Merge pull request #1218 from BRAINSia/use-modern-paradigms

COMP: Use modern ITK paradigms
ANTsX · Aug 6, 2021 · de5c8e7 · de5c8e7
2 parents 61e9501 + bca6205
commit de5c8e7
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Showing 73 changed files with 201 additions and 200 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::FileModeEnum::ReadMode );
+      = itk::ImageIOFactory::CreateImageIO( argv[1], itk::IOFileModeEnum::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::FileModeEnum::ReadMode );
+      = itk::ImageIOFactory::CreateImageIO( argv[2], itk::IOFileModeEnum::ReadMode );
     if( movingImageIO.IsNull() )
       {
       std::cerr << "Invalid moving image: " << argv[2] << std::endl;

diff --git a/Examples/ANTSIntegrateVectorField.cxx b/Examples/ANTSIntegrateVectorField.cxx
@@ -61,7 +61,7 @@ SmoothImage(typename TImage::Pointer image, float sig)
   using dgf = itk::DiscreteGaussianImageFilter<TImage, TImage>;
   typename dgf::Pointer filter = dgf::New();
   filter->SetVariance(sig);
-  filter->SetUseImageSpacingOn();
+  filter->SetUseImageSpacing(true);
   filter->SetMaximumError(.01f);
   filter->SetInput(image);
   filter->Update();
@@ -463,7 +463,7 @@ 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::FileModeEnum::ReadMode);
+    itk::ImageIOFactory::CreateImageIO(ifn.c_str(), itk::IOFileModeEnum::ReadMode);
   imageIO->SetFileName(ifn.c_str() );
   imageIO->ReadImageInformation();
   unsigned int dim =  imageIO->GetNumberOfDimensions();

diff --git a/Examples/ANTSIntegrateVelocityField.cxx b/Examples/ANTSIntegrateVelocityField.cxx
@@ -168,7 +168,7 @@ 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::FileModeEnum::ReadMode);
+    itk::ImageIOFactory::CreateImageIO(ifn.c_str(), itk::IOFileModeEnum::ReadMode);
   imageIO->SetFileName(ifn.c_str() );
   imageIO->ReadImageInformation();
   unsigned int dim =  imageIO->GetNumberOfDimensions();

diff --git a/Examples/ANTSJacobian.cxx b/Examples/ANTSJacobian.cxx
@@ -392,7 +392,7 @@ ComputeJacobian(TDisplacementField* field, char* fnm, char* maskfn, bool uselog
     {
     typename dgf::Pointer filter = dgf::New();
     filter->SetVariance(sig);
-    filter->SetUseImageSpacingOff();
+    filter->SetUseImageSpacing(false);
     filter->SetMaximumError(.01f);
     filter->SetInput(m_FloatImage);
     filter->Update();
@@ -402,7 +402,7 @@ ComputeJacobian(TDisplacementField* field, char* fnm, char* maskfn, bool uselog
     {
     typename dgf::Pointer filter = dgf::New();
     filter->SetVariance(sig);
-    filter->SetUseImageSpacingOff();
+    filter->SetUseImageSpacing(false);
     filter->SetMaximumError(.01f);
     filter->SetInput(temp);
     filter->Update();

diff --git a/Examples/ANTSUseLandmarkImagesToGetAffineTransform.cxx b/Examples/ANTSUseLandmarkImagesToGetAffineTransform.cxx
@@ -432,7 +432,7 @@ 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::FileModeEnum::ReadMode);
+    itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::IOFileModeEnum::ReadMode);
   imageIO->SetFileName(fn.c_str() );
   imageIO->ReadImageInformation();
 

diff --git a/Examples/ANTSUseLandmarkImagesToGetBSplineDisplacementField.cxx b/Examples/ANTSUseLandmarkImagesToGetBSplineDisplacementField.cxx
@@ -540,7 +540,7 @@ 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::FileModeEnum::ReadMode);
+    itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::IOFileModeEnum::ReadMode);
   imageIO->SetFileName(fn.c_str() );
   imageIO->ReadImageInformation();
 

