diff --git a/Modules/Bridge/VTK/include/itkVTKImageExport.h b/Modules/Bridge/VTK/include/itkVTKImageExport.h index 22ca4d28bd7..6984c12ffbb 100644 --- a/Modules/Bridge/VTK/include/itkVTKImageExport.h +++ b/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; diff --git a/Modules/Bridge/VTK/include/itkVTKImageExportBase.h b/Modules/Bridge/VTK/include/itkVTKImageExportBase.h index 57b19095492..d130fe0304c 100644 --- a/Modules/Bridge/VTK/include/itkVTKImageExportBase.h +++ b/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. diff --git a/Modules/Bridge/VTK/include/itkVTKImageImport.h b/Modules/Bridge/VTK/include/itkVTKImageImport.h index 80eddabd1a8..99a9b869fad 100644 --- a/Modules/Bridge/VTK/include/itkVTKImageImport.h +++ b/Modules/Bridge/VTK/include/itkVTKImageImport.h @@ -83,6 +83,7 @@ class ITK_TEMPLATE_EXPORT VTKImageImport : public ImageSource /** 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 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 { 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 { 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; diff --git a/Modules/Core/Common/include/itkAnnulusOperator.h b/Modules/Core/Common/include/itkAnnulusOperator.h index 4c1888f7ab5..f4332ce7f01 100644 --- a/Modules/Core/Common/include/itkAnnulusOperator.h +++ b/Modules/Core/Common/include/itkAnnulusOperator.h @@ -91,6 +91,7 @@ class ITK_TEMPLATE_EXPORT AnnulusOperator : public NeighborhoodOperatorSetNormalize(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 NeighborhoodOperatorSetBrightCenter(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 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 { return static_cast(this->size()); } - + /** @ITKEndGrouping */ /** Get one element */ const TValue & GetElement(SizeValueType i) const diff --git a/Modules/Core/Common/include/itkAutoPointerDataObjectDecorator.h b/Modules/Core/Common/include/itkAutoPointerDataObjectDecorator.h index e4d005687bc..ac1ab35bbe7 100644 --- a/Modules/Core/Common/include/itkAutoPointerDataObjectDecorator.h +++ b/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; diff --git a/Modules/Core/Common/include/itkBinaryThresholdSpatialFunction.h b/Modules/Core/Common/include/itkBinaryThresholdSpatialFunction.h index 036b6b913bd..01b01a4e3f1 100644 --- a/Modules/Core/Common/include/itkBinaryThresholdSpatialFunction.h +++ b/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; diff --git a/Modules/Core/Common/include/itkBuildInformation.h b/Modules/Core/Common/include/itkBuildInformation.h index acf21bc0c6b..87dfd4b7f77 100644 --- a/Modules/Core/Common/include/itkBuildInformation.h +++ b/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 GetAllKeys(); - + /** @ITKEndGrouping */ private: BuildInformation(); diff --git a/Modules/Core/Common/include/itkCellInterface.h b/Modules/Core/Common/include/itkCellInterface.h index 583253b99ef..f5c20236d9b 100644 --- a/Modules/Core/Common/include/itkCellInterface.h +++ b/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; 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 diff --git a/Modules/Core/Common/include/itkColorTable.h b/Modules/Core/Common/include/itkColorTable.h index 1c250e88959..bd687909fb6 100644 --- a/Modules/Core/Common/include/itkColorTable.h +++ b/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 pixel, const char * name = "UserDefined"); - + /** @ITKEndGrouping */ /** Given the position in the table and the color * returns the value. */ diff --git a/Modules/Core/Common/include/itkCommand.h b/Modules/Core/Common/include/itkCommand.h index 9fab6ba028d..573143f9254 100644 --- a/Modules/Core/Common/include/itkCommand.h +++ b/Modules/Core/Common/include/itkCommand.h @@ -89,9 +89,10 @@ class ITK_TEMPLATE_EXPORT MemberCommand : public Command ITK_DISALLOW_COPY_AND_MOVE(MemberCommand); /** pointer to a member function that takes a Object* and the event */ + /** @ITKStartGrouping */ using TMemberFunctionPointer = void (T::*)(Object *, const EventObject &); using TConstMemberFunctionPointer = void (T::*)(const Object *, const EventObject &); - + /** @ITKEndGrouping */ /** Standard class type aliases. */ using Self = MemberCommand; using Pointer = SmartPointer; @@ -358,10 +359,11 @@ class ITKCommon_EXPORT CStyleCommand : public Command { public: /** Typedefs for C-style callbacks. */ + /** @ITKStartGrouping */ using FunctionPointer = void (*)(Object *, const EventObject &, void *); using ConstFunctionPointer = void (*)(const Object *, const EventObject &, void *); using DeleteDataFunctionPointer = void (*)(void *); - + /** @ITKEndGrouping */ /** Standard class type aliases. */ using Self = CStyleCommand; using Pointer = SmartPointer; @@ -378,11 +380,12 @@ class ITKCommon_EXPORT CStyleCommand : public Command SetClientData(void * cd); /** Set the C callback function pointer to be called at Execute time. */ + /** @ITKStartGrouping */ void SetCallback(FunctionPointer f); void SetConstCallback(ConstFunctionPointer f); - + /** @ITKEndGrouping */ /** Set the callback to delete the client data. */ void SetClientDataDeleteCallback(DeleteDataFunctionPointer f); diff --git a/Modules/Core/Common/include/itkCompensatedSummation.h b/Modules/Core/Common/include/itkCompensatedSummation.h index 9c7c2bd5f2c..9b3ac86f61e 100644 --- a/Modules/Core/Common/include/itkCompensatedSummation.h +++ b/Modules/Core/Common/include/itkCompensatedSummation.h @@ -76,34 +76,38 @@ class ITK_TEMPLATE_EXPORT CompensatedSummation using Self = CompensatedSummation; /** Constructors. */ + /** @ITKStartGrouping */ CompensatedSummation() = default; CompensatedSummation(FloatType value); - + /** @ITKEndGrouping */ /** Copy constructor. */ CompensatedSummation(const Self &) = default; + /** Assignment operator. */ Self & operator=(const Self &) = default; /** Add an element to the sum. */ + /** @ITKStartGrouping */ void AddElement(const FloatType & element); Self & operator+=(const FloatType & rhs); Self & operator+=(const Self & rhs); - + /** @ITKEndGrouping */ /** Subtract an element from the sum. */ Self & operator-=(const FloatType & rhs); /** Division and multiplication. These do not provide any numerical advantages * relative to vanilla division and multiplication. */ + /** @ITKStartGrouping */ Self & operator*=(const FloatType & rhs); Self & operator/=(const FloatType & rhs); - + /** @ITKEndGrouping */ /** Reset the sum and compensation to zero. */ void ResetToZero(); diff --git a/Modules/Core/Common/include/itkConceptChecking.h b/Modules/Core/Common/include/itkConceptChecking.h index 88cd7d1aa32..44d00d6f640 100644 --- a/Modules/Core/Common/include/itkConceptChecking.h +++ b/Modules/Core/Common/include/itkConceptChecking.h @@ -76,6 +76,7 @@ * run-time overhead. The "vtable" approach was invented for this * project by Brad King at Kitware. */ +/** @ITKStartGrouping */ # define itkConceptConstraintsMacro() \ virtual void Enforcer() { &Constraints::constraints; } # define itkConceptMacro(name, concept) \ @@ -83,7 +84,7 @@ { \ name = sizeof concept \ } - +/** @ITKEndGrouping */ #elif defined(ITK_CONCEPT_IMPLEMENTATION_CALL) /** Not implemented. */ @@ -112,6 +113,7 @@ namespace itk namespace. */ namespace Concept { + /** * Some concept implementation details are adapted from the BOOST C++ * libraries (www.boost.org). These are marked with "(BOOST)" in the diff --git a/Modules/Core/Common/include/itkConicShellInteriorExteriorSpatialFunction.h b/Modules/Core/Common/include/itkConicShellInteriorExteriorSpatialFunction.h index 07b79d5248b..ade439dac09 100644 --- a/Modules/Core/Common/include/itkConicShellInteriorExteriorSpatialFunction.h +++ b/Modules/Core/Common/include/itkConicShellInteriorExteriorSpatialFunction.h @@ -89,10 +89,12 @@ class ITK_TEMPLATE_EXPORT ConicShellInteriorExteriorSpatialFunction Evaluate(const InputType & position) const override; /** Set/Get the origin of the function. */ + /** @ITKStartGrouping */ itkGetConstMacro(Origin, InputType); itkSetMacro(Origin, InputType); - + /** @ITKEndGrouping */ /** Set/Get the gradient at the origin of the function. */ + /** @ITKStartGrouping */ GradientType GetOriginGradient() { @@ -100,26 +102,30 @@ class ITK_TEMPLATE_EXPORT ConicShellInteriorExteriorSpatialFunction } void SetOriginGradient(GradientType grad); - + /** @ITKEndGrouping */ /** Set/Get the minimum search distance. */ + /** @ITKStartGrouping */ itkGetConstMacro(DistanceMin, double); itkSetMacro(DistanceMin, double); - + /** @ITKEndGrouping */ /** Set/Get the maximum search distance. */ + /** @ITKStartGrouping */ itkGetConstMacro(DistanceMax, double); itkSetMacro(DistanceMax, double); - + /** @ITKEndGrouping */ /** Set/Get the tolerance of the in/out comparison. */ + /** @ITKStartGrouping */ itkGetConstMacro(Epsilon, double); itkSetMacro(Epsilon, double); - + /** @ITKEndGrouping */ /** Set/Get direction along the gradient to search. * Set to true to use the direction that the gradient is pointing; * set to false for the opposite direction. */ + /** @ITKStartGrouping */ itkGetConstMacro(Polarity, bool); itkSetMacro(Polarity, bool); itkBooleanMacro(Polarity); - + /** @ITKEndGrouping */ protected: ConicShellInteriorExteriorSpatialFunction() = default; ~ConicShellInteriorExteriorSpatialFunction() override = default; diff --git a/Modules/Core/Common/include/itkConnectedImageNeighborhoodShape.h b/Modules/Core/Common/include/itkConnectedImageNeighborhoodShape.h index dfc54336d48..714631620a2 100644 --- a/Modules/Core/Common/include/itkConnectedImageNeighborhoodShape.h +++ b/Modules/Core/Common/include/itkConnectedImageNeighborhoodShape.h @@ -83,7 +83,6 @@ namespace itk * \ingroup ImageIterators * \ingroup ITKCommon */ - template class ConnectedImageNeighborhoodShape { @@ -108,7 +107,6 @@ class ConnectedImageNeighborhoodShape , m_NumberOfOffsets{ CalculateNumberOfOffsets(maximumCityblockDistance, includeCenterPixel) } {} - /** Returns the number of offsets needed for this shape. */ constexpr size_t GetNumberOfOffsets() const noexcept diff --git a/Modules/Core/Common/include/itkConstShapedNeighborhoodIterator.h b/Modules/Core/Common/include/itkConstShapedNeighborhoodIterator.h index df804b8af14..60313d23dbe 100644 --- a/Modules/Core/Common/include/itkConstShapedNeighborhoodIterator.h +++ b/Modules/Core/Common/include/itkConstShapedNeighborhoodIterator.h @@ -324,6 +324,7 @@ class ITK_TEMPLATE_EXPORT ConstShapedNeighborhoodIterator : private Neighborhood /** Add/Remove a neighborhood offset (from the center of the neighborhood) * to/from the active list. Active list offsets are the only locations * updated and accessible through the iterator. */ + /** @ITKStartGrouping */ void ActivateOffset(const OffsetType & off) { @@ -334,7 +335,7 @@ class ITK_TEMPLATE_EXPORT ConstShapedNeighborhoodIterator : private Neighborhood { this->DeactivateIndex(Superclass::GetNeighborhoodIndex(off)); } - + /** @ITKEndGrouping */ /** Activates a whole range of offsets, for example, an std::vector, * which could be from GenerateImageNeighborhoodOffsets(shape). */ template @@ -372,6 +373,7 @@ class ITK_TEMPLATE_EXPORT ConstShapedNeighborhoodIterator : private Neighborhood /** Add non-zero neighborhood offsets to the active list. The * radius of the neighborhood must match the radius of the shaped * iterator */ + /** @ITKStartGrouping */ template void CreateActiveListFromNeighborhood(const Neighborhood &); @@ -381,7 +383,7 @@ class ITK_TEMPLATE_EXPORT ConstShapedNeighborhoodIterator : private Neighborhood // just delegate to the templated version this->CreateActiveListFromNeighborhood(neighborhood); } - + /** @ITKEndGrouping */ /** Reimplements the operator++ method so that only active pixel locations * are updated. */ Self & diff --git a/Modules/Core/Common/include/itkConstantBoundaryImageNeighborhoodPixelAccessPolicy.h b/Modules/Core/Common/include/itkConstantBoundaryImageNeighborhoodPixelAccessPolicy.h index bb4d5533723..ea1f7447566 100644 --- a/Modules/Core/Common/include/itkConstantBoundaryImageNeighborhoodPixelAccessPolicy.h +++ b/Modules/Core/Common/include/itkConstantBoundaryImageNeighborhoodPixelAccessPolicy.h @@ -124,7 +124,6 @@ class ConstantBoundaryImageNeighborhoodPixelAccessPolicy final , m_Constant{ constant } {} - /** Retrieves the pixel value from the image buffer, at the current * index. When the index is out of bounds, it returns the constant * value specified during construction. */ diff --git a/Modules/Core/Common/include/itkCovariantVector.h b/Modules/Core/Common/include/itkCovariantVector.h index 790534fbd8c..9232aee5fef 100644 --- a/Modules/Core/Common/include/itkCovariantVector.h +++ b/Modules/Core/Common/include/itkCovariantVector.h @@ -64,7 +64,6 @@ namespace itk * \sphinxexample{Core/Common/CovariantVectorDotProduct, Covariant Vector Dot Product} * \endsphinx */ - template class ITK_TEMPLATE_EXPORT CovariantVector : public FixedArray { diff --git a/Modules/Core/Common/include/itkCreateObjectFunction.h b/Modules/Core/Common/include/itkCreateObjectFunction.h index cfe5018d5c0..adf07d141da 100644 --- a/Modules/Core/Common/include/itkCreateObjectFunction.h +++ b/Modules/Core/Common/include/itkCreateObjectFunction.h @@ -67,13 +67,14 @@ class CreateObjectFunction : public CreateObjectFunctionBase using Pointer = SmartPointer; /** Methods from itk:LightObject. */ + /** @ITKStartGrouping */ itkFactorylessNewMacro(Self); LightObject::Pointer CreateObject() override { return T::New().GetPointer(); } - + /** @ITKEndGrouping */ protected: CreateObjectFunction() = default; ~CreateObjectFunction() override = default; diff --git a/Modules/Core/Common/include/itkDataObject.h b/Modules/Core/Common/include/itkDataObject.h index 7a96941f6eb..a2bbfbabd04 100644 --- a/Modules/Core/Common/include/itkDataObject.h +++ b/Modules/Core/Common/include/itkDataObject.h @@ -77,13 +77,14 @@ class ITKCommon_EXPORT DataObjectError : public ExceptionObject /** Get the data object that is throwing this exception. */ + /** @ITKStartGrouping */ const DataObject * GetDataObject() const noexcept; #if !defined(ITK_LEGACY_REMOVE) DataObject * GetDataObject() noexcept; #endif - + /** @ITKEndGrouping */ protected: /** Print exception information. This method can be overridden by * specific exception subtypes. The default is to print out the @@ -427,13 +428,14 @@ class ITK_FORCE_EXPORT_MACRO(ITKCommon) DataObject : public Object /** The maximum MTime of all upstream filters and data objects. * This does not include the MTime of this data object. */ + /** @ITKStartGrouping */ void SetPipelineMTime(ModifiedTimeType time) { m_PipelineMTime = time; } itkGetConstReferenceMacro(PipelineMTime, ModifiedTimeType); - + /** @ITKEndGrouping */ /** MTime for the last time this DataObject was generated. */ virtual ModifiedTimeType GetUpdateMTime() const; @@ -443,9 +445,10 @@ class ITK_FORCE_EXPORT_MACRO(ITKCommon) DataObject : public Object * the Unix epoch. That is the time 00:00:00 UTC on 1 January 1970 * (or 1970-01-01T00:00:00Z ISO 8601) */ + /** @ITKStartGrouping */ itkSetMacro(RealTimeStamp, RealTimeStamp); itkGetConstReferenceMacro(RealTimeStamp, RealTimeStamp); - + /** @ITKEndGrouping */ /** Setup a DataObject to receive new data. This method is called * by the pipeline mechanism on each output of filter that needs * to execute. The default implementation is to return a DataObject diff --git a/Modules/Core/Common/include/itkDataObjectDecorator.h b/Modules/Core/Common/include/itkDataObjectDecorator.h index 062596f6c8e..b36d51efc89 100644 --- a/Modules/Core/Common/include/itkDataObjectDecorator.h +++ b/Modules/Core/Common/include/itkDataObjectDecorator.h @@ -90,11 +90,12 @@ class ITK_TEMPLATE_EXPORT DataObjectDecorator : public DataObject Set(const ComponentType * val); /** Get the contained object */ + /** @ITKStartGrouping */ virtual const ComponentType * Get() const; virtual ComponentType * GetModifiable(); - + /** @ITKEndGrouping */ /** The most recent MTime of this object and the held component */ ModifiedTimeType GetMTime() const override; diff --git a/Modules/Core/Common/include/itkDeref.h b/Modules/Core/Common/include/itkDeref.h index d9e98254c3f..bd2040b5aba 100644 --- a/Modules/Core/Common/include/itkDeref.h +++ b/Modules/Core/Common/include/itkDeref.h @@ -39,7 +39,6 @@ class DerefError : public ExceptionObject itkOverrideGetNameOfClassMacro(DerefError); }; - /** Dereferences the specified pointer, when the pointer is not null. Throws a `DerefError` exception when the pointer * is null. Aims to avoid undefined behavior from accidentally dereferencing a null pointer. */ diff --git a/Modules/Core/Common/include/itkDiffusionTensor3D.h b/Modules/Core/Common/include/itkDiffusionTensor3D.h index 00553c826dc..b0693dee2a0 100644 --- a/Modules/Core/Common/include/itkDiffusionTensor3D.h +++ b/Modules/Core/Common/include/itkDiffusionTensor3D.h @@ -95,10 +95,11 @@ class ITK_TEMPLATE_EXPORT DiffusionTensor3D : public SymmetricSecondRankTensor DiffusionTensor3D(const DiffusionTensor3D & pa) diff --git a/Modules/Core/Common/include/itkDomainThreader.h b/Modules/Core/Common/include/itkDomainThreader.h index 13b9ea0a7e4..5d2b1f4b239 100644 --- a/Modules/Core/Common/include/itkDomainThreader.h +++ b/Modules/Core/Common/include/itkDomainThreader.h @@ -91,9 +91,10 @@ class ITK_TEMPLATE_EXPORT DomainThreader : public Object Execute(AssociateType * enclosingClass, const DomainType & completeDomain); /** Set/Get the DomainPartitioner. */ + /** @ITKStartGrouping */ itkSetObjectMacro(DomainPartitioner, DomainPartitionerType); itkGetModifiableObjectMacro(DomainPartitioner, DomainPartitionerType); - + /** @ITKEndGrouping */ /** Accessor for number of work units that were actually used in the last * ThreadedExecution. */ itkGetConstMacro(NumberOfWorkUnitsUsed, ThreadIdType); @@ -106,13 +107,15 @@ class ITK_TEMPLATE_EXPORT DomainThreader : public Object * \warning When setting the desired number of work units, it might be clamped by * itk::MultiThreaderBase::GetGlobalMaximumNumberOfThreads(). * */ + /** @ITKStartGrouping */ itkSetClampMacro(NumberOfWorkUnits, ThreadIdType, 1, ITK_MAX_THREADS); itkGetConstMacro(NumberOfWorkUnits, ThreadIdType); - + /** @ITKEndGrouping */ /** Convenience methods to set/get the maximum number of threads to use. * \warning When setting the maximum number of threads, it will be clamped by * itk::MultiThreaderBase::GetGlobalMaximumNumberOfThreads(). * */ + /** @ITKStartGrouping */ ThreadIdType GetMaximumNumberOfThreads() const { @@ -120,7 +123,7 @@ class ITK_TEMPLATE_EXPORT DomainThreader : public Object } void SetMaximumNumberOfThreads(const ThreadIdType threads); - + /** @ITKEndGrouping */ protected: DomainThreader(); ~DomainThreader() override = default; diff --git a/Modules/Core/Common/include/itkEllipsoidInteriorExteriorSpatialFunction.h b/Modules/Core/Common/include/itkEllipsoidInteriorExteriorSpatialFunction.h index de5f9babf2e..bc8542f990d 100644 --- a/Modules/Core/Common/include/itkEllipsoidInteriorExteriorSpatialFunction.h +++ b/Modules/Core/Common/include/itkEllipsoidInteriorExteriorSpatialFunction.h @@ -64,13 +64,15 @@ class ITK_TEMPLATE_EXPORT EllipsoidInteriorExteriorSpatialFunction using OrientationType = vnl_matrix_fixed; /** Set/Get and set the center of the ellipsoid. */ + /** @ITKStartGrouping */ itkGetConstMacro(Center, InputType); itkSetMacro(Center, InputType); - + /** @ITKEndGrouping */ /** Get and set the axes lengths of the ellipsoid. */ + /** @ITKStartGrouping */ itkGetConstMacro(Axes, InputType); itkSetMacro(Axes, InputType); - + /** @ITKEndGrouping */ /** Set the orientation vectors (must be orthogonal) of the ellipsoid axes. * Must be normalized!!!!! */ void diff --git a/Modules/Core/Common/include/itkEquivalencyTable.h b/Modules/Core/Common/include/itkEquivalencyTable.h index 8718412af4e..118e8edbd23 100644 --- a/Modules/Core/Common/include/itkEquivalencyTable.h +++ b/Modules/Core/Common/include/itkEquivalencyTable.h @@ -47,13 +47,14 @@ class ITKCommon_EXPORT EquivalencyTable : public DataObject ITK_DISALLOW_COPY_AND_MOVE(EquivalencyTable); /** Standard smart pointer declarations */ + /** @ITKStartGrouping */ using Self = EquivalencyTable; using Superclass = DataObject; using Pointer = SmartPointer; using ConstPointer = SmartPointer; itkNewMacro(Self); itkOverrideGetNameOfClassMacro(EquivalencyTable); - + /** @ITKEndGrouping */ /** Define the container type for the table. */ using HashTableType = std::unordered_map>; diff --git a/Modules/Core/Common/include/itkEventObject.h b/Modules/Core/Common/include/itkEventObject.h index 6a41cc67695..64182c5ecc0 100644 --- a/Modules/Core/Common/include/itkEventObject.h +++ b/Modules/Core/Common/include/itkEventObject.h @@ -200,6 +200,7 @@ operator<<(std::ostream & os, const EventObject & e) /** * Declare some common ITK events */ +/** @ITKStartGrouping */ itkEventMacroDeclaration(NoEvent, EventObject); itkEventMacroDeclaration(AnyEvent, EventObject); itkEventMacroDeclaration(DeleteEvent, AnyEvent); @@ -220,7 +221,7 @@ itkEventMacroDeclaration(FunctionEvaluationIterationEvent, IterationEvent); itkEventMacroDeclaration(GradientEvaluationIterationEvent, IterationEvent); itkEventMacroDeclaration(FunctionAndGradientEvaluationIterationEvent, IterationEvent); itkEventMacroDeclaration(UserEvent, AnyEvent); - +/** @ITKEndGrouping */ #undef ITKEvent_EXPORT #define ITKEvent_EXPORT ITK_ABI_EXPORT diff --git a/Modules/Core/Common/include/itkExtractImageFilter.h b/Modules/Core/Common/include/itkExtractImageFilter.h index ba41f0d9138..bf7d2c3fa44 100644 --- a/Modules/Core/Common/include/itkExtractImageFilter.h +++ b/Modules/Core/Common/include/itkExtractImageFilter.h @@ -47,6 +47,7 @@ class ExtractImageFilterEnums DIRECTIONCOLLAPSETOGUESS = 3 }; }; + /** Define how to print enumerations */ extern ITKCommon_EXPORT std::ostream & operator<<(std::ostream & out, const ExtractImageFilterEnums::DirectionCollapseStrategy value); @@ -256,10 +257,12 @@ class ITK_TEMPLATE_EXPORT ExtractImageFilter : public InPlaceImageFilter)); + /** @ITKEndGrouping */ protected: ExtractImageFilter(); diff --git a/Modules/Core/Common/include/itkFileOutputWindow.h b/Modules/Core/Common/include/itkFileOutputWindow.h index f2e94506459..e10b80eee08 100644 --- a/Modules/Core/Common/include/itkFileOutputWindow.h +++ b/Modules/Core/Common/include/itkFileOutputWindow.h @@ -67,18 +67,20 @@ class ITKCommon_EXPORT FileOutputWindow : public OutputWindow itkGetStringMacro(FileName); /** Set/Get the buffer flushing mode */ + /** @ITKStartGrouping */ itkSetMacro(Flush, bool); itkGetConstMacro(Flush, bool); itkBooleanMacro(Flush); - + /** @ITKEndGrouping */ /** Setting append will cause the log file to be * opened in append mode. Otherwise, if the log file exists, * it will be overwritten each time the FileOutputWindow * is created. */ + /** @ITKStartGrouping */ itkSetMacro(Append, bool); itkGetConstMacro(Append, bool); itkBooleanMacro(Append); - + /** @ITKEndGrouping */ protected: FileOutputWindow(); ~FileOutputWindow() override; diff --git a/Modules/Core/Common/include/itkFiniteCylinderSpatialFunction.h b/Modules/Core/Common/include/itkFiniteCylinderSpatialFunction.h index 16a16cab9a0..1f1386b0734 100644 --- a/Modules/Core/Common/include/itkFiniteCylinderSpatialFunction.h +++ b/Modules/Core/Common/include/itkFiniteCylinderSpatialFunction.h @@ -60,23 +60,27 @@ class ITK_TEMPLATE_EXPORT FiniteCylinderSpatialFunction : public InteriorExterio using typename Superclass::OutputType; /** Set/Get and set the center of the cylinder. */ + /** @ITKStartGrouping */ itkGetConstMacro(Center, InputType); itkSetMacro(Center, InputType); - + /** @ITKEndGrouping */ /** Get and set the medial axis length of the cylinder. */ + /** @ITKStartGrouping */ itkGetConstMacro(AxisLength, double); itkSetMacro(AxisLength, double); - + /** @ITKEndGrouping */ /** Get and set the radius length of the cylinder. */ + /** @ITKStartGrouping */ itkGetConstMacro(Radius, double); itkSetMacro(Radius, double); - + /** @ITKEndGrouping */ /** Set the orientation vectors (must be orthogonal) of the ellipsoid axes. * Must be normalized!!!!! */ + /** @ITKStartGrouping */ itkGetConstMacro(Orientation, InputType); virtual void SetOrientation(const InputType _Orientation); - + /** @ITKEndGrouping */ /** Evaluates the function at a given position. */ OutputType Evaluate(const InputType & position) const override; diff --git a/Modules/Core/Common/include/itkFixedArray.h b/Modules/Core/Common/include/itkFixedArray.h index 5dfff549fd9..e731e8690d9 100644 --- a/Modules/Core/Common/include/itkFixedArray.h +++ b/Modules/Core/Common/include/itkFixedArray.h @@ -219,9 +219,10 @@ class ITK_TEMPLATE_EXPORT FixedArray * Values are copied individually instead of with a binary copy. This * allows the ValueType's assignment operator to be executed. */ + /** @ITKStartGrouping */ FixedArray(const ValueType r[VLength]); FixedArray(const ValueType &); - + /** @ITKEndGrouping */ /** Explicit constructor for std::array. */ explicit FixedArray(const std::array & stdArray) { @@ -279,6 +280,7 @@ class ITK_TEMPLATE_EXPORT FixedArray /** Allow the FixedArray to be indexed normally. No bounds checking is done. */ + /** @ITKStartGrouping */ // false positive warnings with GCC ITK_GCC_PRAGMA_PUSH ITK_GCC_SUPPRESS_Warray_bounds @@ -293,8 +295,9 @@ class ITK_TEMPLATE_EXPORT FixedArray return m_InternalArray[index]; } ITK_GCC_PRAGMA_POP - + /** @ITKEndGrouping */ /** Set/Get element methods are more convenient in wrapping languages */ + /** @ITKStartGrouping */ void SetElement(unsigned int index, const_reference value) { @@ -305,7 +308,7 @@ class ITK_TEMPLATE_EXPORT FixedArray { return m_InternalArray[index]; } - + /** @ITKEndGrouping */ /** Return a pointer to the data. */ ValueType * GetDataPointer() diff --git a/Modules/Core/Common/include/itkFrustumSpatialFunction.h b/Modules/Core/Common/include/itkFrustumSpatialFunction.h index a436e4d204f..96dad496dde 100644 --- a/Modules/Core/Common/include/itkFrustumSpatialFunction.h +++ b/Modules/Core/Common/include/itkFrustumSpatialFunction.h @@ -98,33 +98,40 @@ class ITK_TEMPLATE_EXPORT FrustumSpatialFunction : public InteriorExteriorSpatia Evaluate(const InputType & position) const override; /** Set/Get the apex of the pyramid. */ + /** @ITKStartGrouping */ itkGetConstMacro(Apex, InputType); itkSetMacro(Apex, InputType); - + /** @ITKEndGrouping */ /** Set/Get the angle of the pyramid axis with respect to the Z axis. */ + /** @ITKStartGrouping */ itkGetConstMacro(AngleZ, double); itkSetMacro(AngleZ, double); - + /** @ITKEndGrouping */ /** Set/Get the aperture angle in the X axis. */ + /** @ITKStartGrouping */ itkGetConstMacro(ApertureAngleX, double); itkSetMacro(ApertureAngleX, double); - + /** @ITKEndGrouping */ /** Set/Get the aperture angle in the Y axis. */ + /** @ITKStartGrouping */ itkGetConstMacro(ApertureAngleY, double); itkSetMacro(ApertureAngleY, double); - + /** @ITKEndGrouping */ /** Set/Get the top plane distance to the apex. */ + /** @ITKStartGrouping */ itkGetConstMacro(TopPlane, double); itkSetMacro(TopPlane, double); - + /** @ITKEndGrouping */ /** Set/Get the bottom plane distance to the apex. */ + /** @ITKStartGrouping */ itkGetConstMacro(BottomPlane, double); itkSetMacro(BottomPlane, double); - + /** @ITKEndGrouping */ /** Set/Get the plane in which the frustum should rotate. */ + /** @ITKStartGrouping */ itkGetConstMacro(RotationPlane, FrustumRotationPlaneType); itkSetMacro(RotationPlane, FrustumRotationPlaneType); - + /** @ITKEndGrouping */ protected: FrustumSpatialFunction() = default; ~FrustumSpatialFunction() override = default; diff --git a/Modules/Core/Common/include/itkGaussianDerivativeOperator.h b/Modules/Core/Common/include/itkGaussianDerivativeOperator.h index a1b6e3cb7b7..b5ebde83b83 100644 --- a/Modules/Core/Common/include/itkGaussianDerivativeOperator.h +++ b/Modules/Core/Common/include/itkGaussianDerivativeOperator.h @@ -123,6 +123,7 @@ class ITK_TEMPLATE_EXPORT GaussianDerivativeOperator : public NeighborhoodOperat * algorithms such as blob detection. The scaling results in the * value of the derivatives being independent of the size of an * object. */ + /** @ITKStartGrouping */ void SetNormalizeAcrossScale(bool flag) { @@ -134,10 +135,11 @@ class ITK_TEMPLATE_EXPORT GaussianDerivativeOperator : public NeighborhoodOperat return m_NormalizeAcrossScale; } itkBooleanMacro(NormalizeAcrossScale); - + /** @ITKEndGrouping */ /** Set/Get the variance of the Gaussian kernel. * */ + /** @ITKStartGrouping */ void SetVariance(const double variance) { @@ -148,8 +150,9 @@ class ITK_TEMPLATE_EXPORT GaussianDerivativeOperator : public NeighborhoodOperat { return m_Variance; } - + /** @ITKEndGrouping */ /** Set/Get the spacing for the direction of this kernel. */ + /** @ITKStartGrouping */ void SetSpacing(const double spacing) { @@ -160,7 +163,7 @@ class ITK_TEMPLATE_EXPORT GaussianDerivativeOperator : public NeighborhoodOperat { return m_Spacing; } - + /** @ITKEndGrouping */ /** Set/Get the desired maximum error of the gaussian approximation. Maximum * error is the difference between the area under the discrete Gaussian curve * and the area under the continuous Gaussian. Maximum error affects the @@ -183,14 +186,16 @@ class ITK_TEMPLATE_EXPORT GaussianDerivativeOperator : public NeighborhoodOperat * large variances will yield very large kernel sizes. This value can be * used to truncate a kernel in such instances. A warning will be given on * truncation of the kernel. */ + /** @ITKStartGrouping */ void SetMaximumKernelWidth(unsigned int n) { m_MaximumKernelWidth = n; } itkGetConstMacro(MaximumKernelWidth, unsigned int); - + /** @ITKEndGrouping */ /** Sets/Get the order of the derivative. */ + /** @ITKStartGrouping */ void SetOrder(const unsigned int order) { @@ -201,7 +206,7 @@ class ITK_TEMPLATE_EXPORT GaussianDerivativeOperator : public NeighborhoodOperat { return m_Order; } - + /** @ITKEndGrouping */ void PrintSelf(std::ostream & os, Indent indent) const override; diff --git a/Modules/Core/Common/include/itkGaussianDerivativeSpatialFunction.h b/Modules/Core/Common/include/itkGaussianDerivativeSpatialFunction.h index 059968be9df..1f9217389b9 100644 --- a/Modules/Core/Common/include/itkGaussianDerivativeSpatialFunction.h +++ b/Modules/Core/Common/include/itkGaussianDerivativeSpatialFunction.h @@ -79,6 +79,7 @@ class ITK_TEMPLATE_EXPORT GaussianDerivativeSpatialFunction : public SpatialFunc EvaluateVector(const TInput & position) const; /** Gets and sets for gaussian parameters */ + /** @ITKStartGrouping */ itkSetMacro(Scale, double); itkGetConstMacro(Scale, double); itkSetMacro(Normalized, bool); @@ -89,7 +90,7 @@ class ITK_TEMPLATE_EXPORT GaussianDerivativeSpatialFunction : public SpatialFunc itkGetConstMacro(Mean, ArrayType); itkSetMacro(Direction, unsigned int); itkGetConstMacro(Direction, unsigned int); - + /** @ITKEndGrouping */ protected: GaussianDerivativeSpatialFunction() = default; ~GaussianDerivativeSpatialFunction() override = default; diff --git a/Modules/Core/Common/include/itkGaussianSpatialFunction.h b/Modules/Core/Common/include/itkGaussianSpatialFunction.h index 94965a76413..8cac689a343 100644 --- a/Modules/Core/Common/include/itkGaussianSpatialFunction.h +++ b/Modules/Core/Common/include/itkGaussianSpatialFunction.h @@ -72,22 +72,26 @@ class ITK_TEMPLATE_EXPORT GaussianSpatialFunction : public SpatialFunction /** Return a pointer to the beginning of the buffer. This is used by * the image iterator class. */ + /** @ITKStartGrouping */ virtual TPixel * GetBufferPointer() { @@ -265,7 +266,7 @@ class ITK_TEMPLATE_EXPORT Image : public ImageBase { return m_Buffer ? m_Buffer->GetBufferPointer() : nullptr; } - + /** @ITKEndGrouping */ /** Return a pointer to the container. */ PixelContainer * GetPixelContainer() diff --git a/Modules/Core/Common/include/itkImageAlgorithm.h b/Modules/Core/Common/include/itkImageAlgorithm.h index 8f072948707..c05b6e14e11 100644 --- a/Modules/Core/Common/include/itkImageAlgorithm.h +++ b/Modules/Core/Common/include/itkImageAlgorithm.h @@ -193,7 +193,6 @@ struct ImageAlgorithm } }; - /** Function to dispatch to std::copy or std::transform. */ template static TType * diff --git a/Modules/Core/Common/include/itkImageBase.h b/Modules/Core/Common/include/itkImageBase.h index 5df26864d02..9809f5db000 100644 --- a/Modules/Core/Common/include/itkImageBase.h +++ b/Modules/Core/Common/include/itkImageBase.h @@ -185,12 +185,13 @@ class ITK_TEMPLATE_EXPORT ImageBase : public DataObject * coordinates of the image origin (pixel [0,0]). It is stored internally * as SpacePrecisionType but may be set from float or double. * \sa GetOrigin() */ + /** @ITKStartGrouping */ itkSetMacro(Origin, PointType); virtual void SetOrigin(const double origin[VImageDimension]); virtual void SetOrigin(const float origin[VImageDimension]); - + /** @ITKEndGrouping */ /** Set the direction cosines of the image. The direction cosines * are vectors that point from one pixel to the next. * @@ -329,6 +330,7 @@ class ITK_TEMPLATE_EXPORT ImageBase : public DataObject /** Convenience methods to set the LargestPossibleRegion, * BufferedRegion and RequestedRegion. Allocate must still be called. */ + /** @ITKStartGrouping */ virtual void SetRegions(const RegionType & region) { @@ -345,6 +347,7 @@ class ITK_TEMPLATE_EXPORT ImageBase : public DataObject this->Self::SetRegions(region); } + /** @ITKEndGrouping */ /** Get the offset table. The offset table gives increments for * moving from one pixel to next in the current row, column, slice, @@ -434,13 +437,14 @@ class ITK_TEMPLATE_EXPORT ImageBase : public DataObject * float. These methods also pre-compute the Index to Physical point * transforms of the image. * \sa GetSpacing() */ + /** @ITKStartGrouping */ virtual void SetSpacing(const SpacingType & spacing); virtual void SetSpacing(const double spacing[VImageDimension]); virtual void SetSpacing(const float spacing[VImageDimension]); - + /** @ITKEndGrouping */ /** Returns the index (discrete) of a voxel from a physical point. * Floating point index results are rounded to integers * \note This specific overload does not figure out whether or not @@ -822,11 +826,12 @@ class ITK_TEMPLATE_EXPORT ImageBase : public DataObject * # returned from NumericTraits for the pixel type, and VectorImage * returns the vector length set by the user. */ + /** @ITKStartGrouping */ virtual unsigned int GetNumberOfComponentsPerPixel() const; virtual void SetNumberOfComponentsPerPixel(unsigned int); - + /** @ITKEndGrouping */ protected: ImageBase() = default; ~ImageBase() override = default; @@ -852,16 +857,18 @@ class ITK_TEMPLATE_EXPORT ImageBase : public DataObject /** Origin, spacing, and direction in physical coordinates. This variables are * protected for efficiency. They are referenced frequently by * inner loop calculations. */ + /** @ITKStartGrouping */ SpacingType m_Spacing{ MakeFilled(1.0) }; PointType m_Origin{}; DirectionType m_Direction{ DirectionType::GetIdentity() }; DirectionType m_InverseDirection{ DirectionType::GetIdentity() }; - + /** @ITKEndGrouping */ /** Matrices intended to help with the conversion of Index coordinates * to PhysicalPoint coordinates */ + /** @ITKStartGrouping */ DirectionType m_IndexToPhysicalPoint{ DirectionType::GetIdentity() }; DirectionType m_PhysicalPointToIndex{ DirectionType::GetIdentity() }; - + /** @ITKEndGrouping */ /** Restores the buffered region to its default state * This method does not call Modify because Initialization is * called by ReleaseData and can not modify the MTime diff --git a/Modules/Core/Common/include/itkImageDuplicator.h b/Modules/Core/Common/include/itkImageDuplicator.h index 63eeb657851..274b7e67736 100644 --- a/Modules/Core/Common/include/itkImageDuplicator.h +++ b/Modules/Core/Common/include/itkImageDuplicator.h @@ -86,6 +86,7 @@ class ITK_TEMPLATE_EXPORT ImageDuplicator : public Object * by returning a non-const pointer * for the generated Object. */ + /** @ITKStartGrouping */ // NOTE: The m_DuplicateImage is only // exposed via the Source generation interface // by the GetOutput() method that mimics @@ -100,7 +101,7 @@ class ITK_TEMPLATE_EXPORT ImageDuplicator : public Object { return this->m_DuplicateImage.GetPointer(); } - + /** @ITKEndGrouping */ #if !defined(ITK_LEGACY_REMOVE) // This interface was exposed in ITKv4 when the itkGetModifiableObjectMacro was used virtual ImageType * diff --git a/Modules/Core/Common/include/itkImageIORegion.h b/Modules/Core/Common/include/itkImageIORegion.h index 000945c2407..041be6eebf2 100644 --- a/Modules/Core/Common/include/itkImageIORegion.h +++ b/Modules/Core/Common/include/itkImageIORegion.h @@ -121,22 +121,24 @@ class ITKCommon_EXPORT ImageIORegion : public Region SetIndex(const IndexType & index); /** Get index defining the corner of the region. */ + /** @ITKStartGrouping */ const IndexType & GetIndex() const; IndexType & GetModifiableIndex(); - + /** @ITKEndGrouping */ /** Set the size of the region. This plus the index determines the * rectangular shape, or extent, of the region. */ void SetSize(const SizeType & size); /** Get the size of the region. */ + /** @ITKStartGrouping */ const SizeType & GetSize() const; SizeType & GetModifiableSize(); - + /** @ITKEndGrouping */ /** Convenience methods to get the size of the image in a particular * coordinate direction i. Do not try to access image sizes beyond the * the ImageDimension. */ diff --git a/Modules/Core/Common/include/itkImageIterator.h b/Modules/Core/Common/include/itkImageIterator.h index d388694dbe1..91bc506e0a9 100644 --- a/Modules/Core/Common/include/itkImageIterator.h +++ b/Modules/Core/Common/include/itkImageIterator.h @@ -134,9 +134,11 @@ class ITK_TEMPLATE_EXPORT ImageIterator : public ImageConstIterator protected: /** This constructor is declared protected in order to enforce const-correctness */ + /** @ITKStartGrouping */ ImageIterator(const ImageConstIterator & it); Self & operator=(const ImageConstIterator & it); + /** @ITKEndGrouping */ }; } // end namespace itk diff --git a/Modules/Core/Common/include/itkImageIteratorWithIndex.h b/Modules/Core/Common/include/itkImageIteratorWithIndex.h index 66e0e27589c..38e7773857a 100644 --- a/Modules/Core/Common/include/itkImageIteratorWithIndex.h +++ b/Modules/Core/Common/include/itkImageIteratorWithIndex.h @@ -124,9 +124,11 @@ class ITK_TEMPLATE_EXPORT ImageIteratorWithIndex : public ImageConstIteratorWith protected: /** This constructor is declared protected in order to enforce const-correctness */ + /** @ITKStartGrouping */ ImageIteratorWithIndex(const ImageConstIteratorWithIndex & it); Self & operator=(const ImageConstIteratorWithIndex & it); + /** @ITKEndGrouping */ }; } // end namespace itk diff --git a/Modules/Core/Common/include/itkImageLinearIteratorWithIndex.h b/Modules/Core/Common/include/itkImageLinearIteratorWithIndex.h index e87eb1f7c67..3b80496fc71 100644 --- a/Modules/Core/Common/include/itkImageLinearIteratorWithIndex.h +++ b/Modules/Core/Common/include/itkImageLinearIteratorWithIndex.h @@ -117,9 +117,11 @@ class ITK_TEMPLATE_EXPORT ImageLinearIteratorWithIndex : public ImageLinearConst protected: /** the construction from a const iterator is declared protected in order to enforce const correctness. */ + /** @ITKStartGrouping */ ImageLinearIteratorWithIndex(const ImageLinearConstIteratorWithIndex & it); Self & operator=(const ImageLinearConstIteratorWithIndex & it); + /** @ITKEndGrouping */ }; } // end namespace itk diff --git a/Modules/Core/Common/include/itkImageRandomConstIteratorWithIndex.h b/Modules/Core/Common/include/itkImageRandomConstIteratorWithIndex.h index 9d573b1d283..0e25a6f47b9 100644 --- a/Modules/Core/Common/include/itkImageRandomConstIteratorWithIndex.h +++ b/Modules/Core/Common/include/itkImageRandomConstIteratorWithIndex.h @@ -137,6 +137,7 @@ class ITK_TEMPLATE_EXPORT ImageRandomConstIteratorWithIndex : public ImageConstI /** Default constructor. Needed since we provide a cast constructor. */ ImageRandomConstIteratorWithIndex() = default; + ~ImageRandomConstIteratorWithIndex() override = default; /** Constructor establishes an iterator to walk a particular image and a diff --git a/Modules/Core/Common/include/itkImageRandomConstIteratorWithOnlyIndex.h b/Modules/Core/Common/include/itkImageRandomConstIteratorWithOnlyIndex.h index 923abbf2b3b..693088d6a8d 100644 --- a/Modules/Core/Common/include/itkImageRandomConstIteratorWithOnlyIndex.h +++ b/Modules/Core/Common/include/itkImageRandomConstIteratorWithOnlyIndex.h @@ -139,6 +139,7 @@ class ITK_TEMPLATE_EXPORT ImageRandomConstIteratorWithOnlyIndex : public ImageCo /** Default constructor. Needed since we provide a cast constructor. */ ImageRandomConstIteratorWithOnlyIndex() = default; + ~ImageRandomConstIteratorWithOnlyIndex() override = default; /** Constructor establishes an iterator to walk a particular image and a diff --git a/Modules/Core/Common/include/itkImageRandomIteratorWithIndex.h b/Modules/Core/Common/include/itkImageRandomIteratorWithIndex.h index 6aaf414628e..a9219227013 100644 --- a/Modules/Core/Common/include/itkImageRandomIteratorWithIndex.h +++ b/Modules/Core/Common/include/itkImageRandomIteratorWithIndex.h @@ -117,9 +117,11 @@ class ITK_TEMPLATE_EXPORT ImageRandomIteratorWithIndex : public ImageRandomConst protected: /** The construction from a const iterator is declared protected in order to enforce const correctness. */ + /** @ITKStartGrouping */ ImageRandomIteratorWithIndex(const ImageRandomConstIteratorWithIndex & it); Self & operator=(const ImageRandomConstIteratorWithIndex & it); + /** @ITKEndGrouping */ }; } // end namespace itk diff --git a/Modules/Core/Common/include/itkImageRandomNonRepeatingConstIteratorWithIndex.h b/Modules/Core/Common/include/itkImageRandomNonRepeatingConstIteratorWithIndex.h index 207c03c68a3..0c5c50be36e 100644 --- a/Modules/Core/Common/include/itkImageRandomNonRepeatingConstIteratorWithIndex.h +++ b/Modules/Core/Common/include/itkImageRandomNonRepeatingConstIteratorWithIndex.h @@ -235,6 +235,7 @@ class ITK_TEMPLATE_EXPORT ImageRandomNonRepeatingConstIteratorWithIndex : public /** Default constructor. Needed since we provide a cast constructor. */ ImageRandomNonRepeatingConstIteratorWithIndex() = default; + ~ImageRandomNonRepeatingConstIteratorWithIndex() override { delete m_Permutation; } /** Constructor establishes an iterator to walk a particular image and a @@ -323,6 +324,7 @@ class ITK_TEMPLATE_EXPORT ImageRandomNonRepeatingConstIteratorWithIndex : public } /** Set/Get number of random samples to extract from the image region. */ + /** @ITKStartGrouping */ void SetNumberOfSamples(SizeValueType number) { @@ -332,12 +334,12 @@ class ITK_TEMPLATE_EXPORT ImageRandomNonRepeatingConstIteratorWithIndex : public m_NumberOfSamplesRequested = m_NumberOfPixelsInRegion; } } - SizeValueType GetNumberOfSamples() const { return m_NumberOfSamplesRequested; } + /** @ITKEndGrouping */ /** Reinitialize the seed of the random number generator. */ void diff --git a/Modules/Core/Common/include/itkImageRandomNonRepeatingIteratorWithIndex.h b/Modules/Core/Common/include/itkImageRandomNonRepeatingIteratorWithIndex.h index e867a17a696..5a1ee63374a 100644 --- a/Modules/Core/Common/include/itkImageRandomNonRepeatingIteratorWithIndex.h +++ b/Modules/Core/Common/include/itkImageRandomNonRepeatingIteratorWithIndex.h @@ -129,9 +129,11 @@ class ITK_TEMPLATE_EXPORT ImageRandomNonRepeatingIteratorWithIndex protected: /** The construction from a const iterator is declared protected in order to enforce const correctness. */ + /** @ITKStartGrouping */ ImageRandomNonRepeatingIteratorWithIndex(const ImageRandomNonRepeatingConstIteratorWithIndex & it); Self & operator=(const ImageRandomNonRepeatingConstIteratorWithIndex & it); + /** @ITKEndGrouping */ }; } // end namespace itk diff --git a/Modules/Core/Common/include/itkImageRegion.h b/Modules/Core/Common/include/itkImageRegion.h index b373c8b27b0..0f8d8765cf9 100644 --- a/Modules/Core/Common/include/itkImageRegion.h +++ b/Modules/Core/Common/include/itkImageRegion.h @@ -184,6 +184,7 @@ class ITK_TEMPLATE_EXPORT ImageRegion final } /** Get index defining the corner of the region. */ + /** @ITKStartGrouping */ const IndexType & GetIndex() const { @@ -194,7 +195,7 @@ class ITK_TEMPLATE_EXPORT ImageRegion final { return m_Index; } - + /** @ITKEndGrouping */ /** Set the size of the region. This plus the index determines the * rectangular shape, or extent, of the region. */ void @@ -204,6 +205,7 @@ class ITK_TEMPLATE_EXPORT ImageRegion final } /** Get the size of the region. */ + /** @ITKStartGrouping */ const SizeType & GetSize() const { @@ -214,9 +216,10 @@ class ITK_TEMPLATE_EXPORT ImageRegion final { return m_Size; } - + /** @ITKEndGrouping */ /** Convenience methods to get and set the size of the particular dimension i. */ + /** @ITKStartGrouping */ void SetSize(unsigned int i, SizeValueType sze) { @@ -227,9 +230,10 @@ class ITK_TEMPLATE_EXPORT ImageRegion final { return m_Size[i]; } - + /** @ITKEndGrouping */ /** Convenience methods to get and set the index of the particular dimension i. */ + /** @ITKStartGrouping */ void SetIndex(unsigned int i, IndexValueType sze) { @@ -240,7 +244,7 @@ class ITK_TEMPLATE_EXPORT ImageRegion final { return m_Index[i]; } - + /** @ITKEndGrouping */ /** Get index defining the upper corner of the region. */ IndexType GetUpperIndex() const; diff --git a/Modules/Core/Common/include/itkImageRegionConstIterator.h b/Modules/Core/Common/include/itkImageRegionConstIterator.h index 7226f4efbb7..a2cc2fab503 100644 --- a/Modules/Core/Common/include/itkImageRegionConstIterator.h +++ b/Modules/Core/Common/include/itkImageRegionConstIterator.h @@ -123,6 +123,7 @@ class ITK_TEMPLATE_EXPORT ImageRegionConstIterator : public ImageConstIterator & it); Self & operator=(const ImageRegionExclusionConstIteratorWithIndex & it); + /** @ITKEndGrouping */ }; } // end namespace itk diff --git a/Modules/Core/Common/include/itkImageRegionIterator.h b/Modules/Core/Common/include/itkImageRegionIterator.h index 7f484dc3898..93babf4631e 100644 --- a/Modules/Core/Common/include/itkImageRegionIterator.h +++ b/Modules/Core/Common/include/itkImageRegionIterator.h @@ -130,9 +130,11 @@ class ITK_TEMPLATE_EXPORT ImageRegionIterator : public ImageRegionConstIterator< protected: /** the construction from a const iterator is declared protected in order to enforce const correctness. */ + /** @ITKStartGrouping */ ImageRegionIterator(const ImageRegionConstIterator & it); Self & operator=(const ImageRegionConstIterator & it); + /** @ITKEndGrouping */ }; } // end namespace itk diff --git a/Modules/Core/Common/include/itkImageRegionIteratorWithIndex.h b/Modules/Core/Common/include/itkImageRegionIteratorWithIndex.h index d533998a6e5..a0c7b813c12 100644 --- a/Modules/Core/Common/include/itkImageRegionIteratorWithIndex.h +++ b/Modules/Core/Common/include/itkImageRegionIteratorWithIndex.h @@ -123,9 +123,11 @@ class ITK_TEMPLATE_EXPORT ImageRegionIteratorWithIndex : public ImageRegionConst protected: /** The construction from a const iterator is declared protected in order to enforce const correctness. */ + /** @ITKStartGrouping */ ImageRegionIteratorWithIndex(const ImageRegionConstIteratorWithIndex & it); Self & operator=(const ImageRegionConstIteratorWithIndex & it); + /** @ITKEndGrouping */ }; } // end namespace itk diff --git a/Modules/Core/Common/include/itkImageRegionReverseIterator.h b/Modules/Core/Common/include/itkImageRegionReverseIterator.h index 1ac655fcf1d..9896a3c33b4 100644 --- a/Modules/Core/Common/include/itkImageRegionReverseIterator.h +++ b/Modules/Core/Common/include/itkImageRegionReverseIterator.h @@ -119,9 +119,11 @@ class ITK_TEMPLATE_EXPORT ImageRegionReverseIterator : public ImageRegionReverse protected: /** the construction from a const iterator is declared protected in order to enforce const correctness. */ + /** @ITKStartGrouping */ ImageRegionReverseIterator(const ImageRegionReverseConstIterator & it); Self & operator=(const ImageRegionReverseConstIterator & it); + /** @ITKEndGrouping */ }; } // end namespace itk diff --git a/Modules/Core/Common/include/itkImageRegionSplitterBase.h b/Modules/Core/Common/include/itkImageRegionSplitterBase.h index f28ea7bdfe6..5852eb2c65f 100644 --- a/Modules/Core/Common/include/itkImageRegionSplitterBase.h +++ b/Modules/Core/Common/include/itkImageRegionSplitterBase.h @@ -75,6 +75,7 @@ class ITKCommon_EXPORT ImageRegionSplitterBase : public Object * a certain dimensions, then some splits will not be possible. This * method returns a number less than or equal to the requested number * of pieces. */ + /** @ITKStartGrouping */ template unsigned int GetNumberOfSplits(const ImageRegion & region, unsigned int requestedNumber) const @@ -88,7 +89,7 @@ class ITKCommon_EXPORT ImageRegionSplitterBase : public Object return this->GetNumberOfSplitsInternal( region.GetImageDimension(), ®ion.GetIndex()[0], ®ion.GetSize()[0], requestedNumber); } - + /** @ITKEndGrouping */ /** \brief Get a region definition that represents the ith piece a * specified region. diff --git a/Modules/Core/Common/include/itkImageRegionSplitterDirection.h b/Modules/Core/Common/include/itkImageRegionSplitterDirection.h index 9e94f78f073..3c276b7dafa 100644 --- a/Modules/Core/Common/include/itkImageRegionSplitterDirection.h +++ b/Modules/Core/Common/include/itkImageRegionSplitterDirection.h @@ -52,9 +52,10 @@ class ITKCommon_EXPORT ImageRegionSplitterDirection : public ImageRegionSplitter * * Defaults to 0. */ + /** @ITKStartGrouping */ itkGetConstMacro(Direction, unsigned int); itkSetMacro(Direction, unsigned int); - + /** @ITKEndGrouping */ protected: ImageRegionSplitterDirection(); diff --git a/Modules/Core/Common/include/itkImageReverseIterator.h b/Modules/Core/Common/include/itkImageReverseIterator.h index 40eed13c7d2..7f824b1b26e 100644 --- a/Modules/Core/Common/include/itkImageReverseIterator.h +++ b/Modules/Core/Common/include/itkImageReverseIterator.h @@ -115,9 +115,11 @@ class ITK_TEMPLATE_EXPORT ImageReverseIterator : public ImageRegionReverseConstI protected: /** the construction from a const iterator is declared protected in order to enforce const correctness. */ + /** @ITKStartGrouping */ ImageReverseIterator(const ImageRegionReverseConstIterator & it); Self & operator=(const ImageRegionReverseConstIterator & it); + /** @ITKEndGrouping */ }; } // end namespace itk diff --git a/Modules/Core/Common/include/itkImageScanlineConstIterator.h b/Modules/Core/Common/include/itkImageScanlineConstIterator.h index 7c4e1906241..5dde1cb09ff 100644 --- a/Modules/Core/Common/include/itkImageScanlineConstIterator.h +++ b/Modules/Core/Common/include/itkImageScanlineConstIterator.h @@ -78,6 +78,7 @@ class ITK_TEMPLATE_EXPORT ImageScanlineConstIterator : public ImageConstIterator * Index type alias support While these were already typedef'ed in the superclass, * they need to be redone here for this subclass to compile properly with gcc. */ + /** Types inherited from the Superclass */ using typename Superclass::IndexType; using typename Superclass::SizeType; @@ -256,7 +257,6 @@ class ITK_TEMPLATE_EXPORT ImageScanlineConstIterator : public ImageConstIterator return *this; } - protected: OffsetValueType m_SpanBeginOffset{}; // one pixel the beginning of the scanline OffsetValueType m_SpanEndOffset{}; // one pixel past the end of the scanline diff --git a/Modules/Core/Common/include/itkImageScanlineIterator.h b/Modules/Core/Common/include/itkImageScanlineIterator.h index 50104fd5057..d98a593165f 100644 --- a/Modules/Core/Common/include/itkImageScanlineIterator.h +++ b/Modules/Core/Common/include/itkImageScanlineIterator.h @@ -92,9 +92,11 @@ class ITK_TEMPLATE_EXPORT ImageScanlineIterator : public ImageScanlineConstItera protected: /** the construction from a const iterator is declared protected in order to enforce const correctness. */ + /** @ITKStartGrouping */ ImageScanlineIterator(const ImageScanlineConstIterator & it); Self & operator=(const ImageScanlineConstIterator & it); + /** @ITKEndGrouping */ }; // Deduction guide for class template argument deduction (CTAD). diff --git a/Modules/Core/Common/include/itkImageSink.h b/Modules/Core/Common/include/itkImageSink.h index ee14040534e..ed9d9de7954 100644 --- a/Modules/Core/Common/include/itkImageSink.h +++ b/Modules/Core/Common/include/itkImageSink.h @@ -110,17 +110,19 @@ class ImageSink * by the input images. ITK has a requirement that multiple input * images be congruent in space by default. */ + /** @ITKStartGrouping */ itkSetMacro(CoordinateTolerance, double); itkGetConstMacro(CoordinateTolerance, double); - + /** @ITKEndGrouping */ /** get/set the direction tolerance * This tolerance is used to make sure that all input * images are oriented the same before performing the filter's * transformations. */ + /** @ITKStartGrouping */ itkSetMacro(DirectionTolerance, double); itkGetConstMacro(DirectionTolerance, double); - + /** @ITKEndGrouping */ /** get/set the global default direction tolerance * * This value is used to initialize the DirectionTolerance upon @@ -183,9 +185,10 @@ class ImageSink /** Set/Get Helper class for dividing the input into regions for * streaming */ + /** @ITKStartGrouping */ itkSetObjectMacro(RegionSplitter, SplitterType); itkGetModifiableObjectMacro(RegionSplitter, SplitterType); - + /** @ITKEndGrouping */ private: unsigned int m_NumberOfStreamDivisions{ 1 }; @@ -196,8 +199,10 @@ class ImageSink * Tolerances for checking whether input images are defined to * occupy the same physical space. */ + /** @ITKStartGrouping */ double m_CoordinateTolerance{ Self::GetGlobalDefaultCoordinateTolerance() }; double m_DirectionTolerance{ Self::GetGlobalDefaultDirectionTolerance() }; + /** @ITKEndGrouping */ }; } // namespace itk diff --git a/Modules/Core/Common/include/itkImageSliceIteratorWithIndex.h b/Modules/Core/Common/include/itkImageSliceIteratorWithIndex.h index 38f86e4ddc2..9b7e73021cf 100644 --- a/Modules/Core/Common/include/itkImageSliceIteratorWithIndex.h +++ b/Modules/Core/Common/include/itkImageSliceIteratorWithIndex.h @@ -119,9 +119,11 @@ class ITK_TEMPLATE_EXPORT ImageSliceIteratorWithIndex : public ImageSliceConstIt protected: /** The construction from a const iterator is declared protected in order to enforce const correctness. */ + /** @ITKStartGrouping */ ImageSliceIteratorWithIndex(const ImageSliceConstIteratorWithIndex & it); Self & operator=(const ImageSliceConstIteratorWithIndex & it); + /** @ITKEndGrouping */ }; } // end namespace itk diff --git a/Modules/Core/Common/include/itkImageSource.h b/Modules/Core/Common/include/itkImageSource.h index fa7b96427d3..0757870b2da 100644 --- a/Modules/Core/Common/include/itkImageSource.h +++ b/Modules/Core/Common/include/itkImageSource.h @@ -142,11 +142,12 @@ class ITK_TEMPLATE_EXPORT ImageSource * types. Derived classes should have names get methods for these * outputs. */ + /** @ITKStartGrouping */ OutputImageType * GetOutput(); const OutputImageType * GetOutput() const; - + /** @ITKEndGrouping */ OutputImageType * GetOutput(unsigned int idx); @@ -221,11 +222,12 @@ class ITK_TEMPLATE_EXPORT ImageSource * SmartPointer to a DataObject. If a subclass of ImageSource has * multiple outputs of different types, then that class must provide * an implementation of MakeOutput(). */ + /** @ITKStartGrouping */ ProcessObject::DataObjectPointer MakeOutput(ProcessObject::DataObjectPointerArraySizeType idx) override; ProcessObject::DataObjectPointer MakeOutput(const ProcessObject::DataObjectIdentifierType &) override; - + /** @ITKEndGrouping */ protected: ImageSource(); ~ImageSource() override = default; @@ -295,11 +297,12 @@ class ITK_TEMPLATE_EXPORT ImageSource * in a single thread being reused to process multiple work units. * * \sa GenerateData(), SplitRequestedRegion() */ + /** @ITKStartGrouping */ virtual void ThreadedGenerateData(const OutputImageRegionType & region, ThreadIdType threadId); virtual void DynamicThreadedGenerateData(const OutputImageRegionType & outputRegionForThread); - + /** @ITKEndGrouping */ /** The GenerateData method normally allocates the buffers for all of the * outputs of a filter. Some filters may want to override this default * behavior. For example, a filter may have multiple outputs with @@ -395,10 +398,11 @@ class ITK_TEMPLATE_EXPORT ImageSource /** Whether to use classic multi-threading infrastructure (OFF by default). * Classic multi-threading uses derived class' ImageRegionSplitter, * thus enabling custom region splitting methods. */ + /** @ITKStartGrouping */ itkGetConstMacro(DynamicMultiThreading, bool); itkSetMacro(DynamicMultiThreading, bool); itkBooleanMacro(DynamicMultiThreading); - + /** @ITKEndGrouping */ bool m_DynamicMultiThreading{ true }; }; } // end namespace itk diff --git a/Modules/Core/Common/include/itkImageToImageFilter.h b/Modules/Core/Common/include/itkImageToImageFilter.h index dd13b4277c1..ddf00106642 100644 --- a/Modules/Core/Common/include/itkImageToImageFilter.h +++ b/Modules/Core/Common/include/itkImageToImageFilter.h @@ -186,17 +186,19 @@ class ITK_TEMPLATE_EXPORT ImageToImageFilter * by the input images. ITK has a requirement that multiple input * images be congruent in space by default. */ + /** @ITKStartGrouping */ itkSetMacro(CoordinateTolerance, double); itkGetConstMacro(CoordinateTolerance, double); - + /** @ITKEndGrouping */ /** get/set the direction tolerance * This tolerance is used to make sure that all input * images are oriented the same before performing the filter's * transformations. */ + /** @ITKStartGrouping */ itkSetMacro(DirectionTolerance, double); itkGetConstMacro(DirectionTolerance, double); - + /** @ITKEndGrouping */ /** get/set the global default direction tolerance * * This value is used to initialize the DirectionTolerance upon @@ -362,9 +364,10 @@ class ITK_TEMPLATE_EXPORT ImageToImageFilter * the versions from ProcessObject to avoid warnings about hiding * methods from the superclass. */ + /** @ITKStartGrouping */ using Superclass::PushBackInput; using Superclass::PushFrontInput; - + /** @ITKEndGrouping */ private: /** * Tolerances for checking whether input images are defined to diff --git a/Modules/Core/Common/include/itkImageToImageFilterDetail.h b/Modules/Core/Common/include/itkImageToImageFilterDetail.h index 0a2873c0acf..a722cf78d89 100644 --- a/Modules/Core/Common/include/itkImageToImageFilterDetail.h +++ b/Modules/Core/Common/include/itkImageToImageFilterDetail.h @@ -43,6 +43,7 @@ namespace itk */ namespace ImageToImageFilterDetail { + /** \struct DispatchBase * \brief Base class for a class used to dispatch to dimension specific implementations. * diff --git a/Modules/Core/Common/include/itkImportImageContainer.h b/Modules/Core/Common/include/itkImportImageContainer.h index 90f25ab04b8..38894c6294c 100644 --- a/Modules/Core/Common/include/itkImportImageContainer.h +++ b/Modules/Core/Common/include/itkImportImageContainer.h @@ -155,10 +155,11 @@ class ITK_TEMPLATE_EXPORT ImportImageContainer : public Object * Note that the normal logic of this class set the value of the boolean * flag. This may override your setting if you call this methods prematurely. * \warning Improper use of these methods will result in memory leaks */ + /** @ITKStartGrouping */ itkSetMacro(ContainerManageMemory, bool); itkGetConstMacro(ContainerManageMemory, bool); itkBooleanMacro(ContainerManageMemory); - + /** @ITKEndGrouping */ protected: ImportImageContainer() = default; ~ImportImageContainer() override; diff --git a/Modules/Core/Common/include/itkImportImageFilter.h b/Modules/Core/Common/include/itkImportImageFilter.h index bd1c3135f33..c35c5251f74 100644 --- a/Modules/Core/Common/include/itkImportImageFilter.h +++ b/Modules/Core/Common/include/itkImportImageFilter.h @@ -117,16 +117,18 @@ class ITK_TEMPLATE_EXPORT ImportImageFilter : public ImageSource; /** Set the direction of the image diff --git a/Modules/Core/Common/include/itkInPlaceImageFilter.h b/Modules/Core/Common/include/itkInPlaceImageFilter.h index df1f8c1f27c..79d296c572e 100644 --- a/Modules/Core/Common/include/itkInPlaceImageFilter.h +++ b/Modules/Core/Common/include/itkInPlaceImageFilter.h @@ -110,10 +110,11 @@ class ITK_TEMPLATE_EXPORT InPlaceImageFilter : public ImageToImageFilter Pointer \ { \ @@ -340,6 +342,7 @@ namespace itk * UnRegister() on the rawPtr to compensate for LightObject's constructor * initializing an object's reference count to 1 (needed for proper * initialization of process objects and data objects cycles). */ +/** @ITKStartGrouping */ #define itkFactorylessNewMacro(x) \ static Pointer New() \ { \ @@ -350,7 +353,7 @@ namespace itk } \ itkCreateAnotherMacro(x); \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ // // A macro to disallow the copy constructor, copy assignment, // move constructor, and move assignment functions. @@ -381,12 +384,13 @@ user-declared destructor [-Wdeprecated]" (Mac10.13-AppleClang) - "warning C5267: definition of implicit copy constructor for '' is deprecated because it has a user-provided destructor." (Visual Studio 2022/MSVC) Intended to be used in the public section of a class. */ +/** @ITKStartGrouping */ #define ITK_DEFAULT_COPY_AND_MOVE(TypeName) \ TypeName(const TypeName &) = default; \ TypeName & operator=(const TypeName &) = default; \ TypeName(TypeName &&) = default; \ TypeName & operator=(TypeName &&) = default - +/** @ITKEndGrouping */ // When ITK_EXPERIMENTAL_CXX20_REWRITTEN_UNEQUAL_OPERATOR is defined, ITK uses // the ability for operator!= to be rewritten automatically in terms of @@ -459,6 +463,7 @@ namespace itk * OutputWindow::GetInstance()->DisplayText(); * This is to avoid Object \#include of OutputWindow * while OutputWindow \#includes Object. */ +/** @ITKStartGrouping */ extern ITKCommon_EXPORT void OutputWindowDisplayText(const char *); @@ -473,6 +478,7 @@ OutputWindowDisplayGenericOutputText(const char *); extern ITKCommon_EXPORT void OutputWindowDisplayDebugText(const char *); +/** @ITKEndGrouping */ } // end namespace itk @@ -481,6 +487,7 @@ OutputWindowDisplayDebugText(const char *); * also used to catch errors, etc. Requires that the caller implements * the GetDebug() method (see itk::Object). Example usage looks like: * itkDebugMacro("this is debug info" << this->SomeVariable); */ +/** @ITKStartGrouping */ #if defined(NDEBUG) # define itkDebugMacro(x) ITK_NOOP_STATEMENT # define itkDebugStatement(x) ITK_NOOP_STATEMENT @@ -501,7 +508,7 @@ OutputWindowDisplayDebugText(const char *); // used in the itkDebugMacro # define itkDebugStatement(x) x #endif - +/** @ITKEndGrouping */ /** This macro is used to print warning information (i.e., unusual circumstance * but not necessarily fatal.) Example usage looks like: * itkWarningMacro("this is warning info" << this->SomeVariable); */ @@ -838,6 +845,7 @@ compilers. #endif /** Set an input. This defines the Set"name"() method */ +/** @ITKStartGrouping */ #define itkSetInputMacro(name, type) \ virtual void Set##name(const type * _arg) \ { \ @@ -849,8 +857,9 @@ compilers. } \ } \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ /** Get an input. This defines the Get"name"() method */ +/** @ITKStartGrouping */ #define itkGetInputMacro(name, type) \ virtual const type * Get##name() const \ { \ @@ -858,9 +867,10 @@ compilers. return itkDynamicCastInDebugMode(this->ProcessObject::GetInput(#name)); \ } \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ // clang-format off /** Set a decorated input. This defines the Set"name"() and a Set"name"Input() method */ +/** @ITKStartGrouping */ #define itkSetDecoratedInputMacro(name, type) \ virtual void Set## name## Input(const SimpleDataObjectDecorator * _arg) \ { \ @@ -891,8 +901,9 @@ compilers. } \ ITK_MACROEND_NOOP_STATEMENT // clang-format on - +/** @ITKEndGrouping */ /** Set a decorated input. This defines the Set"name"() and Set"name"Input() method */ +/** @ITKStartGrouping */ #define itkGetDecoratedInputMacro(name, type) \ virtual const SimpleDataObjectDecorator * Get##name##Input() const \ { \ @@ -912,7 +923,7 @@ compilers. return input->Get(); \ } \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ /** Set a decorated input. This defines the Set"name"() and Set"name"Input() method * and Get"name" and Get"name"Input methods */ #define itkSetGetDecoratedInputMacro(name, type) \ @@ -923,6 +934,7 @@ compilers. * itk::DataObject. This defines the Set"name"() and Set"name"Input * methods. */ +/** @ITKStartGrouping */ #define itkSetDecoratedObjectInputMacro(name, type) \ virtual void Set##name##Input(const DataObjectDecorator * _arg) \ { \ @@ -948,11 +960,12 @@ compilers. this->Set##name##Input(newInput); \ } \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ /** Get a decorated input that derives from itk::Object, but not from * itk::DataObject. This defines the Get"name"() and Get"name"Input * methods. */ +/** @ITKStartGrouping */ #define itkGetDecoratedObjectInputMacro(name, type) \ virtual const DataObjectDecorator * Get##name##Input() const \ { \ @@ -972,7 +985,7 @@ compilers. return input->Get(); \ } \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ /** Set a decorated input. This defines the Set"name"() and Set"name"Input() method * and Get"name" and Get"name"Input methods */ #define itkSetGetDecoratedObjectInputMacro(name, type) \ @@ -996,30 +1009,35 @@ compilers. } \ ITK_MACROEND_NOOP_STATEMENT // clang-format on + /** Get built-in type. Creates member Get"name"() (e.g., GetVisibility()); */ +/** @ITKStartGrouping */ #define itkGetMacro(name, type) \ virtual type Get##name() { return this->m_##name; } \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ /** Get built-in type. Creates member Get"name"() (e.g., GetVisibility()); * This is the "const" form of the itkGetMacro. It should be used unless * the member can be changed through the "Get" access routine. */ +/** @ITKStartGrouping */ #define itkGetConstMacro(name, type) \ virtual type Get##name() const { return this->m_##name; } \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ /** Get built-in type. Creates member Get"name"() (e.g., GetVisibility()); * This is the "const" form of the itkGetMacro. It should be used unless * the member can be changed through the "Get" access routine. * This versions returns a const reference to the variable. */ +/** @ITKStartGrouping */ #define itkGetConstReferenceMacro(name, type) \ virtual const type & Get##name() const { return this->m_##name; } \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ /** Set built-in type. Creates member Set"name"() (e.g., SetVisibility()); * This should be used when the type is an enum. It is used to avoid warnings on * some compilers with non specified enum types passed to * itkDebugMacro. */ +/** @ITKStartGrouping */ #define itkSetEnumMacro(name, type) \ virtual void Set##name(const type _arg) \ { \ @@ -1031,18 +1049,20 @@ compilers. } \ } \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ /** Get built-in type. Creates member Get"name"() (e.g., GetVisibility()); * This should be use when the type is an enum. It is use to avoid warnings on * some compilers with non specified enum types passed to * itkDebugMacro. */ +/** @ITKStartGrouping */ #define itkGetEnumMacro(name, type) \ virtual type Get##name() const { return this->m_##name; } \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ /** Set character string. Creates member Set"name"() * (e.g., SetFilename(char *)). The macro assumes that * the class member (name) is declared a type std::string. */ +/** @ITKStartGrouping */ #define itkSetStringMacro(name) \ virtual void Set##name(const char * _arg) \ { \ @@ -1062,7 +1082,7 @@ compilers. } \ virtual void Set##name(const std::string & _arg) { this->Set##name(_arg.c_str()); } \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ /** Get character string. Creates member Get"name"() * (e.g., SetFilename(char *)). The macro assumes that @@ -1075,6 +1095,7 @@ compilers. /** Set built-in type where value is constrained between min/max limits. * Create member Set"name"() (e.q., SetRadius()). \#defines are * convenience for clamping open-ended values. */ +/** @ITKStartGrouping */ #define itkSetClampMacro(name, type, min, max) \ virtual void Set## name(type _arg) \ { \ @@ -1091,11 +1112,12 @@ compilers. } \ ITK_MACROEND_NOOP_STATEMENT // clang-format on - +/** @ITKEndGrouping */ // clang-format off /** Set pointer to object; uses Object reference counting methodology. * Creates method Set"name"() (e.g., SetPoints()). Note that using * smart pointers requires using raw pointers when setting input. */ +/** @ITKStartGrouping */ #define itkSetObjectMacro(name, type) \ virtual void Set## name(type * _arg) \ { \ @@ -1108,7 +1130,7 @@ compilers. } \ ITK_MACROEND_NOOP_STATEMENT // clang-format on - +/** @ITKEndGrouping */ /** Get a raw pointer to an object. Creates the member * Get"name"() (e.g., GetPoints()). * NOTE: This function returns a non-const @@ -1159,6 +1181,7 @@ compilers. #else // defined ( ITK_FUTURE_LEGACY_REMOVE ) /** Get a raw pointer to an object. Creates the member * Get"name"() (e.g., GetPoints()). */ +/** @ITKStartGrouping */ # define itkGetObjectMacro(name, type) \ virtual type * Get##name() { return this->m_##name.GetPointer(); } \ ITK_MACROEND_NOOP_STATEMENT @@ -1166,6 +1189,7 @@ compilers. virtual type * GetModifiable##name() { return this->m_##name.GetPointer(); } \ itkGetConstObjectMacro(name, type); \ itkGetObjectMacro(name, type) +/** @ITKEndGrouping */ #endif // defined ( ITK_FUTURE_LEGACY_REMOVE ) // For backwards compatibility define ITK_EXPORT to nothing @@ -1181,6 +1205,7 @@ compilers. /** Set const pointer to object; uses Object reference counting methodology. * Creates method Set"name"() (e.g., SetPoints()). Note that using * smart pointers requires using raw pointers when setting input. */ +/** @ITKStartGrouping */ #define itkSetConstObjectMacro(name, type) \ virtual void Set##name(const type * _arg) \ { \ @@ -1192,14 +1217,15 @@ compilers. } \ } \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ /** Create members "name"On() and "name"Off() (e.g., DebugOn() DebugOff()). * Set method must be defined to use this macro. */ +/** @ITKStartGrouping */ #define itkBooleanMacro(name) \ virtual void name##On() { this->Set##name(true); } \ virtual void name##Off() { this->Set##name(false); } \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ /** * \brief A utility function to encapsulate a commonly used paradigm @@ -1259,6 +1285,7 @@ ContainerCopyWithCheck(MemberContainerType & m, const CopyFromContainerType & c, /** General set vector macro creates a single method that copies specified * number of values into object. * Examples: void SetColor(c,3) */ +/** @ITKStartGrouping */ #define itkSetVectorMacro(name, type, count) \ virtual void Set## name(type data[]) \ { \ @@ -1269,7 +1296,7 @@ ContainerCopyWithCheck(MemberContainerType & m, const CopyFromContainerType & c, } \ ITK_MACROEND_NOOP_STATEMENT // clang-format on - +/** @ITKEndGrouping */ /** Get vector macro. Returns pointer to type (i.e., array of type). * This is for efficiency. */ #define itkGetVectorMacro(name, type, count) \ @@ -1287,6 +1314,7 @@ ContainerCopyWithCheck(MemberContainerType & m, const CopyFromContainerType & c, * then without adding the `class` keyword. Useful when an export specifier * needs to be added between the `class` keyword and the class name. */ +/** @ITKStartGrouping */ #define itkGPUKernelMacro(kernel) \ kernel \ { \ @@ -1296,7 +1324,7 @@ ContainerCopyWithCheck(MemberContainerType & m, const CopyFromContainerType & c, ~kernel() = delete; \ static const char * GetOpenCLSource(); \ } - +/** @ITKEndGrouping */ #define itkGetOpenCLSourceFromKernelMacro(kernel) \ static const char * GetOpenCLSource() { return kernel::GetOpenCLSource(); } \ ITK_MACROEND_NOOP_STATEMENT @@ -1324,6 +1352,7 @@ ContainerCopyWithCheck(MemberContainerType & m, const CopyFromContainerType & c, /** Set a decorated output. This defines the Set"name"() and a Set"name"Output() method */ +/** @ITKStartGrouping */ #define itkSetDecoratedOutputMacro(name, type) \ virtual void Set##name##Output(const SimpleDataObjectDecorator * _arg) \ { \ @@ -1358,8 +1387,9 @@ ContainerCopyWithCheck(MemberContainerType & m, const CopyFromContainerType & c, } \ } \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ /** Set a decorated output. This defines the Get"name"() and Get"name"Output() method */ +/** @ITKStartGrouping */ #define itkGetDecoratedOutputMacro(name, type) \ virtual const SimpleDataObjectDecorator * Get##name##Output() const \ { \ @@ -1379,7 +1409,7 @@ ContainerCopyWithCheck(MemberContainerType & m, const CopyFromContainerType & c, return output->Get(); \ } \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ // ITK_FUTURE_DEPRECATED is only for internal use, within the implementation of ITK. It allows triggering "deprecated" // warnings when legacy support is removed, which warn that a specific feature may be removed in the future. #if defined(ITK_LEGACY_REMOVE) && !defined(ITK_LEGACY_SILENT) diff --git a/Modules/Core/Common/include/itkMapContainer.h b/Modules/Core/Common/include/itkMapContainer.h index abb66e2545d..1d550ef0ac6 100644 --- a/Modules/Core/Common/include/itkMapContainer.h +++ b/Modules/Core/Common/include/itkMapContainer.h @@ -73,6 +73,7 @@ class ITK_TEMPLATE_EXPORT MapContainer /** Provide pass-through constructors corresponding to all the STL * map constructors. These are for internal use only since this is also * an Object which must be constructed through the "New()" routine. */ + /** @ITKStartGrouping */ MapContainer() : MapType() {} @@ -88,7 +89,7 @@ class ITK_TEMPLATE_EXPORT MapContainer MapContainer(TInputIterator first, TInputIterator last, const MapKeyCompareType & comp) : MapType(first, last, comp) {} - + /** @ITKEndGrouping */ /** Method for creation through the object factory. */ itkNewMacro(Self); diff --git a/Modules/Core/Common/include/itkMath.h b/Modules/Core/Common/include/itkMath.h index 2f4a87123c2..7f396de8ef9 100644 --- a/Modules/Core/Common/include/itkMath.h +++ b/Modules/Core/Common/include/itkMath.h @@ -737,6 +737,7 @@ NotExactlyEquals(const TInput1 & x1, const TInput2 & x2) * * \note Negative numbers cannot be prime. */ +/** @ITKStartGrouping */ ITKCommon_EXPORT bool IsPrime(unsigned short n); ITKCommon_EXPORT bool @@ -745,9 +746,10 @@ ITKCommon_EXPORT bool IsPrime(unsigned long n); ITKCommon_EXPORT bool IsPrime(unsigned long long n); - +/** @ITKEndGrouping */ /** Return the greatest factor of the decomposition in prime numbers. */ +/** @ITKStartGrouping */ ITKCommon_EXPORT unsigned short GreatestPrimeFactor(unsigned short n); ITKCommon_EXPORT unsigned int @@ -756,7 +758,7 @@ ITKCommon_EXPORT unsigned long GreatestPrimeFactor(unsigned long n); ITKCommon_EXPORT unsigned long long GreatestPrimeFactor(unsigned long long n); - +/** @ITKEndGrouping */ /** Returns `a * b`. Numeric overflow triggers a compilation error in * "constexpr context" and a debug assert failure at run-time. diff --git a/Modules/Core/Common/include/itkMersenneTwisterRandomVariateGenerator.h b/Modules/Core/Common/include/itkMersenneTwisterRandomVariateGenerator.h index 53a06585003..381ecbeab98 100644 --- a/Modules/Core/Common/include/itkMersenneTwisterRandomVariateGenerator.h +++ b/Modules/Core/Common/include/itkMersenneTwisterRandomVariateGenerator.h @@ -236,11 +236,12 @@ class ITKCommon_EXPORT MersenneTwisterRandomVariateGenerator : public RandomVari * * \note This method is thread-safe. */ + /** @ITKStartGrouping */ inline void SetSeed(const IntegerType oneSeed); inline void SetSeed(); - + /** @ITKEndGrouping */ /** Return the current seed * * \note This method is thread-safe. diff --git a/Modules/Core/Common/include/itkMetaDataDictionary.h b/Modules/Core/Common/include/itkMetaDataDictionary.h index 28fb47938f9..c0681ac72ae 100644 --- a/Modules/Core/Common/include/itkMetaDataDictionary.h +++ b/Modules/Core/Common/include/itkMetaDataDictionary.h @@ -145,21 +145,23 @@ class ITKCommon_EXPORT MetaDataDictionary * context cannot be dereferenced safely */ /** Returns an iterator to the beginning of the map */ + /** @ITKStartGrouping */ // Blacklisted by igenerator.py Iterator Begin(); // Blacklisted by igenerator.py ConstIterator Begin() const; - + /** @ITKEndGrouping */ /** Returns an iterator to the end of the map */ + /** @ITKStartGrouping */ // Blacklisted by igenerator.py Iterator End(); // Blacklisted by igenerator.py ConstIterator End() const; - + /** @ITKEndGrouping */ /** Returns an iterator matching the string key */ Iterator Find(const std::string & key); diff --git a/Modules/Core/Common/include/itkMultiThreaderBase.h b/Modules/Core/Common/include/itkMultiThreaderBase.h index 4af5bf37ceb..6dd4908f02d 100644 --- a/Modules/Core/Common/include/itkMultiThreaderBase.h +++ b/Modules/Core/Common/include/itkMultiThreaderBase.h @@ -124,17 +124,19 @@ class ITKCommon_EXPORT MultiThreaderBase : public Object /** Get/Set the number of threads to use. It will be clamped to the range * [ 1, m_GlobalMaximumNumberOfThreads ], so the caller of this method should * check that the requested number of threads was accepted. */ + /** @ITKStartGrouping */ virtual void SetMaximumNumberOfThreads(ThreadIdType numberOfThreads); itkGetConstMacro(MaximumNumberOfThreads, ThreadIdType); - + /** @ITKEndGrouping */ /** Get/Set the number of work units to create. It might be clamped to the range * [ 1, SomeMaximumNumber ], so the caller of this method should * check that the requested number of work units was accepted. */ + /** @ITKStartGrouping */ virtual void SetNumberOfWorkUnits(ThreadIdType numberOfWorkUnits); itkGetConstMacro(NumberOfWorkUnits, ThreadIdType); - + /** @ITKEndGrouping */ virtual void SetUpdateProgress(bool updates); itkGetConstMacro(UpdateProgress, bool); @@ -144,19 +146,21 @@ class ITKCommon_EXPORT MultiThreaderBase : public Object * are already statically allocated using the ITK_MAX_THREADS number. * Therefore the caller of this method should check that the requested number * of threads was accepted. */ + /** @ITKStartGrouping */ static void SetGlobalMaximumNumberOfThreads(ThreadIdType val); static ThreadIdType GetGlobalMaximumNumberOfThreads(); - + /** @ITKEndGrouping */ /** Set/Get whether to use the to use the thread pool * implementation or the spawning implementation of * starting threads. * * Deprecated: use Get/Set GlobalDefaultThreader. */ + /** @ITKStartGrouping */ itkLegacyMacro(static void SetGlobalDefaultUseThreadPool(const bool GlobalDefaultUseThreadPool);) itkLegacyMacro(static bool GetGlobalDefaultUseThreadPool();) - + /** @ITKEndGrouping */ using ThreaderEnum = MultiThreaderBaseEnums::Threader; #if !defined(ITK_LEGACY_REMOVE) using ThreaderType = ThreaderEnum; @@ -201,23 +205,26 @@ class ITKCommon_EXPORT MultiThreaderBase : public Object * * If the SetGlobalDefaultThreaderType API is ever used by the developer, * the developer's choice is respected over the environment variables. */ + /** @ITKStartGrouping */ static void SetGlobalDefaultThreader(ThreaderEnum threaderType); static ThreaderEnum GetGlobalDefaultThreader(); - + /** @ITKEndGrouping */ /** Set/Get the value which is used to initialize the NumberOfThreads in the * constructor. It will be clamped to the range [1, m_GlobalMaximumNumberOfThreads ]. * Therefore the caller of this method should check that the requested number * of threads was accepted. */ + /** @ITKStartGrouping */ static void SetGlobalDefaultNumberOfThreads(ThreadIdType val); static ThreadIdType GetGlobalDefaultNumberOfThreads(); - + /** @ITKEndGrouping */ #if !defined(ITK_LEGACY_REMOVE) /** Get/Set the number of threads to use. * DEPRECATED! Use WorkUnits and MaximumNumberOfThreads instead. */ + /** @ITKStartGrouping */ itkLegacyMacro(virtual void SetNumberOfThreads(ThreadIdType numberOfThreads)) { this->SetMaximumNumberOfThreads(numberOfThreads); @@ -227,7 +234,7 @@ class ITKCommon_EXPORT MultiThreaderBase : public Object { return this->GetNumberOfWorkUnits(); } - + /** @ITKEndGrouping */ /** This is the structure that is passed to the thread that is * created from the SingleMethodExecute. It is passed in as a void *, * and it is up to the method to cast correctly and extract the information. @@ -236,6 +243,7 @@ class ITKCommon_EXPORT MultiThreaderBase : public Object * (void *)arg passed into the SetSingleMethod. * * DEPRECATED! Use WorkUnitInfo instead. */ + /** @ITKStartGrouping */ // clang-format off ITK_GCC_PRAGMA_DIAG_PUSH() ITK_GCC_PRAGMA_DIAG(ignored "-Wattributes") @@ -267,6 +275,7 @@ INTEL_PRAGMA_WARN_POP // clang-format off ITK_GCC_PRAGMA_DIAG_POP() // clang-format on + /** @ITKEndGrouping */ #endif // ITK_LEGACY_REMOVE /** This is the structure that is passed to the thread that is diff --git a/Modules/Core/Common/include/itkNeighborhood.h b/Modules/Core/Common/include/itkNeighborhood.h index ee71574f423..2c75583de10 100644 --- a/Modules/Core/Common/include/itkNeighborhood.h +++ b/Modules/Core/Common/include/itkNeighborhood.h @@ -164,6 +164,7 @@ class ITK_TEMPLATE_EXPORT Neighborhood } /** STL-style iterator support. */ + /** @ITKStartGrouping */ Iterator End() { @@ -184,6 +185,7 @@ class ITK_TEMPLATE_EXPORT Neighborhood { return m_DataBuffer.begin(); } + /** @ITKEndGrouping */ /** More STL-style support. */ NeighborIndexType @@ -193,6 +195,7 @@ class ITK_TEMPLATE_EXPORT Neighborhood } /** Pass-through data access methods to the buffer. */ + /** @ITKStartGrouping */ TPixel & operator[](NeighborIndexType i) { @@ -208,6 +211,7 @@ class ITK_TEMPLATE_EXPORT Neighborhood { return m_DataBuffer[i]; } + /** @ITKEndGrouping */ /** Returns the element at the center of the neighborhood. */ TPixel @@ -245,6 +249,7 @@ class ITK_TEMPLATE_EXPORT Neighborhood } /** Returns a reference to the data buffer structure. */ + /** @ITKStartGrouping */ AllocatorType & GetBufferReference() { @@ -255,8 +260,10 @@ class ITK_TEMPLATE_EXPORT Neighborhood { return m_DataBuffer; } + /** @ITKEndGrouping */ /** Get pixel value by offset */ + /** @ITKStartGrouping */ TPixel & operator[](const OffsetType & o) { @@ -267,6 +274,7 @@ class ITK_TEMPLATE_EXPORT Neighborhood { return this->operator[](this->GetNeighborhoodIndex(o)); } + /** @ITKEndGrouping */ /** Returns the itk::Offset from the center of the Neighborhood to the requested neighbor index. */ diff --git a/Modules/Core/Common/include/itkNeighborhoodAllocator.h b/Modules/Core/Common/include/itkNeighborhoodAllocator.h index 7e7476ed628..c4d6f362fde 100644 --- a/Modules/Core/Common/include/itkNeighborhoodAllocator.h +++ b/Modules/Core/Common/include/itkNeighborhoodAllocator.h @@ -93,7 +93,6 @@ class NeighborhoodAllocator other.m_ElementCount = 0; } - /** Assignment operator. */ Self & operator=(const Self & other) @@ -106,7 +105,6 @@ class NeighborhoodAllocator return *this; } - /** Move-assignment. */ Self & operator=(Self && other) noexcept @@ -120,8 +118,8 @@ class NeighborhoodAllocator return *this; } - /** STL-style iterator support for the memory buffer. */ + /** @ITKStartGrouping */ iterator begin() { @@ -147,8 +145,10 @@ class NeighborhoodAllocator { return m_ElementCount; } + /** @ITKEndGrouping */ /** Data access methods */ + /** @ITKStartGrouping */ const TPixel & operator[](unsigned int i) const { @@ -159,6 +159,7 @@ class NeighborhoodAllocator { return m_Data[i]; } + /** @ITKEndGrouping */ /** Allocates a buffer of size n */ void diff --git a/Modules/Core/Common/include/itkNumericTraitsStdVector.h b/Modules/Core/Common/include/itkNumericTraitsStdVector.h index db00b3b6601..72226b2520b 100644 --- a/Modules/Core/Common/include/itkNumericTraitsStdVector.h +++ b/Modules/Core/Common/include/itkNumericTraitsStdVector.h @@ -96,6 +96,7 @@ class NumericTraits> * \note minimum value for floating pointer types is defined as * minimum positive normalize value. */ + /** @ITKStartGrouping */ static const Self max(const Self & a) { @@ -130,6 +131,7 @@ class NumericTraits> Self b(a.Size(), NumericTraits::NonpositiveMin()); return b; } + /** @ITKEndGrouping */ static constexpr bool IsSigned = std::is_signed_v; static constexpr bool IsInteger = std::is_integral_v; diff --git a/Modules/Core/Common/include/itkObject.h b/Modules/Core/Common/include/itkObject.h index 9c29a6f3977..d5a1fb3852e 100644 --- a/Modules/Core/Common/include/itkObject.h +++ b/Modules/Core/Common/include/itkObject.h @@ -223,11 +223,12 @@ class ITKCommon_EXPORT Object : public LightObject /** * Set the MetaDataDictionary */ + /** @ITKStartGrouping */ void SetMetaDataDictionary(const MetaDataDictionary & rhs); void SetMetaDataDictionary(MetaDataDictionary && rrhs); - + /** @ITKEndGrouping */ /** * A facility to help application programmers set a * human identifiable name for a given object. @@ -235,9 +236,10 @@ class ITKCommon_EXPORT Object : public LightObject * convenience to allow developers to provide a * name for this object. */ + /** @ITKStartGrouping */ itkSetMacro(ObjectName, std::string); itkGetConstReferenceMacro(ObjectName, std::string); - + /** @ITKEndGrouping */ protected: Object(); ~Object() override; diff --git a/Modules/Core/Common/include/itkObjectFactoryBase.h b/Modules/Core/Common/include/itkObjectFactoryBase.h index f45afed5758..f2f53a2bdaf 100644 --- a/Modules/Core/Common/include/itkObjectFactoryBase.h +++ b/Modules/Core/Common/include/itkObjectFactoryBase.h @@ -161,6 +161,7 @@ class ITKCommon_EXPORT ObjectFactoryBase : public Object * versions do not match, an exception will be thrown. When this is false, and * the versions do not match, only a warning message is printed out in the * console, and the factory is still registered. */ + /** @ITKStartGrouping */ static void SetStrictVersionChecking(bool); static void @@ -169,7 +170,7 @@ class ITKCommon_EXPORT ObjectFactoryBase : public Object StrictVersionCheckingOff(); static bool GetStrictVersionChecking(); - + /** @ITKEndGrouping */ /** Return a descriptive string describing the factory. */ virtual const char * GetDescription() const = 0; @@ -262,10 +263,11 @@ class ITKCommon_EXPORT ObjectFactoryBase : public Object /** Set/Get the pointer to ObjectFactoryBasePrivate. * No concurrent thread safe. */ + /** @ITKStartGrouping */ static void SynchronizeObjectFactoryBase(void * objectFactoryBasePrivate); itkGetGlobalDeclarationMacro(ObjectFactoryBasePrivate, PimplGlobals); - + /** @ITKEndGrouping */ const std::unique_ptr m_OverrideMap; /** Load dynamic factories from the ITK_AUTOLOAD_PATH */ diff --git a/Modules/Core/Common/include/itkObjectStore.h b/Modules/Core/Common/include/itkObjectStore.h index 2cd29e891a1..f2a084b8534 100644 --- a/Modules/Core/Common/include/itkObjectStore.h +++ b/Modules/Core/Common/include/itkObjectStore.h @@ -141,13 +141,15 @@ class ITK_TEMPLATE_EXPORT ObjectStore : public Object Clear(); /** Set/Get the linear growth size */ + /** @ITKStartGrouping */ itkSetMacro(LinearGrowthSize, SizeValueType); itkGetConstMacro(LinearGrowthSize, SizeValueType); - + /** @ITKEndGrouping */ /** Set/Get the growth strategy. */ + /** @ITKStartGrouping */ itkSetEnumMacro(GrowthStrategy, GrowthStrategyEnum); itkGetConstMacro(GrowthStrategy, GrowthStrategyEnum); - + /** @ITKEndGrouping */ /** Set growth strategy to exponential */ void SetGrowthStrategyToExponential() diff --git a/Modules/Core/Common/include/itkOctree.h b/Modules/Core/Common/include/itkOctree.h index faa596ea5c9..d47e918934e 100644 --- a/Modules/Core/Common/include/itkOctree.h +++ b/Modules/Core/Common/include/itkOctree.h @@ -135,6 +135,7 @@ class ITK_TEMPLATE_EXPORT Octree : public OctreeBase using Pointer = SmartPointer; using ImageType = Image; using ImageTypePointer = typename ImageType::Pointer; + /** Method for creation through the object factory. */ itkNewMacro(Self); @@ -183,15 +184,17 @@ class ITK_TEMPLATE_EXPORT Octree : public OctreeBase unsigned int GetDepth() override; +#if !defined(ITK_LEGACY_REMOVE) /*** * Exposes enum values for backwards compatibility * */ -#if !defined(ITK_LEGACY_REMOVE) + /** @ITKStartGrouping */ static constexpr OctreeEnum UNKNOWN_PLANE = OctreeEnum::UNKNOWN_PLANE; static constexpr OctreeEnum SAGITTAL_PLANE = OctreeEnum::SAGITTAL_PLANE; [[deprecated("Use SAGITTAL_PLANE instead")]] static constexpr OctreeEnum SAGITAL_PLANE = OctreeEnum::SAGITTAL_PLANE; static constexpr OctreeEnum CORONAL_PLANE = OctreeEnum::CORONAL_PLANE; static constexpr OctreeEnum TRANSVERSE_PLANE = OctreeEnum::TRANSVERSE_PLANE; + /** @ITKEndGrouping */ #endif OctreeNode * diff --git a/Modules/Core/Common/include/itkOctree.hxx b/Modules/Core/Common/include/itkOctree.hxx index 5647696033b..dbab7a3854c 100644 --- a/Modules/Core/Common/include/itkOctree.hxx +++ b/Modules/Core/Common/include/itkOctree.hxx @@ -87,7 +87,7 @@ OCTREE_OCTANT(const unsigned int VoxX, * \defgroup Octant directional identifying functions * These functions determine if the directions are in the "lower" or * "upper" portion of the Octree in the given directions. - * @{ + * @ITKStartGrouping */ inline unsigned int XF(const unsigned int octantID) @@ -107,7 +107,7 @@ ZF(const unsigned int octantID) return (octantID >> 2) & 1; // Just return 1 if 2nd bit is a one } -/** @} */ // End of defgroup +/** @ITKEndGrouping */ // End of defgroup template int diff --git a/Modules/Core/Common/include/itkOctreeNode.h b/Modules/Core/Common/include/itkOctreeNode.h index 0202f1cbb1b..6cd6f328d56 100644 --- a/Modules/Core/Common/include/itkOctreeNode.h +++ b/Modules/Core/Common/include/itkOctreeNode.h @@ -77,15 +77,14 @@ class ITKCommon_EXPORT OctreeNode * \param ChildID The numerical identifier of the desired child. * \return A pointer to the Desired child. NOTE: This is always an * instance of an OctreeNode. - * @{ + * @ITKStartGrouping */ OctreeNode & GetChild(const LeafIdentifierEnum ChildID) const; OctreeNode & GetChild(const LeafIdentifierEnum ChildID); - /** @} - */ + /** @ITKEndGrouping */ /** * Determines the color value of the specified Child for this OctreeNode diff --git a/Modules/Core/Common/include/itkOffset.h b/Modules/Core/Common/include/itkOffset.h index d4617945382..605fee89ee2 100644 --- a/Modules/Core/Common/include/itkOffset.h +++ b/Modules/Core/Common/include/itkOffset.h @@ -170,7 +170,6 @@ struct ITK_TEMPLATE_EXPORT Offset final return *this; } - /** Get the offset. This provides a read only pointer to the offset. * \sa SetOffset() */ const OffsetValueType * diff --git a/Modules/Core/Common/include/itkOptimizerParameters.h b/Modules/Core/Common/include/itkOptimizerParameters.h index 2139b9606cf..e285507f658 100644 --- a/Modules/Core/Common/include/itkOptimizerParameters.h +++ b/Modules/Core/Common/include/itkOptimizerParameters.h @@ -154,6 +154,7 @@ class ITK_TEMPLATE_EXPORT OptimizerParameters : public ArrayArrayType::operator=(rhs); return *this; } + /** @ITKEndGrouping */ ~OptimizerParameters() override = default; diff --git a/Modules/Core/Common/include/itkOrientationAdapterBase.h b/Modules/Core/Common/include/itkOrientationAdapterBase.h index 52c64ae2652..7e7ad026e82 100644 --- a/Modules/Core/Common/include/itkOrientationAdapterBase.h +++ b/Modules/Core/Common/include/itkOrientationAdapterBase.h @@ -63,7 +63,9 @@ class ITK_TEMPLATE_EXPORT [[deprecated("Since ITK 5.3 use SpatialOrientationAdap protected: /** destructor, to silence "virtual class has non-virtual destructor()" warnings */ + /** @ITKStartGrouping */ virtual ~OrientationAdapterBase() = default; + /** @ITKEndGrouping */ }; } // namespace itk #else // ITK_LEGACY_REMOVE diff --git a/Modules/Core/Common/include/itkOutputWindow.h b/Modules/Core/Common/include/itkOutputWindow.h index 8afd0ed7b11..22095c625fa 100644 --- a/Modules/Core/Common/include/itkOutputWindow.h +++ b/Modules/Core/Common/include/itkOutputWindow.h @@ -121,10 +121,11 @@ class ITKCommon_EXPORT OutputWindow : public Object /** If PromptUser is set to true then each time a line of text * is displayed, the user is asked if they want to keep getting * messages. */ + /** @ITKStartGrouping */ itkSetMacro(PromptUser, bool); itkGetConstMacro(PromptUser, bool); itkBooleanMacro(PromptUser); - + /** @ITKEndGrouping */ protected: OutputWindow(); ~OutputWindow() override; diff --git a/Modules/Core/Common/include/itkPlatformMultiThreader.h b/Modules/Core/Common/include/itkPlatformMultiThreader.h index 75ee19088c0..ee0f78f49e4 100644 --- a/Modules/Core/Common/include/itkPlatformMultiThreader.h +++ b/Modules/Core/Common/include/itkPlatformMultiThreader.h @@ -70,6 +70,7 @@ class ITKCommon_EXPORT PlatformMultiThreader : public MultiThreaderBase * are already statically allocated using the ITK_MAX_THREADS number. * Therefore the caller of this method should check that the requested number * of threads was accepted. Legacy: use MultiThreaderBase to invoke these. */ + /** @ITKStartGrouping */ itkLegacyMacro(static void SetGlobalMaximumNumberOfThreads(ThreadIdType val)) { itkGenericOutputMacro("Warning: SetGlobalMaximumNumberOfThreads should now be called on itk::MultiThreaderBase. It " @@ -82,11 +83,13 @@ class ITKCommon_EXPORT PlatformMultiThreader : public MultiThreaderBase "can affect all MultiThreaderBase's derived classes in ITK"); return Superclass::GetGlobalMaximumNumberOfThreads(); } + /** @ITKEndGrouping */ /** Set/Get the value which is used to initialize the NumberOfThreads in the * constructor. It will be clamped to the range [1, m_GlobalMaximumNumberOfThreads ]. * Therefore the caller of this method should check that the requested number * of threads was accepted. Legacy: use MultiThreaderBase to invoke these. */ + /** @ITKStartGrouping */ itkLegacyMacro(static void SetGlobalDefaultNumberOfThreads(ThreadIdType val)) { itkGenericOutputMacro("Warning: SetGlobalDefaultNumberOfThreads should now be called on itk::MultiThreaderBase. It " @@ -99,6 +102,7 @@ class ITKCommon_EXPORT PlatformMultiThreader : public MultiThreaderBase "can affect all MultiThreaderBase's derived classes in ITK"); return Superclass::GetGlobalDefaultNumberOfThreads(); } + /** @ITKEndGrouping */ #endif /** Execute the SingleMethod (as define by SetSingleMethod) using @@ -177,6 +181,7 @@ class ITKCommon_EXPORT PlatformMultiThreader : public MultiThreaderBase /** spawn a new thread for the SingleMethod */ ThreadProcessIdType SpawnDispatchSingleMethodThread(WorkUnitInfo *); + /** wait for a thread in the threadpool to finish work */ void SpawnWaitForSingleMethodThread(ThreadProcessIdType); diff --git a/Modules/Core/Common/include/itkPoint.h b/Modules/Core/Common/include/itkPoint.h index 3af2661fae5..e6570b8ae94 100644 --- a/Modules/Core/Common/include/itkPoint.h +++ b/Modules/Core/Common/include/itkPoint.h @@ -95,7 +95,9 @@ class ITK_TEMPLATE_EXPORT Point : public FixedArray & r) : BaseArray(r) {} + /** Pass-through constructors for plain arrays. */ + /** @ITKStartGrouping */ template Point(const TPointValueType r[VPointDimension]) : BaseArray(r) @@ -103,7 +105,7 @@ class ITK_TEMPLATE_EXPORT Point : public FixedArray diff --git a/Modules/Core/Common/include/itkPointSet.h b/Modules/Core/Common/include/itkPointSet.h index 05e2040675a..00ebff06184 100644 --- a/Modules/Core/Common/include/itkPointSet.h +++ b/Modules/Core/Common/include/itkPointSet.h @@ -157,11 +157,12 @@ class ITK_TEMPLATE_EXPORT PointSet : public PointSetBaseBuildEdges(); } - + /** @ITKEndGrouping */ ~PolygonCell() override = default; protected: diff --git a/Modules/Core/Common/include/itkProcessObject.h b/Modules/Core/Common/include/itkProcessObject.h index 83a0d1564d2..aa5a909a501 100644 --- a/Modules/Core/Common/include/itkProcessObject.h +++ b/Modules/Core/Common/include/itkProcessObject.h @@ -164,7 +164,7 @@ class ITKCommon_EXPORT ProcessObject : public Object /** STL array of data object names */ using NameArray = std::vector; - //** Type of general multi-threader interface */ + /** Type of general multi-threader interface */ using MultiThreaderType = MultiThreaderBase; /** \brief Return an array with the names of the inputs defined. @@ -459,6 +459,7 @@ class ITKCommon_EXPORT ProcessObject : public Object * used by a downstream ProcessObject. Default value is off. Another * options for controlling memory utilization is the * ReleaseDataBeforeUpdateFlag. */ + /** @ITKStartGrouping */ virtual void SetReleaseDataFlag(bool val); virtual bool @@ -473,6 +474,7 @@ class ITKCommon_EXPORT ProcessObject : public Object { this->SetReleaseDataFlag(false); } + /** @ITKEndGrouping */ /** Turn on/off the flags to control whether the bulk data belonging * to the outputs of this ProcessObject are released/reallocated @@ -486,13 +488,17 @@ class ITKCommon_EXPORT ProcessObject : public Object * ReleaseDataBeforeUpdateFlag manages the deallocation/reallocation * of bulk data during a pipeline update to control peak memory * utilization. Default value is on. */ + /** @ITKStartGrouping */ itkSetMacro(ReleaseDataBeforeUpdateFlag, bool); itkGetConstReferenceMacro(ReleaseDataBeforeUpdateFlag, bool); itkBooleanMacro(ReleaseDataBeforeUpdateFlag); + /** @ITKEndGrouping */ /** Get/Set the number of work units to create when executing. */ + /** @ITKStartGrouping */ itkSetClampMacro(NumberOfWorkUnits, ThreadIdType, 1, ITK_MAX_THREADS); itkGetConstReferenceMacro(NumberOfWorkUnits, ThreadIdType); + /** @ITKEndGrouping */ /** Return the multithreader used by this class. */ MultiThreaderType * @@ -536,6 +542,7 @@ class ITKCommon_EXPORT ProcessObject : public Object /** Method used internally for getting an indexed input. */ + /** @ITKStartGrouping */ DataObject * GetInput(DataObjectPointerArraySizeType idx) { @@ -546,6 +553,7 @@ class ITKCommon_EXPORT ProcessObject : public Object { return idx < m_IndexedInputs.size() ? m_IndexedInputs[idx]->second.GetPointer() : nullptr; } + /** @ITKEndGrouping */ /** \brief Protected method for setting indexed and named inputs. * @@ -590,6 +598,7 @@ class ITKCommon_EXPORT ProcessObject : public Object virtual void RemoveInput(DataObjectPointerArraySizeType); /** Return the main input */ + /** @ITKStartGrouping */ DataObject * GetPrimaryInput() { @@ -600,8 +609,10 @@ class ITKCommon_EXPORT ProcessObject : public Object { return m_IndexedInputs[0]->second; } + /** @ITKEndGrouping */ /** Set/Get the name associated with the Primary input. Defaults to "Primary". */ + /** @ITKStartGrouping */ virtual void SetPrimaryInputName(const DataObjectIdentifierType & key); virtual const char * @@ -609,6 +620,7 @@ class ITKCommon_EXPORT ProcessObject : public Object { return this->m_IndexedInputs[0]->first.c_str(); } + /** @ITKEndGrouping */ /** Set the main input */ virtual void @@ -690,12 +702,15 @@ class ITKCommon_EXPORT ProcessObject : public Object // /** Return an output */ + /** @ITKStartGrouping */ DataObject * GetOutput(const DataObjectIdentifierType & key); const DataObject * GetOutput(const DataObjectIdentifierType & key) const; + /** @ITKEndGrouping */ /** Set/Get the name associated with the Primary output. Defaults to "Primary". */ + /** @ITKStartGrouping */ virtual void SetPrimaryOutputName(const DataObjectIdentifierType & key); virtual const char * @@ -703,12 +718,15 @@ class ITKCommon_EXPORT ProcessObject : public Object { return this->m_IndexedOutputs[0]->first.c_str(); } + /** @ITKEndGrouping */ /** Method used internally for getting an indexed output. */ + /** @ITKStartGrouping */ DataObject * GetOutput(DataObjectPointerArraySizeType i); const DataObject * GetOutput(DataObjectPointerArraySizeType i) const; + /** @ITKEndGrouping */ /** Set an output */ virtual void @@ -719,6 +737,7 @@ class ITKCommon_EXPORT ProcessObject : public Object RemoveOutput(const DataObjectIdentifierType & key); /** Return the main output */ + /** @ITKStartGrouping */ DataObject * GetPrimaryOutput() { @@ -729,6 +748,7 @@ class ITKCommon_EXPORT ProcessObject : public Object { return m_IndexedOutputs[0]->second; } + /** @ITKEndGrouping */ /** Set the main output */ virtual void @@ -846,6 +866,7 @@ class ITKCommon_EXPORT ProcessObject : public Object {} /** Called to allocate the input array. Copies old inputs. */ + /** Propagate a call to ResetPipeline() up the pipeline. Called only from * DataObject. */ virtual void @@ -886,11 +907,12 @@ class ITKCommon_EXPORT ProcessObject : public Object * When true, the MultiThreader will report course grain progress. If set to false, a progress must be explicitly * updated in derived filters. */ + /** @ITKStartGrouping */ itkGetConstMacro(ThreaderUpdateProgress, bool); itkBooleanMacro(ThreaderUpdateProgress); virtual void SetThreaderUpdateProgress(bool arg); - + /** @ITKEndGrouping */ /** * Internal method to convert internal integer progress to float [0.0, 1.0] @@ -920,7 +942,6 @@ class ITKCommon_EXPORT ProcessObject : public Object return static_cast(temp); } - /** Sets the required number of outputs, and creates each of them by MakeOutput. */ template static void diff --git a/Modules/Core/Common/include/itkQuadraticEdgeCell.h b/Modules/Core/Common/include/itkQuadraticEdgeCell.h index 55cb9b48ce2..70a11996406 100644 --- a/Modules/Core/Common/include/itkQuadraticEdgeCell.h +++ b/Modules/Core/Common/include/itkQuadraticEdgeCell.h @@ -38,9 +38,10 @@ class ITK_TEMPLATE_EXPORT QuadraticEdgeCell : public TCellInterface ITK_DISALLOW_COPY_AND_MOVE(QuadraticEdgeCell); /** Standard class type aliases. */ + /** @ITKStartGrouping */ itkCellCommonTypedefs(QuadraticEdgeCell); itkCellInheritedTypedefs(TCellInterface); - + /** @ITKEndGrouping */ /** \see LightObject::GetNameOfClass() */ itkOverrideGetNameOfClassMacro(QuadraticEdgeCell); @@ -54,6 +55,7 @@ class ITK_TEMPLATE_EXPORT QuadraticEdgeCell : public TCellInterface static constexpr unsigned int CellDimension = 1; /** Implement the standard CellInterface. */ + /** @ITKStartGrouping */ CellGeometryEnum GetType() const override { @@ -61,7 +63,7 @@ class ITK_TEMPLATE_EXPORT QuadraticEdgeCell : public TCellInterface } void MakeCopy(CellAutoPointer &) const override; - + /** @ITKEndGrouping */ unsigned int GetDimension() const override; diff --git a/Modules/Core/Common/include/itkQuadraticTriangleCell.h b/Modules/Core/Common/include/itkQuadraticTriangleCell.h index a329fea6096..a0f2d1836a7 100644 --- a/Modules/Core/Common/include/itkQuadraticTriangleCell.h +++ b/Modules/Core/Common/include/itkQuadraticTriangleCell.h @@ -41,9 +41,10 @@ class ITK_TEMPLATE_EXPORT QuadraticTriangleCell ITK_DISALLOW_COPY_AND_MOVE(QuadraticTriangleCell); /** Standard class type aliases. */ + /** @ITKStartGrouping */ itkCellCommonTypedefs(QuadraticTriangleCell); itkCellInheritedTypedefs(TCellInterface); - + /** @ITKEndGrouping */ /** \see LightObject::GetNameOfClass() */ itkOverrideGetNameOfClassMacro(QuadraticTriangleCell); @@ -62,6 +63,7 @@ class ITK_TEMPLATE_EXPORT QuadraticTriangleCell static constexpr unsigned int CellDimension = 2; /** Implement the standard CellInterface. */ + /** @ITKStartGrouping */ CellGeometryEnum GetType() const override { @@ -69,7 +71,7 @@ class ITK_TEMPLATE_EXPORT QuadraticTriangleCell } void MakeCopy(CellAutoPointer &) const override; - + /** @ITKEndGrouping */ unsigned int GetDimension() const override; diff --git a/Modules/Core/Common/include/itkQuadrilateralCell.h b/Modules/Core/Common/include/itkQuadrilateralCell.h index 625fc2d12d1..236f2fcf8bf 100644 --- a/Modules/Core/Common/include/itkQuadrilateralCell.h +++ b/Modules/Core/Common/include/itkQuadrilateralCell.h @@ -42,9 +42,10 @@ class ITK_TEMPLATE_EXPORT QuadrilateralCell ITK_DISALLOW_COPY_AND_MOVE(QuadrilateralCell); /** Standard class type aliases. */ + /** @ITKStartGrouping */ itkCellCommonTypedefs(QuadrilateralCell); itkCellInheritedTypedefs(TCellInterface); - + /** @ITKEndGrouping */ /** \see LightObject::GetNameOfClass() */ itkOverrideGetNameOfClassMacro(QuadrilateralCell); @@ -64,6 +65,7 @@ class ITK_TEMPLATE_EXPORT QuadrilateralCell static constexpr unsigned int NumberOfDerivatives = 8; /** Implement the standard CellInterface. */ + /** @ITKStartGrouping */ CellGeometryEnum GetType() const override { @@ -71,7 +73,7 @@ class ITK_TEMPLATE_EXPORT QuadrilateralCell } void MakeCopy(CellAutoPointer &) const override; - + /** @ITKEndGrouping */ unsigned int GetDimension() const override; @@ -128,9 +130,10 @@ class ITK_TEMPLATE_EXPORT QuadrilateralCell itkCellVisitMacro(CellGeometryEnum::QUADRILATERAL_CELL); /** Constructor and destructor */ + /** @ITKStartGrouping */ QuadrilateralCell() = default; ~QuadrilateralCell() override = default; - + /** @ITKEndGrouping */ protected: /** Store the number of points needed for a quadrilateral. */ std::array m_PointIds{ MakeFilled>( diff --git a/Modules/Core/Common/include/itkRGBAPixel.h b/Modules/Core/Common/include/itkRGBAPixel.h index a437cde06b5..a5498984318 100644 --- a/Modules/Core/Common/include/itkRGBAPixel.h +++ b/Modules/Core/Common/include/itkRGBAPixel.h @@ -91,6 +91,7 @@ class ITK_TEMPLATE_EXPORT RGBAPixel : public FixedArray #endif /** Pass-through constructor for the Array base class. */ + /** @ITKStartGrouping */ template RGBAPixel(const RGBAPixel & r) : BaseArray(r) @@ -98,6 +99,7 @@ class ITK_TEMPLATE_EXPORT RGBAPixel : public FixedArray RGBAPixel(const ComponentType r[4]) : BaseArray(r) {} + /** @ITKEndGrouping */ #if defined(ITK_LEGACY_REMOVE) /** Prevents copy-initialization from `nullptr`, as well as from `0` (NULL). */ @@ -114,6 +116,7 @@ class ITK_TEMPLATE_EXPORT RGBAPixel : public FixedArray operator=(const ComponentType r[4]); /** Arithmetic operations between pixels. Return a new RGBAPixel. */ + /** @ITKStartGrouping */ Self operator+(const Self & r) const; Self @@ -122,8 +125,10 @@ class ITK_TEMPLATE_EXPORT RGBAPixel : public FixedArray operator*(const ComponentType & r) const; Self operator/(const ComponentType & r) const; + /** @ITKEndGrouping */ /** Arithmetic-assignment operators. */ + /** @ITKStartGrouping */ const Self & operator+=(const Self & r); const Self & @@ -132,6 +137,7 @@ class ITK_TEMPLATE_EXPORT RGBAPixel : public FixedArray operator*=(const ComponentType & r); const Self & operator/=(const ComponentType & r); + /** @ITKEndGrouping */ /** Implements strict weak ordering. For use in STL, e.g. std::map. */ bool diff --git a/Modules/Core/Common/include/itkRGBPixel.h b/Modules/Core/Common/include/itkRGBPixel.h index 3d5ff32f369..11b97597e42 100644 --- a/Modules/Core/Common/include/itkRGBPixel.h +++ b/Modules/Core/Common/include/itkRGBPixel.h @@ -96,12 +96,14 @@ class ITK_TEMPLATE_EXPORT RGBPixel : public FixedArray /** Prevents copy-initialization from `nullptr`, as well as from `0` (NULL). */ RGBPixel(std::nullptr_t) = delete; #else + /** Constructor to fill Red=Blue=Green= r. * \note ITK_LEGACY_REMOVE=ON will disallow implicit conversion from a component value. */ RGBPixel(const ComponentType & r) { this->Fill(r); } #endif /** Pass-through constructor for the Array base class. */ + /** @ITKStartGrouping */ template RGBPixel(const RGBPixel & r) : BaseArray(r) @@ -109,8 +111,10 @@ class ITK_TEMPLATE_EXPORT RGBPixel : public FixedArray RGBPixel(const ComponentType r[3]) : BaseArray(r) {} + /** @ITKEndGrouping */ /** Pass-through assignment operator for the Array base class. */ + /** @ITKStartGrouping */ template Self & operator=(const RGBPixel & r) @@ -118,11 +122,13 @@ class ITK_TEMPLATE_EXPORT RGBPixel : public FixedArray BaseArray::operator=(r); return *this; } + /** @ITKEndGrouping */ Self & operator=(const ComponentType r[3]); /** Arithmetic operations between pixels. Return a new RGBPixel. */ + /** @ITKStartGrouping */ Self operator+(const Self & r) const; Self @@ -131,8 +137,10 @@ class ITK_TEMPLATE_EXPORT RGBPixel : public FixedArray operator*(const ComponentType & r) const; Self operator/(const ComponentType & r) const; + /** @ITKEndGrouping */ /** Arithmetic-assignment operators. */ + /** @ITKStartGrouping */ const Self & operator+=(const Self & r); const Self & @@ -141,6 +149,7 @@ class ITK_TEMPLATE_EXPORT RGBPixel : public FixedArray operator*=(const ComponentType & r); const Self & operator/=(const ComponentType & r); + /** @ITKEndGrouping */ /** Implements strict weak ordering. For use in STL, e.g. std::map. */ bool diff --git a/Modules/Core/Common/include/itkRealTimeInterval.h b/Modules/Core/Common/include/itkRealTimeInterval.h index 1ff0041649c..8fe97379dad 100644 --- a/Modules/Core/Common/include/itkRealTimeInterval.h +++ b/Modules/Core/Common/include/itkRealTimeInterval.h @@ -64,6 +64,7 @@ class ITKCommon_EXPORT RealTimeInterval using TimeRepresentationType = double; /** Return time in multiple units. */ + /** @ITKStartGrouping */ TimeRepresentationType GetTimeInMicroSeconds() const; TimeRepresentationType @@ -76,8 +77,9 @@ class ITKCommon_EXPORT RealTimeInterval GetTimeInHours() const; TimeRepresentationType GetTimeInDays() const; - + /** @ITKEndGrouping */ /** Arithmetic operations between RealTimeInterval and RealTimeInterval. */ + /** @ITKStartGrouping */ Self operator-(const Self &) const; Self @@ -86,8 +88,9 @@ class ITKCommon_EXPORT RealTimeInterval operator-=(const Self &); const Self & operator+=(const Self &); - + /** @ITKEndGrouping */ /** Comparison operations. */ + /** @ITKStartGrouping */ bool operator>(const Self &) const; bool @@ -99,7 +102,7 @@ class ITKCommon_EXPORT RealTimeInterval operator<=(const Self &) const; bool operator>=(const Self &) const; - + /** @ITKEndGrouping */ /** Set with values. The units and signs of the seconds and microseconds will * be harmonized internally. */ void Set(SecondsDifferenceType, MicroSecondsDifferenceType); diff --git a/Modules/Core/Common/include/itkRealTimeStamp.h b/Modules/Core/Common/include/itkRealTimeStamp.h index 2d67122e98f..c0d8b7a7893 100644 --- a/Modules/Core/Common/include/itkRealTimeStamp.h +++ b/Modules/Core/Common/include/itkRealTimeStamp.h @@ -61,6 +61,7 @@ class ITKCommon_EXPORT RealTimeStamp using TimeRepresentationType = RealTimeInterval::TimeRepresentationType; /** Return time in multiple units. */ + /** @ITKStartGrouping */ TimeRepresentationType GetTimeInMicroSeconds() const; TimeRepresentationType @@ -73,8 +74,9 @@ class ITKCommon_EXPORT RealTimeStamp GetTimeInHours() const; TimeRepresentationType GetTimeInDays() const; - + /** @ITKEndGrouping */ /** Arithmetic operations between RealTimeInterval and RealTimeStamp. */ + /** @ITKStartGrouping */ RealTimeInterval operator-(const Self &) const; Self @@ -85,8 +87,9 @@ class ITKCommon_EXPORT RealTimeStamp operator+=(const RealTimeInterval &); const Self & operator-=(const RealTimeInterval &); - + /** @ITKEndGrouping */ /** Comparison operations. */ + /** @ITKStartGrouping */ bool operator>(const Self &) const; bool @@ -98,7 +101,7 @@ class ITKCommon_EXPORT RealTimeStamp operator<=(const Self &) const; bool operator>=(const Self &) const; - + /** @ITKEndGrouping */ /** Default print out of a RealTimeStamp */ friend ITKCommon_EXPORT std::ostream & operator<<(std::ostream & os, const RealTimeStamp & v); diff --git a/Modules/Core/Common/include/itkShapedNeighborhoodIterator.h b/Modules/Core/Common/include/itkShapedNeighborhoodIterator.h index a35cfee5e16..463170d239e 100644 --- a/Modules/Core/Common/include/itkShapedNeighborhoodIterator.h +++ b/Modules/Core/Common/include/itkShapedNeighborhoodIterator.h @@ -239,6 +239,7 @@ class ITK_TEMPLATE_EXPORT ShapedNeighborhoodIterator /** Returns a const iterator for the neighborhood which points to the first * pixel in the neighborhood. */ + /** @ITKStartGrouping */ Iterator Begin() { @@ -249,6 +250,7 @@ class ITK_TEMPLATE_EXPORT ShapedNeighborhoodIterator { return Iterator(this, this->m_ActiveIndexList.end()); } + /** @ITKEndGrouping */ using Superclass::Begin; using Superclass::End; diff --git a/Modules/Core/Common/include/itkSimpleDataObjectDecorator.h b/Modules/Core/Common/include/itkSimpleDataObjectDecorator.h index 83aadf5dd05..152aefc79e7 100644 --- a/Modules/Core/Common/include/itkSimpleDataObjectDecorator.h +++ b/Modules/Core/Common/include/itkSimpleDataObjectDecorator.h @@ -88,6 +88,7 @@ class ITK_TEMPLATE_EXPORT SimpleDataObjectDecorator : public DataObject Set(const T & val); /** Get the contained object */ + /** @ITKStartGrouping */ virtual T & Get() { @@ -98,7 +99,7 @@ class ITK_TEMPLATE_EXPORT SimpleDataObjectDecorator : public DataObject { return m_Component; } - + /** @ITKEndGrouping */ protected: SimpleDataObjectDecorator() = default; ~SimpleDataObjectDecorator() override = default; diff --git a/Modules/Core/Common/include/itkSimpleFilterWatcher.h b/Modules/Core/Common/include/itkSimpleFilterWatcher.h index 6bfbaa87d06..43740fb6421 100644 --- a/Modules/Core/Common/include/itkSimpleFilterWatcher.h +++ b/Modules/Core/Common/include/itkSimpleFilterWatcher.h @@ -96,6 +96,7 @@ class ITKCommon_EXPORT SimpleFilterWatcher /** Methods to control the verbosity of the messages. Quiet * reporting limits the information emitted at a ProgressEvent. */ + /** @ITKStartGrouping */ void QuietOn() { @@ -106,10 +107,12 @@ class ITKCommon_EXPORT SimpleFilterWatcher { m_Quiet = false; } + /** @ITKEndGrouping */ /** Methods to use to test the AbortEvent of the a filter. If * TestAbort is on, the filter being watched will be aborted when * the progress reaches 30%. */ + /** @ITKStartGrouping */ void TestAbortOn() { @@ -120,8 +123,10 @@ class ITKCommon_EXPORT SimpleFilterWatcher { m_TestAbort = false; } + /** @ITKEndGrouping */ /** Methods to access member data */ + /** Get a pointer to the process object being watched. */ ProcessObject * GetProcess() @@ -130,6 +135,7 @@ class ITKCommon_EXPORT SimpleFilterWatcher } /** Set/Get the steps completed. */ + /** @ITKStartGrouping */ void SetSteps(int val) { @@ -140,8 +146,10 @@ class ITKCommon_EXPORT SimpleFilterWatcher { return m_Steps; } + /** @ITKEndGrouping */ /** Set/Get the number of iterations completed. */ + /** @ITKStartGrouping */ void SetIterations(int val) { @@ -152,9 +160,11 @@ class ITKCommon_EXPORT SimpleFilterWatcher { return m_Iterations; } + /** @ITKEndGrouping */ /** Set/Get the quiet mode boolean. If true, verbose progress is * reported. */ + /** @ITKStartGrouping */ void SetQuiet(bool val) { @@ -165,6 +175,7 @@ class ITKCommon_EXPORT SimpleFilterWatcher { return m_Quiet; } + /** @ITKEndGrouping */ /** Get the comment for the watcher. */ std::string diff --git a/Modules/Core/Common/include/itkSingleton.h b/Modules/Core/Common/include/itkSingleton.h index 19dcf014fe4..fc747dfb717 100644 --- a/Modules/Core/Common/include/itkSingleton.h +++ b/Modules/Core/Common/include/itkSingleton.h @@ -93,12 +93,13 @@ class ITKCommon_EXPORT SingletonIndex /** Set/Get the pointer to GlobalSingleton. * Note that SetGlobalSingleton is not concurrent thread safe. */ + /** @ITKStartGrouping */ static Self * GetInstance(); static void SetInstance(Self * instance); ~SingletonIndex(); - + /** @ITKEndGrouping */ private: // Internal struct to store the instance pointer and the delete function object of a global object. struct GlobalObject diff --git a/Modules/Core/Common/include/itkSmartPointer.h b/Modules/Core/Common/include/itkSmartPointer.h index f027648d70d..7971503e5d5 100644 --- a/Modules/Core/Common/include/itkSmartPointer.h +++ b/Modules/Core/Common/include/itkSmartPointer.h @@ -161,6 +161,7 @@ class SmartPointer * Additionally, it relies on constructors for additional conversion * for pointer types. */ + /** @ITKStartGrouping */ // cppcheck-suppress operatorEqVarError SmartPointer & operator=(SmartPointer r) noexcept @@ -179,6 +180,7 @@ class SmartPointer this->m_Pointer = nullptr; return *this; } + /** @ITKEndGrouping */ /** Function to print object pointed to */ ObjectType * @@ -240,6 +242,7 @@ class SmartPointer /** Comparison of pointers. Equality comparison. */ +/** @ITKStartGrouping */ template bool operator==(const SmartPointer & l, const SmartPointer & r) noexcept @@ -258,8 +261,9 @@ operator==(std::nullptr_t, const SmartPointer & r) noexcept { return (nullptr == r.GetPointer()); } - +/** @ITKEndGrouping */ /** Comparison of pointers. Not equal comparison. */ +/** @ITKStartGrouping */ template bool operator!=(const SmartPointer & l, const SmartPointer & r) noexcept @@ -278,7 +282,7 @@ operator!=(std::nullptr_t, const SmartPointer & r) noexcept { return (nullptr != r.GetPointer()); } - +/** @ITKEndGrouping */ /** Comparison of pointers. Less than comparison. */ template diff --git a/Modules/Core/Common/include/itkSpecialCoordinatesImage.h b/Modules/Core/Common/include/itkSpecialCoordinatesImage.h index 085a31d7f2c..257ce6fdf52 100644 --- a/Modules/Core/Common/include/itkSpecialCoordinatesImage.h +++ b/Modules/Core/Common/include/itkSpecialCoordinatesImage.h @@ -241,6 +241,7 @@ class ITK_TEMPLATE_EXPORT SpecialCoordinatesImage : public ImageBaseGetBufferPointer() : nullptr; } - + /** @ITKEndGrouping */ /** Return a pointer to the container. */ PixelContainer * GetPixelContainer() @@ -289,6 +290,7 @@ class ITK_TEMPLATE_EXPORT SpecialCoordinatesImage : public ImageBase Self Rotate(const Matrix & m) const; @@ -232,6 +233,7 @@ class ITK_TEMPLATE_EXPORT SymmetricSecondRankTensor : public FixedArrayRotate(static_cast>(m)); } + /** @ITKEndGrouping */ /** Pre-Multiply by a Matrix as ResultingMatrix = Matrix * ThisTensor. */ MatrixType diff --git a/Modules/Core/Common/include/itkTetrahedronCell.h b/Modules/Core/Common/include/itkTetrahedronCell.h index 76e68dd3be2..c017d924595 100644 --- a/Modules/Core/Common/include/itkTetrahedronCell.h +++ b/Modules/Core/Common/include/itkTetrahedronCell.h @@ -41,9 +41,10 @@ class ITK_TEMPLATE_EXPORT TetrahedronCell ITK_DISALLOW_COPY_AND_MOVE(TetrahedronCell); /** Standard class type alias. */ + /** @ITKStartGrouping */ itkCellCommonTypedefs(TetrahedronCell); itkCellInheritedTypedefs(TCellInterface); - + /** @ITKEndGrouping */ /** \see LightObject::GetNameOfClass() */ itkOverrideGetNameOfClassMacro(TetrahedronCell); @@ -69,6 +70,7 @@ class ITK_TEMPLATE_EXPORT TetrahedronCell // Standard CellInterface /** Implement the standard CellInterface. */ + /** @ITKStartGrouping */ CellGeometryEnum GetType() const override { @@ -76,7 +78,7 @@ class ITK_TEMPLATE_EXPORT TetrahedronCell } void MakeCopy(CellAutoPointer &) const override; - + /** @ITKEndGrouping */ /** Get the topological dimension of this cell. */ unsigned int GetDimension() const override; diff --git a/Modules/Core/Common/include/itkThreadPool.h b/Modules/Core/Common/include/itkThreadPool.h index 63946122651..1db0c19c45d 100644 --- a/Modules/Core/Common/include/itkThreadPool.h +++ b/Modules/Core/Common/include/itkThreadPool.h @@ -119,11 +119,12 @@ auto result = pool->AddWork([](int param) { return param; }, 7); This function should be used carefully, probably only during static initialization phase to disable waiting for threads when ITK is built as a static library and linked into a shared library (Windows only). */ + /** @ITKStartGrouping */ static bool GetDoNotWaitForThreads(); static void SetDoNotWaitForThreads(bool doNotWaitForThreads); - + /** @ITKEndGrouping */ protected: /** We need access to the mutex in AddWork, and the variable is only * visible in the .cxx file, so this method returns it. */ diff --git a/Modules/Core/Common/include/itkThreadSupport.h b/Modules/Core/Common/include/itkThreadSupport.h index 723225efae4..57d01ff6357 100644 --- a/Modules/Core/Common/include/itkThreadSupport.h +++ b/Modules/Core/Common/include/itkThreadSupport.h @@ -34,6 +34,7 @@ namespace itk { /** Platform specific type alias for simple types */ +/** @ITKStartGrouping */ #if defined(ITK_USE_PTHREADS) constexpr size_t ITK_MAX_THREADS = ITK_DEFAULT_MAX_THREADS; using MutexType = pthread_mutex_t; @@ -44,7 +45,7 @@ using ThreadProcessIdType = pthread_t; constexpr ThreadProcessIdType ITK_DEFAULT_THREAD_ID = 0; # endif using ITK_THREAD_RETURN_TYPE = void *; - +/** @ITKEndGrouping */ constexpr ITK_THREAD_RETURN_TYPE ITK_THREAD_RETURN_DEFAULT_VALUE = nullptr; using itk::ITK_THREAD_RETURN_DEFAULT_VALUE; // We need this out of the itk namespace for #define to work below using ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION = itk::ITK_THREAD_RETURN_TYPE; diff --git a/Modules/Core/Common/include/itkTimeStamp.h b/Modules/Core/Common/include/itkTimeStamp.h index 8509ffb7ef1..34467e89af7 100644 --- a/Modules/Core/Common/include/itkTimeStamp.h +++ b/Modules/Core/Common/include/itkTimeStamp.h @@ -102,6 +102,7 @@ class ITKCommon_EXPORT TimeStamp } /** Support comparisons of time stamp objects directly. */ + /** @ITKStartGrouping */ bool operator>(TimeStamp & ts) const { @@ -112,7 +113,7 @@ class ITKCommon_EXPORT TimeStamp { return (m_ModifiedTime < ts.m_ModifiedTime); } - + /** @ITKEndGrouping */ /** Allow for typecasting to unsigned long. */ operator ModifiedTimeType() const { return m_ModifiedTime; } diff --git a/Modules/Core/Common/include/itkTorusInteriorExteriorSpatialFunction.h b/Modules/Core/Common/include/itkTorusInteriorExteriorSpatialFunction.h index 85b39abc80b..9de5403353a 100644 --- a/Modules/Core/Common/include/itkTorusInteriorExteriorSpatialFunction.h +++ b/Modules/Core/Common/include/itkTorusInteriorExteriorSpatialFunction.h @@ -67,17 +67,20 @@ class ITK_TEMPLATE_EXPORT TorusInteriorExteriorSpatialFunction /** Set/Get the origin of the torus (the point from which the major * radius is measured). */ + /** @ITKStartGrouping */ itkGetConstMacro(Origin, InputType); itkSetMacro(Origin, InputType); - + /** @ITKEndGrouping */ /** Set/Get the major radius of the torus. */ + /** @ITKStartGrouping */ itkGetConstMacro(MajorRadius, double); itkSetMacro(MajorRadius, double); - + /** @ITKEndGrouping */ /** Set/Get the minor radius of the torus (radius of tube). */ + /** @ITKStartGrouping */ itkGetConstMacro(MinorRadius, double); itkSetMacro(MinorRadius, double); - + /** @ITKEndGrouping */ protected: TorusInteriorExteriorSpatialFunction() = default; ~TorusInteriorExteriorSpatialFunction() override = default; diff --git a/Modules/Core/Common/include/itkTriangleCell.h b/Modules/Core/Common/include/itkTriangleCell.h index 223b06c9487..066c8e71978 100644 --- a/Modules/Core/Common/include/itkTriangleCell.h +++ b/Modules/Core/Common/include/itkTriangleCell.h @@ -51,9 +51,10 @@ class ITK_TEMPLATE_EXPORT TriangleCell ITK_DISALLOW_COPY_AND_MOVE(TriangleCell); /** Standard class type aliases. */ + /** @ITKStartGrouping */ itkCellCommonTypedefs(TriangleCell); itkCellInheritedTypedefs(TCellInterface); - + /** @ITKEndGrouping */ /** \see LightObject::GetNameOfClass() */ itkOverrideGetNameOfClassMacro(TriangleCell); @@ -74,6 +75,7 @@ class ITK_TEMPLATE_EXPORT TriangleCell // Standard CellInterface /** Implement the standard CellInterface. */ + /** @ITKStartGrouping */ CellGeometryEnum GetType() const override { @@ -81,7 +83,7 @@ class ITK_TEMPLATE_EXPORT TriangleCell } void MakeCopy(CellAutoPointer &) const override; - + /** @ITKEndGrouping */ /** Get the topological dimension of this cell. */ unsigned int GetDimension() const override; diff --git a/Modules/Core/Common/include/itkUnaryFunctorImageFilter.h b/Modules/Core/Common/include/itkUnaryFunctorImageFilter.h index 79f05dcbd9a..8dc4f41583f 100644 --- a/Modules/Core/Common/include/itkUnaryFunctorImageFilter.h +++ b/Modules/Core/Common/include/itkUnaryFunctorImageFilter.h @@ -81,6 +81,7 @@ class ITK_TEMPLATE_EXPORT UnaryFunctorImageFilter : public InPlaceImageFilter VariableLengthVector(const VariableLengthVectorExpression & rhs); + /** Assignment from an Expression Template vector. * \tparam TExpr1 Type of the left sub-expression * \tparam TExpr2 Type of the right sub-expression @@ -572,6 +574,7 @@ class ITK_TEMPLATE_EXPORT VariableLengthVector operator=(const TValue & v); /** Return the number of elements in the Array */ + /** @ITKStartGrouping */ unsigned int Size() const { @@ -587,13 +590,14 @@ class ITK_TEMPLATE_EXPORT VariableLengthVector { return m_NumElements; } - + /** @ITKEndGrouping */ /** Return reference to the element at specified index. No range checking. */ TValue & operator[](unsigned int i) { return this->m_Data[i]; } + /** Return reference to the element at specified index. No range checking. */ const TValue & operator[](unsigned int i) const @@ -1034,6 +1038,7 @@ template struct GetType { using Type = TExpr; + /** Fetches the i-th element from an array (expression). * \note the default unspecialized behaviour returns the input number \c v. */ @@ -1370,7 +1375,7 @@ GetSquaredNorm(const TExpr & v) } /**\name Serialization */ -//@{ + /** Serialization of \c VariableLengthVector * \relates itk::VariableLengthVector */ @@ -1393,10 +1398,9 @@ operator<<(std::ostream & os, const VariableLengthVector & arr) os << ']'; return os; } -//@} /**\name Standard compliance functions */ -//@{ + /** \c swap() overload for \c VariableLengthVector * \throw None * \relates itk::VariableLengthVector @@ -1420,7 +1424,6 @@ swap(VariableLengthVector & l_, VariableLengthVector & r_) noexcept { l_.Swap(r_); } -//@} } // namespace itk diff --git a/Modules/Core/Common/include/itkVector.h b/Modules/Core/Common/include/itkVector.h index e34a8bb9477..de7684d685b 100644 --- a/Modules/Core/Common/include/itkVector.h +++ b/Modules/Core/Common/include/itkVector.h @@ -114,6 +114,7 @@ class ITK_TEMPLATE_EXPORT Vector : public FixedArray * Deprecated */ Vector(const ValueType & r); #else + /** Constructor to initialize entire vector to one value, * if explicitly invoked. */ explicit Vector(const ValueType & r); @@ -123,6 +124,7 @@ class ITK_TEMPLATE_EXPORT Vector : public FixedArray #endif /** Pass-through constructor for the Array base class. */ + /** @ITKStartGrouping */ template Vector(const Vector & r) : BaseArray(r) @@ -134,6 +136,7 @@ class ITK_TEMPLATE_EXPORT Vector : public FixedArray Vector(const TVectorValueType r[Dimension]) : BaseArray(r) {} + /** @ITKEndGrouping */ /** Explicit constructor for std::array. */ explicit Vector(const std::array & stdArray) diff --git a/Modules/Core/Common/include/itkVectorContainer.h b/Modules/Core/Common/include/itkVectorContainer.h index e5a8f96ee27..5886bb7008c 100644 --- a/Modules/Core/Common/include/itkVectorContainer.h +++ b/Modules/Core/Common/include/itkVectorContainer.h @@ -407,6 +407,7 @@ class ITK_TEMPLATE_EXPORT VectorContainer { return static_cast(m_Pos); } + /** Get the value at this iterator's location in the VectorContainer. */ const_reference Value() const @@ -562,6 +563,7 @@ class ITK_TEMPLATE_EXPORT VectorContainer /** Provide pass-through constructors corresponding to all the STL * vector constructors. These are for internal use only since this is also * an Object which must be constructed through the "New()" routine. */ + /** @ITKStartGrouping */ VectorContainer() = default; VectorContainer(size_type n) : Object() @@ -580,10 +582,10 @@ class ITK_TEMPLATE_EXPORT VectorContainer : Object() , VectorType(first, last) {} + /** @ITKEndGrouping */ }; } // namespace detail - /** Alias template, allowing to use `itk::VectorContainer` without having to explicitly specify its * `ElementIdentifier` type. * diff --git a/Modules/Core/Common/include/itkVectorImage.h b/Modules/Core/Common/include/itkVectorImage.h index 1a40b5e4fce..16cf9344679 100644 --- a/Modules/Core/Common/include/itkVectorImage.h +++ b/Modules/Core/Common/include/itkVectorImage.h @@ -292,6 +292,7 @@ class ITK_TEMPLATE_EXPORT VectorImage : public ImageBase /** Return a pointer to the beginning of the buffer. This is used by * the image iterator class. */ + /** @ITKStartGrouping */ InternalPixelType * GetBufferPointer() { @@ -302,7 +303,7 @@ class ITK_TEMPLATE_EXPORT VectorImage : public ImageBase { return m_Buffer ? m_Buffer->GetBufferPointer() : nullptr; } - + /** @ITKEndGrouping */ /** Return a pointer to the container. */ PixelContainer * GetPixelContainer() @@ -364,9 +365,10 @@ class ITK_TEMPLATE_EXPORT VectorImage : public ImageBase } /** Set/Get macros for the length of each vector in the vector image */ + /** @ITKStartGrouping */ itkSetMacro(VectorLength, VectorLengthType); itkGetConstReferenceMacro(VectorLength, VectorLengthType); - + /** @ITKEndGrouping */ /** Get/Set the number of components each pixel has, ie the VectorLength */ unsigned int GetNumberOfComponentsPerPixel() const override; diff --git a/Modules/Core/Common/include/itkVersor.h b/Modules/Core/Common/include/itkVersor.h index 83b706e5146..d07036eff73 100644 --- a/Modules/Core/Common/include/itkVersor.h +++ b/Modules/Core/Common/include/itkVersor.h @@ -301,6 +301,7 @@ class ITK_TEMPLATE_EXPORT Versor private: /** use different epsilon for float and double */ + /** @ITKStartGrouping */ static inline ValueType Epsilon(double *) { @@ -316,6 +317,7 @@ class ITK_TEMPLATE_EXPORT Versor { return Epsilon((ValueType *)nullptr); } + /** @ITKEndGrouping */ /** Component parallel to x axis. */ ValueType m_X{}; diff --git a/Modules/Core/Common/include/itkVertexCell.h b/Modules/Core/Common/include/itkVertexCell.h index 38886836f8d..102b0812503 100644 --- a/Modules/Core/Common/include/itkVertexCell.h +++ b/Modules/Core/Common/include/itkVertexCell.h @@ -40,9 +40,10 @@ class ITK_TEMPLATE_EXPORT VertexCell : public TCellInterface ITK_DISALLOW_COPY_AND_MOVE(VertexCell); /** Standard class type aliases. */ + /** @ITKStartGrouping */ itkCellCommonTypedefs(VertexCell); itkCellInheritedTypedefs(TCellInterface); - + /** @ITKEndGrouping */ /** \see LightObject::GetNameOfClass() */ itkOverrideGetNameOfClassMacro(VertexCell); @@ -53,6 +54,7 @@ class ITK_TEMPLATE_EXPORT VertexCell : public TCellInterface // Standard CellInterface /** Implement the standard CellInterface. */ + /** @ITKStartGrouping */ CellGeometryEnum GetType() const override { @@ -60,7 +62,7 @@ class ITK_TEMPLATE_EXPORT VertexCell : public TCellInterface } void MakeCopy(CellAutoPointer &) const override; - + /** @ITKEndGrouping */ /** Get the topological dimension of this cell. */ unsigned int GetDimension() const override; diff --git a/Modules/Core/FiniteDifference/include/itkFiniteDifferenceImageFilter.h b/Modules/Core/FiniteDifference/include/itkFiniteDifferenceImageFilter.h index 8a10618524a..c41ea0b198c 100644 --- a/Modules/Core/FiniteDifference/include/itkFiniteDifferenceImageFilter.h +++ b/Modules/Core/FiniteDifference/include/itkFiniteDifferenceImageFilter.h @@ -182,31 +182,36 @@ class ITK_TEMPLATE_EXPORT FiniteDifferenceImageFilter : public InPlaceImageFilte itkSetObjectMacro(DifferenceFunction, FiniteDifferenceFunctionType); /** Set/Get the number of iterations that the filter will run. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfIterations, IdentifierType); itkGetConstReferenceMacro(NumberOfIterations, IdentifierType); - + /** @ITKEndGrouping */ /** Use the image spacing information in calculations. Use this option if you * want derivatives in physical space. Default is UseImageSpacingOn. */ + /** @ITKStartGrouping */ itkSetMacro(UseImageSpacing, bool); itkBooleanMacro(UseImageSpacing); itkGetConstReferenceMacro(UseImageSpacing, bool); - + /** @ITKEndGrouping */ /** Set/Get the maximum error allowed in the solution. This may not be defined for all solvers and its meaning may change with the application. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumRMSError, double); itkGetConstReferenceMacro(MaximumRMSError, double); - + /** @ITKEndGrouping */ /** Set/Get the root mean squared change of the previous iteration. May not be used by all solvers. */ + /** @ITKStartGrouping */ itkSetMacro(RMSChange, double); itkGetConstReferenceMacro(RMSChange, double); - + /** @ITKEndGrouping */ /** Require the filter to be manually reinitialized (by calling SetStateToUninitialized() */ + /** @ITKStartGrouping */ itkSetMacro(ManualReinitialization, bool); itkGetConstReferenceMacro(ManualReinitialization, bool); itkBooleanMacro(ManualReinitialization); - + /** @ITKEndGrouping */ itkSetMacro(IsInitialized, bool); itkGetMacro(IsInitialized, bool); diff --git a/Modules/Core/GPUCommon/include/itkGPUImage.h b/Modules/Core/GPUCommon/include/itkGPUImage.h index 8c00bd7e943..1f502958e0e 100644 --- a/Modules/Core/GPUCommon/include/itkGPUImage.h +++ b/Modules/Core/GPUCommon/include/itkGPUImage.h @@ -152,6 +152,7 @@ class ITK_TEMPLATE_EXPORT GPUImage : public Image SetPixelContainer(PixelContainer * container); /** Return a pointer to the container. */ + /** @ITKStartGrouping */ PixelContainer * GetPixelContainer() { @@ -165,6 +166,7 @@ class ITK_TEMPLATE_EXPORT GPUImage : public Image m_DataManager->UpdateCPUBuffer(); return Superclass::GetPixelContainer(); } + /** @ITKEndGrouping */ void SetCurrentCommandQueue(int queueid) @@ -225,6 +227,7 @@ class ITK_TEMPLATE_EXPORT GPUImageFactory : public itk::ObjectFactoryBase using ConstPointer = itk::SmartPointer; /** Class methods used to interface with the registered factories. */ + /** @ITKStartGrouping */ const char * GetITKSourceVersion() const override { @@ -235,6 +238,7 @@ class ITK_TEMPLATE_EXPORT GPUImageFactory : public itk::ObjectFactoryBase { return "A Factory for GPUImage"; } + /** @ITKEndGrouping */ /** Method for class instantiation. */ itkFactorylessNewMacro(Self); diff --git a/Modules/Core/GPUFiniteDifference/include/itkGPUFiniteDifferenceImageFilter.h b/Modules/Core/GPUFiniteDifference/include/itkGPUFiniteDifferenceImageFilter.h index 24c57c57584..85da97fa900 100644 --- a/Modules/Core/GPUFiniteDifference/include/itkGPUFiniteDifferenceImageFilter.h +++ b/Modules/Core/GPUFiniteDifference/include/itkGPUFiniteDifferenceImageFilter.h @@ -122,19 +122,21 @@ class ITK_TEMPLATE_EXPORT GPUFiniteDifferenceImageFilter } /** Set/Get the state of the filter. */ + /** @ITKStartGrouping */ #if !defined(ITK_WRAPPING_PARSER) itkSetMacro(State, GPUFiniteDifferenceFilterEnum); itkGetConstReferenceMacro(State, GPUFiniteDifferenceFilterEnum); #endif - + /** @ITKEndGrouping */ itkConceptMacro(OutputPixelIsFloatingPointCheck, (Concept::IsFloatingPoint)); /** Methods to get timers */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(InitTime, TimeProbe); itkGetConstReferenceMacro(ComputeUpdateTime, TimeProbe); itkGetConstReferenceMacro(ApplyUpdateTime, TimeProbe); itkGetConstReferenceMacro(SmoothFieldTime, TimeProbe); - + /** @ITKEndGrouping */ protected: GPUFiniteDifferenceImageFilter(); ~GPUFiniteDifferenceImageFilter() override; diff --git a/Modules/Core/ImageAdaptors/include/itkAddPixelAccessor.h b/Modules/Core/ImageAdaptors/include/itkAddPixelAccessor.h index e579d0031ac..0be9853f099 100644 --- a/Modules/Core/ImageAdaptors/include/itkAddPixelAccessor.h +++ b/Modules/Core/ImageAdaptors/include/itkAddPixelAccessor.h @@ -93,13 +93,14 @@ class AddPixelAccessor } /** Constructors */ + /** @ITKStartGrouping */ AddPixelAccessor() : m_Value(TPixel{}) {} AddPixelAccessor(const Self & apa) : m_Value(apa.m_Value) {} - + /** @ITKEndGrouping */ private: TPixel m_Value; }; diff --git a/Modules/Core/ImageFunction/include/itkBSplineInterpolateImageFunction.h b/Modules/Core/ImageFunction/include/itkBSplineInterpolateImageFunction.h index 048d74bc87f..44c6c0875e8 100644 --- a/Modules/Core/ImageFunction/include/itkBSplineInterpolateImageFunction.h +++ b/Modules/Core/ImageFunction/include/itkBSplineInterpolateImageFunction.h @@ -286,9 +286,11 @@ class ITK_TEMPLATE_EXPORT BSplineInterpolateImageFunction : public InterpolateIm * flag is OFF. * The default value of this flag is On. */ + /** @ITKStartGrouping */ itkSetMacro(UseImageDirection, bool); itkGetConstMacro(UseImageDirection, bool); itkBooleanMacro(UseImageDirection); + /** @ITKEndGrouping */ SizeType GetRadius() const override diff --git a/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.h b/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.h index 8f312f59d12..19b74160e42 100644 --- a/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.h +++ b/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.h @@ -199,10 +199,11 @@ class ITK_TEMPLATE_EXPORT CentralDifferenceImageFunction : public ImageFunction< * amount of computation performed when the flag is ON. * The default value of this flag is On. */ + /** @ITKStartGrouping */ itkSetMacro(UseImageDirection, bool); itkGetConstMacro(UseImageDirection, bool); itkBooleanMacro(UseImageDirection); - + /** @ITKEndGrouping */ protected: CentralDifferenceImageFunction(); ~CentralDifferenceImageFunction() override = default; diff --git a/Modules/Core/ImageFunction/include/itkCovarianceImageFunction.h b/Modules/Core/ImageFunction/include/itkCovarianceImageFunction.h index 5bb7d30ca6f..01ef0ddec84 100644 --- a/Modules/Core/ImageFunction/include/itkCovarianceImageFunction.h +++ b/Modules/Core/ImageFunction/include/itkCovarianceImageFunction.h @@ -112,9 +112,10 @@ class ITK_TEMPLATE_EXPORT CovarianceImageFunction /** Get/Set the radius of the neighborhood over which the * statistics are evaluated. */ + /** @ITKStartGrouping */ itkSetMacro(NeighborhoodRadius, unsigned int); itkGetConstReferenceMacro(NeighborhoodRadius, unsigned int); - + /** @ITKEndGrouping */ protected: CovarianceImageFunction(); ~CovarianceImageFunction() override = default; diff --git a/Modules/Core/ImageFunction/include/itkGaussianBlurImageFunction.h b/Modules/Core/ImageFunction/include/itkGaussianBlurImageFunction.h index 884a1bfcaa6..2f80f8d2360 100644 --- a/Modules/Core/ImageFunction/include/itkGaussianBlurImageFunction.h +++ b/Modules/Core/ImageFunction/include/itkGaussianBlurImageFunction.h @@ -129,36 +129,40 @@ class ITK_TEMPLATE_EXPORT GaussianBlurImageFunction : public ImageFunctionSetSigma(sigma); } itkGetConstMacro(Sigma, ArrayType); + /** @ITKEndGrouping */ /** Set/Get alpha. */ + /** @ITKStartGrouping */ virtual void SetAlpha(const RealType a) { @@ -136,6 +139,7 @@ class ITK_TEMPLATE_EXPORT GaussianInterpolateImageFunction : public InterpolateI } } itkGetConstMacro(Alpha, RealType); + /** @ITKEndGrouping */ /** Set/Get sigma and alpha. */ virtual void @@ -179,17 +183,22 @@ class ITK_TEMPLATE_EXPORT GaussianInterpolateImageFunction : public InterpolateI bool evaluateGradient = false) const; /** Set/Get the bounding box starting point. */ + /** @ITKStartGrouping */ itkSetMacro(BoundingBoxStart, ArrayType); itkGetConstMacro(BoundingBoxStart, ArrayType); + /** @ITKEndGrouping */ /** Set/Get the bounding box end point. */ + /** @ITKStartGrouping */ itkSetMacro(BoundingBoxEnd, ArrayType); itkGetConstMacro(BoundingBoxEnd, ArrayType); + /** @ITKEndGrouping */ /** Set/Get the cut-off distance. */ + /** @ITKStartGrouping */ itkSetMacro(CutOffDistance, ArrayType); itkGetConstMacro(CutOffDistance, ArrayType); - + /** @ITKEndGrouping */ private: /** Evaluate function value. */ diff --git a/Modules/Core/ImageFunction/include/itkLabelImageGaussianInterpolateImageFunction.h b/Modules/Core/ImageFunction/include/itkLabelImageGaussianInterpolateImageFunction.h index 851a1649739..9d5344c21e0 100644 --- a/Modules/Core/ImageFunction/include/itkLabelImageGaussianInterpolateImageFunction.h +++ b/Modules/Core/ImageFunction/include/itkLabelImageGaussianInterpolateImageFunction.h @@ -64,7 +64,6 @@ namespace itk * \sphinxexample{Core/ImageFunction/ResampleSegmentedImage,Resample Segmented Image} * \endsphinx */ - template ::RealType>> diff --git a/Modules/Core/ImageFunction/include/itkMahalanobisDistanceThresholdImageFunction.h b/Modules/Core/ImageFunction/include/itkMahalanobisDistanceThresholdImageFunction.h index b66965296e2..aa18dfb5c73 100644 --- a/Modules/Core/ImageFunction/include/itkMahalanobisDistanceThresholdImageFunction.h +++ b/Modules/Core/ImageFunction/include/itkMahalanobisDistanceThresholdImageFunction.h @@ -137,9 +137,10 @@ class ITK_TEMPLATE_EXPORT MahalanobisDistanceThresholdImageFunction EvaluateDistanceAtIndex(const IndexType & index) const; /** Get the lower threshold value. */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(Threshold, double); itkSetMacro(Threshold, double); - + /** @ITKEndGrouping */ /** Set the mean. * Set this mean value to the membership function. */ void diff --git a/Modules/Core/ImageFunction/include/itkMeanImageFunction.h b/Modules/Core/ImageFunction/include/itkMeanImageFunction.h index 1c603567a08..2d864a64ce9 100644 --- a/Modules/Core/ImageFunction/include/itkMeanImageFunction.h +++ b/Modules/Core/ImageFunction/include/itkMeanImageFunction.h @@ -118,10 +118,11 @@ class ITK_TEMPLATE_EXPORT MeanImageFunction /** Get/Set the radius of the neighborhood over which the statistics are evaluated */ + /** @ITKStartGrouping */ void SetNeighborhoodRadius(unsigned int); itkGetConstReferenceMacro(NeighborhoodRadius, unsigned int); - + /** @ITKEndGrouping */ protected: MeanImageFunction(); ~MeanImageFunction() override = default; diff --git a/Modules/Core/ImageFunction/include/itkMedianImageFunction.h b/Modules/Core/ImageFunction/include/itkMedianImageFunction.h index 617a6ecf7bc..44fb06a181b 100644 --- a/Modules/Core/ImageFunction/include/itkMedianImageFunction.h +++ b/Modules/Core/ImageFunction/include/itkMedianImageFunction.h @@ -112,10 +112,11 @@ class ITK_TEMPLATE_EXPORT MedianImageFunction /** Get/Set the radius of the neighborhood over which the statistics are evaluated */ + /** @ITKStartGrouping */ void SetNeighborhoodRadius(unsigned int); itkGetConstReferenceMacro(NeighborhoodRadius, unsigned int); - + /** @ITKEndGrouping */ protected: MedianImageFunction(); ~MedianImageFunction() override = default; diff --git a/Modules/Core/ImageFunction/include/itkRayCastInterpolateImageFunction.h b/Modules/Core/ImageFunction/include/itkRayCastInterpolateImageFunction.h index f8559126294..942c68cafe6 100644 --- a/Modules/Core/ImageFunction/include/itkRayCastInterpolateImageFunction.h +++ b/Modules/Core/ImageFunction/include/itkRayCastInterpolateImageFunction.h @@ -132,22 +132,26 @@ class ITK_TEMPLATE_EXPORT RayCastInterpolateImageFunction : public InterpolateIm /** Connect the Transform. * This Transformation is used to calculate the new focal point position. * */ + /** @ITKStartGrouping */ itkSetObjectMacro(Transform, TransformType); itkGetModifiableObjectMacro(Transform, TransformType); - + /** @ITKEndGrouping */ /** Connect the Interpolator. */ itkSetObjectMacro(Interpolator, InterpolatorType); + /** Get a pointer to the Interpolator. */ itkGetModifiableObjectMacro(Interpolator, InterpolatorType); /** The focal point or position of the ray source. */ + /** @ITKStartGrouping */ itkSetMacro(FocalPoint, InputPointType); itkGetConstMacro(FocalPoint, InputPointType); - + /** @ITKEndGrouping */ /** The threshold above which voxels along the ray path are integrated. */ + /** @ITKStartGrouping */ itkSetMacro(Threshold, double); itkGetConstMacro(Threshold, double); - + /** @ITKEndGrouping */ /** Check if a point is inside the image buffer. * \warning For efficiency, no validity checking of * the input image pointer is done. */ diff --git a/Modules/Core/ImageFunction/include/itkScatterMatrixImageFunction.h b/Modules/Core/ImageFunction/include/itkScatterMatrixImageFunction.h index 8b59df45ee6..43a21a789b9 100644 --- a/Modules/Core/ImageFunction/include/itkScatterMatrixImageFunction.h +++ b/Modules/Core/ImageFunction/include/itkScatterMatrixImageFunction.h @@ -112,9 +112,10 @@ class ITK_TEMPLATE_EXPORT ScatterMatrixImageFunction /** Get/Set the radius of the neighborhood over which the statistics are evaluated */ + /** @ITKStartGrouping */ itkSetMacro(NeighborhoodRadius, unsigned int); itkGetConstReferenceMacro(NeighborhoodRadius, unsigned int); - + /** @ITKEndGrouping */ protected: ScatterMatrixImageFunction(); ~ScatterMatrixImageFunction() override = default; diff --git a/Modules/Core/ImageFunction/include/itkVarianceImageFunction.h b/Modules/Core/ImageFunction/include/itkVarianceImageFunction.h index 55c39b2dfe1..fa59dfa219d 100644 --- a/Modules/Core/ImageFunction/include/itkVarianceImageFunction.h +++ b/Modules/Core/ImageFunction/include/itkVarianceImageFunction.h @@ -106,9 +106,10 @@ class ITK_TEMPLATE_EXPORT VarianceImageFunction /** Get/Set the radius of the neighborhood over which the statistics are evaluated */ + /** @ITKStartGrouping */ itkSetMacro(NeighborhoodRadius, unsigned int); itkGetConstReferenceMacro(NeighborhoodRadius, unsigned int); - + /** @ITKEndGrouping */ protected: VarianceImageFunction(); ~VarianceImageFunction() override = default; diff --git a/Modules/Core/ImageFunction/include/itkVectorMeanImageFunction.h b/Modules/Core/ImageFunction/include/itkVectorMeanImageFunction.h index c757f2cfaa2..136a4543e79 100644 --- a/Modules/Core/ImageFunction/include/itkVectorMeanImageFunction.h +++ b/Modules/Core/ImageFunction/include/itkVectorMeanImageFunction.h @@ -108,9 +108,10 @@ class ITK_TEMPLATE_EXPORT VectorMeanImageFunction /** Get/Set the radius of the neighborhood over which the statistics are evaluated */ + /** @ITKStartGrouping */ itkSetMacro(NeighborhoodRadius, unsigned int); itkGetConstReferenceMacro(NeighborhoodRadius, unsigned int); - + /** @ITKEndGrouping */ protected: VectorMeanImageFunction(); ~VectorMeanImageFunction() override = default; diff --git a/Modules/Core/ImageFunction/include/itkWindowedSincInterpolateImageFunction.h b/Modules/Core/ImageFunction/include/itkWindowedSincInterpolateImageFunction.h index 512bc02fecd..ee2a5efa6dd 100644 --- a/Modules/Core/ImageFunction/include/itkWindowedSincInterpolateImageFunction.h +++ b/Modules/Core/ImageFunction/include/itkWindowedSincInterpolateImageFunction.h @@ -42,6 +42,7 @@ class ITK_TEMPLATE_EXPORT CosineWindowFunction inline TOutput operator()(const TInput & A) const { + /** Equal to \f$ \frac{\pi}{2 m} \f$ */ static constexpr double factor = Math::pi / (2 * VRadius); return static_cast(std::cos(A * factor)); @@ -62,6 +63,7 @@ class ITK_TEMPLATE_EXPORT HammingWindowFunction inline TOutput operator()(const TInput & A) const { + /** Equal to \f$ \frac{\pi}{m} \f$ */ static constexpr double factor = Math::pi / VRadius; return static_cast(0.54 + 0.46 * std::cos(A * factor)); @@ -79,10 +81,11 @@ template (1.0 - A * factor * A); } @@ -108,6 +111,7 @@ class ITK_TEMPLATE_EXPORT LanczosWindowFunction { return static_cast(1.0); } // namespace Function + /** Equal to \f$ \frac{\pi}{m} \f$ */ static constexpr double factor = Math::pi / VRadius; const double z = factor * A; @@ -129,6 +133,7 @@ class ITK_TEMPLATE_EXPORT BlackmanWindowFunction inline TOutput operator()(const TInput & A) const { + /** Equal to \f$ \frac{\pi}{m} \f$ */ static constexpr double factor1 = Math::pi / VRadius; diff --git a/Modules/Core/Mesh/include/itkConnectedRegionsMeshFilter.h b/Modules/Core/Mesh/include/itkConnectedRegionsMeshFilter.h index 1ef911786af..ae89603c1fc 100644 --- a/Modules/Core/Mesh/include/itkConnectedRegionsMeshFilter.h +++ b/Modules/Core/Mesh/include/itkConnectedRegionsMeshFilter.h @@ -125,8 +125,10 @@ class ITK_TEMPLATE_EXPORT ConnectedRegionsMeshFilter : public MeshToMeshFilter using OutputMeshPointer = typename OutputMeshType::Pointer; /** Set the input image of this process object. */ + /** @ITKStartGrouping */ using Superclass::SetInput; void SetInput(unsigned int idx, const InputImageType * input); @@ -73,8 +74,9 @@ class ITK_TEMPLATE_EXPORT ImageToMeshFilter : public MeshSource { this->SetInput(0, input); } - + /** @ITKEndGrouping */ /** Get the input image of this process object. */ + /** @ITKStartGrouping */ const InputImageType * GetInput(unsigned int idx); const InputImageType * @@ -82,7 +84,7 @@ class ITK_TEMPLATE_EXPORT ImageToMeshFilter : public MeshSource { return this->GetInput(0); } - + /** @ITKEndGrouping */ /** Get the output Mesh of this process object. */ OutputMeshType * GetOutput(); diff --git a/Modules/Core/Mesh/include/itkImageToParametricSpaceFilter.h b/Modules/Core/Mesh/include/itkImageToParametricSpaceFilter.h index 6d46715db81..69a47669741 100644 --- a/Modules/Core/Mesh/include/itkImageToParametricSpaceFilter.h +++ b/Modules/Core/Mesh/include/itkImageToParametricSpaceFilter.h @@ -94,10 +94,11 @@ class ITK_TEMPLATE_EXPORT ImageToParametricSpaceFilter : public ImageToMeshFilte * That assumes that the type of PointData in the output * mesh is capable of accepting an itk::Index through * an operator=(). Default value = true */ + /** @ITKStartGrouping */ itkSetMacro(ComputeIndices, bool); itkGetConstMacro(ComputeIndices, bool); itkBooleanMacro(ComputeIndices); - + /** @ITKEndGrouping */ protected: ImageToParametricSpaceFilter(); ~ImageToParametricSpaceFilter() override = default; diff --git a/Modules/Core/Mesh/include/itkInteriorExteriorMeshFilter.h b/Modules/Core/Mesh/include/itkInteriorExteriorMeshFilter.h index a68199c1ab5..5ebb4d77b47 100644 --- a/Modules/Core/Mesh/include/itkInteriorExteriorMeshFilter.h +++ b/Modules/Core/Mesh/include/itkInteriorExteriorMeshFilter.h @@ -78,9 +78,10 @@ class ITK_TEMPLATE_EXPORT InteriorExteriorMeshFilter : public MeshToMeshFilter; using SpatialFunctionDataObjectPointer = typename SpatialFunctionDataObjectType::Pointer; diff --git a/Modules/Core/Mesh/include/itkMesh.h b/Modules/Core/Mesh/include/itkMesh.h index 55348fa9655..400dbc7a3bf 100644 --- a/Modules/Core/Mesh/include/itkMesh.h +++ b/Modules/Core/Mesh/include/itkMesh.h @@ -555,6 +555,7 @@ class ITK_TEMPLATE_EXPORT Mesh : public PointSet; @@ -286,12 +287,13 @@ class ITK_TEMPLATE_EXPORT SimplexMesh : public Mesh /** All these parameter setting function are public temporarily to make the * test easier */ + /** @ITKStartGrouping */ itkSetMacro(ResolutionX, unsigned int); itkSetMacro(ResolutionY, unsigned int); - + /** @ITKEndGrouping */ itkSetMacro(Center, OPointType); itkSetMacro(Scale, OPointType); diff --git a/Modules/Core/Mesh/include/itkTransformMeshFilter.h b/Modules/Core/Mesh/include/itkTransformMeshFilter.h index 0b18a1667ef..7e7dad9d1ce 100644 --- a/Modules/Core/Mesh/include/itkTransformMeshFilter.h +++ b/Modules/Core/Mesh/include/itkTransformMeshFilter.h @@ -72,9 +72,10 @@ class ITK_TEMPLATE_EXPORT TransformMeshFilter : public MeshToMeshFilter /** Set the resolution level to be used for generating cells in the * Sphere. High values of this parameter will produce sphere with more * triangles. */ + /** Set/Get the name of the file to be read. */ + /** @ITKStartGrouping */ itkSetStringMacro(FileName); itkGetStringMacro(FileName); - + /** @ITKEndGrouping */ /** Get the file version line */ itkGetStringMacro(Version); diff --git a/Modules/Core/Mesh/include/itkVTKPolyDataWriter.h b/Modules/Core/Mesh/include/itkVTKPolyDataWriter.h index de118a78f2c..759c19a58f0 100644 --- a/Modules/Core/Mesh/include/itkVTKPolyDataWriter.h +++ b/Modules/Core/Mesh/include/itkVTKPolyDataWriter.h @@ -97,9 +97,10 @@ class ITK_TEMPLATE_EXPORT VTKPolyDataWriter : public Object SetInput(const InputMeshType * input); /** Set/Get the name of the file where data are written. */ + /** @ITKStartGrouping */ itkSetStringMacro(FileName); itkGetStringMacro(FileName); - + /** @ITKEndGrouping */ protected: VTKPolyDataWriter(); ~VTKPolyDataWriter() override = default; diff --git a/Modules/Core/QuadEdgeMesh/include/itkGeometricalQuadEdge.h b/Modules/Core/QuadEdgeMesh/include/itkGeometricalQuadEdge.h index a45e6c5a3dc..3521fe18534 100644 --- a/Modules/Core/QuadEdgeMesh/include/itkGeometricalQuadEdge.h +++ b/Modules/Core/QuadEdgeMesh/include/itkGeometricalQuadEdge.h @@ -88,6 +88,7 @@ class ITK_TEMPLATE_EXPORT GeometricalQuadEdge : public QuadEdge using ConstIteratorGeom = QuadEdgeMeshConstIteratorGeom; /** Basic iterators methods. */ + /** @ITKStartGrouping */ inline itkQEDefineIteratorGeomMethodsMacro(Onext); inline itkQEDefineIteratorGeomMethodsMacro(Sym); inline itkQEDefineIteratorGeomMethodsMacro(Lnext); @@ -101,7 +102,7 @@ class ITK_TEMPLATE_EXPORT GeometricalQuadEdge : public QuadEdge inline itkQEDefineIteratorGeomMethodsMacro(InvLnext); inline itkQEDefineIteratorGeomMethodsMacro(InvRnext); inline itkQEDefineIteratorGeomMethodsMacro(InvDnext); - + /** @ITKEndGrouping */ /** QE macros. */ itkQEAccessorsMacro(Superclass, Self, DualType); @@ -172,6 +173,7 @@ class ITK_TEMPLATE_EXPORT GeometricalQuadEdge : public QuadEdge } /** Get methods. */ + /** @ITKStartGrouping */ // ORIENTATION_NOTE: this definition of GetLeft (or GetRight) // implicitly assumes that the Onext order is counter-clockwise ! inline const OriginRefType @@ -194,7 +196,7 @@ class ITK_TEMPLATE_EXPORT GeometricalQuadEdge : public QuadEdge { return (GetInvRot()->GetOrigin()); } - + /** @ITKEndGrouping */ /** Boolean accessors. */ bool IsOriginSet() const; @@ -209,6 +211,7 @@ class ITK_TEMPLATE_EXPORT GeometricalQuadEdge : public QuadEdge IsLeftSet() const; /** Extra data set methods. */ + /** @ITKStartGrouping */ inline void SetPrimalData(const PrimalDataType data) { @@ -220,7 +223,7 @@ class ITK_TEMPLATE_EXPORT GeometricalQuadEdge : public QuadEdge { this->GetRot()->SetPrimalData(data); } - + /** @ITKEndGrouping */ inline void SetPrimalData() { @@ -244,6 +247,7 @@ class ITK_TEMPLATE_EXPORT GeometricalQuadEdge : public QuadEdge } /** Extra data get methods. */ + /** @ITKStartGrouping */ inline PrimalDataType GetPrimalData() { @@ -254,8 +258,9 @@ class ITK_TEMPLATE_EXPORT GeometricalQuadEdge : public QuadEdge { return (this->GetRot()->GetPrimalData()); } - + /** @ITKEndGrouping */ /** Boolean accessors. */ + /** @ITKStartGrouping */ inline bool IsPrimalDataSet() { @@ -266,7 +271,7 @@ class ITK_TEMPLATE_EXPORT GeometricalQuadEdge : public QuadEdge { return (this->GetRot()->IsPrimalDataSet()); } - + /** @ITKEndGrouping */ /** * @return Returns true when "this" has no faces set on both sides. * Return false otherwise. @@ -323,6 +328,7 @@ class ITK_TEMPLATE_EXPORT GeometricalQuadEdge : public QuadEdge ReorderOnextRingBeforeAddFace(Self * second); /** Disconnection methods. */ + /** @ITKStartGrouping */ inline bool IsOriginDisconnected() { @@ -338,7 +344,7 @@ class ITK_TEMPLATE_EXPORT GeometricalQuadEdge : public QuadEdge { return (this->IsOriginDisconnected() && this->IsDestinationDisconnected()); } - + /** @ITKEndGrouping */ void Disconnect(); diff --git a/Modules/Core/QuadEdgeMesh/include/itkQuadEdge.h b/Modules/Core/QuadEdgeMesh/include/itkQuadEdge.h index fe0d98a3492..b16337af86a 100644 --- a/Modules/Core/QuadEdgeMesh/include/itkQuadEdge.h +++ b/Modules/Core/QuadEdgeMesh/include/itkQuadEdge.h @@ -52,6 +52,7 @@ * @param dt Dual edge type. * \todo Should this macro be added to doxygen macros? */ +/** @ITKStartGrouping */ #define itkQEAccessorsMacro(st, pt, dt) \ pt * GetOnext() { return (dynamic_cast(this->st::GetOnext())); } \ \ @@ -113,7 +114,7 @@ const pt * GetInvDnext() const { return (dynamic_cast(this->st::GetInvDnext())); } \ \ ITK_MACROEND_NOOP_STATEMENT - +/** @ITKEndGrouping */ namespace itk { /** @@ -143,6 +144,7 @@ class ITKQuadEdgeMesh_EXPORT QuadEdge using ConstIterator = QuadEdgeMeshConstIterator; /** Basic iterators methods. */ + /** @ITKStartGrouping */ inline itkQEDefineIteratorMethodsMacro(Onext); // itkQEDefineIteratorMethodsMacro( Sym ); // itkQEDefineIteratorMethodsMacro( Lnext ); @@ -156,8 +158,10 @@ class ITKQuadEdgeMesh_EXPORT QuadEdge // itkQEDefineIteratorMethodsMacro( InvLnext ); // itkQEDefineIteratorMethodsMacro( InvRnext ); // itkQEDefineIteratorMethodsMacro( InvDnext ); + /** @ITKEndGrouping */ /** Object creation methods. */ + /** @ITKStartGrouping */ QuadEdge(); QuadEdge(const QuadEdge &) = default; QuadEdge(QuadEdge &&) = default; @@ -166,8 +170,10 @@ class ITKQuadEdgeMesh_EXPORT QuadEdge QuadEdge & operator=(QuadEdge &&) = default; virtual ~QuadEdge(); + /** @ITKEndGrouping */ /** Sub-algebra Set methods. */ + /** @ITKStartGrouping */ inline void SetOnext(Self * onext) { @@ -178,10 +184,12 @@ class ITKQuadEdgeMesh_EXPORT QuadEdge { this->m_Rot = rot; } + /** @ITKEndGrouping */ /** Sub-algebra Get methods. * Returns edge with same Origin (see * "Accessing adjacent edges"). */ + /** @ITKStartGrouping */ inline Self * GetOnext() { @@ -202,6 +210,7 @@ class ITKQuadEdgeMesh_EXPORT QuadEdge { return this->m_Rot; } + /** @ITKEndGrouping */ /** * \brief Basic quad-edge topological method. @@ -241,6 +250,7 @@ class ITKQuadEdgeMesh_EXPORT QuadEdge /** Returns the symmetric edge * (see "Accessing adjacent edges"). */ + /** @ITKStartGrouping */ inline Self * GetSym() { @@ -260,6 +270,7 @@ class ITKQuadEdgeMesh_EXPORT QuadEdge } return nullptr; } + /** @ITKEndGrouping */ /** Returns next edge with same Left face * (see "Accessing adjacent edges"). */ @@ -323,6 +334,7 @@ class ITKQuadEdgeMesh_EXPORT QuadEdge GetDprev() const; /** Inverse operators */ + /** @ITKStartGrouping */ inline Self * GetInvRot() { @@ -413,8 +425,10 @@ class ITKQuadEdgeMesh_EXPORT QuadEdge { return this->GetDprev(); } + /** @ITKEndGrouping */ /** Queries. */ + /** @ITKStartGrouping */ inline bool IsHalfEdge() const { @@ -427,9 +441,9 @@ class ITKQuadEdgeMesh_EXPORT QuadEdge } bool IsEdgeInOnextRing(Self * testEdge) const; - bool IsLnextGivenSizeCyclic(const int size) const; + /** @ITKEndGrouping */ unsigned int GetOrder() const; diff --git a/Modules/Core/QuadEdgeMesh/include/itkQuadEdgeMesh.h b/Modules/Core/QuadEdgeMesh/include/itkQuadEdgeMesh.h index e687e7a5fce..e7ef3513171 100644 --- a/Modules/Core/QuadEdgeMesh/include/itkQuadEdgeMesh.h +++ b/Modules/Core/QuadEdgeMesh/include/itkQuadEdgeMesh.h @@ -165,8 +165,10 @@ class ITK_TEMPLATE_EXPORT QuadEdgeMesh : public Mesh; using EdgeCellListType = std::vector; - //** */ + /** */ using PointIdIterator = typename CellTraits::PointIdIterator; using PointIdConstIterator = typename CellTraits::PointIdConstIterator; using PointIdInternalIterator = typename CellTraits::PointIdInternalIterator; @@ -97,11 +97,13 @@ class ITK_TEMPLATE_EXPORT QuadEdgeMeshPolygonCell : public TCellInterface itkOverrideGetNameOfClassMacro(QuadEdgeMeshPolygonCell); /** Object memory management methods. */ + /** @ITKStartGrouping */ QuadEdgeMeshPolygonCell(PointIdentifier nPoints = 0); QuadEdgeMeshPolygonCell(QuadEdgeType * e); ~QuadEdgeMeshPolygonCell() override; - + /** @ITKEndGrouping */ /** Accessors for m_Ident. */ + /** @ITKStartGrouping */ void SetIdent(CellIdentifier cid) { @@ -112,8 +114,9 @@ class ITK_TEMPLATE_EXPORT QuadEdgeMeshPolygonCell : public TCellInterface { return (m_Ident); } - + /** @ITKEndGrouping */ /** Lnext ring entry accessors. */ + /** @ITKStartGrouping */ QuadEdgeType * GetEdgeRingEntry() const { @@ -124,7 +127,7 @@ class ITK_TEMPLATE_EXPORT QuadEdgeMeshPolygonCell : public TCellInterface { m_EdgeRingEntry = entry; } - + /** @ITKEndGrouping */ /** Implement the standard CellInterface. */ SelfAutoPointer New(); diff --git a/Modules/Core/QuadEdgeMesh/include/itkQuadEdgeMeshScalarDataVTKPolyDataWriter.h b/Modules/Core/QuadEdgeMesh/include/itkQuadEdgeMeshScalarDataVTKPolyDataWriter.h index c141b8e3e0d..0dfdada6414 100644 --- a/Modules/Core/QuadEdgeMesh/include/itkQuadEdgeMeshScalarDataVTKPolyDataWriter.h +++ b/Modules/Core/QuadEdgeMesh/include/itkQuadEdgeMeshScalarDataVTKPolyDataWriter.h @@ -74,13 +74,15 @@ class ITK_TEMPLATE_EXPORT QuadEdgeMeshScalarDataVTKPolyDataWriter : public VTKPo using CellDataContainerConstPointer = typename CellDataContainer::ConstPointer; /** Set/Get the name of the CellDataName where data are written. */ + /** @ITKStartGrouping */ itkSetStringMacro(CellDataName); itkGetStringMacro(CellDataName); - + /** @ITKEndGrouping */ /** Set/Get the name of the PointDataName where data are written. */ + /** @ITKStartGrouping */ itkSetStringMacro(PointDataName); itkGetStringMacro(PointDataName); - + /** @ITKEndGrouping */ protected: QuadEdgeMeshScalarDataVTKPolyDataWriter(); ~QuadEdgeMeshScalarDataVTKPolyDataWriter() override = default; diff --git a/Modules/Core/SpatialObjects/include/itkGaussianSpatialObject.h b/Modules/Core/SpatialObjects/include/itkGaussianSpatialObject.h index bb68433ad66..5ee2d9f0ba3 100644 --- a/Modules/Core/SpatialObjects/include/itkGaussianSpatialObject.h +++ b/Modules/Core/SpatialObjects/include/itkGaussianSpatialObject.h @@ -69,22 +69,25 @@ class ITK_TEMPLATE_EXPORT GaussianSpatialObject : public SpatialObject GetMTime() const override; /** Set the slice position */ + /** @ITKStartGrouping */ itkSetMacro(SliceNumber, IndexType); void SetSliceNumber(unsigned int dimension, int position); - + /** @ITKEndGrouping */ /** Get the slice position */ + /** @ITKStartGrouping */ itkGetConstMacro(SliceNumber, IndexType); int GetSliceNumber(unsigned int dimension) { return m_SliceNumber[dimension]; } - + /** @ITKEndGrouping */ #if !defined(ITK_LEGACY_REMOVE) itkLegacyMacro(const char * GetPixelTypeName()) { @@ -123,10 +125,11 @@ class ITK_TEMPLATE_EXPORT ImageSpatialObject : public SpatialObject #endif /** Set/Get the interpolator. */ + /** @ITKStartGrouping */ void SetInterpolator(InterpolatorType * interpolator); itkGetConstMacro(Interpolator, InterpolatorType *); - + /** @ITKEndGrouping */ /** Updates the regions of this spatial object in accordance with its current image, and calls its Superclass. */ void Update() override; diff --git a/Modules/Core/SpatialObjects/include/itkMeshSpatialObject.h b/Modules/Core/SpatialObjects/include/itkMeshSpatialObject.h index 1ccef3fea64..2565d695328 100644 --- a/Modules/Core/SpatialObjects/include/itkMeshSpatialObject.h +++ b/Modules/Core/SpatialObjects/include/itkMeshSpatialObject.h @@ -72,11 +72,12 @@ class ITK_TEMPLATE_EXPORT MeshSpatialObject : public SpatialObject; + /** Convert the MetaObject to Spatial Object */ SpatialObjectPointer MetaObjectToSpatialObject(const MetaObjectType * mo) override; @@ -73,11 +74,12 @@ class ITK_TEMPLATE_EXPORT MetaImageConverter : public MetaConverterBasem_DuplicateSpatialObject.GetPointer(); } - + /** @ITKEndGrouping */ #if !defined(ITK_LEGACY_REMOVE) // This interface was exposed in ITKv4 when the itkGetModifiableObjectMacro was used virtual SpatialObjectType * diff --git a/Modules/Core/SpatialObjects/include/itkSpatialObjectToImageFilter.h b/Modules/Core/SpatialObjects/include/itkSpatialObjectToImageFilter.h index b0c72ba749b..ba382094f2b 100644 --- a/Modules/Core/SpatialObjects/include/itkSpatialObjectToImageFilter.h +++ b/Modules/Core/SpatialObjects/include/itkSpatialObjectToImageFilter.h @@ -138,8 +138,10 @@ class ITK_TEMPLATE_EXPORT SpatialObjectToImageFilter : public ImageSource; /** Set/Get the direction of the sample */ + /** @ITKStartGrouping */ itkSetMacro(SampleDirection, unsigned int); itkGetConstMacro(SampleDirection, unsigned int); - + /** @ITKEndGrouping */ /** Set the input image. */ itkSetConstObjectMacro(Image, ImageType); diff --git a/Modules/Core/SpatialObjects/include/itkSpatialObjectToPointSetFilter.h b/Modules/Core/SpatialObjects/include/itkSpatialObjectToPointSetFilter.h index f569219c237..0cb6c954214 100644 --- a/Modules/Core/SpatialObjects/include/itkSpatialObjectToPointSetFilter.h +++ b/Modules/Core/SpatialObjects/include/itkSpatialObjectToPointSetFilter.h @@ -81,18 +81,20 @@ class ITK_TEMPLATE_EXPORT SpatialObjectToPointSetFilter : public MeshSourceGetNumberOfParametersPerDimension() ) to the indices array. */ + /** @ITKStartGrouping */ using Superclass::TransformPoint; void TransformPoint(const InputPointType & point, @@ -237,7 +238,7 @@ class ITK_TEMPLATE_EXPORT BSplineTransform : public BSplineBaseTransformGetCenter(); } - + /** @ITKEndGrouping */ /** Set the matrix of the transform. The matrix should not include * scale */ void @@ -96,6 +97,7 @@ class ITK_TEMPLATE_EXPORT FixedCenterOfRotationAffineTransform { this->SetMatrix(matrix); } + /** Get matrix of the transform */ const MatrixType & GetMatrixComponent() const @@ -119,13 +121,14 @@ class ITK_TEMPLATE_EXPORT FixedCenterOfRotationAffineTransform protected: /** Construct an FixedCenterOfRotationAffineTransform object */ + /** @ITKStartGrouping */ #if !defined(ITK_LEGACY_REMOVE) [[deprecated("Removed unused constructor")]] FixedCenterOfRotationAffineTransform(const MatrixType & matrix, const OutputVectorType & offset); #endif FixedCenterOfRotationAffineTransform(unsigned int outputSpaceDims, unsigned int paramsDims); FixedCenterOfRotationAffineTransform(); - + /** @ITKEndGrouping */ /** Destroy an FixedCenterOfRotationAffineTransform object */ ~FixedCenterOfRotationAffineTransform() override = default; }; // class FixedCenterOfRotationAffineTransform diff --git a/Modules/Core/Transform/include/itkIdentityTransform.h b/Modules/Core/Transform/include/itkIdentityTransform.h index 57d9a5ae058..f7ab4d8901a 100644 --- a/Modules/Core/Transform/include/itkIdentityTransform.h +++ b/Modules/Core/Transform/include/itkIdentityTransform.h @@ -177,7 +177,6 @@ class ITK_TEMPLATE_EXPORT IdentityTransform : public Transform; @@ -228,9 +232,10 @@ class ITK_TEMPLATE_EXPORT KernelTransform : public Transform::max()); itkGetConstMacro(Stiffness, double); - + /** @ITKEndGrouping */ protected: KernelTransform(); ~KernelTransform() override = default; diff --git a/Modules/Core/Transform/include/itkMatrixOffsetTransformBase.h b/Modules/Core/Transform/include/itkMatrixOffsetTransformBase.h index 642a226bc6b..657a3cdcad8 100644 --- a/Modules/Core/Transform/include/itkMatrixOffsetTransformBase.h +++ b/Modules/Core/Transform/include/itkMatrixOffsetTransformBase.h @@ -507,11 +507,13 @@ class ITK_TEMPLATE_EXPORT MatrixOffsetTransformBase * to values specified by the caller. If the arguments are * omitted, then the MatrixOffsetTransformBase is initialized to an identity * transformation in the appropriate number of dimensions. */ + /** @ITKStartGrouping */ #if !defined(ITK_LEGACY_REMOVE) [[deprecated("Removed unused constructor")]] MatrixOffsetTransformBase(const MatrixType & matrix, const OutputVectorType & offset); #endif explicit MatrixOffsetTransformBase(unsigned int paramDims = ParametersDimension); + /** @ITKEndGrouping */ /** Destroy an MatrixOffsetTransformBase object */ ~MatrixOffsetTransformBase() override = default; diff --git a/Modules/Core/Transform/include/itkMultiTransform.h b/Modules/Core/Transform/include/itkMultiTransform.h index ac353539297..db798d08cb2 100644 --- a/Modules/Core/Transform/include/itkMultiTransform.h +++ b/Modules/Core/Transform/include/itkMultiTransform.h @@ -86,12 +86,15 @@ class ITK_TEMPLATE_EXPORT MultiTransform : public TransformGetNameOfClass()); } + /** Method to transform a CovariantVector, using a point. Global transforms * can ignore the \c point parameter. Local transforms (e.g. deformation * field transform) must override and provide required behavior. @@ -557,6 +558,7 @@ class ITK_TEMPLATE_EXPORT Transform : public TransformBaseTemplate std::enable_if_t ApplyToImageMetadata(TImage * image) const; @@ -566,7 +568,7 @@ class ITK_TEMPLATE_EXPORT Transform : public TransformBaseTemplateApplyToImageMetadata(image.GetPointer()); // Delegate to the raw pointer signature } - + /** @ITKEndGrouping */ protected: /** * Clone the current transform. diff --git a/Modules/Core/Transform/include/itkTransformGeometryImageFilter.h b/Modules/Core/Transform/include/itkTransformGeometryImageFilter.h index 25e34453782..709b115a8c7 100644 --- a/Modules/Core/Transform/include/itkTransformGeometryImageFilter.h +++ b/Modules/Core/Transform/include/itkTransformGeometryImageFilter.h @@ -142,9 +142,10 @@ class ITK_TEMPLATE_EXPORT TransformGeometryImageFilter : public InPlaceImageFilt itkSetGetDecoratedObjectInputMacro(Transform, TransformType); /** Set/Get required input image. */ + /** @ITKStartGrouping */ itkSetInputMacro(InputImage, InputImageType); itkGetInputMacro(InputImage, InputImageType); - + /** @ITKEndGrouping */ protected: TransformGeometryImageFilter(); ~TransformGeometryImageFilter() override = default; diff --git a/Modules/Core/Transform/include/itkVersorTransform.h b/Modules/Core/Transform/include/itkVersorTransform.h index 13dedf257d8..1a62f438bd7 100644 --- a/Modules/Core/Transform/include/itkVersorTransform.h +++ b/Modules/Core/Transform/include/itkVersorTransform.h @@ -135,13 +135,14 @@ class ITK_TEMPLATE_EXPORT VersorTransform : public Rigid3DTransform; /** Set/Get the input image. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(Image, ImageType); itkGetConstObjectMacro(Image, ImageType); - + /** @ITKEndGrouping */ /** Set/Get the number of minimum intensity pixels per slice. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfSamples, unsigned int); itkGetConstReferenceMacro(NumberOfSamples, unsigned int); - + /** @ITKEndGrouping */ /** Set/Get the minimum threshold value for the background pixels */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundMinimumThreshold, ImagePixelType); itkGetConstReferenceMacro(BackgroundMinimumThreshold, ImagePixelType); - + /** @ITKEndGrouping */ /** Set/Get the tolerance value. */ + /** @ITKStartGrouping */ itkSetMacro(Tolerance, double); itkGetConstReferenceMacro(Tolerance, double); - + /** @ITKEndGrouping */ /** Set/Get the direction of slicing/ * 0 - x axis, 1 - y axis, 2 - z axis */ + /** @ITKStartGrouping */ itkSetMacro(SlicingDirection, int); itkGetConstReferenceMacro(SlicingDirection, int); - + /** @ITKEndGrouping */ /** Compute the average values of minimum intensity pixels for each slice and * compare the average values with overall averages. */ void diff --git a/Modules/Filtering/BiasCorrection/include/itkMRIBiasFieldCorrectionFilter.h b/Modules/Filtering/BiasCorrection/include/itkMRIBiasFieldCorrectionFilter.h index 349a3f06a0a..1b9111390a0 100644 --- a/Modules/Filtering/BiasCorrection/include/itkMRIBiasFieldCorrectionFilter.h +++ b/Modules/Filtering/BiasCorrection/include/itkMRIBiasFieldCorrectionFilter.h @@ -293,15 +293,19 @@ class ITK_TEMPLATE_EXPORT MRIBiasFieldCorrectionFilter : public ImageToImageFilt /** Set/Get the input mask image pointer. * Without this mask, this filter calculates the energy value using * all pixels in the input image. */ + /** @ITKStartGrouping */ void SetInputMask(ImageMaskType * inputMask); itkGetModifiableObjectMacro(InputMask, ImageMaskType); + /** @ITKEndGrouping */ /** Get/Set the out mask image pointer. * Without this mask, this filter corrects every pixel in the input image. */ + /** @ITKStartGrouping */ void SetOutputMask(ImageMaskType * outputMask); itkGetModifiableObjectMacro(OutputMask, ImageMaskType); + /** @ITKEndGrouping */ #if defined(ITK_LEGACY_REMOVE) /** If this value is true, the filter assumes the bias field is @@ -317,9 +321,11 @@ class ITK_TEMPLATE_EXPORT MRIBiasFieldCorrectionFilter : public ImageToImageFilt /** Set/Get the multiplicative nature of the filter's bias field: if * true, the filter assumes the bias field is multiplicative and * internally uses log intensity values for every calculation. */ + /** @ITKStartGrouping */ itkSetMacro(BiasFieldMultiplicative, bool); itkGetConstMacro(BiasFieldMultiplicative, bool); itkBooleanMacro(BiasFieldMultiplicative); + /** @ITKEndGrouping */ #if defined(ITK_LEGACY_REMOVE) /** If the bias field is multiplicative, it returns true. */ @@ -334,18 +340,22 @@ class ITK_TEMPLATE_EXPORT MRIBiasFieldCorrectionFilter : public ImageToImageFilt * intensity correction will be applied before bias field * correction (default value is true for 3D input images, and false for 2D * input images). */ + /** @ITKStartGrouping */ itkSetMacro(UsingInterSliceIntensityCorrection, bool); itkGetConstMacro(UsingInterSliceIntensityCorrection, bool); itkBooleanMacro(UsingInterSliceIntensityCorrection); + /** @ITKEndGrouping */ /** Set/Get the slab correction flag. If the flag is true, inter-slice * intensity correction and bias field correction will be performed slab by * slab which is identified by the slab identifier (default value is false). * NOTE: if users want to slab identification, all the input image data * should be buffered. */ + /** @ITKStartGrouping */ itkSetMacro(UsingSlabIdentification, bool); itkGetConstMacro(UsingSlabIdentification, bool); itkBooleanMacro(UsingSlabIdentification); + /** @ITKEndGrouping */ itkSetMacro(SlabBackgroundMinimumThreshold, InputImagePixelType); itkGetConstReferenceMacro(SlabBackgroundMinimumThreshold, InputImagePixelType); @@ -361,24 +371,32 @@ class ITK_TEMPLATE_EXPORT MRIBiasFieldCorrectionFilter : public ImageToImageFilt * the inter-slice intensity correction without actual bias correction, * disabling bias field correction would be an useful option (default value * is true). */ + /** @ITKStartGrouping */ itkSetMacro(UsingBiasFieldCorrection, bool); itkGetConstMacro(UsingBiasFieldCorrection, bool); itkBooleanMacro(UsingBiasFieldCorrection); + /** @ITKEndGrouping */ /** Set/Get the flag. If the flag is true, the output image (corrected image) * will be created when this filter is updated (default value is true). */ + /** @ITKStartGrouping */ itkSetMacro(GeneratingOutput, bool); itkGetConstMacro(GeneratingOutput, bool); itkBooleanMacro(GeneratingOutput); + /** @ITKEndGrouping */ /** Sets the direction of slicing. * 0 - x axis, 1 - y axis, 2 - z axis */ + /** @ITKStartGrouping */ itkSetMacro(SlicingDirection, int); itkGetConstMacro(SlicingDirection, int); + /** @ITKEndGrouping */ /** Set/Get the degree of the bias field estimate. */ + /** @ITKStartGrouping */ itkSetMacro(BiasFieldDegree, int); itkGetConstMacro(BiasFieldDegree, int); + /** @ITKEndGrouping */ /** Sets the initial 3D bias field estimate coefficients that will be * used for correcting each slab. */ @@ -406,26 +424,35 @@ class ITK_TEMPLATE_EXPORT MRIBiasFieldCorrectionFilter : public ImageToImageFilt /** Set/Get the maximum iteration termination condition parameter for the * bias field correction. */ + /** @ITKStartGrouping */ itkSetMacro(VolumeCorrectionMaximumIteration, int); itkGetConstMacro(VolumeCorrectionMaximumIteration, int); + /** @ITKEndGrouping */ /** Set/Get the maximum iteration termination condition parameter for the * inter-slice intensity inhomogeneity correction. */ + /** @ITKStartGrouping */ itkSetMacro(InterSliceCorrectionMaximumIteration, int); itkGetConstMacro(InterSliceCorrectionMaximumIteration, int); + /** @ITKEndGrouping */ /** Set/Get the initial search radius. */ + /** @ITKStartGrouping */ itkSetMacro(OptimizerInitialRadius, double); itkGetConstMacro(OptimizerInitialRadius, double); + /** @ITKEndGrouping */ /** Set/Get the search radius grow factor. */ + /** @ITKStartGrouping */ itkSetMacro(OptimizerGrowthFactor, double); itkGetConstMacro(OptimizerGrowthFactor, double); + /** @ITKEndGrouping */ /** Set/Get the search radius shrink factor. */ - + /** @ITKStartGrouping */ itkSetMacro(OptimizerShrinkFactor, double); itkGetConstMacro(OptimizerShrinkFactor, double); + /** @ITKEndGrouping */ /** Set the number of multi-resolution levels. The matrix containing the * schedule will be resized accordingly. The schedule is populated with diff --git a/Modules/Filtering/BiasCorrection/include/itkN4BiasFieldCorrectionImageFilter.h b/Modules/Filtering/BiasCorrection/include/itkN4BiasFieldCorrectionImageFilter.h index 9594d5f74f0..b5d60f2618d 100644 --- a/Modules/Filtering/BiasCorrection/include/itkN4BiasFieldCorrectionImageFilter.h +++ b/Modules/Filtering/BiasCorrection/include/itkN4BiasFieldCorrectionImageFilter.h @@ -146,12 +146,14 @@ class ITK_TEMPLATE_EXPORT N4BiasFieldCorrectionImageFilter : public ImageToImage * those input image voxels inside the mask image values are used in * estimating the bias field. */ + /** @ITKStartGrouping */ itkSetInputMacro(MaskImage, MaskImageType); void SetInput2(const MaskImageType * mask) { this->SetMaskImage(mask); } + /** @ITKEndGrouping */ /** * Get mask image function. If a binary mask image is specified, only @@ -168,15 +170,19 @@ class ITK_TEMPLATE_EXPORT N4BiasFieldCorrectionImageFilter : public ImageToImage * input image voxels corresponding to non-zero voxels in the MaskImage * are used in estimating the bias field. Default = 1. */ + /** @ITKStartGrouping */ itkSetMacro(MaskLabel, MaskPixelType); itkGetConstMacro(MaskLabel, MaskPixelType); + /** @ITKEndGrouping */ /** * Use a mask label for identifying mask functionality. See SetMaskLabel. * Defaults to false. */ + /** @ITKStartGrouping */ itkSetMacro(UseMaskLabel, bool); itkGetConstMacro(UseMaskLabel, bool); itkBooleanMacro(UseMaskLabel); + /** @ITKEndGrouping */ /** * Set confidence image function. If a confidence image is specified, @@ -188,12 +194,14 @@ class ITK_TEMPLATE_EXPORT N4BiasFieldCorrectionImageFilter : public ImageToImage * been done in the literature) as an alternative strategy to estimating the * bias field. */ + /** @ITKStartGrouping */ itkSetInputMacro(ConfidenceImage, RealImageType); void SetInput3(const RealImageType * image) { this->SetConfidenceImage(image); } + /** @ITKEndGrouping */ /** * Get confidence image function. If a confidence image is specified, diff --git a/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryClosingByReconstructionImageFilter.h b/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryClosingByReconstructionImageFilter.h index bf1d448f421..21021427f3b 100644 --- a/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryClosingByReconstructionImageFilter.h +++ b/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryClosingByReconstructionImageFilter.h @@ -90,10 +90,11 @@ class ITK_TEMPLATE_EXPORT BinaryClosingByReconstructionImageFilter * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ protected: BinaryClosingByReconstructionImageFilter(); ~BinaryClosingByReconstructionImageFilter() override = default; diff --git a/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryMorphologicalClosingImageFilter.h b/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryMorphologicalClosingImageFilter.h index 2596a51302b..259c4c9d5ac 100644 --- a/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryMorphologicalClosingImageFilter.h +++ b/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryMorphologicalClosingImageFilter.h @@ -95,10 +95,11 @@ class ITK_TEMPLATE_EXPORT BinaryMorphologicalClosingImageFilter /** A safe border is added to input image to avoid borders effects * and remove it once the closing is done */ + /** @ITKStartGrouping */ itkSetMacro(SafeBorder, bool); itkGetConstReferenceMacro(SafeBorder, bool); itkBooleanMacro(SafeBorder); - + /** @ITKEndGrouping */ protected: BinaryMorphologicalClosingImageFilter(); ~BinaryMorphologicalClosingImageFilter() override = default; diff --git a/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryMorphologyImageFilter.h b/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryMorphologyImageFilter.h index 65b7f8ef376..b77ea3f1da4 100644 --- a/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryMorphologyImageFilter.h +++ b/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryMorphologyImageFilter.h @@ -166,10 +166,11 @@ class ITK_TEMPLATE_EXPORT BinaryMorphologyImageFilter : public KernelImageFilter /** Get/Set the borders as foreground (true) or background (false). */ + /** @ITKStartGrouping */ itkSetMacro(BoundaryToForeground, bool); itkGetConstReferenceMacro(BoundaryToForeground, bool); itkBooleanMacro(BoundaryToForeground); - + /** @ITKEndGrouping */ /** Set kernel (structuring element). */ void SetKernel(const KernelType & kernel) override; diff --git a/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryOpeningByReconstructionImageFilter.h b/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryOpeningByReconstructionImageFilter.h index a42f2074510..a92bc0ddd63 100644 --- a/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryOpeningByReconstructionImageFilter.h +++ b/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryOpeningByReconstructionImageFilter.h @@ -95,10 +95,11 @@ class ITK_TEMPLATE_EXPORT BinaryOpeningByReconstructionImageFilter * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ protected: BinaryOpeningByReconstructionImageFilter(); ~BinaryOpeningByReconstructionImageFilter() override = default; diff --git a/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryPruningImageFilter.h b/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryPruningImageFilter.h index 4d18abc35f3..4fe8ebe992c 100644 --- a/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryPruningImageFilter.h +++ b/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryPruningImageFilter.h @@ -101,9 +101,10 @@ class ITK_TEMPLATE_EXPORT BinaryPruningImageFilter : public ImageToImageFilterrgb mapping operation on one image. @@ -181,18 +182,20 @@ class ITK_TEMPLATE_EXPORT ScalarToRGBColormapImageFilter : public ImageToImageFi #endif /** Set/Get the colormap object. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Colormap, ColormapType); itkGetModifiableObjectMacro(Colormap, ColormapType); - + /** @ITKEndGrouping */ void SetColormap(RGBColormapFilterEnum); /** Set/Get UseInputImageExtremaForScaling. If true, the colormap uses the * min and max values from the image to scale appropriately. Otherwise, * these values can be set in the colormap manually. */ + /** @ITKStartGrouping */ itkSetMacro(UseInputImageExtremaForScaling, bool); itkGetConstMacro(UseInputImageExtremaForScaling, bool); itkBooleanMacro(UseInputImageExtremaForScaling); - + /** @ITKEndGrouping */ protected: ScalarToRGBColormapImageFilter(); ~ScalarToRGBColormapImageFilter() override = default; diff --git a/Modules/Filtering/Convolution/include/itkConvolutionImageFilterBase.h b/Modules/Filtering/Convolution/include/itkConvolutionImageFilterBase.h index be046213d62..52de9a0605e 100644 --- a/Modules/Filtering/Convolution/include/itkConvolutionImageFilterBase.h +++ b/Modules/Filtering/Convolution/include/itkConvolutionImageFilterBase.h @@ -41,6 +41,7 @@ class ConvolutionImageFilterBaseEnums VALID }; }; + /** Define how to print enumerations */ extern ITKConvolution_EXPORT std::ostream & operator<<(std::ostream & out, const ConvolutionImageFilterBaseEnums::ConvolutionImageFilterOutputRegion value); @@ -95,19 +96,22 @@ class ITK_TEMPLATE_EXPORT ConvolutionImageFilterBase : public ImageToImageFilter using DefaultBoundaryConditionType = ZeroFluxNeumannBoundaryCondition; /** Set/get the boundary condition. */ + /** @ITKStartGrouping */ itkSetMacro(BoundaryCondition, BoundaryConditionType *); itkGetConstMacro(BoundaryCondition, BoundaryConditionType *); - + /** @ITKEndGrouping */ /** Set/get the image kernel. */ + /** @ITKStartGrouping */ itkSetInputMacro(KernelImage, KernelImageType); itkGetInputMacro(KernelImage, KernelImageType); - + /** @ITKEndGrouping */ /** Normalize the output image by the sum of the kernel * components. Defaults to off. */ + /** @ITKStartGrouping */ itkSetMacro(Normalize, bool); itkGetConstMacro(Normalize, bool); itkBooleanMacro(Normalize); - + /** @ITKEndGrouping */ /** Reverse compatibility for enumerations */ using OutputRegionModeEnum = ConvolutionImageFilterBaseEnums::ConvolutionImageFilterOutputRegion; #if !defined(ITK_LEGACY_REMOVE) @@ -127,13 +131,14 @@ class ITK_TEMPLATE_EXPORT ConvolutionImageFilterBase : public ImageToImageFilter * (no extrapolated contributions from the boundary condition are * needed). The output is therefore smaller than the input * region. Default output region mode is SAME. */ + /** @ITKStartGrouping */ itkSetEnumMacro(OutputRegionMode, OutputRegionModeEnum); itkGetEnumMacro(OutputRegionMode, OutputRegionModeEnum); virtual void SetOutputRegionModeToSame(); virtual void SetOutputRegionModeToValid(); - + /** @ITKEndGrouping */ protected: ConvolutionImageFilterBase(); ~ConvolutionImageFilterBase() override = default; diff --git a/Modules/Filtering/Convolution/include/itkFFTNormalizedCorrelationImageFilter.h b/Modules/Filtering/Convolution/include/itkFFTNormalizedCorrelationImageFilter.h index 1b9924508bf..a135d67a2a6 100644 --- a/Modules/Filtering/Convolution/include/itkFFTNormalizedCorrelationImageFilter.h +++ b/Modules/Filtering/Convolution/include/itkFFTNormalizedCorrelationImageFilter.h @@ -93,7 +93,6 @@ namespace itk * \sphinxexample{Filtering/Convolution/NormalizedCorrelationUsingFFT,Normalized Correlation Using FFT} * \endsphinx */ - template class ITK_TEMPLATE_EXPORT FFTNormalizedCorrelationImageFilter : public MaskedFFTNormalizedCorrelationImageFilter diff --git a/Modules/Filtering/Convolution/include/itkMaskedFFTNormalizedCorrelationImageFilter.h b/Modules/Filtering/Convolution/include/itkMaskedFFTNormalizedCorrelationImageFilter.h index d8a3b384ed1..73346f14a29 100644 --- a/Modules/Filtering/Convolution/include/itkMaskedFFTNormalizedCorrelationImageFilter.h +++ b/Modules/Filtering/Convolution/include/itkMaskedFFTNormalizedCorrelationImageFilter.h @@ -135,7 +135,6 @@ namespace itk With Mask Images For Input Images} * \endsphinx */ - template class ITK_TEMPLATE_EXPORT MaskedFFTNormalizedCorrelationImageFilter : public ImageToImageFilter @@ -186,29 +185,35 @@ class ITK_TEMPLATE_EXPORT MaskedFFTNormalizedCorrelationImageFilter using FFTImagePointer = typename FFTImageType::Pointer; /** Set and get the fixed image */ + /** @ITKStartGrouping */ itkSetInputMacro(FixedImage, InputImageType); itkGetInputMacro(FixedImage, InputImageType); - + /** @ITKEndGrouping */ /** Set and get the moving image */ + /** @ITKStartGrouping */ itkSetInputMacro(MovingImage, InputImageType); itkGetInputMacro(MovingImage, InputImageType); - + /** @ITKEndGrouping */ /** Set and get the fixed mask */ + /** @ITKStartGrouping */ itkSetInputMacro(FixedImageMask, MaskImageType); itkGetInputMacro(FixedImageMask, MaskImageType); - + /** @ITKEndGrouping */ /** Set and get the moving mask */ + /** @ITKStartGrouping */ itkSetInputMacro(MovingImageMask, MaskImageType); itkGetInputMacro(MovingImageMask, MaskImageType); - + /** @ITKEndGrouping */ /** Set and get the required number of overlapping pixels */ + /** @ITKStartGrouping */ itkSetMacro(RequiredNumberOfOverlappingPixels, SizeValueType); itkGetMacro(RequiredNumberOfOverlappingPixels, SizeValueType); - + /** @ITKEndGrouping */ /** Set and get the required fraction of overlapping pixels */ + /** @ITKStartGrouping */ itkGetMacro(RequiredFractionOfOverlappingPixels, RealPixelType); itkSetClampMacro(RequiredFractionOfOverlappingPixels, RealPixelType, 0.0f, 1.0f); - + /** @ITKEndGrouping */ /** Get the maximum number of overlapping pixels. */ itkGetMacro(MaximumNumberOfOverlappingPixels, SizeValueType); @@ -323,14 +328,17 @@ class ITK_TEMPLATE_EXPORT MaskedFFTNormalizedCorrelationImageFilter * Thus, larger values remove less stable computations but also limit the capture range. * The default is set to 0. */ SizeValueType m_RequiredNumberOfOverlappingPixels{}; + /** Similar to m_RequiredNumberOfOverlappingPixels except that the m_RequiredFractionOfOverlappingPixels is multiplied * by the m_MaximumNumberOfOverlappingPixels to determine the requiredNumberOfOverlappingPixels. The default is 0. */ RealPixelType m_RequiredFractionOfOverlappingPixels{}; + /** This is computed internally */ SizeValueType m_MaximumNumberOfOverlappingPixels{}; /** This is used for the progress reporter */ const unsigned int m_TotalForwardAndInverseFFTs{ 12 }; + /** The total accumulated progress */ float m_AccumulatedProgress{}; }; diff --git a/Modules/Filtering/CurvatureFlow/include/itkBinaryMinMaxCurvatureFlowFunction.h b/Modules/Filtering/CurvatureFlow/include/itkBinaryMinMaxCurvatureFlowFunction.h index 71e5573d1ae..3d4c4d336b8 100644 --- a/Modules/Filtering/CurvatureFlow/include/itkBinaryMinMaxCurvatureFlowFunction.h +++ b/Modules/Filtering/CurvatureFlow/include/itkBinaryMinMaxCurvatureFlowFunction.h @@ -68,6 +68,7 @@ class ITK_TEMPLATE_EXPORT BinaryMinMaxCurvatureFlowFunction : public MinMaxCurva static constexpr unsigned int ImageDimension = Superclass::ImageDimension; /** Set/Get the threshold value. */ + /** @ITKStartGrouping */ void SetThreshold(const double thresh) { @@ -78,7 +79,7 @@ class ITK_TEMPLATE_EXPORT BinaryMinMaxCurvatureFlowFunction : public MinMaxCurva { return m_Threshold; } - + /** @ITKEndGrouping */ /** Compute the solution update for each pixel that does not lie on a the data set boundary. */ PixelType ComputeUpdate(const NeighborhoodType & it, diff --git a/Modules/Filtering/CurvatureFlow/include/itkBinaryMinMaxCurvatureFlowImageFilter.h b/Modules/Filtering/CurvatureFlow/include/itkBinaryMinMaxCurvatureFlowImageFilter.h index 5d066345b41..5a8221c9260 100644 --- a/Modules/Filtering/CurvatureFlow/include/itkBinaryMinMaxCurvatureFlowImageFilter.h +++ b/Modules/Filtering/CurvatureFlow/include/itkBinaryMinMaxCurvatureFlowImageFilter.h @@ -104,9 +104,10 @@ class ITK_TEMPLATE_EXPORT BinaryMinMaxCurvatureFlowImageFilter static constexpr unsigned int ImageDimension = Superclass::ImageDimension; /** Set/Get the threshold value. */ + /** @ITKStartGrouping */ itkSetMacro(Threshold, double); itkGetConstMacro(Threshold, double); - + /** @ITKEndGrouping */ itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); diff --git a/Modules/Filtering/CurvatureFlow/include/itkMinMaxCurvatureFlowImageFilter.h b/Modules/Filtering/CurvatureFlow/include/itkMinMaxCurvatureFlowImageFilter.h index d7c8bf45508..db897a401ee 100644 --- a/Modules/Filtering/CurvatureFlow/include/itkMinMaxCurvatureFlowImageFilter.h +++ b/Modules/Filtering/CurvatureFlow/include/itkMinMaxCurvatureFlowImageFilter.h @@ -109,9 +109,10 @@ class ITK_TEMPLATE_EXPORT MinMaxCurvatureFlowImageFilter : public CurvatureFlowI using RadiusValueType = typename RadiusType::SizeValueType; /** Set/Get the stencil radius. */ + /** @ITKStartGrouping */ itkSetMacro(StencilRadius, RadiusValueType); itkGetConstMacro(StencilRadius, RadiusValueType); - + /** @ITKEndGrouping */ itkConceptMacro(UnsignedLongConvertibleToOutputCheck, (Concept::Convertible)); itkConceptMacro(OutputLessThanComparableCheck, (Concept::LessThanComparable)); diff --git a/Modules/Filtering/Deconvolution/include/itkInverseDeconvolutionImageFilter.h b/Modules/Filtering/Deconvolution/include/itkInverseDeconvolutionImageFilter.h index 6d2c555b77c..db1c3bfd6de 100644 --- a/Modules/Filtering/Deconvolution/include/itkInverseDeconvolutionImageFilter.h +++ b/Modules/Filtering/Deconvolution/include/itkInverseDeconvolutionImageFilter.h @@ -103,9 +103,10 @@ class ITK_TEMPLATE_EXPORT InverseDeconvolutionImageFilter /** Set/get the threshold value used to determine whether a * frequency of the Fourier transform of the blurring kernel is * considered to be zero. Default value is 1.0e-4. */ + /** @ITKStartGrouping */ itkSetMacro(KernelZeroMagnitudeThreshold, double); itkGetConstMacro(KernelZeroMagnitudeThreshold, double); - + /** @ITKEndGrouping */ protected: InverseDeconvolutionImageFilter(); ~InverseDeconvolutionImageFilter() override = default; @@ -152,6 +153,7 @@ class ITK_TEMPLATE_EXPORT InverseDeconvolutionFunctor /** Set/get the threshold value below which complex magnitudes are considered * to be zero. */ + /** @ITKStartGrouping */ void SetKernelZeroMagnitudeThreshold(double mu) { @@ -162,7 +164,7 @@ class ITK_TEMPLATE_EXPORT InverseDeconvolutionFunctor { return m_KernelZeroMagnitudeThreshold; } - + /** @ITKEndGrouping */ private: double m_KernelZeroMagnitudeThreshold; }; diff --git a/Modules/Filtering/Deconvolution/include/itkIterativeDeconvolutionImageFilter.h b/Modules/Filtering/Deconvolution/include/itkIterativeDeconvolutionImageFilter.h index 4775244cbf2..18cbbf23329 100644 --- a/Modules/Filtering/Deconvolution/include/itkIterativeDeconvolutionImageFilter.h +++ b/Modules/Filtering/Deconvolution/include/itkIterativeDeconvolutionImageFilter.h @@ -80,14 +80,16 @@ class ITK_TEMPLATE_EXPORT IterativeDeconvolutionImageFilter itkOverrideGetNameOfClassMacro(IterativeDeconvolutionImageFilter); /** Set/get the number of iterations. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfIterations, unsigned int); itkGetMacro(NumberOfIterations, unsigned int); - + /** @ITKEndGrouping */ /** Set/get the current estimate. */ itkGetModifiableObjectMacro(CurrentEstimate, InternalImageType); /** Stop iteration. When this method is called, the iteration will * halt after the current iteration has completed. */ + /** @ITKStartGrouping */ void SetStopIteration(bool stop) { @@ -95,7 +97,7 @@ class ITK_TEMPLATE_EXPORT IterativeDeconvolutionImageFilter m_StopIteration = stop; } itkGetConstMacro(StopIteration, bool); - + /** @ITKEndGrouping */ /** Get the current iteration. */ itkGetConstMacro(Iteration, unsigned int); diff --git a/Modules/Filtering/Deconvolution/include/itkLandweberDeconvolutionImageFilter.h b/Modules/Filtering/Deconvolution/include/itkLandweberDeconvolutionImageFilter.h index bccd5143c50..9cb8a89ef86 100644 --- a/Modules/Filtering/Deconvolution/include/itkLandweberDeconvolutionImageFilter.h +++ b/Modules/Filtering/Deconvolution/include/itkLandweberDeconvolutionImageFilter.h @@ -126,9 +126,10 @@ class ITK_TEMPLATE_EXPORT LandweberDeconvolutionImageFilter itkOverrideGetNameOfClassMacro(LandweberDeconvolutionImageFilter); /** Set/get relaxation factor. */ + /** @ITKStartGrouping */ itkSetMacro(Alpha, double); itkGetMacro(Alpha, double); - + /** @ITKEndGrouping */ protected: LandweberDeconvolutionImageFilter(); ~LandweberDeconvolutionImageFilter() override; diff --git a/Modules/Filtering/Deconvolution/include/itkParametricBlindLeastSquaresDeconvolutionImageFilter.h b/Modules/Filtering/Deconvolution/include/itkParametricBlindLeastSquaresDeconvolutionImageFilter.h index 5aedd365a2f..dcbd4acb90d 100644 --- a/Modules/Filtering/Deconvolution/include/itkParametricBlindLeastSquaresDeconvolutionImageFilter.h +++ b/Modules/Filtering/Deconvolution/include/itkParametricBlindLeastSquaresDeconvolutionImageFilter.h @@ -91,20 +91,23 @@ class ITK_TEMPLATE_EXPORT ParametricBlindLeastSquaresDeconvolutionImageFilter itkOverrideGetNameOfClassMacro(ParametricBlindLeastSquaresDeconvolutionImageFilter); /** Set/get the parametric kernel source. */ + /** @ITKStartGrouping */ void SetKernelSource(KernelSourceType * kernelSource); itkGetModifiableObjectMacro(KernelSource, KernelSourceType); - + /** @ITKEndGrouping */ /** Set/get the scale factor (also known as learning rate) for the * image intensity gradient descent. */ + /** @ITKStartGrouping */ itkSetMacro(Alpha, double); itkGetMacro(Alpha, double); - + /** @ITKEndGrouping */ /** Set/get the scale factor (also known as learning rate) for the * parameter gradient descent. */ + /** @ITKStartGrouping */ itkSetMacro(Beta, double); itkGetMacro(Beta, double); - + /** @ITKEndGrouping */ protected: ParametricBlindLeastSquaresDeconvolutionImageFilter(); ~ParametricBlindLeastSquaresDeconvolutionImageFilter() override = default; diff --git a/Modules/Filtering/Deconvolution/include/itkTikhonovDeconvolutionImageFilter.h b/Modules/Filtering/Deconvolution/include/itkTikhonovDeconvolutionImageFilter.h index 2e51062fcc0..6e80672a9cf 100644 --- a/Modules/Filtering/Deconvolution/include/itkTikhonovDeconvolutionImageFilter.h +++ b/Modules/Filtering/Deconvolution/include/itkTikhonovDeconvolutionImageFilter.h @@ -99,9 +99,10 @@ class ITK_TEMPLATE_EXPORT TikhonovDeconvolutionImageFilter * noise in the solution, but results in higher approximation error * in the deblurred image. Default value is 0.0, yielding the same * results as the InverseDeconvolutionImageFilter. */ + /** @ITKStartGrouping */ itkSetMacro(RegularizationConstant, double); itkGetConstMacro(RegularizationConstant, double); - + /** @ITKEndGrouping */ protected: TikhonovDeconvolutionImageFilter(); ~TikhonovDeconvolutionImageFilter() override = default; @@ -154,6 +155,7 @@ class ITK_TEMPLATE_EXPORT TikhonovDeconvolutionFunctor /** Set/get the regular constant. This needs to be a non-negative * real value. */ + /** @ITKStartGrouping */ void SetRegularizationConstant(double constant) { @@ -164,9 +166,10 @@ class ITK_TEMPLATE_EXPORT TikhonovDeconvolutionFunctor { return m_RegularizationConstant; } - + /** @ITKEndGrouping */ /** Set/get the threshold value below which complex magnitudes are considered * to be zero. */ + /** @ITKStartGrouping */ void SetKernelZeroMagnitudeThreshold(double mu) { @@ -177,7 +180,7 @@ class ITK_TEMPLATE_EXPORT TikhonovDeconvolutionFunctor { return m_KernelZeroMagnitudeThreshold; } - + /** @ITKEndGrouping */ private: double m_RegularizationConstant = 0.0; double m_KernelZeroMagnitudeThreshold = 0.0; diff --git a/Modules/Filtering/Deconvolution/include/itkWienerDeconvolutionImageFilter.h b/Modules/Filtering/Deconvolution/include/itkWienerDeconvolutionImageFilter.h index cd13ae20e81..ca17f48b7e9 100644 --- a/Modules/Filtering/Deconvolution/include/itkWienerDeconvolutionImageFilter.h +++ b/Modules/Filtering/Deconvolution/include/itkWienerDeconvolutionImageFilter.h @@ -123,9 +123,10 @@ class ITK_TEMPLATE_EXPORT WienerDeconvolutionImageFilter /** Set/get the variance of the zero-mean Gaussian white noise * assumed to be added to the input. */ + /** @ITKStartGrouping */ itkSetMacro(NoiseVariance, double); itkGetConstMacro(NoiseVariance, double); - + /** @ITKEndGrouping */ protected: WienerDeconvolutionImageFilter(); ~WienerDeconvolutionImageFilter() override = default; @@ -184,6 +185,7 @@ class ITK_TEMPLATE_EXPORT WienerDeconvolutionFunctor /** Set/get the constant defining the noise power spectral density * constant. */ + /** @ITKStartGrouping */ void SetNoisePowerSpectralDensityConstant(double constant) { @@ -194,9 +196,10 @@ class ITK_TEMPLATE_EXPORT WienerDeconvolutionFunctor { return m_NoisePowerSpectralDensityConstant; } - + /** @ITKEndGrouping */ /** Set/get the threshold value below which complex magnitudes are considered * to be zero. */ + /** @ITKStartGrouping */ void SetKernelZeroMagnitudeThreshold(double mu) { @@ -207,7 +210,7 @@ class ITK_TEMPLATE_EXPORT WienerDeconvolutionFunctor { return m_KernelZeroMagnitudeThreshold; } - + /** @ITKEndGrouping */ private: double m_NoisePowerSpectralDensityConstant = 0.0; double m_KernelZeroMagnitudeThreshold = 0.0; diff --git a/Modules/Filtering/Denoising/include/itkPatchBasedDenoisingBaseImageFilter.h b/Modules/Filtering/Denoising/include/itkPatchBasedDenoisingBaseImageFilter.h index 366f6f58eb9..f0a02954f9a 100644 --- a/Modules/Filtering/Denoising/include/itkPatchBasedDenoisingBaseImageFilter.h +++ b/Modules/Filtering/Denoising/include/itkPatchBasedDenoisingBaseImageFilter.h @@ -180,6 +180,7 @@ class ITK_TEMPLATE_EXPORT PatchBasedDenoisingBaseImageFilter : public ImageToIma * make the patch more isotropic and less rectangular. */ using PatchWeightsType = Array; + /** This data structure type is used for efficiently accessing patch values * from the image data structure. */ @@ -194,9 +195,10 @@ class ITK_TEMPLATE_EXPORT PatchBasedDenoisingBaseImageFilter : public ImageToIma * Currently, only isotropic patches in physical space are allowed; * patches can be anisotropic in voxel space. */ + /** @ITKStartGrouping */ itkSetMacro(PatchRadius, unsigned int); itkGetConstMacro(PatchRadius, unsigned int); - + /** @ITKEndGrouping */ PatchRadiusType GetPatchRadiusInVoxels() const; @@ -220,49 +222,55 @@ class ITK_TEMPLATE_EXPORT PatchBasedDenoisingBaseImageFilter : public ImageToIma * Defaults to NOMODEL. * To use the noise model during denoising, NoiseModelFidelityWeight must be positive. */ + /** @ITKStartGrouping */ itkSetEnumMacro(NoiseModel, NoiseModelEnum); itkGetConstMacro(NoiseModel, NoiseModelEnum); - + /** @ITKEndGrouping */ /** Set/Get the weight on the smoothing term. * This option is used when a noise model is specified. * This weight controls the balance between the smoothing and the closeness to the noisy data. * Large step sizes may cause instabilities. */ + /** @ITKStartGrouping */ itkSetClampMacro(SmoothingWeight, double, 0.0, 1.0); itkGetConstMacro(SmoothingWeight, double); - + /** @ITKEndGrouping */ /** Set/Get the weight on the fidelity term (penalizes deviations from the noisy data). * This option is used when a noise model is specified. * This weight controls the balance between the smoothing and the closeness to the noisy data. * Use a positive weight to prevent oversmoothing. */ + /** @ITKStartGrouping */ itkSetClampMacro(NoiseModelFidelityWeight, double, 0.0, 1.0); itkGetConstMacro(NoiseModelFidelityWeight, double); - + /** @ITKEndGrouping */ /** Set/Get flag indicating whether kernel-bandwidth should be estimated * automatically from the image data. * Defaults to false. */ + /** @ITKStartGrouping */ itkSetMacro(KernelBandwidthEstimation, bool); itkBooleanMacro(KernelBandwidthEstimation); itkGetConstMacro(KernelBandwidthEstimation, bool); - + /** @ITKEndGrouping */ /** Set/Get the update frequency for the kernel bandwidth estimation. * An optimal bandwidth will be re-estimated * based on the denoised image after every 'n' iterations. * Must be a positive integer. * Defaults to 3, i.e. bandwidth updated after every 3 denoising iteration. */ + /** @ITKStartGrouping */ itkSetClampMacro(KernelBandwidthUpdateFrequency, unsigned int, 1, NumericTraits::max()); itkGetConstMacro(KernelBandwidthUpdateFrequency, unsigned int); - + /** @ITKEndGrouping */ /** Set/Get the number of denoising iterations to perform. * Must be a positive integer. * Defaults to 1. */ + /** @ITKStartGrouping */ itkSetClampMacro(NumberOfIterations, unsigned int, 1, NumericTraits::max()); itkGetConstReferenceMacro(NumberOfIterations, unsigned int); - + /** @ITKEndGrouping */ /** Get the number of elapsed iterations of the filter. */ itkGetConstReferenceMacro(ElapsedIterations, unsigned int); @@ -270,10 +278,11 @@ class ITK_TEMPLATE_EXPORT PatchBasedDenoisingBaseImageFilter : public ImageToIma * as if they are in euclidean space regardless of pixel type. * Defaults to false. */ + /** @ITKStartGrouping */ itkSetMacro(AlwaysTreatComponentsAsEuclidean, bool); itkBooleanMacro(AlwaysTreatComponentsAsEuclidean); itkGetConstMacro(AlwaysTreatComponentsAsEuclidean, bool); - + /** @ITKEndGrouping */ /** Set the state of the filter to INITIALIZED. */ virtual void SetStateToInitialized(); @@ -283,19 +292,21 @@ class ITK_TEMPLATE_EXPORT PatchBasedDenoisingBaseImageFilter : public ImageToIma SetStateToUninitialized(); /** Set/Get the state of the filter. */ + /** @ITKStartGrouping */ #if !defined(ITK_WRAPPING_PARSER) itkSetEnumMacro(State, FilterStateEnum); itkGetConstReferenceMacro(State, FilterStateEnum); #endif - + /** @ITKEndGrouping */ /** Indicates whether the filter automatically resets to UNINITIALIZED state * after completing, or whether filter must be manually reset. * Require the filter to be manually reinitialized (by calling * SetStateToUninitialized(). */ + /** @ITKStartGrouping */ itkSetMacro(ManualReinitialization, bool); itkGetConstReferenceMacro(ManualReinitialization, bool); itkBooleanMacro(ManualReinitialization); - + /** @ITKEndGrouping */ protected: PatchBasedDenoisingBaseImageFilter(); ~PatchBasedDenoisingBaseImageFilter() override = default; @@ -386,9 +397,10 @@ class ITK_TEMPLATE_EXPORT PatchBasedDenoisingBaseImageFilter : public ImageToIma } /** Set/Get the component space type. */ + /** @ITKStartGrouping */ itkSetEnumMacro(ComponentSpace, ComponentSpaceEnum); itkGetConstMacro(ComponentSpace, ComponentSpaceEnum); - + /** @ITKEndGrouping */ // Cache input and output pointer to get rid of thousands of calls // to GetInput and GetOutput. const InputImageType * m_InputImage{}; diff --git a/Modules/Filtering/Denoising/include/itkPatchBasedDenoisingImageFilter.h b/Modules/Filtering/Denoising/include/itkPatchBasedDenoisingImageFilter.h index 4c7b2acef7b..e691a735699 100644 --- a/Modules/Filtering/Denoising/include/itkPatchBasedDenoisingImageFilter.h +++ b/Modules/Filtering/Denoising/include/itkPatchBasedDenoisingImageFilter.h @@ -141,31 +141,35 @@ class ITK_TEMPLATE_EXPORT PatchBasedDenoisingImageFilter * If this flag is true, the smooth-disc patch weights will override any * weights provided via the SetPatchWeights method. */ + /** @ITKStartGrouping */ itkSetMacro(UseSmoothDiscPatchWeights, bool); itkBooleanMacro(UseSmoothDiscPatchWeights); itkGetConstMacro(UseSmoothDiscPatchWeights, bool); - + /** @ITKEndGrouping */ /** Set/Get initial kernel bandwidth estimate. * To prevent the class from automatically modifying this estimate, * set KernelBandwidthEstimation to false in the base class. */ + /** @ITKStartGrouping */ void SetKernelBandwidthSigma(const RealArrayType & kernelSigma); itkGetConstMacro(KernelBandwidthSigma, RealArrayType); - + /** @ITKEndGrouping */ /** Set/Get the fraction of the image to use for kernel bandwidth sigma estimation. * To reduce the computational burden for computing sigma, * a small random fraction of the image pixels can be used. */ + /** @ITKStartGrouping */ itkSetClampMacro(KernelBandwidthFractionPixelsForEstimation, double, 0.01, 1.0); itkGetConstReferenceMacro(KernelBandwidthFractionPixelsForEstimation, double); - + /** @ITKEndGrouping */ /** Set/Get flag indicating whether conditional derivatives should be used estimating sigma. */ + /** @ITKStartGrouping */ itkSetMacro(ComputeConditionalDerivatives, bool); itkBooleanMacro(ComputeConditionalDerivatives); itkGetConstMacro(ComputeConditionalDerivatives, bool); - + /** @ITKEndGrouping */ /** Set/Get flag indicating whether the fast algorithm for tensor computations should be used. * * Specifically, when this flag is true (default) or On, a faster implementation of the 3x3 @@ -177,10 +181,11 @@ class ITK_TEMPLATE_EXPORT PatchBasedDenoisingImageFilter * However, you may want to turn this option off if you have concerns about numerical * performance. */ + /** @ITKStartGrouping */ itkSetMacro(UseFastTensorComputations, bool); itkBooleanMacro(UseFastTensorComputations); itkGetConstMacro(UseFastTensorComputations, bool); - + /** @ITKEndGrouping */ /** Maximum number of Newton-Raphson iterations for sigma update. */ static constexpr unsigned int MaxSigmaUpdateIterations = 20; @@ -190,9 +195,10 @@ class ITK_TEMPLATE_EXPORT PatchBasedDenoisingImageFilter * isn't very far from 1. * Note: This is used only when KernelBandwidthEstimation is True/On. */ + /** @ITKStartGrouping */ itkSetClampMacro(KernelBandwidthMultiplicationFactor, double, 0.01, 100); itkGetConstReferenceMacro(KernelBandwidthMultiplicationFactor, double); - + /** @ITKEndGrouping */ /** Set/Get the noise sigma. * Used by the noise model where appropriate, defaults to 5% of the image intensity range */ @@ -202,9 +208,10 @@ class ITK_TEMPLATE_EXPORT PatchBasedDenoisingImageFilter itkGetConstMacro(NoiseSigma, RealType); /** Set/Get the class used for creating a subsample of patches. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Sampler, BaseSamplerType); itkGetModifiableObjectMacro(Sampler, BaseSamplerType); - + /** @ITKEndGrouping */ /** Get the number of independent components of the input. */ itkGetConstMacro(NumIndependentComponents, unsigned int); diff --git a/Modules/Filtering/DiffusionTensorImage/include/itkDiffusionTensor3DReconstructionImageFilter.h b/Modules/Filtering/DiffusionTensorImage/include/itkDiffusionTensor3DReconstructionImageFilter.h index 5df5d76efba..8d5c0f052d6 100644 --- a/Modules/Filtering/DiffusionTensorImage/include/itkDiffusionTensor3DReconstructionImageFilter.h +++ b/Modules/Filtering/DiffusionTensorImage/include/itkDiffusionTensor3DReconstructionImageFilter.h @@ -199,10 +199,12 @@ class ITK_TEMPLATE_EXPORT DiffusionTensor3DReconstructionImageFilter using GradientDirectionContainerType = VectorContainer; /** Set method to add a gradient direction and its corresponding image. */ + /** @ITKStartGrouping */ void AddGradientImage(const GradientDirectionType &, const GradientImageType * gradientImage); const GradientImageType * GetGradientImage(unsigned int index) const; + /** @ITKEndGrouping */ /** Another set method to add a gradient directions and its corresponding * image. The image here is a VectorImage. The user is expected to pass the @@ -251,6 +253,7 @@ class ITK_TEMPLATE_EXPORT DiffusionTensor3DReconstructionImageFilter /** set an image mask */ void SetMaskImage(MaskImageType * maskImage); + /** set a spatial object mask */ void SetMaskSpatialObject(MaskSpatialObjectType * maskSpatialObject); @@ -259,8 +262,10 @@ class ITK_TEMPLATE_EXPORT DiffusionTensor3DReconstructionImageFilter /** Threshold on the reference image data. The output tensor will be a null * tensor for pixels in the reference image that have a value less than this * threshold. */ + /** @ITKStartGrouping */ itkSetMacro(Threshold, ReferencePixelType); itkGetConstMacro(Threshold, ReferencePixelType); + /** @ITKEndGrouping */ /** * The BValue \f$ (s/mm^2) \f$ value used in normalizing the tensors to @@ -268,11 +273,13 @@ class ITK_TEMPLATE_EXPORT DiffusionTensor3DReconstructionImageFilter * a description of how this is applied to the tensor estimation. * Equation (1) of the same reference describes the physical significance. */ + /** @ITKStartGrouping */ itkSetMacro(BValue, TTensorPixelType); #ifdef GetBValue # undef GetBValue #endif itkGetConstReferenceMacro(BValue, TTensorPixelType); + /** @ITKEndGrouping */ itkConceptMacro(ReferenceEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(TensorEqualityComparableCheck, (Concept::EqualityComparable)); diff --git a/Modules/Filtering/DisplacementField/include/itkBSplineExponentialDiffeomorphicTransform.h b/Modules/Filtering/DisplacementField/include/itkBSplineExponentialDiffeomorphicTransform.h index e43efa94c50..33b218ae6e5 100644 --- a/Modules/Filtering/DisplacementField/include/itkBSplineExponentialDiffeomorphicTransform.h +++ b/Modules/Filtering/DisplacementField/include/itkBSplineExponentialDiffeomorphicTransform.h @@ -121,9 +121,10 @@ class ITK_TEMPLATE_EXPORT BSplineExponentialDiffeomorphicTransform /** * Set/Get the spline order. */ + /** @ITKStartGrouping */ itkSetMacro(SplineOrder, SplineOrderType); itkGetConstMacro(SplineOrder, SplineOrderType); - + /** @ITKEndGrouping */ /** * Set/Get the control point grid size defining the B-spline estimate of the * smoothed velocity field. In each dimension, the B-spline mesh size is equal @@ -131,9 +132,10 @@ class ITK_TEMPLATE_EXPORT BSplineExponentialDiffeomorphicTransform * Default = 4 control points in each dimension for a mesh size of 1 in each * dimension. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfControlPointsForTheConstantVelocityField, ArrayType); itkGetConstMacro(NumberOfControlPointsForTheConstantVelocityField, ArrayType); - + /** @ITKEndGrouping */ /** * Set the control point grid size defining the B-spline estimate of the * smoothed update field. In each dimension, the B-spline mesh size is equal @@ -141,9 +143,10 @@ class ITK_TEMPLATE_EXPORT BSplineExponentialDiffeomorphicTransform * Default = 4 control points in each dimension for a mesh size of 1 in each * dimension. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfControlPointsForTheUpdateField, ArrayType); itkGetConstMacro(NumberOfControlPointsForTheUpdateField, ArrayType); - + /** @ITKEndGrouping */ /** * Set the update field mesh size which is used to specify the control point * grid size. The mesh size in each dimension is calculated as the diff --git a/Modules/Filtering/DisplacementField/include/itkBSplineSmoothingOnUpdateDisplacementFieldTransform.h b/Modules/Filtering/DisplacementField/include/itkBSplineSmoothingOnUpdateDisplacementFieldTransform.h index 05fd0661668..eec8046bad2 100644 --- a/Modules/Filtering/DisplacementField/include/itkBSplineSmoothingOnUpdateDisplacementFieldTransform.h +++ b/Modules/Filtering/DisplacementField/include/itkBSplineSmoothingOnUpdateDisplacementFieldTransform.h @@ -168,10 +168,11 @@ class ITK_TEMPLATE_EXPORT BSplineSmoothingOnUpdateDisplacementFieldTransform /** * Enforce stationary boundaries. Important for diffeomorphic transforms. */ + /** @ITKStartGrouping */ itkBooleanMacro(EnforceStationaryBoundary); itkSetMacro(EnforceStationaryBoundary, bool); itkGetConstMacro(EnforceStationaryBoundary, bool); - + /** @ITKEndGrouping */ protected: BSplineSmoothingOnUpdateDisplacementFieldTransform(); ~BSplineSmoothingOnUpdateDisplacementFieldTransform() override = default; diff --git a/Modules/Filtering/DisplacementField/include/itkConstantVelocityFieldTransform.h b/Modules/Filtering/DisplacementField/include/itkConstantVelocityFieldTransform.h index 1627742775f..2a156365963 100644 --- a/Modules/Filtering/DisplacementField/include/itkConstantVelocityFieldTransform.h +++ b/Modules/Filtering/DisplacementField/include/itkConstantVelocityFieldTransform.h @@ -119,19 +119,21 @@ class ITK_TEMPLATE_EXPORT ConstantVelocityFieldTransform * Set the displacement field. Create special set accessor to update * interpolator and assign displacement field to transform parameters * container. */ + /** @ITKStartGrouping */ virtual void SetConstantVelocityField(ConstantVelocityFieldType *); itkGetModifiableObjectMacro(ConstantVelocityField, ConstantVelocityFieldType); - + /** @ITKEndGrouping */ void SetFixedParameters(const FixedParametersType &) override; /** Get/Set the interpolator. * Create out own set accessor that assigns the velocity field */ + /** @ITKStartGrouping */ virtual void SetConstantVelocityFieldInterpolator(ConstantVelocityFieldInterpolatorType *); itkGetModifiableObjectMacro(ConstantVelocityFieldInterpolator, ConstantVelocityFieldInterpolatorType); - + /** @ITKEndGrouping */ /** Get the modification time of velocity field */ itkGetConstReferenceMacro(ConstantVelocityFieldSetTime, ModifiedTimeType); diff --git a/Modules/Filtering/DisplacementField/include/itkDisplacementFieldJacobianDeterminantFilter.h b/Modules/Filtering/DisplacementField/include/itkDisplacementFieldJacobianDeterminantFilter.h index cf9e1dabc77..a02e6363680 100644 --- a/Modules/Filtering/DisplacementField/include/itkDisplacementFieldJacobianDeterminantFilter.h +++ b/Modules/Filtering/DisplacementField/include/itkDisplacementFieldJacobianDeterminantFilter.h @@ -176,11 +176,12 @@ class ITK_TEMPLATE_EXPORT DisplacementFieldJacobianDeterminantFilter * 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. */ + /** @ITKStartGrouping */ void SetUseImageSpacing(bool); itkGetConstMacro(UseImageSpacing, bool); itkBooleanMacro(UseImageSpacing); - + /** @ITKEndGrouping */ #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 @@ -208,10 +209,11 @@ class ITK_TEMPLATE_EXPORT DisplacementFieldJacobianDeterminantFilter /** Directly Set/Get the array of weights used in the gradient calculations. Note that calling UseImageSpacingOn will clobber these values. */ + /** @ITKStartGrouping */ void SetDerivativeWeights(const WeightsType &); itkGetConstReferenceMacro(DerivativeWeights, WeightsType); - + /** @ITKEndGrouping */ protected: DisplacementFieldJacobianDeterminantFilter(); ~DisplacementFieldJacobianDeterminantFilter() override = default; @@ -247,14 +249,16 @@ class ITK_TEMPLATE_EXPORT DisplacementFieldJacobianDeterminantFilter itkGetConstObjectMacro(RealValuedInputImage, ImageBaseType); /** Get/Set the neighborhood radius used for gradient computation */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(NeighborhoodRadius, RadiusType); itkSetMacro(NeighborhoodRadius, RadiusType); - + /** @ITKEndGrouping */ virtual TRealType EvaluateAtNeighborhood(const ConstNeighborhoodIteratorType & it) const; /** The weights used to scale partial derivatives during processing */ WeightsType m_DerivativeWeights{}; + /** Pre-compute 0.5*m_DerivativeWeights since that is the only thing used in the computations. */ WeightsType m_HalfDerivativeWeights{}; diff --git a/Modules/Filtering/DisplacementField/include/itkDisplacementFieldToBSplineImageFilter.h b/Modules/Filtering/DisplacementField/include/itkDisplacementFieldToBSplineImageFilter.h index 4391babe19d..3d44b3cd795 100644 --- a/Modules/Filtering/DisplacementField/include/itkDisplacementFieldToBSplineImageFilter.h +++ b/Modules/Filtering/DisplacementField/include/itkDisplacementFieldToBSplineImageFilter.h @@ -113,6 +113,7 @@ class ITK_TEMPLATE_EXPORT DisplacementFieldToBSplineImageFilter : public ImageTo * estimation of the displacement field weights the contribution of each voxel * according the value of the corresponding voxel in the confidence image. */ + /** @ITKStartGrouping */ void SetConfidenceImage(const RealImageType * image) { @@ -123,6 +124,7 @@ class ITK_TEMPLATE_EXPORT DisplacementFieldToBSplineImageFilter : public ImageTo { this->SetConfidenceImage(image); } + /** @ITKEndGrouping */ /** Get confidence image function. */ const RealImageType * @@ -132,6 +134,7 @@ class ITK_TEMPLATE_EXPORT DisplacementFieldToBSplineImageFilter : public ImageTo } /** Set the input point set */ + /** @ITKStartGrouping */ void SetPointSet(const InputPointSetType * points) { @@ -142,6 +145,7 @@ class ITK_TEMPLATE_EXPORT DisplacementFieldToBSplineImageFilter : public ImageTo { this->SetPointSet(points); } + /** @ITKEndGrouping */ /** Get the input point set. */ const InputPointSetType * @@ -263,16 +267,20 @@ class ITK_TEMPLATE_EXPORT DisplacementFieldToBSplineImageFilter : public ImageTo /** * Estimate the inverse field instead of the forward field. Default = false. */ + /** @ITKStartGrouping */ itkBooleanMacro(EstimateInverse); itkSetMacro(EstimateInverse, bool); itkGetConstMacro(EstimateInverse, bool); + /** @ITKEndGrouping */ /** * Enforce stationary boundary conditions. Default = false. */ + /** @ITKStartGrouping */ itkBooleanMacro(EnforceStationaryBoundary); itkSetMacro(EnforceStationaryBoundary, bool); itkGetConstMacro(EnforceStationaryBoundary, bool); + /** @ITKEndGrouping */ protected: /** Constructor */ diff --git a/Modules/Filtering/DisplacementField/include/itkDisplacementFieldTransform.h b/Modules/Filtering/DisplacementField/include/itkDisplacementFieldTransform.h index 50167ded8e3..76a9fbf512f 100644 --- a/Modules/Filtering/DisplacementField/include/itkDisplacementFieldTransform.h +++ b/Modules/Filtering/DisplacementField/include/itkDisplacementFieldTransform.h @@ -150,6 +150,7 @@ class ITK_TEMPLATE_EXPORT DisplacementFieldTransform : public Transform; using OutputTensorEigenVectorType = CovariantVector; + /** Derivative type */ using typename Superclass::DerivativeType; @@ -181,30 +182,38 @@ class ITK_TEMPLATE_EXPORT DisplacementFieldTransform : public Transform::Pointer; /** Get the time-varying velocity field. */ + /** @ITKStartGrouping */ #if !defined(ITK_LEGACY_REMOVE) VelocityFieldType * GetTimeVaryingVelocityField() @@ -116,7 +117,7 @@ class ITK_TEMPLATE_EXPORT TimeVaryingVelocityFieldTransform { return this->GetVelocityField(); } - + /** @ITKEndGrouping */ /** Set the time-varying velocity field. */ virtual void SetTimeVaryingVelocityField(VelocityFieldType * field) diff --git a/Modules/Filtering/DisplacementField/include/itkTransformToDisplacementFieldFilter.h b/Modules/Filtering/DisplacementField/include/itkTransformToDisplacementFieldFilter.h index 7612a0fd7df..1f638a1f5f8 100644 --- a/Modules/Filtering/DisplacementField/include/itkTransformToDisplacementFieldFilter.h +++ b/Modules/Filtering/DisplacementField/include/itkTransformToDisplacementFieldFilter.h @@ -97,42 +97,48 @@ class ITK_TEMPLATE_EXPORT TransformToDisplacementFieldFilter : public ImageSourc * Set the coordinate transform to use for resampling. Note that this must * be in physical coordinates and it is the output-to-input transform, NOT * the input-to-output transform that you might naively expect. */ + /** @ITKStartGrouping */ using Superclass::SetInput; virtual void SetInput(const TransformInputType * input); const TransformInputType * GetInput() const; itkSetGetDecoratedObjectInputMacro(Transform, TransformType); - + /** @ITKEndGrouping */ /** Set/Get the start index of the output largest possible region. * The default is an index of all zeros. */ + /** @ITKStartGrouping */ itkSetMacro(OutputStartIndex, IndexType); itkGetConstReferenceMacro(OutputStartIndex, IndexType); - + /** @ITKEndGrouping */ /** Set/Get the size of the output image. */ + /** @ITKStartGrouping */ itkSetMacro(Size, SizeType); itkGetConstReferenceMacro(Size, SizeType); - + /** @ITKEndGrouping */ /** Set the output image spacing. */ + /** @ITKStartGrouping */ itkSetMacro(OutputSpacing, SpacingType); virtual void SetOutputSpacing(const SpacePrecisionType * spacing); - + /** @ITKEndGrouping */ /** Get the output image spacing. */ itkGetConstReferenceMacro(OutputSpacing, SpacingType); /** Set the output image origin. */ + /** @ITKStartGrouping */ itkSetMacro(OutputOrigin, OriginType); virtual void SetOutputOrigin(const SpacePrecisionType * origin); - + /** @ITKEndGrouping */ /** Get the output image origin. */ itkGetConstReferenceMacro(OutputOrigin, OriginType); /** Set the output direction cosine matrix. */ + /** @ITKStartGrouping */ itkSetMacro(OutputDirection, DirectionType); itkGetConstReferenceMacro(OutputDirection, DirectionType); - + /** @ITKEndGrouping */ /** Set a reference image to use to define the output information. * By default, output information is specified through the * SetOutputSpacing, Origin, and Direction methods. Alternatively, @@ -146,10 +152,11 @@ class ITK_TEMPLATE_EXPORT TransformToDisplacementFieldFilter : public ImageSourc /** Turn on/off whether a specified reference image should be used to define * the output information. */ + /** @ITKStartGrouping */ itkSetMacro(UseReferenceImage, bool); itkBooleanMacro(UseReferenceImage); itkGetConstMacro(UseReferenceImage, bool); - + /** @ITKEndGrouping */ static constexpr unsigned int PixelDimension = PixelType::Dimension; itkConceptMacro(SameDimensionCheck, (Concept::SameDimension)); diff --git a/Modules/Filtering/DisplacementField/include/itkVelocityFieldTransform.h b/Modules/Filtering/DisplacementField/include/itkVelocityFieldTransform.h index 78730aaf8d6..08af8706c99 100644 --- a/Modules/Filtering/DisplacementField/include/itkVelocityFieldTransform.h +++ b/Modules/Filtering/DisplacementField/include/itkVelocityFieldTransform.h @@ -121,18 +121,22 @@ class ITK_TEMPLATE_EXPORT VelocityFieldTransform : public DisplacementFieldTrans * Set the displacement field. Create special set accessor to update * interpolator and assign displacement field to transform parameters * container. */ + /** @ITKStartGrouping */ virtual void SetVelocityField(VelocityFieldType *); itkGetModifiableObjectMacro(VelocityField, VelocityFieldType); + /** @ITKEndGrouping */ void SetFixedParameters(const FixedParametersType &) override; /** Get/Set the interpolator. * Create out own set accessor that assigns the velocity field */ + /** @ITKStartGrouping */ virtual void SetVelocityFieldInterpolator(VelocityFieldInterpolatorType *); itkGetModifiableObjectMacro(VelocityFieldInterpolator, VelocityFieldInterpolatorType); + /** @ITKEndGrouping */ /** Get the modification time of velocity field */ itkGetConstReferenceMacro(VelocityFieldSetTime, unsigned long); diff --git a/Modules/Filtering/DistanceMap/include/itkApproximateSignedDistanceMapImageFilter.h b/Modules/Filtering/DistanceMap/include/itkApproximateSignedDistanceMapImageFilter.h index e23411f9ce2..051058c9d75 100644 --- a/Modules/Filtering/DistanceMap/include/itkApproximateSignedDistanceMapImageFilter.h +++ b/Modules/Filtering/DistanceMap/include/itkApproximateSignedDistanceMapImageFilter.h @@ -105,6 +105,7 @@ class ITK_TEMPLATE_EXPORT ApproximateSignedDistanceMapImageFilter : public Image /** Type of input image size and size value */ using OutputSizeType = typename OutputImageType::SizeType; using OutputSizeValueType = typename OutputSizeType::SizeValueType; + /** The dimension of the input image. */ static constexpr unsigned int InputImageDimension = InputImageType::ImageDimension; @@ -116,13 +117,15 @@ class ITK_TEMPLATE_EXPORT ApproximateSignedDistanceMapImageFilter : public Image /** Set/Get intensity value representing the interior of objects in the mask. */ + /** @ITKStartGrouping */ itkSetMacro(InsideValue, InputPixelType); itkGetConstMacro(InsideValue, InputPixelType); - + /** @ITKEndGrouping */ /** Set/Get intensity value representing non-objects in the mask. */ + /** @ITKStartGrouping */ itkSetMacro(OutsideValue, InputPixelType); itkGetConstMacro(OutsideValue, InputPixelType); - + /** @ITKEndGrouping */ itkConceptMacro(InputEqualityComparableCheck, (Concept::EqualityComparable)); protected: diff --git a/Modules/Filtering/DistanceMap/include/itkContourDirectedMeanDistanceImageFilter.h b/Modules/Filtering/DistanceMap/include/itkContourDirectedMeanDistanceImageFilter.h index ef276990e01..dc84f5133ea 100644 --- a/Modules/Filtering/DistanceMap/include/itkContourDirectedMeanDistanceImageFilter.h +++ b/Modules/Filtering/DistanceMap/include/itkContourDirectedMeanDistanceImageFilter.h @@ -119,10 +119,11 @@ class ITK_TEMPLATE_EXPORT ContourDirectedMeanDistanceImageFilter : public ImageT itkGetConstMacro(ContourDirectedMeanDistance, RealType); /** Set/Get if image spacing should be used in computing distances. */ + /** @ITKStartGrouping */ itkSetMacro(UseImageSpacing, bool); itkGetConstMacro(UseImageSpacing, bool); itkBooleanMacro(UseImageSpacing); - + /** @ITKEndGrouping */ itkConceptMacro(InputHasNumericTraitsCheck, (Concept::HasNumericTraits)); protected: diff --git a/Modules/Filtering/DistanceMap/include/itkContourMeanDistanceImageFilter.h b/Modules/Filtering/DistanceMap/include/itkContourMeanDistanceImageFilter.h index 1563f8dbb16..5c59880d458 100644 --- a/Modules/Filtering/DistanceMap/include/itkContourMeanDistanceImageFilter.h +++ b/Modules/Filtering/DistanceMap/include/itkContourMeanDistanceImageFilter.h @@ -125,10 +125,11 @@ class ITK_TEMPLATE_EXPORT ContourMeanDistanceImageFilter : public ImageToImageFi itkGetConstMacro(MeanDistance, RealType); /** Set if image spacing should be used in computing distances. */ + /** @ITKStartGrouping */ itkSetMacro(UseImageSpacing, bool); itkGetConstMacro(UseImageSpacing, bool); itkBooleanMacro(UseImageSpacing); - + /** @ITKEndGrouping */ itkConceptMacro(InputHasNumericTraitsCheck, (Concept::HasNumericTraits)); protected: diff --git a/Modules/Filtering/DistanceMap/include/itkDanielssonDistanceMapImageFilter.h b/Modules/Filtering/DistanceMap/include/itkDanielssonDistanceMapImageFilter.h index 2ccc361685f..9818b2873a8 100644 --- a/Modules/Filtering/DistanceMap/include/itkDanielssonDistanceMapImageFilter.h +++ b/Modules/Filtering/DistanceMap/include/itkDanielssonDistanceMapImageFilter.h @@ -124,24 +124,27 @@ class ITK_TEMPLATE_EXPORT DanielssonDistanceMapImageFilter : public ImageToImage using VectorImagePointer = typename VectorImageType::Pointer; /** Set/Get if the distance should be squared. */ + /** @ITKStartGrouping */ itkSetMacro(SquaredDistance, bool); itkGetConstReferenceMacro(SquaredDistance, bool); itkBooleanMacro(SquaredDistance); - + /** @ITKEndGrouping */ /** Set/Get if the input is binary. If this variable is set, each * nonzero pixel in the input image will be given a unique numeric * code to be used by the Voronoi partition. If the image is binary * but you are not interested in the Voronoi regions of the * different nonzero pixels, then you need not set this. */ + /** @ITKStartGrouping */ itkSetMacro(InputIsBinary, bool); itkGetConstReferenceMacro(InputIsBinary, bool); itkBooleanMacro(InputIsBinary); - + /** @ITKEndGrouping */ /** Set/Get if image spacing should be used in computing distances. */ + /** @ITKStartGrouping */ itkSetMacro(UseImageSpacing, bool); itkGetConstReferenceMacro(UseImageSpacing, bool); itkBooleanMacro(UseImageSpacing); - + /** @ITKEndGrouping */ /** Get Voronoi Map * This map shows for each pixel what object is closest to it. * Each object should be labeled by a number (larger than 0), diff --git a/Modules/Filtering/DistanceMap/include/itkDirectedHausdorffDistanceImageFilter.h b/Modules/Filtering/DistanceMap/include/itkDirectedHausdorffDistanceImageFilter.h index b92fe4afc04..d474468b69b 100644 --- a/Modules/Filtering/DistanceMap/include/itkDirectedHausdorffDistanceImageFilter.h +++ b/Modules/Filtering/DistanceMap/include/itkDirectedHausdorffDistanceImageFilter.h @@ -126,14 +126,16 @@ class ITK_TEMPLATE_EXPORT DirectedHausdorffDistanceImageFilter : public ImageToI GetInput2(); /** Set/Get if image spacing should be used in computing distances. */ + /** @ITKStartGrouping */ itkSetMacro(UseImageSpacing, bool); itkGetConstMacro(UseImageSpacing, bool); itkBooleanMacro(UseImageSpacing); - + /** @ITKEndGrouping */ /** Return the computed directed Hausdorff distance. */ + /** @ITKStartGrouping */ itkGetConstMacro(DirectedHausdorffDistance, RealType); itkGetConstMacro(AverageHausdorffDistance, RealType); - + /** @ITKEndGrouping */ itkConceptMacro(InputHasNumericTraitsCheck, (Concept::HasNumericTraits)); protected: diff --git a/Modules/Filtering/DistanceMap/include/itkFastChamferDistanceImageFilter.h b/Modules/Filtering/DistanceMap/include/itkFastChamferDistanceImageFilter.h index 91ad2d0b747..f55eb4b39b1 100644 --- a/Modules/Filtering/DistanceMap/include/itkFastChamferDistanceImageFilter.h +++ b/Modules/Filtering/DistanceMap/include/itkFastChamferDistanceImageFilter.h @@ -109,13 +109,15 @@ class ITK_TEMPLATE_EXPORT FastChamferDistanceImageFilter : public ImageToImageFi using WeightsType = FixedArray; /** coefficients of the Chamfer distance for each kind of neighbor. */ + /** @ITKStartGrouping */ itkSetMacro(Weights, WeightsType); itkGetConstReferenceMacro(Weights, WeightsType); - + /** @ITKEndGrouping */ /** Maximal computed distance */ + /** @ITKStartGrouping */ itkSetMacro(MaximumDistance, float); itkGetConstMacro(MaximumDistance, float); - + /** @ITKEndGrouping */ /** */ void SetRegionToProcess(const RegionType & r); diff --git a/Modules/Filtering/DistanceMap/include/itkHausdorffDistanceImageFilter.h b/Modules/Filtering/DistanceMap/include/itkHausdorffDistanceImageFilter.h index 8c804746025..ba800aab67d 100644 --- a/Modules/Filtering/DistanceMap/include/itkHausdorffDistanceImageFilter.h +++ b/Modules/Filtering/DistanceMap/include/itkHausdorffDistanceImageFilter.h @@ -115,13 +115,15 @@ class ITK_TEMPLATE_EXPORT HausdorffDistanceImageFilter : public ImageToImageFilt GetInput2(); /** Set if image spacing should be used in computing distances. */ + /** @ITKStartGrouping */ itkSetMacro(UseImageSpacing, bool); itkGetConstMacro(UseImageSpacing, bool); - + /** @ITKEndGrouping */ /** Return the computed Hausdorff distance. */ + /** @ITKStartGrouping */ itkGetConstMacro(HausdorffDistance, RealType); itkGetConstMacro(AverageHausdorffDistance, RealType); - + /** @ITKEndGrouping */ itkConceptMacro(Input1HasNumericTraitsCheck, (Concept::HasNumericTraits)); protected: diff --git a/Modules/Filtering/DistanceMap/include/itkIsoContourDistanceImageFilter.h b/Modules/Filtering/DistanceMap/include/itkIsoContourDistanceImageFilter.h index af1c7403b8e..1af425c790b 100644 --- a/Modules/Filtering/DistanceMap/include/itkIsoContourDistanceImageFilter.h +++ b/Modules/Filtering/DistanceMap/include/itkIsoContourDistanceImageFilter.h @@ -110,20 +110,23 @@ class ITK_TEMPLATE_EXPORT IsoContourDistanceImageFilter : public ImageToImageFil /** Set/Get the value of the level set to be located. The default value is * 0. */ + /** @ITKStartGrouping */ itkSetMacro(LevelSetValue, PixelRealType); itkGetConstMacro(LevelSetValue, PixelRealType); - + /** @ITKEndGrouping */ /** Set/Get the value of the level set to be located. The default value is * 0. */ + /** @ITKStartGrouping */ itkSetMacro(FarValue, PixelType); itkGetConstMacro(FarValue, PixelType); - + /** @ITKEndGrouping */ /** Set/Get the narrowbanding flag. By default, narrowbanding is switched * off. */ + /** @ITKStartGrouping */ itkSetMacro(NarrowBanding, bool); itkGetConstMacro(NarrowBanding, bool); itkBooleanMacro(NarrowBanding); - + /** @ITKEndGrouping */ /** Set/Get the narrowband. */ void SetNarrowBand(NarrowBandType * ptr); diff --git a/Modules/Filtering/DistanceMap/include/itkSignedMaurerDistanceMapImageFilter.h b/Modules/Filtering/DistanceMap/include/itkSignedMaurerDistanceMapImageFilter.h index e6dd110a724..f7c1f6d81aa 100644 --- a/Modules/Filtering/DistanceMap/include/itkSignedMaurerDistanceMapImageFilter.h +++ b/Modules/Filtering/DistanceMap/include/itkSignedMaurerDistanceMapImageFilter.h @@ -146,9 +146,10 @@ class ITK_TEMPLATE_EXPORT SignedMaurerDistanceMapImageFilter : public ImageToIma * Set the background value which defines the object. Usually this * value is = 0. */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, InputPixelType); itkGetConstReferenceMacro(BackgroundValue, InputPixelType); - + /** @ITKEndGrouping */ itkConceptMacro(IntConvertibleToInputCheck, (Concept::Convertible)); itkConceptMacro(InputHasNumericTraitsCheck, (Concept::HasNumericTraits)); itkConceptMacro(OutputImagePixelTypeIsFloatingPointCheck, (Concept::IsFloatingPoint)); diff --git a/Modules/Filtering/FFT/include/itkComplexToComplex1DFFTImageFilter.h b/Modules/Filtering/FFT/include/itkComplexToComplex1DFFTImageFilter.h index b914fa2909e..50fe554aefd 100644 --- a/Modules/Filtering/FFT/include/itkComplexToComplex1DFFTImageFilter.h +++ b/Modules/Filtering/FFT/include/itkComplexToComplex1DFFTImageFilter.h @@ -79,9 +79,10 @@ class ITK_TEMPLATE_EXPORT ComplexToComplex1DFFTImageFilter : public ImageToImage * Transform. * By selecting INVERSE, this filter will perform an inverse Fourier * Transform. */ + /** @ITKStartGrouping */ itkSetMacro(TransformDirection, TransformDirectionType); itkGetConstMacro(TransformDirection, TransformDirectionType); - + /** @ITKEndGrouping */ /** Get the direction in which the filter is to be applied. */ itkGetConstMacro(Direction, unsigned int); diff --git a/Modules/Filtering/FFT/include/itkComplexToComplexFFTImageFilter.h b/Modules/Filtering/FFT/include/itkComplexToComplexFFTImageFilter.h index bafb24046f9..1226cff5b3a 100644 --- a/Modules/Filtering/FFT/include/itkComplexToComplexFFTImageFilter.h +++ b/Modules/Filtering/FFT/include/itkComplexToComplexFFTImageFilter.h @@ -112,9 +112,10 @@ class ITK_TEMPLATE_EXPORT ComplexToComplexFFTImageFilter : public ImageToImageFi * By selecting FORWARD, this filter will perform a direct, i.e. forward, Fourier Transform, * By selecting INVERSE, this filter will perform an inverse, i.e. backward, Fourier Transform, */ + /** @ITKStartGrouping */ itkSetEnumMacro(TransformDirection, TransformDirectionEnum); itkGetConstMacro(TransformDirection, TransformDirectionEnum); - + /** @ITKEndGrouping */ protected: ComplexToComplexFFTImageFilter() = default; diff --git a/Modules/Filtering/FFT/include/itkFFTImageFilterFactory.h b/Modules/Filtering/FFT/include/itkFFTImageFilterFactory.h index 0cb1d241e6d..728d12eb314 100644 --- a/Modules/Filtering/FFT/include/itkFFTImageFilterFactory.h +++ b/Modules/Filtering/FFT/include/itkFFTImageFilterFactory.h @@ -97,6 +97,7 @@ class FFTImageFilterFactory : public itk::ObjectFactoryBase using ConstPointer = SmartPointer; /** Class methods used to interface with the registered factories. */ + /** @ITKStartGrouping */ const char * GetITKSourceVersion() const override { @@ -107,7 +108,7 @@ class FFTImageFilterFactory : public itk::ObjectFactoryBase { return "An FFTImageFilter factory"; } - + /** @ITKEndGrouping */ /** Method for class instantiation. */ itkFactorylessNewMacro(Self); @@ -128,6 +129,7 @@ class FFTImageFilterFactory : public itk::ObjectFactoryBase * with distinct specialization. * Requires TFFTImageFilter to have the template signature . */ + /** @ITKStartGrouping */ template void OverrideFFTImageFilterType(const std::integer_sequence &) @@ -146,7 +148,7 @@ class FFTImageFilterFactory : public itk::ObjectFactoryBase void OverrideFFTImageFilterType(const std::integer_sequence &) {} - + /** @ITKEndGrouping */ FFTImageFilterFactory() { OverrideFFTImageFilterType::template InputPixelType, diff --git a/Modules/Filtering/FFT/include/itkFFTPadImageFilter.h b/Modules/Filtering/FFT/include/itkFFTPadImageFilter.h index a97d0e8560d..6cab46c2ef5 100644 --- a/Modules/Filtering/FFT/include/itkFFTPadImageFilter.h +++ b/Modules/Filtering/FFT/include/itkFFTPadImageFilter.h @@ -89,9 +89,10 @@ class ITK_TEMPLATE_EXPORT FFTPadImageFilter : public PadImageFilterBase; using DefaultBoundaryConditionType = ZeroFluxNeumannBoundaryCondition; diff --git a/Modules/Filtering/FFT/include/itkFFTShiftImageFilter.h b/Modules/Filtering/FFT/include/itkFFTShiftImageFilter.h index 833df6e6016..0e5403e0435 100644 --- a/Modules/Filtering/FFT/include/itkFFTShiftImageFilter.h +++ b/Modules/Filtering/FFT/include/itkFFTShiftImageFilter.h @@ -84,10 +84,11 @@ class ITK_TEMPLATE_EXPORT FFTShiftImageFilter : public CyclicShiftImageFilterSetPlanRigor(FFTWGlobalConfiguration::GetPlanRigorValue(name)); #endif } - + /** @ITKEndGrouping */ protected: FFTWComplexToComplexFFTImageFilter(); ~FFTWComplexToComplexFFTImageFilter() override = default; diff --git a/Modules/Filtering/FFT/include/itkFFTWForwardFFTImageFilter.h b/Modules/Filtering/FFT/include/itkFFTWForwardFFTImageFilter.h index bc245637c3f..83f1b77f5e1 100644 --- a/Modules/Filtering/FFT/include/itkFFTWForwardFFTImageFilter.h +++ b/Modules/Filtering/FFT/include/itkFFTWForwardFFTImageFilter.h @@ -98,6 +98,7 @@ class ITK_TEMPLATE_EXPORT FFTWForwardFFTImageFilter : public ForwardFFTImageFilt * * /sa FFTWGlobalConfiguration */ + /** @ITKStartGrouping */ virtual void SetPlanRigor(const int & value) { @@ -112,7 +113,7 @@ class ITK_TEMPLATE_EXPORT FFTWForwardFFTImageFilter : public ForwardFFTImageFilt } } itkGetConstReferenceMacro(PlanRigor, int); - + /** @ITKEndGrouping */ SizeValueType GetSizeGreatestPrimeFactor() const override; diff --git a/Modules/Filtering/FFT/include/itkFFTWHalfHermitianToRealInverseFFTImageFilter.h b/Modules/Filtering/FFT/include/itkFFTWHalfHermitianToRealInverseFFTImageFilter.h index 1ec374db482..7e68ee1fa97 100644 --- a/Modules/Filtering/FFT/include/itkFFTWHalfHermitianToRealInverseFFTImageFilter.h +++ b/Modules/Filtering/FFT/include/itkFFTWHalfHermitianToRealInverseFFTImageFilter.h @@ -94,6 +94,7 @@ class ITK_TEMPLATE_EXPORT FFTWHalfHermitianToRealInverseFFTImageFilter * This has no effect with ITK_USE_CUFFTW enabled. * /sa FFTWGlobalConfiguration */ + /** @ITKStartGrouping */ virtual void SetPlanRigor(const int & value) { @@ -115,7 +116,7 @@ class ITK_TEMPLATE_EXPORT FFTWHalfHermitianToRealInverseFFTImageFilter this->SetPlanRigor(FFTWGlobalConfiguration::GetPlanRigorValue(name)); #endif } - + /** @ITKEndGrouping */ SizeValueType GetSizeGreatestPrimeFactor() const override; diff --git a/Modules/Filtering/FFT/include/itkFFTWInverseFFTImageFilter.h b/Modules/Filtering/FFT/include/itkFFTWInverseFFTImageFilter.h index 724c5813083..51e0467c667 100644 --- a/Modules/Filtering/FFT/include/itkFFTWInverseFFTImageFilter.h +++ b/Modules/Filtering/FFT/include/itkFFTWInverseFFTImageFilter.h @@ -93,6 +93,7 @@ class ITK_TEMPLATE_EXPORT FFTWInverseFFTImageFilter : public InverseFFTImageFilt * This has no effect with ITK_USE_CUFFTW. * /sa FFTWGlobalConfiguration */ + /** @ITKStartGrouping */ virtual void SetPlanRigor(const int & value) { @@ -114,7 +115,7 @@ class ITK_TEMPLATE_EXPORT FFTWInverseFFTImageFilter : public InverseFFTImageFilt this->SetPlanRigor(FFTWGlobalConfiguration::GetPlanRigorValue(name)); #endif } - + /** @ITKEndGrouping */ SizeValueType GetSizeGreatestPrimeFactor() const override; diff --git a/Modules/Filtering/FFT/include/itkFFTWRealToHalfHermitianForwardFFTImageFilter.h b/Modules/Filtering/FFT/include/itkFFTWRealToHalfHermitianForwardFFTImageFilter.h index d67b38ccb66..06430e12a7e 100644 --- a/Modules/Filtering/FFT/include/itkFFTWRealToHalfHermitianForwardFFTImageFilter.h +++ b/Modules/Filtering/FFT/include/itkFFTWRealToHalfHermitianForwardFFTImageFilter.h @@ -97,6 +97,7 @@ class ITK_TEMPLATE_EXPORT FFTWRealToHalfHermitianForwardFFTImageFilter * This has no effect when ITK_USE_CUFFTW is enabled. * /sa FFTWGlobalConfiguration */ + /** @ITKStartGrouping */ virtual void SetPlanRigor(const int & value) { @@ -111,7 +112,7 @@ class ITK_TEMPLATE_EXPORT FFTWRealToHalfHermitianForwardFFTImageFilter } } itkGetConstReferenceMacro(PlanRigor, int); - + /** @ITKEndGrouping */ SizeValueType GetSizeGreatestPrimeFactor() const override; diff --git a/Modules/Filtering/FFT/include/itkHalfHermitianToRealInverseFFTImageFilter.h b/Modules/Filtering/FFT/include/itkHalfHermitianToRealInverseFFTImageFilter.h index 216f0c111d5..ae4035b7765 100644 --- a/Modules/Filtering/FFT/include/itkHalfHermitianToRealInverseFFTImageFilter.h +++ b/Modules/Filtering/FFT/include/itkHalfHermitianToRealInverseFFTImageFilter.h @@ -84,9 +84,10 @@ class ITK_TEMPLATE_EXPORT HalfHermitianToRealInverseFFTImageFilter itkFactoryOnlyNewMacro(Self); /** Was the original truncated dimension size odd? */ + /** @ITKStartGrouping */ itkSetGetDecoratedInputMacro(ActualXDimensionIsOdd, bool); itkBooleanMacro(ActualXDimensionIsOdd); - + /** @ITKEndGrouping */ /* Return the preferred greatest prime factor supported for the input image * size. Defaults to 2 as many implementations work only for sizes that are * power of 2. diff --git a/Modules/Filtering/FFT/include/itkHalfToFullHermitianImageFilter.h b/Modules/Filtering/FFT/include/itkHalfToFullHermitianImageFilter.h index 21cb1dae15f..3ada992d993 100644 --- a/Modules/Filtering/FFT/include/itkHalfToFullHermitianImageFilter.h +++ b/Modules/Filtering/FFT/include/itkHalfToFullHermitianImageFilter.h @@ -79,9 +79,10 @@ class ITK_TEMPLATE_EXPORT HalfToFullHermitianImageFilter : public ImageToImageFi static constexpr unsigned int ImageDimension = TInputImage::ImageDimension; /** Was the original truncated dimension size in the x-dimension odd? */ + /** @ITKStartGrouping */ itkSetGetDecoratedInputMacro(ActualXDimensionIsOdd, bool); itkBooleanMacro(ActualXDimensionIsOdd); - + /** @ITKEndGrouping */ protected: HalfToFullHermitianImageFilter(); ~HalfToFullHermitianImageFilter() override = default; diff --git a/Modules/Filtering/FastMarching/include/itkFastMarchingBase.h b/Modules/Filtering/FastMarching/include/itkFastMarchingBase.h index be7bbbe16ef..4dea1013d3e 100644 --- a/Modules/Filtering/FastMarching/include/itkFastMarchingBase.h +++ b/Modules/Filtering/FastMarching/include/itkFastMarchingBase.h @@ -181,25 +181,30 @@ class ITK_TEMPLATE_EXPORT FastMarchingBase : public FastMarchingTraits)); protected: diff --git a/Modules/Filtering/FastMarching/include/itkFastMarchingImageFilter.h b/Modules/Filtering/FastMarching/include/itkFastMarchingImageFilter.h index 48a1a3d9b25..3a6104e470f 100644 --- a/Modules/Filtering/FastMarching/include/itkFastMarchingImageFilter.h +++ b/Modules/Filtering/FastMarching/include/itkFastMarchingImageFilter.h @@ -313,8 +313,10 @@ class ITK_TEMPLATE_EXPORT FastMarchingImageFilter : public ImageToImageFilter)); itkConceptMacro(SpeedConvertibleToDoubleCheck, (Concept::Convertible)); diff --git a/Modules/Filtering/FastMarching/include/itkFastMarchingImageFilterBase.h b/Modules/Filtering/FastMarching/include/itkFastMarchingImageFilterBase.h index 1cf2feb1ce1..0d7352a8431 100644 --- a/Modules/Filtering/FastMarching/include/itkFastMarchingImageFilterBase.h +++ b/Modules/Filtering/FastMarching/include/itkFastMarchingImageFilterBase.h @@ -135,6 +135,7 @@ class ITK_TEMPLATE_EXPORT FastMarchingImageFilterBase : public FastMarchingBase< * SetOutputSpacing(), SetOutputDirection(), and SetOutputOrigin(). * Else if the speed image is not nullptr, the output information * is copied from the input speed image. */ + /** @ITKStartGrouping */ virtual void SetOutputSize(const OutputSizeType & size) { @@ -156,7 +157,7 @@ class ITK_TEMPLATE_EXPORT FastMarchingImageFilterBase : public FastMarchingBase< itkSetMacro(OverrideOutputInformation, bool); itkGetConstReferenceMacro(OverrideOutputInformation, bool); itkBooleanMacro(OverrideOutputInformation); - + /** @ITKEndGrouping */ protected: FastMarchingImageFilterBase(); @@ -212,11 +213,12 @@ class ITK_TEMPLATE_EXPORT FastMarchingImageFilterBase : public FastMarchingBase< UpdateValue(OutputImageType * oImage, const NodeType & iNode) override; /** Make sure the given node does not violate any topological constraint*/ + /** @ITKStartGrouping */ bool CheckTopology(OutputImageType * oImage, const NodeType & iNode) override; void InitializeOutput(OutputImageType * oImage) override; - + /** @ITKEndGrouping */ /** Find the nodes were the front will propagate given a node */ void GetInternalNodesUsed(OutputImageType * oImage, const NodeType & iNode, InternalNodeStructureArray & ioNodesUsed); diff --git a/Modules/Filtering/FastMarching/include/itkFastMarchingNumberOfElementsStoppingCriterion.h b/Modules/Filtering/FastMarching/include/itkFastMarchingNumberOfElementsStoppingCriterion.h index 88f8fb15bb3..83d47db3f10 100644 --- a/Modules/Filtering/FastMarching/include/itkFastMarchingNumberOfElementsStoppingCriterion.h +++ b/Modules/Filtering/FastMarching/include/itkFastMarchingNumberOfElementsStoppingCriterion.h @@ -59,9 +59,10 @@ class ITK_TEMPLATE_EXPORT FastMarchingNumberOfElementsStoppingCriterion using typename Superclass::NodeType; /** Get/set the threshold used by the stopping criteria. */ + /** @ITKStartGrouping */ itkSetMacro(TargetNumberOfElements, IdentifierType); itkGetMacro(TargetNumberOfElements, IdentifierType); - + /** @ITKEndGrouping */ bool IsSatisfied() const override { diff --git a/Modules/Filtering/FastMarching/include/itkFastMarchingReachedTargetNodesStoppingCriterion.h b/Modules/Filtering/FastMarching/include/itkFastMarchingReachedTargetNodesStoppingCriterion.h index e7f2b69fda8..63fa054a680 100644 --- a/Modules/Filtering/FastMarching/include/itkFastMarchingReachedTargetNodesStoppingCriterion.h +++ b/Modules/Filtering/FastMarching/include/itkFastMarchingReachedTargetNodesStoppingCriterion.h @@ -46,6 +46,7 @@ class FastMarchingReachedTargetNodesStoppingCriterionEnums // Define how to print enumeration extern ITKFastMarching_EXPORT std::ostream & operator<<(std::ostream & out, const FastMarchingReachedTargetNodesStoppingCriterionEnums::TargetCondition value); + /** * \class FastMarchingReachedTargetNodesStoppingCriterion * \brief Stopping criterion for FastMarchingFilterBase. @@ -87,6 +88,7 @@ class ITK_TEMPLATE_EXPORT FastMarchingReachedTargetNodesStoppingCriterion /** Set/Get TargetCondition to indicate if the user wants the front to reach one, some or all target nodes. */ + /** @ITKStartGrouping */ void SetTargetCondition(const TargetConditionEnum & iCondition) { @@ -96,10 +98,13 @@ class ITK_TEMPLATE_EXPORT FastMarchingReachedTargetNodesStoppingCriterion } itkGetConstReferenceMacro(TargetCondition, TargetConditionEnum); + /** @ITKEndGrouping */ /** Set/Get TargetOffset */ + /** @ITKStartGrouping */ itkSetMacro(TargetOffset, OutputPixelType); itkGetMacro(TargetOffset, OutputPixelType); + /** @ITKEndGrouping */ /** \brief Set the number of target nodes to be reached */ void diff --git a/Modules/Filtering/FastMarching/include/itkFastMarchingThresholdStoppingCriterion.h b/Modules/Filtering/FastMarching/include/itkFastMarchingThresholdStoppingCriterion.h index e7c6966ff90..4931cc6ca66 100644 --- a/Modules/Filtering/FastMarching/include/itkFastMarchingThresholdStoppingCriterion.h +++ b/Modules/Filtering/FastMarching/include/itkFastMarchingThresholdStoppingCriterion.h @@ -53,9 +53,10 @@ class ITK_TEMPLATE_EXPORT FastMarchingThresholdStoppingCriterion using typename Superclass::NodeType; /** Get/set the threshold used by the stopping criteria. */ + /** @ITKStartGrouping */ itkSetMacro(Threshold, OutputPixelType); itkGetMacro(Threshold, OutputPixelType); - + /** @ITKEndGrouping */ bool IsSatisfied() const override { diff --git a/Modules/Filtering/FastMarching/include/itkFastMarchingUpwindGradientImageFilter.h b/Modules/Filtering/FastMarching/include/itkFastMarchingUpwindGradientImageFilter.h index 33774a55532..8c8135f5988 100644 --- a/Modules/Filtering/FastMarching/include/itkFastMarchingUpwindGradientImageFilter.h +++ b/Modules/Filtering/FastMarching/include/itkFastMarchingUpwindGradientImageFilter.h @@ -180,19 +180,22 @@ class ITK_TEMPLATE_EXPORT FastMarchingUpwindGradientImageFilter : public FastMar itkSetMacro(GenerateGradientImage, bool); /** Get the GenerateGradientImage flag. */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(GenerateGradientImage, bool); itkBooleanMacro(GenerateGradientImage); - + /** @ITKEndGrouping */ /** Set how long (in terms of arrival times) after targets are reached the * front must stop. This is useful to ensure that the level set of target * arrival time is smooth. */ itkSetMacro(TargetOffset, double); + /** Get the TargetOffset ivar. */ itkGetConstReferenceMacro(TargetOffset, double); /** Choose whether the front must stop when the first target has been reached * or all targets have been reached. */ + /** @ITKStartGrouping */ itkSetMacro(TargetReachedMode, TargetConditionEnum); itkGetConstReferenceMacro(TargetReachedMode, TargetConditionEnum); void @@ -213,7 +216,7 @@ class ITK_TEMPLATE_EXPORT FastMarchingUpwindGradientImageFilter : public FastMar this->SetTargetReachedMode(TargetConditionEnum::SomeTargets); m_NumberOfTargets = numberOfTargets; } - + /** @ITKEndGrouping */ void SetTargetReachedModeToAllTargets() { diff --git a/Modules/Filtering/FastMarching/include/itkLevelSetNode.h b/Modules/Filtering/FastMarching/include/itkLevelSetNode.h index 202af2be7e2..b60eafa3b59 100644 --- a/Modules/Filtering/FastMarching/include/itkLevelSetNode.h +++ b/Modules/Filtering/FastMarching/include/itkLevelSetNode.h @@ -99,6 +99,7 @@ class LevelSetNode } /** Get/Set level set value. */ + /** @ITKStartGrouping */ PixelType & GetValue() { @@ -114,8 +115,10 @@ class LevelSetNode { m_Value = input; } + /** @ITKEndGrouping */ /** Get/Set index. */ + /** @ITKStartGrouping */ IndexType & GetIndex() { @@ -131,6 +134,7 @@ class LevelSetNode { m_Index = input; } + /** @ITKEndGrouping */ /** Default constructor */ LevelSetNode() diff --git a/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUGradientAnisotropicDiffusionImageFilterFactory.h b/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUGradientAnisotropicDiffusionImageFilterFactory.h index b61573daf29..fa2153f0d09 100644 --- a/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUGradientAnisotropicDiffusionImageFilterFactory.h +++ b/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUGradientAnisotropicDiffusionImageFilterFactory.h @@ -40,6 +40,7 @@ class GPUGradientAnisotropicDiffusionImageFilterFactory : public ObjectFactoryBa using ConstPointer = SmartPointer; /** Class methods used to interface with the registered factories. */ + /** @ITKStartGrouping */ const char * GetITKSourceVersion() const override { @@ -50,7 +51,7 @@ class GPUGradientAnisotropicDiffusionImageFilterFactory : public ObjectFactoryBa { return "A Factory for GPUGradientAnisotropicDiffusionImageFilter"; } - + /** @ITKEndGrouping */ /** Method for class instantiation. */ itkFactorylessNewMacro(Self); diff --git a/Modules/Filtering/GPUSmoothing/include/itkGPUMeanImageFilter.h b/Modules/Filtering/GPUSmoothing/include/itkGPUMeanImageFilter.h index 1bdbc228712..f1c01ac22b6 100644 --- a/Modules/Filtering/GPUSmoothing/include/itkGPUMeanImageFilter.h +++ b/Modules/Filtering/GPUSmoothing/include/itkGPUMeanImageFilter.h @@ -110,6 +110,7 @@ class GPUMeanImageFilterFactory : public ObjectFactoryBase using ConstPointer = SmartPointer; /** Class methods used to interface with the registered factories. */ + /** @ITKStartGrouping */ const char * GetITKSourceVersion() const override { @@ -120,7 +121,7 @@ class GPUMeanImageFilterFactory : public ObjectFactoryBase { return "A Factory for GPUMeanImageFilter"; } - + /** @ITKEndGrouping */ /** Method for class instantiation. */ itkFactorylessNewMacro(Self); diff --git a/Modules/Filtering/GPUThresholding/include/itkGPUBinaryThresholdImageFilter.h b/Modules/Filtering/GPUThresholding/include/itkGPUBinaryThresholdImageFilter.h index 792964bbe00..0e856cc7f9c 100644 --- a/Modules/Filtering/GPUThresholding/include/itkGPUBinaryThresholdImageFilter.h +++ b/Modules/Filtering/GPUThresholding/include/itkGPUBinaryThresholdImageFilter.h @@ -163,6 +163,7 @@ class GPUBinaryThresholdImageFilterFactory : public ObjectFactoryBase using ConstPointer = SmartPointer; /** Class methods used to interface with the registered factories. */ + /** @ITKStartGrouping */ const char * GetITKSourceVersion() const override { @@ -173,6 +174,7 @@ class GPUBinaryThresholdImageFilterFactory : public ObjectFactoryBase { return "A Factory for GPUBinaryThresholdImageFilter"; } + /** @ITKEndGrouping */ /** Method for class instantiation. */ itkFactorylessNewMacro(Self); diff --git a/Modules/Filtering/ImageCompare/include/itkCheckerBoardImageFilter.h b/Modules/Filtering/ImageCompare/include/itkCheckerBoardImageFilter.h index e7d9ae79a1a..542babb2c28 100644 --- a/Modules/Filtering/ImageCompare/include/itkCheckerBoardImageFilter.h +++ b/Modules/Filtering/ImageCompare/include/itkCheckerBoardImageFilter.h @@ -82,9 +82,10 @@ class ITK_TEMPLATE_EXPORT CheckerBoardImageFilter : public ImageToImageFilter of * all Specificity (true negative fraction, q) values for the expert @@ -199,8 +201,10 @@ class ITK_TEMPLATE_EXPORT STAPLEImageFilter : public ImageToImageFilter::max()); itkGetConstMacro(MaximumIterations, unsigned int); + /** @ITKEndGrouping */ /** Scales the estimated prior probability that a pixel will be inside the * targeted object of segmentation. The default prior probability g_t is @@ -209,8 +213,10 @@ class ITK_TEMPLATE_EXPORT STAPLEImageFilter : public ImageToImageFilter> class ITK_TEMPLATE_EXPORT ComposeImageFilter : public ImageToImageFilter diff --git a/Modules/Filtering/ImageCompose/include/itkJoinSeriesImageFilter.h b/Modules/Filtering/ImageCompose/include/itkJoinSeriesImageFilter.h index d59db6636e6..c8f36b7be6b 100644 --- a/Modules/Filtering/ImageCompose/include/itkJoinSeriesImageFilter.h +++ b/Modules/Filtering/ImageCompose/include/itkJoinSeriesImageFilter.h @@ -78,13 +78,15 @@ class ITK_TEMPLATE_EXPORT JoinSeriesImageFilter : public ImageToImageFilter)); diff --git a/Modules/Filtering/ImageFeature/include/itkBilateralImageFilter.h b/Modules/Filtering/ImageFeature/include/itkBilateralImageFilter.h index ac26858d08e..254f14a8871 100644 --- a/Modules/Filtering/ImageFeature/include/itkBilateralImageFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkBilateralImageFilter.h @@ -128,6 +128,7 @@ class ITK_TEMPLATE_EXPORT BilateralImageFilter : public ImageToImageFilter)); protected: diff --git a/Modules/Filtering/ImageFeature/include/itkCannyEdgeDetectionImageFilter.h b/Modules/Filtering/ImageFeature/include/itkCannyEdgeDetectionImageFilter.h index 45e9d66e41e..42e5e3fadc4 100644 --- a/Modules/Filtering/ImageFeature/include/itkCannyEdgeDetectionImageFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkCannyEdgeDetectionImageFilter.h @@ -138,13 +138,17 @@ class ITK_TEMPLATE_EXPORT CannyEdgeDetectionImageFilter : public ImageToImageFil using ArrayType = FixedArray; /** Set/Get the variance of the Gaussian smoothing filter. */ + /** @ITKStartGrouping */ itkSetMacro(Variance, ArrayType); itkGetConstMacro(Variance, const ArrayType); + /** @ITKEndGrouping */ /** Set/Get the maximum error of the Gaussian smoothing kernel in each dimensional * direction. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumError, ArrayType); itkGetConstMacro(MaximumError, const ArrayType); + /** @ITKEndGrouping */ /** Set/Get the variance of the Gaussian smoothing filter. */ void diff --git a/Modules/Filtering/ImageFeature/include/itkDerivativeImageFilter.h b/Modules/Filtering/ImageFeature/include/itkDerivativeImageFilter.h index 71dd7bb74fd..fc205d92cde 100644 --- a/Modules/Filtering/ImageFeature/include/itkDerivativeImageFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkDerivativeImageFilter.h @@ -83,19 +83,21 @@ class ITK_TEMPLATE_EXPORT DerivativeImageFilter : public ImageToImageFilter)); /** Standard get/set macros for filter parameters. */ + /** @ITKStartGrouping */ itkSetMacro(Order, unsigned int); itkGetConstMacro(Order, unsigned int); itkSetMacro(Direction, unsigned int); itkGetConstMacro(Direction, unsigned int); - + /** @ITKEndGrouping */ /** Set/Get whether or not the filter will use the spacing of the input * image in its calculations. Use On to compute the derivatives in physical * space; use Off to ignore the image spacing and to compute the derivatives * in isotropic voxel space. Default is On. */ + /** @ITKStartGrouping */ itkSetMacro(UseImageSpacing, bool); itkGetConstMacro(UseImageSpacing, bool); itkBooleanMacro(UseImageSpacing); - + /** @ITKEndGrouping */ #if !defined(ITK_FUTURE_LEGACY_REMOVE) /** Use the image spacing information in calculations. Use this option if you * want derivatives in physical space. Default is UseImageSpacingOn. */ diff --git a/Modules/Filtering/ImageFeature/include/itkDiscreteGaussianDerivativeImageFilter.h b/Modules/Filtering/ImageFeature/include/itkDiscreteGaussianDerivativeImageFilter.h index b65a8019a0c..75859f75368 100644 --- a/Modules/Filtering/ImageFeature/include/itkDiscreteGaussianDerivativeImageFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkDiscreteGaussianDerivativeImageFilter.h @@ -96,29 +96,33 @@ class ITK_TEMPLATE_EXPORT DiscreteGaussianDerivativeImageFilter : public ImageTo /** Order of derivatives in each dimension. Sets the derivative order * independently for each dimension, but see also * SetOrder(const unsigned int v). The default is 1 in each dimension. */ + /** @ITKStartGrouping */ itkSetMacro(Order, OrderArrayType); itkGetConstMacro(Order, const OrderArrayType); - + /** @ITKEndGrouping */ /** The variance for the discrete Gaussian kernel. Sets the variance * independently for each dimension, but * see also SetVariance(const double v). The default is 0.0 in each * dimension. If UseImageSpacing is true, the units are the physical units * of your image. If UseImageSpacing is false then the units are * pixels. */ + /** @ITKStartGrouping */ itkSetMacro(Variance, ArrayType); itkGetConstMacro(Variance, const ArrayType); - + /** @ITKEndGrouping */ /** The algorithm will size the discrete kernel so that the error * resulting from truncation of the kernel is no greater than * MaximumError. The default is 0.01 in each dimension. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumError, ArrayType); itkGetConstMacro(MaximumError, const ArrayType); - + /** @ITKEndGrouping */ /** Set the kernel to be no wider than MaximumKernelWidth pixels, * even if MaximumError demands it. The default is 32 pixels. */ + /** @ITKStartGrouping */ itkGetConstMacro(MaximumKernelWidth, int); itkSetMacro(MaximumKernelWidth, int); - + /** @ITKEndGrouping */ /** \brief Set/Get number of pieces to divide the input for the * internal composite pipeline. The upstream pipeline will not be * effected. @@ -134,7 +138,7 @@ class ITK_TEMPLATE_EXPORT DiscreteGaussianDerivativeImageFilter : public ImageTo /** Convenience Set methods for setting all dimensional parameters * to the same values. */ - /*@{*/ + /** @ITKStartGrouping */ void SetOrder(const typename OrderArrayType::ValueType v) { @@ -155,22 +159,23 @@ class ITK_TEMPLATE_EXPORT DiscreteGaussianDerivativeImageFilter : public ImageTo auto a = MakeFilled(v); this->SetMaximumError(a); } - - /*@}*/ + /** @ITKEndGrouping */ /** Set/Get whether or not the filter will use the spacing of the input image in its calculations. Default is ImageSpacingOn. */ + /** @ITKStartGrouping */ itkSetMacro(UseImageSpacing, bool); itkGetConstMacro(UseImageSpacing, bool); itkBooleanMacro(UseImageSpacing); - + /** @ITKEndGrouping */ /** Set/Get the flag for calculating scale-space normalized derivatives. * Normalized derivatives are obtained multiplying by the scale * parameter t. */ + /** @ITKStartGrouping */ itkSetMacro(NormalizeAcrossScale, bool); itkGetConstMacro(NormalizeAcrossScale, bool); itkBooleanMacro(NormalizeAcrossScale); - + /** @ITKEndGrouping */ itkConceptMacro(OutputHasNumericTraitsCheck, (Concept::HasNumericTraits)); protected: diff --git a/Modules/Filtering/ImageFeature/include/itkHessian3DToVesselnessMeasureImageFilter.h b/Modules/Filtering/ImageFeature/include/itkHessian3DToVesselnessMeasureImageFilter.h index cf43d321e1d..f087f8596d8 100644 --- a/Modules/Filtering/ImageFeature/include/itkHessian3DToVesselnessMeasureImageFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkHessian3DToVesselnessMeasureImageFilter.h @@ -109,14 +109,16 @@ class ITK_TEMPLATE_EXPORT Hessian3DToVesselnessMeasureImageFilter /** Set/Get macros for alpha_1. Please refer to * http://www.image.med.osaka-u.ac.jp/member/yoshi/paper/linefilter.pdf */ + /** @ITKStartGrouping */ itkSetMacro(Alpha1, double); itkGetConstMacro(Alpha1, double); - + /** @ITKEndGrouping */ /** Set/Get macros for alpha_2. Please refer to * http://www.image.med.osaka-u.ac.jp/member/yoshi/paper/linefilter.pdf */ + /** @ITKStartGrouping */ itkSetMacro(Alpha2, double); itkGetConstMacro(Alpha2, double); - + /** @ITKEndGrouping */ itkConceptMacro(DoubleConvertibleToOutputCheck, (Concept::Convertible)); protected: diff --git a/Modules/Filtering/ImageFeature/include/itkHessianRecursiveGaussianImageFilter.h b/Modules/Filtering/ImageFeature/include/itkHessianRecursiveGaussianImageFilter.h index 16aaadb6b9d..dc3633686cb 100644 --- a/Modules/Filtering/ImageFeature/include/itkHessianRecursiveGaussianImageFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkHessianRecursiveGaussianImageFilter.h @@ -113,19 +113,21 @@ class ITK_TEMPLATE_EXPORT HessianRecursiveGaussianImageFilter : public ImageToIm itkNewMacro(Self); /** Set/Get Sigma value. Sigma is measured in the units of image spacing. */ + /** @ITKStartGrouping */ void SetSigma(RealType sigma); RealType GetSigma() const; - + /** @ITKEndGrouping */ /** Define which normalization factor will be used for the Gaussian * \sa RecursiveGaussianImageFilter::SetNormalizeAcrossScale */ + /** @ITKStartGrouping */ void SetNormalizeAcrossScale(bool normalize); itkGetConstMacro(NormalizeAcrossScale, bool); itkBooleanMacro(NormalizeAcrossScale); - + /** @ITKEndGrouping */ /** HessianRecursiveGaussianImageFilter needs all of the input to produce an * output. Therefore, HessianRecursiveGaussianImageFilter needs to provide * an implementation for GenerateInputRequestedRegion in order to inform diff --git a/Modules/Filtering/ImageFeature/include/itkHessianToObjectnessMeasureImageFilter.h b/Modules/Filtering/ImageFeature/include/itkHessianToObjectnessMeasureImageFilter.h index d1fae6ee165..f189127b80b 100644 --- a/Modules/Filtering/ImageFeature/include/itkHessianToObjectnessMeasureImageFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkHessianToObjectnessMeasureImageFilter.h @@ -84,38 +84,44 @@ class ITK_TEMPLATE_EXPORT HessianToObjectnessMeasureImageFilter : public ImageTo /** Set/Get Alpha, the weight corresponding to R_A * (the ratio of the smallest eigenvalue that has to be large to the larger ones). * Smaller values lead to increased sensitivity to the object dimensionality. */ + /** @ITKStartGrouping */ itkSetMacro(Alpha, double); itkGetConstMacro(Alpha, double); - + /** @ITKEndGrouping */ /** Set/Get Beta, the weight corresponding to R_B * (the ratio of the largest eigenvalue that has to be small to the larger ones). * Smaller values lead to increased sensitivity to the object dimensionality. */ + /** @ITKStartGrouping */ itkSetMacro(Beta, double); itkGetConstMacro(Beta, double); - + /** @ITKEndGrouping */ /** Set/Get Gamma, the weight corresponding to S * (the Frobenius norm of the Hessian matrix, or second-order structureness) */ + /** @ITKStartGrouping */ itkSetMacro(Gamma, double); itkGetConstMacro(Gamma, double); - + /** @ITKEndGrouping */ /** Toggle scaling the objectness measure with the magnitude of the largest absolute eigenvalue */ + /** @ITKStartGrouping */ itkSetMacro(ScaleObjectnessMeasure, bool); itkGetConstMacro(ScaleObjectnessMeasure, bool); itkBooleanMacro(ScaleObjectnessMeasure); - + /** @ITKEndGrouping */ /** Set/Get the dimensionality of the object (0: points (blobs), * 1: lines (vessels), 2: planes (plate-like structures), 3: hyper-planes. * ObjectDimension must be smaller than ImageDimension. */ + /** @ITKStartGrouping */ itkSetMacro(ObjectDimension, unsigned int); itkGetConstMacro(ObjectDimension, unsigned int); - + /** @ITKEndGrouping */ /** Enhance bright structures on a dark background if true, the opposite if false. Default is "On" (equivalent to vesselness). */ + /** @ITKStartGrouping */ itkSetMacro(BrightObject, bool); itkGetConstMacro(BrightObject, bool); itkBooleanMacro(BrightObject); - + /** @ITKEndGrouping */ itkConceptMacro(DoubleConvertibleToOutputCheck, (Concept::Convertible)); protected: diff --git a/Modules/Filtering/ImageFeature/include/itkHoughTransform2DCirclesImageFilter.h b/Modules/Filtering/ImageFeature/include/itkHoughTransform2DCirclesImageFilter.h index e699dd64a86..cbd0a182ca7 100644 --- a/Modules/Filtering/ImageFeature/include/itkHoughTransform2DCirclesImageFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkHoughTransform2DCirclesImageFilter.h @@ -118,13 +118,15 @@ class ITK_TEMPLATE_EXPORT HoughTransform2DCirclesImageFilter SetRadius(double radius); /** Set the minimum radius value the filter should look for. */ + /** @ITKStartGrouping */ itkSetMacro(MinimumRadius, double); itkGetConstMacro(MinimumRadius, double); - + /** @ITKEndGrouping */ /** Set the maximum radius value the filter should look for. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumRadius, double); itkGetConstMacro(MaximumRadius, double); - + /** @ITKEndGrouping */ /** Set the threshold above which the filter should consider * the point as a valid point. */ itkSetMacro(Threshold, double); @@ -134,9 +136,10 @@ class ITK_TEMPLATE_EXPORT HoughTransform2DCirclesImageFilter /** Threshold for the norm of the gradient: Only pixels whose gradient norm is * above this threshold are processed by the filter. The threshold must be >= 0. */ + /** @ITKStartGrouping */ itkSetMacro(GradientNormThreshold, double); itkGetConstMacro(GradientNormThreshold, double); - + /** @ITKEndGrouping */ /** Get the radius image. */ itkGetModifiableObjectMacro(RadiusImage, RadiusImageType); @@ -154,27 +157,32 @@ class ITK_TEMPLATE_EXPORT HoughTransform2DCirclesImageFilter GetCircles(); /** Set/Get the number of circles to extract. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfCircles, CirclesListSizeType); itkGetConstMacro(NumberOfCircles, CirclesListSizeType); - + /** @ITKEndGrouping */ /** Set/Get the radius of the disc to remove from the accumulator * for each circle found. */ + /** @ITKStartGrouping */ itkSetMacro(DiscRadiusRatio, double); itkGetConstMacro(DiscRadiusRatio, double); - + /** @ITKEndGrouping */ /** Set/Get the variance of the Gaussian blurring for the accumulator. */ + /** @ITKStartGrouping */ itkSetMacro(Variance, double); itkGetConstMacro(Variance, double); - + /** @ITKEndGrouping */ /** Set/Get the sweep angle. */ + /** @ITKStartGrouping */ itkSetMacro(SweepAngle, double); itkGetConstMacro(SweepAngle, double); - + /** @ITKEndGrouping */ /** Specifies whether to use the spacing of the input image internally, when * doing Gaussian Derivative calculation and Gaussian image filtering. */ + /** @ITKStartGrouping */ itkSetMacro(UseImageSpacing, bool); itkGetConstMacro(UseImageSpacing, bool); - + /** @ITKEndGrouping */ itkConceptMacro(IntConvertibleToOutputCheck, (Concept::Convertible)); itkConceptMacro(InputGreaterThanDoubleCheck, (Concept::GreaterThanComparable)); itkConceptMacro(OutputPlusIntCheck, (Concept::AdditiveOperators)); diff --git a/Modules/Filtering/ImageFeature/include/itkHoughTransform2DLinesImageFilter.h b/Modules/Filtering/ImageFeature/include/itkHoughTransform2DLinesImageFilter.h index b6abb57610c..f9b0d0b6cd7 100644 --- a/Modules/Filtering/ImageFeature/include/itkHoughTransform2DLinesImageFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkHoughTransform2DLinesImageFilter.h @@ -113,15 +113,17 @@ class ITK_TEMPLATE_EXPORT HoughTransform2DLinesImageFilter /** Set/Get the threshold above which the filter should consider * the point as a valid point. */ + /** @ITKStartGrouping */ itkSetMacro(Threshold, double); itkGetConstMacro(Threshold, double); - + /** @ITKEndGrouping */ /** Set/Get the resolution angle. * The Hough space describes (in the angle direction) [-PI,PI[ * with a constant step AngleResolution. */ + /** @ITKStartGrouping */ itkSetMacro(AngleResolution, double); itkGetConstMacro(AngleResolution, double); - + /** @ITKEndGrouping */ /** Simplify the accumulator. * Performs the same iteration process as the Update() method, but finds * the maximum along the curve and then removes the curve. */ @@ -136,18 +138,21 @@ class ITK_TEMPLATE_EXPORT HoughTransform2DLinesImageFilter GetLines(); /** Set/Get the number of lines to extract */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfLines, LinesListSizeType); itkGetConstMacro(NumberOfLines, LinesListSizeType); - + /** @ITKEndGrouping */ /** Set/Get the radius of the disc to remove from the accumulator * for each line found. */ + /** @ITKStartGrouping */ itkSetMacro(DiscRadius, double); itkGetConstMacro(DiscRadius, double); - + /** @ITKEndGrouping */ /** Set/Get the variance of the Gaussian blurring for the accumulator. */ + /** @ITKStartGrouping */ itkSetMacro(Variance, double); itkGetConstMacro(Variance, double); - + /** @ITKEndGrouping */ itkConceptMacro(IntConvertibleToOutputCheck, (Concept::Convertible)); itkConceptMacro(InputGreaterThanFloatCheck, (Concept::GreaterThanComparable)); itkConceptMacro(OutputPlusIntCheck, (Concept::AdditiveOperators)); diff --git a/Modules/Filtering/ImageFeature/include/itkLaplacianImageFilter.h b/Modules/Filtering/ImageFeature/include/itkLaplacianImageFilter.h index 73d78430114..866f366e0c9 100644 --- a/Modules/Filtering/ImageFeature/include/itkLaplacianImageFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkLaplacianImageFilter.h @@ -110,9 +110,10 @@ class ITK_TEMPLATE_EXPORT LaplacianImageFilter : public ImageToImageFilter)); itkConceptMacro(InputPixelTypeIsFloatingPointCheck, (Concept::IsFloatingPoint)); itkConceptMacro(OutputPixelTypeIsFloatingPointCheck, (Concept::IsFloatingPoint)); diff --git a/Modules/Filtering/ImageFeature/include/itkLaplacianRecursiveGaussianImageFilter.h b/Modules/Filtering/ImageFeature/include/itkLaplacianRecursiveGaussianImageFilter.h index 7a8293f6f27..dd80cde57d1 100644 --- a/Modules/Filtering/ImageFeature/include/itkLaplacianRecursiveGaussianImageFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkLaplacianRecursiveGaussianImageFilter.h @@ -100,18 +100,20 @@ class ITK_TEMPLATE_EXPORT LaplacianRecursiveGaussianImageFilter : public ImageTo itkOverrideGetNameOfClassMacro(LaplacianRecursiveGaussianImageFilter); /** Set/Get Sigma value. Sigma is measured in the units of image spacing. */ + /** @ITKStartGrouping */ void SetSigma(RealType sigma); RealType GetSigma() const; - + /** @ITKEndGrouping */ /** Define which normalization factor will be used for the Gaussian * \sa RecursiveGaussianImageFilter::SetNormalizeAcrossScale */ + /** @ITKStartGrouping */ void SetNormalizeAcrossScale(bool normalize); itkGetConstMacro(NormalizeAcrossScale, bool); - + /** @ITKEndGrouping */ protected: LaplacianRecursiveGaussianImageFilter(); ~LaplacianRecursiveGaussianImageFilter() override = default; diff --git a/Modules/Filtering/ImageFeature/include/itkLaplacianSharpeningImageFilter.h b/Modules/Filtering/ImageFeature/include/itkLaplacianSharpeningImageFilter.h index b8f79f6a087..60db441f6ea 100644 --- a/Modules/Filtering/ImageFeature/include/itkLaplacianSharpeningImageFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkLaplacianSharpeningImageFilter.h @@ -86,10 +86,11 @@ class ITK_TEMPLATE_EXPORT LaplacianSharpeningImageFilter : public ImageToImageFi /** Set/Get whether or not the filter will use the spacing information of the input image in its calculations. Use * this option if derivatives are required in physical space. */ + /** @ITKStartGrouping */ itkBooleanMacro(UseImageSpacing); itkSetMacro(UseImageSpacing, bool); itkGetConstMacro(UseImageSpacing, bool); - + /** @ITKEndGrouping */ itkConceptMacro(SameDimensionCheck, (Concept::SameDimension)); protected: diff --git a/Modules/Filtering/ImageFeature/include/itkMaskFeaturePointSelectionFilter.h b/Modules/Filtering/ImageFeature/include/itkMaskFeaturePointSelectionFilter.h index e304c84ff5c..c3ff4ad0725 100644 --- a/Modules/Filtering/ImageFeature/include/itkMaskFeaturePointSelectionFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkMaskFeaturePointSelectionFilter.h @@ -111,26 +111,31 @@ class ITK_TEMPLATE_EXPORT MaskFeaturePointSelectionFilter : public ImageToMeshFi * 0 <= connect < ImageDimension; 0 is vertex connectivity (e.g., 26 in 3D), * 1 is edge connectivity (e.g., 18 in 3D), 2 is face connectivity * (e.g., 6 in 3D), etc */ + /** @ITKStartGrouping */ itkSetMacro(NonConnectivity, unsigned int); itkGetMacro(NonConnectivity, unsigned int); - + /** @ITKEndGrouping */ /** set/get mask */ + /** @ITKStartGrouping */ itkSetInputMacro(MaskImage, MaskType); itkGetInputMacro(MaskImage, MaskType); - + /** @ITKEndGrouping */ /** set/get half size of the block for calculating variance */ + /** @ITKStartGrouping */ itkSetMacro(BlockRadius, SizeType); itkGetConstReferenceMacro(BlockRadius, SizeType); - + /** @ITKEndGrouping */ /** enable/disable tensor computations */ + /** @ITKStartGrouping */ itkSetMacro(ComputeStructureTensors, bool); itkGetMacro(ComputeStructureTensors, bool); itkBooleanMacro(ComputeStructureTensors); - + /** @ITKEndGrouping */ /** set fraction of eligible points to select */ + /** @ITKStartGrouping */ itkSetClampMacro(SelectFraction, double, 0, 1); itkGetMacro(SelectFraction, double); - + /** @ITKEndGrouping */ itkConceptMacro(ImageDimensionShouldBe3, (Concept::SameDimension)); itkConceptMacro(MaskDimensionShouldBe3, (Concept::SameDimension)); itkConceptMacro(PointDimensionShouldBe3, (Concept::SameDimension)); diff --git a/Modules/Filtering/ImageFeature/include/itkMultiScaleHessianBasedMeasureImageFilter.h b/Modules/Filtering/ImageFeature/include/itkMultiScaleHessianBasedMeasureImageFilter.h index 923ef1769d6..bcabffe96b7 100644 --- a/Modules/Filtering/ImageFeature/include/itkMultiScaleHessianBasedMeasureImageFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkMultiScaleHessianBasedMeasureImageFilter.h @@ -132,33 +132,38 @@ class ITK_TEMPLATE_EXPORT MultiScaleHessianBasedMeasureImageFilter itkOverrideGetNameOfClassMacro(MultiScaleHessianBasedMeasureImageFilter); /** Set/Get macros for SigmaMin */ + /** @ITKStartGrouping */ itkSetMacro(SigmaMinimum, double); itkGetConstMacro(SigmaMinimum, double); - + /** @ITKEndGrouping */ /** Set/Get macros for SigmaMax */ + /** @ITKStartGrouping */ itkSetMacro(SigmaMaximum, double); itkGetConstMacro(SigmaMaximum, double); - + /** @ITKEndGrouping */ /** Set/Get macros for Number of Scales */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfSigmaSteps, unsigned int); itkGetConstMacro(NumberOfSigmaSteps, unsigned int); - + /** @ITKEndGrouping */ /** Set/Get HessianToMeasureFilter. This will be a filter that takes Hessian input image and produces enhanced output scalar image. The filter must derive from itk::ImageToImage filter */ + /** @ITKStartGrouping */ itkSetObjectMacro(HessianToMeasureFilter, HessianToMeasureFilterType); itkGetModifiableObjectMacro(HessianToMeasureFilter, HessianToMeasureFilterType); - + /** @ITKEndGrouping */ /** Methods to turn on/off flag to inform the filter that the Hessian-based measure is non-negative (classical measures like Sato's and Frangi's are), hence it has a minimum at zero. In this case, the update buffer is initialized at zero, and the output scale and Hessian are zero in case the Hessian-based measure returns zero for all scales. Otherwise, the minimum output scale and Hessian are the ones obtained at scale SigmaMinimum. On by default. */ + /** @ITKStartGrouping */ itkSetMacro(NonNegativeHessianBasedMeasure, bool); itkGetConstMacro(NonNegativeHessianBasedMeasure, bool); itkBooleanMacro(NonNegativeHessianBasedMeasure); - + /** @ITKEndGrouping */ using SigmaStepMethodEnum = MultiScaleHessianBasedMeasureImageFilterEnums::SigmaStepMethod; #if !defined(ITK_LEGACY_REMOVE) /**Exposes enums values for backwards compatibility*/ @@ -168,9 +173,10 @@ class ITK_TEMPLATE_EXPORT MultiScaleHessianBasedMeasureImageFilter /** Set/Get the method used to generate scale sequence (Equispaced * or Logarithmic) */ + /** @ITKStartGrouping */ itkSetEnumMacro(SigmaStepMethod, SigmaStepMethodEnum); itkGetConstMacro(SigmaStepMethod, SigmaStepMethodEnum); - + /** @ITKEndGrouping */ /**Set equispaced sigma step method */ void SetSigmaStepMethodToEquispaced(); @@ -191,16 +197,18 @@ class ITK_TEMPLATE_EXPORT MultiScaleHessianBasedMeasureImageFilter /** Methods to turn on/off flag to generate an image with scale values at * each pixel for the best vesselness response */ + /** @ITKStartGrouping */ itkSetMacro(GenerateScalesOutput, bool); itkGetConstMacro(GenerateScalesOutput, bool); itkBooleanMacro(GenerateScalesOutput); - + /** @ITKEndGrouping */ /** Methods to turn on/off flag to generate an image with hessian values at * each pixel for the best vesselness response */ + /** @ITKStartGrouping */ itkSetMacro(GenerateHessianOutput, bool); itkGetConstMacro(GenerateHessianOutput, bool); itkBooleanMacro(GenerateHessianOutput); - + /** @ITKEndGrouping */ /** This is overloaded to create the Scales and Hessian output images */ using DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType; diff --git a/Modules/Filtering/ImageFeature/include/itkUnsharpMaskImageFilter.h b/Modules/Filtering/ImageFeature/include/itkUnsharpMaskImageFilter.h index 9c20d1c7e13..4c53a45aac8 100644 --- a/Modules/Filtering/ImageFeature/include/itkUnsharpMaskImageFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkUnsharpMaskImageFilter.h @@ -110,8 +110,10 @@ class ITK_TEMPLATE_EXPORT UnsharpMaskImageFilter : public ImageToImageFilter; /** Standard get/set macros for Gaussian filter parameters. */ + /** @ITKStartGrouping */ itkSetMacro(Variance, ArrayType); itkGetConstMacro(Variance, const ArrayType); itkSetMacro(MaximumError, ArrayType); itkGetConstMacro(MaximumError, const ArrayType); - + /** @ITKEndGrouping */ /** Get/Set the label values for the ZeroCrossingImageFilter */ + /** @ITKStartGrouping */ itkGetConstMacro(BackgroundValue, OutputImagePixelType); itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(ForegroundValue, OutputImagePixelType); itkSetMacro(ForegroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** Set the variance parameter needed by the embedded gaussian filter */ void SetVariance(const typename ArrayType::ValueType v) diff --git a/Modules/Filtering/ImageFeature/include/itkZeroCrossingImageFilter.h b/Modules/Filtering/ImageFeature/include/itkZeroCrossingImageFilter.h index 7005679ce29..c740338c5e7 100644 --- a/Modules/Filtering/ImageFeature/include/itkZeroCrossingImageFilter.h +++ b/Modules/Filtering/ImageFeature/include/itkZeroCrossingImageFilter.h @@ -107,13 +107,15 @@ class ITK_TEMPLATE_EXPORT ZeroCrossingImageFilter : public ImageToImageFilter)); itkConceptMacro(SameDimensionCheck, (Concept::SameDimension)); itkConceptMacro(InputComparableCheck, (Concept::Comparable)); diff --git a/Modules/Filtering/ImageFilterBase/include/itkBinaryFunctorImageFilter.h b/Modules/Filtering/ImageFilterBase/include/itkBinaryFunctorImageFilter.h index 083727de742..cc1647c9eca 100644 --- a/Modules/Filtering/ImageFilterBase/include/itkBinaryFunctorImageFilter.h +++ b/Modules/Filtering/ImageFilterBase/include/itkBinaryFunctorImageFilter.h @@ -87,12 +87,14 @@ class ITK_TEMPLATE_EXPORT BinaryFunctorImageFilter : public InPlaceImageFilterGetConstant2(); } + /** @ITKEndGrouping */ /** Get the constant value of the second operand. An exception is sent if * the second operand is not a constant. */ diff --git a/Modules/Filtering/ImageFilterBase/include/itkBinaryGeneratorImageFilter.h b/Modules/Filtering/ImageFilterBase/include/itkBinaryGeneratorImageFilter.h index 5f74a40a336..eaff295dc4f 100644 --- a/Modules/Filtering/ImageFilterBase/include/itkBinaryGeneratorImageFilter.h +++ b/Modules/Filtering/ImageFilterBase/include/itkBinaryGeneratorImageFilter.h @@ -94,13 +94,14 @@ class ITK_TEMPLATE_EXPORT BinaryGeneratorImageFilter : public InPlaceImageFilter using ValueFunctionType = OutputImagePixelType(Input1ImagePixelType, Input2ImagePixelType); /** Connect the first operand for pixel-wise operation. */ + /** @ITKStartGrouping */ virtual void SetInput1(const TInputImage1 * image1); virtual void SetInput1(const DecoratedInput1ImagePixelType * input1); virtual void SetInput1(const Input1ImagePixelType & input1); - + /** @ITKEndGrouping */ /** Set the first operand as a constant. */ virtual void SetConstant1(const Input1ImagePixelType & input1); @@ -111,15 +112,17 @@ class ITK_TEMPLATE_EXPORT BinaryGeneratorImageFilter : public InPlaceImageFilter GetConstant1() const; /** Connect the second operand for pixel-wise operation. */ + /** @ITKStartGrouping */ virtual void SetInput2(const TInputImage2 * image2); virtual void SetInput2(const DecoratedInput2ImagePixelType * input2); virtual void SetInput2(const Input2ImagePixelType & input2); - + /** @ITKEndGrouping */ /** Set the second operand as a constant. */ + /** @ITKStartGrouping */ virtual void SetConstant2(const Input2ImagePixelType & input2); void @@ -127,16 +130,18 @@ class ITK_TEMPLATE_EXPORT BinaryGeneratorImageFilter : public InPlaceImageFilter { this->SetConstant2(ct); } + /** @ITKEndGrouping */ + /** Get the constant value of the second operand. An exception is thrown if + * the second operand is not a constant. */ + /** @ITKStartGrouping */ + virtual const Input2ImagePixelType & + GetConstant2() const; const Input2ImagePixelType & GetConstant() const { return this->GetConstant2(); } - - /** Get the constant value of the second operand. An exception is thrown if - * the second operand is not a constant. */ - virtual const Input2ImagePixelType & - GetConstant2() const; + /** @ITKEndGrouping */ #if !defined(ITK_WRAPPING_PARSER) /** Set the pixel functor @@ -233,6 +238,7 @@ class ITK_TEMPLATE_EXPORT BinaryGeneratorImageFilter : public InPlaceImageFilter * * \sa ImageToImageFilter::ThreadedGenerateData(), * ImageToImageFilter::GenerateData() */ + /** @ITKStartGrouping */ template void DynamicThreadedGenerateDataWithFunctor(const TFunctor &, const OutputImageRegionType & outputRegionForThread); @@ -243,7 +249,7 @@ class ITK_TEMPLATE_EXPORT BinaryGeneratorImageFilter : public InPlaceImageFilter { this->UpdateProgress(1.0); } - + /** @ITKEndGrouping */ // Needed to take the image information from the 2nd input, if the first one is // a simple decorated object. void diff --git a/Modules/Filtering/ImageFilterBase/include/itkTernaryGeneratorImageFilter.h b/Modules/Filtering/ImageFilterBase/include/itkTernaryGeneratorImageFilter.h index d1cedf73b51..7a7a24c296d 100644 --- a/Modules/Filtering/ImageFilterBase/include/itkTernaryGeneratorImageFilter.h +++ b/Modules/Filtering/ImageFilterBase/include/itkTernaryGeneratorImageFilter.h @@ -103,13 +103,14 @@ class ITK_TEMPLATE_EXPORT TernaryGeneratorImageFilter : public InPlaceImageFilte using ValueFunctionType = OutputImagePixelType(Input1ImagePixelType, Input2ImagePixelType, Input3ImagePixelType); /** Connect one of the operands for pixel-wise operation. */ + /** @ITKStartGrouping */ void SetInput1(const TInputImage1 * image1); virtual void SetInput1(const DecoratedInput1ImagePixelType * input1); virtual void SetInput1(const Input1ImagePixelType & input1); - + /** @ITKEndGrouping */ /** Set the first operand as a constant. */ virtual void SetConstant1(const Input1ImagePixelType & input1); @@ -120,13 +121,14 @@ class ITK_TEMPLATE_EXPORT TernaryGeneratorImageFilter : public InPlaceImageFilte GetConstant1() const; /** Connect one of the operands for pixel-wise operation. */ + /** @ITKStartGrouping */ void SetInput2(const TInputImage2 * image2); virtual void SetInput2(const DecoratedInput2ImagePixelType * input2); virtual void SetInput2(const Input2ImagePixelType & input2); - + /** @ITKEndGrouping */ /** Set the second operand as a constant. */ virtual void SetConstant2(const Input2ImagePixelType & input2); @@ -137,13 +139,14 @@ class ITK_TEMPLATE_EXPORT TernaryGeneratorImageFilter : public InPlaceImageFilte GetConstant2() const; /** Connect one of the operands for pixel-wise operation. */ + /** @ITKStartGrouping */ void SetInput3(const TInputImage3 * image3); virtual void SetInput3(const DecoratedInput3ImagePixelType * input3); virtual void SetInput3(const Input3ImagePixelType & input3); - + /** @ITKEndGrouping */ /** Set the second operand as a constant. */ virtual void SetConstant3(const Input3ImagePixelType & input3); @@ -159,6 +162,7 @@ class ITK_TEMPLATE_EXPORT TernaryGeneratorImageFilter : public InPlaceImageFilte * * The functor defines an operation done per pixel. */ + /** @ITKStartGrouping */ void SetFunctor(const std::function & f) { @@ -179,11 +183,13 @@ class ITK_TEMPLATE_EXPORT TernaryGeneratorImageFilter : public InPlaceImageFilte this->Modified(); } + /** @ITKEndGrouping */ /** Set the pixel functor by a C function pointer * * The functor defines an operation done per pixel. */ + /** @ITKStartGrouping */ void SetFunctor(ConstRefFunctionType * funcPointer) { @@ -202,6 +208,7 @@ class ITK_TEMPLATE_EXPORT TernaryGeneratorImageFilter : public InPlaceImageFilte this->Modified(); } + /** @ITKEndGrouping */ /** Set the pixel functor by a "Functor Object" @@ -252,12 +259,13 @@ class ITK_TEMPLATE_EXPORT TernaryGeneratorImageFilter : public InPlaceImageFilte * * \sa ImageToImageFilter::ThreadedGenerateData(), * ImageToImageFilter::GenerateData() */ + /** @ITKStartGrouping */ template void DynamicThreadedGenerateDataWithFunctor(const TFunctor &, const OutputImageRegionType & outputRegionForThread); void DynamicThreadedGenerateData(const OutputImageRegionType & outputRegionForThread) override; - + /** @ITKEndGrouping */ private: std::function m_DynamicThreadedGenerateDataFunction{}; diff --git a/Modules/Filtering/ImageFilterBase/include/itkUnaryGeneratorImageFilter.h b/Modules/Filtering/ImageFilterBase/include/itkUnaryGeneratorImageFilter.h index 25181ab510c..4c0049935d8 100644 --- a/Modules/Filtering/ImageFilterBase/include/itkUnaryGeneratorImageFilter.h +++ b/Modules/Filtering/ImageFilterBase/include/itkUnaryGeneratorImageFilter.h @@ -88,6 +88,7 @@ class ITK_TEMPLATE_EXPORT UnaryGeneratorImageFilter : public InPlaceImageFilter< * * The functor defines an operation done per pixel. */ + /** @ITKStartGrouping */ void SetFunctor(const std::function & f) { @@ -106,12 +107,14 @@ class ITK_TEMPLATE_EXPORT UnaryGeneratorImageFilter : public InPlaceImageFilter< this->Modified(); } + /** @ITKEndGrouping */ /** Set the pixel functor by a C function pointer * * The functor defines an operation done per pixel. */ + /** @ITKStartGrouping */ void SetFunctor(ConstRefFunctionType * funcPointer) { @@ -130,6 +133,7 @@ class ITK_TEMPLATE_EXPORT UnaryGeneratorImageFilter : public InPlaceImageFilter< this->Modified(); } + /** @ITKEndGrouping */ /** Set the pixel functor by a "Functor Object" @@ -177,12 +181,13 @@ class ITK_TEMPLATE_EXPORT UnaryGeneratorImageFilter : public InPlaceImageFilter< * * \sa ImageToImageFilter::ThreadedGenerateData(), * ImageToImageFilter::GenerateData() */ + /** @ITKStartGrouping */ template void DynamicThreadedGenerateDataWithFunctor(const TFunctor &, const OutputImageRegionType & outputRegionForThread); void DynamicThreadedGenerateData(const OutputImageRegionType & outputRegionForThread) override; - + /** @ITKEndGrouping */ private: std::function m_DynamicThreadedGenerateDataFunction{}; }; diff --git a/Modules/Filtering/ImageFrequency/include/itkFrequencyBandImageFilter.h b/Modules/Filtering/ImageFrequency/include/itkFrequencyBandImageFilter.h index 310d12d48ab..0ce3a7bdef0 100644 --- a/Modules/Filtering/ImageFrequency/include/itkFrequencyBandImageFilter.h +++ b/Modules/Filtering/ImageFrequency/include/itkFrequencyBandImageFilter.h @@ -84,9 +84,11 @@ class ITK_TEMPLATE_EXPORT FrequencyBandImageFilter : public UnaryFrequencyDomain using FrequencyValueType = typename FrequencyIteratorType::FrequencyValueType; /****** Frequency Threshold Getters/Setters *****/ + /** Band range: Low threshold/boundary in Hertz */ itkGetConstReferenceMacro(LowFrequencyThreshold, FrequencyValueType); itkSetMacro(LowFrequencyThreshold, FrequencyValueType); + /** * Set low frequency threshold when input frequency is in radians. * @param freqLowInRadians low freq in radians. @@ -95,11 +97,12 @@ class ITK_TEMPLATE_EXPORT FrequencyBandImageFilter : public UnaryFrequencyDomain SetLowFrequencyThresholdInRadians(const FrequencyValueType & freqLowInRadians); /** Band range: High threshold/boundary in Hertz */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(HighFrequencyThreshold, FrequencyValueType); itkSetMacro(HighFrequencyThreshold, FrequencyValueType); void SetHighFrequencyThresholdInRadians(const FrequencyValueType & freqHighInRadians); - + /** @ITKEndGrouping */ /** * Set LowFrequencyThreshold and HighFrequencyThreshold at the same time, * input frequencies in Hertz. @@ -123,21 +126,24 @@ class ITK_TEMPLATE_EXPORT FrequencyBandImageFilter : public UnaryFrequencyDomain /** The pixel values that correspond to m_LowFrequencyThreshold are passed to the output image, * independent of m_PassBand */ + /** @ITKStartGrouping */ itkSetMacro(PassLowFrequencyThreshold, bool); itkGetConstReferenceMacro(PassLowFrequencyThreshold, bool); itkBooleanMacro(PassLowFrequencyThreshold); - + /** @ITKEndGrouping */ /** The pixel values that correspond to m_HighFrequencyThreshold are passed to the output image, * independent of m_PassBand */ + /** @ITKStartGrouping */ itkSetMacro(PassHighFrequencyThreshold, bool); itkGetConstReferenceMacro(PassHighFrequencyThreshold, bool); itkBooleanMacro(PassHighFrequencyThreshold); - + /** @ITKEndGrouping */ /** True: the band is a PassBand. False: StopBand **/ + /** @ITKStartGrouping */ itkSetMacro(PassBand, bool); itkGetConstReferenceMacro(PassBand, bool); itkBooleanMacro(PassBand); - + /** @ITKEndGrouping */ /** * Utility method equivalent to: * SetPassBand(true) @@ -164,22 +170,25 @@ class ITK_TEMPLATE_EXPORT FrequencyBandImageFilter : public UnaryFrequencyDomain /** If true the frequency cut-off uses the radius of the frequency vector. If false, it uses the max absolute value of * the frequency vector. */ + /** @ITKStartGrouping */ itkSetMacro(RadialBand, bool); itkGetConstReferenceMacro(RadialBand, bool); itkBooleanMacro(RadialBand); - + /** @ITKEndGrouping */ /** Control if negative frequencies with absolute value equal to low frequency threshold are passing. * Only effective when RadialBand is false **/ + /** @ITKStartGrouping */ itkSetMacro(PassNegativeLowFrequencyThreshold, bool); itkGetConstReferenceMacro(PassNegativeLowFrequencyThreshold, bool); itkBooleanMacro(PassNegativeLowFrequencyThreshold); - + /** @ITKEndGrouping */ /** Control if negative frequencies with absolute value equal to high frequency threshold are passing. * Only effective when RadialBand is false **/ + /** @ITKStartGrouping */ itkSetMacro(PassNegativeHighFrequencyThreshold, bool); itkGetConstReferenceMacro(PassNegativeHighFrequencyThreshold, bool); itkBooleanMacro(PassNegativeHighFrequencyThreshold); - + /** @ITKEndGrouping */ protected: FrequencyBandImageFilter(); diff --git a/Modules/Filtering/ImageFrequency/include/itkFrequencyFFTLayoutImageRegionConstIteratorWithIndex.h b/Modules/Filtering/ImageFrequency/include/itkFrequencyFFTLayoutImageRegionConstIteratorWithIndex.h index 2075784a919..081699eb5a4 100644 --- a/Modules/Filtering/ImageFrequency/include/itkFrequencyFFTLayoutImageRegionConstIteratorWithIndex.h +++ b/Modules/Filtering/ImageFrequency/include/itkFrequencyFFTLayoutImageRegionConstIteratorWithIndex.h @@ -239,8 +239,10 @@ class ITK_TEMPLATE_EXPORT FrequencyFFTLayoutImageRegionConstIteratorWithIndex * (Odd Size) LargestPositiveFrequencyIndex = originIndex + (N + 1) / 2 */ itkGetConstReferenceMacro(LargestPositiveFrequencyIndex, IndexType); + /** Default to first index of the largest possible Region. */ itkGetConstReferenceMacro(MinIndex, IndexType); + /** Default to UpperIndex of the largest possible Region. */ itkGetConstReferenceMacro(MaxIndex, IndexType); @@ -257,6 +259,7 @@ class ITK_TEMPLATE_EXPORT FrequencyFFTLayoutImageRegionConstIteratorWithIndex /** Does nothing. This member only affects HalfHermitianFrequencyIterator. * Provided for homogeneous interface between iterators. */ + /** @ITKStartGrouping */ void SetActualXDimensionIsOdd(bool value) { @@ -264,7 +267,7 @@ class ITK_TEMPLATE_EXPORT FrequencyFFTLayoutImageRegionConstIteratorWithIndex } itkGetMacro(ActualXDimensionIsOdd, bool); itkBooleanMacro(ActualXDimensionIsOdd); - + /** @ITKEndGrouping */ private: /** Calculate Nyquist frequency index (m_LargestPositiveFrequencyIndex), Min/Max indices from LargestPossibleRegion. * Also sets FrequencySpacing and FrequencyOrigin. diff --git a/Modules/Filtering/ImageFrequency/include/itkFrequencyHalfHermitianFFTLayoutImageRegionConstIteratorWithIndex.h b/Modules/Filtering/ImageFrequency/include/itkFrequencyHalfHermitianFFTLayoutImageRegionConstIteratorWithIndex.h index ae3f32c03df..f754ddf39c8 100644 --- a/Modules/Filtering/ImageFrequency/include/itkFrequencyHalfHermitianFFTLayoutImageRegionConstIteratorWithIndex.h +++ b/Modules/Filtering/ImageFrequency/include/itkFrequencyHalfHermitianFFTLayoutImageRegionConstIteratorWithIndex.h @@ -247,8 +247,10 @@ class FrequencyHalfHermitianFFTLayoutImageRegionConstIteratorWithIndex * (Odd Size) LargestPositiveFrequencyIndex = originIndex + (N + 1) / 2 */ itkGetConstReferenceMacro(LargestPositiveFrequencyIndex, IndexType); + /** Default to first index of the largest possible Region. */ itkGetConstReferenceMacro(MinIndex, IndexType); + /** Default to UpperIndex of the largest possible Region. */ itkGetConstReferenceMacro(MaxIndex, IndexType); @@ -268,6 +270,7 @@ class FrequencyHalfHermitianFFTLayoutImageRegionConstIteratorWithIndex * To compute the right frequency spacing and the original size, * this information has to be provided. */ + /** @ITKStartGrouping */ void SetActualXDimensionIsOdd(bool value) { @@ -279,7 +282,7 @@ class FrequencyHalfHermitianFFTLayoutImageRegionConstIteratorWithIndex } itkGetMacro(ActualXDimensionIsOdd, bool); itkBooleanMacro(ActualXDimensionIsOdd); - + /** @ITKEndGrouping */ private: /** Calculate Nyquist frequency index (m_LargestPositiveFrequencyIndex), Min/Max indices from LargestPossibleRegion. * Also sets FrequencySpacing and FrequencyOrigin. diff --git a/Modules/Filtering/ImageFrequency/include/itkFrequencyShiftedFFTLayoutImageRegionConstIteratorWithIndex.h b/Modules/Filtering/ImageFrequency/include/itkFrequencyShiftedFFTLayoutImageRegionConstIteratorWithIndex.h index aa9528617fb..d1ce32b4d63 100644 --- a/Modules/Filtering/ImageFrequency/include/itkFrequencyShiftedFFTLayoutImageRegionConstIteratorWithIndex.h +++ b/Modules/Filtering/ImageFrequency/include/itkFrequencyShiftedFFTLayoutImageRegionConstIteratorWithIndex.h @@ -220,6 +220,7 @@ class ITK_TEMPLATE_EXPORT FrequencyShiftedFFTLayoutImageRegionConstIteratorWithI * This is: N/2 if N even, (N - 1)/2 if N odd. */ itkGetConstReferenceMacro(ZeroFrequencyIndex, IndexType); + /** Origin of frequencies is zero for FFT output. */ itkGetConstReferenceMacro(FrequencyOrigin, FrequencyType); @@ -233,6 +234,7 @@ class ITK_TEMPLATE_EXPORT FrequencyShiftedFFTLayoutImageRegionConstIteratorWithI /** Does nothing. This member only affects HalfHermitianFrequencyIterator. * Provided for homogeneous interface between iterators. */ + /** @ITKStartGrouping */ void SetActualXDimensionIsOdd(bool value) { @@ -240,7 +242,7 @@ class ITK_TEMPLATE_EXPORT FrequencyShiftedFFTLayoutImageRegionConstIteratorWithI } itkGetMacro(ActualXDimensionIsOdd, bool); itkBooleanMacro(ActualXDimensionIsOdd); - + /** @ITKEndGrouping */ private: /** Calculate m_ZeroFrequencyIndex, and frequency spacing/origin. * Called by constructors. */ diff --git a/Modules/Filtering/ImageFrequency/include/itkUnaryFrequencyDomainFilter.h b/Modules/Filtering/ImageFrequency/include/itkUnaryFrequencyDomainFilter.h index 9a6083d478a..fe0a27ce361 100644 --- a/Modules/Filtering/ImageFrequency/include/itkUnaryFrequencyDomainFilter.h +++ b/Modules/Filtering/ImageFrequency/include/itkUnaryFrequencyDomainFilter.h @@ -98,10 +98,11 @@ class ITK_TEMPLATE_EXPORT UnaryFrequencyDomainFilter : public InPlaceImageFilter * original image in the spatial domain was odd. * Only needed when using HermitianFrequencyIterator and the original * image was odd. **/ + /** @ITKStartGrouping */ itkSetMacro(ActualXDimensionIsOdd, bool); itkGetConstReferenceMacro(ActualXDimensionIsOdd, bool); itkBooleanMacro(ActualXDimensionIsOdd); - + /** @ITKEndGrouping */ /** Returns factor with which the current frequency should be multiplied. */ using ConstRefFunctionType = double(const FrequencyIteratorType &); @@ -192,12 +193,13 @@ class ITK_TEMPLATE_EXPORT UnaryFrequencyDomainFilter : public InPlaceImageFilter * * \sa ImageToImageFilter::ThreadedGenerateData(), * ImageToImageFilter::GenerateData() */ + /** @ITKStartGrouping */ template void DynamicThreadedGenerateDataWithFunctor(const TFunctor &, const ImageRegionType & outputRegionForThread); void DynamicThreadedGenerateData(const ImageRegionType & outputRegionForThread) override; - + /** @ITKEndGrouping */ private: std::function m_DynamicThreadedGenerateDataFunction{}; diff --git a/Modules/Filtering/ImageFusion/include/itkLabelMapContourOverlayImageFilter.h b/Modules/Filtering/ImageFusion/include/itkLabelMapContourOverlayImageFilter.h index 098dfa7e0bc..d74143acc5c 100644 --- a/Modules/Filtering/ImageFusion/include/itkLabelMapContourOverlayImageFilter.h +++ b/Modules/Filtering/ImageFusion/include/itkLabelMapContourOverlayImageFilter.h @@ -151,37 +151,44 @@ class ITK_TEMPLATE_EXPORT LabelMapContourOverlayImageFilter : public LabelMapFil /** Set/Get the opacity of the colored label image. The value must be * between 0 and 1 */ + /** @ITKStartGrouping */ itkSetMacro(Opacity, double); itkGetConstReferenceMacro(Opacity, double); - + /** @ITKEndGrouping */ /** Set/Get the overlay type - CONTOUR is used by default. */ + /** @ITKStartGrouping */ itkSetMacro(Type, int); itkGetConstReferenceMacro(Type, int); - + /** @ITKEndGrouping */ /** Set/Get the object priority - HIGH_LABEL_ON_TOP by default. */ + /** @ITKStartGrouping */ itkSetMacro(Priority, int); itkGetConstReferenceMacro(Priority, int); - + /** @ITKEndGrouping */ /** Set/Get the object dilation radius - 0 by default. */ + /** @ITKStartGrouping */ itkSetMacro(DilationRadius, SizeType); itkGetConstReferenceMacro(DilationRadius, SizeType); - + /** @ITKEndGrouping */ /** Set/Get the contour thickness - 1 by default. */ + /** @ITKStartGrouping */ itkSetMacro(ContourThickness, SizeType); itkGetConstReferenceMacro(ContourThickness, SizeType); - + /** @ITKEndGrouping */ /** Set/Get the slice dimension - defaults to image dimension - 1. */ + /** @ITKStartGrouping */ itkSetMacro(SliceDimension, int); itkGetConstReferenceMacro(SliceDimension, int); - + /** @ITKEndGrouping */ /** Set/Get the overlay functor - defaults to a reasonable set of colors. * This can be used to apply a different colormap. */ + /** @ITKStartGrouping */ virtual void SetFunctor(const FunctorType & functor) { @@ -201,7 +208,7 @@ class ITK_TEMPLATE_EXPORT LabelMapContourOverlayImageFilter : public LabelMapFil { return m_Functor; } - + /** @ITKEndGrouping */ protected: LabelMapContourOverlayImageFilter(); ~LabelMapContourOverlayImageFilter() override = default; diff --git a/Modules/Filtering/ImageFusion/include/itkLabelMapOverlayImageFilter.h b/Modules/Filtering/ImageFusion/include/itkLabelMapOverlayImageFilter.h index 4b5b0a155e8..0eaef91ed8c 100644 --- a/Modules/Filtering/ImageFusion/include/itkLabelMapOverlayImageFilter.h +++ b/Modules/Filtering/ImageFusion/include/itkLabelMapOverlayImageFilter.h @@ -138,12 +138,14 @@ class ITK_TEMPLATE_EXPORT LabelMapOverlayImageFilter : public LabelMapFilter)); itkConceptMacro(OutputPixelShouldHaveBracketOperator, (Concept::BracketOperator)); diff --git a/Modules/Filtering/ImageFusion/include/itkLabelToRGBImageFilter.h b/Modules/Filtering/ImageFusion/include/itkLabelToRGBImageFilter.h index 08cfa4a745c..d6af12a61b1 100644 --- a/Modules/Filtering/ImageFusion/include/itkLabelToRGBImageFilter.h +++ b/Modules/Filtering/ImageFusion/include/itkLabelToRGBImageFilter.h @@ -80,13 +80,15 @@ class ITK_TEMPLATE_EXPORT LabelToRGBImageFilter itkNewMacro(Self); /** Set/Get the background value */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, LabelPixelType); itkGetConstReferenceMacro(BackgroundValue, LabelPixelType); - + /** @ITKEndGrouping */ /** Set/Get the background color in the output image */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundColor, OutputPixelType); itkGetConstReferenceMacro(BackgroundColor, OutputPixelType); - + /** @ITKEndGrouping */ /** Empty the color LUT container */ void ResetColors(); diff --git a/Modules/Filtering/ImageGradient/include/itkDifferenceOfGaussiansGradientImageFilter.h b/Modules/Filtering/ImageGradient/include/itkDifferenceOfGaussiansGradientImageFilter.h index 2a10570b245..e67d04c25cf 100644 --- a/Modules/Filtering/ImageGradient/include/itkDifferenceOfGaussiansGradientImageFilter.h +++ b/Modules/Filtering/ImageGradient/include/itkDifferenceOfGaussiansGradientImageFilter.h @@ -75,9 +75,10 @@ class ITK_TEMPLATE_EXPORT DifferenceOfGaussiansGradientImageFilter using OutputImageRegionType = typename TInputImage::RegionType; /** Set/Get the member variables. */ + /** @ITKStartGrouping */ itkGetConstMacro(Width, unsigned int); itkSetMacro(Width, unsigned int); - + /** @ITKEndGrouping */ itkConceptMacro(DataTypeHasNumericTraitsCheck, (Concept::HasNumericTraits)); protected: diff --git a/Modules/Filtering/ImageGradient/include/itkGradientImageFilter.h b/Modules/Filtering/ImageGradient/include/itkGradientImageFilter.h index b0519e3e9ae..1ee72a36b01 100644 --- a/Modules/Filtering/ImageGradient/include/itkGradientImageFilter.h +++ b/Modules/Filtering/ImageGradient/include/itkGradientImageFilter.h @@ -114,10 +114,11 @@ class ITK_TEMPLATE_EXPORT GradientImageFilter : public ImageToImageFilter ) ); diff --git a/Modules/Filtering/ImageGradient/include/itkVectorGradientMagnitudeImageFilter.h b/Modules/Filtering/ImageGradient/include/itkVectorGradientMagnitudeImageFilter.h index cdfc0986fcf..b0c5eb7a708 100644 --- a/Modules/Filtering/ImageGradient/include/itkVectorGradientMagnitudeImageFilter.h +++ b/Modules/Filtering/ImageGradient/include/itkVectorGradientMagnitudeImageFilter.h @@ -100,7 +100,7 @@ namespace itk * derivative values are summed during computation. Specify these weights * using the SetComponentWeights method. The argument to this method is a C * array of TRealValue type. - + * * \par Constraints * The filter requires an image with at least two dimensions and a vector * length of at least 2. The theory supports extension to scalar images, but @@ -195,11 +195,12 @@ class ITK_TEMPLATE_EXPORT VectorGradientMagnitudeImageFilter : public ImageToIma if you want to calculate the gradient in the space in which the data was acquired; use Off to ignore image spacing and to calculate the gradient in the image space. Default is On. */ + /** @ITKStartGrouping */ void SetUseImageSpacing(bool); itkGetConstMacro(UseImageSpacing, bool); itkBooleanMacro(UseImageSpacing); - + /** @ITKEndGrouping */ #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 gradient in the @@ -231,23 +232,26 @@ class ITK_TEMPLATE_EXPORT VectorGradientMagnitudeImageFilter : public ImageToIma /** Directly Set/Get the array of weights used in the gradient calculations. Note that calling UseImageSpacingOn will clobber these values. */ + /** @ITKStartGrouping */ itkSetMacro(DerivativeWeights, DerivativeWeightsType); itkGetConstReferenceMacro(DerivativeWeights, DerivativeWeightsType); - + /** @ITKEndGrouping */ /** Set/Get the array of weightings for the different components of the vector. Default values are 1.0. */ + /** @ITKStartGrouping */ itkSetMacro(ComponentWeights, ComponentWeightsType); itkGetConstReferenceMacro(ComponentWeights, ComponentWeightsType); - + /** @ITKEndGrouping */ /** Set/Get principle components calculation mode. When this is set to TRUE/ON, the gradient calculation will involve a principle component analysis of the partial derivatives of the color components. When this value is set to FALSE/OFF, the calculation is done as a square root of weighted sum of the derivatives squared. Default is UsePrincipleComponents = true. */ + /** @ITKStartGrouping */ itkSetMacro(UsePrincipleComponents, bool); itkGetConstMacro(UsePrincipleComponents, bool); itkBooleanMacro(UsePrincipleComponents); - + /** @ITKEndGrouping */ #if !defined(ITK_FUTURE_LEGACY_REMOVE) /** \deprecated Use VectorGradientMagnitudeImageFilter::UsePrincipleComponentsOn instead. */ void @@ -485,9 +489,10 @@ class ITK_TEMPLATE_EXPORT VectorGradientMagnitudeImageFilter : public ImageToIma /** These weights are used to scale vector component values when they are combined to produce a scalar. The square root */ + /** @ITKStartGrouping */ ComponentWeightsType m_ComponentWeights = ComponentWeightsType::Filled(1); ComponentWeightsType m_SqrtComponentWeights = ComponentWeightsType::Filled(1); - + /** @ITKEndGrouping */ private: bool m_UseImageSpacing{ true }; bool m_UsePrincipleComponents{}; diff --git a/Modules/Filtering/ImageGrid/include/itkBSplineControlPointImageFilter.h b/Modules/Filtering/ImageGrid/include/itkBSplineControlPointImageFilter.h index b0d0439a4a2..df4a6f674b7 100644 --- a/Modules/Filtering/ImageGrid/include/itkBSplineControlPointImageFilter.h +++ b/Modules/Filtering/ImageGrid/include/itkBSplineControlPointImageFilter.h @@ -144,27 +144,31 @@ class ITK_TEMPLATE_EXPORT BSplineControlPointImageFilter : public ImageToImageFi * they were also located at the end of the domain. The number of points to * be reused will depend on the spline order. As a user, you don't need to * replicate the points, the filter will do this for you. */ + /** @ITKStartGrouping */ itkSetMacro(CloseDimension, ArrayType); itkGetConstReferenceMacro(CloseDimension, ArrayType); - + /** @ITKEndGrouping */ /** * Set/Get the parametric spacing of the B-spline object domain. */ + /** @ITKStartGrouping */ itkSetMacro(Spacing, SpacingType); itkGetConstMacro(Spacing, SpacingType); - + /** @ITKEndGrouping */ /** * Set/Get the parametric origin of the B-spline object domain. */ + /** @ITKStartGrouping */ itkSetMacro(Origin, OriginType); itkGetConstMacro(Origin, OriginType); - + /** @ITKEndGrouping */ /** * Set/Get the parametric size of the B-spline object domain. */ + /** @ITKStartGrouping */ itkSetMacro(Size, SizeType); itkGetConstMacro(Size, SizeType); - + /** @ITKEndGrouping */ /** * Set the sampled object direction. Note that this is not used in any of the * calculations in this class. The only reason why it is included is due diff --git a/Modules/Filtering/ImageGrid/include/itkBSplineControlPointImageFunction.h b/Modules/Filtering/ImageGrid/include/itkBSplineControlPointImageFunction.h index a2a2854506c..467e4795049 100644 --- a/Modules/Filtering/ImageGrid/include/itkBSplineControlPointImageFunction.h +++ b/Modules/Filtering/ImageGrid/include/itkBSplineControlPointImageFunction.h @@ -164,21 +164,24 @@ class ITK_TEMPLATE_EXPORT BSplineControlPointImageFunction /** * Set/Get the parametric spacing of the B-spline object domain. */ + /** @ITKStartGrouping */ itkSetMacro(Spacing, SpacingType); itkGetConstMacro(Spacing, SpacingType); - + /** @ITKEndGrouping */ /** * Set/Get the parametric origin of the B-spline object domain. */ + /** @ITKStartGrouping */ itkSetMacro(Origin, OriginType); itkGetConstMacro(Origin, OriginType); - + /** @ITKEndGrouping */ /** * Set/Get the parametric size of the B-spline object domain. */ + /** @ITKStartGrouping */ itkSetMacro(Size, SizeType); itkGetConstMacro(Size, SizeType); - + /** @ITKEndGrouping */ /** * Set/Get the epsilon used for B-splines. The B-spline parametric domain in * 1-D is defined on the half-closed interval [a,b). Extension to n-D is @@ -187,9 +190,10 @@ class ITK_TEMPLATE_EXPORT BSplineControlPointImageFunction * the B-spline epsilon to push the edge of the image boundary inside the * B-spline parametric domain. */ + /** @ITKStartGrouping */ itkSetMacro(BSplineEpsilon, RealType); itkGetConstMacro(BSplineEpsilon, RealType); - + /** @ITKEndGrouping */ /** * Evaluate the resulting B-spline object at a specified point in the * parametric domain. diff --git a/Modules/Filtering/ImageGrid/include/itkBSplineScatteredDataPointSetToImageFilter.h b/Modules/Filtering/ImageGrid/include/itkBSplineScatteredDataPointSetToImageFilter.h index 2d9a4e9054b..afaae1d126f 100644 --- a/Modules/Filtering/ImageGrid/include/itkBSplineScatteredDataPointSetToImageFilter.h +++ b/Modules/Filtering/ImageGrid/include/itkBSplineScatteredDataPointSetToImageFilter.h @@ -199,9 +199,10 @@ class ITK_TEMPLATE_EXPORT BSplineScatteredDataPointSetToImageFilter * initial fitting level. The B-spline mesh size is equal to the number * of control points minus the spline order. Default = 4 in each dimension. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfControlPoints, ArrayType); itkGetConstReferenceMacro(NumberOfControlPoints, ArrayType); - + /** @ITKEndGrouping */ /** Get the number of current control points for each parametric dimension at * the current fitting level. The B-spline mesh size is equal to the number * of control points minus the spline order. Default = 4 in each dimension. @@ -234,9 +235,10 @@ class ITK_TEMPLATE_EXPORT BSplineScatteredDataPointSetToImageFilter * the image domain to be co-extensive with the parametric domain. We use * the B-spline epsilon to push the edge of the image boundary inside the * B-spline parametric domain. */ + /** @ITKStartGrouping */ itkSetMacro(BSplineEpsilon, RealType); itkGetConstMacro(BSplineEpsilon, RealType); - + /** @ITKEndGrouping */ /** Set/Get the array to define the periodicity of the dimensions in the * parametric space is to be. * This array of 0/1 values defines whether a particular dimension of the @@ -253,9 +255,10 @@ class ITK_TEMPLATE_EXPORT BSplineScatteredDataPointSetToImageFilter * they were also located at the end of the domain. The number of points to * be reused will depend on the spline order. As a user, you don't need to * replicate the points, the filter will do this for you. */ + /** @ITKStartGrouping */ itkSetMacro(CloseDimension, ArrayType); itkGetConstReferenceMacro(CloseDimension, ArrayType); - + /** @ITKEndGrouping */ /** A weighted fitting is possible where each input point is assigned a * relative weighting. */ void @@ -264,10 +267,11 @@ class ITK_TEMPLATE_EXPORT BSplineScatteredDataPointSetToImageFilter /** Set/Get whether or not the sampled output B-spline object is constructed. * The result of the fitting process is an n-D grid of control points which * describe the continuous B-spline object. */ + /** @ITKStartGrouping */ itkSetMacro(GenerateOutputImage, bool); itkGetConstReferenceMacro(GenerateOutputImage, bool); itkBooleanMacro(GenerateOutputImage); - + /** @ITKEndGrouping */ /** Get the control point lattice produced by the fitting process. */ PointDataImagePointer GetPhiLattice() diff --git a/Modules/Filtering/ImageGrid/include/itkBinShrinkImageFilter.h b/Modules/Filtering/ImageGrid/include/itkBinShrinkImageFilter.h index 9cd95ebe6bb..941e76c00c5 100644 --- a/Modules/Filtering/ImageGrid/include/itkBinShrinkImageFilter.h +++ b/Modules/Filtering/ImageGrid/include/itkBinShrinkImageFilter.h @@ -94,12 +94,13 @@ class ITK_TEMPLATE_EXPORT BinShrinkImageFilter : public ImageToImageFilter)); itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); itkConceptMacro(SameDimensionCheck, (Concept::SameDimension)); diff --git a/Modules/Filtering/ImageGrid/include/itkCropImageFilter.h b/Modules/Filtering/ImageGrid/include/itkCropImageFilter.h index cefb547a064..0fc19e75272 100644 --- a/Modules/Filtering/ImageGrid/include/itkCropImageFilter.h +++ b/Modules/Filtering/ImageGrid/include/itkCropImageFilter.h @@ -78,11 +78,12 @@ class ITK_TEMPLATE_EXPORT CropImageFilter : public ExtractImageFilter; /** Get/Set the interpolator function. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Interpolator, InterpolatorType); itkGetModifiableObjectMacro(Interpolator, InterpolatorType); - + /** @ITKEndGrouping */ /** The type of the expand factors representation */ using ExpandFactorsType = FixedArray; /** Set the expand factors. Values are clamped to * a minimum value of 1. Default is 1 for all dimensions. */ + /** @ITKStartGrouping */ itkSetMacro(ExpandFactors, ExpandFactorsType); virtual void SetExpandFactors(const unsigned int factor); - + /** @ITKEndGrouping */ /** Get the expand factors. */ itkGetConstReferenceMacro(ExpandFactors, ExpandFactorsType); diff --git a/Modules/Filtering/ImageGrid/include/itkFlipImageFilter.h b/Modules/Filtering/ImageGrid/include/itkFlipImageFilter.h index 7d651cbd3c2..2d30e96b576 100644 --- a/Modules/Filtering/ImageGrid/include/itkFlipImageFilter.h +++ b/Modules/Filtering/ImageGrid/include/itkFlipImageFilter.h @@ -85,16 +85,18 @@ class ITK_TEMPLATE_EXPORT FlipImageFilter : public ImageToImageFilter; /** Set/Get the first image */ + /** @ITKStartGrouping */ void SetInput1(const InputImageType * image) { @@ -86,7 +87,7 @@ class ITK_TEMPLATE_EXPORT InterpolateImageFilter : public ImageToImageFilterGetInput(); } - + /** @ITKEndGrouping */ /** Set/Get the second image */ void SetInput2(const InputImageType * image); @@ -96,13 +97,15 @@ class ITK_TEMPLATE_EXPORT InterpolateImageFilter : public ImageToImageFilter::min(), 1.0); - + /** @ITKEndGrouping */ itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); protected: diff --git a/Modules/Filtering/ImageGrid/include/itkOrientImageFilter.h b/Modules/Filtering/ImageGrid/include/itkOrientImageFilter.h index 6c874fe794f..7194957b240 100644 --- a/Modules/Filtering/ImageGrid/include/itkOrientImageFilter.h +++ b/Modules/Filtering/ImageGrid/include/itkOrientImageFilter.h @@ -114,9 +114,11 @@ class ITK_TEMPLATE_EXPORT OrientImageFilter : public ImageToImageFilter)); protected: diff --git a/Modules/Filtering/ImageGrid/include/itkShrinkImageFilter.h b/Modules/Filtering/ImageGrid/include/itkShrinkImageFilter.h index 98dcba6c1ec..3ad027972cf 100644 --- a/Modules/Filtering/ImageGrid/include/itkShrinkImageFilter.h +++ b/Modules/Filtering/ImageGrid/include/itkShrinkImageFilter.h @@ -104,12 +104,13 @@ class ITK_TEMPLATE_EXPORT ShrinkImageFilter : public ImageToImageFilter; /** Set/Get the first index extracted from the input image */ + /** @ITKStartGrouping */ itkSetMacro(Start, IndexType); itkGetConstReferenceMacro(Start, IndexType); void SetStart(IndexValueType start); - + /** @ITKEndGrouping */ /** Set/Get the excluded end of the range */ + /** @ITKStartGrouping */ itkSetMacro(Stop, IndexType); itkGetConstReferenceMacro(Stop, IndexType); void SetStop(IndexValueType stop); - + /** @ITKEndGrouping */ /** Set/Get the stride of indexes extracted * * An exception will be generated if 0. */ + /** @ITKStartGrouping */ itkSetMacro(Step, ArrayType); itkGetConstReferenceMacro(Step, ArrayType); void SetStep(int step); - + /** @ITKEndGrouping */ itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); diff --git a/Modules/Filtering/ImageGrid/include/itkTileImageFilter.h b/Modules/Filtering/ImageGrid/include/itkTileImageFilter.h index 266a2fed933..1c3f906d96d 100644 --- a/Modules/Filtering/ImageGrid/include/itkTileImageFilter.h +++ b/Modules/Filtering/ImageGrid/include/itkTileImageFilter.h @@ -86,6 +86,7 @@ class ITK_TEMPLATE_EXPORT TileImageFilter : public ImageToImageFilter; @@ -151,29 +152,33 @@ class ITK_TEMPLATE_EXPORT WarpImageFilter : public ImageToImageFilter class ITK_TEMPLATE_EXPORT AddImageFilter : public BinaryGeneratorImageFilter - { public: ITK_DISALLOW_COPY_AND_MOVE(AddImageFilter); diff --git a/Modules/Filtering/ImageIntensity/include/itkDiscreteGaussianDerivativeImageFunction.h b/Modules/Filtering/ImageIntensity/include/itkDiscreteGaussianDerivativeImageFunction.h index 56e0cf987c1..bf1291e1e6a 100644 --- a/Modules/Filtering/ImageIntensity/include/itkDiscreteGaussianDerivativeImageFunction.h +++ b/Modules/Filtering/ImageIntensity/include/itkDiscreteGaussianDerivativeImageFunction.h @@ -121,9 +121,11 @@ class ITK_TEMPLATE_EXPORT DiscreteGaussianDerivativeImageFunction : public Image * physical units of your image. If UseImageSpacing is false then * the units are pixels. */ + /** @ITKStartGrouping */ itkSetMacro(Variance, VarianceArrayType); itkGetConstMacro(Variance, const VarianceArrayType); itkSetVectorMacro(Variance, double, VarianceArrayType::Length); + /** @ITKEndGrouping */ /** Convenience method for setting the variance for all dimensions. */ virtual void @@ -148,13 +150,17 @@ class ITK_TEMPLATE_EXPORT DiscreteGaussianDerivativeImageFunction : public Image * Gaussian operator size. The value is clamped between 0.00001 and * 0.99999. */ + /** @ITKStartGrouping */ itkSetClampMacro(MaximumError, double, 0.00001, 0.99999); itkGetConstMacro(MaximumError, double); + /** @ITKEndGrouping */ /** Set/Get the derivative order for an individual dimension. */ + /** @ITKStartGrouping */ itkSetMacro(Order, OrderArrayType); itkGetConstMacro(Order, const OrderArrayType); itkSetVectorMacro(Order, unsigned int, OrderArrayType::Length); + /** @ITKEndGrouping */ /** Convenience method for setting the order for all dimensions. */ virtual void @@ -167,25 +173,33 @@ class ITK_TEMPLATE_EXPORT DiscreteGaussianDerivativeImageFunction : public Image /** Set/Get the flag for calculating scale-space normalized derivatives. * Normalized derivatives are obtained multiplying by the scale * parameter t. */ + /** @ITKStartGrouping */ itkSetMacro(NormalizeAcrossScale, bool); itkGetConstMacro(NormalizeAcrossScale, bool); itkBooleanMacro(NormalizeAcrossScale); + /** @ITKEndGrouping */ /** Set/Get the flag for using image spacing when calculating derivatives. */ + /** @ITKStartGrouping */ itkSetMacro(UseImageSpacing, bool); itkGetConstMacro(UseImageSpacing, bool); itkBooleanMacro(UseImageSpacing); + /** @ITKEndGrouping */ /** Set/Get a limit for growth of the kernel. Small maximum error values with * large variances will yield very large kernel sizes. This value can be * used to truncate a kernel in such instances. A warning will be given on * truncation of the kernel. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumKernelWidth, unsigned int); itkGetConstMacro(MaximumKernelWidth, unsigned int); + /** @ITKEndGrouping */ /** Set/Get the interpolation mode. */ + /** @ITKStartGrouping */ itkSetEnumMacro(InterpolationMode, InterpolationModeEnum); itkGetEnumMacro(InterpolationMode, InterpolationModeEnum); + /** @ITKEndGrouping */ /** Set the input image. * \warning this method caches BufferedRegion information. diff --git a/Modules/Filtering/ImageIntensity/include/itkDiscreteGradientMagnitudeGaussianImageFunction.h b/Modules/Filtering/ImageIntensity/include/itkDiscreteGradientMagnitudeGaussianImageFunction.h index d2d8be6dce0..d82fa5c0938 100644 --- a/Modules/Filtering/ImageIntensity/include/itkDiscreteGradientMagnitudeGaussianImageFunction.h +++ b/Modules/Filtering/ImageIntensity/include/itkDiscreteGradientMagnitudeGaussianImageFunction.h @@ -123,9 +123,11 @@ class ITK_TEMPLATE_EXPORT DiscreteGradientMagnitudeGaussianImageFunction * Sets the variance for individual dimensions. The default is 0.0 in each dimension. * If UseImageSpacing is true, the units are the physical units of your image. * If UseImageSpacing is false then the units are pixels */ + /** @ITKStartGrouping */ itkSetMacro(Variance, VarianceArrayType); itkGetConstMacro(Variance, const VarianceArrayType); itkSetVectorMacro(Variance, double, VarianceArrayType::Length); + /** @ITKEndGrouping */ /** Convenience method for setting the variance for all dimensions */ virtual void @@ -148,31 +150,41 @@ class ITK_TEMPLATE_EXPORT DiscreteGradientMagnitudeGaussianImageFunction * and the area under the continuous Gaussian. Maximum error affects the * Gaussian operator size. The value is clamped between 0.00001 and * 0.99999. */ + /** @ITKStartGrouping */ itkSetClampMacro(MaximumError, double, 0.00001, 0.99999); itkGetConstMacro(MaximumError, double); + /** @ITKEndGrouping */ /** Set/Get the flag for calculating scale-space normalized derivatives. * Normalized derivatives are obtained multiplying by the scale * parameter t. */ + /** @ITKStartGrouping */ itkSetMacro(NormalizeAcrossScale, bool); itkGetConstMacro(NormalizeAcrossScale, bool); itkBooleanMacro(NormalizeAcrossScale); + /** @ITKEndGrouping */ /** Set/Get the flag for using image spacing when calculating derivatives. */ + /** @ITKStartGrouping */ itkSetMacro(UseImageSpacing, bool); itkGetConstMacro(UseImageSpacing, bool); itkBooleanMacro(UseImageSpacing); + /** @ITKEndGrouping */ /** Set/Get a limit for growth of the kernel. Small maximum error values with * large variances will yield very large kernel sizes. This value can be * used to truncate a kernel in such instances. A warning will be given on * truncation of the kernel. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumKernelWidth, unsigned int); itkGetConstMacro(MaximumKernelWidth, unsigned int); + /** @ITKEndGrouping */ /** Set/Get the interpolation mode. */ + /** @ITKStartGrouping */ itkSetEnumMacro(InterpolationMode, InterpolationModeEnum); itkGetEnumMacro(InterpolationMode, InterpolationModeEnum); + /** @ITKEndGrouping */ /** Set the input image. * \warning this method caches BufferedRegion information. diff --git a/Modules/Filtering/ImageIntensity/include/itkDiscreteHessianGaussianImageFunction.h b/Modules/Filtering/ImageIntensity/include/itkDiscreteHessianGaussianImageFunction.h index 03ed4fc757d..df70c58bc59 100644 --- a/Modules/Filtering/ImageIntensity/include/itkDiscreteHessianGaussianImageFunction.h +++ b/Modules/Filtering/ImageIntensity/include/itkDiscreteHessianGaussianImageFunction.h @@ -123,9 +123,11 @@ class ITK_TEMPLATE_EXPORT DiscreteHessianGaussianImageFunction * Sets the variance for individual dimensions. The default is 0.0 in each dimension. * If UseImageSpacing is true, the units are the physical units of your image. * If UseImageSpacing is false then the units are pixels. */ + /** @ITKStartGrouping */ itkSetMacro(Variance, VarianceArrayType); itkGetConstMacro(Variance, const VarianceArrayType); itkSetVectorMacro(Variance, double, VarianceArrayType::Length); + /** @ITKEndGrouping */ /** Convenience method for setting the variance for all dimensions */ virtual void @@ -148,31 +150,41 @@ class ITK_TEMPLATE_EXPORT DiscreteHessianGaussianImageFunction * and the area under the continuous Gaussian. Maximum error affects the * Gaussian operator size. The value is clamped between 0.00001 and * 0.99999. */ + /** @ITKStartGrouping */ itkSetClampMacro(MaximumError, double, 0.00001, 0.99999); itkGetConstMacro(MaximumError, double); + /** @ITKEndGrouping */ /** Set/Get the flag for calculating scale-space normalized derivatives. * Normalized derivatives are obtained multiplying by the scale * parameter t. */ + /** @ITKStartGrouping */ itkSetMacro(NormalizeAcrossScale, bool); itkGetConstMacro(NormalizeAcrossScale, bool); itkBooleanMacro(NormalizeAcrossScale); + /** @ITKEndGrouping */ /** Set/Get the flag for using image spacing when calculating derivatives. */ + /** @ITKStartGrouping */ itkSetMacro(UseImageSpacing, bool); itkGetConstMacro(UseImageSpacing, bool); itkBooleanMacro(UseImageSpacing); + /** @ITKEndGrouping */ /** Set/Get a limit for growth of the kernel. Small maximum error values with * large variances will yield very large kernel sizes. This value can be * used to truncate a kernel in such instances. A warning will be given on * truncation of the kernel. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumKernelWidth, unsigned int); itkGetConstMacro(MaximumKernelWidth, unsigned int); + /** @ITKEndGrouping */ /** Set/Get the interpolation mode. */ + /** @ITKStartGrouping */ itkSetEnumMacro(InterpolationMode, InterpolationModeEnum); itkGetEnumMacro(InterpolationMode, InterpolationModeEnum); + /** @ITKEndGrouping */ /** Set the input image. * \warning this method caches BufferedRegion information. diff --git a/Modules/Filtering/ImageIntensity/include/itkDivideOrZeroOutImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkDivideOrZeroOutImageFilter.h index 660e1998d57..abdaf9232d7 100644 --- a/Modules/Filtering/ImageIntensity/include/itkDivideOrZeroOutImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkDivideOrZeroOutImageFilter.h @@ -73,6 +73,7 @@ class ITK_TEMPLATE_EXPORT DivideOrZeroOutImageFilter /** Set/get the threshold below which pixels in the denominator will * be considered zero. */ + /** @ITKStartGrouping */ void SetThreshold(DenominatorPixelType threshold) { @@ -87,9 +88,11 @@ class ITK_TEMPLATE_EXPORT DivideOrZeroOutImageFilter { return this->GetFunctor().m_Threshold; } + /** @ITKEndGrouping */ /** Set/get the constant value returned when the denominator input * value is considered zero. */ + /** @ITKStartGrouping */ void SetConstant(OutputPixelType constant) { @@ -104,7 +107,7 @@ class ITK_TEMPLATE_EXPORT DivideOrZeroOutImageFilter { return this->GetFunctor().m_Constant; } - + /** @ITKEndGrouping */ protected: DivideOrZeroOutImageFilter() = default; ~DivideOrZeroOutImageFilter() override = default; diff --git a/Modules/Filtering/ImageIntensity/include/itkExpNegativeImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkExpNegativeImageFilter.h index e4cdb85b11a..cce59809524 100644 --- a/Modules/Filtering/ImageIntensity/include/itkExpNegativeImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkExpNegativeImageFilter.h @@ -37,7 +37,6 @@ class ExpNegative ExpNegative() { m_Factor = 1.0; } ~ExpNegative() = default; - bool operator==(const ExpNegative & other) const { diff --git a/Modules/Filtering/ImageIntensity/include/itkHistogramMatchingImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkHistogramMatchingImageFilter.h index 1aa656362c8..19c7b6f96c0 100644 --- a/Modules/Filtering/ImageIntensity/include/itkHistogramMatchingImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkHistogramMatchingImageFilter.h @@ -109,13 +109,15 @@ class ITK_TEMPLATE_EXPORT HistogramMatchingImageFilter : public ImageToImageFilt using HistogramPointer = typename HistogramType::Pointer; /** Set and Get the source image */ + /** @ITKStartGrouping */ itkSetInputMacro(SourceImage, InputImageType); itkGetInputMacro(SourceImage, InputImageType); - + /** @ITKEndGrouping */ /** Set/Get the reference image. */ + /** @ITKStartGrouping */ itkSetInputMacro(ReferenceImage, InputImageType); itkGetInputMacro(ReferenceImage, InputImageType); - + /** @ITKEndGrouping */ /** Set the reference histogram. The reference histogram must * have the first bin minimum be the smallest intensity value for the * reference image space and the last bin maximum must contain the largest @@ -124,26 +126,30 @@ class ITK_TEMPLATE_EXPORT HistogramMatchingImageFilter : public ImageToImageFilt * that are used to populate the histogram to a smaller intensity range * than is represented by the smallest and largest intensity values.) */ + /** @ITKStartGrouping */ itkSetInputMacro(ReferenceHistogram, HistogramType); itkGetInputMacro(ReferenceHistogram, HistogramType); - + /** @ITKEndGrouping */ /** Set/Get the number of histogram levels used. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfHistogramLevels, SizeValueType); itkGetConstMacro(NumberOfHistogramLevels, SizeValueType); - + /** @ITKEndGrouping */ /** Set/Get the number of match points used. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfMatchPoints, SizeValueType); itkGetConstMacro(NumberOfMatchPoints, SizeValueType); - + /** @ITKEndGrouping */ /** Set/Get the threshold at mean intensity flag. * If true, only source (reference) pixels which are greater * than the mean source (reference) intensity is used in * the histogram matching. If false, all pixels are * used. */ + /** @ITKStartGrouping */ itkSetMacro(ThresholdAtMeanIntensity, bool); itkGetConstMacro(ThresholdAtMeanIntensity, bool); itkBooleanMacro(ThresholdAtMeanIntensity); - + /** @ITKEndGrouping */ /** Set/Get if the reference histogram is regenerated from * the supplied ReferenceImage (true) or supplied directly * as in input argument (false). If SetReferenceHistogram(myhistogram) @@ -153,10 +159,11 @@ class ITK_TEMPLATE_EXPORT HistogramMatchingImageFilter : public ImageToImageFilt * indicated by GenerateReferenceHistogramFromImage choice will be used * and the other object will be ignored. */ + /** @ITKStartGrouping */ itkSetMacro(GenerateReferenceHistogramFromImage, bool); itkGetConstMacro(GenerateReferenceHistogramFromImage, bool); itkBooleanMacro(GenerateReferenceHistogramFromImage); - + /** @ITKEndGrouping */ /** This filter requires all of the input to be in the buffer. */ void GenerateInputRequestedRegion() override; @@ -164,9 +171,10 @@ class ITK_TEMPLATE_EXPORT HistogramMatchingImageFilter : public ImageToImageFilt /** Methods to get the histograms of the source, reference, and * output. Objects are only valid after Update() has been called * on this filter. */ + /** @ITKStartGrouping */ itkGetModifiableObjectMacro(SourceHistogram, HistogramType); itkGetModifiableObjectMacro(OutputHistogram, HistogramType); - + /** @ITKEndGrouping */ itkConceptMacro(IntConvertibleToInputCheck, (Concept::Convertible)); itkConceptMacro(SameDimensionCheck, (Concept::SameDimension)); itkConceptMacro(DoubleConvertibleToInputCheck, (Concept::Convertible)); diff --git a/Modules/Filtering/ImageIntensity/include/itkIntensityWindowingImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkIntensityWindowingImageFilter.h index 3ce07d1832b..6398a64827d 100644 --- a/Modules/Filtering/ImageIntensity/include/itkIntensityWindowingImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkIntensityWindowingImageFilter.h @@ -170,18 +170,20 @@ class ITK_TEMPLATE_EXPORT IntensityWindowingImageFilter /** Set/Get the values of the maximum and minimum * intensities of the output image. */ + /** @ITKStartGrouping */ itkSetMacro(OutputMinimum, OutputPixelType); itkSetMacro(OutputMaximum, OutputPixelType); itkGetConstReferenceMacro(OutputMinimum, OutputPixelType); itkGetConstReferenceMacro(OutputMaximum, OutputPixelType); - + /** @ITKEndGrouping */ /** Set/Get the values of the maximum and minimum * intensities of the input intensity window. */ + /** @ITKStartGrouping */ itkSetMacro(WindowMinimum, InputPixelType); itkSetMacro(WindowMaximum, InputPixelType); itkGetConstReferenceMacro(WindowMinimum, InputPixelType); itkGetConstReferenceMacro(WindowMaximum, InputPixelType); - + /** @ITKEndGrouping */ /** Set/Get the window width and level. This is an alternative API * to using the SetWindowMinimum()/SetWindowMaximum(). The window * minimum and maximum are set as [level-window/2, @@ -198,9 +200,10 @@ class ITK_TEMPLATE_EXPORT IntensityWindowingImageFilter /** Get the Scale and Shift used for the linear transformation of gray level values. \warning These Values are only valid after the filter has been updated. */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(Scale, RealType); itkGetConstReferenceMacro(Shift, RealType); - + /** @ITKEndGrouping */ /** Process to execute before entering the multithreaded section. */ void BeforeThreadedGenerateData() override; diff --git a/Modules/Filtering/ImageIntensity/include/itkInvertIntensityImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkInvertIntensityImageFilter.h index 877aae48db9..ba1e66521e2 100644 --- a/Modules/Filtering/ImageIntensity/include/itkInvertIntensityImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkInvertIntensityImageFilter.h @@ -115,9 +115,10 @@ class ITK_TEMPLATE_EXPORT InvertIntensityImageFilter itkOverrideGetNameOfClassMacro(InvertIntensityImageFilter); /** Set/Get the maximum intensity value for the inversion. */ + /** @ITKStartGrouping */ itkSetMacro(Maximum, InputPixelType); itkGetConstReferenceMacro(Maximum, InputPixelType); - + /** @ITKEndGrouping */ void PrintSelf(std::ostream & os, Indent indent) const override; diff --git a/Modules/Filtering/ImageIntensity/include/itkLogicOpsFunctors.h b/Modules/Filtering/ImageIntensity/include/itkLogicOpsFunctors.h index 01d425e7234..28f1917c64d 100644 --- a/Modules/Filtering/ImageIntensity/include/itkLogicOpsFunctors.h +++ b/Modules/Filtering/ImageIntensity/include/itkLogicOpsFunctors.h @@ -55,6 +55,7 @@ namespace Functor * * \ingroup ITKImageIntensity */ + template class ITK_TEMPLATE_EXPORT LogicOpBase { diff --git a/Modules/Filtering/ImageIntensity/include/itkMaskImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkMaskImageFilter.h index fbb3c3746e0..ef36a7cc8a2 100644 --- a/Modules/Filtering/ImageIntensity/include/itkMaskImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkMaskImageFilter.h @@ -80,6 +80,7 @@ class MaskInput { m_MaskingValue = maskingValue; } + /** Method to get the masking value */ const TMask & GetMaskingValue() const @@ -171,6 +172,7 @@ class ITK_TEMPLATE_EXPORT MaskImageFilter : public BinaryGeneratorImageFilter(this->ProcessObject::GetInput(1)); } + /** @ITKEndGrouping */ /** Method to explicitly set the outside value of the mask. Defaults to 0 */ void diff --git a/Modules/Filtering/ImageIntensity/include/itkModulusImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkModulusImageFilter.h index 833d9cf4f1d..a2539190dcd 100644 --- a/Modules/Filtering/ImageIntensity/include/itkModulusImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkModulusImageFilter.h @@ -66,6 +66,7 @@ class ITK_TEMPLATE_EXPORT ModulusImageFilter itkOverrideGetNameOfClassMacro(ModulusImageFilter); /** Set/Get the dividend */ + /** @ITKStartGrouping */ virtual void SetDividend(InputPixelType _arg) { @@ -76,7 +77,7 @@ class ITK_TEMPLATE_EXPORT ModulusImageFilter { return this->GetConstant2(); } - + /** @ITKEndGrouping */ itkConceptMacro(InputHasNumericTraitsCheck, (Concept::HasNumericTraits)); diff --git a/Modules/Filtering/ImageIntensity/include/itkNaryFunctorImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkNaryFunctorImageFilter.h index eb30eaa6fb9..2c18c106db2 100644 --- a/Modules/Filtering/ImageIntensity/include/itkNaryFunctorImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkNaryFunctorImageFilter.h @@ -50,6 +50,7 @@ class ITK_TEMPLATE_EXPORT NaryFunctorImageFilter : public InPlaceImageFilter; using Pointer = SmartPointer; using ConstPointer = SmartPointer; + /** Method for creation through the object factory. */ itkNewMacro(Self); diff --git a/Modules/Filtering/ImageIntensity/include/itkNormalizeToConstantImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkNormalizeToConstantImageFilter.h index 9bcaff2e774..2d02b9f8164 100644 --- a/Modules/Filtering/ImageIntensity/include/itkNormalizeToConstantImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkNormalizeToConstantImageFilter.h @@ -92,9 +92,10 @@ class ITK_TEMPLATE_EXPORT NormalizeToConstantImageFilter : public ImageToImageFi itkOverrideGetNameOfClassMacro(NormalizeToConstantImageFilter); /** Set/get the normalization constant. */ + /** @ITKStartGrouping */ itkSetMacro(Constant, RealType); itkGetConstMacro(Constant, RealType); - + /** @ITKEndGrouping */ itkConceptMacro(InputHasPixelTraitsCheck, (Concept::HasPixelTraits)); itkConceptMacro(InputHasNumericTraitsCheck, (Concept::HasNumericTraits)); diff --git a/Modules/Filtering/ImageIntensity/include/itkNotImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkNotImageFilter.h index f845a80225e..a83e8aa4a4c 100644 --- a/Modules/Filtering/ImageIntensity/include/itkNotImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkNotImageFilter.h @@ -80,6 +80,7 @@ class NotImageFilter /** Set/Get the value used to mark the false pixels of the result of * the operator. Defaults to 0 */ + /** @ITKStartGrouping */ void SetBackgroundValue(const typename TOutputImage::PixelType & backgroundValue) { @@ -94,10 +95,11 @@ class NotImageFilter { return this->GetFunctor().GetBackgroundValue(); } - + /** @ITKEndGrouping */ /** Set/Get the value used to mark the false pixels of the result of * the operator. Defaults to 1 */ + /** @ITKStartGrouping */ void SetForegroundValue(const typename TOutputImage::PixelType & foregroundValue) { @@ -114,7 +116,7 @@ class NotImageFilter { return this->GetFunctor().GetForegroundValue(); } - + /** @ITKEndGrouping */ itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); itkConceptMacro(OutputConvertibleToOutputCheck, (Concept::Convertible)); diff --git a/Modules/Filtering/ImageIntensity/include/itkPolylineMaskImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkPolylineMaskImageFilter.h index 0cf525c8ab9..692cf885ca6 100644 --- a/Modules/Filtering/ImageIntensity/include/itkPolylineMaskImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkPolylineMaskImageFilter.h @@ -89,25 +89,30 @@ class ITK_TEMPLATE_EXPORT PolylineMaskImageFilter : public ImageToImageFilter class ITK_TEMPLATE_EXPORT PowImageFilter : public BinaryGeneratorImageFilter - { public: ITK_DISALLOW_COPY_AND_MOVE(PowImageFilter); diff --git a/Modules/Filtering/ImageIntensity/include/itkRescaleIntensityImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkRescaleIntensityImageFilter.h index 22b8475f406..bddfe0f437e 100644 --- a/Modules/Filtering/ImageIntensity/include/itkRescaleIntensityImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkRescaleIntensityImageFilter.h @@ -167,14 +167,16 @@ class ITK_TEMPLATE_EXPORT RescaleIntensityImageFilter /** Get the Scale and Shift used for the linear transformation of gray level values. \warning These Values are only valid after the filter has been updated */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(Scale, RealType); itkGetConstReferenceMacro(Shift, RealType); - + /** @ITKEndGrouping */ /** Get the Minimum and Maximum values of the input image. \warning These Values are only valid after the filter has been updated */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(InputMinimum, InputPixelType); itkGetConstReferenceMacro(InputMaximum, InputPixelType); - + /** @ITKEndGrouping */ /** Process to execute before entering the multithreaded section */ void BeforeThreadedGenerateData() override; diff --git a/Modules/Filtering/ImageIntensity/include/itkShiftScaleImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkShiftScaleImageFilter.h index 723af7aa6cd..2a85ef372c8 100644 --- a/Modules/Filtering/ImageIntensity/include/itkShiftScaleImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkShiftScaleImageFilter.h @@ -82,18 +82,21 @@ class ITK_TEMPLATE_EXPORT ShiftScaleImageFilter : public ImageToImageFilter)); itkConceptMacro(InputPlusRealTypeCheck, (Concept::AdditiveOperators)); itkConceptMacro(RealTypeMultiplyOperatorCheck, (Concept::MultiplyOperator)); diff --git a/Modules/Filtering/ImageIntensity/include/itkSymmetricEigenAnalysisImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkSymmetricEigenAnalysisImageFilter.h index 1d30c05fca0..e71e8327597 100644 --- a/Modules/Filtering/ImageIntensity/include/itkSymmetricEigenAnalysisImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkSymmetricEigenAnalysisImageFilter.h @@ -63,6 +63,7 @@ class SymmetricEigenAnalysisFunction } /** Method to explicitly set the dimension of the matrix */ + /** @ITKStartGrouping */ void SetDimension(unsigned int n) { @@ -73,6 +74,7 @@ class SymmetricEigenAnalysisFunction { return m_Calculator.GetDimension(); } + /** @ITKEndGrouping */ #if !defined(ITK_LEGACY_REMOVE) /** Enables reverse compatibility for enumeration values */ @@ -88,6 +90,7 @@ class SymmetricEigenAnalysisFunction /** Order eigen values. Default is to OrderByValue: lambda_1 < * lambda_2 < .... */ + /** @ITKStartGrouping */ void OrderEigenValuesBy(EigenValueOrderEnum order) { @@ -118,7 +121,7 @@ class SymmetricEigenAnalysisFunction } return EigenValueOrderEnum::DoNotOrder; } - + /** @ITKEndGrouping */ private: CalculatorType m_Calculator; @@ -242,6 +245,7 @@ class SymmetricEigenAnalysisImageFilter /** Order eigen values. Default is to OrderByValue: lambda_1 < * lambda_2 < .... */ + /** @ITKStartGrouping */ void OrderEigenValuesBy(EigenValueOrderEnum order) { @@ -257,6 +261,7 @@ class SymmetricEigenAnalysisImageFilter { return this->GetFunctor().GetOrderEigenValuesBy(); } + /** @ITKEndGrouping */ /** \see LightObject::GetNameOfClass() */ itkOverrideGetNameOfClassMacro(SymmetricEigenAnalysisImageFilter); @@ -271,8 +276,9 @@ class SymmetricEigenAnalysisImageFilter this->Superclass::PrintSelf(os, indent); } - /** Set the dimension of the tensor. (For example the SymmetricSecondRankTensor + /** Set/Get the dimension of the tensor. (For example the SymmetricSecondRankTensor * is a pxp matrix) */ + /** @ITKStartGrouping */ void SetDimension(unsigned int p) { @@ -283,6 +289,7 @@ class SymmetricEigenAnalysisImageFilter { return this->GetFunctor().GetDimension(); } + /** @ITKEndGrouping */ itkConceptMacro(InputHasNumericTraitsCheck, (Concept::HasNumericTraits)); diff --git a/Modules/Filtering/ImageIntensity/include/itkVectorExpandImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkVectorExpandImageFilter.h index 663af910bd3..75b4d61c828 100644 --- a/Modules/Filtering/ImageIntensity/include/itkVectorExpandImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkVectorExpandImageFilter.h @@ -127,16 +127,18 @@ class ITK_TEMPLATE_EXPORT VectorExpandImageFilter : public ImageToImageFilter; /** Get/Set the interpolator function. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Interpolator, InterpolatorType); itkGetModifiableObjectMacro(Interpolator, InterpolatorType); - + /** @ITKEndGrouping */ /** Set the expand factors. Values are clamped to * a minimum value of 1. Default is 1 for all dimensions. */ + /** @ITKStartGrouping */ itkSetMacro(ExpandFactors, ExpandFactorsArrayType); virtual void SetExpandFactors(const float factor); itkSetVectorMacro(ExpandFactors, const unsigned int, ImageDimension); - + /** @ITKEndGrouping */ /** Get the expand factors. */ itkGetConstReferenceMacro(ExpandFactors, ExpandFactorsArrayType); diff --git a/Modules/Filtering/ImageIntensity/include/itkVectorIndexSelectionCastImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkVectorIndexSelectionCastImageFilter.h index 151ef706674..83d376fbf56 100644 --- a/Modules/Filtering/ImageIntensity/include/itkVectorIndexSelectionCastImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkVectorIndexSelectionCastImageFilter.h @@ -110,6 +110,7 @@ class VectorIndexSelectionCastImageFilter itkOverrideGetNameOfClassMacro(VectorIndexSelectionCastImageFilter); /** Get/Set methods for the index */ + /** @ITKStartGrouping */ void SetIndex(unsigned int i) { @@ -125,6 +126,7 @@ class VectorIndexSelectionCastImageFilter { return this->GetFunctor().GetIndex(); } + /** @ITKEndGrouping */ itkConceptMacro(InputHasNumericTraitsCheck, (Concept::HasNumericTraits)); diff --git a/Modules/Filtering/ImageIntensity/include/itkVectorRescaleIntensityImageFilter.h b/Modules/Filtering/ImageIntensity/include/itkVectorRescaleIntensityImageFilter.h index 4b541f0aa8d..0cb131da44e 100644 --- a/Modules/Filtering/ImageIntensity/include/itkVectorRescaleIntensityImageFilter.h +++ b/Modules/Filtering/ImageIntensity/include/itkVectorRescaleIntensityImageFilter.h @@ -134,9 +134,10 @@ class ITK_TEMPLATE_EXPORT VectorRescaleIntensityImageFilter /** Get the Scale and Shift used for the linear transformation of magnitude values. \warning These values are only valid after the filter has been updated. */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(Scale, InputRealType); itkGetConstReferenceMacro(Shift, InputRealType); - + /** @ITKEndGrouping */ /** Get the Maximum value of the input image magnitudes. \warning These values are only valid after the filter has been updated. */ itkGetConstReferenceMacro(InputMaximumMagnitude, InputRealType); diff --git a/Modules/Filtering/ImageLabel/include/itkBinaryContourImageFilter.h b/Modules/Filtering/ImageLabel/include/itkBinaryContourImageFilter.h index 0b332b93da0..9371ff9dac9 100644 --- a/Modules/Filtering/ImageLabel/include/itkBinaryContourImageFilter.h +++ b/Modules/Filtering/ImageLabel/include/itkBinaryContourImageFilter.h @@ -105,24 +105,27 @@ class ITK_TEMPLATE_EXPORT BinaryContourImageFilter * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ /** * Set/Get the background value used to mark the pixels not on the border of the * objects. */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the foreground value used to identify the objects in the input and * output images. */ + /** @ITKStartGrouping */ itkSetMacro(ForegroundValue, InputImagePixelType); itkGetConstMacro(ForegroundValue, InputImagePixelType); - + /** @ITKEndGrouping */ protected: BinaryContourImageFilter(); ~BinaryContourImageFilter() override = default; diff --git a/Modules/Filtering/ImageLabel/include/itkLabelContourImageFilter.h b/Modules/Filtering/ImageLabel/include/itkLabelContourImageFilter.h index a29212cfc09..5b94da806cb 100644 --- a/Modules/Filtering/ImageLabel/include/itkLabelContourImageFilter.h +++ b/Modules/Filtering/ImageLabel/include/itkLabelContourImageFilter.h @@ -106,17 +106,19 @@ class ITK_TEMPLATE_EXPORT LabelContourImageFilter * FullyConnectedOff. * \note For objects that are 1 pixel wide, use FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ /** * Set/Get the background value used to identify the objects and mark the * pixels not on the border of the objects. */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ protected: LabelContourImageFilter(); ~LabelContourImageFilter() override = default; diff --git a/Modules/Filtering/ImageNoise/include/itkAdditiveGaussianNoiseImageFilter.h b/Modules/Filtering/ImageNoise/include/itkAdditiveGaussianNoiseImageFilter.h index b28247daee0..477ec66a53f 100644 --- a/Modules/Filtering/ImageNoise/include/itkAdditiveGaussianNoiseImageFilter.h +++ b/Modules/Filtering/ImageNoise/include/itkAdditiveGaussianNoiseImageFilter.h @@ -83,14 +83,16 @@ class ITK_TEMPLATE_EXPORT AdditiveGaussianNoiseImageFilter : public NoiseBaseIma /** Set/Get the mean of the Gaussian distribution. * Defaults to 0.0. */ + /** @ITKStartGrouping */ itkGetConstMacro(Mean, double); itkSetMacro(Mean, double); - + /** @ITKEndGrouping */ /** Set/Get the standard deviation of the Gaussian distribution. * Defaults to 1.0. */ + /** @ITKStartGrouping */ itkGetConstMacro(StandardDeviation, double); itkSetMacro(StandardDeviation, double); - + /** @ITKEndGrouping */ itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); diff --git a/Modules/Filtering/ImageNoise/include/itkNoiseBaseImageFilter.h b/Modules/Filtering/ImageNoise/include/itkNoiseBaseImageFilter.h index b69affc42dc..b5fddf70b1a 100644 --- a/Modules/Filtering/ImageNoise/include/itkNoiseBaseImageFilter.h +++ b/Modules/Filtering/ImageNoise/include/itkNoiseBaseImageFilter.h @@ -53,9 +53,10 @@ class ITK_TEMPLATE_EXPORT NoiseBaseImageFilter : public InPlaceImageFilter::max(). */ + /** @ITKStartGrouping */ itkSetMacro(SaltValue, OutputImagePixelType); itkGetConstMacro(SaltValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** Set/Get the pepper/low pixel value. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(PepperValue, OutputImagePixelType); itkGetConstMacro(PepperValue, OutputImagePixelType); - + /** @ITKEndGrouping */ itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); diff --git a/Modules/Filtering/ImageNoise/include/itkShotNoiseImageFilter.h b/Modules/Filtering/ImageNoise/include/itkShotNoiseImageFilter.h index a2f8672aece..9065a82f4d3 100644 --- a/Modules/Filtering/ImageNoise/include/itkShotNoiseImageFilter.h +++ b/Modules/Filtering/ImageNoise/include/itkShotNoiseImageFilter.h @@ -125,9 +125,10 @@ class ITK_TEMPLATE_EXPORT ShotNoiseImageFilter : public NoiseBaseImageFilter)); diff --git a/Modules/Filtering/ImageNoise/include/itkSpeckleNoiseImageFilter.h b/Modules/Filtering/ImageNoise/include/itkSpeckleNoiseImageFilter.h index 648fcf18172..5e37ed3631d 100644 --- a/Modules/Filtering/ImageNoise/include/itkSpeckleNoiseImageFilter.h +++ b/Modules/Filtering/ImageNoise/include/itkSpeckleNoiseImageFilter.h @@ -84,9 +84,10 @@ class ITK_TEMPLATE_EXPORT SpeckleNoiseImageFilter : public NoiseBaseImageFilter< /** Set/Get the standard deviation of the gamma distribution. * Defaults to 1.0. */ + /** @ITKStartGrouping */ itkGetConstMacro(StandardDeviation, double); itkSetMacro(StandardDeviation, double); - + /** @ITKEndGrouping */ itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); diff --git a/Modules/Filtering/ImageSources/include/itkGaborImageSource.h b/Modules/Filtering/ImageSources/include/itkGaborImageSource.h index 1d90c7aa29c..0aaa6b5c778 100644 --- a/Modules/Filtering/ImageSources/include/itkGaborImageSource.h +++ b/Modules/Filtering/ImageSources/include/itkGaborImageSource.h @@ -79,23 +79,27 @@ class ITK_TEMPLATE_EXPORT GaborImageSource : public GenerateImageSource; /** Set/Get the standard deviation in each direction. */ + /** @ITKStartGrouping */ itkSetMacro(Sigma, ArrayType); itkGetConstReferenceMacro(Sigma, ArrayType); - + /** @ITKEndGrouping */ /** Set/Get the mean in each direction. */ + /** @ITKStartGrouping */ itkSetMacro(Mean, ArrayType); itkGetConstReferenceMacro(Mean, ArrayType); - + /** @ITKEndGrouping */ /** Set/Get the modulation frequency of the sine or cosine component. */ + /** @ITKStartGrouping */ itkSetMacro(Frequency, double); itkGetConstReferenceMacro(Frequency, double); - + /** @ITKEndGrouping */ /** Set/Get whether the evaluation is performed using the using the imaginary * part. Default is false. */ + /** @ITKStartGrouping */ itkSetMacro(CalculateImaginaryPart, bool); itkGetConstReferenceMacro(CalculateImaginaryPart, bool); itkBooleanMacro(CalculateImaginaryPart); - + /** @ITKEndGrouping */ protected: GaborImageSource(); ~GaborImageSource() override = default; diff --git a/Modules/Filtering/ImageSources/include/itkGaborKernelFunction.h b/Modules/Filtering/ImageSources/include/itkGaborKernelFunction.h index 70e4fb0b597..be44e4158c1 100644 --- a/Modules/Filtering/ImageSources/include/itkGaborKernelFunction.h +++ b/Modules/Filtering/ImageSources/include/itkGaborKernelFunction.h @@ -76,23 +76,27 @@ class ITK_TEMPLATE_EXPORT GaborKernelFunction : public KernelFunctionBase /** * Set/Get the size of the output image **/ + /** @ITKStartGrouping */ itkSetMacro(Size, SizeType); itkGetConstReferenceMacro(Size, SizeType); itkSetVectorMacro(Size, SizeValueType, NDimensions); - + /** @ITKEndGrouping */ /** * Set/Get the output image spacing. This parameter defaults to all ones. **/ + /** @ITKStartGrouping */ itkSetMacro(Spacing, SpacingType); itkGetConstReferenceMacro(Spacing, SpacingType); itkSetVectorMacro(Spacing, const float, NDimensions); - + /** @ITKEndGrouping */ /** * Set/Get the output image origin. This parameter defaults to all zeros. **/ + /** @ITKStartGrouping */ itkSetMacro(Origin, PointType); itkGetConstReferenceMacro(Origin, PointType); itkSetVectorMacro(Origin, const float, NDimensions); - + /** @ITKEndGrouping */ /** * Set/Get the output image direction cosine. This parameter * defaults to the identity matrix. **/ + /** @ITKStartGrouping */ itkSetMacro(Direction, DirectionType); itkGetConstReferenceMacro(Direction, DirectionType); - + /** @ITKEndGrouping */ /** * Set/Get the output image direction cosine. This parameter * defaults to the identity matrix. **/ + /** @ITKStartGrouping */ itkSetMacro(StartIndex, IndexType); itkGetConstReferenceMacro(StartIndex, IndexType); - + /** @ITKEndGrouping */ /** Helper method to set the output parameters based on an image. */ void SetOutputParametersFromImage(const ReferenceImageBaseType * image); @@ -121,6 +126,7 @@ class ITK_TEMPLATE_EXPORT GenerateImageSource : public ImageSource * copy the information. UseReferenceImageOn must be set to utilize the * reference image. */ itkSetInputMacro(ReferenceImage, ReferenceImageBaseType); + /** Get the reference image that is defining the output information. */ itkGetInputMacro(ReferenceImage, ReferenceImageBaseType); diff --git a/Modules/Filtering/ImageSources/include/itkGridImageSource.h b/Modules/Filtering/ImageSources/include/itkGridImageSource.h index 56ee1bbfcd6..327b477e6c8 100644 --- a/Modules/Filtering/ImageSources/include/itkGridImageSource.h +++ b/Modules/Filtering/ImageSources/include/itkGridImageSource.h @@ -94,30 +94,36 @@ class ITK_TEMPLATE_EXPORT GridImageSource : public GenerateImageSource; /** Set/Get kernel function used to create the grid. */ + /** @ITKStartGrouping */ itkSetObjectMacro(KernelFunction, KernelFunctionType); itkGetConstReferenceObjectMacro(KernelFunction, KernelFunctionType); - + /** @ITKEndGrouping */ /** Set/Get the standard deviation of the Gaussians or width of the box * functions.*/ + /** @ITKStartGrouping */ itkSetMacro(Sigma, ArrayType); itkGetConstReferenceMacro(Sigma, ArrayType); - + /** @ITKEndGrouping */ /** Set/Get the grid spacing of the peaks. */ + /** @ITKStartGrouping */ itkSetMacro(GridSpacing, ArrayType); itkGetConstReferenceMacro(GridSpacing, ArrayType); - + /** @ITKEndGrouping */ /** Set/Get the grid offset. */ + /** @ITKStartGrouping */ itkSetMacro(GridOffset, ArrayType); itkGetConstReferenceMacro(GridOffset, ArrayType); - + /** @ITKEndGrouping */ /** Set/Get the dimensions which are gridded. */ + /** @ITKStartGrouping */ itkSetMacro(WhichDimensions, BoolArrayType); itkGetConstReferenceMacro(WhichDimensions, BoolArrayType); - + /** @ITKEndGrouping */ /** Set/Get the scale factor to multiply the true value of the grid. */ + /** @ITKStartGrouping */ itkSetMacro(Scale, RealType); itkGetConstReferenceMacro(Scale, RealType); - + /** @ITKEndGrouping */ protected: GridImageSource(); ~GridImageSource() override = default; diff --git a/Modules/Filtering/ImageStatistics/include/itkAccumulateImageFilter.h b/Modules/Filtering/ImageStatistics/include/itkAccumulateImageFilter.h index 5c896371975..fc877d211ad 100644 --- a/Modules/Filtering/ImageStatistics/include/itkAccumulateImageFilter.h +++ b/Modules/Filtering/ImageStatistics/include/itkAccumulateImageFilter.h @@ -90,18 +90,20 @@ class ITK_TEMPLATE_EXPORT AccumulateImageFilter : public ImageToImageFilterModified(); } } - + /** @ITKEndGrouping */ itkGetConstMacro(UseLookupTable, bool); itkBooleanMacro(UseLookupTable); #endif diff --git a/Modules/Filtering/ImageStatistics/include/itkGetAverageSliceImageFilter.h b/Modules/Filtering/ImageStatistics/include/itkGetAverageSliceImageFilter.h index 4803ffe4fa1..406d188e0e8 100644 --- a/Modules/Filtering/ImageStatistics/include/itkGetAverageSliceImageFilter.h +++ b/Modules/Filtering/ImageStatistics/include/itkGetAverageSliceImageFilter.h @@ -63,9 +63,10 @@ class ITK_TEMPLATE_EXPORT GetAverageSliceImageFilter : public AccumulateImageFil itkOverrideGetNameOfClassMacro(GetAverageSliceImageFilter); /** Set the direction in which to reflect the data. */ + /** @ITKStartGrouping */ itkGetConstMacro(AveragedOutDimension, unsigned int); itkSetMacro(AveragedOutDimension, unsigned int); - + /** @ITKEndGrouping */ protected: GetAverageSliceImageFilter(); ~GetAverageSliceImageFilter() override = default; diff --git a/Modules/Filtering/ImageStatistics/include/itkImagePCADecompositionCalculator.h b/Modules/Filtering/ImageStatistics/include/itkImagePCADecompositionCalculator.h index ca95a43691f..c499100d37a 100644 --- a/Modules/Filtering/ImageStatistics/include/itkImagePCADecompositionCalculator.h +++ b/Modules/Filtering/ImageStatistics/include/itkImagePCADecompositionCalculator.h @@ -87,6 +87,7 @@ class ITK_TEMPLATE_EXPORT ImagePCADecompositionCalculator : public Object /** Basis image pixel type: this is also the type of the output vector */ using BasisPixelType = typename TBasisImage::PixelType; + /** Input Image dimension */ static constexpr unsigned int InputImageDimension = TInputImage::ImageDimension; @@ -101,13 +102,15 @@ class ITK_TEMPLATE_EXPORT ImagePCADecompositionCalculator : public Object using BasisVectorType = vnl_vector; /** Set and get the input image. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(Image, InputImageType); itkGetConstObjectMacro(Image, InputImageType); - + /** @ITKEndGrouping */ /** Set and get the mean image. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(MeanImage, BasisImageType); itkGetConstObjectMacro(MeanImage, BasisImageType); - + /** @ITKEndGrouping */ /** Set and get the basis images. */ void SetBasisImages(const BasisImagePointerVector &); @@ -120,6 +123,7 @@ class ITK_TEMPLATE_EXPORT ImagePCADecompositionCalculator : public Object /** Type definition of a compatible ImagePCAShapeModelEstimator */ using ModelPointerType = typename ImagePCAShapeModelEstimator::Pointer; + /** Set the basis images from a ImagePCAShapeModelEstimator */ void SetBasisFromModel(ModelPointerType model); diff --git a/Modules/Filtering/ImageStatistics/include/itkLabelOverlapMeasuresImageFilter.h b/Modules/Filtering/ImageStatistics/include/itkLabelOverlapMeasuresImageFilter.h index 6e050636d6d..2ca3429b979 100644 --- a/Modules/Filtering/ImageStatistics/include/itkLabelOverlapMeasuresImageFilter.h +++ b/Modules/Filtering/ImageStatistics/include/itkLabelOverlapMeasuresImageFilter.h @@ -97,11 +97,12 @@ class ITK_TEMPLATE_EXPORT LabelOverlapMeasuresImageFilter : public ImageSinkGetUnionOverlap(); } - + /** @ITKEndGrouping */ /** Get the union overlap (Jaccard coefficient) for the specified individual * label. */ + /** @ITKStartGrouping */ RealType GetUnionOverlap(LabelType) const; RealType GetJaccardCoefficient(LabelType label) const { return this->GetUnionOverlap(label); } - + /** @ITKEndGrouping */ /** Get the mean overlap (Dice coefficient) over all labels. */ + /** @ITKStartGrouping */ RealType GetMeanOverlap() const; RealType @@ -145,16 +149,17 @@ class ITK_TEMPLATE_EXPORT LabelOverlapMeasuresImageFilter : public ImageSinkGetMeanOverlap(); } - + /** @ITKEndGrouping */ /** Get the mean overlap (Dice coefficient) for the specified individual * label. */ + /** @ITKStartGrouping */ RealType GetMeanOverlap(LabelType) const; RealType GetDiceCoefficient(LabelType label) const { return this->GetMeanOverlap(label); } - + /** @ITKEndGrouping */ /** Get the volume similarity over all labels. */ RealType GetVolumeSimilarity() const; diff --git a/Modules/Filtering/ImageStatistics/include/itkLabelStatisticsImageFilter.h b/Modules/Filtering/ImageStatistics/include/itkLabelStatisticsImageFilter.h index 438f0874425..cd48a826579 100644 --- a/Modules/Filtering/ImageStatistics/include/itkLabelStatisticsImageFilter.h +++ b/Modules/Filtering/ImageStatistics/include/itkLabelStatisticsImageFilter.h @@ -289,9 +289,10 @@ class ITK_TEMPLATE_EXPORT LabelStatisticsImageFilter : public ImageSinkModified(); } + /** @ITKEndGrouping */ /** * Set/Get whether the objects with the specified attribute values should be kept * or excluded. */ + /** @ITKStartGrouping */ itkGetConstMacro(Exclude, bool); itkSetMacro(Exclude, bool); itkBooleanMacro(Exclude); + /** @ITKEndGrouping */ /** Clear the attribute set, and add the attribute passed in parameter */ void diff --git a/Modules/Filtering/LabelMap/include/itkAttributeUniqueLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkAttributeUniqueLabelMapFilter.h index 7be12ebcfab..27ec729687f 100644 --- a/Modules/Filtering/LabelMap/include/itkAttributeUniqueLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkAttributeUniqueLabelMapFilter.h @@ -91,10 +91,11 @@ class ITK_TEMPLATE_EXPORT AttributeUniqueLabelMapFilter : public InPlaceLabelMap * the highest attribute values are labeled first. Set ReverseOrdering to true * make the one with the smallest attributes be labeled first. */ + /** @ITKStartGrouping */ itkSetMacro(ReverseOrdering, bool); itkGetConstReferenceMacro(ReverseOrdering, bool); itkBooleanMacro(ReverseOrdering); - + /** @ITKEndGrouping */ protected: AttributeUniqueLabelMapFilter(); ~AttributeUniqueLabelMapFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkAutoCropLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkAutoCropLabelMapFilter.h index 6b62e4207f6..10ef20716b7 100644 --- a/Modules/Filtering/LabelMap/include/itkAutoCropLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkAutoCropLabelMapFilter.h @@ -96,9 +96,10 @@ class ITK_TEMPLATE_EXPORT AutoCropLabelMapFilter : public ChangeRegionLabelMapFi /** * Set/Get the border added to the mask before the crop. The default is 0 on * all the axis. */ + /** @ITKStartGrouping */ itkSetMacro(CropBorder, SizeType); itkGetConstReferenceMacro(CropBorder, SizeType); - + /** @ITKEndGrouping */ protected: AutoCropLabelMapFilter(); ~AutoCropLabelMapFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkBinaryFillholeImageFilter.h b/Modules/Filtering/LabelMap/include/itkBinaryFillholeImageFilter.h index bce7a46016a..15311d7cad9 100644 --- a/Modules/Filtering/LabelMap/include/itkBinaryFillholeImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkBinaryFillholeImageFilter.h @@ -81,10 +81,11 @@ class ITK_TEMPLATE_EXPORT BinaryFillholeImageFilter : public ImageToImageFilter< * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); /** Set the value in the image to consider as "foreground". Defaults to diff --git a/Modules/Filtering/LabelMap/include/itkBinaryGrindPeakImageFilter.h b/Modules/Filtering/LabelMap/include/itkBinaryGrindPeakImageFilter.h index 97e15bddbc3..d69238a6cb3 100644 --- a/Modules/Filtering/LabelMap/include/itkBinaryGrindPeakImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkBinaryGrindPeakImageFilter.h @@ -81,10 +81,11 @@ class ITK_TEMPLATE_EXPORT BinaryGrindPeakImageFilter : public ImageToImageFilter * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); /** Set the value in the image to consider as "foreground". Defaults to diff --git a/Modules/Filtering/LabelMap/include/itkBinaryImageToLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkBinaryImageToLabelMapFilter.h index 81b68309a51..47475e1e0d4 100644 --- a/Modules/Filtering/LabelMap/include/itkBinaryImageToLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkBinaryImageToLabelMapFilter.h @@ -117,10 +117,11 @@ class ITK_TEMPLATE_EXPORT BinaryImageToLabelMapFilter * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ // only set after completion itkGetConstReferenceMacro(NumberOfObjects, SizeValueType); @@ -128,16 +129,18 @@ class ITK_TEMPLATE_EXPORT BinaryImageToLabelMapFilter * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(OutputBackgroundValue, OutputPixelType); itkGetConstMacro(OutputBackgroundValue, OutputPixelType); - + /** @ITKEndGrouping */ /** * Set/Get the value to be consider "foreground" in the input image. * Defaults to NumericTraits::max(). */ + /** @ITKStartGrouping */ itkSetMacro(InputForegroundValue, InputPixelType); itkGetConstMacro(InputForegroundValue, InputPixelType); - + /** @ITKEndGrouping */ protected: BinaryImageToLabelMapFilter(); ~BinaryImageToLabelMapFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkBinaryImageToShapeLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkBinaryImageToShapeLabelMapFilter.h index fe5536108f3..ea727bdf0ec 100644 --- a/Modules/Filtering/LabelMap/include/itkBinaryImageToShapeLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkBinaryImageToShapeLabelMapFilter.h @@ -104,10 +104,11 @@ class ITK_TEMPLATE_EXPORT BinaryImageToShapeLabelMapFilter : public ImageToImage * by face+edge+vertex connectivity. Default is FullyConnectedOff. For objects that * are 1 pixel wide, use FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ itkConceptMacro(InputEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(IntConvertibleToInputCheck, (Concept::Convertible)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); @@ -116,41 +117,46 @@ class ITK_TEMPLATE_EXPORT BinaryImageToShapeLabelMapFilter : public ImageToImage * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(OutputBackgroundValue, OutputImagePixelType); itkGetConstMacro(OutputBackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the value used as "foreground" in the output image. * Defaults to NumericTraits::max(). */ + /** @ITKStartGrouping */ itkSetMacro(InputForegroundValue, InputImagePixelType); itkGetConstMacro(InputForegroundValue, InputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get whether the maximum Feret diameter should be computed or not. * Default value is false, because of the high computation time required. */ + /** @ITKStartGrouping */ itkSetMacro(ComputeFeretDiameter, bool); itkGetConstReferenceMacro(ComputeFeretDiameter, bool); itkBooleanMacro(ComputeFeretDiameter); - + /** @ITKEndGrouping */ /** * Set/Get whether the perimeter should be computed or not. * Default value is false, because of the high computation time required. */ + /** @ITKStartGrouping */ itkSetMacro(ComputePerimeter, bool); itkGetConstReferenceMacro(ComputePerimeter, bool); itkBooleanMacro(ComputePerimeter); - + /** @ITKEndGrouping */ /** * Set/Get whether the oriented bounding box should be * computed or not. Default value is false because of potential * memory consumption issues with sparse labels. */ + /** @ITKStartGrouping */ itkSetMacro(ComputeOrientedBoundingBox, bool); itkGetConstReferenceMacro(ComputeOrientedBoundingBox, bool); itkBooleanMacro(ComputeOrientedBoundingBox); - + /** @ITKEndGrouping */ protected: BinaryImageToShapeLabelMapFilter(); ~BinaryImageToShapeLabelMapFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkBinaryImageToStatisticsLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkBinaryImageToStatisticsLabelMapFilter.h index 0c0ee89dc71..02b62583d7a 100644 --- a/Modules/Filtering/LabelMap/include/itkBinaryImageToStatisticsLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkBinaryImageToStatisticsLabelMapFilter.h @@ -90,10 +90,11 @@ class ITK_TEMPLATE_EXPORT BinaryImageToStatisticsLabelMapFilter : public ImageTo * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ itkConceptMacro(InputEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(IntConvertibleToInputCheck, (Concept::Convertible)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); @@ -102,32 +103,36 @@ class ITK_TEMPLATE_EXPORT BinaryImageToStatisticsLabelMapFilter : public ImageTo * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(OutputBackgroundValue, OutputImagePixelType); itkGetConstMacro(OutputBackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the value used as "foreground" in the output image. * Defaults to NumericTraits::max(). */ + /** @ITKStartGrouping */ itkSetMacro(InputForegroundValue, InputImagePixelType); itkGetConstMacro(InputForegroundValue, InputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get whether the maximum Feret diameter should be computed or not. The * default value is false, because of the high computation time required. */ + /** @ITKStartGrouping */ itkSetMacro(ComputeFeretDiameter, bool); itkGetConstReferenceMacro(ComputeFeretDiameter, bool); itkBooleanMacro(ComputeFeretDiameter); - + /** @ITKEndGrouping */ /** * Set/Get whether the perimeter should be computed or not. The default value * is false, because of the high computation time required. */ + /** @ITKStartGrouping */ itkSetMacro(ComputePerimeter, bool); itkGetConstReferenceMacro(ComputePerimeter, bool); itkBooleanMacro(ComputePerimeter); - + /** @ITKEndGrouping */ /** Set the feature image */ void SetFeatureImage(const TFeatureImage * input) @@ -163,18 +168,20 @@ class ITK_TEMPLATE_EXPORT BinaryImageToStatisticsLabelMapFilter : public ImageTo * compared to the other attributes, this option is useful to reduce the memory usage * when the histogram is not required. */ + /** @ITKStartGrouping */ itkSetMacro(ComputeHistogram, bool); itkGetConstReferenceMacro(ComputeHistogram, bool); itkBooleanMacro(ComputeHistogram); - + /** @ITKEndGrouping */ /** * Set/Get the number of bins in the histogram. Note that the histogram is used * to compute the median value, and that this option may have an effect on the * value of the median. