DOC: Fix "unbalanced grouping commands" Doxygen warnings

Fix "unbalanced grouping commands" Doxygen warnings:
- Use a brute force approach to fix the "unbalanced grouping commands"
  Doxygen warnings by explicitly placing the `ALIASES`
 `ITKStartGrouping` and `ITKEndGrouping` around the appropriate code
  blocks. This involved a multi-step, trial and error process where an
  initial attempt was made to address such warnings by inserting the
  Doxygen commands `@{` and `@}` around the identified faulty blocks,
  and then any new warnings appeared as a result of those changes was
  solved in an interative, manual process.
- Remove grouping around single functions.
- Remove grouping from `Examples`: the code in the `Examples` folder
  is meant to serve as files hosting code blocks used by the ITK
  Software Guide and such files do not appear in the ITK Doxygen
  documentaion. Thus, grouping has no meaningful application within
  these files.

The use of the `Utilities/Doxygen/itkgroup.py` script to introduce the
Doxygen grouping markers at the appropriate places has been abandoned as
this implicitly added the commands based on the layout. Grouping is hard
to enforce automatically and it is also hard to get an error-free output
from this script (would nearly require a compiler).

Virtually all of the grouping in ITK happens around `Get`/`Set` method
pairs.

Doxygen grouping documentation:
https://www.doxygen.nl/manual/grouping.html

Author: albert-github

Modules/Bridge/VTK/include/itkVTKImageExport.h

@@ -76,12 +76,13 @@ class ITK_TEMPLATE_EXPORT VTKImageExport : public VTKImageExportBase
   itkConceptMacro(ImageDimensionCheck, (Concept::SameDimensionOrMinusOneOrTwo<3, Self::InputImageDimension>));
 
   /** Set the input image of this image exporter. */
+  /** @ITKStartGrouping */
   using Superclass::SetInput;
   void
   SetInput(const InputImageType *);
   InputImageType *
   GetInput();
-
+  /** @ITKEndGrouping */
 protected:
   VTKImageExport();
   ~VTKImageExport() override = default;

Modules/Bridge/VTK/include/itkVTKImageExportBase.h

@@ -54,6 +54,7 @@ class ITKVTK_EXPORT VTKImageExportBase : public ProcessObject
   GetCallbackUserData();
 
   /** The function pointer type expected for a callback. */
+  /** @ITKStartGrouping */
   using UpdateInformationCallbackType = void (*)(void *);
   using PipelineModifiedCallbackType = int (*)(void *);
   using WholeExtentCallbackType = int * (*)(void *);
@@ -66,11 +67,12 @@ class ITKVTK_EXPORT VTKImageExportBase : public ProcessObject
   using UpdateDataCallbackType = void (*)(void *);
   using DataExtentCallbackType = int * (*)(void *);
   using BufferPointerCallbackType = void * (*)(void *);
-
+  /** @ITKEndGrouping */
   /** Compatibility for VTK older than 4.4.  */
+  /** @ITKStartGrouping */
   using FloatSpacingCallbackType = float * (*)(void *);
   using FloatOriginCallbackType = float * (*)(void *);
-
+  /** @ITKEndGrouping */
   /**
    * \class CallbackTypeProxy
    * \brief Provide compatibility between VTK 4.4 and earlier versions.

Modules/Bridge/VTK/include/itkVTKImageImport.h

@@ -83,6 +83,7 @@ class ITK_TEMPLATE_EXPORT VTKImageImport : public ImageSource<TOutputImage>
 