diff --git a/Examples/AddNoiseToImage.cxx b/Examples/AddNoiseToImage.cxx
@@ -507,7 +507,7 @@ int AddNoiseToImage( std::vector<std::string> args, std::ostream* /*out_stream =
       return EXIT_FAILURE;
       }
     itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(
-        filename.c_str(), itk::ImageIOFactory::FileModeEnum::ReadMode );
+        filename.c_str(), itk::IOFileModeEnum::ReadMode );
     dimension = imageIO->GetNumberOfDimensions();
     }
 

diff --git a/Examples/Atropos.cxx b/Examples/Atropos.cxx
@@ -1766,7 +1766,7 @@ 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::FileModeEnum::ReadMode );
+        filename.c_str(), itk::IOFileModeEnum::ReadMode );
     dimension = imageIO->GetNumberOfDimensions();
     }
 

diff --git a/Examples/AverageImages.cxx b/Examples/AverageImages.cxx
@@ -63,7 +63,7 @@ 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::FileModeEnum::ReadMode);
+      itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::IOFileModeEnum::ReadMode);
     imageIO->SetFileName(fn.c_str() );
     imageIO->ReadImageInformation();
 
@@ -186,7 +186,7 @@ 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::FileModeEnum::ReadMode);
+      itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::IOFileModeEnum::ReadMode);
     imageIO->SetFileName( fn.c_str() );
     imageIO->ReadImageInformation();
 
@@ -319,7 +319,7 @@ 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::FileModeEnum::ReadMode);
+    itk::ImageIOFactory::CreateImageIO(argv[4], itk::IOFileModeEnum::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::FileModeEnum::ReadMode);
+      itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::IOFileModeEnum::ReadMode);
     imageIO->SetFileName(fn.c_str() );
     imageIO->ReadImageInformation();
     for( unsigned int i = 0; i < imageIO->GetNumberOfDimensions(); i++ )

diff --git a/Examples/CheckTopology.cxx b/Examples/CheckTopology.cxx
@@ -131,7 +131,7 @@ typename TImage::Pointer SmoothImage( typename TImage::Pointer image, float sig
   using dgf = itk::DiscreteGaussianImageFilter<ImageType, ImageType>;
   typename dgf::Pointer filter = dgf::New();
   filter->SetVariance(sig);
-  filter->SetUseImageSpacingOff();
+  filter->SetUseImageSpacing(false);
   filter->SetMaximumError(.01f);
   filter->SetInput(image);
   filter->Update();

diff --git a/Examples/ConformalMapping.cxx b/Examples/ConformalMapping.cxx
@@ -246,7 +246,7 @@ SmoothImage( typename TImage::Pointer input, double var)
   typename dgf::Pointer filter = dgf::New();
   filter->SetVariance(var);
   filter->SetMaximumError(.01f);
-  filter->SetUseImageSpacingOn();
+  filter->SetUseImageSpacing(true);
   filter->SetInput(input);
   filter->Update();
 

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::FileModeEnum::ReadMode);
+      fn.c_str(), itk::IOFileModeEnum::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::FileModeEnum::ReadMode);
+      fn.c_str(), itk::IOFileModeEnum::ReadMode);
   imageIO->SetFileName(fn.c_str() );
   imageIO->ReadImageInformation();
 

diff --git a/Examples/ConvertScalarImageToRGB.cxx b/Examples/ConvertScalarImageToRGB.cxx
@@ -72,67 +72,67 @@ int ConvertScalarImageToRGB( int argc, char *argv[] )
 