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfBins, unsigned int); itkGetConstReferenceMacro(NumberOfBins, unsigned int); - + /** @ITKEndGrouping */ protected: BinaryImageToStatisticsLabelMapFilter(); ~BinaryImageToStatisticsLabelMapFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkBinaryNotImageFilter.h b/Modules/Filtering/LabelMap/include/itkBinaryNotImageFilter.h index 2e232747f85..c163d5152c4 100644 --- a/Modules/Filtering/LabelMap/include/itkBinaryNotImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkBinaryNotImageFilter.h @@ -105,14 +105,16 @@ class BinaryNotImageFilter /** Set/Get the value in the image considered as "foreground". Defaults to * maximum value of PixelType. */ + /** @ITKStartGrouping */ itkSetMacro(ForegroundValue, PixelType); itkGetConstMacro(ForegroundValue, PixelType); - + /** @ITKEndGrouping */ /** Set/Get the value used as "background". Defaults to * NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, PixelType); itkGetConstMacro(BackgroundValue, PixelType); - + /** @ITKEndGrouping */ protected: BinaryNotImageFilter() { diff --git a/Modules/Filtering/LabelMap/include/itkBinaryReconstructionByDilationImageFilter.h b/Modules/Filtering/LabelMap/include/itkBinaryReconstructionByDilationImageFilter.h index 4f505325a2a..2447219af8d 100644 --- a/Modules/Filtering/LabelMap/include/itkBinaryReconstructionByDilationImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkBinaryReconstructionByDilationImageFilter.h @@ -99,10 +99,11 @@ class ITK_TEMPLATE_EXPORT BinaryReconstructionByDilationImageFilter * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ itkConceptMacro(InputEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(IntConvertibleToInputCheck, (Concept::Convertible)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); @@ -111,24 +112,28 @@ class ITK_TEMPLATE_EXPORT BinaryReconstructionByDilationImageFilter * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the value used as "foreground" in the output image. * Defaults to NumericTraits::max(). */ + /** @ITKStartGrouping */ itkSetMacro(ForegroundValue, OutputImagePixelType); itkGetConstMacro(ForegroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** Set/Get the marker image */ + /** @ITKStartGrouping */ itkSetInputMacro(MarkerImage, InputImageType); itkGetInputMacro(MarkerImage, InputImageType); - + /** @ITKEndGrouping */ /** Set/Get the mask image */ + /** @ITKStartGrouping */ itkSetInputMacro(MaskImage, InputImageType); itkGetInputMacro(MaskImage, InputImageType); - + /** @ITKEndGrouping */ protected: BinaryReconstructionByDilationImageFilter(); ~BinaryReconstructionByDilationImageFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkBinaryReconstructionByErosionImageFilter.h b/Modules/Filtering/LabelMap/include/itkBinaryReconstructionByErosionImageFilter.h index cb721c7f0b3..57517fbc43c 100644 --- a/Modules/Filtering/LabelMap/include/itkBinaryReconstructionByErosionImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkBinaryReconstructionByErosionImageFilter.h @@ -99,10 +99,11 @@ class ITK_TEMPLATE_EXPORT BinaryReconstructionByErosionImageFilter : public Imag * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ itkConceptMacro(InputEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(IntConvertibleToInputCheck, (Concept::Convertible)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); @@ -111,24 +112,28 @@ class ITK_TEMPLATE_EXPORT BinaryReconstructionByErosionImageFilter : public Imag * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the value used as "foreground" in the output image. * Defaults to NumericTraits::max(). */ + /** @ITKStartGrouping */ itkSetMacro(ForegroundValue, OutputImagePixelType); itkGetConstMacro(ForegroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** Set/Get the marker image */ + /** @ITKStartGrouping */ itkSetInputMacro(MarkerImage, InputImageType); itkGetInputMacro(MarkerImage, InputImageType); - + /** @ITKEndGrouping */ /** Set/Get the mask image */ + /** @ITKStartGrouping */ itkSetInputMacro(MaskImage, InputImageType); itkGetInputMacro(MaskImage, InputImageType); - + /** @ITKEndGrouping */ protected: BinaryReconstructionByErosionImageFilter(); ~BinaryReconstructionByErosionImageFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkBinaryReconstructionLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkBinaryReconstructionLabelMapFilter.h index d246814e362..1ea37b5e30a 100644 --- a/Modules/Filtering/LabelMap/include/itkBinaryReconstructionLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkBinaryReconstructionLabelMapFilter.h @@ -88,9 +88,10 @@ class ITK_TEMPLATE_EXPORT BinaryReconstructionLabelMapFilter : public InPlaceLab (Concept::OStreamWritable));*/ /** Set/Get the marker image */ + /** @ITKStartGrouping */ itkSetInputMacro(MarkerImage, MarkerImageType); itkGetInputMacro(MarkerImage, MarkerImageType); - + /** @ITKEndGrouping */ /** Set the input image */ void SetInput1(TImage * input) @@ -109,9 +110,10 @@ class ITK_TEMPLATE_EXPORT BinaryReconstructionLabelMapFilter : public InPlaceLab * Set/Get the value used as "foreground" in the output image. * Defaults to NumericTraits::max(). */ + /** @ITKStartGrouping */ itkSetMacro(ForegroundValue, MarkerImagePixelType); itkGetConstMacro(ForegroundValue, MarkerImagePixelType); - + /** @ITKEndGrouping */ protected: BinaryReconstructionLabelMapFilter(); ~BinaryReconstructionLabelMapFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkBinaryShapeKeepNObjectsImageFilter.h b/Modules/Filtering/LabelMap/include/itkBinaryShapeKeepNObjectsImageFilter.h index 8f88c3fd85a..61ce5821407 100644 --- a/Modules/Filtering/LabelMap/include/itkBinaryShapeKeepNObjectsImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkBinaryShapeKeepNObjectsImageFilter.h @@ -95,10 +95,11 @@ class ITK_TEMPLATE_EXPORT BinaryShapeKeepNObjectsImageFilter : public ImageToIma * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ itkConceptMacro(InputEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(IntConvertibleToInputCheck, (Concept::Convertible)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); @@ -107,35 +108,40 @@ class ITK_TEMPLATE_EXPORT BinaryShapeKeepNObjectsImageFilter : public ImageToIma * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the value used as "foreground" in the output image. * Defaults to NumericTraits::max(). */ + /** @ITKStartGrouping */ itkSetMacro(ForegroundValue, OutputImagePixelType); itkGetConstMacro(ForegroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the number of objects to keep */ + /** @ITKStartGrouping */ itkGetConstMacro(NumberOfObjects, SizeValueType); itkSetMacro(NumberOfObjects, SizeValueType); - + /** @ITKEndGrouping */ /** * Set/Get the ordering of the objects. By default, the ones with the * highest value are kept. Turming ReverseOrdering to true make this filter * keep the objects with the smallest values */ + /** @ITKStartGrouping */ itkGetConstMacro(ReverseOrdering, bool); itkSetMacro(ReverseOrdering, bool); itkBooleanMacro(ReverseOrdering); - + /** @ITKEndGrouping */ /** * Set/Get the attribute to use to select the object to keep. The default * is "NumberOfPixels". */ + /** @ITKStartGrouping */ itkGetConstMacro(Attribute, AttributeType); itkSetMacro(Attribute, AttributeType); void @@ -143,7 +149,7 @@ class ITK_TEMPLATE_EXPORT BinaryShapeKeepNObjectsImageFilter : public ImageToIma { this->SetAttribute(LabelObjectType::GetAttributeFromName(s)); } - + /** @ITKEndGrouping */ protected: BinaryShapeKeepNObjectsImageFilter(); ~BinaryShapeKeepNObjectsImageFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkBinaryShapeOpeningImageFilter.h b/Modules/Filtering/LabelMap/include/itkBinaryShapeOpeningImageFilter.h index a90b8427ddd..7b50380aaac 100644 --- a/Modules/Filtering/LabelMap/include/itkBinaryShapeOpeningImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkBinaryShapeOpeningImageFilter.h @@ -95,10 +95,11 @@ class ITK_TEMPLATE_EXPORT BinaryShapeOpeningImageFilter : public ImageToImageFil * Default is FullyConnectedOff. * For objects that are 1 pixel wide, use FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ itkConceptMacro(InputEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(IntConvertibleToInputCheck, (Concept::Convertible)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); @@ -107,36 +108,41 @@ class ITK_TEMPLATE_EXPORT BinaryShapeOpeningImageFilter : public ImageToImageFil * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the value used as "foreground" in the output image. * Defaults to NumericTraits::max(). */ + /** @ITKStartGrouping */ itkSetMacro(ForegroundValue, OutputImagePixelType); itkGetConstMacro(ForegroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the threshold used to keep or remove the objects. */ + /** @ITKStartGrouping */ itkGetConstMacro(Lambda, double); itkSetMacro(Lambda, double); - + /** @ITKEndGrouping */ /** * Set/Get the ordering of the objects. By default, the objects with * an attribute value smaller than Lamba are removed. Turning ReverseOrdering * to true make this filter remove objects with an attribute value greater * than Lambda instead. */ + /** @ITKStartGrouping */ itkGetConstMacro(ReverseOrdering, bool); itkSetMacro(ReverseOrdering, bool); itkBooleanMacro(ReverseOrdering); - + /** @ITKEndGrouping */ /** * Set/Get the attribute to use to select the object to remove. * Default is "Size". */ + /** @ITKStartGrouping */ itkGetConstMacro(Attribute, AttributeType); itkSetMacro(Attribute, AttributeType); void @@ -144,7 +150,7 @@ class ITK_TEMPLATE_EXPORT BinaryShapeOpeningImageFilter : public ImageToImageFil { this->SetAttribute(LabelObjectType::GetAttributeFromName(s)); } - + /** @ITKEndGrouping */ protected: BinaryShapeOpeningImageFilter(); ~BinaryShapeOpeningImageFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkBinaryStatisticsKeepNObjectsImageFilter.h b/Modules/Filtering/LabelMap/include/itkBinaryStatisticsKeepNObjectsImageFilter.h index 6cd59527355..349a0651721 100644 --- a/Modules/Filtering/LabelMap/include/itkBinaryStatisticsKeepNObjectsImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkBinaryStatisticsKeepNObjectsImageFilter.h @@ -98,10 +98,11 @@ class ITK_TEMPLATE_EXPORT BinaryStatisticsKeepNObjectsImageFilter : public Image * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ itkConceptMacro(InputEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(IntConvertibleToInputCheck, (Concept::Convertible)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); @@ -110,35 +111,40 @@ class ITK_TEMPLATE_EXPORT BinaryStatisticsKeepNObjectsImageFilter : public Image * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the value used as "foreground" in the output image. * Defaults to NumericTraits::max(). */ + /** @ITKStartGrouping */ itkSetMacro(ForegroundValue, OutputImagePixelType); itkGetConstMacro(ForegroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the number of objects to keep */ + /** @ITKStartGrouping */ itkGetConstMacro(NumberOfObjects, SizeValueType); itkSetMacro(NumberOfObjects, SizeValueType); - + /** @ITKEndGrouping */ /** * Set/Get the ordering of the objects. By default, the ones with the * highest value are kept. Turming ReverseOrdering to true make this filter * keep the objects with the smallest values */ + /** @ITKStartGrouping */ itkGetConstMacro(ReverseOrdering, bool); itkSetMacro(ReverseOrdering, bool); itkBooleanMacro(ReverseOrdering); - + /** @ITKEndGrouping */ /** * Set/Get the attribute to use to select the object to keep. The default * is "Mean". */ + /** @ITKStartGrouping */ itkGetConstMacro(Attribute, AttributeType); itkSetMacro(Attribute, AttributeType); void @@ -146,7 +152,7 @@ class ITK_TEMPLATE_EXPORT BinaryStatisticsKeepNObjectsImageFilter : public Image { this->SetAttribute(LabelObjectType::GetAttributeFromName(s)); } - + /** @ITKEndGrouping */ /** Set the feature image */ void SetFeatureImage(const TFeatureImage * input) diff --git a/Modules/Filtering/LabelMap/include/itkBinaryStatisticsOpeningImageFilter.h b/Modules/Filtering/LabelMap/include/itkBinaryStatisticsOpeningImageFilter.h index a3b93d8362b..e7f561974e5 100644 --- a/Modules/Filtering/LabelMap/include/itkBinaryStatisticsOpeningImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkBinaryStatisticsOpeningImageFilter.h @@ -102,10 +102,11 @@ class ITK_TEMPLATE_EXPORT BinaryStatisticsOpeningImageFilter : public ImageToIma * Default is FullyConnectedOff. * For objects that are 1 pixel wide, use FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ itkConceptMacro(InputEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(IntConvertibleToInputCheck, (Concept::Convertible)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); @@ -114,36 +115,41 @@ class ITK_TEMPLATE_EXPORT BinaryStatisticsOpeningImageFilter : public ImageToIma * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the value used as "foreground" in the output image. * Defaults to NumericTraits::max(). */ + /** @ITKStartGrouping */ itkSetMacro(ForegroundValue, OutputImagePixelType); itkGetConstMacro(ForegroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the threshold used to keep or remove the objects. */ + /** @ITKStartGrouping */ itkGetConstMacro(Lambda, double); itkSetMacro(Lambda, double); - + /** @ITKEndGrouping */ /** * Set/Get the ordering of the objects. By default, the objects with * an attribute value smaller than Lamba are removed. Turning ReverseOrdering * to true make this filter remove objects with an attribute value greater * than Lambda instead. */ + /** @ITKStartGrouping */ itkGetConstMacro(ReverseOrdering, bool); itkSetMacro(ReverseOrdering, bool); itkBooleanMacro(ReverseOrdering); - + /** @ITKEndGrouping */ /** * Set/Get the attribute to use to select the object to remove. * Default is "Size". */ + /** @ITKStartGrouping */ itkGetConstMacro(Attribute, AttributeType); itkSetMacro(Attribute, AttributeType); void @@ -151,7 +157,7 @@ class ITK_TEMPLATE_EXPORT BinaryStatisticsOpeningImageFilter : public ImageToIma { this->SetAttribute(LabelObjectType::GetAttributeFromName(s)); } - + /** @ITKEndGrouping */ /** Set the feature image */ void SetFeatureImage(const TFeatureImage * input) diff --git a/Modules/Filtering/LabelMap/include/itkChangeRegionLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkChangeRegionLabelMapFilter.h index 080d4887786..35e0fed0a2f 100644 --- a/Modules/Filtering/LabelMap/include/itkChangeRegionLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkChangeRegionLabelMapFilter.h @@ -98,9 +98,10 @@ class ITK_TEMPLATE_EXPORT ChangeRegionLabelMapFilter : public InPlaceLabelMapFil static constexpr unsigned int ImageDimension = TOutputImage::ImageDimension; /** The output region to use */ + /** @ITKStartGrouping */ itkSetMacro(Region, OutputImageRegionType); itkGetConstReferenceMacro(Region, OutputImageRegionType); - + /** @ITKEndGrouping */ protected: ChangeRegionLabelMapFilter() = default; ~ChangeRegionLabelMapFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkCropLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkCropLabelMapFilter.h index 8260bace19c..dd678911667 100644 --- a/Modules/Filtering/LabelMap/include/itkCropLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkCropLabelMapFilter.h @@ -96,11 +96,12 @@ class ITK_TEMPLATE_EXPORT CropLabelMapFilter : public ChangeRegionLabelMapFilter static constexpr unsigned int ImageDimension = TOutputImage::ImageDimension; /** Set/Get the cropping sizes for the upper and lower boundaries. */ + /** @ITKStartGrouping */ itkSetMacro(UpperBoundaryCropSize, SizeType); itkGetMacro(UpperBoundaryCropSize, SizeType); itkSetMacro(LowerBoundaryCropSize, SizeType); itkGetMacro(LowerBoundaryCropSize, SizeType); - + /** @ITKEndGrouping */ void SetCropSize(const SizeType & size) { diff --git a/Modules/Filtering/LabelMap/include/itkInPlaceLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkInPlaceLabelMapFilter.h index 761467e9fba..5fda6b33403 100644 --- a/Modules/Filtering/LabelMap/include/itkInPlaceLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkInPlaceLabelMapFilter.h @@ -123,10 +123,11 @@ class ITK_TEMPLATE_EXPORT InPlaceLabelMapFilter : public LabelMapFilter::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ itkConceptMacro(SameDimensionCheck, (Concept::SameDimension)); protected: diff --git a/Modules/Filtering/LabelMap/include/itkLabelImageToShapeLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkLabelImageToShapeLabelMapFilter.h index df1a517c2df..c5f1616b662 100644 --- a/Modules/Filtering/LabelMap/include/itkLabelImageToShapeLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkLabelImageToShapeLabelMapFilter.h @@ -95,34 +95,38 @@ class ITK_TEMPLATE_EXPORT LabelImageToShapeLabelMapFilter : public ImageToImageF * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get whether the maximum Feret diameter should be computed or not. * Default value is false, because of the high computation time required. */ + /** @ITKStartGrouping */ itkSetMacro(ComputeFeretDiameter, bool); itkGetConstReferenceMacro(ComputeFeretDiameter, bool); itkBooleanMacro(ComputeFeretDiameter); - + /** @ITKEndGrouping */ /** * Set/Get whether the perimeter should be computed or not. * Default value is false, because of the high computation time required. */ + /** @ITKStartGrouping */ itkSetMacro(ComputePerimeter, bool); itkGetConstReferenceMacro(ComputePerimeter, bool); itkBooleanMacro(ComputePerimeter); - + /** @ITKEndGrouping */ /** * Set/Get whether the oriented bounding box should be * computed or not. Default value is false because of potential * memory consumption issues with sparse labels. */ + /** @ITKStartGrouping */ itkSetMacro(ComputeOrientedBoundingBox, bool); itkGetConstReferenceMacro(ComputeOrientedBoundingBox, bool); itkBooleanMacro(ComputeOrientedBoundingBox); - + /** @ITKEndGrouping */ protected: LabelImageToShapeLabelMapFilter(); diff --git a/Modules/Filtering/LabelMap/include/itkLabelImageToStatisticsLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkLabelImageToStatisticsLabelMapFilter.h index e8fb003bdf4..623dd997453 100644 --- a/Modules/Filtering/LabelMap/include/itkLabelImageToStatisticsLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkLabelImageToStatisticsLabelMapFilter.h @@ -93,25 +93,28 @@ class ITK_TEMPLATE_EXPORT LabelImageToStatisticsLabelMapFilter : public ImageToI * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get whether the maximum Feret diameter should be computed or not. The * default value is false, because of the high computation time required. */ + /** @ITKStartGrouping */ itkSetMacro(ComputeFeretDiameter, bool); itkGetConstReferenceMacro(ComputeFeretDiameter, bool); itkBooleanMacro(ComputeFeretDiameter); - + /** @ITKEndGrouping */ /** * Set/Get whether the perimeter should be computed or not. The default value * is false, because of the high computation time required. */ + /** @ITKStartGrouping */ itkSetMacro(ComputePerimeter, bool); itkGetConstReferenceMacro(ComputePerimeter, bool); itkBooleanMacro(ComputePerimeter); - + /** @ITKEndGrouping */ /** Set the feature image */ void SetFeatureImage(const TFeatureImage * input) @@ -147,18 +150,20 @@ class ITK_TEMPLATE_EXPORT LabelImageToStatisticsLabelMapFilter : public ImageToI * compared to the other attributes, this option is useful to reduce the memory usage * when the histogram is not required. */ + /** @ITKStartGrouping */ itkSetMacro(ComputeHistogram, bool); itkGetConstReferenceMacro(ComputeHistogram, bool); itkBooleanMacro(ComputeHistogram); - + /** @ITKEndGrouping */ /** * Set/Get the number of bins in the histogram. Note that the histogram is used * to compute the median value, and that this option may have an effect on the * value of the median. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfBins, unsigned int); itkGetConstReferenceMacro(NumberOfBins, unsigned int); - + /** @ITKEndGrouping */ protected: LabelImageToStatisticsLabelMapFilter(); ~LabelImageToStatisticsLabelMapFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkLabelMap.h b/Modules/Filtering/LabelMap/include/itkLabelMap.h index f0b1a33c342..715098400e8 100644 --- a/Modules/Filtering/LabelMap/include/itkLabelMap.h +++ b/Modules/Filtering/LabelMap/include/itkLabelMap.h @@ -150,11 +150,12 @@ class ITK_TEMPLATE_EXPORT LabelMap : public ImageBase::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ protected: LabelMapToAttributeImageFilter(); ~LabelMapToAttributeImageFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkLabelMapToBinaryImageFilter.h b/Modules/Filtering/LabelMap/include/itkLabelMapToBinaryImageFilter.h index 5fcf677cdb7..6da50fd801e 100644 --- a/Modules/Filtering/LabelMap/include/itkLabelMapToBinaryImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkLabelMapToBinaryImageFilter.h @@ -82,16 +82,18 @@ class ITK_TEMPLATE_EXPORT LabelMapToBinaryImageFilter : public LabelMapFilter::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the value used as "foreground" in the output image. * Defaults to NumericTraits::max(). */ + /** @ITKStartGrouping */ itkSetMacro(ForegroundValue, OutputImagePixelType); itkGetConstMacro(ForegroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** Set/Get the background image top be used to restore the background values */ void diff --git a/Modules/Filtering/LabelMap/include/itkLabelShapeKeepNObjectsImageFilter.h b/Modules/Filtering/LabelMap/include/itkLabelShapeKeepNObjectsImageFilter.h index f08079c2b96..d6daf99885f 100644 --- a/Modules/Filtering/LabelMap/include/itkLabelShapeKeepNObjectsImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkLabelShapeKeepNObjectsImageFilter.h @@ -99,28 +99,32 @@ class ITK_TEMPLATE_EXPORT LabelShapeKeepNObjectsImageFilter : public ImageToImag * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the number of objects to keep */ + /** @ITKStartGrouping */ itkGetConstMacro(NumberOfObjects, SizeValueType); itkSetMacro(NumberOfObjects, SizeValueType); - + /** @ITKEndGrouping */ /** * Set/Get the ordering of the objects. By default, the ones with the * highest value are kept. Turming ReverseOrdering to true make this filter * keep the objects with the smallest values */ + /** @ITKStartGrouping */ itkGetConstMacro(ReverseOrdering, bool); itkSetMacro(ReverseOrdering, bool); itkBooleanMacro(ReverseOrdering); - + /** @ITKEndGrouping */ /** * Set/Get the attribute to use to select the object to keep. The default * is "Size". */ + /** @ITKStartGrouping */ itkGetConstMacro(Attribute, AttributeType); itkSetMacro(Attribute, AttributeType); void @@ -128,7 +132,7 @@ class ITK_TEMPLATE_EXPORT LabelShapeKeepNObjectsImageFilter : public ImageToImag { this->SetAttribute(LabelObjectType::GetAttributeFromName(s)); } - + /** @ITKEndGrouping */ protected: LabelShapeKeepNObjectsImageFilter(); ~LabelShapeKeepNObjectsImageFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkLabelShapeOpeningImageFilter.h b/Modules/Filtering/LabelMap/include/itkLabelShapeOpeningImageFilter.h index c17c96d3993..e43146c0f34 100644 --- a/Modules/Filtering/LabelMap/include/itkLabelShapeOpeningImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkLabelShapeOpeningImageFilter.h @@ -95,29 +95,33 @@ class ITK_TEMPLATE_EXPORT LabelShapeOpeningImageFilter : public ImageToImageFilt * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the threshold used to keep or remove the objects. */ + /** @ITKStartGrouping */ itkGetConstMacro(Lambda, double); itkSetMacro(Lambda, double); - + /** @ITKEndGrouping */ /** * Set/Get the ordering of the objects. By default, the objects with * an attribute value smaller than Lamba are removed. Turning ReverseOrdering * to true make this filter remove the object with an attribute value greater * than Lambda instead. */ + /** @ITKStartGrouping */ itkGetConstMacro(ReverseOrdering, bool); itkSetMacro(ReverseOrdering, bool); itkBooleanMacro(ReverseOrdering); - + /** @ITKEndGrouping */ /** * Set/Get the attribute to use to select the object to remove. The default * is "Size". */ + /** @ITKStartGrouping */ itkGetConstMacro(Attribute, AttributeType); itkSetMacro(Attribute, AttributeType); void @@ -125,7 +129,7 @@ class ITK_TEMPLATE_EXPORT LabelShapeOpeningImageFilter : public ImageToImageFilt { this->SetAttribute(LabelObjectType::GetAttributeFromName(s)); } - + /** @ITKEndGrouping */ protected: LabelShapeOpeningImageFilter(); ~LabelShapeOpeningImageFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkLabelStatisticsKeepNObjectsImageFilter.h b/Modules/Filtering/LabelMap/include/itkLabelStatisticsKeepNObjectsImageFilter.h index 689297fc1b2..494f84bf10c 100644 --- a/Modules/Filtering/LabelMap/include/itkLabelStatisticsKeepNObjectsImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkLabelStatisticsKeepNObjectsImageFilter.h @@ -98,28 +98,32 @@ class ITK_TEMPLATE_EXPORT LabelStatisticsKeepNObjectsImageFilter : public ImageT * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the number of objects to keep */ + /** @ITKStartGrouping */ itkGetConstMacro(NumberOfObjects, SizeValueType); itkSetMacro(NumberOfObjects, SizeValueType); - + /** @ITKEndGrouping */ /** * Set/Get the ordering of the objects. By default, the ones with the * highest value are kept. Turming ReverseOrdering to true make this filter * keep the objects with the smallest values */ + /** @ITKStartGrouping */ itkGetConstMacro(ReverseOrdering, bool); itkSetMacro(ReverseOrdering, bool); itkBooleanMacro(ReverseOrdering); - + /** @ITKEndGrouping */ /** * Set/Get the attribute to use to select the object to keep. The default * is "Mean". */ + /** @ITKStartGrouping */ itkGetConstMacro(Attribute, AttributeType); itkSetMacro(Attribute, AttributeType); void @@ -127,7 +131,7 @@ class ITK_TEMPLATE_EXPORT LabelStatisticsKeepNObjectsImageFilter : public ImageT { this->SetAttribute(LabelObjectType::GetAttributeFromName(s)); } - + /** @ITKEndGrouping */ /** Set the feature image */ void SetFeatureImage(const TFeatureImage * input) diff --git a/Modules/Filtering/LabelMap/include/itkLabelStatisticsOpeningImageFilter.h b/Modules/Filtering/LabelMap/include/itkLabelStatisticsOpeningImageFilter.h index 0da49d7ffc2..cb20a4892bf 100644 --- a/Modules/Filtering/LabelMap/include/itkLabelStatisticsOpeningImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkLabelStatisticsOpeningImageFilter.h @@ -98,29 +98,33 @@ class ITK_TEMPLATE_EXPORT LabelStatisticsOpeningImageFilter : public ImageToImag * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the threshold used to keep or remove the objects. */ + /** @ITKStartGrouping */ itkGetConstMacro(Lambda, double); itkSetMacro(Lambda, double); - + /** @ITKEndGrouping */ /** * Set/Get the ordering of the objects. By default, the objects with * an attribute value smaller than Lamba are removed. Turning ReverseOrdering * to true make this filter remove the object with an attribute value greater * than Lambda instead. */ + /** @ITKStartGrouping */ itkGetConstMacro(ReverseOrdering, bool); itkSetMacro(ReverseOrdering, bool); itkBooleanMacro(ReverseOrdering); - + /** @ITKEndGrouping */ /** * Set/Get the attribute to use to select the object to remove. The default * is "Mean". */ + /** @ITKStartGrouping */ itkGetConstMacro(Attribute, AttributeType); itkSetMacro(Attribute, AttributeType); void @@ -128,7 +132,7 @@ class ITK_TEMPLATE_EXPORT LabelStatisticsOpeningImageFilter : public ImageToImag { this->SetAttribute(LabelObjectType::GetAttributeFromName(s)); } - + /** @ITKEndGrouping */ /** Set the feature image */ void SetFeatureImage(const TFeatureImage * input) diff --git a/Modules/Filtering/LabelMap/include/itkMergeLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkMergeLabelMapFilter.h index df8244a4421..416477d9b17 100644 --- a/Modules/Filtering/LabelMap/include/itkMergeLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkMergeLabelMapFilter.h @@ -144,9 +144,10 @@ class ITK_TEMPLATE_EXPORT MergeLabelMapFilter : public InPlaceLabelMapFilterSetAttribute(LabelObjectType::GetAttributeFromName(s)); } - + /** @ITKEndGrouping */ protected: ShapeOpeningLabelMapFilter(); ~ShapeOpeningLabelMapFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkShapePositionLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkShapePositionLabelMapFilter.h index cb3b6b6947b..16a091586ba 100644 --- a/Modules/Filtering/LabelMap/include/itkShapePositionLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkShapePositionLabelMapFilter.h @@ -77,6 +77,7 @@ class ITK_TEMPLATE_EXPORT ShapePositionLabelMapFilter : public InPlaceLabelMapFi * Set/Get the attribute to use to get the object position. The default * is "Centroid". */ + /** @ITKStartGrouping */ itkGetConstMacro(Attribute, AttributeType); itkSetMacro(Attribute, AttributeType); void @@ -84,7 +85,7 @@ class ITK_TEMPLATE_EXPORT ShapePositionLabelMapFilter : public InPlaceLabelMapFi { this->SetAttribute(LabelObjectType::GetAttributeFromName(s)); } - + /** @ITKEndGrouping */ protected: ShapePositionLabelMapFilter(); ~ShapePositionLabelMapFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkShapeRelabelImageFilter.h b/Modules/Filtering/LabelMap/include/itkShapeRelabelImageFilter.h index c98e225bae6..b208f5d358a 100644 --- a/Modules/Filtering/LabelMap/include/itkShapeRelabelImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkShapeRelabelImageFilter.h @@ -94,21 +94,24 @@ class ITK_TEMPLATE_EXPORT ShapeRelabelImageFilter : public ImageToImageFilter::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the order of labeling of the objects. By default, the objects with * the highest attribute values are labeled first. Set ReverseOrdering to true * make the one with the smallest attributes be labeled first. */ + /** @ITKStartGrouping */ itkGetConstMacro(ReverseOrdering, bool); itkSetMacro(ReverseOrdering, bool); itkBooleanMacro(ReverseOrdering); - + /** @ITKEndGrouping */ /** * Set/Get the attribute to use. Default is "Size". */ + /** @ITKStartGrouping */ itkGetConstMacro(Attribute, AttributeType); itkSetMacro(Attribute, AttributeType); void @@ -116,7 +119,7 @@ class ITK_TEMPLATE_EXPORT ShapeRelabelImageFilter : public ImageToImageFilterSetAttribute(LabelObjectType::GetAttributeFromName(s)); } - + /** @ITKEndGrouping */ protected: ShapeRelabelImageFilter(); ~ShapeRelabelImageFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkShapeRelabelLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkShapeRelabelLabelMapFilter.h index 9574a876c6e..f650fc19cb2 100644 --- a/Modules/Filtering/LabelMap/include/itkShapeRelabelLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkShapeRelabelLabelMapFilter.h @@ -85,14 +85,16 @@ class ITK_TEMPLATE_EXPORT ShapeRelabelLabelMapFilter : public InPlaceLabelMapFil * the highest attribute values are labeled first. Setting ReverseOrdering to true * causes the object with the smallest attributes to be labeled first. */ + /** @ITKStartGrouping */ itkSetMacro(ReverseOrdering, bool); itkGetConstReferenceMacro(ReverseOrdering, bool); itkBooleanMacro(ReverseOrdering); - + /** @ITKEndGrouping */ /** * Set/Get the attribute to use. * Default is "Size". */ + /** @ITKStartGrouping */ itkGetConstMacro(Attribute, AttributeType); itkSetMacro(Attribute, AttributeType); void @@ -100,7 +102,7 @@ class ITK_TEMPLATE_EXPORT ShapeRelabelLabelMapFilter : public InPlaceLabelMapFil { this->SetAttribute(LabelObjectType::GetAttributeFromName(s)); } - + /** @ITKEndGrouping */ protected: ShapeRelabelLabelMapFilter(); ~ShapeRelabelLabelMapFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkShapeUniqueLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkShapeUniqueLabelMapFilter.h index 3b4685aa7a6..21ba0000078 100644 --- a/Modules/Filtering/LabelMap/include/itkShapeUniqueLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkShapeUniqueLabelMapFilter.h @@ -84,14 +84,16 @@ class ITK_TEMPLATE_EXPORT ShapeUniqueLabelMapFilter : public InPlaceLabelMapFilt * a the largest attribute value are kept. If set to true, the filter * to keeps the object with the smallest attribute instead. */ + /** @ITKStartGrouping */ itkGetConstMacro(ReverseOrdering, bool); itkSetMacro(ReverseOrdering, bool); itkBooleanMacro(ReverseOrdering); - + /** @ITKEndGrouping */ /** * Set/Get the attribute to use to select the object to remove. The default * is "Size". */ + /** @ITKStartGrouping */ itkGetConstMacro(Attribute, AttributeType); itkSetMacro(Attribute, AttributeType); void @@ -99,7 +101,7 @@ class ITK_TEMPLATE_EXPORT ShapeUniqueLabelMapFilter : public InPlaceLabelMapFilt { this->SetAttribute(LabelObjectType::GetAttributeFromName(s)); } - + /** @ITKEndGrouping */ protected: ShapeUniqueLabelMapFilter(); ~ShapeUniqueLabelMapFilter() override = default; diff --git a/Modules/Filtering/LabelMap/include/itkStatisticsLabelMapFilter.h b/Modules/Filtering/LabelMap/include/itkStatisticsLabelMapFilter.h index 7f3c2b35b58..9ad9168cade 100644 --- a/Modules/Filtering/LabelMap/include/itkStatisticsLabelMapFilter.h +++ b/Modules/Filtering/LabelMap/include/itkStatisticsLabelMapFilter.h @@ -117,18 +117,20 @@ class ITK_TEMPLATE_EXPORT StatisticsLabelMapFilter * compared to the other attributes, this option is useful to reduce the memory usage * when the histogram is not required. */ + /** @ITKStartGrouping */ itkSetMacro(ComputeHistogram, bool); itkGetConstReferenceMacro(ComputeHistogram, bool); itkBooleanMacro(ComputeHistogram); - + /** @ITKEndGrouping */ /** * Set/Get the number of bins in the histogram. Note that the histogram is used * to compute the median value, and that this option may have an effect on the * value of the median. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfBins, unsigned int); itkGetConstReferenceMacro(NumberOfBins, unsigned int); - + /** @ITKEndGrouping */ // Set the default number of bins to match the number of values for 8 or 16-bit integers; otherwise 128 static constexpr unsigned int GetDefaultNumberOfBins() diff --git a/Modules/Filtering/LabelMap/include/itkStatisticsRelabelImageFilter.h b/Modules/Filtering/LabelMap/include/itkStatisticsRelabelImageFilter.h index d94ce73f6a4..c382ace8c5c 100644 --- a/Modules/Filtering/LabelMap/include/itkStatisticsRelabelImageFilter.h +++ b/Modules/Filtering/LabelMap/include/itkStatisticsRelabelImageFilter.h @@ -97,21 +97,24 @@ class ITK_TEMPLATE_EXPORT StatisticsRelabelImageFilter : public ImageToImageFilt * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the order of labeling of the objects. By default, the objects with * the highest attribute values are labeled first. Set ReverseOrdering to true * make the one with the smallest attributes be labeled first. */ + /** @ITKStartGrouping */ itkGetConstMacro(ReverseOrdering, bool); itkSetMacro(ReverseOrdering, bool); itkBooleanMacro(ReverseOrdering); - + /** @ITKEndGrouping */ /** * Set/Get the attribute to use. Default is "Mean". */ + /** @ITKStartGrouping */ itkGetConstMacro(Attribute, AttributeType); itkSetMacro(Attribute, AttributeType); void @@ -119,7 +122,7 @@ class ITK_TEMPLATE_EXPORT StatisticsRelabelImageFilter : public ImageToImageFilt { this->SetAttribute(LabelObjectType::GetAttributeFromName(s)); } - + /** @ITKEndGrouping */ /** Set the feature image */ void SetFeatureImage(TFeatureImage * input) diff --git a/Modules/Filtering/MathematicalMorphology/include/itkAnchorErodeDilateImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkAnchorErodeDilateImageFilter.h index fce888161b8..be576032097 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkAnchorErodeDilateImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkAnchorErodeDilateImageFilter.h @@ -48,6 +48,7 @@ class ITK_TEMPLATE_EXPORT AnchorErodeDilateImageFilter : public KernelImageFilte using ConstPointer = SmartPointer; /** Some convenient type alias. */ + /** Kernel type alias. */ using KernelType = TKernel; @@ -70,9 +71,10 @@ class ITK_TEMPLATE_EXPORT AnchorErodeDilateImageFilter : public KernelImageFilte itkOverrideGetNameOfClassMacro(AnchorErodeDilateImageFilter); /** Set/Get the boundary value. */ + /** @ITKStartGrouping */ itkSetMacro(Boundary, InputImagePixelType); itkGetConstMacro(Boundary, InputImagePixelType); - + /** @ITKEndGrouping */ protected: AnchorErodeDilateImageFilter(); ~AnchorErodeDilateImageFilter() override = default; diff --git a/Modules/Filtering/MathematicalMorphology/include/itkAnchorOpenCloseLine.h b/Modules/Filtering/MathematicalMorphology/include/itkAnchorOpenCloseLine.h index 81e4f01644c..00ab4d29234 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkAnchorOpenCloseLine.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkAnchorOpenCloseLine.h @@ -37,10 +37,11 @@ class ITK_TEMPLATE_EXPORT AnchorOpenCloseLine { public: /** Some convenient type alias. */ + /** @ITKStartGrouping */ using InputImagePixelType = TInputPix; AnchorOpenCloseLine(); ~AnchorOpenCloseLine() = default; - + /** @ITKEndGrouping */ void PrintSelf(std::ostream & os, Indent indent) const; diff --git a/Modules/Filtering/MathematicalMorphology/include/itkBlackTopHatImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkBlackTopHatImageFilter.h index 1b2daf68243..85a5fe922a8 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkBlackTopHatImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkBlackTopHatImageFilter.h @@ -89,14 +89,16 @@ class ITK_TEMPLATE_EXPORT BlackTopHatImageFilter : public KernelImageFilter)); protected: diff --git a/Modules/Filtering/MathematicalMorphology/include/itkDoubleThresholdImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkDoubleThresholdImageFilter.h index 6dbf96ba052..8f45e34d909 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkDoubleThresholdImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkDoubleThresholdImageFilter.h @@ -95,27 +95,30 @@ class ITK_TEMPLATE_EXPORT DoubleThresholdImageFilter : public ImageToImageFilter * NumericTraits::NonpositiveMin(). The two upper * thresholds default NumericTraits::max. * Threshold1 <= Threshold2 <= Threshold3 <= Threshold4. */ + /** @ITKStartGrouping */ itkSetMacro(Threshold1, InputPixelType); itkSetMacro(Threshold2, InputPixelType); itkSetMacro(Threshold3, InputPixelType); itkSetMacro(Threshold4, InputPixelType); - + /** @ITKEndGrouping */ /** Get the threshold values. */ + /** @ITKStartGrouping */ itkGetConstMacro(Threshold1, InputPixelType); itkGetConstMacro(Threshold2, InputPixelType); itkGetConstMacro(Threshold3, InputPixelType); itkGetConstMacro(Threshold4, InputPixelType); - + /** @ITKEndGrouping */ /** * Set/Get whether the connected components are defined strictly by * face connectivity or by face+edge+vertex connectivity. Default is * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ itkConceptMacro(OutputEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(InputComparableCheck, (Concept::Comparable)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); diff --git a/Modules/Filtering/MathematicalMorphology/include/itkFlatStructuringElement.h b/Modules/Filtering/MathematicalMorphology/include/itkFlatStructuringElement.h index 099c10719c0..532ef64f81c 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkFlatStructuringElement.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkFlatStructuringElement.h @@ -164,6 +164,7 @@ class ITK_TEMPLATE_EXPORT FlatStructuringElement : public Neighborhood)); itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); diff --git a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleConnectedOpeningImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleConnectedOpeningImageFilter.h index c0a829698ab..9a358f8053b 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleConnectedOpeningImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleConnectedOpeningImageFilter.h @@ -76,19 +76,21 @@ class ITK_TEMPLATE_EXPORT GrayscaleConnectedOpeningImageFilter : public ImageToI itkOverrideGetNameOfClassMacro(GrayscaleConnectedOpeningImageFilter); /** Set/Get the seed pixel for the segmentation */ + /** @ITKStartGrouping */ itkSetMacro(Seed, InputImageIndexType); itkGetConstMacro(Seed, InputImageIndexType); - + /** @ITKEndGrouping */ /** * Set/Get whether the connected components are defined strictly by * face connectivity or by face+edge+vertex connectivity. Default is * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ itkConceptMacro(InputEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); diff --git a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleDilateImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleDilateImageFilter.h index 60ec7178d18..10316b8e62d 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleDilateImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleDilateImageFilter.h @@ -124,10 +124,11 @@ class ITK_TEMPLATE_EXPORT GrayscaleDilateImageFilter : public KernelImageFilter< itkGetConstMacro(Boundary, PixelType); /** Set/Get the backend filter class. */ + /** @ITKStartGrouping */ void SetAlgorithm(AlgorithmEnum algo); itkGetConstMacro(Algorithm, AlgorithmEnum); - + /** @ITKEndGrouping */ /** GrayscaleDilateImageFilter need to set its internal filters as modified */ void Modified() const override; diff --git a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleErodeImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleErodeImageFilter.h index c2a6e9fccb3..eb7fc0aba11 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleErodeImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleErodeImageFilter.h @@ -124,10 +124,11 @@ class ITK_TEMPLATE_EXPORT GrayscaleErodeImageFilter : public KernelImageFilter)); protected: diff --git a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleGeodesicDilateImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleGeodesicDilateImageFilter.h index 2daabfd3d91..60cd88cfadb 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleGeodesicDilateImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleGeodesicDilateImageFilter.h @@ -119,10 +119,11 @@ class ITK_TEMPLATE_EXPORT GrayscaleGeodesicDilateImageFilter : public ImageToIma /** Set/Get whether the filter should run one iteration or until * convergence. When run to convergence, this filter is equivalent * to "reconstruction by dilation". Default is off. */ + /** @ITKStartGrouping */ itkSetMacro(RunOneIteration, bool); itkGetConstMacro(RunOneIteration, bool); itkBooleanMacro(RunOneIteration); - + /** @ITKEndGrouping */ /** Get the number of iterations used to produce the current * output. */ itkGetConstMacro(NumberOfIterationsUsed, unsigned long); @@ -133,10 +134,11 @@ class ITK_TEMPLATE_EXPORT GrayscaleGeodesicDilateImageFilter : public ImageToIma * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ itkConceptMacro(SameDimensionCheck, (Concept::SameDimension)); itkConceptMacro(InputComparableCheck, (Concept::Comparable)); itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); diff --git a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleGeodesicErodeImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleGeodesicErodeImageFilter.h index 0577a095872..b38440b141b 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleGeodesicErodeImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleGeodesicErodeImageFilter.h @@ -120,10 +120,11 @@ class ITK_TEMPLATE_EXPORT GrayscaleGeodesicErodeImageFilter : public ImageToImag /** Set/Get whether the filter should run one iteration or until * convergence. When run to convergence, this filter is equivalent * to "reconstruction by erosion". Default is off. */ + /** @ITKStartGrouping */ itkSetMacro(RunOneIteration, bool); itkGetConstMacro(RunOneIteration, bool); itkBooleanMacro(RunOneIteration); - + /** @ITKEndGrouping */ /** Get the number of iterations used to produce the current * output. */ itkGetConstMacro(NumberOfIterationsUsed, unsigned long); @@ -134,10 +135,11 @@ class ITK_TEMPLATE_EXPORT GrayscaleGeodesicErodeImageFilter : public ImageToImag * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ itkConceptMacro(SameDimensionCheck, (Concept::SameDimension)); itkConceptMacro(InputComparableCheck, (Concept::Comparable)); itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); diff --git a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleGrindPeakImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleGrindPeakImageFilter.h index 538fa5cfe39..720b3d0e0a9 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleGrindPeakImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleGrindPeakImageFilter.h @@ -105,10 +105,11 @@ class ITK_TEMPLATE_EXPORT GrayscaleGrindPeakImageFilter : public ImageToImageFil * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); protected: diff --git a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleMorphologicalClosingImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleMorphologicalClosingImageFilter.h index 83cec6a437d..a77b7253538 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleMorphologicalClosingImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleMorphologicalClosingImageFilter.h @@ -113,10 +113,11 @@ class ITK_TEMPLATE_EXPORT GrayscaleMorphologicalClosingImageFilter SetKernel(const KernelType & kernel) override; /** Set/Get the backend filter class. */ + /** @ITKStartGrouping */ void SetAlgorithm(AlgorithmEnum algo); itkGetConstMacro(Algorithm, AlgorithmEnum); - + /** @ITKEndGrouping */ /** GrayscaleMorphologicalClosingImageFilter need to set its internal filters as modified */ void @@ -124,10 +125,11 @@ class ITK_TEMPLATE_EXPORT GrayscaleMorphologicalClosingImageFilter /** A safe border is added to input image to avoid borders effects * and remove it once the closing is done */ + /** @ITKStartGrouping */ itkSetMacro(SafeBorder, bool); itkGetConstReferenceMacro(SafeBorder, bool); itkBooleanMacro(SafeBorder); - + /** @ITKEndGrouping */ protected: GrayscaleMorphologicalClosingImageFilter(); ~GrayscaleMorphologicalClosingImageFilter() override = default; diff --git a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleMorphologicalOpeningImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleMorphologicalOpeningImageFilter.h index df6c8505863..915709748db 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleMorphologicalOpeningImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkGrayscaleMorphologicalOpeningImageFilter.h @@ -112,10 +112,11 @@ class ITK_TEMPLATE_EXPORT GrayscaleMorphologicalOpeningImageFilter SetKernel(const KernelType & kernel) override; /** Set/Get the backend filter class. */ + /** @ITKStartGrouping */ void SetAlgorithm(AlgorithmEnum algo); itkGetConstMacro(Algorithm, AlgorithmEnum); - + /** @ITKEndGrouping */ /** GrayscaleMorphologicalOpeningImageFilter need to set its internal filters as modified */ void @@ -123,10 +124,11 @@ class ITK_TEMPLATE_EXPORT GrayscaleMorphologicalOpeningImageFilter /** A safe border is added to input image to avoid borders effects * and remove it once the closing is done */ + /** @ITKStartGrouping */ itkSetMacro(SafeBorder, bool); itkGetConstReferenceMacro(SafeBorder, bool); itkBooleanMacro(SafeBorder); - + /** @ITKEndGrouping */ protected: GrayscaleMorphologicalOpeningImageFilter(); ~GrayscaleMorphologicalOpeningImageFilter() override = default; diff --git a/Modules/Filtering/MathematicalMorphology/include/itkHConcaveImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkHConcaveImageFilter.h index d438de68141..6bf2ae36f89 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkHConcaveImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkHConcaveImageFilter.h @@ -78,19 +78,21 @@ class ITK_TEMPLATE_EXPORT HConcaveImageFilter : public ImageToImageFilter)); itkConceptMacro(IntConvertibleToInputCheck, (Concept::Convertible)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); diff --git a/Modules/Filtering/MathematicalMorphology/include/itkHConvexImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkHConvexImageFilter.h index f6a610ea250..91e9c7a0b47 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkHConvexImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkHConvexImageFilter.h @@ -78,19 +78,21 @@ class ITK_TEMPLATE_EXPORT HConvexImageFilter : public ImageToImageFilter)); itkConceptMacro(IntConvertibleToInputCheck, (Concept::Convertible)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); diff --git a/Modules/Filtering/MathematicalMorphology/include/itkHMaximaImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkHMaximaImageFilter.h index ed8ae30f9d9..29dd4830277 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkHMaximaImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkHMaximaImageFilter.h @@ -90,19 +90,21 @@ class ITK_TEMPLATE_EXPORT HMaximaImageFilter : public ImageToImageFilter)); itkConceptMacro(IntConvertibleToInputCheck, (Concept::Convertible)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); diff --git a/Modules/Filtering/MathematicalMorphology/include/itkHMinimaImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkHMinimaImageFilter.h index 71e62f9b04e..a8dea4c18d8 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkHMinimaImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkHMinimaImageFilter.h @@ -88,19 +88,21 @@ class ITK_TEMPLATE_EXPORT HMinimaImageFilter : public ImageToImageFilter)); itkConceptMacro(IntConvertibleToInputCheck, (Concept::Convertible)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); diff --git a/Modules/Filtering/MathematicalMorphology/include/itkMorphologicalGradientImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkMorphologicalGradientImageFilter.h index 87e4251ccc9..6f4eaab94eb 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkMorphologicalGradientImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkMorphologicalGradientImageFilter.h @@ -111,10 +111,11 @@ class ITK_TEMPLATE_EXPORT MorphologicalGradientImageFilter SetKernel(const KernelType & kernel) override; /** Set/Get the backend filter class. */ + /** @ITKStartGrouping */ void SetAlgorithm(AlgorithmEnum algo); itkGetConstMacro(Algorithm, AlgorithmEnum); - + /** @ITKEndGrouping */ /** MorphologicalGradientImageFilter need to set its internal filters as modified */ void diff --git a/Modules/Filtering/MathematicalMorphology/include/itkMovingHistogramMorphologyImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkMovingHistogramMorphologyImageFilter.h index 154547dac46..318ef33c754 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkMovingHistogramMorphologyImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkMovingHistogramMorphologyImageFilter.h @@ -88,9 +88,10 @@ class ITK_TEMPLATE_EXPORT MovingHistogramMorphologyImageFilter /** Set/Get the boundary value. * Subclasses should set their own values. */ + /** @ITKStartGrouping */ itkSetMacro(Boundary, PixelType); itkGetConstMacro(Boundary, PixelType); - + /** @ITKEndGrouping */ /** Return true if the vector based algorithm is used, and * false if the map based algorithm is used */ static bool diff --git a/Modules/Filtering/MathematicalMorphology/include/itkOpeningByReconstructionImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkOpeningByReconstructionImageFilter.h index b51a4bb1619..c641bbba24a 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkOpeningByReconstructionImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkOpeningByReconstructionImageFilter.h @@ -98,18 +98,20 @@ class ITK_TEMPLATE_EXPORT OpeningByReconstructionImageFilter : public ImageToIma * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ /** * Set/Get whether the original intensities of the image retained for * those pixels unaffected by the opening by reconstruction. If Off, * the output pixel contrast will be reduced. */ + /** @ITKStartGrouping */ itkSetMacro(PreserveIntensities, bool); itkGetConstReferenceMacro(PreserveIntensities, bool); itkBooleanMacro(PreserveIntensities); - + /** @ITKEndGrouping */ itkConceptMacro(InputEqualityComparableCheck, (Concept::EqualityComparable)); protected: diff --git a/Modules/Filtering/MathematicalMorphology/include/itkReconstructionImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkReconstructionImageFilter.h index 7568d12f7c7..77124c006a5 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkReconstructionImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkReconstructionImageFilter.h @@ -85,6 +85,7 @@ class ITK_TEMPLATE_EXPORT ReconstructionImageFilter : public ImageToImageFilter< using OutputImageIndexType = typename OutputImageType::IndexType; /** ImageDimension constants */ + /** ImageDimension constants */ static constexpr unsigned int MarkerImageDimension = TInputImage::ImageDimension; static constexpr unsigned int MaskImageDimension = TInputImage::ImageDimension; @@ -101,34 +102,38 @@ class ITK_TEMPLATE_EXPORT ReconstructionImageFilter : public ImageToImageFilter< * however this filter implicitly applies a mask to force the * constraint to hold. The marker image the * image that is dilated by this filter. */ + /** @ITKStartGrouping */ itkSetInputMacro(MarkerImage, MarkerImageType); itkGetInputMacro(MarkerImage, MarkerImageType); - + /** @ITKEndGrouping */ /** Set/Get the mask image. The mask image is used to "mask" the * dilated marker image. The mask operation is a pixelwise * minimum. */ + /** @ITKStartGrouping */ itkSetInputMacro(MaskImage, MaskImageType); itkGetInputMacro(MaskImage, MaskImageType); - + /** @ITKEndGrouping */ /** * Set/Get whether the connected components are defined strictly by * face connectivity or by face+edge+vertex connectivity. Default is * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ /** * Perform a padding of the image internally to increase the performance * of the filter. UseInternalCopy can be set to false to reduce the memory * usage. */ + /** @ITKStartGrouping */ itkSetMacro(UseInternalCopy, bool); itkGetConstReferenceMacro(UseInternalCopy, bool); itkBooleanMacro(UseInternalCopy); - + /** @ITKEndGrouping */ protected: ReconstructionImageFilter(); ~ReconstructionImageFilter() override = default; diff --git a/Modules/Filtering/MathematicalMorphology/include/itkRegionalMaximaImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkRegionalMaximaImageFilter.h index a97c2df8590..9454b43ea37 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkRegionalMaximaImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkRegionalMaximaImageFilter.h @@ -90,32 +90,36 @@ class ITK_TEMPLATE_EXPORT RegionalMaximaImageFilter : public ImageToImageFilter< * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ /** * Set/Get the value in the output image to consider as "foreground". * Defaults to maximum value of PixelType. */ + /** @ITKStartGrouping */ itkSetMacro(ForegroundValue, OutputImagePixelType); itkGetConstMacro(ForegroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get whether a flat image must be considered as a maxima or not. * Defaults to true. */ + /** @ITKStartGrouping */ itkSetMacro(FlatIsMaxima, bool); itkGetConstMacro(FlatIsMaxima, bool); itkBooleanMacro(FlatIsMaxima); - + /** @ITKEndGrouping */ itkConceptMacro(InputHasPixelTraitsCheck, (Concept::HasPixelTraits)); itkConceptMacro(InputHasNumericTraitsCheck, (Concept::HasNumericTraits)); diff --git a/Modules/Filtering/MathematicalMorphology/include/itkRegionalMinimaImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkRegionalMinimaImageFilter.h index 05bc45fce9c..db4697cac5b 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkRegionalMinimaImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkRegionalMinimaImageFilter.h @@ -88,32 +88,36 @@ class ITK_TEMPLATE_EXPORT RegionalMinimaImageFilter : public ImageToImageFilter< * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ /** * Set/Get the value in the output image to consider as "foreground". * Defaults to maximum value of PixelType. */ + /** @ITKStartGrouping */ itkSetMacro(ForegroundValue, OutputImagePixelType); itkGetConstMacro(ForegroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get the value used as "background" in the output image. * Defaults to NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** * Set/Get whether a flat image must be considered as a minima or not. * Defaults to true. */ + /** @ITKStartGrouping */ itkSetMacro(FlatIsMinima, bool); itkGetConstMacro(FlatIsMinima, bool); itkBooleanMacro(FlatIsMinima); - + /** @ITKEndGrouping */ itkConceptMacro(InputHasPixelTraitsCheck, (Concept::HasPixelTraits)); itkConceptMacro(InputHasNumericTraitsCheck, (Concept::HasNumericTraits)); diff --git a/Modules/Filtering/MathematicalMorphology/include/itkValuedRegionalExtremaImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkValuedRegionalExtremaImageFilter.h index 53bdfc333c5..65e6d6169d9 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkValuedRegionalExtremaImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkValuedRegionalExtremaImageFilter.h @@ -114,16 +114,18 @@ class ITK_TEMPLATE_EXPORT ValuedRegionalExtremaImageFilter : public ImageToImage * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ /** * Set/Get the value used to mark all pixels which are not extrema. */ + /** @ITKStartGrouping */ itkSetMacro(MarkerValue, typename TInputImage::PixelType); itkGetConstReferenceMacro(MarkerValue, typename TInputImage::PixelType); - + /** @ITKEndGrouping */ /** * Get whether the image is flat or not. */ diff --git a/Modules/Filtering/MathematicalMorphology/include/itkVanHerkGilWermanErodeDilateImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkVanHerkGilWermanErodeDilateImageFilter.h index 5e641061a19..25095f8491d 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkVanHerkGilWermanErodeDilateImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkVanHerkGilWermanErodeDilateImageFilter.h @@ -51,6 +51,7 @@ class ITK_TEMPLATE_EXPORT VanHerkGilWermanErodeDilateImageFilter : public Kernel using ConstPointer = SmartPointer; /** Some convenient type alias. */ + /** Kernel type alias. */ using KernelType = TKernel; @@ -73,9 +74,10 @@ class ITK_TEMPLATE_EXPORT VanHerkGilWermanErodeDilateImageFilter : public Kernel itkOverrideGetNameOfClassMacro(VanHerkGilWermanErodeDilateImageFilter); /** Set/Get the boundary value. */ + /** @ITKStartGrouping */ itkSetMacro(Boundary, InputImagePixelType); itkGetConstMacro(Boundary, InputImagePixelType); - + /** @ITKEndGrouping */ protected: VanHerkGilWermanErodeDilateImageFilter(); ~VanHerkGilWermanErodeDilateImageFilter() override = default; diff --git a/Modules/Filtering/MathematicalMorphology/include/itkWhiteTopHatImageFilter.h b/Modules/Filtering/MathematicalMorphology/include/itkWhiteTopHatImageFilter.h index 7526a65d932..1b0c3b146fe 100644 --- a/Modules/Filtering/MathematicalMorphology/include/itkWhiteTopHatImageFilter.h +++ b/Modules/Filtering/MathematicalMorphology/include/itkWhiteTopHatImageFilter.h @@ -87,14 +87,16 @@ class ITK_TEMPLATE_EXPORT WhiteTopHatImageFilter : public KernelImageFilter } /** Insert a new step into the chaincode at a specified position */ + /** @ITKStartGrouping */ inline void InsertStep(InputType position, int encodedStep) { @@ -124,8 +125,10 @@ class ITK_TEMPLATE_EXPORT ChainCodePath2D : public ChainCodePath<2> m_Chain2D.insert(m_Chain2D.begin() + position, EncodeOffset(step)); this->Modified(); } + /** @ITKEndGrouping */ /** Change the direction of a step in the chaincode */ + /** @ITKStartGrouping */ inline void ChangeStep(InputType position, int encodedStep) { @@ -139,6 +142,7 @@ class ITK_TEMPLATE_EXPORT ChainCodePath2D : public ChainCodePath<2> m_Chain2D[position] = EncodeOffset(step); this->Modified(); } + /** @ITKEndGrouping */ /** Remove all steps from the chain code */ void diff --git a/Modules/Filtering/Path/include/itkContourExtractor2DImageFilter.h b/Modules/Filtering/Path/include/itkContourExtractor2DImageFilter.h index 4df2bc93423..501508a8f11 100644 --- a/Modules/Filtering/Path/include/itkContourExtractor2DImageFilter.h +++ b/Modules/Filtering/Path/include/itkContourExtractor2DImageFilter.h @@ -153,22 +153,25 @@ class ITK_TEMPLATE_EXPORT ContourExtractor2DImageFilter /** Control the orientation of the contours with reference to the image * gradient. (See class documentation.) */ + /** @ITKStartGrouping */ itkSetMacro(ReverseContourOrientation, bool); itkGetConstReferenceMacro(ReverseContourOrientation, bool); itkBooleanMacro(ReverseContourOrientation); - + /** @ITKEndGrouping */ /** Control whether high- or low-valued pixels are vertex-connected. * Default is for low-valued pixels to be vertex-connected. * (See class documentation.) */ + /** @ITKStartGrouping */ itkSetMacro(VertexConnectHighPixels, bool); itkGetConstReferenceMacro(VertexConnectHighPixels, bool); itkBooleanMacro(VertexConnectHighPixels); - + /** @ITKEndGrouping */ /** Return contours for all distinct labels */ + /** @ITKStartGrouping */ itkSetMacro(LabelContours, bool); itkGetConstReferenceMacro(LabelContours, bool); itkBooleanMacro(LabelContours); - + /** @ITKEndGrouping */ /** Control whether the largest possible input region is used, or if a * custom requested region is to be used. */ void @@ -180,9 +183,10 @@ class ITK_TEMPLATE_EXPORT ContourExtractor2DImageFilter /** Set/Get the image intensity value that the contours should follow. * This is the equivalent of an iso-value in Marching Squares. */ + /** @ITKStartGrouping */ itkSetMacro(ContourValue, InputRealType); itkGetConstReferenceMacro(ContourValue, InputRealType); - + /** @ITKEndGrouping */ itkConceptMacro(DimensionShouldBe2, (Concept::SameDimension)); itkConceptMacro(InputPixelTypeComparable, (Concept::Comparable)); itkConceptMacro(InputHasPixelTraitsCheck, (Concept::HasPixelTraits)); diff --git a/Modules/Filtering/Path/include/itkHilbertPath.h b/Modules/Filtering/Path/include/itkHilbertPath.h index a055e446302..fb658b8a978 100644 --- a/Modules/Filtering/Path/include/itkHilbertPath.h +++ b/Modules/Filtering/Path/include/itkHilbertPath.h @@ -145,8 +145,10 @@ class ITK_TEMPLATE_EXPORT HilbertPath : public Path::max()); itkGetConstMacro(HilbertOrder, HilbertOrderType); + /** @ITKEndGrouping */ /** Convert the path index to the multidimensional index location */ IndexType diff --git a/Modules/Filtering/Path/include/itkParametricPath.h b/Modules/Filtering/Path/include/itkParametricPath.h index 53212cd468a..edb4b4dd99c 100644 --- a/Modules/Filtering/Path/include/itkParametricPath.h +++ b/Modules/Filtering/Path/include/itkParametricPath.h @@ -67,6 +67,7 @@ class ITK_TEMPLATE_EXPORT ParametricPath /** Standard class type aliases. */ using Self = ParametricPath; + /** All paths must be mappable to index space */ using ContinuousIndexType = ContinuousIndex; using Superclass = Path; diff --git a/Modules/Filtering/Path/include/itkPathSource.h b/Modules/Filtering/Path/include/itkPathSource.h index fcf389a96cb..8d0a80c5671 100644 --- a/Modules/Filtering/Path/include/itkPathSource.h +++ b/Modules/Filtering/Path/include/itkPathSource.h @@ -107,11 +107,13 @@ class ITK_TEMPLATE_EXPORT PathSource : public ProcessObject * Region, which can be set using ImageBase::SetRequestedRegion(). * By default, the largest possible region is requested. */ + /** @ITKStartGrouping */ OutputPathType * GetOutput(); OutputPathType * GetOutput(unsigned int idx); + /** @ITKEndGrouping */ /** Graft the specified DataObject onto this ProcessObject's output. * This method grabs a handle to the specified DataObject's path @@ -173,10 +175,12 @@ class ITK_TEMPLATE_EXPORT PathSource : public ProcessObject * SmartPointer to a DataObject. If a subclass of ImageSource has * multiple outputs of different types, then that class must provide * an implementation of MakeOutput(). */ + /** @ITKStartGrouping */ using DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType; using Superclass::MakeOutput; DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx) override; + /** @ITKEndGrouping */ protected: PathSource(); diff --git a/Modules/Filtering/Path/include/itkPathToChainCodePathFilter.h b/Modules/Filtering/Path/include/itkPathToChainCodePathFilter.h index d267a8b2bb0..d2bd1a23793 100644 --- a/Modules/Filtering/Path/include/itkPathToChainCodePathFilter.h +++ b/Modules/Filtering/Path/include/itkPathToChainCodePathFilter.h @@ -64,10 +64,11 @@ class ITK_TEMPLATE_EXPORT PathToChainCodePathFilter : public PathToPathFilter /** Set/Get the value for pixels on and off the path. * By default, this filter will return a "0" image with path pixels set to 1 */ + /** @ITKStartGrouping */ itkSetMacro(PathValue, ValueType); itkGetConstMacro(PathValue, ValueType); itkSetMacro(BackgroundValue, ValueType); itkGetConstMacro(BackgroundValue, ValueType); - + /** @ITKEndGrouping */ /** The origin of the output image. The origin is the geometric * coordinates of the index (0,0,...,0). It is stored internally * as double but may be set from float. @@ -112,9 +113,10 @@ class ITK_TEMPLATE_EXPORT PathToImageFilter : public ImageSource GetOrigin() const; /** Set/Get Size */ + /** @ITKStartGrouping */ itkSetMacro(Size, SizeType); itkGetConstMacro(Size, SizeType); - + /** @ITKEndGrouping */ protected: PathToImageFilter(); ~PathToImageFilter() override = default; diff --git a/Modules/Filtering/Path/include/itkPolyLineParametricPath.h b/Modules/Filtering/Path/include/itkPolyLineParametricPath.h index 6dd82009c7d..6deb871c4df 100644 --- a/Modules/Filtering/Path/include/itkPolyLineParametricPath.h +++ b/Modules/Filtering/Path/include/itkPolyLineParametricPath.h @@ -88,7 +88,7 @@ class ITK_TEMPLATE_EXPORT PolyLineParametricPath : public ParametricPathGetOutput(); OutputCellsContainerPointer cells = output->GetCells(); - + /** @ITKEndGrouping */ OutputQEType * qe = iEdge; OutputQEType * qe_it = qe->GetOnext(); diff --git a/Modules/Filtering/QuadEdgeMeshFiltering/include/itkLaplacianDeformationQuadEdgeMeshFilter.h b/Modules/Filtering/QuadEdgeMeshFiltering/include/itkLaplacianDeformationQuadEdgeMeshFilter.h index d848f637a1c..42880a627a9 100644 --- a/Modules/Filtering/QuadEdgeMeshFiltering/include/itkLaplacianDeformationQuadEdgeMeshFilter.h +++ b/Modules/Filtering/QuadEdgeMeshFiltering/include/itkLaplacianDeformationQuadEdgeMeshFilter.h @@ -42,6 +42,7 @@ class LaplacianDeformationQuadEdgeMeshFilterEnums { /** Do not use any area information*/ NONE = 0, + /** Use a mixed area*/ MIXEDAREA }; @@ -179,8 +180,10 @@ class ITK_TEMPLATE_EXPORT LaplacianDeformationQuadEdgeMeshFilter ClearConstraints(); /** Set/Get the Laplacian order */ + /** @ITKStartGrouping */ itkSetMacro(Order, unsigned int); itkGetMacro(Order, unsigned int); + /** @ITKEndGrouping */ using AreaEnum = LaplacianDeformationQuadEdgeMeshFilterEnums::Area; #if !defined(ITK_LEGACY_REMOVE) @@ -190,16 +193,20 @@ class ITK_TEMPLATE_EXPORT LaplacianDeformationQuadEdgeMeshFilter #endif /** Set/Get the area normalization type */ + /** @ITKStartGrouping */ itkSetEnumMacro(AreaComputationType, AreaEnum); itkGetMacro(AreaComputationType, AreaEnum); + /** @ITKEndGrouping */ itkConceptMacro(SameDimensionCheck1, (Concept::SameDimension)); itkConceptMacro(SameDimensionCheck2, (Concept::SameDimension)); protected: /** Default constructor*/ + /** @ITKStartGrouping */ LaplacianDeformationQuadEdgeMeshFilter(); ~LaplacianDeformationQuadEdgeMeshFilter() override = default; + /** @ITKEndGrouping */ using OutputMapPointIdentifier = std::unordered_map; using OutputMapPointIdentifierIterator = typename OutputMapPointIdentifier::iterator; diff --git a/Modules/Filtering/QuadEdgeMeshFiltering/include/itkSmoothingQuadEdgeMeshFilter.h b/Modules/Filtering/QuadEdgeMeshFiltering/include/itkSmoothingQuadEdgeMeshFilter.h index 178b361dff0..ccc34e15c1b 100644 --- a/Modules/Filtering/QuadEdgeMeshFiltering/include/itkSmoothingQuadEdgeMeshFilter.h +++ b/Modules/Filtering/QuadEdgeMeshFiltering/include/itkSmoothingQuadEdgeMeshFilter.h @@ -68,6 +68,7 @@ class ITK_TEMPLATE_EXPORT SmoothingQuadEdgeMeshFilter : public QuadEdgeMeshToQua /** \see LightObject::GetNameOfClass() */ itkOverrideGetNameOfClassMacro(SmoothingQuadEdgeMeshFilter); + /** New macro for creation of through a Smart Pointer */ itkNewMacro(Self); @@ -97,18 +98,21 @@ class ITK_TEMPLATE_EXPORT SmoothingQuadEdgeMeshFilter : public QuadEdgeMeshToQua SetCoefficientsMethod(CoefficientsComputation * iMethod); /** Set/Get the number of iterations */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfIterations, unsigned int); itkGetConstMacro(NumberOfIterations, unsigned int); - + /** @ITKEndGrouping */ /** Set/Get if DelaunayConformingQuadEdgeMeshFilter is used at the end of each iterations */ + /** @ITKStartGrouping */ itkBooleanMacro(DelaunayConforming); itkSetMacro(DelaunayConforming, bool); itkGetConstMacro(DelaunayConforming, bool); - + /** @ITKEndGrouping */ /** Set/Get relaxation factor applied for each iteration */ + /** @ITKStartGrouping */ itkSetMacro(RelaxationFactor, OutputCoordType); itkGetConstMacro(RelaxationFactor, OutputCoordType); - + /** @ITKEndGrouping */ protected: SmoothingQuadEdgeMeshFilter(); ~SmoothingQuadEdgeMeshFilter() override; diff --git a/Modules/Filtering/Smoothing/include/itkBinomialBlurImageFilter.h b/Modules/Filtering/Smoothing/include/itkBinomialBlurImageFilter.h index c02d6149c0e..969d1abf951 100644 --- a/Modules/Filtering/Smoothing/include/itkBinomialBlurImageFilter.h +++ b/Modules/Filtering/Smoothing/include/itkBinomialBlurImageFilter.h @@ -82,9 +82,10 @@ class ITK_TEMPLATE_EXPORT BinomialBlurImageFilter : public ImageToImageFilterSetVariance(variance); } + /** SetSigmaArray is preserved for interface * backwards compatibility. */ + /** @ITKStartGrouping */ void SetSigmaArray(const ArrayType & sigmas) { @@ -217,6 +229,7 @@ class ITK_TEMPLATE_EXPORT DiscreteGaussianImageFilter : public ImageToImageFilte { this->SetVariance(sigma * sigma); } + /** @ITKEndGrouping */ /** Get the Sigma value. */ ArrayType @@ -280,9 +293,11 @@ class ITK_TEMPLATE_EXPORT DiscreteGaussianImageFilter : public ImageToImageFilte * into account and to specify the Gaussian variance in real world units; * use Off to ignore the image spacing and to specify the Gaussian variance * in voxel units. Default is On. */ + /** @ITKStartGrouping */ itkSetMacro(UseImageSpacing, bool); itkGetConstMacro(UseImageSpacing, bool); itkBooleanMacro(UseImageSpacing); + /** @ITKEndGrouping */ #if !defined(ITK_FUTURE_LEGACY_REMOVE) /** Use the image spacing information in calculations. Use this option if you diff --git a/Modules/Filtering/Smoothing/include/itkFFTDiscreteGaussianImageFilterFactory.h b/Modules/Filtering/Smoothing/include/itkFFTDiscreteGaussianImageFilterFactory.h index b007a65d825..301aaab5949 100644 --- a/Modules/Filtering/Smoothing/include/itkFFTDiscreteGaussianImageFilterFactory.h +++ b/Modules/Filtering/Smoothing/include/itkFFTDiscreteGaussianImageFilterFactory.h @@ -51,6 +51,7 @@ class FFTDiscreteGaussianImageFilterFactory : public itk::ObjectFactoryBase using ConstPointer = SmartPointer; /** Class methods used to interface with the registered factories. */ + /** @ITKStartGrouping */ const char * GetITKSourceVersion() const override { @@ -61,7 +62,7 @@ class FFTDiscreteGaussianImageFilterFactory : public itk::ObjectFactoryBase { return "An FFTDiscreteGaussianImageFilterFactory factory"; } - + /** @ITKEndGrouping */ /** Method for class instantiation. */ itkFactorylessNewMacro(Self); @@ -81,6 +82,7 @@ class FFTDiscreteGaussianImageFilterFactory : public itk::ObjectFactoryBase /** Override base DiscreteGaussianImageFilter constructor at runtime to return * an upcast FFTDiscreteGaussianImageFilter instance through the object factory */ + /** @ITKStartGrouping */ template void OverrideSuperclassType(const std::integer_sequence &) @@ -99,7 +101,7 @@ class FFTDiscreteGaussianImageFilterFactory : public itk::ObjectFactoryBase void OverrideSuperclassType(const std::integer_sequence &) {} - + /** @ITKEndGrouping */ FFTDiscreteGaussianImageFilterFactory() { OverrideSuperclassType(std::integer_sequence{}); diff --git a/Modules/Filtering/Smoothing/include/itkRecursiveGaussianImageFilter.h b/Modules/Filtering/Smoothing/include/itkRecursiveGaussianImageFilter.h index 16f6b695e92..c5793f056dd 100644 --- a/Modules/Filtering/Smoothing/include/itkRecursiveGaussianImageFilter.h +++ b/Modules/Filtering/Smoothing/include/itkRecursiveGaussianImageFilter.h @@ -116,9 +116,10 @@ class ITK_TEMPLATE_EXPORT RecursiveGaussianImageFilter : public RecursiveSeparab * kernel. The default is 1.0. An exception will be generated if * the Sigma value is less than or equal to zero. */ + /** @ITKStartGrouping */ itkGetConstMacro(Sigma, ScalarRealType); itkSetMacro(Sigma, ScalarRealType); - + /** @ITKEndGrouping */ /** Type of the output image */ using OutputImageType = TOutputImage; @@ -132,6 +133,7 @@ class ITK_TEMPLATE_EXPORT RecursiveGaussianImageFilter : public RecursiveSeparab static constexpr GaussianOrderEnum FirstOrder = GaussianOrderEnum::FirstOrder; static constexpr GaussianOrderEnum SecondOrder = GaussianOrderEnum::SecondOrder; #endif + /** Set/Get the flag for normalizing the gaussian over scale-space. This flag enables the analysis of the differential shape of @@ -181,9 +183,10 @@ class ITK_TEMPLATE_EXPORT RecursiveGaussianImageFilter : public RecursiveSeparab \li FirstOrder is equivalent to convolving with the first derivative of a Gaussian. \li SecondOrder is equivalent to convolving with the second derivative of a Gaussian. */ + /** @ITKStartGrouping */ itkSetMacro(Order, GaussianOrderEnum); itkGetConstMacro(Order, GaussianOrderEnum); - + /** @ITKEndGrouping */ /** Explicitly set a zeroth order derivative. */ void SetZeroOrder(); diff --git a/Modules/Filtering/Smoothing/include/itkSmoothingRecursiveGaussianImageFilter.h b/Modules/Filtering/Smoothing/include/itkSmoothingRecursiveGaussianImageFilter.h index 4a7d038920d..90c596c0b39 100644 --- a/Modules/Filtering/Smoothing/include/itkSmoothingRecursiveGaussianImageFilter.h +++ b/Modules/Filtering/Smoothing/include/itkSmoothingRecursiveGaussianImageFilter.h @@ -108,11 +108,12 @@ class ITK_TEMPLATE_EXPORT SmoothingRecursiveGaussianImageFilter : public InPlace * Sigma is measured in the units of image spacing. You may use the method * SetSigma to set the same value across each axis or use the method * SetSigmaArray if you need different values along each axis. */ + /** @ITKStartGrouping */ void SetSigmaArray(const SigmaArrayType & sigma); void SetSigma(ScalarRealType sigma); - + /** @ITKEndGrouping */ /** Get the Sigma value. */ SigmaArrayType GetSigmaArray() const; @@ -126,11 +127,12 @@ class ITK_TEMPLATE_EXPORT SmoothingRecursiveGaussianImageFilter : public InPlace * This method does not effect the output of this filter. * * \sa RecursiveGaussianImageFilter::SetNormalizeAcrossScale */ + /** @ITKStartGrouping */ void SetNormalizeAcrossScale(bool normalize); itkGetConstMacro(NormalizeAcrossScale, bool); itkBooleanMacro(NormalizeAcrossScale); - + /** @ITKEndGrouping */ /** Set the number of work units to create. */ void SetNumberOfWorkUnits(ThreadIdType nb) override; diff --git a/Modules/Filtering/Thresholding/include/itkBinaryThresholdProjectionImageFilter.h b/Modules/Filtering/Thresholding/include/itkBinaryThresholdProjectionImageFilter.h index a013e641e8e..0cb1c0dcb05 100644 --- a/Modules/Filtering/Thresholding/include/itkBinaryThresholdProjectionImageFilter.h +++ b/Modules/Filtering/Thresholding/include/itkBinaryThresholdProjectionImageFilter.h @@ -125,19 +125,22 @@ class BinaryThresholdProjectionImageFilter /** Set/Get the output value used as "foreground". Defaults to * maximum value of PixelType. */ + /** @ITKStartGrouping */ itkSetMacro(ForegroundValue, OutputPixelType); itkGetConstMacro(ForegroundValue, OutputPixelType); - + /** @ITKEndGrouping */ /** Set/Get the output value used as "background". Defaults to * NumericTraits::NonpositiveMin(). */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputPixelType); itkGetConstMacro(BackgroundValue, OutputPixelType); - + /** @ITKEndGrouping */ /** Set/Get the input value consider as "threshold". Defaults to * NumericTraits::max() */ + /** @ITKStartGrouping */ itkSetMacro(ThresholdValue, InputPixelType); itkGetConstMacro(ThresholdValue, InputPixelType); - + /** @ITKEndGrouping */ itkConceptMacro(InputPixelTypeGreaterThanComparable, (Concept::GreaterThanComparable)); itkConceptMacro(InputHasNumericTraitsCheck, (Concept::HasNumericTraits)); diff --git a/Modules/Filtering/Thresholding/include/itkHistogramThresholdImageFilter.h b/Modules/Filtering/Thresholding/include/itkHistogramThresholdImageFilter.h index 2a02009ace1..302010a0044 100644 --- a/Modules/Filtering/Thresholding/include/itkHistogramThresholdImageFilter.h +++ b/Modules/Filtering/Thresholding/include/itkHistogramThresholdImageFilter.h @@ -120,9 +120,10 @@ class ITK_TEMPLATE_EXPORT HistogramThresholdImageFilter : public ImageToImageFil static constexpr unsigned int MaskImageDimension = MaskImageType::ImageDimension; /** Set and Get the mask image */ + /** @ITKStartGrouping */ itkSetInputMacro(MaskImage, TMaskImage); itkGetInputMacro(MaskImage, TMaskImage); - + /** @ITKEndGrouping */ /** Set the input image */ void SetInput1(const TInputImage * input) @@ -152,35 +153,40 @@ class ITK_TEMPLATE_EXPORT HistogramThresholdImageFilter : public ImageToImageFil itkGetConstMacro(InsideValue, OutputPixelType); /** Set the number of histogram bins */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfHistogramBins, unsigned int); itkGetConstMacro(NumberOfHistogramBins, unsigned int); - + /** @ITKEndGrouping */ /** Does histogram generator compute min and max from data? * Default is true for all but char types */ + /** @ITKStartGrouping */ itkSetMacro(AutoMinimumMaximum, bool); itkGetConstMacro(AutoMinimumMaximum, bool); itkBooleanMacro(AutoMinimumMaximum); - + /** @ITKEndGrouping */ /** Do you want the output to be masked by the mask used in * histogram construction. Only relevant if masking is in * use. Default is true. */ + /** @ITKStartGrouping */ itkSetMacro(MaskOutput, bool); itkGetConstMacro(MaskOutput, bool); itkBooleanMacro(MaskOutput); - + /** @ITKEndGrouping */ /** The value in the mask image, if used, indicating voxels that should be included. Default is the max of pixel type, as in the MaskedImageToHistogramFilter */ + /** @ITKStartGrouping */ itkSetMacro(MaskValue, MaskPixelType); itkGetConstMacro(MaskValue, MaskPixelType); - + /** @ITKEndGrouping */ /** Get the computed threshold. */ itkGetConstMacro(Threshold, InputPixelType); /** Set/Get the calculator to use to compute the threshold */ + /** @ITKStartGrouping */ itkSetObjectMacro(Calculator, CalculatorType); itkGetModifiableObjectMacro(Calculator, CalculatorType); - + /** @ITKEndGrouping */ itkConceptMacro(OutputEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(InputOStreamWritableCheck, (Concept::OStreamWritable)); itkConceptMacro(OutputOStreamWritableCheck, (Concept::OStreamWritable)); diff --git a/Modules/Filtering/Thresholding/include/itkIntermodesThresholdCalculator.h b/Modules/Filtering/Thresholding/include/itkIntermodesThresholdCalculator.h index cac3a0c8886..6ff8d213495 100644 --- a/Modules/Filtering/Thresholding/include/itkIntermodesThresholdCalculator.h +++ b/Modules/Filtering/Thresholding/include/itkIntermodesThresholdCalculator.h @@ -78,10 +78,11 @@ class ITK_TEMPLATE_EXPORT IntermodesThresholdCalculator : public HistogramThresh /** Select whether midpoint (intermode = true) or minimum between peaks is used. Default is "On". */ + /** @ITKStartGrouping */ itkSetMacro(UseInterMode, bool); itkGetConstMacro(UseInterMode, bool); itkBooleanMacro(UseInterMode); - + /** @ITKEndGrouping */ protected: IntermodesThresholdCalculator() { diff --git a/Modules/Filtering/Thresholding/include/itkIntermodesThresholdImageFilter.h b/Modules/Filtering/Thresholding/include/itkIntermodesThresholdImageFilter.h index 32703ac4fcc..3a141b2aeb0 100644 --- a/Modules/Filtering/Thresholding/include/itkIntermodesThresholdImageFilter.h +++ b/Modules/Filtering/Thresholding/include/itkIntermodesThresholdImageFilter.h @@ -99,10 +99,11 @@ class ITK_TEMPLATE_EXPORT IntermodesThresholdImageFilter /** Select whether midpoint (intermode=true) or minimum between peaks is used. */ + /** @ITKStartGrouping */ itkSetMacro(UseInterMode, bool); itkGetConstReferenceMacro(UseInterMode, bool); itkBooleanMacro(UseInterMode); - + /** @ITKEndGrouping */ /** Image related type alias. */ static constexpr unsigned int InputImageDimension = InputImageType::ImageDimension; static constexpr unsigned int OutputImageDimension = OutputImageType::ImageDimension; diff --git a/Modules/Filtering/Thresholding/include/itkKappaSigmaThresholdImageCalculator.h b/Modules/Filtering/Thresholding/include/itkKappaSigmaThresholdImageCalculator.h index 5bf5e3f2f5b..d874998cc7d 100644 --- a/Modules/Filtering/Thresholding/include/itkKappaSigmaThresholdImageCalculator.h +++ b/Modules/Filtering/Thresholding/include/itkKappaSigmaThresholdImageCalculator.h @@ -93,17 +93,20 @@ class ITK_TEMPLATE_EXPORT KappaSigmaThresholdImageCalculator : public Object /** Set the mask value used to select which pixels will be considered in the * computation (e.g. only pixels which satisfy (m_Mask->GetPixel(Index()) == m_MaskValue) * are considered). */ + /** @ITKStartGrouping */ itkSetMacro(MaskValue, MaskPixelType); itkGetConstMacro(MaskValue, MaskPixelType); - + /** @ITKEndGrouping */ /** Set the Sigma multiplier (Kappa) to adjust the pixel rejection rate. */ + /** @ITKStartGrouping */ itkSetMacro(SigmaFactor, double); itkGetConstMacro(SigmaFactor, double); - + /** @ITKEndGrouping */ /** Set the number of rejection passes. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfIterations, unsigned int); itkGetConstMacro(NumberOfIterations, unsigned int); - + /** @ITKEndGrouping */ /** Run and compute threshold. */ void Compute(); diff --git a/Modules/Filtering/Thresholding/include/itkKappaSigmaThresholdImageFilter.h b/Modules/Filtering/Thresholding/include/itkKappaSigmaThresholdImageFilter.h index 4ca2147c95b..c65414eb5de 100644 --- a/Modules/Filtering/Thresholding/include/itkKappaSigmaThresholdImageFilter.h +++ b/Modules/Filtering/Thresholding/include/itkKappaSigmaThresholdImageFilter.h @@ -96,17 +96,20 @@ class ITK_TEMPLATE_EXPORT KappaSigmaThresholdImageFilter : public ImageToImageFi /** Set the mask value used to select which pixels will be considered in the * threshold computation (optional, only in case a MaskImage is set). */ + /** @ITKStartGrouping */ itkSetMacro(MaskValue, MaskPixelType); itkGetConstMacro(MaskValue, MaskPixelType); - + /** @ITKEndGrouping */ /** Set the Sigma multiplier (Kappa) to adjust the pixel rejection rate. */ + /** @ITKStartGrouping */ itkSetMacro(SigmaFactor, double); itkGetConstMacro(SigmaFactor, double); - + /** @ITKEndGrouping */ /** Set the number of rejection passes. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfIterations, unsigned int); itkGetConstMacro(NumberOfIterations, unsigned int); - + /** @ITKEndGrouping */ itkConceptMacro(OutputComparableCheck, (Concept::Comparable)); itkConceptMacro(OutputOStreamWritableCheck, (Concept::OStreamWritable)); diff --git a/Modules/Filtering/Thresholding/include/itkOtsuMultipleThresholdsCalculator.h b/Modules/Filtering/Thresholding/include/itkOtsuMultipleThresholdsCalculator.h index 9c9e4be7a1a..633c0e03fc0 100644 --- a/Modules/Filtering/Thresholding/include/itkOtsuMultipleThresholdsCalculator.h +++ b/Modules/Filtering/Thresholding/include/itkOtsuMultipleThresholdsCalculator.h @@ -70,10 +70,11 @@ class ITK_TEMPLATE_EXPORT OtsuMultipleThresholdsCalculator : public HistogramAlg using InstanceIdentifierType = typename TInputHistogram::InstanceIdentifier; using InstanceIdentifierVectorType = std::vector; - /**Standard Macros */ + /** Standard Macros */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(OtsuMultipleThresholdsCalculator); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Typedef for the thresholds output */ using OutputType = std::vector; @@ -82,24 +83,27 @@ class ITK_TEMPLATE_EXPORT OtsuMultipleThresholdsCalculator : public HistogramAlg GetOutput(); /** Set/Get the number of thresholds. */ + /** @ITKStartGrouping */ itkSetClampMacro(NumberOfThresholds, SizeValueType, 1, NumericTraits::max()); itkGetConstMacro(NumberOfThresholds, SizeValueType); - + /** @ITKEndGrouping */ /** Calculates Otsu's thresholds and saves them. */ void Compute() override; /** Set/Get the use of valley emphasis. Default is false. */ + /** @ITKStartGrouping */ itkSetMacro(ValleyEmphasis, bool); itkGetConstReferenceMacro(ValleyEmphasis, bool); itkBooleanMacro(ValleyEmphasis); - + /** @ITKEndGrouping */ /** Should the threshold value be mid-point of the bin or the maximum? * Default is to return bin maximum. */ + /** @ITKStartGrouping */ itkSetMacro(ReturnBinMidpoint, bool); itkGetConstReferenceMacro(ReturnBinMidpoint, bool); itkBooleanMacro(ReturnBinMidpoint); - + /** @ITKEndGrouping */ protected: OtsuMultipleThresholdsCalculator(); diff --git a/Modules/Filtering/Thresholding/include/itkOtsuMultipleThresholdsImageFilter.h b/Modules/Filtering/Thresholding/include/itkOtsuMultipleThresholdsImageFilter.h index 535086492c5..2afac7bd095 100644 --- a/Modules/Filtering/Thresholding/include/itkOtsuMultipleThresholdsImageFilter.h +++ b/Modules/Filtering/Thresholding/include/itkOtsuMultipleThresholdsImageFilter.h @@ -101,28 +101,33 @@ class ITK_TEMPLATE_EXPORT OtsuMultipleThresholdsImageFilter : public ImageToImag static constexpr unsigned int OutputImageDimension = TOutputImage::ImageDimension; /** Set/Get the number of histogram bins. Default is 128. */ + /** @ITKStartGrouping */ itkSetClampMacro(NumberOfHistogramBins, SizeValueType, 1, NumericTraits::max()); itkGetConstMacro(NumberOfHistogramBins, SizeValueType); - + /** @ITKEndGrouping */ /** Set/Get the number of thresholds. Default is 1. */ + /** @ITKStartGrouping */ itkSetClampMacro(NumberOfThresholds, SizeValueType, 1, NumericTraits::max()); itkGetConstMacro(NumberOfThresholds, SizeValueType); - + /** @ITKEndGrouping */ /** Set/Get the offset which labels have to start from. Default is 0. */ + /** @ITKStartGrouping */ itkSetClampMacro(LabelOffset, OutputPixelType, OutputPixelType{}, NumericTraits::max()); itkGetConstMacro(LabelOffset, OutputPixelType); - + /** @ITKEndGrouping */ /** Set/Get the use of valley emphasis. Default is false. */ + /** @ITKStartGrouping */ itkSetMacro(ValleyEmphasis, bool); itkGetConstReferenceMacro(ValleyEmphasis, bool); itkBooleanMacro(ValleyEmphasis); - + /** @ITKEndGrouping */ /** Should the threshold value be mid-point of the bin or the maximum? * Default is to return bin maximum. */ + /** @ITKStartGrouping */ itkSetMacro(ReturnBinMidpoint, bool); itkGetConstReferenceMacro(ReturnBinMidpoint, bool); itkBooleanMacro(ReturnBinMidpoint); - + /** @ITKEndGrouping */ /** Get the computed threshold. */ const ThresholdVectorType & GetThresholds() const diff --git a/Modules/Filtering/Thresholding/include/itkOtsuThresholdCalculator.h b/Modules/Filtering/Thresholding/include/itkOtsuThresholdCalculator.h index d5cb94e6609..65f658987c0 100644 --- a/Modules/Filtering/Thresholding/include/itkOtsuThresholdCalculator.h +++ b/Modules/Filtering/Thresholding/include/itkOtsuThresholdCalculator.h @@ -65,10 +65,11 @@ class ITK_TEMPLATE_EXPORT OtsuThresholdCalculator : public HistogramThresholdCal /** Should the threshold value be mid-point of the bin or the maximum? * Default is to return bin maximum. */ + /** @ITKStartGrouping */ itkSetMacro(ReturnBinMidpoint, bool); itkGetConstReferenceMacro(ReturnBinMidpoint, bool); itkBooleanMacro(ReturnBinMidpoint); - + /** @ITKEndGrouping */ /** for backward compatibility. Update() should be preferred. */ void Compute() diff --git a/Modules/Filtering/Thresholding/include/itkOtsuThresholdImageFilter.h b/Modules/Filtering/Thresholding/include/itkOtsuThresholdImageFilter.h index dd68d830f3f..362c3432205 100644 --- a/Modules/Filtering/Thresholding/include/itkOtsuThresholdImageFilter.h +++ b/Modules/Filtering/Thresholding/include/itkOtsuThresholdImageFilter.h @@ -102,10 +102,11 @@ class ITK_TEMPLATE_EXPORT OtsuThresholdImageFilter /** Should the threshold value be mid-point of the bin or the maximum? * Default is to return bin maximum. */ + /** @ITKStartGrouping */ itkSetMacro(ReturnBinMidpoint, bool); itkGetConstReferenceMacro(ReturnBinMidpoint, bool); itkBooleanMacro(ReturnBinMidpoint); - + /** @ITKEndGrouping */ protected: OtsuThresholdImageFilter() { this->SetCalculator(CalculatorType::New()); } ~OtsuThresholdImageFilter() override = default; diff --git a/Modules/Filtering/Thresholding/include/itkThresholdImageFilter.h b/Modules/Filtering/Thresholding/include/itkThresholdImageFilter.h index 83368ca0936..fa9e6196e85 100644 --- a/Modules/Filtering/Thresholding/include/itkThresholdImageFilter.h +++ b/Modules/Filtering/Thresholding/include/itkThresholdImageFilter.h @@ -89,9 +89,10 @@ class ITK_TEMPLATE_EXPORT ThresholdImageFilter : public InPlaceImageFilter)); itkConceptMacro(PixelTypeOStreamWritableCheck, (Concept::OStreamWritable)); - + /** @ITKEndGrouping */ /** Set the "outside" pixel value. The default value * PixelType{}. */ itkSetMacro(OutsideValue, PixelType); @@ -112,13 +113,15 @@ class ITK_TEMPLATE_EXPORT ThresholdImageFilter : public InPlaceImageFilter; /** The input and output pixel types must support comparison operators. */ + /** @ITKStartGrouping */ itkConceptMacro(PixelTypeComparable, (Concept::Comparable)); itkConceptMacro(OutputPixelTypeComparable, (Concept::Comparable)); itkConceptMacro(OutputPixelTypeOStreamWritable, (Concept::OStreamWritable)); - + /** @ITKEndGrouping */ /** Set the vector of thresholds. */ void SetThresholds(const ThresholdVector & thresholds) @@ -193,9 +194,10 @@ class ITK_TEMPLATE_EXPORT ThresholdLabelerImageFilter } /** Set the offset which labels have to start from. */ + /** @ITKStartGrouping */ itkSetClampMacro(LabelOffset, OutputPixelType, OutputPixelType{}, NumericTraits::max()); itkGetConstMacro(LabelOffset, OutputPixelType); - + /** @ITKEndGrouping */ protected: ThresholdLabelerImageFilter(); ~ThresholdLabelerImageFilter() override = default; diff --git a/Modules/IO/CSV/include/itkCSVArray2DDataObject.h b/Modules/IO/CSV/include/itkCSVArray2DDataObject.h index 9caa7ac6b1e..76c6eab8ee7 100644 --- a/Modules/IO/CSV/include/itkCSVArray2DDataObject.h +++ b/Modules/IO/CSV/include/itkCSVArray2DDataObject.h @@ -69,15 +69,17 @@ class ITK_TEMPLATE_EXPORT CSVArray2DDataObject : public DataObject using MatrixType = typename itk::Array2D; /** Set macros */ + /** @ITKStartGrouping */ itkSetMacro(HasColumnHeaders, bool); itkSetMacro(HasRowHeaders, bool); itkBooleanMacro(HasColumnHeaders); itkBooleanMacro(HasRowHeaders); - + /** @ITKEndGrouping */ /** Get macros for Column and Row headers. */ + /** @ITKStartGrouping */ itkGetConstMacro(HasColumnHeaders, bool); itkGetConstMacro(HasRowHeaders, bool); - + /** @ITKEndGrouping */ /** Get macro for the matrix. */ itkGetMacro(Matrix, MatrixType); diff --git a/Modules/IO/CSV/include/itkCSVFileReaderBase.h b/Modules/IO/CSV/include/itkCSVFileReaderBase.h index 69dfd93aed9..2634c33f1e2 100644 --- a/Modules/IO/CSV/include/itkCSVFileReaderBase.h +++ b/Modules/IO/CSV/include/itkCSVFileReaderBase.h @@ -117,10 +117,11 @@ class ITKIOCSV_EXPORT CSVFileReaderBase : public LightProcessObject /** Boolean macros for setting HasRowHeaders, HasColumnHeaders and * UseStringDelimiterCharacter. They can conveniently be set by appending * On() or Off() to each of the variable names. */ + /** @ITKStartGrouping */ itkBooleanMacro(HasRowHeaders); itkBooleanMacro(HasColumnHeaders); itkBooleanMacro(UseStringDelimiterCharacter); - + /** @ITKEndGrouping */ /** Counts the number of rows and columns in a file and prepares the file * for iterative reading using the GetNextField() method. */ void diff --git a/Modules/IO/GDCM/include/itkGDCMImageIO.h b/Modules/IO/GDCM/include/itkGDCMImageIO.h index 66784e95017..5a5403b3dce 100644 --- a/Modules/IO/GDCM/include/itkGDCMImageIO.h +++ b/Modules/IO/GDCM/include/itkGDCMImageIO.h @@ -135,9 +135,10 @@ class ITKIOGDCM_EXPORT GDCMImageIO : public ImageIOBase /** Set/Get the original component type of the image. This differs from * ComponentType which may change as a function of rescale slope and * intercept. */ + /** @ITKStartGrouping */ itkGetEnumMacro(InternalComponentType, itk::CommonEnums::IOComponent); itkSetEnumMacro(InternalComponentType, itk::CommonEnums::IOComponent); - + /** @ITKEndGrouping */ /*-------- This part of the interfaces deals with writing data. ----- */ /** Determine the file type. Returns true if this ImageIO can write the @@ -156,37 +157,43 @@ class ITKIOGDCM_EXPORT GDCMImageIO : public ImageIOBase Write(const void * buffer) override; /** Macro to access Rescale Slope and Rescale Intercept. */ + /** @ITKStartGrouping */ itkGetConstMacro(RescaleSlope, double); itkGetConstMacro(RescaleIntercept, double); - + /** @ITKEndGrouping */ /** Macro to access the DICOM UID prefix. By default this is the ITK * root id. This default can be overridden if the exam is for example * part of an existing study. */ + /** @ITKStartGrouping */ itkGetStringMacro(UIDPrefix); itkSetStringMacro(UIDPrefix); - + /** @ITKEndGrouping */ /** Access the generated DICOM UIDs. */ + /** @ITKStartGrouping */ itkGetStringMacro(StudyInstanceUID); itkGetStringMacro(SeriesInstanceUID); itkGetStringMacro(FrameOfReferenceInstanceUID); - + /** @ITKEndGrouping */ /** Preserve the original DICOM UIDs of the input files. */ + /** @ITKStartGrouping */ itkSetMacro(KeepOriginalUID, bool); itkGetConstMacro(KeepOriginalUID, bool); itkBooleanMacro(KeepOriginalUID); - + /** @ITKEndGrouping */ /** Parse and load any private tags in the DICOM file. Loading DICOM * files is faster when private tags are not needed. Default is false. */ + /** @ITKStartGrouping */ itkSetMacro(LoadPrivateTags, bool); itkGetConstMacro(LoadPrivateTags, bool); itkBooleanMacro(LoadPrivateTags); - + /** @ITKEndGrouping */ /** Convert Y'CbCr (YBR_FULL, YBR_FULL_422) to RGB. Default is true, * not required for YBR_RCT and YBR_ICT. */ + /** @ITKStartGrouping */ itkSetMacro(ReadYBRtoRGB, bool); itkGetConstMacro(ReadYBRtoRGB, bool); itkBooleanMacro(ReadYBRtoRGB); - + /** @ITKEndGrouping */ /** More general method to retrieve an arbitrary DICOM value based * on a DICOM Tag (eg "0123|45ef"). */ bool @@ -223,6 +230,14 @@ class ITKIOGDCM_EXPORT GDCMImageIO : public ImageIOBase * @param _arg */ itkSetEnumMacro(CompressionType, CompressionEnum); + /** Get the compression type to use for writing. + * + * Currently only JPEG2000 and JPEG are supported. + * These map to the following DICOM standards: + * JPEG2000: JPEG 2000 Image Compression (Lossless Only) + * JPEG: JPEG Lossless, Non-Hierarchical, First-Order Prediction + * + */ itkGetEnumMacro(CompressionType, CompressionEnum); void diff --git a/Modules/IO/GDCM/include/itkGDCMSeriesFileNames.h b/Modules/IO/GDCM/include/itkGDCMSeriesFileNames.h index f4d13e08866..b646a365d8a 100644 --- a/Modules/IO/GDCM/include/itkGDCMSeriesFileNames.h +++ b/Modules/IO/GDCM/include/itkGDCMSeriesFileNames.h @@ -55,6 +55,7 @@ namespace itk * * \ingroup ITKIOGDCM */ + /** \todo: remove these from the itk:: namespace */ using FilenamesContainer = std::vector; using SerieUIDContainer = std::vector; @@ -139,9 +140,11 @@ class ITKIOGDCM_EXPORT GDCMSeriesFileNames : public ProcessObject /** Recursively parse the input directory. * Must be set before the call to SetInputDirectory(). */ + /** @ITKStartGrouping */ itkSetMacro(Recursive, bool); itkGetConstMacro(Recursive, bool); itkBooleanMacro(Recursive); + /** @ITKEndGrouping */ /** Use additional series information such as ProtocolName * and SeriesName to identify when a single SeriesUID contains @@ -173,18 +176,21 @@ class ITKIOGDCM_EXPORT GDCMSeriesFileNames : public ProcessObject * to skip sequences. This makes loading DICOM files faster when * sequences are not needed. */ + /** @ITKStartGrouping */ itkSetMacro(LoadSequences, bool); itkGetConstMacro(LoadSequences, bool); itkBooleanMacro(LoadSequences); + /** @ITKEndGrouping */ /** Parse any private tags in the DICOM file. Defaults to false * to skip private tags. This makes loading DICOM files faster when * private tags are not needed. */ + /** @ITKStartGrouping */ itkSetMacro(LoadPrivateTags, bool); itkGetConstMacro(LoadPrivateTags, bool); itkBooleanMacro(LoadPrivateTags); - + /** @ITKEndGrouping */ protected: GDCMSeriesFileNames(); ~GDCMSeriesFileNames() override; diff --git a/Modules/IO/ImageBase/include/itkImageFileReader.h b/Modules/IO/ImageBase/include/itkImageFileReader.h index 5c7d4db5277..71568877083 100644 --- a/Modules/IO/ImageBase/include/itkImageFileReader.h +++ b/Modules/IO/ImageBase/include/itkImageFileReader.h @@ -109,15 +109,18 @@ class ITK_TEMPLATE_EXPORT ImageFileReader : public ImageSource * instance that is created. Or you can directly specify the ImageIO * to use to read a particular file in case the factory mechanism will * not work properly (e.g., unknown or unusual extension). */ + /** @ITKStartGrouping */ void SetImageIO(ImageIOBase * imageIO); itkGetModifiableObjectMacro(ImageIO, ImageIOBase); + /** @ITKEndGrouping */ /** Set the stream On or Off */ + /** @ITKStartGrouping */ itkSetMacro(UseStreaming, bool); itkGetConstReferenceMacro(UseStreaming, bool); itkBooleanMacro(UseStreaming); - + /** @ITKEndGrouping */ protected: ImageFileReader(); ~ImageFileReader() override = default; @@ -189,7 +192,6 @@ ReadImage(const std::string & filename) return reader->GetOutput(); } - } // namespace itk #ifndef ITK_MANUAL_INSTANTIATION diff --git a/Modules/IO/ImageBase/include/itkImageFileWriter.h b/Modules/IO/ImageBase/include/itkImageFileWriter.h index 5e9ff41a680..7a179612cc3 100644 --- a/Modules/IO/ImageBase/include/itkImageFileWriter.h +++ b/Modules/IO/ImageBase/include/itkImageFileWriter.h @@ -113,9 +113,10 @@ class ITK_TEMPLATE_EXPORT ImageFileWriter : public ProcessObject GetInput(unsigned int idx); /** Specify the name of the output file to write. */ + /** @ITKStartGrouping */ itkSetStringMacro(FileName); itkGetStringMacro(FileName); - + /** @ITKEndGrouping */ /** Set/Get the ImageIO helper class. Usually this is created via the object * factory mechanism that determines whether a particular ImageIO can * write a certain file. This method provides a way to get the ImageIO @@ -126,6 +127,7 @@ class ITK_TEMPLATE_EXPORT ImageFileWriter : public ProcessObject * correct choice and will allow a file to be created regardless of * the file extension. If the factory has set the ImageIO, the * extension must be supported by the specified ImageIO. */ + /** @ITKStartGrouping */ void SetImageIO(ImageIOBase * io) { @@ -137,7 +139,7 @@ class ITK_TEMPLATE_EXPORT ImageFileWriter : public ProcessObject m_FactorySpecifiedImageIO = false; } itkGetModifiableObjectMacro(ImageIO, ImageIOBase); - + /** @ITKEndGrouping */ /** A special version of the Update() method for writers. It * invokes start and end events and handles releasing data. It * eventually calls GenerateData() which does the actual writing. @@ -161,9 +163,10 @@ class ITK_TEMPLATE_EXPORT ImageFileWriter : public ProcessObject /** Set/Get the number of pieces to divide the input. The upstream pipeline * will try to be executed this many times. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfStreamDivisions, unsigned int); itkGetConstReferenceMacro(NumberOfStreamDivisions, unsigned int); - + /** @ITKEndGrouping */ /** Aliased to the Write() method to be consistent with the rest of the * pipeline. */ void @@ -186,25 +189,28 @@ class ITK_TEMPLATE_EXPORT ImageFileWriter : public ProcessObject } /** Set the compression On or Off */ + /** @ITKStartGrouping */ itkSetMacro(UseCompression, bool); itkGetConstReferenceMacro(UseCompression, bool); itkBooleanMacro(UseCompression); - + /** @ITKEndGrouping */ /** Set the compression level. \sa ImageIOBase for details. * Set to a negative number to use ImageIO's default compression level. */ + /** @ITKStartGrouping */ itkSetMacro(CompressionLevel, int); itkGetConstReferenceMacro(CompressionLevel, int); - + /** @ITKEndGrouping */ /** By default the MetaDataDictionary is taken from the input image and * passed to the ImageIO. In some cases, however, a user may prefer to * introduce her/his own MetaDataDictionary. This is often the case of * the ImageSeriesWriter. This flag defined whether the MetaDataDictionary * to use will be the one from the input image or the one already set in * the ImageIO object. */ + /** @ITKStartGrouping */ itkSetMacro(UseInputMetaDataDictionary, bool); itkGetConstReferenceMacro(UseInputMetaDataDictionary, bool); itkBooleanMacro(UseInputMetaDataDictionary); - + /** @ITKEndGrouping */ protected: ImageFileWriter() = default; ~ImageFileWriter() override = default; diff --git a/Modules/IO/ImageBase/include/itkImageIOBase.h b/Modules/IO/ImageBase/include/itkImageIOBase.h index ae0158f78c6..95a2ad34dc3 100644 --- a/Modules/IO/ImageBase/include/itkImageIOBase.h +++ b/Modules/IO/ImageBase/include/itkImageIOBase.h @@ -89,8 +89,10 @@ class ITKIOImageBase_EXPORT ImageIOBase : public LightProcessObject itkOverrideGetNameOfClassMacro(ImageIOBase); /** Set/Get the name of the file to be read. */ + /** @ITKStartGrouping */ itkSetStringMacro(FileName); itkGetStringMacro(FileName); + /** @ITKEndGrouping */ /** Types for managing image size and image index components. */ using IndexValueType = itk::IndexValueType; @@ -169,14 +171,16 @@ class ITKIOImageBase_EXPORT ImageIOBase : public LightProcessObject /** Set/Get the image dimensions in the x, y, z, etc. directions. * GetDimensions() is typically used after reading the data; the * SetDimensions() is used prior to writing the data. */ + /** @ITKStartGrouping */ virtual void SetDimensions(unsigned int i, SizeValueType dim); - virtual SizeValueType + GetDimensions(unsigned int i) const { return m_Dimensions[i]; } + /** @ITKEndGrouping */ /** Set/Get the image origin on a axis-by-axis basis. The SetOrigin() method * is required when writing the image. */ @@ -225,21 +229,26 @@ class ITKIOImageBase_EXPORT ImageIOBase : public LightProcessObject * vectors define the start (lower-left corner) and length of the * region within the image. Make sure that the IORegion lies within * the image. */ + /** @ITKStartGrouping */ itkSetMacro(IORegion, ImageIORegion); itkGetConstReferenceMacro(IORegion, ImageIORegion); + /** @ITKEndGrouping */ /** Set/Get the type of the pixel. The PixelTypes provides context * to the IO mechanisms for data conversions. PixelTypes can be * SCALAR, RGB, RGBA, VECTOR, COVARIANTVECTOR, POINT, INDEX. If * the PIXELTYPE is SCALAR, then the NumberOfComponents should be 1. * Any other of PIXELTYPE will have more than one component. */ + /** @ITKStartGrouping */ itkSetEnumMacro(PixelType, itk::CommonEnums::IOPixel); itkGetEnumMacro(PixelType, itk::CommonEnums::IOPixel); + /** @ITKEndGrouping */ /** Set/Get the component type of the image. This is always a native * type. */ itkSetEnumMacro(ComponentType, IOComponentEnum); itkGetEnumMacro(ComponentType, IOComponentEnum); + /** get the type_info for the current pixel component type. * This function is DEPRECATED and only provided for backwards * compatibility. There is no use for this method that can't @@ -252,13 +261,17 @@ class ITKIOImageBase_EXPORT ImageIOBase : public LightProcessObject * be set by the reading process. For SCALAR pixel types, * NumberOfComponents will be 1. For other pixel types, * NumberOfComponents will be greater than or equal to one. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfComponents, unsigned int); itkGetConstReferenceMacro(NumberOfComponents, unsigned int); + /** @ITKEndGrouping */ /** Set/Get a boolean to use the compression or not. */ + /** @ITKStartGrouping */ itkSetMacro(UseCompression, bool); itkGetConstMacro(UseCompression, bool); itkBooleanMacro(UseCompression); + /** @ITKEndGrouping */ /** \brief Set/Get a compression level hint * @@ -284,28 +297,36 @@ class ITKIOImageBase_EXPORT ImageIOBase : public LightProcessObject itkGetConstReferenceMacro(Compressor, std::string); /** Set/Get a boolean to use streaming while reading or not. */ + /** @ITKStartGrouping */ itkSetMacro(UseStreamedReading, bool); itkGetConstMacro(UseStreamedReading, bool); itkBooleanMacro(UseStreamedReading); + /** @ITKEndGrouping */ /** Set/Get a boolean to use streaming while writing or not. */ + /** @ITKStartGrouping */ itkSetMacro(UseStreamedWriting, bool); itkGetConstMacro(UseStreamedWriting, bool); itkBooleanMacro(UseStreamedWriting); + /** @ITKEndGrouping */ /** Set/Get a boolean to perform RGB palette expansion. * If true, palette image is read as RGB, * if false, palette image is read as Scalar+Palette. * A RGB image is always read as RGB.*/ + /** @ITKStartGrouping */ itkSetMacro(ExpandRGBPalette, bool); itkGetConstMacro(ExpandRGBPalette, bool); itkBooleanMacro(ExpandRGBPalette); + /** @ITKEndGrouping */ /** Set/Get a boolean to include a color palette while writing * the image file. Applies only for scalar Pixels*/ + /** @ITKStartGrouping */ itkSetMacro(WritePalette, bool); itkGetConstMacro(WritePalette, bool); itkBooleanMacro(WritePalette); + /** @ITKEndGrouping */ /** Determine whether a palletized image file has been read as a scalar image * plus a color palette. @@ -331,6 +352,7 @@ class ITKIOImageBase_EXPORT ImageIOBase : public LightProcessObject /** These methods control whether the file is written binary or ASCII. * Many file formats (i.e., subclasses) ignore this flag. */ + /** @ITKStartGrouping */ itkSetEnumMacro(FileType, IOFileEnum); itkGetEnumMacro(FileType, IOFileEnum); void @@ -338,6 +360,7 @@ class ITKIOImageBase_EXPORT ImageIOBase : public LightProcessObject { this->SetFileType(IOFileEnum::ASCII); } + /** @ITKEndGrouping */ void SetFileTypeToBinary() @@ -356,6 +379,7 @@ class ITKIOImageBase_EXPORT ImageIOBase : public LightProcessObject * a VAX or PC, SetByteOrderToLittleEndian() otherwise * SetByteOrderToBigEndian(). Some ImageIOBase subclasses * ignore these methods. */ + /** @ITKStartGrouping */ itkSetEnumMacro(ByteOrder, IOByteOrderEnum); itkGetEnumMacro(ByteOrder, IOByteOrderEnum); void @@ -363,6 +387,7 @@ class ITKIOImageBase_EXPORT ImageIOBase : public LightProcessObject { this->SetByteOrder(IOByteOrderEnum::BigEndian); } + /** @ITKEndGrouping */ void SetByteOrderToLittleEndian() @@ -550,6 +575,7 @@ class ITKIOImageBase_EXPORT ImageIOBase : public LightProcessObject SetTypeInfo(const TPixel *); /** Map between C++ Pixel type and ImageIOBase ComponentType */ + /** @ITKStartGrouping */ template struct MapPixelType { @@ -675,7 +701,7 @@ class ITKIOImageBase_EXPORT ImageIOBase : public LightProcessObject this->SetPixelType(IOPixelEnum::VARIABLESIZEMATRIX); this->SetComponentType(MapPixelType::CType); } - + /** @ITKEndGrouping */ protected: ImageIOBase(); @@ -690,10 +716,12 @@ class ITKIOImageBase_EXPORT ImageIOBase : public LightProcessObject * extension list. If ignoreCase is true, the case of the characters * is ignored. */ + /** @ITKStartGrouping */ virtual bool HasSupportedReadExtension(const char * fileName, bool ignoreCase = true); virtual bool HasSupportedWriteExtension(const char * fileName, bool ignoreCase = true); + /** @ITKEndGrouping */ /** Used internally to keep track of the type of the pixel. */ IOPixelEnum m_PixelType{ IOPixelEnum::SCALAR }; @@ -729,9 +757,11 @@ class ITKIOImageBase_EXPORT ImageIOBase : public LightProcessObject std::string m_Compressor{ "uninitialized" }; /** Set/Get enforced maximum compression level value to limit range */ + /** @ITKStartGrouping */ virtual void SetMaximumCompressionLevel(int); itkGetConstMacro(MaximumCompressionLevel, int); + /** @ITKEndGrouping */ /** Called when the compressor changes value. The compressor string * is converted to uppercase for case insensitive comparisons. diff --git a/Modules/IO/ImageBase/include/itkImageSeriesReader.h b/Modules/IO/ImageBase/include/itkImageSeriesReader.h index a4db232965b..56a3fa174e7 100644 --- a/Modules/IO/ImageBase/include/itkImageSeriesReader.h +++ b/Modules/IO/ImageBase/include/itkImageSeriesReader.h @@ -78,8 +78,9 @@ class ITK_TEMPLATE_EXPORT ImageSeriesReader : public ImageSource using FileNamesContainer = std::vector; - /** Set the vector of strings that contains the file names. Files + /** Set/Get the vector of strings that contains the file names. Files * are processed in sequential order. */ + /** @ITKStartGrouping */ void SetFileNames(const FileNamesContainer & name) { @@ -95,6 +96,7 @@ class ITK_TEMPLATE_EXPORT ImageSeriesReader : public ImageSource { return m_FileNames; } + /** @ITKEndGrouping */ /** Set the first file name to be processed. This deletes previous * filenames. */ @@ -116,22 +118,28 @@ class ITK_TEMPLATE_EXPORT ImageSeriesReader : public ImageSource /** ReverseOrderOn changes the order of traversal of the file names * from last to first */ + /** @ITKStartGrouping */ itkSetMacro(ReverseOrder, bool); itkGetConstMacro(ReverseOrder, bool); itkBooleanMacro(ReverseOrder); + /** @ITKEndGrouping */ /** Do we want to force orthogonal direction cosines? On by default. * Turning it off enables proper reading of DICOM series with gantry tilt. */ + /** @ITKStartGrouping */ itkSetMacro(ForceOrthogonalDirection, bool); itkGetConstMacro(ForceOrthogonalDirection, bool); itkBooleanMacro(ForceOrthogonalDirection); + /** @ITKEndGrouping */ /** Set/Get the ImageIO helper class. By default, the * ImageSeriesReader uses the factory mechanism of the * ImageFileReader to determine the file type. This method can be * used to specify which IO to use. */ + /** @ITKStartGrouping */ itkSetObjectMacro(ImageIO, ImageIOBase); itkGetModifiableObjectMacro(ImageIO, ImageIOBase); + /** @ITKEndGrouping */ /** \brief Set/Get MetaDataDictionaryArrayUpdate enables the updating of * the MetaDataDictionaryArray. @@ -165,14 +173,17 @@ class ITK_TEMPLATE_EXPORT ImageSeriesReader : public ImageSource GetMetaDataDictionaryArray() const; /** Set the stream On or Off */ + /** @ITKStartGrouping */ itkSetMacro(UseStreaming, bool); itkGetConstReferenceMacro(UseStreaming, bool); itkBooleanMacro(UseStreaming); + /** @ITKEndGrouping */ /** Set the relative threshold for issuing warnings about non-uniform sampling */ + /** @ITKStartGrouping */ itkSetMacro(SpacingWarningRelThreshold, double); itkGetConstMacro(SpacingWarningRelThreshold, double); - + /** @ITKEndGrouping */ protected: ImageSeriesReader() : m_ImageIO(nullptr) diff --git a/Modules/IO/ImageBase/include/itkImageSeriesWriter.h b/Modules/IO/ImageBase/include/itkImageSeriesWriter.h index ad3901ecd5b..876d92cde21 100644 --- a/Modules/IO/ImageBase/include/itkImageSeriesWriter.h +++ b/Modules/IO/ImageBase/include/itkImageSeriesWriter.h @@ -120,8 +120,10 @@ class ITK_TEMPLATE_EXPORT ImageSeriesWriter : public ProcessObject * get the ImageIO instance that is created, or to manually set one * when the factory mechanism may not work (e.g., for raw files or * for non-standard file suffix). */ + /** @ITKStartGrouping */ itkSetObjectMacro(ImageIO, ImageIOBase); itkGetModifiableObjectMacro(ImageIO, ImageIOBase); + /** @ITKEndGrouping */ /** A special version of the Update() method for writers. It * invokes start and end events and handles releasing data. It @@ -140,23 +142,30 @@ class ITK_TEMPLATE_EXPORT ImageSeriesWriter : public ProcessObject /** Use this method to set the starting index of the series. * The default value is 1. */ + /** @ITKStartGrouping */ itkSetMacro(StartIndex, SizeValueType); itkGetConstMacro(StartIndex, SizeValueType); + /** @ITKEndGrouping */ /** Set the increment of the index of the series. The * default value is 1. */ + /** @ITKStartGrouping */ itkSetMacro(IncrementIndex, SizeValueType); itkGetConstMacro(IncrementIndex, SizeValueType); + /** @ITKEndGrouping */ /** The format string used to generate each filename in the * series. The filename is built with snprintf(filename, length, SeriesFormat, * number) where number starts at StartIndex and is incremented by * IncrementIndex. */ + /** @ITKStartGrouping */ itkSetStringMacro(SeriesFormat); itkGetStringMacro(SeriesFormat); + /** @ITKEndGrouping */ /** Set/Get the vector of strings that contains the file names. Files * are processed in sequential order. */ + /** @ITKStartGrouping */ void SetFileNames(const FileNamesContainer & name) { @@ -172,6 +181,7 @@ class ITK_TEMPLATE_EXPORT ImageSeriesWriter : public ProcessObject { return m_FileNames; } + /** @ITKEndGrouping */ /** Set the first file name to be processed. This deletes previous * filenames. */ @@ -197,10 +207,11 @@ class ITK_TEMPLATE_EXPORT ImageSeriesWriter : public ProcessObject itkSetMacro(MetaDataDictionaryArray, DictionaryArrayRawPointer); /** Set the compression On or Off */ + /** @ITKStartGrouping */ itkSetMacro(UseCompression, bool); itkGetConstReferenceMacro(UseCompression, bool); itkBooleanMacro(UseCompression); - + /** @ITKEndGrouping */ protected: ImageSeriesWriter(); ~ImageSeriesWriter() override = default; diff --git a/Modules/IO/ImageBase/include/itkNumericSeriesFileNames.h b/Modules/IO/ImageBase/include/itkNumericSeriesFileNames.h index c1da226fe8e..38688b38e43 100644 --- a/Modules/IO/ImageBase/include/itkNumericSeriesFileNames.h +++ b/Modules/IO/ImageBase/include/itkNumericSeriesFileNames.h @@ -71,26 +71,30 @@ class ITKIOImageBase_EXPORT NumericSeriesFileNames : public Object /** Use this method to set the starting index of the numeric series. * The default value is 1. */ + /** @ITKStartGrouping */ itkSetMacro(StartIndex, SizeValueType); itkGetConstMacro(StartIndex, SizeValueType); - + /** @ITKEndGrouping */ /** Set the end index of the numeric series. The default is 1. */ + /** @ITKStartGrouping */ itkSetMacro(EndIndex, SizeValueType); itkGetConstMacro(EndIndex, SizeValueType); - + /** @ITKEndGrouping */ /** Set the increment of the index of the numeric series. The * default value is 1. */ + /** @ITKStartGrouping */ itkSetMacro(IncrementIndex, SizeValueType); itkGetConstMacro(IncrementIndex, SizeValueType); - + /** @ITKEndGrouping */ /** The format string used to generate the series. Different subclasses * require different characteristics of this string. For example, the * subclass NumericSeriesFileNames requires a "%d" or some integral * format specified to be embedded in the string. Default is "%d". */ + /** @ITKStartGrouping */ itkSetStringMacro(SeriesFormat); itkGetStringMacro(SeriesFormat); - + /** @ITKEndGrouping */ /** Returns a vector containing the series' file names. The file * names are ordered by Index. */ const std::vector & diff --git a/Modules/IO/ImageBase/include/itkRegularExpressionSeriesFileNames.h b/Modules/IO/ImageBase/include/itkRegularExpressionSeriesFileNames.h index 25682b67b03..cbe819e0238 100644 --- a/Modules/IO/ImageBase/include/itkRegularExpressionSeriesFileNames.h +++ b/Modules/IO/ImageBase/include/itkRegularExpressionSeriesFileNames.h @@ -86,25 +86,29 @@ class ITKIOImageBase_EXPORT RegularExpressionSeriesFileNames : public Object /* -------- Define the API for RegularExpressionSeriesFileNames ---------- */ /** The directory containing the files. */ + /** @ITKStartGrouping */ itkSetStringMacro(Directory); itkGetStringMacro(Directory); - + /** @ITKEndGrouping */ /** The RegularExpression. Refer to the description for valid expressions */ + /** @ITKStartGrouping */ itkSetStringMacro(RegularExpression); itkGetStringMacro(RegularExpression); - + /** @ITKEndGrouping */ /** The index of the submatch that will be used to sort the * matches. */ + /** @ITKStartGrouping */ itkSetMacro(SubMatch, unsigned int); itkGetConstMacro(SubMatch, unsigned int); - + /** @ITKEndGrouping */ /** NumericSortOn changes the sort of the submatch field to a * numeric sort. NumericSortOff is the default, and sorts the * submatch alphabetically. */ + /** @ITKStartGrouping */ itkSetMacro(NumericSort, bool); itkGetConstMacro(NumericSort, bool); itkBooleanMacro(NumericSort); - + /** @ITKEndGrouping */ /** Returns a vector containing the series' file names. The file * names are sorted by the sub expression selected by the SubMatch id. */ const std::vector & diff --git a/Modules/IO/JPEG/include/itkJPEGImageIO.h b/Modules/IO/JPEG/include/itkJPEGImageIO.h index c836e831f40..56bdc48c948 100644 --- a/Modules/IO/JPEG/include/itkJPEGImageIO.h +++ b/Modules/IO/JPEG/include/itkJPEGImageIO.h @@ -53,6 +53,7 @@ class ITKIOJPEG_EXPORT JPEGImageIO : public ImageIOBase itkOverrideGetNameOfClassMacro(JPEGImageIO); /** Set/Get the level of quality for the output images. */ + /** @ITKStartGrouping */ virtual void SetQuality(int _JPEGQuality) { @@ -63,17 +64,19 @@ class ITKIOJPEG_EXPORT JPEGImageIO : public ImageIOBase { return this->GetCompressionLevel(); } - + /** @ITKEndGrouping */ /** */ + /** @ITKStartGrouping */ itkSetMacro(Progressive, bool); itkGetConstMacro(Progressive, bool); itkBooleanMacro(Progressive); - + /** @ITKEndGrouping */ /** Convert to RGB if out_color_space is CMYK, default is true */ + /** @ITKStartGrouping */ itkSetMacro(CMYKtoRGB, bool); itkGetConstMacro(CMYKtoRGB, bool); itkBooleanMacro(CMYKtoRGB); - + /** @ITKEndGrouping */ /*-------- This part of the interface deals with reading data. ------ */ /** Determine the file type. Returns true if this ImageIO can read the diff --git a/Modules/IO/JPEG2000/include/itkJPEG2000ImageIOFactory.h b/Modules/IO/JPEG2000/include/itkJPEG2000ImageIOFactory.h index d1cba6f2261..b1d4c662dd0 100644 --- a/Modules/IO/JPEG2000/include/itkJPEG2000ImageIOFactory.h +++ b/Modules/IO/JPEG2000/include/itkJPEG2000ImageIOFactory.h @@ -60,13 +60,14 @@ class ITKIOJPEG2000_EXPORT JPEG2000ImageIOFactory : public ObjectFactoryBase GetDescription() const override; /** Method for class instantiation. */ + /** @ITKStartGrouping */ itkFactorylessNewMacro(Self); static JPEG2000ImageIOFactory * FactoryNew() { return new JPEG2000ImageIOFactory; } - + /** @ITKEndGrouping */ /** \see LightObject::GetNameOfClass() */ itkOverrideGetNameOfClassMacro(JPEG2000ImageIOFactory); diff --git a/Modules/IO/MINC/include/itkMINCImageIO.h b/Modules/IO/MINC/include/itkMINCImageIO.h index 822b4535567..2dbe8f5f848 100644 --- a/Modules/IO/MINC/include/itkMINCImageIO.h +++ b/Modules/IO/MINC/include/itkMINCImageIO.h @@ -78,6 +78,7 @@ class ITKIOMINC_EXPORT MINCImageIO : public ImageIOBase using Superclass = ImageIOBase; using Pointer = SmartPointer; using MatrixType = Matrix; + /** Method for creation through the object factory. */ itkNewMacro(Self); @@ -124,10 +125,11 @@ class ITKIOMINC_EXPORT MINCImageIO : public ImageIOBase Write(const void * buffer) override; /** Set to automatically convert from PositiveCoordinateOrientation RAS to PositiveCoordinateOrientation LPS*/ + /** @ITKStartGrouping */ itkSetMacro(RAStoLPS, bool); itkGetConstMacro(RAStoLPS, bool); itkBooleanMacro(RAStoLPS); - + /** @ITKEndGrouping */ protected: MINCImageIO(); ~MINCImageIO() override; diff --git a/Modules/IO/MeshBase/include/itkMeshFileReader.h b/Modules/IO/MeshBase/include/itkMeshFileReader.h index 4b26ca7af9d..ccff05ae477 100644 --- a/Modules/IO/MeshBase/include/itkMeshFileReader.h +++ b/Modules/IO/MeshBase/include/itkMeshFileReader.h @@ -126,8 +126,10 @@ class ITK_TEMPLATE_EXPORT MeshFileReader : public MeshSource static constexpr unsigned int OutputPointDimension = OutputMeshType::PointDimension; /** Specify the file to read. This is forwarded to the IO instance. */ + /** @ITKStartGrouping */ itkSetStringMacro(FileName); itkGetStringMacro(FileName); + /** @ITKEndGrouping */ /** Set/Get the MeshIO helper class. Often this is created via the object * factory mechanism that determines whether a particular MeshIO can @@ -135,9 +137,11 @@ class ITK_TEMPLATE_EXPORT MeshFileReader : public MeshSource * instance that is created. Or you can directly specify the MeshIO * to use to read a particular file in case the factory mechanism will * not work properly (e.g., unknown or unusual extension). */ + /** @ITKStartGrouping */ void SetMeshIO(MeshIOBase * meshIO); itkGetModifiableObjectMacro(MeshIO, MeshIOBase); + /** @ITKEndGrouping */ /** Prepare the allocation of the output mesh during the first back * propagation of the pipeline. */ @@ -223,7 +227,6 @@ ReadMesh(const std::string & filename) reader->Update(); return reader->GetOutput(); } - } // end namespace itk #ifndef ITK_MANUAL_INSTANTIATION diff --git a/Modules/IO/MeshBase/include/itkMeshFileWriter.h b/Modules/IO/MeshBase/include/itkMeshFileWriter.h index f9501cf1158..283dfe3e88a 100644 --- a/Modules/IO/MeshBase/include/itkMeshFileWriter.h +++ b/Modules/IO/MeshBase/include/itkMeshFileWriter.h @@ -86,9 +86,10 @@ class ITK_TEMPLATE_EXPORT MeshFileWriter : public ProcessObject GetInput(unsigned int idx); /** Specify the name of the output file to write. */ + /** @ITKStartGrouping */ itkSetStringMacro(FileName); itkGetStringMacro(FileName); - + /** @ITKEndGrouping */ /** Set/Get the MeshIO helper class. Usually this is created via the object * factory mechanism that determines whether a particular MeshIO can * write a certain file. This method provides a way to get the MeshIO @@ -98,6 +99,7 @@ class ITK_TEMPLATE_EXPORT MeshFileWriter : public ProcessObject * correct choice and will allow a file to be created regardless of * the file extension. If the factory has set the MeshIO, the * extension must be supported by the specified MeshIO. */ + /** @ITKStartGrouping */ void SetMeshIO(MeshIOBase * io) { @@ -110,7 +112,7 @@ class ITK_TEMPLATE_EXPORT MeshFileWriter : public ProcessObject m_UserSpecifiedMeshIO = true; } itkGetModifiableObjectMacro(MeshIO, MeshIOBase); - + /** @ITKEndGrouping */ void SetFileTypeAsASCII() { @@ -137,10 +139,11 @@ class ITK_TEMPLATE_EXPORT MeshFileWriter : public ProcessObject } /** Set the compression On or Off */ + /** @ITKStartGrouping */ itkSetMacro(UseCompression, bool); itkGetConstReferenceMacro(UseCompression, bool); itkBooleanMacro(UseCompression); - + /** @ITKEndGrouping */ protected: MeshFileWriter() = default; ~MeshFileWriter() override = default; diff --git a/Modules/IO/MeshBase/include/itkMeshIOBase.h b/Modules/IO/MeshBase/include/itkMeshIOBase.h index 6b443120803..12fced90e49 100644 --- a/Modules/IO/MeshBase/include/itkMeshIOBase.h +++ b/Modules/IO/MeshBase/include/itkMeshIOBase.h @@ -100,9 +100,10 @@ class ITKIOMeshBase_EXPORT MeshIOBase : public LightProcessObject itkOverrideGetNameOfClassMacro(MeshIOBase); /** Set/Get the name of the file to be read. */ + /** @ITKStartGrouping */ itkSetStringMacro(FileName); itkGetStringMacro(FileName); - + /** @ITKEndGrouping */ #if !defined(ITK_LEGACY_REMOVE) /**Exposes enums values for backwards compatibility*/ static constexpr IOPixelEnum UNKNOWNPIXELTYPE = IOPixelEnum::UNKNOWNPIXELTYPE; @@ -181,13 +182,15 @@ class ITKIOMeshBase_EXPORT MeshIOBase : public LightProcessObject * SCALAR, RGB, RGBA, VECTOR, COVARIANTVECTOR, POINT, INDEX. If * the PIXELTYPE is SCALAR, then the NumberOfComponents should be 1. * Any other of PIXELTYPE will have more than one component. */ + /** @ITKStartGrouping */ itkSetEnumMacro(PointPixelType, itk::CommonEnums::IOPixel); itkGetEnumMacro(PointPixelType, itk::CommonEnums::IOPixel); itkSetEnumMacro(CellPixelType, itk::CommonEnums::IOPixel); itkGetEnumMacro(CellPixelType, itk::CommonEnums::IOPixel); - + /** @ITKEndGrouping */ /** Set/Get the component type of the point, cell, point data and cell data. This is always a native type. */ + /** @ITKStartGrouping */ itkSetEnumMacro(PointComponentType, itk::CommonEnums::IOComponent); itkGetEnumMacro(PointComponentType, itk::CommonEnums::IOComponent); itkSetEnumMacro(CellComponentType, itk::CommonEnums::IOComponent); @@ -196,7 +199,7 @@ class ITKIOMeshBase_EXPORT MeshIOBase : public LightProcessObject itkGetEnumMacro(PointPixelComponentType, itk::CommonEnums::IOComponent); itkSetEnumMacro(CellPixelComponentType, itk::CommonEnums::IOComponent); itkGetEnumMacro(CellPixelComponentType, itk::CommonEnums::IOComponent); - + /** @ITKEndGrouping */ template struct MapComponentType { @@ -441,6 +444,7 @@ class ITKIOMeshBase_EXPORT MeshIOBase : public LightProcessObject * be set by the reading process. For SCALAR pixel types, * NumberOfComponents will be 1. For other pixel types, * NumberOfComponents will be greater than or equal to one. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfPointPixelComponents, unsigned int); itkGetConstMacro(NumberOfPointPixelComponents, unsigned int); itkSetMacro(NumberOfCellPixelComponents, unsigned int); @@ -469,7 +473,7 @@ class ITKIOMeshBase_EXPORT MeshIOBase : public LightProcessObject itkSetMacro(UpdateCellData, bool); itkGetConstMacro(UpdateCellData, bool); itkBooleanMacro(UpdateCellData); - + /** @ITKEndGrouping */ unsigned int GetComponentSize(IOComponentEnum componentType) const; @@ -483,9 +487,10 @@ class ITKIOMeshBase_EXPORT MeshIOBase : public LightProcessObject /** These methods control whether the file is written binary or ASCII. * Many file formats (i.e., subclasses) ignore this flag. */ + /** @ITKStartGrouping */ itkSetEnumMacro(FileType, IOFileEnum); itkGetEnumMacro(FileType, IOFileEnum); - + /** @ITKEndGrouping */ void SetFileTypeToASCII() { @@ -509,9 +514,10 @@ class ITKIOMeshBase_EXPORT MeshIOBase : public LightProcessObject * a VAX or PC, SetByteOrderToLittleEndian() otherwise * SetByteOrderToBigEndian(). Some MeshIOBase subclasses * ignore these methods. */ + /** @ITKStartGrouping */ itkSetEnumMacro(ByteOrder, IOByteOrderEnum); itkGetEnumMacro(ByteOrder, IOByteOrderEnum); - + /** @ITKEndGrouping */ void SetByteOrderToBigEndian() { @@ -525,10 +531,11 @@ class ITKIOMeshBase_EXPORT MeshIOBase : public LightProcessObject } /** Set/Get a boolean to use the compression or not. */ + /** @ITKStartGrouping */ itkSetMacro(UseCompression, bool); itkGetConstMacro(UseCompression, bool); itkBooleanMacro(UseCompression); - + /** @ITKEndGrouping */ /** Convenience method returns the IOFileEnum as a string. This can be * used for writing output files. */ std::string GetFileTypeAsString(IOFileEnum) const; diff --git a/Modules/IO/MeshFreeSurfer/include/itkFreeSurferAsciiMeshIO.h b/Modules/IO/MeshFreeSurfer/include/itkFreeSurferAsciiMeshIO.h index bd22c8b26eb..0358d9c6533 100644 --- a/Modules/IO/MeshFreeSurfer/include/itkFreeSurferAsciiMeshIO.h +++ b/Modules/IO/MeshFreeSurfer/include/itkFreeSurferAsciiMeshIO.h @@ -129,6 +129,7 @@ class ITKIOMeshFreeSurfer_EXPORT FreeSurferAsciiMeshIO : public MeshIOBase } } + /** Write cells to output stream */ template void WriteCells(T * buffer, std::ofstream & outputFile, T label = T{}) @@ -161,6 +162,7 @@ class ITKIOMeshFreeSurfer_EXPORT FreeSurferAsciiMeshIO : public MeshIOBase { for (unsigned int jj = 0; jj < 3; ++jj) { + /** point identifiers start from the third elements, first element is cellType, the second is numberOfPoints */ output[ii * 3 + jj] = static_cast(input[5 * ii + jj + 2]); diff --git a/Modules/IO/MeshVTK/include/itkVTKPolyDataMeshIO.h b/Modules/IO/MeshVTK/include/itkVTKPolyDataMeshIO.h index 7d7598cb8f4..dbcce0ce4df 100644 --- a/Modules/IO/MeshVTK/include/itkVTKPolyDataMeshIO.h +++ b/Modules/IO/MeshVTK/include/itkVTKPolyDataMeshIO.h @@ -412,6 +412,7 @@ class ITKIOMeshVTK_EXPORT VTKPolyDataMeshIO : public MeshIOBase itkExceptionMacro("UnExpected end of line while trying to read LOOKUP_TABLE"); } } + /** For VECTORS or NORMALS or TENSORS, we could read them directly */ const SizeValueType numberOfComponents = this->m_NumberOfCellPixels * this->m_NumberOfCellPixelComponents; inputFile.read(reinterpret_cast(buffer), numberOfComponents * sizeof(T)); diff --git a/Modules/IO/Meta/include/itkMetaArrayWriter.h b/Modules/IO/Meta/include/itkMetaArrayWriter.h index 612ca26cb0b..b726e6f2e8b 100644 --- a/Modules/IO/Meta/include/itkMetaArrayWriter.h +++ b/Modules/IO/Meta/include/itkMetaArrayWriter.h @@ -44,22 +44,25 @@ class ITKIOMeta_EXPORT MetaArrayWriter : public LightProcessObject itkOverrideGetNameOfClassMacro(MetaArrayWriter); /** Set/Get the filename. */ + /** @ITKStartGrouping */ itkSetStringMacro(FileName); itkGetStringMacro(FileName); - + /** @ITKEndGrouping */ /** Set/Get the filename to which the data is written. * Optional: use if header and data should be in separate files. */ + /** @ITKStartGrouping */ itkSetStringMacro(DataFileName); itkGetStringMacro(DataFileName); - + /** @ITKEndGrouping */ /** Boolean to set binary mode. * If set to On, data will be stored in the file in binary format; if set * to Off, data will be stored in ascii format. * Default is Off. */ + /** @ITKStartGrouping */ itkBooleanMacro(Binary); itkSetMacro(Binary, bool); itkGetConstMacro(Binary, bool); - + /** @ITKEndGrouping */ /** Set the input itk Array to write. */ template void @@ -131,9 +134,10 @@ class ITKIOMeta_EXPORT MetaArrayWriter : public LightProcessObject } /** Set/Get the precision of the writing. */ + /** @ITKStartGrouping */ itkSetMacro(Precision, unsigned int); itkGetConstMacro(Precision, unsigned int); - + /** @ITKEndGrouping */ /** Set the data type written to the file. */ void ConvertTo(MET_ValueEnumType _metaElementType); diff --git a/Modules/IO/Meta/include/itkMetaImageIO.h b/Modules/IO/Meta/include/itkMetaImageIO.h index 0190ea9b3e8..947976525cd 100644 --- a/Modules/IO/Meta/include/itkMetaImageIO.h +++ b/Modules/IO/Meta/include/itkMetaImageIO.h @@ -164,8 +164,10 @@ class ITKIOMeta_EXPORT MetaImageIO : public ImageIOBase /** Determining the subsampling factor in case * we want a coarse version of the image/ * \warning this is only used when streaming is on. */ + /** @ITKStartGrouping */ itkSetMacro(SubSamplingFactor, unsigned int); itkGetConstMacro(SubSamplingFactor, unsigned int); + /** @ITKEndGrouping */ /** * Set the default precision when writing out the MetaImage header. @@ -177,11 +179,12 @@ class ITKIOMeta_EXPORT MetaImageIO : public ImageIOBase * This function is not thread safe. * Default value after static initialization is 17. */ + /** @ITKStartGrouping */ static void SetDefaultDoublePrecision(unsigned int precision); static unsigned int GetDefaultDoublePrecision(); - + /** @ITKEndGrouping */ protected: MetaImageIO(); ~MetaImageIO() override; diff --git a/Modules/IO/NIFTI/include/itkNiftiImageIO.h b/Modules/IO/NIFTI/include/itkNiftiImageIO.h index d19089c252f..6bc992b1534 100644 --- a/Modules/IO/NIFTI/include/itkNiftiImageIO.h +++ b/Modules/IO/NIFTI/include/itkNiftiImageIO.h @@ -41,14 +41,19 @@ class NiftiImageIOEnums */ enum class Analyze75Flavor : uint8_t { + /** Behavior introduced in ITK4.0 by NIFTI reader interpreting Analyze files */ AnalyzeITK4 = 4, + /** Will ignore orientation code and negative pixel dimensions */ AnalyzeFSL = 3, + /** Will ignore orientation code and respect negative pixel dimensions */ AnalyzeSPM = 2, + /** Same as AnalyzeITK4 but will show warning about deprecated file format (Default)*/ AnalyzeITK4Warning = 1, + /** Reject Analyze files as potentially wrong */ AnalyzeReject = 0 }; @@ -61,10 +66,13 @@ class NiftiImageIOEnums { /** 2-file Nifti (consisting of .hdr and .img file). */ TwoFileNifti = 2, + /** 1-file Nifti (consisting of .nii file). */ OneFileNifti = 1, + /** Legacy Analyze 7.5 format (consisting of .hdr and .img file). */ Analyze75 = 0, + /** Some other file format, or file system error. */ OtherOrError = -1, }; @@ -76,11 +84,12 @@ using Analyze75Flavor = NiftiImageIOEnums::Analyze75Flavor; #endif /** Define how to print enumerations */ +/** @ITKStartGrouping */ extern ITKIONIFTI_EXPORT std::ostream & operator<<(std::ostream & out, const NiftiImageIOEnums::Analyze75Flavor value); extern ITKIONIFTI_EXPORT std::ostream & operator<<(std::ostream & out, const NiftiImageIOEnums::NiftiFileEnum value); - +/** @ITKEndGrouping */ /** * \class NiftiImageIO * @@ -178,16 +187,18 @@ class ITKIONIFTI_EXPORT NiftiImageIO : public ImageIOBase GenerateStreamableReadRegionFromRequestedRegion(const ImageIORegion & requestedRegion) const override; /** Set the slope and intercept for voxel value rescaling. */ + /** @ITKStartGrouping */ itkSetMacro(RescaleSlope, double); itkSetMacro(RescaleIntercept, double); - + /** @ITKEndGrouping */ /** A mode to allow the Nifti filter to read and write to the LegacyAnalyze75 format as interpreted by * the nifti library maintainers. This format does not properly respect the file orientation fields. * By default this is set by configuration option ITK_NIFTI_IO_ANALYZE_FLAVOR */ + /** @ITKStartGrouping */ itkSetMacro(LegacyAnalyze75Mode, NiftiImageIOEnums::Analyze75Flavor); itkGetConstMacro(LegacyAnalyze75Mode, NiftiImageIOEnums::Analyze75Flavor); - + /** @ITKEndGrouping */ /** Enable conversion of vector coordinates between RAS coordinate system (in NIFTI file) and * LPS (ITK convention) when reading or writing a generic vector image file (intent code: 1007). * @@ -196,10 +207,11 @@ class ITKIONIFTI_EXPORT NiftiImageIO : public ImageIOBase * By default an ITK vector image is written to NIFTI file as a generic vector image, unless * "intent_code" field is set explicitly to set to "1006" (displacement vector). */ + /** @ITKStartGrouping */ itkSetMacro(ConvertRASVectors, bool); itkGetConstMacro(ConvertRASVectors, bool); itkBooleanMacro(ConvertRASVectors); - + /** @ITKEndGrouping */ /** Enable conversion of vector coordinates between RAS coordinate system (in NIFTI file) and * LPS (ITK convention) when reading or writing a "displacement vector" file (intent code: 1006). * @@ -215,15 +227,17 @@ class ITKIONIFTI_EXPORT NiftiImageIO : public ImageIOBase \endcode * */ + /** @ITKStartGrouping */ itkSetMacro(ConvertRASDisplacementVectors, bool); itkGetConstMacro(ConvertRASDisplacementVectors, bool); itkBooleanMacro(ConvertRASDisplacementVectors); - + /** @ITKEndGrouping */ /** Allow to read nifti files with non-orthogonal sform*/ + /** @ITKStartGrouping */ itkSetMacro(SFORM_Permissive, bool); itkGetConstMacro(SFORM_Permissive, bool); itkBooleanMacro(SFORM_Permissive); - + /** @ITKEndGrouping */ protected: NiftiImageIO(); ~NiftiImageIO() override; diff --git a/Modules/IO/RAW/include/itkRawImageIO.h b/Modules/IO/RAW/include/itkRawImageIO.h index 8a64a8a484f..f561ea5a5e3 100644 --- a/Modules/IO/RAW/include/itkRawImageIO.h +++ b/Modules/IO/RAW/include/itkRawImageIO.h @@ -86,9 +86,10 @@ class ITK_TEMPLATE_EXPORT RawImageIO : public ImageIOBase /** The number of dimensions stored in a file. Defaults to two. If two, * each file contains one "slice". If three, each file will contain one * "volume". */ + /** @ITKStartGrouping */ itkSetMacro(FileDimensionality, unsigned long); itkGetConstMacro(FileDimensionality, unsigned long); - + /** @ITKEndGrouping */ /** The different types of ImageIO's can support data of varying * dimensionality. For example, some file formats are strictly 2D * while others can support 2D, 3D, or even n-D. This method returns @@ -124,6 +125,7 @@ class ITK_TEMPLATE_EXPORT RawImageIO : public ImageIOBase Read(void * buffer) override; /** Set/Get the Data mask. */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(ImageMask, unsigned short); void SetImageMask(unsigned long val) @@ -135,7 +137,7 @@ class ITK_TEMPLATE_EXPORT RawImageIO : public ImageIOBase m_ImageMask = (static_cast(val)); this->Modified(); } - + /** @ITKEndGrouping */ /** Read a file's header to determine image dimensions, etc. */ virtual void ReadHeader(const std::string = std::string()) diff --git a/Modules/IO/SpatialObjects/include/itkSpatialObjectReader.h b/Modules/IO/SpatialObjects/include/itkSpatialObjectReader.h index a923fdacd29..13655d39536 100644 --- a/Modules/IO/SpatialObjects/include/itkSpatialObjectReader.h +++ b/Modules/IO/SpatialObjects/include/itkSpatialObjectReader.h @@ -63,11 +63,13 @@ class ITK_TEMPLATE_EXPORT SpatialObjectReader : public Object void Update(); - /** Set the version of MetaIO to use */ + /** Set/Get the version of MetaIO to use */ + /** @ITKStartGrouping */ void SetMetaIOVersion(unsigned int ver); unsigned int GetMetaIOVersion() const; + /** @ITKEndGrouping */ /** Set the filename */ itkSetStringMacro(FileName); @@ -104,6 +106,7 @@ class ITK_TEMPLATE_EXPORT SpatialObjectReader : public Object } /** Set/GetEvent */ + /** @ITKStartGrouping */ const MetaEvent * GetEvent() { @@ -115,6 +118,7 @@ class ITK_TEMPLATE_EXPORT SpatialObjectReader : public Object { m_MetaToSpatialConverter->SetEvent(event); } + /** @ITKEndGrouping */ /** Add a converter for a new MetaObject/SpatialObject type */ void diff --git a/Modules/IO/SpatialObjects/include/itkSpatialObjectWriter.h b/Modules/IO/SpatialObjects/include/itkSpatialObjectWriter.h index f246523404c..518ac28f79c 100644 --- a/Modules/IO/SpatialObjects/include/itkSpatialObjectWriter.h +++ b/Modules/IO/SpatialObjects/include/itkSpatialObjectWriter.h @@ -98,10 +98,11 @@ class ITK_TEMPLATE_EXPORT SpatialObjectWriter : public Object GetTransformPrecision(); /** Set/Get if the images should be written in a different file */ + /** @ITKStartGrouping */ itkSetMacro(WriteImagesInSeparateFile, bool); itkGetConstMacro(WriteImagesInSeparateFile, bool); itkBooleanMacro(WriteImagesInSeparateFile); - + /** @ITKEndGrouping */ /** Add a converter for a new MetaObject/SpatialObject type */ void RegisterMetaConverter(const char * metaTypeName, diff --git a/Modules/IO/Stimulate/include/itkStimulateImageIO.h b/Modules/IO/Stimulate/include/itkStimulateImageIO.h index 2148f4a47d8..a798b8fb765 100644 --- a/Modules/IO/Stimulate/include/itkStimulateImageIO.h +++ b/Modules/IO/Stimulate/include/itkStimulateImageIO.h @@ -114,6 +114,7 @@ class ITKIOStimulate_EXPORT StimulateImageIO : public ImageIOBase * high_value will be displayed as white. Pixels with values within the display * range are displayed with a grey value that is scaled linearly between the * low_value and high_value. */ + /** @ITKStartGrouping */ itkGetVectorMacro(DisplayRange, const float, 2); const float & GetHighDisplayValue() @@ -125,7 +126,7 @@ class ITKIOStimulate_EXPORT StimulateImageIO : public ImageIOBase { return m_DisplayRange[1]; } - + /** @ITKEndGrouping */ protected: StimulateImageIO(); ~StimulateImageIO() override; diff --git a/Modules/IO/TIFF/include/itkTIFFImageIO.h b/Modules/IO/TIFF/include/itkTIFFImageIO.h index 2ef065bd366..961ee60919c 100644 --- a/Modules/IO/TIFF/include/itkTIFFImageIO.h +++ b/Modules/IO/TIFF/include/itkTIFFImageIO.h @@ -160,6 +160,7 @@ class ITKIOTIFF_EXPORT TIFFImageIO : public ImageIOBase /** Set/Get the level of quality for the output images if * Compression is JPEG. Settings vary from 1 to 100. * 100 is the highest quality. Default is 75 */ + /** @ITKStartGrouping */ virtual void SetJPEGQuality(int _JPEGQuality) { @@ -170,7 +171,7 @@ class ITKIOTIFF_EXPORT TIFFImageIO : public ImageIOBase { return this->GetCompressionLevel(); } - + /** @ITKEndGrouping */ /** Get a const ref to the palette of the image. In the case of non palette * image or ExpandRGBPalette set to true, a vector of size diff --git a/Modules/IO/TransformBase/include/itkTransformFileReader.h b/Modules/IO/TransformBase/include/itkTransformFileReader.h index d48f5bbb49e..3033ca6c8e3 100644 --- a/Modules/IO/TransformBase/include/itkTransformFileReader.h +++ b/Modules/IO/TransformBase/include/itkTransformFileReader.h @@ -95,9 +95,10 @@ class ITK_TEMPLATE_EXPORT TransformFileReaderTemplate : public LightProcessObjec } /** Set/Get the TransformIO class used internally to read to transform. */ + /** @ITKStartGrouping */ itkSetObjectMacro(TransformIO, TransformIOType); itkGetConstObjectMacro(TransformIO, TransformIOType); - + /** @ITKEndGrouping */ protected: void PrintSelf(std::ostream & os, Indent indent) const override; diff --git a/Modules/IO/TransformBase/include/itkTransformFileWriter.h b/Modules/IO/TransformBase/include/itkTransformFileWriter.h index 3a0c326de9d..2497cc5622d 100644 --- a/Modules/IO/TransformBase/include/itkTransformFileWriter.h +++ b/Modules/IO/TransformBase/include/itkTransformFileWriter.h @@ -81,15 +81,17 @@ class ITKIOTransformBase_TEMPLATE_EXPORT TransformFileWriterTemplate : public Li #endif /** Set/Get the write mode (append/overwrite) for the filter. */ + /** @ITKStartGrouping */ itkSetMacro(AppendMode, bool); itkGetConstMacro(AppendMode, bool); itkBooleanMacro(AppendMode); - + /** @ITKEndGrouping */ /** Set/Get a boolean to use the compression or not. */ + /** @ITKStartGrouping */ itkSetMacro(UseCompression, bool); itkGetConstMacro(UseCompression, bool); itkBooleanMacro(UseCompression); - + /** @ITKEndGrouping */ /** Set/Get the input transform to write */ void SetInput(const Object * transform); @@ -106,9 +108,10 @@ class ITKIOTransformBase_TEMPLATE_EXPORT TransformFileWriterTemplate : public Li Update(); /** Set/Get the TransformIO class used internally to read to transform. */ + /** @ITKStartGrouping */ itkSetObjectMacro(TransformIO, TransformIOType); itkGetConstObjectMacro(TransformIO, TransformIOType); - + /** @ITKEndGrouping */ protected: TransformFileWriterTemplate(); ~TransformFileWriterTemplate() override; @@ -135,13 +138,14 @@ ITK_GCC_PRAGMA_DIAG_PUSH() ITK_GCC_PRAGMA_DIAG(ignored "-Wattributes") /** Declare specializations */ +/** @ITKStartGrouping */ template <> void ITKIOTransformBase_TEMPLATE_EXPORT TransformFileWriterTemplate::PushBackTransformList(const Object * transObj); template <> void ITKIOTransformBase_TEMPLATE_EXPORT TransformFileWriterTemplate::PushBackTransformList(const Object * transObj); - +/** @ITKEndGrouping */ ITK_GCC_PRAGMA_DIAG_POP() } // namespace itk diff --git a/Modules/IO/TransformBase/include/itkTransformIOBase.h b/Modules/IO/TransformBase/include/itkTransformIOBase.h index 0980617a489..49f82c1f7a0 100644 --- a/Modules/IO/TransformBase/include/itkTransformIOBase.h +++ b/Modules/IO/TransformBase/include/itkTransformIOBase.h @@ -82,9 +82,10 @@ class ITKIOTransformBase_TEMPLATE_EXPORT TransformIOBaseTemplate : public LightP using ConstTransformListType = std::list; /** Set/Get the name of the file to be read. */ + /** @ITKStartGrouping */ itkSetStringMacro(FileName); itkGetStringMacro(FileName); - + /** @ITKEndGrouping */ /** Reads the data from disk into the memory buffer provided. */ virtual void Read() = 0; @@ -104,6 +105,7 @@ class ITKIOTransformBase_TEMPLATE_EXPORT TransformIOBaseTemplate : public LightP CanWriteFile(const char *) = 0; /** Get the list of transforms resulting from a file read */ + /** @ITKStartGrouping */ TransformListType & GetTransformList() { @@ -119,21 +121,23 @@ class ITKIOTransformBase_TEMPLATE_EXPORT TransformIOBaseTemplate : public LightP { return m_WriteTransformList; } - + /** @ITKEndGrouping */ /** Set the list of transforms before writing */ void SetTransformList(ConstTransformListType & transformList); /** Set the writer to append to the specified file */ + /** @ITKStartGrouping */ itkSetMacro(AppendMode, bool); itkGetConstMacro(AppendMode, bool); itkBooleanMacro(AppendMode); - + /** @ITKEndGrouping */ /** Set/Get a boolean to use the compression or not. */ + /** @ITKStartGrouping */ itkSetMacro(UseCompression, bool); itkGetConstMacro(UseCompression, bool); itkBooleanMacro(UseCompression); - + /** @ITKEndGrouping */ /** The transform type has a string representation used when reading * and writing transform files. In the case where a double-precision * transform is to be written as float, or vice versa, the transform diff --git a/Modules/IO/TransformHDF5/include/itkHDF5TransformIO.h b/Modules/IO/TransformHDF5/include/itkHDF5TransformIO.h index 48461b81e8f..21740e3aef5 100644 --- a/Modules/IO/TransformHDF5/include/itkHDF5TransformIO.h +++ b/Modules/IO/TransformHDF5/include/itkHDF5TransformIO.h @@ -102,9 +102,10 @@ class ITK_TEMPLATE_EXPORT HDF5TransformIOTemplate using ConstTransformListType = typename TransformIOBaseTemplate::ConstTransformListType; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(HDF5TransformIOTemplate); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Determine the file type. Returns true if this ImageIO can read the * file specified. */ bool @@ -131,25 +132,28 @@ class ITK_TEMPLATE_EXPORT HDF5TransformIOTemplate private: /** Read a parameter array from the file location name */ + /** @ITKStartGrouping */ ParametersType ReadParameters(const std::string & DataSetName) const; FixedParametersType ReadFixedParameters(const std::string & DataSetName) const; - + /** @ITKEndGrouping */ /** Write a parameter array to the file location name */ + /** @ITKStartGrouping */ void WriteParameters(const std::string & name, const ParametersType & parameters); void WriteFixedParameters(const std::string & name, const FixedParametersType & fixedParameters); - + /** @ITKEndGrouping */ /** write a string variable */ + /** @ITKStartGrouping */ void WriteString(const std::string & path, const std::string & value); void WriteString(const std::string & path, const char * s); void WriteOneTransform(const int transformIndex, const TransformType * curTransform); - + /** @ITKEndGrouping */ std::unique_ptr m_H5File; /** Utility function for inferring data storage type diff --git a/Modules/IO/TransformInsightLegacy/include/itkTxtTransformIO.h b/Modules/IO/TransformInsightLegacy/include/itkTxtTransformIO.h index 9b04c3c91d2..df83363d6fa 100644 --- a/Modules/IO/TransformInsightLegacy/include/itkTxtTransformIO.h +++ b/Modules/IO/TransformInsightLegacy/include/itkTxtTransformIO.h @@ -46,9 +46,10 @@ class ITK_TEMPLATE_EXPORT TxtTransformIOTemplate : public TransformIOBaseTemplat using FixedParametersValueType = typename TransformType::FixedParametersValueType; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(TxtTransformIOTemplate); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Determine the file type. Returns true if this ImageIO can read the * file specified. */ bool diff --git a/Modules/IO/TransformMatlab/include/itkMatlabTransformIO.h b/Modules/IO/TransformMatlab/include/itkMatlabTransformIO.h index 0a000d28b61..6a5626b2ec9 100644 --- a/Modules/IO/TransformMatlab/include/itkMatlabTransformIO.h +++ b/Modules/IO/TransformMatlab/include/itkMatlabTransformIO.h @@ -42,9 +42,10 @@ class ITK_TEMPLATE_EXPORT MatlabTransformIOTemplate : public TransformIOBaseTemp using ConstTransformListType = typename TransformIOBaseTemplate::ConstTransformListType; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(MatlabTransformIOTemplate); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Determine the file type. Returns true if this ImageIO can read the * file specified. */ bool diff --git a/Modules/IO/XML/include/itkDOMNode.h b/Modules/IO/XML/include/itkDOMNode.h index 98c42e0f161..fa621530567 100644 --- a/Modules/IO/XML/include/itkDOMNode.h +++ b/Modules/IO/XML/include/itkDOMNode.h @@ -85,30 +85,36 @@ class ITKIOXML_EXPORT DOMNode : public Object using OffsetType = int; /** Retrieve the parent node. */ + /** @ITKStartGrouping */ virtual void SetParent(DOMNode * node); DOMNode * GetParent(); const DOMNode * GetParent() const; - + /** @ITKEndGrouping */ /** Retrieve the tag name of this node. */ + /** @ITKStartGrouping */ itkSetMacro(Name, const std::string &); itkGetConstReferenceMacro(Name, std::string); - + /** @ITKEndGrouping */ /** Retrieve the special attribute "id" of this node. */ + /** @ITKStartGrouping */ itkSetMacro(ID, const std::string &); itkGetConstReferenceMacro(ID, std::string); - + /** @ITKEndGrouping */ /** Retrieve an attribute by key (return an empty string if not found). */ virtual std::string GetAttribute(const std::string & key) const; + /** Check whether has an attribute. */ virtual bool HasAttribute(const std::string & key) const; + /** Add or replace an attribute. */ virtual void SetAttribute(const std::string & key, const std::string & value); + /** Remove an attribute by key (throw exception if not found). */ virtual void RemoveAttribute(const std::string & key); @@ -119,6 +125,7 @@ class ITKIOXML_EXPORT DOMNode : public Object */ virtual void GetAllAttributes(AttributesListType & output, bool keepOriginalOrder = true) const; + /** Remove all attributes. */ virtual void RemoveAllAttributes(); @@ -130,6 +137,7 @@ class ITKIOXML_EXPORT DOMNode : public Object /** Return all children. */ virtual void GetAllChildren(ChildrenListType & output); + /** Return all children for read-only access. */ virtual void GetAllChildren(ConstChildrenListType & output) const; @@ -137,6 +145,7 @@ class ITKIOXML_EXPORT DOMNode : public Object /** Return all children of a same tag name. */ virtual void GetChildren(const std::string & tag, ChildrenListType & output); + /** Return all children of a same tag name for read-only access. */ virtual void GetChildren(const std::string & tag, ConstChildrenListType & output) const; @@ -148,9 +157,11 @@ class ITKIOXML_EXPORT DOMNode : public Object /** Add a child in front of another child (throw exception if not able to add). */ virtual void AddChild(DOMNode * node, IdentifierType i = 0); + /** Add a child in front of the children list (throw exception if not able to add). */ virtual void AddChildAtBegin(DOMNode * node); + /** Add a child at the end of the children list (throw exception if not able to add). */ virtual void AddChildAtEnd(DOMNode * node); @@ -168,36 +179,41 @@ class ITKIOXML_EXPORT DOMNode : public Object RemoveAllAttributesAndChildren(); /** Retrieve a child by index (return nullptr if i is out of range). */ + /** @ITKStartGrouping */ virtual DOMNode * GetChild(IdentifierType i = 0); virtual const DOMNode * GetChild(IdentifierType i = 0) const; - + /** @ITKEndGrouping */ /** Retrieve a child by tag name and an index (multiple children can have a same tag name, return nullptr if no such * child). */ + /** @ITKStartGrouping */ virtual DOMNode * GetChild(const std::string & tag, IdentifierType i = 0); virtual const DOMNode * GetChild(const std::string & tag, IdentifierType i = 0) const; - + /** @ITKEndGrouping */ /** Retrieve a child by its unique "id" attribute value (return nullptr if not found). */ + /** @ITKStartGrouping */ virtual DOMNode * GetChildByID(const std::string & value); virtual const DOMNode * GetChildByID(const std::string & value) const; - + /** @ITKEndGrouping */ /** Retrieve an older or younger sibling by distance (return nullptr if no such sibling). */ + /** @ITKStartGrouping */ virtual DOMNode * GetSibling(OffsetType i); virtual const DOMNode * GetSibling(OffsetType i) const; - + /** @ITKEndGrouping */ /** Return the root node. */ + /** @ITKStartGrouping */ virtual DOMNode * GetRoot(); virtual const DOMNode * GetRoot() const; - + /** @ITKEndGrouping */ /** Test whether the input node and this node share the same root. */ virtual bool ShareRoot(const DOMNode * node) const; @@ -219,27 +235,31 @@ class ITKIOXML_EXPORT DOMNode : public Object * * The method returns nullptr if queried node does not exist. */ + /** @ITKStartGrouping */ virtual DOMNode * Find(const std::string & path); virtual const DOMNode * Find(const std::string & path) const; - + /** @ITKEndGrouping */ /** Return the path of this node within its root, in the form of a query string that uses only indices. */ virtual std::string GetPath() const; /** Get a child and cast it to a text node (return nullptr if out of range or not a text node). */ + /** @ITKStartGrouping */ virtual DOMTextNode * GetTextChild(IdentifierType i = 0); virtual const DOMTextNode * GetTextChild(IdentifierType i = 0) const; - + /** @ITKEndGrouping */ /** Generate a text node from a string and add/insert it as a child (see AddChild(node,i)). */ virtual void AddTextChild(const std::string & text, IdentifierType i = 0); + /** Generate a text node from a string and add/insert in front of all children. */ virtual void AddTextChildAtBegin(const std::string & text); + /** Generate a text node from a string and add/insert at the end of all children. */ virtual void AddTextChildAtEnd(const std::string & text); diff --git a/Modules/IO/XML/include/itkDOMNodeXMLReader.h b/Modules/IO/XML/include/itkDOMNodeXMLReader.h index adfe8ac8daa..05c1521a380 100644 --- a/Modules/IO/XML/include/itkDOMNodeXMLReader.h +++ b/Modules/IO/XML/include/itkDOMNodeXMLReader.h @@ -88,6 +88,7 @@ class ITKIOXML_EXPORT DOMNodeXMLReader : public Object * Get/Set The output DOM object will be created automatically, but the user * can appoint a user DOM object as the output by calling this function. */ + /** @ITKStartGrouping */ itkSetObjectMacro(DOMNodeXML, OutputType); #if !defined(ITK_LEGACY_REMOVE) // Provide backwards compatible interface @@ -97,7 +98,7 @@ class ITKIOXML_EXPORT DOMNodeXMLReader : public Object this->SetDOMNodeXML(_arg); } #endif - + /** @ITKEndGrouping */ /** * Provide an interface to match that * of other ProcessObjects @@ -105,6 +106,7 @@ class ITKIOXML_EXPORT DOMNodeXMLReader : public Object * by returning a non-const pointer * for the generated Object. */ + /** @ITKStartGrouping */ // NOTE: The m_DOMNodeXML is only // exposed via the Source generation interface // by the GetOutput() method that mimics @@ -119,7 +121,7 @@ class ITKIOXML_EXPORT DOMNodeXMLReader : public Object { return this->m_DOMNodeXML.GetPointer(); } - + /** @ITKEndGrouping */ #if !defined(ITK_LEGACY_REMOVE) // This interface was exposed in ITKv4 when the itkGetModifiableObjectMacro was used virtual OutputType * @@ -185,5 +187,4 @@ operator>>(std::istream & is, itk::DOMNode & object) reader->Update(is); return is; } - #endif // itkDOMNodeXMLReader_h diff --git a/Modules/IO/XML/include/itkDOMNodeXMLWriter.h b/Modules/IO/XML/include/itkDOMNodeXMLWriter.h index 2a88ad9a072..857f343f435 100644 --- a/Modules/IO/XML/include/itkDOMNodeXMLWriter.h +++ b/Modules/IO/XML/include/itkDOMNodeXMLWriter.h @@ -85,9 +85,10 @@ class ITKIOXML_EXPORT DOMNodeXMLWriter : public Object itkGetStringMacro(FileName); /** Get/Set the input DOM object to be written. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(Input, InputType); itkGetConstObjectMacro(Input, InputType); - + /** @ITKEndGrouping */ /** * Function called by Update() or end-users to write the input DOM object * to an output stream such as file, string, console, etc. @@ -126,5 +127,4 @@ operator<<(std::ostream & os, const itk::DOMNode & object) writer->Update(os); return os; } - #endif // itkDOMNodeXMLWriter_h diff --git a/Modules/IO/XML/include/itkDOMReader.h b/Modules/IO/XML/include/itkDOMReader.h index 9e0b0da8210..060e0679e0e 100644 --- a/Modules/IO/XML/include/itkDOMReader.h +++ b/Modules/IO/XML/include/itkDOMReader.h @@ -136,14 +136,16 @@ class ITK_TEMPLATE_EXPORT DOMReader : public Object private: /** Get/Set the intermediate DOM object. */ + /** @ITKStartGrouping */ itkSetObjectMacro(IntermediateDOM, DOMNodeType); itkGetModifiableObjectMacro(IntermediateDOM, DOMNodeType); - + /** @ITKEndGrouping */ /** Variable to hold the input XML file name. */ std::string m_FileName{}; /** Variable to hold the output object, created internally or supplied by the user. */ OutputType * m_Output{}; + /** Variable to hold the output object if it is a smart object. */ typename LightObject::Pointer m_OutputHolder{}; diff --git a/Modules/IO/XML/include/itkDOMTextNode.h b/Modules/IO/XML/include/itkDOMTextNode.h index 5a71986b914..884ab4bcc10 100644 --- a/Modules/IO/XML/include/itkDOMTextNode.h +++ b/Modules/IO/XML/include/itkDOMTextNode.h @@ -55,9 +55,10 @@ class DOMTextNode : public DOMNode itkOverrideGetNameOfClassMacro(DOMTextNode); /** Functions to set/get the enclosed text of this node. */ + /** @ITKStartGrouping */ itkSetMacro(Text, const std::string &); itkGetConstReferenceMacro(Text, std::string); - + /** @ITKEndGrouping */ protected: DOMTextNode() { this->SetName("!"); } diff --git a/Modules/IO/XML/include/itkDOMWriter.h b/Modules/IO/XML/include/itkDOMWriter.h index ada1ef16fcb..ed54b3ff24a 100644 --- a/Modules/IO/XML/include/itkDOMWriter.h +++ b/Modules/IO/XML/include/itkDOMWriter.h @@ -131,14 +131,16 @@ class ITK_TEMPLATE_EXPORT DOMWriter : public Object private: /** Get/Set the intermediate DOM object. */ + /** @ITKStartGrouping */ itkSetObjectMacro(IntermediateDOM, DOMNodeType); itkGetModifiableObjectMacro(IntermediateDOM, DOMNodeType); - + /** @ITKEndGrouping */ /** Variable to hold the output XML file name. */ std::string m_FileName{}; /** Variable to hold the input object. */ const InputType * m_Input{}; + /** Variable to hold the input object if it is a smart object. */ typename LightObject::ConstPointer m_InputHolder{}; diff --git a/Modules/Numerics/NarrowBand/include/itkNarrowBandImageFilterBase.h b/Modules/Numerics/NarrowBand/include/itkNarrowBandImageFilterBase.h index f696415f9e6..1150001fc76 100644 --- a/Modules/Numerics/NarrowBand/include/itkNarrowBandImageFilterBase.h +++ b/Modules/Numerics/NarrowBand/include/itkNarrowBandImageFilterBase.h @@ -113,8 +113,10 @@ class ITK_TEMPLATE_EXPORT NarrowBandImageFilterBase : public FiniteDifferenceIma using NarrowBandIterator = typename NarrowBandType::Iterator; /** Set/Get IsoSurfaceValue to use in the input image */ + /** @ITKStartGrouping */ itkSetMacro(IsoSurfaceValue, ValueType); itkGetConstMacro(IsoSurfaceValue, ValueType); + /** @ITKEndGrouping */ /** Root Mean Square Change between successive iterations */ // itkGetConstMacro( RMSChange, ValueType); @@ -123,6 +125,7 @@ class ITK_TEMPLATE_EXPORT NarrowBandImageFilterBase : public FiniteDifferenceIma * entire narrow band can be constructed using this method. Usually, * however, the narrow band is initialized and reinitialized automatically * by the subclass. */ + /** @ITKStartGrouping */ void InsertNarrowBandNode(const BandNodeType & node) { @@ -152,6 +155,7 @@ class ITK_TEMPLATE_EXPORT NarrowBandImageFilterBase : public FiniteDifferenceIma m_NarrowBand->PushBack(tmpnode); this->Modified(); } + /** @ITKEndGrouping */ /** Set the narrow band total radius. The narrow band width will be * twice this value (positive and negative distance to the zero level @@ -237,6 +241,7 @@ class ITK_TEMPLATE_EXPORT NarrowBandImageFilterBase : public FiniteDifferenceIma Defines a subregion of the narrowband. */ struct ThreadRegionType { + /** this is the actual first element */ NarrowBandIterator first; diff --git a/Modules/Numerics/Optimizers/include/itkAmoebaOptimizer.h b/Modules/Numerics/Optimizers/include/itkAmoebaOptimizer.h index 7cb6a4c8720..c68b1a38764 100644 --- a/Modules/Numerics/Optimizers/include/itkAmoebaOptimizer.h +++ b/Modules/Numerics/Optimizers/include/itkAmoebaOptimizer.h @@ -100,9 +100,10 @@ class ITKOptimizers_EXPORT AmoebaOptimizer : public SingleValuedNonLinearVnlOpti /** Set/Get the maximum number of iterations. The optimization algorithm will * terminate after the maximum number of iterations has been reached. * The default value is defined as DEFAULT_MAXIMAL_NUMBER_OF_ITERATIONS. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumNumberOfIterations, NumberOfIterationsType); itkGetConstMacro(MaximumNumberOfIterations, NumberOfIterationsType); - + /** @ITKEndGrouping */ /** Set/Get the mode which determines how the amoeba algorithm * defines the initial simplex. Default is * AutomaticInitialSimplexOn. If AutomaticInitialSimplex is on, the @@ -111,40 +112,45 @@ class ITKOptimizers_EXPORT AmoebaOptimizer : public SingleValuedNonLinearVnlOpti * used to define the initial simplex, setting the ith corner of the * simplex as [x0[0], x0[1], ..., x0[i]+InitialSimplexDelta[i], ..., * x0[d-1]]. */ + /** @ITKStartGrouping */ itkSetMacro(AutomaticInitialSimplex, bool); itkBooleanMacro(AutomaticInitialSimplex); itkGetConstMacro(AutomaticInitialSimplex, bool); - + /** @ITKEndGrouping */ /** Set/Get the mode that determines if we want to use multiple runs of the * Amoeba optimizer. If true, then the optimizer is rerun after it converges. * The additional runs are performed using a simplex initialized with the * best solution obtained by the previous runs. The edge length is half of * that from the previous iteration. */ + /** @ITKStartGrouping */ itkSetMacro(OptimizeWithRestarts, bool); itkBooleanMacro(OptimizeWithRestarts); itkGetConstMacro(OptimizeWithRestarts, bool); - + /** @ITKEndGrouping */ /** Set/Get the deltas that are used to define the initial simplex * when AutomaticInitialSimplex is off. */ + /** @ITKStartGrouping */ void SetInitialSimplexDelta(ParametersType initialSimplexDelta, bool automaticInitialSimplex = false); itkGetConstMacro(InitialSimplexDelta, ParametersType); - + /** @ITKEndGrouping */ /** The optimization algorithm will terminate when the simplex * diameter and the difference in cost function values at the corners of * the simplex falls below user specified thresholds. The simplex * diameter threshold is set via SetParametersConvergenceTolerance().