STYLE: Use itk::ReadImage and itk::WriteImage in remaining modules at src/

src/Bridge/VtkGlue/ConvertAnRGBitkImageTovtkImageData/Code.cxx

@@ -40,13 +40,11 @@ main(int argc, char * argv[])
   using PixelType = itk::RGBPixel<PixelComponentType>;
   using ImageType = itk::Image<PixelType, Dimension>;
 
-  using ReaderType = itk::ImageFileReader<ImageType>;
-  ReaderType::Pointer reader = ReaderType::New();
-  reader->SetFileName(inputFileName);
+  const auto input = itk::ReadImage<ImageType>(inputFileName);
 
   using FilterType = itk::ImageToVTKImageFilter<ImageType>;
   FilterType::Pointer filter = FilterType::New();
-  filter->SetInput(reader->GetOutput());
+  filter->SetInput(input);
 
   try
   {

src/Bridge/VtkGlue/ConvertAnitkImageTovtkImageData/Code.cxx

@@ -38,13 +38,11 @@ main(int argc, char * argv[])
   using PixelType = unsigned char;
   using ImageType = itk::Image<PixelType, Dimension>;
 
-  using ReaderType = itk::ImageFileReader<ImageType>;
-  ReaderType::Pointer reader = ReaderType::New();
-  reader->SetFileName(inputFileName);
+  const auto input = itk::ReadImage<ImageType>(inputFileName);
 
   using FilterType = itk::ImageToVTKImageFilter<ImageType>;
   FilterType::Pointer filter = FilterType::New();
-  filter->SetInput(reader->GetOutput());
+  filter->SetInput(input);
 
   try
   {

src/Bridge/VtkGlue/VisualizeEvolvingDense2DLevelSetAsElevationMap/Code.cxx

@@ -48,13 +48,7 @@ main(int argc, char * argv[])
   using InputPixelType = unsigned char;
   using InputImageType = itk::Image<InputPixelType, Dimension>;
 
-  // Read input image (to be processed).
-  using ReaderType = itk::ImageFileReader<InputImageType>;
-  ReaderType::Pointer reader = ReaderType::New();
-  reader->SetFileName(argv[1]);
-  reader->Update();
-
-  InputImageType::Pointer input = reader->GetOutput();
+  InputImageType::Pointer input = itk::ReadImage<InputImageType>(argv[1]);
 
   int numberOfIterations = std::stoi(argv[2]);
 

src/Bridge/VtkGlue/VisualizeEvolvingDense2DLevelSetZeroSet/Code.cxx

@@ -48,13 +48,7 @@ main(int argc, char * argv[])
   using InputPixelType = unsigned char;
   using InputImageType = itk::Image<InputPixelType, Dimension>;
 
-  // Read input image (to be processed).
-  using ReaderType = itk::ImageFileReader<InputImageType>;
-  ReaderType::Pointer reader = ReaderType::New();
-  reader->SetFileName(argv[1]);
-  reader->Update();
-
-  InputImageType::Pointer input = reader->GetOutput();
+  InputImageType::Pointer input = itk::ReadImage<InputImageType>(argv[1]);
 
   int numberOfIterations = std::stoi(argv[2]);
 

src/Bridge/VtkGlue/VisualizeStaticDense2DLevelSetAsElevationMap/Code.cxx

@@ -51,12 +51,7 @@ main(int argc, char * argv[])
   using InputPixelType = unsigned char;
   using InputImageType = itk::Image<InputPixelType, Dimension>;
 
-  // Read input image (to be processed).
-  using ReaderType = itk::ImageFileReader<InputImageType>;
-  ReaderType::Pointer reader = ReaderType::New();
-  reader->SetFileName(argv[1]);
-
-  InputImageType::Pointer input = reader->GetOutput();
+  InputImageType::Pointer input = itk::ReadImage<InputImageType>(argv[1]);
 
   using LevelSetPixelType = float;
   using LevelSetImageType = itk::Image<LevelSetPixelType, Dimension>;

src/Bridge/VtkGlue/VisualizeStaticDense2DLevelSetZeroSet/Code.cxx

@@ -51,12 +51,7 @@ main(int argc, char * argv[])
   using InputPixelType = unsigned char;
   using InputImageType = itk::Image<InputPixelType, Dimension>;
 