   /** These are function pointer types for the pipeline connection
    * callbacks. */
+  /** @ITKStartGrouping */
   using UpdateInformationCallbackType = void (*)(void *);
   using PipelineModifiedCallbackType = int (*)(void *);
   using WholeExtentCallbackType = int * (*)(void *);
@@ -95,24 +96,29 @@ class ITK_TEMPLATE_EXPORT VTKImageImport : public ImageSource<TOutputImage>
   using UpdateDataCallbackType = void (*)(void *);
   using DataExtentCallbackType = int * (*)(void *);
   using BufferPointerCallbackType = void * (*)(void *);
-
+  /** @ITKEndGrouping */
   /** Compatibility for VTK older than 4.4.  */
+  /** @ITKStartGrouping */
   using FloatSpacingCallbackType = float * (*)(void *);
   using FloatOriginCallbackType = float * (*)(void *);
-
+  /** @ITKEndGrouping */
   /** What to do when receiving UpdateInformation(). */
+  /** @ITKStartGrouping */
   itkSetMacro(UpdateInformationCallback, UpdateInformationCallbackType);
   itkGetConstMacro(UpdateInformationCallback, UpdateInformationCallbackType);
-
+  /** @ITKEndGrouping */
   /** What to do when receiving PipelineModified(). */
+  /** @ITKStartGrouping */
   itkSetMacro(PipelineModifiedCallback, PipelineModifiedCallbackType);
   itkGetConstMacro(PipelineModifiedCallback, PipelineModifiedCallbackType);
-
+  /** @ITKEndGrouping */
   /** What to do when receiving SetWholeExtent(). */
+  /** @ITKStartGrouping */
   itkSetMacro(WholeExtentCallback, WholeExtentCallbackType);
   itkGetConstMacro(WholeExtentCallback, WholeExtentCallbackType);
-
+  /** @ITKEndGrouping */
   /** What to do when receiving SetSpacing(). */
+  /** @ITKStartGrouping */
   itkSetMacro(SpacingCallback, SpacingCallbackType);
   itkGetConstMacro(SpacingCallback, SpacingCallbackType);
   itkSetMacro(FloatSpacingCallback, FloatSpacingCallbackType);
@@ -122,8 +128,9 @@ class ITK_TEMPLATE_EXPORT VTKImageImport : public ImageSource<TOutputImage>
   {
     this->SetFloatSpacingCallback(f);
   }
-
+  /** @ITKEndGrouping */
   /** What to do when receiving SetOrigin(). */
+  /** @ITKStartGrouping */
   itkSetMacro(OriginCallback, OriginCallbackType);
   itkGetConstMacro(OriginCallback, OriginCallbackType);
   itkSetMacro(FloatOriginCallback, FloatOriginCallbackType);
@@ -133,39 +140,47 @@ class ITK_TEMPLATE_EXPORT VTKImageImport : public ImageSource<TOutputImage>
   {
     this->SetFloatOriginCallback(f);
   }
-
+  /** @ITKEndGrouping */
   /** What to do when receiving SetDirection(). */
+  /** @ITKStartGrouping */
   itkSetMacro(DirectionCallback, DirectionCallbackType);
   itkGetConstMacro(DirectionCallback, DirectionCallbackType);
-
+  /** @ITKEndGrouping */
   /** What to do when receiving UpdateInformation(). */
+  /** @ITKStartGrouping */
   itkSetMacro(ScalarTypeCallback, ScalarTypeCallbackType);
   itkGetConstMacro(ScalarTypeCallback, ScalarTypeCallbackType);
-
+  /** @ITKEndGrouping */
   /** What to do when receiving SetNumberOfComponents(). */
+  /** @ITKStartGrouping */
   itkSetMacro(NumberOfComponentsCallback, NumberOfComponentsCallbackType);
   itkGetConstMacro(NumberOfComponentsCallback, NumberOfComponentsCallbackType);
-
+  /** @ITKEndGrouping */
   /** What to do when receiving PropagateUpdateExtent(). */
+  /** @ITKStartGrouping */
   itkSetMacro(PropagateUpdateExtentCallback, PropagateUpdateExtentCallbackType);
   itkGetConstMacro(PropagateUpdateExtentCallback, PropagateUpdateExtentCallbackType);
-
+  /** @ITKEndGrouping */
   /** What to do when receiving UpdateData(). */
+  /** @ITKStartGrouping */
   itkSetMacro(UpdateDataCallback, UpdateDataCallbackType);
   itkGetConstMacro(UpdateDataCallback, UpdateDataCallbackType);
-
+  /** @ITKEndGrouping */
   /** What to do when receiving DataExtent(). */
+  /** @ITKStartGrouping */
   itkSetMacro(DataExtentCallback, DataExtentCallbackType);
   itkGetConstMacro(DataExtentCallback, DataExtentCallbackType);
-
+  /** @ITKEndGrouping */
   /** What to do when receiving BufferPointer(). */
+  /** @ITKStartGrouping */
   itkSetMacro(BufferPointerCallback, BufferPointerCallbackType);
   itkGetConstMacro(BufferPointerCallback, BufferPointerCallbackType);
-
+  /** @ITKEndGrouping */
   /** Specify callback data. */
+  /** @ITKStartGrouping */
   itkSetMacro2(CallbackUserData, void *);
   itkGetConstMacro(CallbackUserData, void *);
-
+  /** @ITKEndGrouping */
 protected:
   VTKImageImport();
   ~VTKImageImport() override = default;

