ENH: Increase coverage

Modules/Filtering/BiasCorrection/test/itkN4BiasFieldCorrectionImageFilterTest.cxx

@@ -128,7 +128,7 @@ N4(int argc, char * argv[])
   ImagePointer inputImage = reader->GetOutput();
   inputImage->DisconnectPipeline();
 
-  // handle the mask image
+  // Handle the mask image
   using MaskImageType = itk::Image<unsigned char, ImageDimension>;
   typename MaskImageType::Pointer maskImage = nullptr;
 
@@ -164,15 +164,44 @@ N4(int argc, char * argv[])
     maskImage->DisconnectPipeline();
   }
 
-  // instantiate N4 and assign variables not exposed to the user in this test.
+  // Instantiate N4 and assign variables not exposed to the user in this test.
   using CorrecterType = itk::N4BiasFieldCorrectionImageFilter<ImageType, MaskImageType, ImageType>;
   typename CorrecterType::Pointer correcter = CorrecterType::New();
-  correcter->SetSplineOrder(3);
+
+  ITK_EXERCISE_BASIC_OBJECT_METHODS(correcter, N4BiasFieldCorrectionImageFilter, ImageToImageFilter);
+
+
+  unsigned int splineOrder = 3;
+  correcter->SetSplineOrder(splineOrder);
+  ITK_TEST_SET_GET_VALUE(splineOrder, correcter->GetSplineOrder());
+
   correcter->SetWienerFilterNoise(0.01);
-  correcter->SetBiasFieldFullWidthAtHalfMaximum(0.15);
-  correcter->SetConvergenceThreshold(0.0000001);
 
-  // handle the number of iterations
+  typename CorrecterType::RealType biasFieldFullWidthAtHalfMaximum = 0.15;
+  correcter->SetBiasFieldFullWidthAtHalfMaximum(biasFieldFullWidthAtHalfMaximum);
+  ITK_TEST_SET_GET_VALUE(biasFieldFullWidthAtHalfMaximum, correcter->GetBiasFieldFullWidthAtHalfMaximum());
+
+  typename CorrecterType::RealType convergenceThreshold = 0.0000001;
+  correcter->SetConvergenceThreshold(convergenceThreshold);
+  ITK_TEST_SET_GET_VALUE(convergenceThreshold, correcter->GetConvergenceThreshold());
+
+  unsigned int numberOfHistogramBins = 200;
+  correcter->SetNumberOfHistogramBins(numberOfHistogramBins);
+  ITK_TEST_SET_GET_VALUE(numberOfHistogramBins, correcter->GetNumberOfHistogramBins());
+
+  typename CorrecterType::RealType wienerFilterNoise = 0.01;
+  correcter->SetWienerFilterNoise(wienerFilterNoise);
+  ITK_TEST_SET_GET_VALUE(wienerFilterNoise, correcter->GetWienerFilterNoise());
+
+  typename CorrecterType::MaskPixelType maskLabel =
+    itk::NumericTraits<typename CorrecterType::MaskPixelType>::OneValue();
+  correcter->SetMaskLabel(maskLabel);
+  ITK_TEST_SET_GET_VALUE(maskLabel, correcter->GetMaskLabel());
+
+  bool useMaskLabel = false;
+  ITK_TEST_SET_GET_BOOLEAN(correcter, UseMaskLabel, useMaskLabel);
+
+  // Handle the number of iterations
   std::vector<unsigned int> numIters = ConvertVector<unsigned int>(std::string("100x50x50"));
   if (argc > 5)
   {
@@ -185,17 +214,18 @@ N4(int argc, char * argv[])
     maximumNumberOfIterations[d] = numIters[d];
   }
   correcter->SetMaximumNumberOfIterations(maximumNumberOfIterations);
+  ITK_TEST_SET_GET_VALUE(maximumNumberOfIterations, correcter->GetMaximumNumberOfIterations());
 
   typename CorrecterType::ArrayType numberOfFittingLevels;
   numberOfFittingLevels.Fill(
     static_cast<typename CorrecterType::VariableSizeArrayType::SizeValueType>(numIters.size()));
   correcter->SetNumberOfFittingLevels(numberOfFittingLevels);
+  ITK_TEST_SET_GET_VALUE(numberOfFittingLevels, correcter->GetNumberOfFittingLevels());
 