-  // Read input image (to be processed).
-  using ReaderType = itk::ImageFileReader<InputImageType>;
-  ReaderType::Pointer reader = ReaderType::New();
-  reader->SetFileName(argv[1]);
-
-  InputImageType::Pointer input = reader->GetOutput();
+  InputImageType::Pointer input = itk::ReadImage<InputImageType>(argv[1]);
 
   using LevelSetPixelType = float;
   using LevelSetImageType = itk::Image<LevelSetPixelType, Dimension>;

src/Bridge/VtkGlue/VisualizeStaticMalcolm2DLevelSetLayers/Code.cxx

@@ -43,12 +43,7 @@ main(int argc, char * argv[])
   using InputPixelType = unsigned char;
   using InputImageType = itk::Image<InputPixelType, Dimension>;
 
-  // Read input image (to be processed).
-  using ReaderType = itk::ImageFileReader<InputImageType>;
-  ReaderType::Pointer reader = ReaderType::New();
-  reader->SetFileName(argv[1]);
-
-  InputImageType::Pointer input = reader->GetOutput();
+  InputImageType::Pointer input = itk::ReadImage<InputImageType>(argv[1]);
 
   using LevelSetType = itk::MalcolmSparseLevelSetImage<Dimension>;
 

src/Bridge/VtkGlue/VisualizeStaticShi2DLevelSetLayers/Code.cxx

@@ -43,13 +43,7 @@ main(int argc, char * argv[])
   using InputPixelType = unsigned char;
   using InputImageType = itk::Image<InputPixelType, Dimension>;
 
-  // Read input image (to be processed).
-  using ReaderType = itk::ImageFileReader<InputImageType>;
-  ReaderType::Pointer reader = ReaderType::New();
-  reader->SetFileName(argv[1]);
-  reader->Update();
-
-  InputImageType::Pointer input = reader->GetOutput();
+  InputImageType::Pointer input = itk::ReadImage<InputImageType>(argv[1]);
 
   using LevelSetType = itk::ShiSparseLevelSetImage<Dimension>;
 

src/Bridge/VtkGlue/VisualizeStaticWhitaker2DLevelSetLayers/Code.cxx

@@ -43,12 +43,7 @@ main(int argc, char * argv[])
   using InputPixelType = unsigned char;
   using InputImageType = itk::Image<InputPixelType, Dimension>;
 
-  // Read input image (to be processed).
-  using ReaderType = itk::ImageFileReader<InputImageType>;
-  ReaderType::Pointer reader = ReaderType::New();
-  reader->SetFileName(argv[1]);
-
-  InputImageType::Pointer input = reader->GetOutput();
+  InputImageType::Pointer input = itk::ReadImage<InputImageType>(argv[1]);
 
   using LevelSetPixelType = float;
   using LevelSetType = itk::WhitakerSparseLevelSetImage<LevelSetPixelType, Dimension>;

src/Developer/Exceptions.cxx

@@ -1,6 +1,4 @@
 #include "itkImage.h"
-#include "itkImageFileReader.h"
-#include "itkImageFileWriter.h"
 
 #include "ImageSource.h"
 

src/Developer/ImageFilter.cxx

@@ -1,6 +1,4 @@
 #include "itkImage.h"
-#include "itkImageFileReader.h"
-#include "itkImageFileWriter.h"
 
 #include "ImageFilter.h"
 

src/Developer/ImageFilterMultipleInputs.cxx

@@ -1,6 +1,4 @@
 #include "itkImage.h"
-#include "itkImageFileReader.h"
-#include "itkImageFileWriter.h"
 
 #include "ImageFilterMultipleInputs.h"
 

src/Developer/ImageFilterMultipleInputsDifferentType.cxx

@@ -13,21 +13,14 @@ main(int, char *[])
   using ScalarImageType = itk::Image<unsigned char, 2>;
   using FilterType = itk::ImageFilterMultipleInputsDifferentType<VectorImageType, ScalarImageType>;
 
-  using ReaderType = itk::ImageFileReader<VectorImageType>;
-  ReaderType::Pointer reader = ReaderType::New();
-  reader->SetFileName("Test.jpg");
-  reader->Update();
+  const auto input = itk::ReadImage<VectorImageType>("Test.jpg");
 
   // Create and the filter
   FilterType::Pointer filter = FilterType::New();
-  filter->SetInput(reader->GetOutput());
+  filter->SetInput(input);
   filter->Update();
 
-  using WriterType = itk::ImageFileWriter<VectorImageType>;
-  WriterType::Pointer writer = WriterType::New();
-  writer->SetFileName("TestOutput.jpg");
-  writer->SetInput(filter->GetOutput());
-  writer->Update();
+  itk::WriteImage(filter->GetOutput(), "TestOutput.jpg");
 
   return EXIT_SUCCESS;
 }

src/Developer/ImageFilterMultipleOutputs.cxx

@@ -1,5 +1,4 @@
 #include "itkImage.h"
-#include "itkImageFileReader.h"
 #include "itkImageFileWriter.h"
 