Modules/Core/Common/include/itkAnnulusOperator.h

@@ -91,6 +91,7 @@ class ITK_TEMPLATE_EXPORT AnnulusOperator : public NeighborhoodOperator<TPixel,
 
   /** Set/Get the inner radius of the annulus. Radius is specified in
    * physical units (mm). */
+  /** @ITKStartGrouping */
   void
   SetInnerRadius(double r)
   {
@@ -101,10 +102,11 @@ class ITK_TEMPLATE_EXPORT AnnulusOperator : public NeighborhoodOperator<TPixel,
   {
     return m_InnerRadius;
   }
-
+  /** @ITKEndGrouping */
   /** Set/Get the thickness of the annulus.  The outer radius of the
    * annulus is defined as r = InnerRadius + Thickness. Thickness is
    * specified in physical units (mm). */
+  /** @ITKStartGrouping */
   void
   SetThickness(double t)
   {
@@ -115,9 +117,10 @@ class ITK_TEMPLATE_EXPORT AnnulusOperator : public NeighborhoodOperator<TPixel,
   {
     return m_Thickness;
   }
-
+  /** @ITKEndGrouping */
   /** Set/Get the pixel spacings.  Setting these ensures the annulus
    * is round in physical space. Defaults to 1. */
+  /** @ITKStartGrouping */
   void
   SetSpacing(SpacingType & s)
   {
@@ -128,9 +131,10 @@ class ITK_TEMPLATE_EXPORT AnnulusOperator : public NeighborhoodOperator<TPixel,
   {
     return m_Spacing;
   }
-
+  /** @ITKEndGrouping */
   /** Set/Get whether kernel values are computed automatically or
    * specified manually */
+  /** @ITKStartGrouping */
   void
   SetNormalize(bool b)
   {
@@ -151,9 +155,10 @@ class ITK_TEMPLATE_EXPORT AnnulusOperator : public NeighborhoodOperator<TPixel,
   {
     this->SetNormalize(false);
   }
-
+  /** @ITKEndGrouping */
   /** If Normalize is on, you define the annulus to have a bright
    * center or a dark center. */
+  /** @ITKStartGrouping */
   void
   SetBrightCenter(bool b)
   {
@@ -174,11 +179,12 @@ class ITK_TEMPLATE_EXPORT AnnulusOperator : public NeighborhoodOperator<TPixel,
   {
     this->SetBrightCenter(false);
   }
-
+  /** @ITKEndGrouping */
   /** If Normalize is off, the interior to annulus, the
    * annulus (region between the two circles), and the region exterior to the
    * annulus to be defined manually.  Defaults are 0, 1, 0
    * respectively. */
+  /** @ITKStartGrouping */
   void
   SetInteriorValue(TPixel v)
   {
@@ -209,7 +215,7 @@ class ITK_TEMPLATE_EXPORT AnnulusOperator : public NeighborhoodOperator<TPixel,
   {
     return m_ExteriorValue;
   }
-
+  /** @ITKEndGrouping */
   void
   PrintSelf(std::ostream & os, Indent indent) const override
   {

Modules/Core/Common/include/itkArray.h

@@ -125,6 +125,7 @@ class ITK_TEMPLATE_EXPORT Array : public vnl_vector<TValue>
   operator=(const VnlVectorType & rhs);
 
