort.cxx
@@ -1180,7 +1180,7 @@ int CreateDTICohort( std::vector<std::string> args, std::ostream* /*out_stream =
       return EXIT_FAILURE;
       }
     itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(
-        filename.c_str(), itk::ImageIOFactory::FileModeType::ReadMode );
+        filename.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode );
     dimension = imageIO->GetNumberOfDimensions();
     }
 

diff --git a/Examples/CreateTiledMosaic.cxx b/Examples/CreateTiledMosaic.cxx
@@ -1286,7 +1286,7 @@ int CreateTiledMosaic( std::vector<std::string> args, std::ostream* /*out_stream
     filename = imageOption->GetFunction( 0 )->GetName();
 
     itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(
-        filename.c_str(), itk::ImageIOFactory::FileModeType::ReadMode );
+        filename.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode );
     unsigned int dimension = imageIO->GetNumberOfDimensions();
 
     if( dimension == 3 )

diff --git a/Examples/DenoiseImage.cxx b/Examples/DenoiseImage.cxx
@@ -649,7 +649,7 @@ int DenoiseImage( std::vector<std::string> args, std::ostream* /*out_stream = nu
       return EXIT_FAILURE;
       }
     itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(
-        filename.c_str(), itk::ImageIOFactory::FileModeType::ReadMode );
+        filename.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode );
     dimension = imageIO->GetNumberOfDimensions();
     }
 

diff --git a/Examples/ImageMath_Templates.hxx b/Examples/ImageMath_Templates.hxx
@@ -1106,7 +1106,7 @@ int TileImages(unsigned int argc, char *argv[])
     // Get the image dimension
     std::string fn = std::string(argv[j]);
     typename itk::ImageIOBase::Pointer imageIO =
-      itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+      itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
     imageIO->SetFileName(fn.c_str() );
     imageIO->ReadImageInformation();
 
@@ -5818,7 +5818,7 @@ int TensorFunctions(int argc, char *argv[])
       " Convert a 4D tensor to a 3D tensor --- if there are 7 components to the tensor, we throw away the first component b/c its probably b0 "
       << std::endl;
     itk::ImageIOBase::Pointer imageIO =
-      itk::ImageIOFactory::CreateImageIO(fn1.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+      itk::ImageIOFactory::CreateImageIO(fn1.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
     imageIO->SetFileName(fn1.c_str() );
     imageIO->ReadImageInformation();
     unsigned int dim = imageIO->GetNumberOfDimensions();
@@ -11022,7 +11022,7 @@ int ConvertImageSetToMatrix(unsigned int argc, char *argv[])
     // Get the image dimension
     std::string fn = std::string(argv[j]);
     typename itk::ImageIOBase::Pointer imageIO =
-      itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+      itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
     imageIO->SetFileName(fn.c_str() );
     imageIO->ReadImageInformation();
     for( unsigned int i = 0; i < imageIO->GetNumberOfDimensions(); i++ )
@@ -11319,7 +11319,7 @@ int ConvertImageSetToEigenvectors(unsigned int argc, char *argv[])
     // Get the image dimension
     std::string fn = std::string(argv[j]);
     typename itk::ImageIOBase::Pointer imageIO =
-      itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+      itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
     imageIO->SetFileName(fn.c_str() );
     imageIO->ReadImageInformation();
     for( unsigned int i = 0; i < imageIO->GetNumberOfDimensions(); i++ )

diff --git a/Examples/KellyKapowski.cxx b/Examples/KellyKapowski.cxx
@@ -834,7 +834,7 @@ int KellyKapowski( std::vector<std::string> args, std::ostream* /*out_stream = n
       return EXIT_FAILURE;
       }
     itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(
-        filename.c_str(), itk::ImageIOFactory::FileModeType::ReadMode );
+        filename.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode );
     dimension = imageIO->GetNumberOfDimensions();
     }
 

diff --git a/Examples/LaplacianThickness.cxx b/Examples/LaplacianThickness.cxx
@@ -1008,7 +1008,7 @@ int LaplacianThickness( std::vector<std::string> args, std::ostream* /*out_strea
   //  std::cout << " image " << ifn << std::endl;
   // Get the image dimension
   itk::ImageIOBase::Pointer imageIO =
-    itk::ImageIOFactory::CreateImageIO(ifn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+    itk::ImageIOFactory::CreateImageIO(ifn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(ifn.c_str() );
   imageIO->ReadImageInformation();
   unsigned int dim =  imageIO->GetNumberOfDimensions();

