Miscellaneous examples fixes

examples/CMakeLists.txt

@@ -12,7 +12,7 @@ if(NOT ITK_SOURCE_DIR)
 else()
   # when being built as part of ITK, ITKImageIO and ITKTransformIO
   # lists of modules are not yet ready, causing a configure error
-  find_package(ITK REQUIRED COMPONENTS Montage ITKIOTransformInsightLegacy ITKIOHDF5 ITKTestKernel ${ExampleSpecificComponents})
+  find_package(ITK REQUIRED COMPONENTS Montage ITKIOTransformInsightLegacy ITKIONRRD ITKIOPNG ITKTestKernel ${ExampleSpecificComponents})
 endif()
 include(${ITK_USE_FILE})
 

examples/CompleteMontage.cxx

@@ -91,7 +91,7 @@ denoiseImage(typename itk::Image<PixelType, Dimension>::Pointer image, double si
 {
   using ImageType = itk::Image<PixelType, Dimension>;
   using DensoingType = itk::BilateralImageFilter<ImageType, ImageType>;
-  DensoingType::Pointer denoiser = DensoingType::New();
+  typename DensoingType::Pointer denoiser = DensoingType::New();
   denoiser->SetInput(image);
   denoiser->SetRangeSigma(itk::NumericTraits<PixelType>::max() / 20.0);
   denoiser->SetDomainSigma(sigma);
@@ -110,9 +110,9 @@ denoiseImage(typename itk::Image<PixelType, Dimension>::Pointer image, double si
   using DensoingType = itk::BilateralImageFilter<ScalarImageType, ScalarImageType>;
   using ComposeType = itk::ComposeImageFilter<ScalarImageType, ColorImageType>;
 
-  ImageAdaptorType::Pointer cAdaptor = ImageAdaptorType::New();
+  typename ImageAdaptorType::Pointer cAdaptor = ImageAdaptorType::New();
   cAdaptor->SetInput(image);
-  DensoingType::Pointer denoiser = DensoingType::New();
+  typename DensoingType::Pointer denoiser = DensoingType::New();
   denoiser->SetInput(cAdaptor->GetOutput());
   denoiser->SetRangeSigma(itk::NumericTraits<ComponentType>::max() / 20.0);
   denoiser->SetDomainSigma(sigma);
@@ -127,7 +127,7 @@ denoiseImage(typename itk::Image<PixelType, Dimension>::Pointer image, double si
   }
 
   // compose an RGB(A) image from the filtered component images
-  ComposeType::Pointer compose = ComposeType::New();
+  typename ComposeType::Pointer compose = ComposeType::New();
   for (unsigned c = 0; c < PixelType::Length; c++)
   {
     compose->SetInput(c, cImages[c]);
@@ -152,7 +152,7 @@ class CommandIterationUpdate : public itk::Command
   void
   Execute(itk::Object * caller, const itk::EventObject & event) override
   {
-    Execute((const itk::Object *)caller, event);
+    Execute(static_cast<const itk::Object *>(caller), event);
   }
 
   void
@@ -165,7 +165,7 @@ class CommandIterationUpdate : public itk::Command
       return;
     }
 
-    std::cout << '.' << std::flush; // minimal progress feedback
+    std::cout << ' ' << filter->GetElapsedIterations() << std::flush;
   }
 };
 
@@ -190,9 +190,9 @@ GetLogBiasField(typename itk::Image<PixelType, Dimension>::Pointer scalarImage,
   using CorrecterType = itk::N4BiasFieldCorrectionImageFilter<RealImageType>;
   typename CorrecterType::Pointer correcter = CorrecterType::New();
   correcter->SetSplineOrder(splineOrder);
-  correcter->SetWienerFilterNoise(0.01);
-  correcter->SetBiasFieldFullWidthAtHalfMaximum(0.15);
-  correcter->SetConvergenceThreshold(0.00001);
+  correcter->SetWienerFilterNoise(0.01f);
+  correcter->SetBiasFieldFullWidthAtHalfMaximum(0.15f);
+  correcter->SetConvergenceThreshold(0.00001f);
 