-  /* B-spline options -- we place this here to take care of the case where
-   * the user wants to specify things in terms of the spline distance.
-   *  1. need to pad the images to get as close to possible to the
-   *     requested domain size.
-   */
+  // B-spline options -- we place this here to take care of the case where
+  // the user wants to specify things in terms of the spline distance.
+  //  1. need to pad the images to get as close to possible to the
+  //     requested domain size.
   typename ImageType::PointType newOrigin = inputImage->GetOrigin();
 
   typename CorrecterType::ArrayType numberOfControlPoints;
@@ -245,8 +275,9 @@ N4(int argc, char * argv[])
   maskImage->DisconnectPipeline();
 
   correcter->SetNumberOfControlPoints(numberOfControlPoints);
+  ITK_TEST_SET_GET_VALUE(numberOfControlPoints, correcter->GetNumberOfControlPoints());
 
-  // handle the shrink factor
+  // Handle the shrink factor
   using ShrinkerType = itk::ShrinkImageFilter<ImageType, ImageType>;
   typename ShrinkerType::Pointer shrinker = ShrinkerType::New();
   shrinker->SetInput(inputImage);
@@ -270,26 +301,16 @@ N4(int argc, char * argv[])
   maskImage = maskshrinker->GetOutput();
   maskImage->DisconnectPipeline();
 
-  // set the input image and mask image
+  // Set the input image and mask image
   correcter->SetInput(inputImage);
   correcter->SetMaskImage(maskImage);
 
   using CommandType = CommandIterationUpdate<CorrecterType>;
   typename CommandType::Pointer observer = CommandType::New();
   correcter->AddObserver(itk::IterationEvent(), observer);
 
-  try
-  {
-    correcter->Update();
-  }
-  catch (const itk::ExceptionObject & excep)
-  {
-    std::cerr << "Exception caught !" << std::endl;
-    std::cerr << excep << std::endl;
-    return EXIT_FAILURE;
-  }
+  ITK_TRY_EXPECT_NO_EXCEPTION(correcter->Update());
 
-  correcter->Print(std::cout, 3);
 
   // Test the reconstruction of the log bias field
   ImagePointer originalInputImage = reader->GetOutput();
@@ -300,7 +321,7 @@ N4(int argc, char * argv[])
     correcter->ReconstructBiasField(correcter->GetLogBiasFieldControlPointLattice());
   WriteImage(biasField.GetPointer(), (std::string(argv[3]) + "-LogBiasField.nrrd").c_str());
 
-  // output the log bias field control point lattice
+  // Output the log bias field control point lattice
   WriteImage(correcter->GetLogBiasFieldControlPointLattice(), argv[3]);
 
   return EXIT_SUCCESS;
@@ -315,7 +336,7 @@ itkN4BiasFieldCorrectionImageFilterTest(int argc, char * argv[])
               << "outputLogControlPointLattice [shrinkFactor,default=1] "
               << "[numberOfIterations,default=100x50x50] "
               << " [maskImageWithLabelEqualTo1] [splineDistance,default=200]" << std::endl;
-    exit(EXIT_FAILURE);
+    return EXIT_FAILURE;
   }
 
   switch (std::stoi(argv[1]))
@@ -328,6 +349,6 @@ itkN4BiasFieldCorrectionImageFilterTest(int argc, char * argv[])
 
     default:
       std::cerr << "Unsupported dimension" << std::endl;
-      exit(EXIT_FAILURE);
+      return EXIT_FAILURE;
   }
 }

Modules/Filtering/BinaryMathematicalMorphology/test/itkBinaryClosingByReconstructionImageFilterTest.cxx

@@ -28,42 +28,61 @@ int
 itkBinaryClosingByReconstructionImageFilterTest(int argc, char * argv[])
 {
 
-  if (argc != 6)
+  if (argc < 6)
   {
-    std::cerr << "usage: " << itkNameOfTestExecutableMacro(argv) << " input output conn fg kernelSize" << std::endl;
-    // std::cerr << "  : " << std::endl;
-    exit(1);
+    std::cerr << "Missing Parameters." << std::endl;
+    std::cerr << "Usage: " << itkNameOfTestExecutableMacro(argv)
+              << " inputFileName outputFileName fullyConnected foregroundValue kernelSize" << std::endl;
+    return EXIT_FAILURE;
   }
 
-  constexpr int dim = 2;
+  constexpr unsigned int Dimension = 2;
 
-  using IType = itk::Image<unsigned char, dim>;
+  using PixelType = unsigned char;
 
-  using ReaderType = itk::ImageFileReader<IType>;
+  using ImageType = itk::Image<PixelType, Dimension>;
+
+  using ReaderType = itk::ImageFileReader<ImageType>;
   ReaderType::Pointer reader = ReaderType::New();
   reader->SetFileName(argv[1]);
-  reader->Update();
 