diff --git a/Examples/MeasureMinMaxMean.cxx b/Examples/MeasureMinMaxMean.cxx
@@ -187,7 +187,7 @@ int MeasureMinMaxMean( std::vector<std::string> args, std::ostream* /*out_stream
     }
   int                       dim = std::stoi( argv[1] );
   itk::ImageIOBase::Pointer imageIO =
-    itk::ImageIOFactory::CreateImageIO(argv[2], itk::ImageIOFactory::FileModeType::ReadMode);
+    itk::ImageIOFactory::CreateImageIO(argv[2], itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(argv[2]);
   imageIO->ReadImageInformation();
   unsigned int ncomponents = imageIO->GetNumberOfComponents();

diff --git a/Examples/MultiplyImages.cxx b/Examples/MultiplyImages.cxx
@@ -185,7 +185,7 @@ int MultiplyImages( std::vector<std::string> args, std::ostream* /*out_stream =
 
   int                       dim = std::stoi( argv[1] );
   itk::ImageIOBase::Pointer imageIO =
-    itk::ImageIOFactory::CreateImageIO(argv[2], itk::ImageIOFactory::FileModeType::ReadMode);
+    itk::ImageIOFactory::CreateImageIO(argv[2], itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(argv[2]);
   imageIO->ReadImageInformation();
   unsigned int ncomponents = imageIO->GetNumberOfComponents();

diff --git a/Examples/N4BiasFieldCorrection.cxx b/Examples/N4BiasFieldCorrection.cxx
@@ -946,7 +946,7 @@ int N4BiasFieldCorrection( std::vector<std::string> args, std::ostream* /*out_st
       return EXIT_FAILURE;
       }
     itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(
-        filename.c_str(), itk::ImageIOFactory::FileModeType::ReadMode );
+        filename.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode );
     dimension = imageIO->GetNumberOfDimensions();
     }
 

diff --git a/Examples/NonLocalSuperResolution.cxx b/Examples/NonLocalSuperResolution.cxx
@@ -717,7 +717,7 @@ int NonLocalSuperResolution( std::vector<std::string> args, std::ostream* /*out_
       return EXIT_FAILURE;
       }
     itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(
-        filename.c_str(), itk::ImageIOFactory::FileModeType::ReadMode );
+        filename.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode );
     dimension = imageIO->GetNumberOfDimensions();
     }
 

diff --git a/Examples/PrintHeader.cxx b/Examples/PrintHeader.cxx
@@ -456,7 +456,7 @@ int PrintHeader( std::vector<std::string> args, std::ostream* /*out_stream = nul
     }
   itk::ImageIOBase::Pointer imageIO =
     itk::ImageIOFactory::CreateImageIO(
-      fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+      fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(fn.c_str() );
   try
     {

diff --git a/Examples/ResetDirection.cxx b/Examples/ResetDirection.cxx
@@ -136,7 +136,7 @@ int ResetDirection( std::vector<std::string> args, std::ostream* /*out_stream =
   std::string               fn = std::string(argv[1]);
   itk::ImageIOBase::Pointer imageIO =
     itk::ImageIOFactory::CreateImageIO(
-      fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+      fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(fn.c_str() );
   imageIO->ReadImageInformation();
 

diff --git a/Examples/SetDirectionByMatrix.cxx b/Examples/SetDirectionByMatrix.cxx
@@ -155,7 +155,7 @@ int SetDirectionByMatrix( std::vector<std::string> args, std::ostream* /*out_str
   std::string               fn = std::string(argv[1]);
   itk::ImageIOBase::Pointer imageIO =
     itk::ImageIOFactory::CreateImageIO(
-      fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+      fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(fn.c_str() );
   imageIO->ReadImageInformation();
 

diff --git a/Examples/StudentsTestOnImages.cxx b/Examples/StudentsTestOnImages.cxx
@@ -454,7 +454,7 @@ int StudentsTestOnImages(int argc, char *argv[])
   // Get the image dimension
   std::string               fn = std::string(argv[5]);
   itk::ImageIOBase::Pointer imageIO =
-    itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+    itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(fn.c_str() );
   imageIO->ReadImageInformation();
   typename ImageType::SizeType size;

diff --git a/Examples/WarpImageMultiTransform.cxx b/Examples/WarpImageMultiTransform.cxx
@@ -808,7 +808,7 @@ int WarpImageMultiTransform( std::vector<std::string> args, std::ostream* /*out_
   if( is_parsing_ok )
     {
     itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(moving_image_filename,
-                                                                           itk::ImageIOFactory::FileModeType::ReadMode);
+                                                                           itk::ImageIOFactory::FileModeEnum::ReadMode);
     imageIO->SetFileName(moving_image_filename);
     imageIO->ReadImageInformation();
     unsigned int ncomponents = imageIO->GetNumberOfComponents();

diff --git a/Examples/WarpTimeSeriesImageMultiTransform.cxx b/Examples/WarpTimeSeriesImageMultiTransform.cxx
@@ -483,7 +483,7 @@ void WarpImageMultiTransform(char *moving_image_filename, char *output_image_fil
 