 #include "ImageFilterMultipleOutputs.h"
@@ -15,21 +14,9 @@ main(int, char *[])
   FilterType::Pointer filter = FilterType::New();
   filter->Update();
 
-  {
-    using WriterType = itk::ImageFileWriter<ImageType>;
-    WriterType::Pointer writer = WriterType::New();
-    writer->SetFileName("TestOutput1.jpg");
-    writer->SetInput(filter->GetOutput1());
-    writer->Update();
-  }
+  itk::WriteImage(filter->GetOutput1(), "TestOutput1.jpg");
 
-  {
-    using WriterType = itk::ImageFileWriter<ImageType>;
-    WriterType::Pointer writer = WriterType::New();
-    writer->SetFileName("TestOutput2.jpg");
-    writer->SetInput(filter->GetOutput2());
-    writer->Update();
-  }
+  itk::WriteImage(filter->GetOutput2(), "TestOutput2.jpg");
 
   return EXIT_SUCCESS;
 }

src/Developer/ImageFilterMultipleOutputsDifferentType.cxx

@@ -17,21 +17,9 @@ main(int, char *[])
   FilterType::Pointer filter = FilterType::New();
   filter->Update();
 
-  {
-    using WriterType = itk::ImageFileWriter<OutputImageType1>;
-    WriterType::Pointer writer = WriterType::New();
-    writer->SetFileName("TestOutput1.jpg");
-    writer->SetInput(filter->GetOutput1());
-    writer->Update();
-  }
+  itk::WriteImage(filter->GetOutput1(), "TestOutput1.jpg");
 
-  {
-    using WriterType = itk::ImageFileWriter<OutputImageType2>;
-    WriterType::Pointer writer = WriterType::New();
-    writer->SetFileName("TestOutput2.jpg");
-    writer->SetInput(filter->GetOutput2());
-    writer->Update();
-  }
+  itk::WriteImage(filter->GetOutput2(), "TestOutput2.jpg");
 
   return EXIT_SUCCESS;
 }

src/Developer/InplaceImageFilter.cxx

@@ -1,6 +1,4 @@
 #include "itkImage.h"
-#include "itkImageFileReader.h"
-#include "itkImageFileWriter.h"
 
 #include "MyInPlaceImageFilter.h"
 

src/Developer/MiniPipeline.cxx

@@ -1,5 +1,4 @@
 #include "itkImage.h"
-#include "itkImageFileReader.h"
 #include "itkImageFileWriter.h"
 
 #include "ImageFilterY.h"
@@ -28,11 +27,7 @@ main(int, char *[])
   std::cout << "Input:" << std::endl;
   std::cout << filter->GetOutput()->GetLargestPossibleRegion() << std::endl;
 
-  using WriterType = itk::ImageFileWriter<ImageType>;
-  WriterType::Pointer writer = WriterType::New();
-  writer->SetFileName("Output.png");
-  writer->SetInput(filter->GetOutput());
-  writer->Update();
+  itk::WriteImage(filter->GetOutput(), "Output.png");
 
   return EXIT_SUCCESS;
 }

src/Developer/MultiThreadedImageFilter.cxx

@@ -1,6 +1,4 @@
 #include "itkImage.h"
-#include "itkImageFileReader.h"
-#include "itkImageFileWriter.h"
 
 #include "MultiThreadedImageFilter.h"
 

src/Developer/OilPaintingImageFilter.cxx

@@ -30,20 +30,17 @@ main(int argc, char * argv[])
   using ImageType = itk::Image<unsigned char, 2>;
   using FilterType = itk::OilPaintingImageFilter<ImageType>;
 
-  using ReaderType = itk::ImageFileReader<ImageType>;
-  ReaderType::Pointer reader = ReaderType::New();
-  reader->SetFileName(argv[1]);
-  reader->Update();
+  const auto input = itk::ReadImage<ImageType>(argv[1]);
 
   FilterType::Pointer filter = FilterType::New();
-  filter->SetInput(reader->GetOutput());
+  filter->SetInput(input);
   filter->SetNumberOfBins(numberOfBins);
   filter->SetRadius(radius);
   filter->Update();
 
 #ifdef ENABLE_QUICKVIEW
   QuickView viewer;
-  viewer.AddImage(reader->GetOutput(), true, itksys::SystemTools::GetFilenameName(reader->GetFileName()));
+  viewer.AddImage(input, true, itksys::SystemTools::GetFilenameName(reader->GetFileName()));
 
   std::stringstream desc;
   desc << "OilPaintingImageFilter, bins = " << numberOfBins << " radius = " << radius;

src/Developer/SetGetMacro.cxx

@@ -1,6 +1,4 @@
 #include "itkImage.h"
-#include "itkImageFileReader.h"
-#include "itkImageFileWriter.h"
 
