ENH: Update Doxygen to 1.8.15

CODE_OF_CONDUCT.md

@@ -210,7 +210,7 @@ participants. We will not accept harassment or other exclusionary behavior.
 
 Be aware of your impact and how intense interactions may be affecting people.
 Be direct, constructive and positive. We can all make mistakes; when we do, we
-take responsibility for your impact and your mistakes – if someone says they
+take responsibility for your impact and your mistakes - if someone says they
 have been harmed through your words or actions, listen carefully, apologize
 sincerely, and correct the behavior going forward. If someone has been harmed
 or offended, we listen carefully and respectfully, and work to right the wrong.

Modules/Core/Common/include/itkBackwardDifferenceOperator.h

@@ -24,17 +24,17 @@ namespace itk
 {
 /**
  * \class BackwardDifferenceOperator
+ *
  * \brief Operator whose inner product with a neighborhood returns
  * a "half" derivative at the center of the neighborhood.
  *
  * BackwardDifferenceOperator uses backward differences
- * i.e. F(x) - F(x-1) to calculate a "half" derivative useful, among
+ * i.e. \f$ F(x) - F(x-1) \f$ to calculate a "half" derivative useful, among
  * other things, in solving differential equations. It is a directional
  * NeighborhoodOperator that should be applied to a Neighborhood using the
  * inner product.
  *
  * \ingroup Operators
- *
  * \ingroup ITKCommon
  *
  * \wiki

Modules/Core/Common/include/itkBoundingBox.h

@@ -36,7 +36,9 @@
 
 namespace itk
 {
+
 /** \class BoundingBox
+ *
  * \brief Represent and compute information about bounding boxes.
  *
  * BoundingBox is a supporting class that represents, computes, and
@@ -51,14 +53,9 @@ namespace itk
  *
  * Template parameters for BoundingBox:
  *
- * TPointIdentifier =
- *     The type used to access a particular point (i.e., a point's id)
- *
- * TCoordRep =
- *     Numerical type with which to represent each coordinate value.
- *
- * VPointDimension =
- *    Geometric dimension of space.
+ * \tparam TPointIdentifier The type used to access a particular point (i.e., a point's id)
+ * \tparam TCoordRep Numerical type with which to represent each coordinate value.
+ * \tparam VPointDimension Geometric dimension of space.
  *
  * \ingroup DataRepresentation
  * \ingroup ImageObjects
@@ -68,7 +65,6 @@ namespace itk
  * \wikiexample{Utilities/BoundingBox,Bounding box}
  * \endwiki
  */
-
 template<
   typename TPointIdentifier = IdentifierType,
   unsigned int VPointDimension = 3,

Modules/Core/ImageFunction/include/itkBSplineInterpolateImageFunction.h

@@ -39,23 +39,27 @@
 
 namespace itk
 {
-/** \class BSplineInterpolateImageFunction
+/**
+ * \class BSplineInterpolateImageFunction
+ *
  * \brief Evaluates the B-Spline interpolation of an image.  Spline order may be from 0 to 5.
  *
  * This class defines N-Dimension B-Spline transformation.
  * It is based on:
- *    [1] M. Unser,
- *       "Splines: A Perfect Fit for Signal and Image Processing,"
- *        IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38,
- *        November 1999.
- *    [2] M. Unser, A. Aldroubi and M. Eden,
- *        "B-Spline Signal Processing: Part I--Theory,"
- *        IEEE Transactions on Signal Processing, vol. 41, no. 2, pp. 821-832,
- *        February 1993.
- *    [3] M. Unser, A. Aldroubi and M. Eden,
- *        "B-Spline Signal Processing: Part II--Efficient Design and Applications,"
- *        IEEE Transactions on Signal Processing, vol. 41, no. 2, pp. 834-848,
- *        February 1993.
+\verbatim
+[1] M. Unser,
+    "Splines: A Perfect Fit for Signal and Image Processing,"
+    IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38,
+    November 1999.
+[2] M. Unser, A. Aldroubi and M. Eden,
+    "B-Spline Signal Processing: Part I--Theory,"
+    IEEE Transactions on Signal Processing, vol. 41, no. 2, pp. 821-832,
+    February 1993.
+[3] M. Unser, A. Aldroubi and M. Eden,
+    "B-Spline Signal Processing: Part II--Efficient Design and Applications,"
+     IEEE Transactions on Signal Processing, vol. 41, no. 2, pp. 834-848,
+     February 1993.
+\endverbatim
  * And code obtained from bigwww.epfl.ch by Philippe Thevenaz
  *
  * The B spline coefficients are calculated through the