   typename VectorImageType::Pointer img_mov;
   typename itk::ImageIOBase::Pointer imageIO =
-    itk::ImageIOFactory::CreateImageIO(moving_image_filename, itk::ImageIOFactory::FileModeType::ReadMode);
+    itk::ImageIOFactory::CreateImageIO(moving_image_filename, itk::ImageIOFactory::FileModeEnum::ReadMode);
   imageIO->SetFileName(moving_image_filename);
   imageIO->ReadImageInformation();
   //    std::cout << " Dimension " << imageIO->GetNumberOfDimensions()  << " Components "

diff --git a/Examples/antsAI.cxx b/Examples/antsAI.cxx
@@ -959,18 +959,18 @@ int antsAI( itk::ants::CommandLineParser *parser )
 
       if( ImageDimension == 2 )
         {
-        fixedPrimaryEigenVector = fixedImagePrincipalAxes.GetVnlMatrix().get_row( 1 );
-        movingPrimaryEigenVector = movingImagePrincipalAxes.GetVnlMatrix().get_row( 1 );
+        fixedPrimaryEigenVector = fixedImagePrincipalAxes.GetVnlMatrix().get_row( 1 ).as_ref();
+        movingPrimaryEigenVector = movingImagePrincipalAxes.GetVnlMatrix().get_row( 1 ).as_ref();
 
         B = outer_product( movingPrimaryEigenVector, fixedPrimaryEigenVector );
         }
       else if( ImageDimension == 3 )
         {
-        fixedPrimaryEigenVector = fixedImagePrincipalAxes.GetVnlMatrix().get_row( 2 );
-        fixedSecondaryEigenVector = fixedImagePrincipalAxes.GetVnlMatrix().get_row( 1 );
+        fixedPrimaryEigenVector = fixedImagePrincipalAxes.GetVnlMatrix().get_row( 2 ).as_ref();
+        fixedSecondaryEigenVector = fixedImagePrincipalAxes.GetVnlMatrix().get_row( 1 ).as_ref();
 
-        movingPrimaryEigenVector = movingImagePrincipalAxes.GetVnlMatrix().get_row( 2 );
-        movingSecondaryEigenVector = movingImagePrincipalAxes.GetVnlMatrix().get_row( 1 );
+        movingPrimaryEigenVector = movingImagePrincipalAxes.GetVnlMatrix().get_row( 2 ).as_ref();
+        movingSecondaryEigenVector = movingImagePrincipalAxes.GetVnlMatrix().get_row( 1 ).as_ref();
 
         B = outer_product( movingPrimaryEigenVector, fixedPrimaryEigenVector ) +
           outer_product( movingSecondaryEigenVector, fixedSecondaryEigenVector );

diff --git a/Examples/antsAlignOrigin.cxx b/Examples/antsAlignOrigin.cxx
@@ -323,7 +323,7 @@ int antsAlignOrigin( std::vector<std::string> args, std::ostream* /*out_stream =
     parser->GetOption( "input-image-type" );
 
   itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(
-      filename.c_str(), itk::ImageIOFactory::FileModeType::ReadMode );
+      filename.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode );
   unsigned int dimension = imageIO->GetNumberOfDimensions();
 
   itk::ants::CommandLineParser::OptionType::Pointer dimOption =

diff --git a/Examples/antsJointFusion.cxx b/Examples/antsJointFusion.cxx
@@ -1002,7 +1002,7 @@ int antsJointFusion( std::vector<std::string> args, std::ostream* /*out_stream =
       return EXIT_FAILURE;
       }
     itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(
-        filename.c_str(), itk::ImageIOFactory::FileModeType::ReadMode );
+        filename.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode );
     dimension = imageIO->GetNumberOfDimensions();
     }
 

diff --git a/Examples/antsJointTensorFusion.cxx b/Examples/antsJointTensorFusion.cxx
@@ -974,7 +974,7 @@ int antsJointTensorFusion( std::vector<std::string> args, std::ostream* /*out_st
       return EXIT_FAILURE;
       }
     itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(
-        filename.c_str(), itk::ImageIOFactory::FileModeType::ReadMode );
+        filename.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode );
     dimension = imageIO->GetNumberOfDimensions();
     }
 

diff --git a/Examples/antsMotionCorrDiffusionDirection.cxx b/Examples/antsMotionCorrDiffusionDirection.cxx
@@ -319,7 +319,7 @@ int ants_motion_directions( itk::ants::CommandLineParser *parser )
   // Therefore check reference image is 3D, and fail if not
   //
  itk::ImageIOBase::Pointer imageIO =
-   itk::ImageIOFactory::CreateImageIO(physicalName.c_str(), itk::ImageIOFactory::FileModeType::ReadMode);
+   itk::ImageIOFactory::CreateImageIO(physicalName.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode);
  imageIO->SetFileName(physicalName.c_str() );
  try
    {