   /** Return the number of elements in the Array  */
+  /** @ITKStartGrouping */
   SizeValueType
   Size() const
   {
@@ -135,7 +136,7 @@ class ITK_TEMPLATE_EXPORT Array : public vnl_vector<TValue>
   {
     return static_cast<SizeValueType>(this->size());
   }
-
+  /** @ITKEndGrouping */
   /** Get one element */
   const TValue &
   GetElement(SizeValueType i) const

Modules/Core/Common/include/itkAutoPointerDataObjectDecorator.h

@@ -84,6 +84,7 @@ class ITK_TEMPLATE_EXPORT AutoPointerDataObjectDecorator : public DataObject
   Set(T * val);
 
   /** Get the contained object */
+  /** @ITKStartGrouping */
   virtual T *
   Get()
   {
@@ -94,7 +95,7 @@ class ITK_TEMPLATE_EXPORT AutoPointerDataObjectDecorator : public DataObject
   {
     return m_Component.get();
   }
-
+  /** @ITKEndGrouping */
 protected:
   AutoPointerDataObjectDecorator() = default;
   ~AutoPointerDataObjectDecorator() override = default;

Modules/Core/Common/include/itkBinaryThresholdSpatialFunction.h

@@ -71,17 +71,20 @@ class ITK_TEMPLATE_EXPORT BinaryThresholdSpatialFunction
   using FunctionOutputType = typename TFunction::OutputType;
 
   /** Set/Get the lower threshold. */
+  /** @ITKStartGrouping */
   itkSetMacro(LowerThreshold, FunctionOutputType);
   itkGetConstReferenceMacro(LowerThreshold, FunctionOutputType);
-
+  /** @ITKEndGrouping */
   /** Set/Get the upper threshold. */
+  /** @ITKStartGrouping */
   itkSetMacro(UpperThreshold, FunctionOutputType);
   itkGetConstReferenceMacro(UpperThreshold, FunctionOutputType);
-
+  /** @ITKEndGrouping */
   /** Set/Get the underlying function. */
+  /** @ITKStartGrouping */
   itkSetObjectMacro(Function, FunctionType);
   itkGetModifiableObjectMacro(Function, FunctionType);
-
+  /** @ITKEndGrouping */
   /** Evaluate the function at a given position. */
   OutputType
   Evaluate(const InputType & point) const override;

Modules/Core/Common/include/itkBuildInformation.h

@@ -85,6 +85,7 @@ class ITKCommon_EXPORT BuildInformation final : public Object
   New();
 
   /** Returns the global singleton instance of the BuildInformation */
+  /** @ITKStartGrouping */
   static Pointer
   GetInstance();
   static const MapType &
@@ -95,7 +96,7 @@ class ITKCommon_EXPORT BuildInformation final : public Object
   GetDescription(const MapKeyType &);
   static const std::vector<MapKeyType>
   GetAllKeys();
-
+  /** @ITKEndGrouping */
 private:
   BuildInformation();
 

Modules/Core/Common/include/itkCellInterface.h

@@ -306,12 +306,13 @@ class ITK_TEMPLATE_EXPORT CellInterface
   PointIdsEnd() const = 0;
 
   /** Get/Set the point id list used by the cell */
+  /** @ITKStartGrouping */
   using PointIdentifierContainerType = itk::Array<PointIdentifier>;
   PointIdentifierContainerType
   GetPointIdsContainer() const;
   void
   SetPointIdsContainer(const PointIdentifierContainerType &);
-
+  /** @ITKEndGrouping */
   /** Given the parametric coordinates of a point in the cell
    * (pCoords[CellDimension]), get the closest cell boundary feature of
    * topological dimension CellDimension-1.  If the "inside" pointer is not

Modules/Core/Common/include/itkColorTable.h

@@ -95,11 +95,12 @@ class ITK_TEMPLATE_EXPORT ColorTable : public Object
    * the color. If a name is not provided, the name "UserDefined" is
    * used.
    */
+  /** @ITKStartGrouping */
   bool
   SetColor(unsigned int c, TComponent r, TComponent g, TComponent b, const char * name = "UserDefined");
   bool
   SetColor(unsigned int c, RGBPixel<TComponent> pixel, const char * name = "UserDefined");
-
+  /** @ITKEndGrouping */
   /** Given the position in the table and the color
    * returns the value.
    */