 #include "ImageFilterX.h"
 

src/IO/GDCM/ReadDICOMSeriesAndWrite3DImage/Code.cxx

@@ -102,9 +102,7 @@ main(int argc, char * argv[])
       reader->SetFileNames(fileNames);
       reader->ForceOrthogonalDirectionOff(); // properly read CTs with gantry tilt
 
-      using WriterType = itk::ImageFileWriter<ImageType>;
-      WriterType::Pointer writer = WriterType::New();
-      std::string         outFileName;
+      std::string outFileName;
       if (argc > 2)
       {
         outFileName = argv[2];
@@ -113,13 +111,10 @@ main(int argc, char * argv[])
       {
         outFileName = dirName + std::string("/") + seriesIdentifier + ".nrrd";
       }
-      writer->SetFileName(outFileName);
-      writer->UseCompressionOn();
-      writer->SetInput(reader->GetOutput());
       std::cout << "Writing: " << outFileName << std::endl;
       try
       {
-        writer->Update();
+        itk::WriteImage(reader->GetOutput(), outFileName, true); // compression
       }
       catch (itk::ExceptionObject & ex)
       {

src/IO/ImageBase/ConvertFileFormats/Code.cxx

@@ -36,18 +36,11 @@ main(int argc, char * argv[])
   using PixelType = unsigned char;
   using ImageType = itk::Image<PixelType, Dimension>;
 
-  using ReaderType = itk::ImageFileReader<ImageType>;
-  ReaderType::Pointer reader = ReaderType::New();
-  reader->SetFileName(argv[1]);
-
-  using WriterType = itk::ImageFileWriter<ImageType>;
-  WriterType::Pointer writer = WriterType::New();
-  writer->SetFileName(argv[2]);
-  writer->SetInput(reader->GetOutput());
+  const auto input = itk::ReadImage<ImageType>(argv[1]);
 
   try
   {
-    writer->Update();
+    itk::WriteImage(input, argv[2]);
   }
   catch (itk::ExceptionObject & error)
   {

src/IO/ImageBase/Create3DFromSeriesOf2D/Code.cxx

@@ -36,15 +36,13 @@ main(int argc, char * argv[])
 
   using ImageType = itk::Image<PixelType, Dimension>;
   using ReaderType = itk::ImageSeriesReader<ImageType>;
-  using WriterType = itk::ImageFileWriter<ImageType>;
 
   ReaderType::Pointer reader = ReaderType::New();
-  WriterType::Pointer writer = WriterType::New();
 
   const unsigned int first = std::stoi(argv[2]);
   const unsigned int last = std::stoi(argv[3]);
 
-  const char * outputFilename = argv[4];
+  const char * outputFileName = argv[4];
 
   using NameGeneratorType = itk::NumericSeriesFileNames;
 
@@ -67,11 +65,9 @@ main(int argc, char * argv[])
 
   reader->SetFileNames(names);
 
-  writer->SetFileName(outputFilename);
-  writer->SetInput(reader->GetOutput());
   try
   {
-    writer->Update();
+    itk::WriteImage(reader->GetOutput(), outputFileName);
   }
   catch (itk::ExceptionObject & err)
   {

src/IO/ImageBase/GenerateSlicesFromVolume/Code.cxx

@@ -44,21 +44,19 @@ main(int argc, char * argv[])
   using PixelType = unsigned char;
   using InputImageType = itk::Image<PixelType, Dimension>;
 
-  using ReaderType = itk::ImageFileReader<InputImageType>;
-  ReaderType::Pointer reader = ReaderType::New();
-  reader->SetFileName(inputFileName);
+  const auto input = itk::ReadImage<InputImageType>(inputFileName);
 
   using OutputPixelType = unsigned char;
   using RescaleImageType = itk::Image<OutputPixelType, Dimension>;
 
   using RescaleFilterType = itk::RescaleIntensityImageFilter<InputImageType, RescaleImageType>;
   RescaleFilterType::Pointer rescale = RescaleFilterType::New();
-  rescale->SetInput(reader->GetOutput());
+  rescale->SetInput(input);
   rescale->SetOutputMinimum(0);
   rescale->SetOutputMaximum(255);
   rescale->UpdateLargestPossibleRegion();
 
-  InputImageType::RegionType region = reader->GetOutput()->GetLargestPossibleRegion();
+  InputImageType::RegionType region = input->GetLargestPossibleRegion();
   InputImageType::SizeType   size = region.GetSize();
 
   itk::NumericSeriesFileNames::Pointer fnames = itk::NumericSeriesFileNames::New();