Modules/Core/SpatialObjects/include/itkBlobSpatialObject.h

@@ -24,8 +24,10 @@
 
 namespace itk
 {
+
 /**
  * \class BlobSpatialObject
+ *
  * \brief Spatial object representing a potentially amorphous object.
  *
  * The BlobSpatialObject is a discretized representation of a "blob",
@@ -35,13 +37,13 @@ namespace itk
  * represent a binary image.
  *
  * \sa SpatialObjectPoint
+ *
  * \ingroup ITKSpatialObjects
  *
  * \wiki
  * \wikiexample{SpatialObjects/BlobSpatialObject,Blob}
  * \endwiki
  */
-
 template< unsigned int TDimension = 3 >
 class ITK_TEMPLATE_EXPORT BlobSpatialObject:
   public PointBasedSpatialObject<  TDimension,

Modules/Core/Transform/include/itkAzimuthElevationToCartesianTransform.h

@@ -24,6 +24,7 @@
 namespace itk
 {
 /** \class AzimuthElevationToCartesianTransform
+ *
  * \brief Transforms from an azimuth, elevation, radius coordinate system to
  * a Cartesian coordinate system, or vice versa.
  *
@@ -37,15 +38,18 @@ namespace itk
  *
  * The equations form performing the conversion from azimuth-elevation
  * coordinates to cartesian coordinates are as follows:
- * z = std::sqrt((r^2*(cos(azimuth))^2)/(1 + (cos(azimuth))^2 *
- *     (tan(elevation))^2);
- * x = z * std::tan(azimuth)
- * y = z * std::tan(elevation)
+\code
+z = std::sqrt((r^2*(cos(azimuth))^2)/(1 + (cos(azimuth))^2 * (tan(elevation))^2);
+x = z * std::tan(azimuth)
+y = z * std::tan(elevation)
+\endcode
  *
  * The reversed transforms are:
- * azimuth = arctan(x/y)
- * elevation = arctan(y/z)
- * r = std::sqrt(x^2 + y^2 + z^2)
+\code
+azimuth = arctan(x/y)
+elevation = arctan(y/z)
+r = std::sqrt(x^2 + y^2 + z^2)
+\endcode
  *
  * In this class, we can also set what a "forward" transform means.  If we call
  * SetForwardAzimuthElevationToCartesian(), a forward transform will return
@@ -67,12 +71,12 @@ namespace itk
  * over the scalar type?  Perhaps it should always be double, unless
  * there's a compatibility problem with the Point class.
  *
- * \todo  Derive this class from a yet undefined TransformBase class.
- *        Currently, this class derives from AffineTransform, although
- *        it is not an affine transform.
+ * \todo Derive this class from TransformBase class.
+ * Currently, this class derives from AffineTransform, although
+ * it is not an affine transform.
  *
- * \todo  Add a figure in the documentation that informs the formulas used in this class
- *        that are used to transform Cartesian to azimuth-elevation-radius
+ * \todo Add a figure in the documentation that informs the formulas used in this class
+ * that are used to transform Cartesian to azimuth-elevation-radius
  *
  * \ingroup ITKTransform
  *