   if( colormapString == "red" )
     {
-    rgbfilter->SetColormap( RGBFilterType::ColormapEnumType::Red );
+      rgbfilter->SetColormap( RGBFilterType::RGBColormapFilterEnum::Red );
     }
   else if( colormapString == "green"  )
     {
-    rgbfilter->SetColormap( RGBFilterType::ColormapEnumType::Green );
+      rgbfilter->SetColormap( RGBFilterType::RGBColormapFilterEnum::Green );
     }
   else if( colormapString == "blue"  )
     {
-    rgbfilter->SetColormap( RGBFilterType::ColormapEnumType::Blue );
+      rgbfilter->SetColormap( RGBFilterType::RGBColormapFilterEnum::Blue );
     }
   else if( colormapString == "grey"  )
     {
-    rgbfilter->SetColormap( RGBFilterType::ColormapEnumType::Grey );
+      rgbfilter->SetColormap( RGBFilterType::RGBColormapFilterEnum::Grey );
     }
   else if( colormapString == "cool"  )
     {
-    rgbfilter->SetColormap( RGBFilterType::ColormapEnumType::Cool );
+      rgbfilter->SetColormap( RGBFilterType::RGBColormapFilterEnum::Cool );
     }
   else if( colormapString == "hot"  )
     {
-    rgbfilter->SetColormap( RGBFilterType::ColormapEnumType::Hot );
+      rgbfilter->SetColormap( RGBFilterType::RGBColormapFilterEnum::Hot );
     }
   else if( colormapString == "spring"  )
     {
-    rgbfilter->SetColormap( RGBFilterType::ColormapEnumType::Spring );
+      rgbfilter->SetColormap( RGBFilterType::RGBColormapFilterEnum::Spring );
     }
   else if( colormapString == "autumn"  )
     {
-    rgbfilter->SetColormap( RGBFilterType::ColormapEnumType::Autumn );
+      rgbfilter->SetColormap( RGBFilterType::RGBColormapFilterEnum::Autumn );
     }
   else if( colormapString == "winter"  )
     {
-    rgbfilter->SetColormap( RGBFilterType::ColormapEnumType::Winter );
+      rgbfilter->SetColormap( RGBFilterType::RGBColormapFilterEnum::Winter );
     }
   else if( colormapString == "copper"  )
     {
-    rgbfilter->SetColormap( RGBFilterType::ColormapEnumType::Copper );
+    rgbfilter->SetColormap( RGBFilterType::RGBColormapFilterEnum::Copper );
     }
   else if( colormapString == "summer"  )
     {
-    rgbfilter->SetColormap( RGBFilterType::ColormapEnumType::Summer );
+    rgbfilter->SetColormap( RGBFilterType::RGBColormapFilterEnum::Summer );
     }
   else if( colormapString == "jet"  )
     {
-    rgbfilter->SetColormap( RGBFilterType::ColormapEnumType::Jet );
+    rgbfilter->SetColormap( RGBFilterType::RGBColormapFilterEnum::Jet );
 //    typedef itk::Function::JetColormapFunction<typename RealImageType::PixelType,
 //      typename RGBImageType::PixelType> ColormapType;
 //    typename ColormapType::Pointer colormap = ColormapType::New();
 //    rgbfilter->SetColormap( colormap );
     }
   else if( colormapString == "hsv"  )
     {
-    rgbfilter->SetColormap( RGBFilterType::ColormapEnumType::HSV );
+    rgbfilter->SetColormap( RGBFilterType::RGBColormapFilterEnum::HSV );
 //    typedef itk::Function::HSVColormapFunction<typename RealImageType::PixelType,
 //      typename RGBImageType::PixelType> ColormapType;
 //    typename ColormapType::Pointer colormap = ColormapType::New();
 //    rgbfilter->SetColormap( colormap );
     }
   else if( colormapString == "overunder"  )
     {
-    rgbfilter->SetColormap( RGBFilterType::ColormapEnumType::OverUnder );
+    rgbfilter->SetColormap( RGBFilterType::RGBColormapFilterEnum::OverUnder );
     }
   else if( colormapString == "custom"  )
     {

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::FileModeEnum::ReadMode);
+        fn.c_str(), itk::IOFileModeEnum::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::FileModeEnum::ReadMode);
+      fn.c_str(), itk::IOFileModeEnum::ReadMode);
   imageIO->SetFileName(fn.c_str() );
   imageIO->ReadImageInformation();
   unsigned int dim = imageIO->GetNumberOfDimensions();

diff --git a/Examples/CreateDTICohort.cxx b/Examples/CreateDTICohort.cxx
@@ -1177,7 +1177,7 @@ 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::FileModeEnum::ReadMode );
+        filename.c_str(), itk::IOFileModeEnum::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::FileModeEnum::ReadMode );
+        filename.c_str(), itk::IOFileModeEnum::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::FileModeEnum::ReadMode );
+        filename.c_str(), itk::IOFileModeEnum::ReadMode );
     dimension = imageIO->GetNumberOfDimensions();
     }