   typename CorrecterType::VariableSizeArrayType maximumNumberOfIterations(
     static_cast<typename CorrecterType::VariableSizeArrayType::SizeValueType>(iterations.size()));
@@ -203,8 +203,7 @@ GetLogBiasField(typename itk::Image<PixelType, Dimension>::Pointer scalarImage,
   correcter->SetMaximumNumberOfIterations(maximumNumberOfIterations);
 
   typename CorrecterType::ArrayType numberOfFittingLevels;
-  numberOfFittingLevels.Fill(
-    static_cast<typename CorrecterType::VariableSizeArrayType::SizeValueType>(iterations.size()));
+  numberOfFittingLevels.Fill(iterations.size());
   correcter->SetNumberOfFittingLevels(numberOfFittingLevels);
 
   typename CorrecterType::ArrayType numberOfControlPoints;
@@ -323,8 +322,6 @@ CorrectBias(typename itk::Image<PixelType, Dimension>::Pointer image,
   mt->ParallelizeImageRegion<Dimension>(
     region,
     [mulField, diff](const typename ImageType::RegionType & subRegion) {
-      double threadSum = 0.0;
-
       itk::ImageRegionIterator<RealImageType> ItM(mulField, subRegion);
       for (ItM.GoToBegin(); !ItM.IsAtEnd(); ++ItM)
       {
@@ -471,8 +468,8 @@ completeMontage(const itk::TileConfiguration<Dimension> & stageTiles,
   std::cout << "Writing transform for each input tile...";
   for (size_t t = 0; t < stageTiles.LinearSize(); t++)
   {
-    typename MontageType::TileIndexType ind = stageTiles.LinearIndexToNDIndex(t);
-    const TransformType *               regTr = montage->GetOutputTransform(ind);
+    ind = stageTiles.LinearIndexToNDIndex(t);
+    const TransformType * regTr = montage->GetOutputTransform(ind);
     WriteTransform(regTr, outputPath + stageTiles.Tiles[t].FileName + ".tfm");
 
     // set inputs to resampler class

include/itkTileConfiguration.h

@@ -176,7 +176,6 @@ struct ITK_TEMPLATE_EXPORT TileConfiguration
       // check consistency with previously established size
       for (unsigned d = 0; d < maxAxis; d++)
       {
-        SizeValueType axisSize = (d == maxAxis - 1) ? AxisSizes[d] : AxisSizes[d] - 1;
         itkAssertOrThrowMacro(cInd[d] == AxisSizes[d] - 1,
                               "Axis sizes: " << AxisSizes << " current index: " << cInd
                                              << ". We have reached the end along axis " << maxAxis
@@ -220,8 +219,8 @@ struct ITK_TEMPLATE_EXPORT TileConfiguration
 
     tileFile << "# Tile coordinates are in index space, not physical space\n";
     tileFile << "dim = " << Dimension << "\n\n";
-    char                             buffer[20];
-    double_conversion::StringBuilder conversionResult(buffer, 20);
+    char                             buffer[25];
+    double_conversion::StringBuilder conversionResult(buffer, 25);
 
     size_t totalTiles = this->LinearSize();
     for (SizeValueType linearIndex = 0; linearIndex < totalTiles; linearIndex++)

test/CMakeLists.txt

@@ -315,7 +315,7 @@ endfunction()
 
 GroundTruthTest2D(10-129 DATA{Input/10-129-C_2/10-129-C_2_p00.jpg} 6 4 15 25)
 GroundTruthTest2D(run2 DATA{Input/05MAR09_run2_64-Raw/05MAR09_run2_64-Raw_p0.bmp} 4 5 15 10)
-GroundTruthTest2D(MediumCarbonSteel DATA{Input/MediumCarbonSteel/1701701_000000_Fused.bmp} 11 3 20 20)
+GroundTruthTest2D(MediumCarbonSteel DATA{Input/MediumCarbonSteel/1701701_000000_Fused.tif} 11 3 20 20)
 
 itk_add_test(NAME itkMontage-10-129-C_2
   COMMAND MontageTestDriver

test/itkMontageTest.cxx

@@ -149,17 +149,33 @@ itkMontageTest(int argc, char * argv[])
     inputPath += '/';
   }
 