Modules/Core/Transform/include/itkBSplineDeformableTransform.h

@@ -59,41 +59,41 @@ namespace itk
  * is managed by the caller.
  *
  * The following illustrates the typical usage of this class:
- * \verbatim
- * using TransformType = BSplineDeformableTransform<double,2,3>;
- * TransformType::Pointer transform = TransformType::New();
- *
- * transform->SetGridRegion( region );
- * transform->SetGridSpacing( spacing );
- * transform->SetGridOrigin( origin );
- *
- * // NB: the region must be set first before setting the parameters
- *
- * TransformType::ParametersType parameters(
- *                                       transform->GetNumberOfParameters() );
- *
- * // Fill the parameters with values
- *
- * transform->SetParameters( parameters )
- *
- * outputPoint = transform->TransformPoint( inputPoint );
- *
- * \endverbatim
+\code
+using TransformType = BSplineDeformableTransform<double,2,3>;
+TransformType::Pointer transform = TransformType::New();
+
+transform->SetGridRegion( region );
+transform->SetGridSpacing( spacing );
+transform->SetGridOrigin( origin );
+
+// NB: the region must be set first before setting the parameters
+
+TransformType::ParametersType parameters( transform->GetNumberOfParameters() );
+
+// Fill the parameters with values
+
+transform->SetParameters( parameters )
+
+outputPoint = transform->TransformPoint( inputPoint );
+
+\endcode
  *
  * An alternative way to set the B-spline coefficients is via array of
  * images. The grid region, spacing and origin information is taken
  * directly from the first image. It is assumed that the subsequent images
  * are the same buffered region. The following illustrates the API:
- * \verbatim
- *
- * TransformType::ImageConstPointer images[2];
- *
- * // Fill the images up with values
  *
- * transform->SetCoefficientImages( images );
- * outputPoint = transform->TransformPoint( inputPoint );
- *
- * \endverbatim
+\code
+
+TransformType::ImageConstPointer images[2];
+
+// Fill the images up with values
+
+transform->SetCoefficientImages( images );
+outputPoint = transform->TransformPoint( inputPoint );
+
+\endcode
  *
  * Warning: use either the SetParameters() or SetCoefficientImages()
  * API. Mixing the two modes may results in unexpected results.

Modules/Filtering/ImageFilterBase/include/itkBinaryFunctorImageFilter.h

@@ -39,7 +39,8 @@ namespace itk
  * \sa BinaryGeneratorImagFilter
  * \sa UnaryFunctorImageFilter TernaryFunctorImageFilter
  *
- * \ingroup IntensityImageFilters   MultiThreaded
+ * \ingroup IntensityImageFilters
+ * \ingroup MultiThreaded
  * \ingroup ITKImageFilterBase
  *
  * \wiki

Modules/Numerics/Optimizersv4/include/itkLBFGS2Optimizerv4.h

@@ -81,15 +81,15 @@ namespace itk
  *
  * [4] Jorge Nocedal.
  * Updating Quasi-Newton Matrices with Limited Storage.
- * Mathematics of Computation, Vol. 35, No. 151, pp. 773–782, 1980.
+ * Mathematics of Computation, Vol. 35, No. 151, pp. 773-782, 1980.
  *
  * [5] Dong C. Liu and Jorge Nocedal.
  * On the limited memory BFGS method for large scale optimization.
  * Mathematical Programming B, Vol. 45, No. 3, pp. 503-528, 1989.
  *
  * [6] More, J. J. and D. J. Thuente.
  * Line Search Algorithms with Guaranteed Sufficient Decrease.
- * ACM Transactions on Mathematical Software 20, no. 3 (1994): 286–307.
+ * ACM Transactions on Mathematical Software 20, no. 3 (1994): 286-307.
  *
  * [7] John E. Dennis and Robert B. Schnabel.
  * Numerical Methods for Unconstrained Optimization and Nonlinear Equations,

Modules/Numerics/Optimizersv4/include/itkLBFGSOptimizerv4.h

@@ -69,15 +69,15 @@ namespace itk
  *
  * [2] Jorge Nocedal.
  * Updating Quasi-Newton Matrices with Limited Storage.
- * Mathematics of Computation, Vol. 35, No. 151, pp. 773–782, 1980.
+ * Mathematics of Computation, Vol. 35, No. 151, pp. 773-782, 1980.
  *
  * [3] Dong C. Liu and Jorge Nocedal.
  * On the limited memory BFGS method for large scale optimization.
  * Mathematical Programming B, Vol. 45, No. 3, pp. 503-528, 1989.
  *
  * [4] More, J. J. and D. J. Thuente.
  * Line Search Algorithms with Guaranteed Sufficient Decrease.
- * ACM Transactions on Mathematical Software 20, no. 3 (1994): 286–307.
+ * ACM Transactions on Mathematical Software 20, no. 3 (1994): 286-307.
  *
  * \ingroup ITKOptimizersv4
  */