-  using KernelType = itk::BinaryBallStructuringElement<bool, dim>;
+  ITK_TRY_EXPECT_NO_EXCEPTION(reader->Update());
+
+
+  using KernelType = itk::BinaryBallStructuringElement<bool, Dimension>;
   KernelType           ball;
   KernelType::SizeType ballSize;
   ballSize.Fill(std::stoi(argv[5]));
   ball.SetRadius(ballSize);
   ball.CreateStructuringElement();
 
-  using I2LType = itk::BinaryClosingByReconstructionImageFilter<IType, KernelType>;
-  I2LType::Pointer reconstruction = I2LType::New();
-  reconstruction->SetInput(reader->GetOutput());
-  reconstruction->SetKernel(ball);
-  reconstruction->SetFullyConnected(std::stoi(argv[3]));
-  reconstruction->SetForegroundValue(std::stoi(argv[4]));
-  //   reconstruction->SetBackgroundValue( std::stoi(argv[6]) );
-  itk::SimpleFilterWatcher watcher(reconstruction, "filter");
+  using FilterType = itk::BinaryClosingByReconstructionImageFilter<ImageType, KernelType>;
+  FilterType::Pointer reconstructionFilter = FilterType::New();
+
+  ITK_EXERCISE_BASIC_OBJECT_METHODS(reconstructionFilter, BinaryClosingByReconstructionImageFilter, KernelImageFilter);
+
+
+  itk::SimpleFilterWatcher watcher(reconstructionFilter, "filter");
+
+  auto fullyConnected = static_cast<bool>(std::stoi(argv[3]));
+  ITK_TEST_SET_GET_BOOLEAN(reconstructionFilter, FullyConnected, fullyConnected);
 
-  using WriterType = itk::ImageFileWriter<IType>;
+  typename FilterType::InputImagePixelType foregroundValue = std::stoi(argv[4]);
+  reconstructionFilter->SetForegroundValue(foregroundValue);
+  ITK_TEST_SET_GET_VALUE(foregroundValue, reconstructionFilter->GetForegroundValue());
+
+  reconstructionFilter->SetKernel(ball);
+
+  reconstructionFilter->SetInput(reader->GetOutput());
+
+  using WriterType = itk::ImageFileWriter<ImageType>;
   WriterType::Pointer writer = WriterType::New();
-  writer->SetInput(reconstruction->GetOutput());
+  writer->SetInput(reconstructionFilter->GetOutput());
   writer->SetFileName(argv[2]);
-  writer->Update();
-  return 0;
+
+  ITK_TRY_EXPECT_NO_EXCEPTION(writer->Update());
+
+
+  std::cout << "Test finished." << std::endl;
+  return EXIT_SUCCESS;
 }

Modules/Filtering/DisplacementField/include/itkDisplacementFieldJacobianDeterminantFilter.h

@@ -67,10 +67,10 @@ namespace itk
  * itk::Image<TRealType, N>.
  *
  * \par Filter Parameters
- * The method SetUseImageSpacingOn will cause derivatives in the image to be
+ * The method UseImageSpacingOn will cause derivatives in the image to be
  * scaled (inversely) with the pixel size of the input image, effectively
  * taking derivatives in world coordinates (versus isotropic image
- * space). SetUseImageSpacingOff turns this functionality off.  Default is
+ * space). UseImageSpacingOff turns this functionality off.  Default is
  * UseImageSpacingOn.  The parameter UseImageSpacing can
  * be set directly with the method SetUseImageSpacing(bool).
  *
@@ -170,10 +170,23 @@ class ITK_TEMPLATE_EXPORT DisplacementFieldJacobianDeterminantFilter
   void
   GenerateInputRequestedRegion() override;
 
+  /** Set/Get whether or not the filter will use the spacing of the input
+   * image (1/spacing) in the calculation of the Jacobian determinant. Use On
+   * to compute the Jacobian determinant in the space in which the data was
+   * acquired; use Off to reset the derivative weights, ignore the image
+   * spacing, and to compute the Jacobian determinant in the image space.
+   * Default is On. */
+  void
+  SetUseImageSpacing(bool);
+  itkGetConstMacro(UseImageSpacing, bool);
+  itkBooleanMacro(UseImageSpacing);
+
+#if !defined(ITK_FUTURE_LEGACY_REMOVE)
   /** Set the derivative weights according to the spacing of the input image
       (1/spacing). Use this option if you want to calculate the Jacobian
       determinant in the space in which the data was acquired. Default
-      is ImageSpacingOn. */
+      is ImageSpacingOn.
+      \deprecated Use DisplacementFieldJacobianDeterminantFilter::UseImageSpacingOn instead. */
   void
   SetUseImageSpacingOn()
   {
@@ -182,19 +195,14 @@ class ITK_TEMPLATE_EXPORT DisplacementFieldJacobianDeterminantFilter
 