-  unsigned dim;
-  itk::TileConfiguration<2>::TryParse(inputPath + "TileConfiguration.txt", dim);
+  try
+  {
+    unsigned dim;
+    itk::TileConfiguration<2>::TryParse(inputPath + "TileConfiguration.txt", dim);
 
-  switch (dim)
+    switch (dim)
+    {
+      case 2:
+        return itkMontageTestHelper<2>(argc, argv, inputPath);
+      case 3:
+        return itkMontageTestHelper<3>(argc, argv, inputPath);
+      default:
+        std::cerr << "Only dimensions 2 and 3 are supported. You are attempting to montage dimension " << dim;
+        return EXIT_FAILURE;
+    }
+  }
+  catch (itk::ExceptionObject & exc)
+  {
+    std::cerr << exc;
+  }
+  catch (std::runtime_error & exc)
+  {
+    std::cerr << exc.what();
+  }
+  catch (...)
   {
-    case 2:
-      return itkMontageTestHelper<2>(argc, argv, inputPath);
-    case 3:
-      return itkMontageTestHelper<3>(argc, argv, inputPath);
-    default:
-      std::cerr << "Only dimensions 2 and 3 are supported. You are attempting to montage dimension " << dim;
-      return EXIT_FAILURE;
+    std::cerr << "Unknown error has occurred" << std::endl;
   }
+  return EXIT_FAILURE;
 }

test/itkMontageTruthCreator.cxx

@@ -196,28 +196,43 @@ itkMontageTruthCreator(int argc, char * argv[])
     return EXIT_FAILURE;
   }
 
-  itk::ImageIOBase::Pointer imageIO =
-    itk::ImageIOFactory::CreateImageIO(argv[1], itk::ImageIOFactory::FileModeType::ReadMode);
-  imageIO->SetFileName(argv[1]);
-  imageIO->ReadImageInformation();
-  unsigned                                dim = imageIO->GetNumberOfDimensions();
-  const itk::ImageIOBase::IOComponentType cType = imageIO->GetComponentType();
-
-  if (cType == itk::ImageIOBase::IOComponentType::UCHAR)
+  try
   {
-    return CreateGroundTruth<unsigned char>(argc, argv, dim, imageIO->GetPixelType());
+    itk::ImageIOBase::Pointer imageIO =
+      itk::ImageIOFactory::CreateImageIO(argv[1], itk::ImageIOFactory::FileModeType::ReadMode);
+    imageIO->SetFileName(argv[1]);
+    imageIO->ReadImageInformation();
+    unsigned                                dim = imageIO->GetNumberOfDimensions();
+    const itk::ImageIOBase::IOComponentType cType = imageIO->GetComponentType();
+
+    if (cType == itk::ImageIOBase::IOComponentType::UCHAR)
+    {
+      return CreateGroundTruth<unsigned char>(argc, argv, dim, imageIO->GetPixelType());
+    }
+    else if (cType == itk::ImageIOBase::IOComponentType::USHORT)
+    {
+      return CreateGroundTruth<unsigned short>(argc, argv, dim, imageIO->GetPixelType());
+    }
+    else if (cType == itk::ImageIOBase::IOComponentType::SHORT)
+    {
+      return CreateGroundTruth<short>(argc, argv, dim, imageIO->GetPixelType());
+    }
+    else
+    {
+      std::cerr << "Unsupported component type: " << itk::ImageIOBase::GetComponentTypeAsString(cType) << std::endl;
+    }
   }
-  else if (cType == itk::ImageIOBase::IOComponentType::USHORT)
+  catch (itk::ExceptionObject & exc)
   {
-    return CreateGroundTruth<unsigned short>(argc, argv, dim, imageIO->GetPixelType());
+    std::cerr << exc;
   }
-  else if (cType == itk::ImageIOBase::IOComponentType::SHORT)
+  catch (std::runtime_error & exc)
   {
-    return CreateGroundTruth<short>(argc, argv, dim, imageIO->GetPixelType());
+    std::cerr << exc.what();
   }
-  else
+  catch (...)
   {
-    std::cerr << "Unsupported component type: " << itk::ImageIOBase::GetComponentTypeAsString(cType) << std::endl;
-    return EXIT_FAILURE;
+    std::cerr << "Unknown error has occurred" << std::endl;
   }
+  return EXIT_FAILURE;
 }