   /** Reset the derivative weights to ignore image spacing.  Use this option if
       you want to calculate the Jacobian determinant in the image space.
-      Default is ImageSpacingOn. */
+      Default is ImageSpacingOn.
+      \deprecated Use DisplacementFieldJacobianDeterminantFilter::UseImageSpacingOff instead. */
   void
   SetUseImageSpacingOff()
   {
     this->SetUseImageSpacing(false);
   }
-
-  /** Set/Get whether or not the filter will use the spacing of the input
-      image in its calculations */
-  void
-  SetUseImageSpacing(bool);
-
-  itkGetConstMacro(UseImageSpacing, bool);
+#endif
 
   using WeightsType = FixedArray<TRealType, ImageDimension>;
 

Modules/Filtering/DisplacementField/include/itkDisplacementFieldJacobianDeterminantFilter.hxx

@@ -27,7 +27,7 @@
 #include "itkCastImageFilter.h"
 
 #include "itkMath.h"
-#include "itkMath.h"
+#include "itkPrintHelper.h"
 
 namespace itk
 {
@@ -234,25 +234,19 @@ void
 DisplacementFieldJacobianDeterminantFilter<TInputImage, TRealType, TOutputImage>::PrintSelf(std::ostream & os,
                                                                                             Indent         indent) const
 {
-  unsigned int i;
+  using namespace print_helper;
 
   Superclass::PrintSelf(os, indent);
-  os << indent << "m_UseImageSpacing = " << m_UseImageSpacing << std::endl;
-  os << indent << "m_RequestedNumberOfThreads = " << m_RequestedNumberOfThreads << std::endl;
-  os << indent << "m_DerivativeWeights = ";
-  for (i = 0; i < ImageDimension; i++)
-  {
-    os << m_DerivativeWeights[i] << " ";
-  }
-  os << std::endl;
-  os << indent << "m_HalfDerivativeWeights = ";
-  for (i = 0; i < ImageDimension; i++)
-  {
-    os << m_HalfDerivativeWeights[i] << " ";
-  }
-  os << std::endl;
-  os << indent << "m_NeighborhoodRadius = " << m_NeighborhoodRadius << std::endl;
-  os << indent << "m_RealValuedInputImage = " << m_RealValuedInputImage.GetPointer() << std::endl;
+
+  os << indent << "DerivativeWeights: " << m_DerivativeWeights << std::endl;
+  os << indent << "HalfDerivativeWeights: " << m_HalfDerivativeWeights << std::endl;
+  os << indent << "UseImageSpacing: " << m_UseImageSpacing << std::endl;
+  os << indent << "RequestedNumberOfThreads: "
+     << static_cast<typename NumericTraits<ThreadIdType>::PrintType>(m_RequestedNumberOfThreads) << std::endl;
+  os << indent << "RealValuedInputImage: " << m_RealValuedInputImage.GetPointer() << std::endl;
+  os << indent
+     << "NeighborhoodRadius: " << static_cast<typename NumericTraits<RadiusType>::PrintType>(m_NeighborhoodRadius)
+     << std::endl;
 }
 } // end namespace itk
 

Modules/Filtering/DisplacementField/test/CMakeLists.txt

@@ -80,7 +80,7 @@ itk_add_test(NAME itkTransformToDisplacementFieldFilterTest03
         --compare ${ITK_TEST_OUTPUT_DIR}/transformedImage.nii
                   ${ITK_TEST_OUTPUT_DIR}/warpedImage.nii
         --compareNumberOfPixelsTolerance 20
-        itkTransformToDisplacementFieldFilterTest1 ${ITK_TEST_OUTPUT_DIR}/transformedImage.nii ${ITK_TEST_OUTPUT_DIR}/warpedImage.nii)
+        itkTransformToDisplacementFieldFilterTest1 ${ITK_TEST_OUTPUT_DIR}/transformedImage.nii ${ITK_TEST_OUTPUT_DIR}/warpedImage.nii 1)
 itk_add_test(NAME itkDisplacementFieldTransformCloneTest
   COMMAND ITKDisplacementFieldTestDriver itkDisplacementFieldTransformCloneTest)
 itk_add_test(NAME itkExponentialDisplacementFieldImageFilterTest