*/ + /** @ITKStartGrouping */ itkSetMacro(ParametersConvergenceTolerance, double); itkGetConstMacro(ParametersConvergenceTolerance, double); - + /** @ITKEndGrouping */ /** The optimization algorithm will terminate when the simplex * diameter and the difference in cost function values at the corners of * the simplex falls below user specified thresholds. The cost function * convergence threshold is set via SetFunctionConvergenceTolerance().*/ + /** @ITKStartGrouping */ itkSetMacro(FunctionConvergenceTolerance, double); itkGetConstMacro(FunctionConvergenceTolerance, double); - + /** @ITKEndGrouping */ /** Report the reason for stopping. */ std::string GetStopConditionDescription() const override; diff --git a/Modules/Numerics/Optimizers/include/itkCumulativeGaussianOptimizer.h b/Modules/Numerics/Optimizers/include/itkCumulativeGaussianOptimizer.h index 62dcfb42e3f..b55dbe80c0d 100644 --- a/Modules/Numerics/Optimizers/include/itkCumulativeGaussianOptimizer.h +++ b/Modules/Numerics/Optimizers/include/itkCumulativeGaussianOptimizer.h @@ -68,6 +68,7 @@ class ITKOptimizers_EXPORT CumulativeGaussianOptimizer : public MultipleValuedNo itkOverrideGetNameOfClassMacro(CumulativeGaussianOptimizer); /** Set and get macros. */ + /** @ITKStartGrouping */ itkSetMacro(DifferenceTolerance, double); itkGetMacro(DifferenceTolerance, double); itkSetMacro(Verbose, bool); @@ -79,7 +80,7 @@ class ITKOptimizers_EXPORT CumulativeGaussianOptimizer : public MultipleValuedNo itkGetMacro(LowerAsymptote, double); itkGetMacro(FinalSampledArray, MeasureType *); itkGetMacro(FitError, double); - + /** @ITKEndGrouping */ void SetDataArray(MeasureType * cumGaussianArray); diff --git a/Modules/Numerics/Optimizers/include/itkFRPROptimizer.h b/Modules/Numerics/Optimizers/include/itkFRPROptimizer.h index 204f774358b..5e44728d7ba 100644 --- a/Modules/Numerics/Optimizers/include/itkFRPROptimizer.h +++ b/Modules/Numerics/Optimizers/include/itkFRPROptimizer.h @@ -90,10 +90,11 @@ class ITKOptimizers_EXPORT FRPROptimizer : public PowellOptimizer using CostFunctionPointer = CostFunctionType::Pointer; /** Convert gradient to a unit length vector */ + /** @ITKStartGrouping */ itkSetMacro(UseUnitLengthGradient, bool); itkGetConstMacro(UseUnitLengthGradient, bool); itkBooleanMacro(UseUnitLengthGradient); - + /** @ITKEndGrouping */ /** Start optimization. */ void StartOptimization() override; diff --git a/Modules/Numerics/Optimizers/include/itkGradientDescentOptimizer.h b/Modules/Numerics/Optimizers/include/itkGradientDescentOptimizer.h index ee802a3642a..c8c429185a4 100644 --- a/Modules/Numerics/Optimizers/include/itkGradientDescentOptimizer.h +++ b/Modules/Numerics/Optimizers/include/itkGradientDescentOptimizer.h @@ -98,6 +98,7 @@ class ITKOptimizers_EXPORT GradientDescentOptimizer : public SingleValuedNonLine #endif /** Methods to configure the cost function. */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(Maximize, bool); itkSetMacro(Maximize, bool); itkBooleanMacro(Maximize); @@ -121,7 +122,7 @@ class ITKOptimizers_EXPORT GradientDescentOptimizer : public SingleValuedNonLine { this->MaximizeOn(); } - + /** @ITKEndGrouping */ /** Advance one step following the gradient direction. */ virtual void AdvanceOneStep(); @@ -159,10 +160,11 @@ class ITKOptimizers_EXPORT GradientDescentOptimizer : public SingleValuedNonLine itkGetConstReferenceMacro(Value, double); /** Get Stop condition. */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(StopCondition, StopConditionGradientDescentOptimizerEnum); std::string GetStopConditionDescription() const override; - + /** @ITKEndGrouping */ /** Get Gradient condition. */ itkGetConstReferenceMacro(Gradient, DerivativeType); diff --git a/Modules/Numerics/Optimizers/include/itkInitializationBiasedParticleSwarmOptimizer.h b/Modules/Numerics/Optimizers/include/itkInitializationBiasedParticleSwarmOptimizer.h index e34032290db..78b01be92e3 100644 --- a/Modules/Numerics/Optimizers/include/itkInitializationBiasedParticleSwarmOptimizer.h +++ b/Modules/Numerics/Optimizers/include/itkInitializationBiasedParticleSwarmOptimizer.h @@ -101,6 +101,7 @@ class ITKOptimizers_EXPORT InitializationBiasedParticleSwarmOptimizer : public P * \f$p_g\f$ - parameters yielding the best function value obtained by all particles * \f$x_{init}\f$ - initial parameter values provided by user */ + /** @ITKStartGrouping */ itkSetMacro(InertiaCoefficient, CoefficientType); itkGetMacro(InertiaCoefficient, CoefficientType); itkSetMacro(PersonalCoefficient, CoefficientType); @@ -109,7 +110,7 @@ class ITKOptimizers_EXPORT InitializationBiasedParticleSwarmOptimizer : public P itkGetMacro(GlobalCoefficient, CoefficientType); itkSetMacro(InitializationCoefficient, CoefficientType); itkGetMacro(InitializationCoefficient, CoefficientType); - + /** @ITKEndGrouping */ protected: InitializationBiasedParticleSwarmOptimizer(); ~InitializationBiasedParticleSwarmOptimizer() override = default; diff --git a/Modules/Numerics/Optimizers/include/itkLBFGSBOptimizer.h b/Modules/Numerics/Optimizers/include/itkLBFGSBOptimizer.h index 3402da3ece3..866fbefe99f 100644 --- a/Modules/Numerics/Optimizers/include/itkLBFGSBOptimizer.h +++ b/Modules/Numerics/Optimizers/include/itkLBFGSBOptimizer.h @@ -104,25 +104,28 @@ class ITKOptimizers_EXPORT LBFGSBOptimizer : public SingleValuedNonLinearVnlOpti itkBooleanMacro(Trace); /** Set the lower bound value for each variable. */ + /** @ITKStartGrouping */ virtual void SetLowerBound(const BoundValueType & value); itkGetConstReferenceMacro(LowerBound, BoundValueType); - + /** @ITKEndGrouping */ /** Set the upper bound value for each variable. */ + /** @ITKStartGrouping */ virtual void SetUpperBound(const BoundValueType & value); itkGetConstReferenceMacro(UpperBound, BoundValueType); - + /** @ITKEndGrouping */ /** Set the boundary condition for each variable, where * select[i] = 0 if x[i] is unbounded, * = 1 if x[i] has only a lower bound, * = 2 if x[i] has both lower and upper bounds, and * = 3 if x[1] has only an upper bound */ + /** @ITKStartGrouping */ virtual void SetBoundSelection(const BoundSelectionType & value); itkGetConstReferenceMacro(BoundSelection, BoundSelectionType); - + /** @ITKEndGrouping */ /** Set/Get the CostFunctionConvergenceFactor. Algorithm terminates * when the reduction in cost function is less than factor * epsmcj * where epsmch is the machine precision. diff --git a/Modules/Numerics/Optimizers/include/itkMultipleValuedNonLinearVnlOptimizer.h b/Modules/Numerics/Optimizers/include/itkMultipleValuedNonLinearVnlOptimizer.h index e80b233d8ff..1c822b45dce 100644 --- a/Modules/Numerics/Optimizers/include/itkMultipleValuedNonLinearVnlOptimizer.h +++ b/Modules/Numerics/Optimizers/include/itkMultipleValuedNonLinearVnlOptimizer.h @@ -90,10 +90,11 @@ class ITKOptimizers_EXPORT MultipleValuedNonLinearVnlOptimizer : public Multiple * current parameters. For GUI update purposes, this method is a * good option, for mathematical validation you should rather call * GetValue(). */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(CachedValue, MeasureType); itkGetConstReferenceMacro(CachedDerivative, DerivativeType); itkGetConstReferenceMacro(CachedCurrentPosition, ParametersType); - + /** @ITKEndGrouping */ protected: MultipleValuedNonLinearVnlOptimizer(); ~MultipleValuedNonLinearVnlOptimizer() override; diff --git a/Modules/Numerics/Optimizers/include/itkOnePlusOneEvolutionaryOptimizer.h b/Modules/Numerics/Optimizers/include/itkOnePlusOneEvolutionaryOptimizer.h index 2438fe6112c..ecd51d5d479 100644 --- a/Modules/Numerics/Optimizers/include/itkOnePlusOneEvolutionaryOptimizer.h +++ b/Modules/Numerics/Optimizers/include/itkOnePlusOneEvolutionaryOptimizer.h @@ -84,10 +84,11 @@ class ITKOptimizers_EXPORT OnePlusOneEvolutionaryOptimizer : public SingleValued using NormalVariateGeneratorType = Statistics::RandomVariateGeneratorBase; /** Set if the Optimizer should Maximize the metric */ + /** @ITKStartGrouping */ itkSetMacro(Maximize, bool); itkBooleanMacro(Maximize); itkGetConstReferenceMacro(Maximize, bool); - + /** @ITKEndGrouping */ bool GetMinimize() const { @@ -110,26 +111,31 @@ class ITKOptimizers_EXPORT OnePlusOneEvolutionaryOptimizer : public SingleValued } /** Set/Get maximum iteration limit. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumIteration, unsigned int); itkGetConstReferenceMacro(MaximumIteration, unsigned int); - + /** @ITKEndGrouping */ /** Set/Get the search radius grow factor in parameter space. */ + /** @ITKStartGrouping */ itkSetMacro(GrowthFactor, double); itkGetConstReferenceMacro(GrowthFactor, double); - + /** @ITKEndGrouping */ /** Set/Get the search radius shrink factor. */ + /** @ITKStartGrouping */ itkSetMacro(ShrinkFactor, double); itkGetConstReferenceMacro(ShrinkFactor, double); - + /** @ITKEndGrouping */ /** Set/Get initial search radius in parameter space */ + /** @ITKStartGrouping */ itkSetMacro(InitialRadius, double); itkGetConstReferenceMacro(InitialRadius, double); - + /** @ITKEndGrouping */ /** Set/Get the minimal size of search radius * (frobenius_norm of covariance matrix). */ + /** @ITKStartGrouping */ itkSetMacro(Epsilon, double); itkGetConstReferenceMacro(Epsilon, double); - + /** @ITKEndGrouping */ /** Get the current Frobenius norm of covariance matrix */ itkGetConstReferenceMacro(FrobeniusNorm, double); @@ -146,13 +152,14 @@ class ITKOptimizers_EXPORT OnePlusOneEvolutionaryOptimizer : public SingleValued Initialize(double initialRadius, double grow = -1, double shrink = -1); /** Return Current Value */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(CurrentCost, MeasureType); MeasureType GetValue() const { return this->GetCurrentCost(); } - + /** @ITKEndGrouping */ /** Return Current Iteration */ itkGetConstReferenceMacro(CurrentIteration, unsigned int); diff --git a/Modules/Numerics/Optimizers/include/itkOptimizer.h b/Modules/Numerics/Optimizers/include/itkOptimizer.h index 0ac2d7fb8a0..264b1b7d28b 100644 --- a/Modules/Numerics/Optimizers/include/itkOptimizer.h +++ b/Modules/Numerics/Optimizers/include/itkOptimizer.h @@ -76,9 +76,10 @@ class ITKOptimizers_EXPORT Optimizer : public Object SetScales(const ScalesType & scales); /** Get current parameters scaling. */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(Scales, ScalesType); itkGetConstReferenceMacro(InverseScales, ScalesType); - + /** @ITKEndGrouping */ /** Get current position of the optimization. */ itkGetConstReferenceMacro(CurrentPosition, ParametersType); diff --git a/Modules/Numerics/Optimizers/include/itkParticleSwarmOptimizer.h b/Modules/Numerics/Optimizers/include/itkParticleSwarmOptimizer.h index c3033293e68..1fdfc4c4c8c 100644 --- a/Modules/Numerics/Optimizers/include/itkParticleSwarmOptimizer.h +++ b/Modules/Numerics/Optimizers/include/itkParticleSwarmOptimizer.h @@ -84,13 +84,14 @@ class ITKOptimizers_EXPORT ParticleSwarmOptimizer : public ParticleSwarmOptimize * p_i - parameters yielding the best function value obtained by this particle * p_g - parameters yielding the best function value obtained by all particles */ + /** @ITKStartGrouping */ itkSetMacro(InertiaCoefficient, double); itkGetMacro(InertiaCoefficient, double); itkSetMacro(PersonalCoefficient, double); itkGetMacro(PersonalCoefficient, double); itkSetMacro(GlobalCoefficient, double); itkGetMacro(GlobalCoefficient, double); - + /** @ITKEndGrouping */ protected: ParticleSwarmOptimizer(); ~ParticleSwarmOptimizer() override; diff --git a/Modules/Numerics/Optimizers/include/itkParticleSwarmOptimizerBase.h b/Modules/Numerics/Optimizers/include/itkParticleSwarmOptimizerBase.h index 05bb7916224..a24c02118f0 100644 --- a/Modules/Numerics/Optimizers/include/itkParticleSwarmOptimizerBase.h +++ b/Modules/Numerics/Optimizers/include/itkParticleSwarmOptimizerBase.h @@ -89,29 +89,32 @@ class ITKOptimizers_EXPORT ParticleSwarmOptimizerBase : public SingleValuedNonLi * If the optimum is expected to be near the initial value it is likely * that initializing with a normal distribution will result in faster * convergence.*/ + /** @ITKStartGrouping */ itkSetMacro(InitializeNormalDistribution, bool); itkGetMacro(InitializeNormalDistribution, bool); itkBooleanMacro(InitializeNormalDistribution); - + /** @ITKEndGrouping */ /** * Specify the initial swarm. Useful for evaluating PSO variants. If the * initial swarm is set it will be used. To revert to random initialization * (uniform or normal particle distributions) set using an empty swarm. */ + /** @ITKStartGrouping */ void SetInitialSwarm(const SwarmType & initialSwarm); void ClearSwarm(); - + /** @ITKEndGrouping */ /** * Indicate whether or not to output the swarm information when printing an * object. By default this option is turned off as it generates too much * information. */ + /** @ITKStartGrouping */ itkSetMacro(PrintSwarm, bool); itkGetMacro(PrintSwarm, bool); itkBooleanMacro(PrintSwarm); - + /** @ITKEndGrouping */ /** Start optimization. */ void StartOptimization() override; @@ -119,30 +122,34 @@ class ITKOptimizers_EXPORT ParticleSwarmOptimizerBase : public SingleValuedNonLi /** Set/Get number of particles in the swarm - the maximal number of function evaluations is m_MaximalNumberOfIterations*m_NumberOfParticles */ + /** @ITKStartGrouping */ void SetNumberOfParticles(NumberOfParticlesType n); itkGetMacro(NumberOfParticles, NumberOfParticlesType); - + /** @ITKEndGrouping */ /** Set/Get maximal number of iterations - the maximal number of function evaluations is m_MaximalNumberOfIterations*m_NumberOfParticles */ + /** @ITKStartGrouping */ itkSetMacro(MaximalNumberOfIterations, NumberOfIterationsType); itkGetMacro(MaximalNumberOfIterations, NumberOfIterationsType); - + /** @ITKEndGrouping */ /** Set/Get the number of generations to continue with minimal improvement in * the function value, |f_best(g_i) - f_best(g_k)| & bounds, unsigned int n); - + /** @ITKEndGrouping */ ParameterBoundsType GetParameterBounds() const; @@ -162,28 +169,32 @@ class ITKOptimizers_EXPORT ParticleSwarmOptimizerBase : public SingleValuedNonLi */ itkSetMacro(FunctionConvergenceTolerance, MeasureType); itkGetMacro(FunctionConvergenceTolerance, MeasureType); - /**Set parameters convergence tolerance using the same value for all, sz, + + /** Set parameters convergence tolerance using the same value for all, sz, parameters*/ + /** @ITKStartGrouping */ void SetParametersConvergenceTolerance(ValueType convergenceTolerance, unsigned int sz); itkSetMacro(ParametersConvergenceTolerance, ParametersType); itkGetMacro(ParametersConvergenceTolerance, ParametersType); itkGetMacro(PercentageParticlesConverged, double); itkSetMacro(PercentageParticlesConverged, double); - - /**Set the random number seed for the swarm. Use this method to + /** @ITKEndGrouping */ + /** Set the random number seed for the swarm. Use this method to * produce repeatable results, typically, for testing. */ + /** @ITKStartGrouping */ itkSetMacro(Seed, RandomVariateGeneratorType::IntegerType); itkGetMacro(Seed, RandomVariateGeneratorType::IntegerType); - + /** @ITKEndGrouping */ /** Use a specific seed to initialize the random number * generator. If On, use m_Seed to seed the random number * generator. Default is Off. */ + /** @ITKStartGrouping */ itkSetMacro(UseSeed, bool); itkGetMacro(UseSeed, bool); itkBooleanMacro(UseSeed); - + /** @ITKEndGrouping */ /** Get the function value for the current position. * NOTE: This value is only valid during and after the execution of the * StartOptimization() method.*/ diff --git a/Modules/Numerics/Optimizers/include/itkPowellOptimizer.h b/Modules/Numerics/Optimizers/include/itkPowellOptimizer.h index 1b09fda5f38..f21501a51e1 100644 --- a/Modules/Numerics/Optimizers/include/itkPowellOptimizer.h +++ b/Modules/Numerics/Optimizers/include/itkPowellOptimizer.h @@ -81,42 +81,49 @@ class ITKOptimizers_EXPORT PowellOptimizer : public SingleValuedNonLinearOptimiz using CostFunctionPointer = CostFunctionType::Pointer; /** Set if the Optimizer should Maximize the metric */ + /** @ITKStartGrouping */ itkSetMacro(Maximize, bool); itkBooleanMacro(Maximize); itkGetConstReferenceMacro(Maximize, bool); - + /** @ITKEndGrouping */ /** Set/Get maximum iteration limit. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumIteration, unsigned int); itkGetConstReferenceMacro(MaximumIteration, unsigned int); - + /** @ITKEndGrouping */ /** Set/Get the maximum number of line search iterations */ + /** @ITKStartGrouping */ itkSetMacro(MaximumLineIteration, unsigned int); itkGetConstMacro(MaximumLineIteration, unsigned int); - + /** @ITKEndGrouping */ /** Set/Get StepLength for the (scaled) spacing of the sampling of * parameter space while bracketing the extremum */ + /** @ITKStartGrouping */ itkSetMacro(StepLength, double); itkGetConstReferenceMacro(StepLength, double); - + /** @ITKEndGrouping */ /** Set/Get StepTolerance. Once the local extreme is known to be within this * distance of the current parameter values, optimization terminates */ + /** @ITKStartGrouping */ itkSetMacro(StepTolerance, double); itkGetConstReferenceMacro(StepTolerance, double); - + /** @ITKEndGrouping */ /** Set/Get ValueTolerance. Once this current cost function value is known * to be within this tolerance of the cost function value at the local * extreme, optimization terminates */ + /** @ITKStartGrouping */ itkSetMacro(ValueTolerance, double); itkGetConstReferenceMacro(ValueTolerance, double); - + /** @ITKEndGrouping */ /** Return Current Value */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(CurrentCost, MeasureType); MeasureType GetValue() const { return this->GetCurrentCost(); } - + /** @ITKEndGrouping */ /** Return Current Iteration */ itkGetConstReferenceMacro(CurrentIteration, unsigned int); diff --git a/Modules/Numerics/Optimizers/include/itkRegularStepGradientDescentBaseOptimizer.h b/Modules/Numerics/Optimizers/include/itkRegularStepGradientDescentBaseOptimizer.h index 1beb716d798..7d026c957f1 100644 --- a/Modules/Numerics/Optimizers/include/itkRegularStepGradientDescentBaseOptimizer.h +++ b/Modules/Numerics/Optimizers/include/itkRegularStepGradientDescentBaseOptimizer.h @@ -84,6 +84,7 @@ class ITKOptimizers_EXPORT RegularStepGradientDescentBaseOptimizer : public Sing static constexpr StopConditionEnum Unknown = StopConditionEnum::Unknown; #endif /** Specify whether to minimize or maximize the cost function. */ + /** @ITKStartGrouping */ itkSetMacro(Maximize, bool); itkGetConstReferenceMacro(Maximize, bool); itkBooleanMacro(Maximize); @@ -107,7 +108,7 @@ class ITKOptimizers_EXPORT RegularStepGradientDescentBaseOptimizer : public Sing { SetMaximize(true); } - + /** @ITKEndGrouping */ /** Start optimization. */ void StartOptimization() override; @@ -123,6 +124,7 @@ class ITKOptimizers_EXPORT RegularStepGradientDescentBaseOptimizer : public Sing StopOptimization(); /** Set/Get parameters to control the optimization process. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumStepLength, double); itkSetMacro(MinimumStepLength, double); itkSetMacro(RelaxationFactor, double); @@ -138,7 +140,7 @@ class ITKOptimizers_EXPORT RegularStepGradientDescentBaseOptimizer : public Sing itkGetConstReferenceMacro(StopCondition, StopConditionEnum); itkGetConstReferenceMacro(Value, MeasureType); itkGetConstReferenceMacro(Gradient, DerivativeType); - + /** @ITKEndGrouping */ /** Get the reason for termination */ std::string GetStopConditionDescription() const override; diff --git a/Modules/Numerics/Optimizers/include/itkSPSAOptimizer.h b/Modules/Numerics/Optimizers/include/itkSPSAOptimizer.h index e9dbcb9a77a..a7e9bd18bb1 100644 --- a/Modules/Numerics/Optimizers/include/itkSPSAOptimizer.h +++ b/Modules/Numerics/Optimizers/include/itkSPSAOptimizer.h @@ -139,6 +139,7 @@ class ITKOptimizers_EXPORT SPSAOptimizer : public SingleValuedNonLinearOptimizer itkGetConstReferenceMacro(Gradient, DerivativeType); /** Set/Get a. */ + /** @ITKStartGrouping */ itkSetMacro(Sa, double); itkGetConstMacro(Sa, double); // For backward compatibility @@ -152,8 +153,9 @@ class ITKOptimizers_EXPORT SPSAOptimizer : public SingleValuedNonLinearOptimizer { return GetSa(); } - + /** @ITKEndGrouping */ /** Set/Get c. */ + /** @ITKStartGrouping */ itkSetMacro(Sc, double); itkGetConstMacro(Sc, double); // For backward compatibility @@ -167,20 +169,24 @@ class ITKOptimizers_EXPORT SPSAOptimizer : public SingleValuedNonLinearOptimizer { return GetSc(); } - + /** @ITKEndGrouping */ /** Set/Get A. */ + /** @ITKStartGrouping */ itkSetMacro(A, double); itkGetConstMacro(A, double); - + /** @ITKEndGrouping */ /** Set/Get alpha. */ + /** @ITKStartGrouping */ itkSetMacro(Alpha, double); itkGetConstMacro(Alpha, double); - + /** @ITKEndGrouping */ /** Set/Get gamma. */ + /** @ITKStartGrouping */ itkSetMacro(Gamma, double); itkGetConstMacro(Gamma, double); - + /** @ITKEndGrouping */ /** Methods to configure the cost function. */ + /** @ITKStartGrouping */ itkGetConstMacro(Maximize, bool); itkSetMacro(Maximize, bool); itkBooleanMacro(Maximize); @@ -204,15 +210,16 @@ class ITKOptimizers_EXPORT SPSAOptimizer : public SingleValuedNonLinearOptimizer { this->MaximizeOn(); } - + /** @ITKEndGrouping */ /** Set/Get the number of perturbation used to construct * a gradient estimate g_k. * q = NumberOfPerturbations * g_k = 1/q sum_{j=1..q} g^(j)_k */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfPerturbations, SizeValueType); itkGetConstMacro(NumberOfPerturbations, SizeValueType); - + /** @ITKEndGrouping */ /** * Get the state of convergence in the last iteration. When the * StateOfConvergence is lower than the Tolerance, and the minimum @@ -227,21 +234,25 @@ class ITKOptimizers_EXPORT SPSAOptimizer : public SingleValuedNonLinearOptimizer itkGetConstMacro(StateOfConvergence, double); /** Set/Get StateOfConvergenceDecayRate (number between 0 and 1). */ + /** @ITKStartGrouping */ itkSetMacro(StateOfConvergenceDecayRate, double); itkGetConstMacro(StateOfConvergenceDecayRate, double); - + /** @ITKEndGrouping */ /** Set/Get the minimum number of iterations */ + /** @ITKStartGrouping */ itkSetMacro(MinimumNumberOfIterations, SizeValueType); itkGetConstMacro(MinimumNumberOfIterations, SizeValueType); - + /** @ITKEndGrouping */ /** Set/Get the maximum number of iterations. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumNumberOfIterations, SizeValueType); itkGetConstMacro(MaximumNumberOfIterations, SizeValueType); - + /** @ITKEndGrouping */ /** Set/Get Tolerance */ + /** @ITKStartGrouping */ itkSetMacro(Tolerance, double); itkGetConstMacro(Tolerance, double); - + /** @ITKEndGrouping */ /** Get the reason for termination */ std::string GetStopConditionDescription() const override; diff --git a/Modules/Numerics/Optimizers/include/itkSingleValuedNonLinearVnlOptimizer.h b/Modules/Numerics/Optimizers/include/itkSingleValuedNonLinearVnlOptimizer.h index a4e4c545d75..a3d3665519f 100644 --- a/Modules/Numerics/Optimizers/include/itkSingleValuedNonLinearVnlOptimizer.h +++ b/Modules/Numerics/Optimizers/include/itkSingleValuedNonLinearVnlOptimizer.h @@ -70,6 +70,7 @@ class ITKOptimizers_EXPORT SingleValuedNonLinearVnlOptimizer : public SingleValu * Maximization is implemented here by notifying the CostFunctionAdaptor * which in its turn will multiply the function values and its derivative by * -1.0. */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(Maximize, bool); itkSetMacro(Maximize, bool); itkBooleanMacro(Maximize); @@ -93,16 +94,17 @@ class ITKOptimizers_EXPORT SingleValuedNonLinearVnlOptimizer : public SingleValu { this->MaximizeOn(); } - + /** @ITKEndGrouping */ /** Return Cached Values. These method have the advantage of not triggering a * recomputation of the metric value, but it has the disadvantage of returning * a value that may not be the one corresponding to the current parameters. For * GUI update purposes, this method is a good option, for mathematical * validation you should rather call GetValue(). */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(CachedValue, MeasureType); itkGetConstReferenceMacro(CachedDerivative, DerivativeType); itkGetConstReferenceMacro(CachedCurrentPosition, ParametersType); - + /** @ITKEndGrouping */ /** Returns true if derived optimizer supports using scales. * For optimizers that do not support scaling, this * default function is overridden to return false.*/ diff --git a/Modules/Numerics/Optimizersv4/include/itkAmoebaOptimizerv4.h b/Modules/Numerics/Optimizersv4/include/itkAmoebaOptimizerv4.h index 26c46ec8a2d..191708efd51 100644 --- a/Modules/Numerics/Optimizersv4/include/itkAmoebaOptimizerv4.h +++ b/Modules/Numerics/Optimizersv4/include/itkAmoebaOptimizerv4.h @@ -99,40 +99,45 @@ class ITKOptimizersv4_EXPORT AmoebaOptimizerv4 : public SingleValuedNonLinearVnl * used to define the initial simplex, setting the ith corner of the * simplex as [x0[0], x0[1], ..., x0[i]+InitialSimplexDelta[i], ..., * x0[d-1]]. */ + /** @ITKStartGrouping */ itkSetMacro(AutomaticInitialSimplex, bool); itkBooleanMacro(AutomaticInitialSimplex); itkGetConstMacro(AutomaticInitialSimplex, bool); - + /** @ITKEndGrouping */ /** Set/Get the mode that determines if we want to use multiple runs of the * Amoeba optimizer. If true, then the optimizer is rerun after it converges. * The additional runs are performed using a simplex initialized with the * best solution obtained by the previous runs. The edge length is half of * that from the previous iteration. */ + /** @ITKStartGrouping */ itkSetMacro(OptimizeWithRestarts, bool); itkBooleanMacro(OptimizeWithRestarts); itkGetConstMacro(OptimizeWithRestarts, bool); - + /** @ITKEndGrouping */ /** Set/Get the deltas that are used to define the initial simplex * when AutomaticInitialSimplex is off. */ + /** @ITKStartGrouping */ void SetInitialSimplexDelta(ParametersType initialSimplexDelta, bool automaticInitialSimplex = false); itkGetConstMacro(InitialSimplexDelta, ParametersType); - + /** @ITKEndGrouping */ /** The optimization algorithm will terminate when the simplex * diameter and the difference in cost function values at the corners of * the simplex falls below user specified thresholds. The simplex * diameter threshold is set via SetParametersConvergenceTolerance().*/ + /** @ITKStartGrouping */ itkSetMacro(ParametersConvergenceTolerance, double); itkGetConstMacro(ParametersConvergenceTolerance, double); - + /** @ITKEndGrouping */ /** The optimization algorithm will terminate when the simplex * diameter and the difference in cost function values at the corners of * the simplex falls below user specified thresholds. The cost function * convergence threshold is set via SetFunctionConvergenceTolerance().*/ + /** @ITKStartGrouping */ itkSetMacro(FunctionConvergenceTolerance, double); itkGetConstMacro(FunctionConvergenceTolerance, double); - + /** @ITKEndGrouping */ /** Report the reason for stopping. */ std::string GetStopConditionDescription() const override; diff --git a/Modules/Numerics/Optimizersv4/include/itkCommandIterationUpdatev4.h b/Modules/Numerics/Optimizersv4/include/itkCommandIterationUpdatev4.h index 9ab6b4b9dc4..f6bae52ab32 100644 --- a/Modules/Numerics/Optimizersv4/include/itkCommandIterationUpdatev4.h +++ b/Modules/Numerics/Optimizersv4/include/itkCommandIterationUpdatev4.h @@ -126,10 +126,11 @@ class CommandIterationUpdatev4 : public Command /** * Print parameters at each iteration */ + /** @ITKStartGrouping */ itkSetMacro(PrintParameters, bool); itkGetMacro(PrintParameters, bool); itkBooleanMacro(PrintParameters); - + /** @ITKEndGrouping */ protected: /** diff --git a/Modules/Numerics/Optimizersv4/include/itkGradientDescentLineSearchOptimizerv4.h b/Modules/Numerics/Optimizersv4/include/itkGradientDescentLineSearchOptimizerv4.h index ae818d1fd24..b94d529c479 100644 --- a/Modules/Numerics/Optimizersv4/include/itkGradientDescentLineSearchOptimizerv4.h +++ b/Modules/Numerics/Optimizersv4/include/itkGradientDescentLineSearchOptimizerv4.h @@ -91,9 +91,10 @@ class ITK_TEMPLATE_EXPORT GradientDescentLineSearchOptimizerv4Template /** The epsilon determines the accuracy of the line search * i.e. the energy alteration that is considered convergent. */ + /** @ITKStartGrouping */ itkSetMacro(Epsilon, TInternalComputationValueType); itkGetMacro(Epsilon, TInternalComputationValueType); - + /** @ITKEndGrouping */ /** The upper and lower limit below determine the range * of values over which the learning rate can be adjusted * by the golden section line search. The update can then @@ -103,13 +104,14 @@ class ITK_TEMPLATE_EXPORT GradientDescentLineSearchOptimizerv4Template * NewParams = OldParams + UpperLimit * gradient * Reasonable values might be 0 and 2. */ + /** @ITKStartGrouping */ itkSetMacro(LowerLimit, TInternalComputationValueType); itkGetMacro(LowerLimit, TInternalComputationValueType); itkSetMacro(UpperLimit, TInternalComputationValueType); itkGetMacro(UpperLimit, TInternalComputationValueType); itkSetMacro(MaximumLineSearchIterations, unsigned int); itkGetMacro(MaximumLineSearchIterations, unsigned int); - + /** @ITKEndGrouping */ protected: /** Advance one Step following the gradient direction. * Includes transform update. */ @@ -147,6 +149,7 @@ class ITK_TEMPLATE_EXPORT GradientDescentLineSearchOptimizerv4Template /** Controls the maximum recursion depth for the golden section search */ unsigned int m_MaximumLineSearchIterations{}; + /** Counts the recursion depth for the golden section search */ unsigned int m_LineSearchIterations{}; }; diff --git a/Modules/Numerics/Optimizersv4/include/itkGradientDescentOptimizerBasev4.h b/Modules/Numerics/Optimizersv4/include/itkGradientDescentOptimizerBasev4.h index ce9a486d39a..4d43f995e50 100644 --- a/Modules/Numerics/Optimizersv4/include/itkGradientDescentOptimizerBasev4.h +++ b/Modules/Numerics/Optimizersv4/include/itkGradientDescentOptimizerBasev4.h @@ -133,11 +133,12 @@ class ITK_TEMPLATE_EXPORT GradientDescentOptimizerBasev4Template * * \sa EstimateLearningRate() */ + /** @ITKStartGrouping */ virtual void ModifyGradientByScales(); virtual void ModifyGradientByLearningRate(); - + /** @ITKEndGrouping */ using IndexRangeType = ThreadedIndexedContainerPartitioner::IndexRangeType; /** Derived classes define this worker method to modify the gradient by scales. @@ -161,9 +162,10 @@ class ITK_TEMPLATE_EXPORT GradientDescentOptimizerBasev4Template protected: /** Default constructor */ + /** @ITKStartGrouping */ GradientDescentOptimizerBasev4Template(); ~GradientDescentOptimizerBasev4Template() override = default; - + /** @ITKEndGrouping */ /** Flag to control use of the ScalesEstimator (if set) for * automatic learning step estimation at *each* iteration. */ diff --git a/Modules/Numerics/Optimizersv4/include/itkGradientDescentOptimizerv4.h b/Modules/Numerics/Optimizersv4/include/itkGradientDescentOptimizerv4.h index 0738f530958..cfa0b13e30e 100644 --- a/Modules/Numerics/Optimizersv4/include/itkGradientDescentOptimizerv4.h +++ b/Modules/Numerics/Optimizersv4/include/itkGradientDescentOptimizerv4.h @@ -110,18 +110,20 @@ class ITK_TEMPLATE_EXPORT GradientDescentOptimizerv4Template * Set/Get the learning rate to apply. It is overridden by * automatic learning rate estimation if enabled. See main documentation. */ + /** @ITKStartGrouping */ itkSetMacro(LearningRate, TInternalComputationValueType); itkGetConstReferenceMacro(LearningRate, TInternalComputationValueType); - + /** @ITKEndGrouping */ /** Set/Get the maximum step size, in physical space units. * * Only relevant when m_ScalesEstimator is set by user, * and automatic learning rate estimation is enabled. * See main documentation. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumStepSizeInPhysicalUnits, TInternalComputationValueType); itkGetConstReferenceMacro(MaximumStepSizeInPhysicalUnits, TInternalComputationValueType); - + /** @ITKEndGrouping */ /** Option to use ScalesEstimator for learning rate estimation at * *each* iteration. The estimation overrides the learning rate * set by SetLearningRate(). Default is false. @@ -129,10 +131,11 @@ class ITK_TEMPLATE_EXPORT GradientDescentOptimizerv4Template * \sa SetDoEstimateLearningRateOnce() * \sa SetScalesEstimator() */ + /** @ITKStartGrouping */ itkSetMacro(DoEstimateLearningRateAtEachIteration, bool); itkGetConstReferenceMacro(DoEstimateLearningRateAtEachIteration, bool); itkBooleanMacro(DoEstimateLearningRateAtEachIteration); - + /** @ITKEndGrouping */ /** Option to use ScalesEstimator for learning rate estimation * only *once*, during first iteration. The estimation overrides the * learning rate set by SetLearningRate(). Default is true. @@ -140,10 +143,11 @@ class ITK_TEMPLATE_EXPORT GradientDescentOptimizerv4Template * \sa SetDoEstimateLearningRateAtEachIteration() * \sa SetScalesEstimator() */ + /** @ITKStartGrouping */ itkSetMacro(DoEstimateLearningRateOnce, bool); itkGetConstReferenceMacro(DoEstimateLearningRateOnce, bool); itkBooleanMacro(DoEstimateLearningRateOnce); - + /** @ITKEndGrouping */ /** Minimum convergence value for convergence checking. * The convergence checker calculates convergence value by fitting to * a window of the energy profile. When the convergence value reaches @@ -181,10 +185,11 @@ class ITK_TEMPLATE_EXPORT GradientDescentOptimizerv4Template * parameters, which can be large when working with high-dimensional * transforms such as DisplacementFieldTransform. */ + /** @ITKStartGrouping */ itkSetMacro(ReturnBestParametersAndValue, bool); itkGetConstReferenceMacro(ReturnBestParametersAndValue, bool); itkBooleanMacro(ReturnBestParametersAndValue); - + /** @ITKEndGrouping */ /** Start and run the optimization. */ void StartOptimization(bool doOnlyInitialization = false) override; diff --git a/Modules/Numerics/Optimizersv4/include/itkLBFGS2Optimizerv4.h b/Modules/Numerics/Optimizersv4/include/itkLBFGS2Optimizerv4.h index 171e48ea1e5..2fcbcbb2e49 100644 --- a/Modules/Numerics/Optimizersv4/include/itkLBFGS2Optimizerv4.h +++ b/Modules/Numerics/Optimizersv4/include/itkLBFGS2Optimizerv4.h @@ -41,8 +41,10 @@ class LBFGS2Optimizerv4Enums { /** The default algorithm (MoreThuente method). */ LINESEARCH_DEFAULT = 0, + /** MoreThuente method proposed by More and Thuente \cite more1994. */ LINESEARCH_MORETHUENTE = 0, + /** * Backtracking method with the Armijo condition. * The backtracking method finds the step length such that it satisfies @@ -53,8 +55,10 @@ class LBFGS2Optimizerv4Enums * a is the step length. */ LINESEARCH_BACKTRACKING_ARMIJO = 1, + /** The backtracking method with the default (regular Wolfe) condition. */ LINESEARCH_BACKTRACKING = 2, + /** * Backtracking method with regular Wolfe condition. * The backtracking method finds the step length such that it satisfies @@ -66,6 +70,7 @@ class LBFGS2Optimizerv4Enums * a is the step length. */ LINESEARCH_BACKTRACKING_WOLFE = 2, + /** * Backtracking method with strong Wolfe condition. * The backtracking method finds the step length such that it satisfies @@ -139,7 +144,6 @@ template class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template : public GradientDescentOptimizerv4Template { - public: ITK_DISALLOW_COPY_AND_MOVE(LBFGS2Optimizerv4Template); @@ -165,6 +169,7 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template using PrecisionType = double; static_assert(std::is_same::value, "LBFGS2Optimizerv4Template only supports double precision"); + /** Standard "Self" type alias. */ using Self = LBFGS2Optimizerv4Template; using Superclass = GradientDescentOptimizerv4Template; @@ -205,11 +210,12 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template * (corrections). The default value is \c 6. Values less than \c 3 are * not recommended. Large values will result in excessive computing time. */ + /** @ITKStartGrouping */ void SetHessianApproximationAccuracy(int m); int GetHessianApproximationAccuracy() const; - + /** @ITKEndGrouping */ /** * Set/Get epsilon for convergence test. * This parameter determines the accuracy with which the solution is to @@ -218,11 +224,12 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template * where ||.|| denotes the Euclidean (L2) norm. The default value is * \c 1e-5. */ + /** @ITKStartGrouping */ void SetSolutionAccuracy(PrecisionType epsilon); PrecisionType GetSolutionAccuracy() const; - + /** @ITKEndGrouping */ /** * Set/Get distance for delta-based convergence test. * This parameter determines the distance, in iterations, to compute @@ -230,11 +237,12 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template * parameter is zero, the library does not perform the delta-based * convergence test. The default value is \c 0. */ + /** @ITKStartGrouping */ void SetDeltaConvergenceDistance(int nPast); int GetDeltaConvergenceDistance() const; - + /** @ITKEndGrouping */ /** * Delta for convergence test. * This parameter determines the minimum rate of decrease of the @@ -245,11 +253,12 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template * the objective value of the current iteration. * The default value is \c 0. */ + /** @ITKStartGrouping */ void SetDeltaConvergenceTolerance(PrecisionType tol); PrecisionType GetDeltaConvergenceTolerance() const; - + /** @ITKEndGrouping */ /** * The maximum number of iterations. * The lbfgs() function terminates an optimization process with @@ -258,13 +267,15 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template * optimization process until a convergence or error. The default value * is \c 0. */ + /** @ITKStartGrouping */ void SetMaximumIterations(int maxIterations); int GetMaximumIterations() const; - + /** @ITKEndGrouping */ /** Aliased to Set/Get MaximumIterations to match base class interface. */ + /** @ITKStartGrouping */ SizeValueType GetNumberOfIterations() const override { @@ -275,28 +286,30 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template { SetMaximumIterations(static_cast(_arg)); } - + /** @ITKEndGrouping */ /** * The line search algorithm. * This parameter specifies a line search algorithm to be used by the * L-BFGS routine. See lbfgs.h for enumeration of line search type. * Defaults to More-Thuente's method. */ + /** @ITKStartGrouping */ void SetLineSearch(const LineSearchMethodEnum & linesearch); LineSearchMethodEnum GetLineSearch() const; - + /** @ITKEndGrouping */ /** * The maximum number of trials for the line search. * This parameter controls the number of function and gradients evaluations * per iteration for the line search routine. The default value is \c 20. */ + /** @ITKStartGrouping */ void SetMaximumLineSearchEvaluations(int n); int GetMaximumLineSearchEvaluations() const; - + /** @ITKEndGrouping */ /** * The minimum step of the line search routine. * The default value is \c 1e-20. This value need not be modified unless @@ -304,11 +317,12 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template * problem is extremely badly scaled (in which case the exponents should * be increased). */ + /** @ITKStartGrouping */ void SetMinimumLineSearchStep(PrecisionType step); PrecisionType GetMinimumLineSearchStep() const; - + /** @ITKEndGrouping */ /** * The maximum step of the line search. * The default value is \c 1e+20. This value need not be modified unless @@ -316,21 +330,23 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template * problem is extremely badly scaled (in which case the exponents should * be increased). */ + /** @ITKStartGrouping */ void SetMaximumLineSearchStep(PrecisionType step); PrecisionType GetMaximumLineSearchStep() const; - + /** @ITKEndGrouping */ /** * A parameter to control the accuracy of the line search routine. * The default value is \c 1e-4. This parameter should be greater * than zero and smaller than \c 0.5. */ + /** @ITKStartGrouping */ void SetLineSearchAccuracy(PrecisionType ftol); PrecisionType GetLineSearchAccuracy() const; - + /** @ITKEndGrouping */ /** * A coefficient for the Wolfe condition. * This parameter is valid only when the backtracking line-search @@ -340,11 +356,12 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template * The default value is \c 0.9. This parameter should be greater * than the \c ftol parameter and smaller than \c 1.0. */ + /** @ITKStartGrouping */ void SetWolfeCoefficient(PrecisionType wc); PrecisionType GetWolfeCoefficient() const; - + /** @ITKEndGrouping */ /** * A parameter to control the gradient accuracy of the More-Thuente * line search routine. @@ -356,11 +373,12 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template * greater than the \c ftol parameter (\c 1e-4) and smaller than * \c 1.0. */ + /** @ITKStartGrouping */ void SetLineSearchGradientAccuracy(PrecisionType gtol); PrecisionType GetLineSearchGradientAccuracy() const; - + /** @ITKEndGrouping */ /** * The machine precision for floating-point values. * This parameter must be a positive value set by a client program to @@ -368,11 +386,12 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template * with the status code (\c LBFGSERR_ROUNDING_ERROR) if the relative width * of the interval of uncertainty is less than this parameter. */ + /** @ITKStartGrouping */ void SetMachinePrecisionTolerance(PrecisionType xtol); PrecisionType GetMachinePrecisionTolerance() const; - + /** @ITKEndGrouping */ /** * Coefficient for the L1 norm of variables. * This parameter should be set to zero for standard minimization @@ -386,11 +405,12 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template * the function value F(x) and gradients G(x) as usual. The default value * is zero. */ + /** @ITKStartGrouping */ void SetOrthantwiseCoefficient(PrecisionType orthant_c); PrecisionType GetOrthantwiseCoefficient() const; - + /** @ITKEndGrouping */ /** * Start index for computing L1 norm of the variables. * This parameter is valid only for OWL-QN method @@ -405,11 +425,12 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template * variables, \f$x_1, ..., x_{b-1}\f$ (e.g., a bias term of logistic * regression) from being regularized. The default value is zero. */ + /** @ITKStartGrouping */ void SetOrthantwiseStart(int start); int GetOrthantwiseStart() const; - + /** @ITKEndGrouping */ /** * End index for computing L1 norm of the variables. * This parameter is valid only for OWL-QN method @@ -417,13 +438,15 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template * specifies the index number at which the library stops computing the * L1 norm of the variables x, */ + /** @ITKStartGrouping */ void SetOrthantwiseEnd(int end); int GetOrthantwiseEnd() const; - + /** @ITKEndGrouping */ /** Get parameter norm of current iteration */ itkGetConstMacro(CurrentParameterNorm, PrecisionType); + /** Get gradient norm of current iteration */ itkGetConstMacro(CurrentGradientNorm, PrecisionType); @@ -437,10 +460,11 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template * *each* iteration. The estimation overrides the scales * set by SetScales(). Default is true. */ + /** @ITKStartGrouping */ itkSetMacro(EstimateScalesAtEachIteration, bool); itkGetConstReferenceMacro(EstimateScalesAtEachIteration, bool); itkBooleanMacro(EstimateScalesAtEachIteration); - + /** @ITKEndGrouping */ protected: LBFGS2Optimizerv4Template(); ~LBFGS2Optimizerv4Template() override; @@ -473,7 +497,7 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template int k, int ls); - //** Function evaluation callback from libLBFGS forward to instance */ + /** Function evaluation callback from libLBFGS forward to instance */ static PrecisionType EvaluateCostCallback(void * instance, const PrecisionType * x, @@ -499,6 +523,7 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template /** * itkGradientDecentOptimizerv4Template specific non supported methods. */ + /** @ITKStartGrouping */ void SetMinimumConvergenceValue(PrecisionType) override { @@ -516,7 +541,7 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template static const PrecisionType value{}; return value; } - + /** @ITKEndGrouping */ void AdvanceOneStep() override { diff --git a/Modules/Numerics/Optimizersv4/include/itkLBFGSOptimizerv4.h b/Modules/Numerics/Optimizersv4/include/itkLBFGSOptimizerv4.h index 462434c3ced..f982756e914 100644 --- a/Modules/Numerics/Optimizersv4/include/itkLBFGSOptimizerv4.h +++ b/Modules/Numerics/Optimizersv4/include/itkLBFGSOptimizerv4.h @@ -68,7 +68,6 @@ namespace itk * * \ingroup ITKOptimizersv4 */ - class ITKOptimizersv4_EXPORT LBFGSOptimizerv4 : public LBFGSOptimizerBasev4 { public: diff --git a/Modules/Numerics/Optimizersv4/include/itkMultiGradientOptimizerv4.h b/Modules/Numerics/Optimizersv4/include/itkMultiGradientOptimizerv4.h index 592da0c505a..07c792934a2 100644 --- a/Modules/Numerics/Optimizersv4/include/itkMultiGradientOptimizerv4.h +++ b/Modules/Numerics/Optimizersv4/include/itkMultiGradientOptimizerv4.h @@ -130,9 +130,10 @@ class ITK_TEMPLATE_EXPORT MultiGradientOptimizerv4Template protected: /** Default constructor */ + /** @ITKStartGrouping */ MultiGradientOptimizerv4Template(); ~MultiGradientOptimizerv4Template() override = default; - + /** @ITKEndGrouping */ void PrintSelf(std::ostream & os, Indent indent) const override; diff --git a/Modules/Numerics/Optimizersv4/include/itkMultiStartOptimizerv4.h b/Modules/Numerics/Optimizersv4/include/itkMultiStartOptimizerv4.h index 0735dbe31dc..2af9c74b9ed 100644 --- a/Modules/Numerics/Optimizersv4/include/itkMultiStartOptimizerv4.h +++ b/Modules/Numerics/Optimizersv4/include/itkMultiStartOptimizerv4.h @@ -89,6 +89,7 @@ class ITK_TEMPLATE_EXPORT MultiStartOptimizerv4Template /** Stop condition internal string type */ using typename Superclass::StopConditionDescriptionType; + /** Stop condition return string type */ /** It should be possible to derive the internal computation type from the class object. */ @@ -147,9 +148,10 @@ class ITK_TEMPLATE_EXPORT MultiStartOptimizerv4Template GetBestParameters(); /** Set/Get the optimizer. */ + /** @ITKStartGrouping */ itkSetObjectMacro(LocalOptimizer, OptimizerType); itkGetModifiableObjectMacro(LocalOptimizer, OptimizerType); - + /** @ITKEndGrouping */ inline ParameterListSizeType GetBestParametersIndex() { @@ -158,9 +160,10 @@ class ITK_TEMPLATE_EXPORT MultiStartOptimizerv4Template protected: /** Default constructor */ + /** @ITKStartGrouping */ MultiStartOptimizerv4Template(); ~MultiStartOptimizerv4Template() override = default; - + /** @ITKEndGrouping */ void PrintSelf(std::ostream & os, Indent indent) const override; diff --git a/Modules/Numerics/Optimizersv4/include/itkObjectToObjectMetric.h b/Modules/Numerics/Optimizersv4/include/itkObjectToObjectMetric.h index 6de22e1f197..5ec2b77d447 100644 --- a/Modules/Numerics/Optimizersv4/include/itkObjectToObjectMetric.h +++ b/Modules/Numerics/Optimizersv4/include/itkObjectToObjectMetric.h @@ -309,11 +309,12 @@ class ITK_TEMPLATE_EXPORT ObjectToObjectMetric : public ObjectToObjectMetricBase * \note Returns true if the virtual domain has not been defined. This * allows, for example, use in point set metrics where the virtual domain * is implicitly defined by the point sets and transforms. */ + /** @ITKStartGrouping */ bool IsInsideVirtualDomain(const VirtualPointType & point) const; bool IsInsideVirtualDomain(const VirtualIndexType & index) const; - + /** @ITKEndGrouping */ using MetricCategoryType = typename Superclass::MetricCategoryEnum; /** Get metric category */ diff --git a/Modules/Numerics/Optimizersv4/include/itkObjectToObjectMetricBase.h b/Modules/Numerics/Optimizersv4/include/itkObjectToObjectMetricBase.h index b2e86e1d3a7..46fd9216c58 100644 --- a/Modules/Numerics/Optimizersv4/include/itkObjectToObjectMetricBase.h +++ b/Modules/Numerics/Optimizersv4/include/itkObjectToObjectMetricBase.h @@ -62,6 +62,7 @@ extern ITKOptimizersv4_EXPORT std::ostream & operator<<(std::ostream & out, const ObjectToObjectMetricBaseTemplateEnums::GradientSource value); extern ITKOptimizersv4_EXPORT std::ostream & operator<<(std::ostream & out, const ObjectToObjectMetricBaseTemplateEnums::MetricCategory value); + /** * \class ObjectToObjectMetricBaseTemplate * \brief Base class for all object-to-object similarity metrics added in ITKv4. @@ -120,13 +121,15 @@ class ITK_TEMPLATE_EXPORT ObjectToObjectMetricBaseTemplate using ObjectConstPointer = typename ObjectType::ConstPointer; /** Get/Set the Fixed Object. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(FixedObject, ObjectType); itkGetConstObjectMacro(FixedObject, ObjectType); - + /** @ITKEndGrouping */ /** Get/Set the Moving Object. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(MovingObject, ObjectType); itkGetConstObjectMacro(MovingObject, ObjectType); - + /** @ITKEndGrouping */ using GradientSourceEnum = itk::ObjectToObjectMetricBaseTemplateEnums::GradientSource; #if !defined(ITK_LEGACY_REMOVE) /** Enables backwards compatibility for enum values */ @@ -192,11 +195,12 @@ class ITK_TEMPLATE_EXPORT ObjectToObjectMetricBaseTemplate /** Methods for working with the metric's 'active' transform, e.g. the * transform being optimized in the case of registration. Some of these are * used in non-metric classes, e.g. optimizers. */ + /** @ITKStartGrouping */ NumberOfParametersType GetNumberOfParameters() const override = 0; virtual NumberOfParametersType GetNumberOfLocalParameters() const = 0; - + /** @ITKEndGrouping */ /** Set the active transform's parameters by value*/ virtual void SetParameters(ParametersType & params) = 0; diff --git a/Modules/Numerics/Optimizersv4/include/itkObjectToObjectOptimizerBase.h b/Modules/Numerics/Optimizersv4/include/itkObjectToObjectOptimizerBase.h index d6504c26291..5acc5155a0e 100644 --- a/Modules/Numerics/Optimizersv4/include/itkObjectToObjectOptimizerBase.h +++ b/Modules/Numerics/Optimizersv4/include/itkObjectToObjectOptimizerBase.h @@ -151,8 +151,10 @@ class ITK_TEMPLATE_EXPORT ObjectToObjectOptimizerBaseTemplate : public Object using StopConditionDescriptionType = std::ostringstream; /** Accessors for Metric */ + /** @ITKStartGrouping */ itkSetObjectMacro(Metric, MetricType); itkGetModifiableObjectMacro(Metric, MetricType); + /** @ITKEndGrouping */ /** Accessor for metric value. Returns the value * stored in m_CurrentMetricValue from the most recent @@ -212,9 +214,11 @@ class ITK_TEMPLATE_EXPORT ObjectToObjectOptimizerBaseTemplate : public Object * optimization, and overrides any scales set using SetScales(). * Default is true. */ + /** @ITKStartGrouping */ itkSetMacro(DoEstimateScales, bool); itkGetConstReferenceMacro(DoEstimateScales, bool); itkBooleanMacro(DoEstimateScales); + /** @ITKEndGrouping */ /** Set the number of work units to use when threading. * The default is the global default number of work units @@ -223,9 +227,10 @@ class ITK_TEMPLATE_EXPORT ObjectToObjectOptimizerBaseTemplate : public Object SetNumberOfWorkUnits(ThreadIdType number); #if !defined(ITK_LEGACY_REMOVE) - /** Set the number of work units to use when threading. + /** Set/Get the number of work units to use when threading. * * NOTE: deprecated. Use SetNumberOfWorkUnits() */ + /** @ITKStartGrouping */ itkLegacyMacro(virtual void SetNumberOfThreads(ThreadIdType number)) { return this->SetNumberOfWorkUnits(number); @@ -234,6 +239,7 @@ class ITK_TEMPLATE_EXPORT ObjectToObjectOptimizerBaseTemplate : public Object { return this->m_NumberOfWorkUnits; } + /** @ITKEndGrouping */ #endif // !ITK_LEGACY_REMOVE /** Get the number of work units set to be used. */ diff --git a/Modules/Numerics/Optimizersv4/include/itkOnePlusOneEvolutionaryOptimizerv4.h b/Modules/Numerics/Optimizersv4/include/itkOnePlusOneEvolutionaryOptimizerv4.h index bae9c11f1ed..dab6165b5d3 100644 --- a/Modules/Numerics/Optimizersv4/include/itkOnePlusOneEvolutionaryOptimizerv4.h +++ b/Modules/Numerics/Optimizersv4/include/itkOnePlusOneEvolutionaryOptimizerv4.h @@ -93,26 +93,31 @@ class ITK_TEMPLATE_EXPORT OnePlusOneEvolutionaryOptimizerv4 using typename Superclass::ScalesType; /** Set/Get maximum iteration limit. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumIteration, unsigned int); itkGetConstReferenceMacro(MaximumIteration, unsigned int); - + /** @ITKEndGrouping */ /** Set/Get the search radius grow factor in parameter space. */ + /** @ITKStartGrouping */ itkSetMacro(GrowthFactor, double); itkGetConstReferenceMacro(GrowthFactor, double); - + /** @ITKEndGrouping */ /** Set/Get the search radius shrink factor. */ + /** @ITKStartGrouping */ itkSetMacro(ShrinkFactor, double); itkGetConstReferenceMacro(ShrinkFactor, double); - + /** @ITKEndGrouping */ /** Set/Get initial search radius in parameter space */ + /** @ITKStartGrouping */ itkSetMacro(InitialRadius, double); itkGetConstReferenceMacro(InitialRadius, double); - + /** @ITKEndGrouping */ /** Set/Get the minimal size of search radius * (frobenius_norm of covariance matrix). */ + /** @ITKStartGrouping */ itkSetMacro(Epsilon, double); itkGetConstReferenceMacro(Epsilon, double); - + /** @ITKEndGrouping */ /** Get the current Frobenius norm of covariance matrix */ itkGetConstReferenceMacro(FrobeniusNorm, double); @@ -129,10 +134,11 @@ class ITK_TEMPLATE_EXPORT OnePlusOneEvolutionaryOptimizerv4 Initialize(double initialRadius, double grow = -1, double shrink = -1); /** Return Current Value */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(CurrentCost, MeasureType); const MeasureType & GetValue() const override; - + /** @ITKEndGrouping */ /** Return if optimizer has been initialized */ itkGetConstReferenceMacro(Initialized, bool); diff --git a/Modules/Numerics/Optimizersv4/include/itkPowellOptimizerv4.h b/Modules/Numerics/Optimizersv4/include/itkPowellOptimizerv4.h index 543e4bd7e17..33e6bcc3411 100644 --- a/Modules/Numerics/Optimizersv4/include/itkPowellOptimizerv4.h +++ b/Modules/Numerics/Optimizersv4/include/itkPowellOptimizerv4.h @@ -77,37 +77,43 @@ class ITK_TEMPLATE_EXPORT PowellOptimizerv4 : public ObjectToObjectOptimizerBase using typename Superclass::ScalesType; /** Set/Get maximum iteration limit. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumIteration, unsigned int); itkGetConstReferenceMacro(MaximumIteration, unsigned int); - + /** @ITKEndGrouping */ /** Set/Get the maximum number of line search iterations */ + /** @ITKStartGrouping */ itkSetMacro(MaximumLineIteration, unsigned int); itkGetConstMacro(MaximumLineIteration, unsigned int); - + /** @ITKEndGrouping */ /** Set/Get StepLength for the (scaled) spacing of the sampling of * parameter space while bracketing the extremum */ + /** @ITKStartGrouping */ itkSetMacro(StepLength, double); itkGetConstReferenceMacro(StepLength, double); - + /** @ITKEndGrouping */ /** Set/Get StepTolerance. Once the local extreme is known to be within this * distance of the current parameter values, optimization terminates */ + /** @ITKStartGrouping */ itkSetMacro(StepTolerance, double); itkGetConstReferenceMacro(StepTolerance, double); - + /** @ITKEndGrouping */ /** Set/Get ValueTolerance. Once this current cost function value is known * to be within this tolerance of the cost function value at the local * extreme, optimization terminates */ + /** @ITKStartGrouping */ itkSetMacro(ValueTolerance, double); itkGetConstReferenceMacro(ValueTolerance, double); - + /** @ITKEndGrouping */ /** Return Current Value */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(CurrentCost, MeasureType); const MeasureType & GetValue() const override { return this->GetCurrentCost(); } - + /** @ITKEndGrouping */ /** Get the current line search iteration */ itkGetConstReferenceMacro(CurrentLineIteration, unsigned int); diff --git a/Modules/Numerics/Optimizersv4/include/itkRegistrationParameterScalesEstimator.h b/Modules/Numerics/Optimizersv4/include/itkRegistrationParameterScalesEstimator.h index c317aa2203c..5ed23d54695 100644 --- a/Modules/Numerics/Optimizersv4/include/itkRegistrationParameterScalesEstimator.h +++ b/Modules/Numerics/Optimizersv4/include/itkRegistrationParameterScalesEstimator.h @@ -94,8 +94,10 @@ class ITK_TEMPLATE_EXPORT RegistrationParameterScalesEstimator /** Type of scales */ using typename Superclass::ScalesType; + /** Type of parameters of the optimizer */ using typename Superclass::ParametersType; + /** Type of float */ using typename Superclass::FloatType; @@ -149,18 +151,21 @@ class ITK_TEMPLATE_EXPORT RegistrationParameterScalesEstimator * The transforms from the metric will be used for estimation, along * with the images when appropriate. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Metric, MetricType); itkGetConstObjectMacro(Metric, MetricType); - + /** @ITKEndGrouping */ /** m_TransformForward specifies which transform scales to be estimated. * m_TransformForward = true (default) for the moving transform parameters. * m_TransformForward = false for the fixed transform parameters. */ + /** @ITKStartGrouping */ itkSetMacro(TransformForward, bool); itkGetConstMacro(TransformForward, bool); itkBooleanMacro(TransformForward); - + /** @ITKEndGrouping */ /** Get/Set a point set for virtual domain sampling. */ + /** @ITKStartGrouping */ #ifndef ITK_FUTURE_LEGACY_REMOVE virtual void SetVirtualDomainPointSet(VirtualPointSetType * const arg) @@ -172,11 +177,12 @@ class ITK_TEMPLATE_EXPORT RegistrationParameterScalesEstimator #endif itkSetConstObjectMacro(VirtualDomainPointSet, VirtualPointSetType); itkGetConstObjectMacro(VirtualDomainPointSet, VirtualPointSetType); - + /** @ITKEndGrouping */ /** the radius of the central region for sampling. */ + /** @ITKStartGrouping */ itkSetMacro(CentralRegionRadius, IndexValueType); itkGetConstMacro(CentralRegionRadius, IndexValueType); - + /** @ITKEndGrouping */ /** Estimate parameter scales */ void EstimateScales(ScalesType & scales) override = 0; diff --git a/Modules/Numerics/Optimizersv4/include/itkRegistrationParameterScalesFromShiftBase.h b/Modules/Numerics/Optimizersv4/include/itkRegistrationParameterScalesFromShiftBase.h index 84e6f1a54a8..80c0fa52643 100644 --- a/Modules/Numerics/Optimizersv4/include/itkRegistrationParameterScalesFromShiftBase.h +++ b/Modules/Numerics/Optimizersv4/include/itkRegistrationParameterScalesFromShiftBase.h @@ -58,9 +58,11 @@ class ITK_TEMPLATE_EXPORT RegistrationParameterScalesFromShiftBase /** Type of scales */ using typename Superclass::ScalesType; + /** Type of parameters of the optimizer */ using typename Superclass::ParametersType; using ParametersValueType = typename ParametersType::ValueType; + /** Type of float */ using typename Superclass::FloatType; @@ -84,9 +86,10 @@ class ITK_TEMPLATE_EXPORT RegistrationParameterScalesFromShiftBase EstimateLocalStepScales(const ParametersType & step, ScalesType & localStepScales) override; /** Set/get small parameter variation */ + /** @ITKStartGrouping */ itkSetMacro(SmallParameterVariation, ParametersValueType); itkGetConstMacro(SmallParameterVariation, ParametersValueType); - + /** @ITKEndGrouping */ protected: RegistrationParameterScalesFromShiftBase(); ~RegistrationParameterScalesFromShiftBase() override = default; diff --git a/Modules/Numerics/Optimizersv4/include/itkRegularStepGradientDescentOptimizerv4.h b/Modules/Numerics/Optimizersv4/include/itkRegularStepGradientDescentOptimizerv4.h index 64ef1aae437..dc8388a13cd 100644 --- a/Modules/Numerics/Optimizersv4/include/itkRegularStepGradientDescentOptimizerv4.h +++ b/Modules/Numerics/Optimizersv4/include/itkRegularStepGradientDescentOptimizerv4.h @@ -87,21 +87,25 @@ class ITK_TEMPLATE_EXPORT RegularStepGradientDescentOptimizerv4 * * The default value is set to 1e-4 to pass all tests. */ + /** @ITKStartGrouping */ itkSetMacro(MinimumStepLength, TInternalComputationValueType); itkGetConstReferenceMacro(MinimumStepLength, TInternalComputationValueType); - + /** @ITKEndGrouping */ /** Set/Get relaxation factor value. */ + /** @ITKStartGrouping */ itkSetMacro(RelaxationFactor, TInternalComputationValueType); itkGetConstReferenceMacro(RelaxationFactor, TInternalComputationValueType); - + /** @ITKEndGrouping */ /** Set/Get gradient magnitude tolerance value for convergence checking. */ + /** @ITKStartGrouping */ itkSetMacro(GradientMagnitudeTolerance, TInternalComputationValueType); itkGetConstReferenceMacro(GradientMagnitudeTolerance, TInternalComputationValueType); - + /** @ITKEndGrouping */ /** Set/Get current scale for learning rate. */ + /** @ITKStartGrouping */ itkSetMacro(CurrentLearningRateRelaxation, MeasureType); itkGetConstReferenceMacro(CurrentLearningRateRelaxation, MeasureType); - + /** @ITKEndGrouping */ /** Start and run the optimization. */ void StartOptimization(bool doOnlyInitialization = false) override; @@ -121,11 +125,12 @@ class ITK_TEMPLATE_EXPORT RegularStepGradientDescentOptimizerv4 AdvanceOneStep() override; /** Modify the input gradient over a given index range. */ + /** @ITKStartGrouping */ void ModifyGradientByScalesOverSubRange(const IndexRangeType & subrange) override; void ModifyGradientByLearningRateOverSubRange(const IndexRangeType & subrange) override; - + /** @ITKEndGrouping */ /** Default constructor. */ RegularStepGradientDescentOptimizerv4(); diff --git a/Modules/Numerics/Optimizersv4/include/itkSingleValuedNonLinearVnlOptimizerv4.h b/Modules/Numerics/Optimizersv4/include/itkSingleValuedNonLinearVnlOptimizerv4.h index 7f96a010d20..ef461659ab3 100644 --- a/Modules/Numerics/Optimizersv4/include/itkSingleValuedNonLinearVnlOptimizerv4.h +++ b/Modules/Numerics/Optimizersv4/include/itkSingleValuedNonLinearVnlOptimizerv4.h @@ -85,9 +85,10 @@ class ITKOptimizersv4_EXPORT SingleValuedNonLinearVnlOptimizerv4 : public Object * a value that may not be the one corresponding to the current parameters. For * GUI update purposes, this method is a good option. * \note The metric value is cached in the base class, retrieved via GetValue(). */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(CachedDerivative, DerivativeType); itkGetConstReferenceMacro(CachedCurrentPosition, ParametersType); - + /** @ITKEndGrouping */ /** Get the reason for termination */ StopConditionReturnStringType GetStopConditionDescription() const override = 0; diff --git a/Modules/Numerics/Optimizersv4/include/itkWindowConvergenceMonitoringFunction.h b/Modules/Numerics/Optimizersv4/include/itkWindowConvergenceMonitoringFunction.h index a40723d03cf..241f05b0b14 100644 --- a/Modules/Numerics/Optimizersv4/include/itkWindowConvergenceMonitoringFunction.h +++ b/Modules/Numerics/Optimizersv4/include/itkWindowConvergenceMonitoringFunction.h @@ -70,9 +70,10 @@ class ITK_TEMPLATE_EXPORT WindowConvergenceMonitoringFunction : public Convergen ClearEnergyValues() override; /** Set/Get window size over which the convergence value is calculated */ + /** @ITKStartGrouping */ itkSetMacro(WindowSize, EnergyValueContainerSizeType); itkGetConstMacro(WindowSize, EnergyValueContainerSizeType); - + /** @ITKEndGrouping */ /** Calculate convergence value by fitting to a window of the energy profile */ RealType GetConvergenceValue() const override; diff --git a/Modules/Numerics/Polynomials/include/itkMultivariateLegendrePolynomial.h b/Modules/Numerics/Polynomials/include/itkMultivariateLegendrePolynomial.h index aef1628dcf5..510f75ed23b 100644 --- a/Modules/Numerics/Polynomials/include/itkMultivariateLegendrePolynomial.h +++ b/Modules/Numerics/Polynomials/include/itkMultivariateLegendrePolynomial.h @@ -64,7 +64,6 @@ namespace itk * \note For more details refer to \cite styner2000 and \cite styner1997. * \ingroup ITKPolynomials */ - class ITKPolynomials_EXPORT MultivariateLegendrePolynomial { public: @@ -87,6 +86,7 @@ class ITKPolynomials_EXPORT MultivariateLegendrePolynomial /** Constructor. */ MultivariateLegendrePolynomial(unsigned int dimension, unsigned int degree, const DomainSizeType & domainSize); + /** Destructor. */ virtual ~MultivariateLegendrePolynomial(); diff --git a/Modules/Numerics/Statistics/include/itkCovarianceSampleFilter.h b/Modules/Numerics/Statistics/include/itkCovarianceSampleFilter.h index 9bfdb691d39..00306f0e9d3 100644 --- a/Modules/Numerics/Statistics/include/itkCovarianceSampleFilter.h +++ b/Modules/Numerics/Statistics/include/itkCovarianceSampleFilter.h @@ -63,9 +63,10 @@ class ITK_TEMPLATE_EXPORT CovarianceSampleFilter : public ProcessObject using SampleType = TSample; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(CovarianceSampleFilter); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Type of each measurement vector in sample */ using MeasurementVectorType = typename SampleType::MeasurementVectorType; diff --git a/Modules/Numerics/Statistics/include/itkDistanceMetric.h b/Modules/Numerics/Statistics/include/itkDistanceMetric.h index b2ba1214791..2e48796b45b 100644 --- a/Modules/Numerics/Statistics/include/itkDistanceMetric.h +++ b/Modules/Numerics/Statistics/include/itkDistanceMetric.h @@ -58,6 +58,7 @@ class ITK_TEMPLATE_EXPORT DistanceMetric : public FunctionBase using MeasurementVectorType = TVector; /** declare Measurement vector component type */ + /** Type used to represent the number of components oft he MeasurementVectorType */ using MeasurementVectorSizeType = unsigned int; diff --git a/Modules/Numerics/Statistics/include/itkDistanceToCentroidMembershipFunction.h b/Modules/Numerics/Statistics/include/itkDistanceToCentroidMembershipFunction.h index a6e72b7b6e3..e4488d793fb 100644 --- a/Modules/Numerics/Statistics/include/itkDistanceToCentroidMembershipFunction.h +++ b/Modules/Numerics/Statistics/include/itkDistanceToCentroidMembershipFunction.h @@ -54,9 +54,10 @@ class ITK_TEMPLATE_EXPORT DistanceToCentroidMembershipFunction : public Membersh using ConstPointer = SmartPointer; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(DistanceToCentroidMembershipFunction); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** SmartPointer class for superclass */ using MembershipFunctionPointer = typename Superclass::Pointer; diff --git a/Modules/Numerics/Statistics/include/itkExpectationMaximizationMixtureModelEstimator.h b/Modules/Numerics/Statistics/include/itkExpectationMaximizationMixtureModelEstimator.h index 3331ae9afee..79d3dc5c1fe 100644 --- a/Modules/Numerics/Statistics/include/itkExpectationMaximizationMixtureModelEstimator.h +++ b/Modules/Numerics/Statistics/include/itkExpectationMaximizationMixtureModelEstimator.h @@ -80,7 +80,6 @@ operator<<(std::ostream & out, const ExpectationMaximizationMixtureModelEstimato * \sphinxexample{Numerics/Statistics/DistributeSamplingUsingGMM,Distribute Sampling Using GMM EM} * \endsphinx */ - template class ITK_TEMPLATE_EXPORT ExpectationMaximizationMixtureModelEstimator : public Object { @@ -92,9 +91,10 @@ class ITK_TEMPLATE_EXPORT ExpectationMaximizationMixtureModelEstimator : public using ConstPointer = SmartPointer; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(ExpectationMaximizationMixtureModelEstimator); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** TSample template argument related type alias */ using SampleType = TSample; using MeasurementType = typename TSample::MeasurementType; diff --git a/Modules/Numerics/Statistics/include/itkGaussianMembershipFunction.h b/Modules/Numerics/Statistics/include/itkGaussianMembershipFunction.h index 0d1123bcced..3f734476d43 100644 --- a/Modules/Numerics/Statistics/include/itkGaussianMembershipFunction.h +++ b/Modules/Numerics/Statistics/include/itkGaussianMembershipFunction.h @@ -65,9 +65,10 @@ class ITK_TEMPLATE_EXPORT GaussianMembershipFunction : public MembershipFunction using ConstPointer = SmartPointer; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(GaussianMembershipFunction); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** SmartPointer class for superclass */ using MembershipFunctionPointer = typename Superclass::Pointer; diff --git a/Modules/Numerics/Statistics/include/itkGaussianMixtureModelComponent.h b/Modules/Numerics/Statistics/include/itkGaussianMixtureModelComponent.h index aa344e5d7c3..b1e82821cf2 100644 --- a/Modules/Numerics/Statistics/include/itkGaussianMixtureModelComponent.h +++ b/Modules/Numerics/Statistics/include/itkGaussianMixtureModelComponent.h @@ -57,10 +57,11 @@ class ITK_TEMPLATE_EXPORT GaussianMixtureModelComponent : public MixtureModelCom using Pointer = SmartPointer; using ConstPointer = SmartPointer; - /**Standard Macros */ + /** Standard Macros */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(GaussianMixtureModelComponent); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Typedefs from the superclass */ using typename Superclass::MeasurementVectorType; using typename Superclass::MeasurementVectorSizeType; diff --git a/Modules/Numerics/Statistics/include/itkHistogram.h b/Modules/Numerics/Statistics/include/itkHistogram.h index da094194db1..1ec586ccf0f 100644 --- a/Modules/Numerics/Statistics/include/itkHistogram.h +++ b/Modules/Numerics/Statistics/include/itkHistogram.h @@ -157,10 +157,11 @@ class ITK_TEMPLATE_EXPORT Histogram : public Sample> GetIndex(InstanceIdentifier id) const; /** Set/Get whether the bins at the edges of the histogram extend to +/- infinity. */ + /** @ITKStartGrouping */ itkGetConstMacro(ClipBinsAtEnds, bool); itkSetMacro(ClipBinsAtEnds, bool); itkBooleanMacro(ClipBinsAtEnds); - + /** @ITKEndGrouping */ /** Returns true if the given index is out of bound meaning one of index * is not between [0, last index] */ bool diff --git a/Modules/Numerics/Statistics/include/itkHistogramToImageFilter.h b/Modules/Numerics/Statistics/include/itkHistogramToImageFilter.h index 348f9c2897e..c43947672bc 100644 --- a/Modules/Numerics/Statistics/include/itkHistogramToImageFilter.h +++ b/Modules/Numerics/Statistics/include/itkHistogramToImageFilter.h @@ -111,6 +111,7 @@ class ITK_TEMPLATE_EXPORT HistogramToImageFilter : public ImageSource * (Functors do not have to derive from itk::LightObject, so they do * not necessarily have a reference count. So we cannot return a * SmartPointer.) */ + /** @ITKStartGrouping */ FunctorType & GetFunctor() { @@ -121,6 +122,7 @@ class ITK_TEMPLATE_EXPORT HistogramToImageFilter : public ImageSource { return m_Functor; } + /** @ITKEndGrouping */ void SetTotalFrequency(SizeValueType n); diff --git a/Modules/Numerics/Statistics/include/itkHistogramToRunLengthFeaturesFilter.h b/Modules/Numerics/Statistics/include/itkHistogramToRunLengthFeaturesFilter.h index 0fef5ff4db5..1d615ec7ec2 100644 --- a/Modules/Numerics/Statistics/include/itkHistogramToRunLengthFeaturesFilter.h +++ b/Modules/Numerics/Statistics/include/itkHistogramToRunLengthFeaturesFilter.h @@ -57,6 +57,7 @@ using RunLengthFeatureEnum = HistogramToRunLengthFeaturesFilterEnums::RunLengthF // Define how to print enumeration extern ITKStatistics_EXPORT std::ostream & operator<<(std::ostream & out, const HistogramToRunLengthFeaturesFilterEnums::RunLengthFeature value); + /** * \class HistogramToRunLengthFeaturesFilter * \brief This class computes texture feature coefficients from a grey level @@ -112,12 +113,13 @@ class ITK_TEMPLATE_EXPORT HistogramToRunLengthFeaturesFilter : public ProcessObj using FrequencyType = typename HistogramType::TotalAbsoluteFrequencyType; /** Method to Set/Get the input Histogram */ + /** @ITKStartGrouping */ using Superclass::SetInput; void SetInput(const HistogramType * histogram); const HistogramType * GetInput() const; - + /** @ITKEndGrouping */ /** Smart Pointer type to a DataObject. */ using DataObjectPointer = DataObject::Pointer; @@ -125,65 +127,75 @@ class ITK_TEMPLATE_EXPORT HistogramToRunLengthFeaturesFilter : public ProcessObj using MeasurementObjectType = SimpleDataObjectDecorator; /** Methods to return the short run emphasis. */ + /** @ITKStartGrouping */ MeasurementType GetShortRunEmphasis() const; const MeasurementObjectType * GetShortRunEmphasisOutput() const; - + /** @ITKEndGrouping */ /** Methods to return the long run emphasis. */ + /** @ITKStartGrouping */ MeasurementType GetLongRunEmphasis() const; const MeasurementObjectType * GetLongRunEmphasisOutput() const; - + /** @ITKEndGrouping */ /** Methods to return the grey level nonuniformity. */ + /** @ITKStartGrouping */ MeasurementType GetGreyLevelNonuniformity() const; const MeasurementObjectType * GetGreyLevelNonuniformityOutput() const; - + /** @ITKEndGrouping */ /** Methods to return the run length nonuniformity. */ + /** @ITKStartGrouping */ MeasurementType GetRunLengthNonuniformity() const; const MeasurementObjectType * GetRunLengthNonuniformityOutput() const; - + /** @ITKEndGrouping */ /** Methods to return the low grey level run emphasis. */ + /** @ITKStartGrouping */ MeasurementType GetLowGreyLevelRunEmphasis() const; const MeasurementObjectType * GetLowGreyLevelRunEmphasisOutput() const; - + /** @ITKEndGrouping */ /** Methods to return the high grey level run emphasis. */ + /** @ITKStartGrouping */ MeasurementType GetHighGreyLevelRunEmphasis() const; const MeasurementObjectType * GetHighGreyLevelRunEmphasisOutput() const; - + /** @ITKEndGrouping */ /** Methods to return the short run low grey level run emphasis. */ + /** @ITKStartGrouping */ MeasurementType GetShortRunLowGreyLevelEmphasis() const; const MeasurementObjectType * GetShortRunLowGreyLevelEmphasisOutput() const; - + /** @ITKEndGrouping */ /** Methods to return the short run high grey level run emphasis. */ + /** @ITKStartGrouping */ MeasurementType GetShortRunHighGreyLevelEmphasis() const; const MeasurementObjectType * GetShortRunHighGreyLevelEmphasisOutput() const; - + /** @ITKEndGrouping */ /** Methods to return the long run low grey level run emphasis. */ + /** @ITKStartGrouping */ MeasurementType GetLongRunLowGreyLevelEmphasis() const; const MeasurementObjectType * GetLongRunLowGreyLevelEmphasisOutput() const; - + /** @ITKEndGrouping */ /** Methods to return the long run high grey level run emphasis. */ + /** @ITKStartGrouping */ MeasurementType GetLongRunHighGreyLevelEmphasis() const; const MeasurementObjectType * GetLongRunHighGreyLevelEmphasisOutput() const; - + /** @ITKEndGrouping */ itkGetMacro(TotalNumberOfRuns, unsigned long); #if !defined(ITK_LEGACY_REMOVE) diff --git a/Modules/Numerics/Statistics/include/itkHistogramToTextureFeaturesFilter.h b/Modules/Numerics/Statistics/include/itkHistogramToTextureFeaturesFilter.h index 19be0c080af..bc590d93922 100644 --- a/Modules/Numerics/Statistics/include/itkHistogramToTextureFeaturesFilter.h +++ b/Modules/Numerics/Statistics/include/itkHistogramToTextureFeaturesFilter.h @@ -113,7 +113,6 @@ operator<<(std::ostream & out, const HistogramToTextureFeaturesFilterEnums::Text * Author: Zachary Pincus * \ingroup ITKStatistics */ - template class ITK_TEMPLATE_EXPORT HistogramToTextureFeaturesFilter : public ProcessObject { diff --git a/Modules/Numerics/Statistics/include/itkImageClassifierFilter.h b/Modules/Numerics/Statistics/include/itkImageClassifierFilter.h index 69c9a1251eb..c9fb3bf6326 100644 --- a/Modules/Numerics/Statistics/include/itkImageClassifierFilter.h +++ b/Modules/Numerics/Statistics/include/itkImageClassifierFilter.h @@ -58,9 +58,10 @@ class ITK_TEMPLATE_EXPORT ImageClassifierFilter : public ImageToImageFilter; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(ImageClassifierFilter); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Image pixel value type alias. */ using InputImageType = TInputImage; using OutputImageType = TOutputImage; @@ -122,13 +123,15 @@ class ITK_TEMPLATE_EXPORT ImageClassifierFilter : public ImageToImageFilter public: /** Return the output histogram. */ + /** @ITKStartGrouping */ const HistogramType * GetOutput() const; HistogramType * GetOutput(); - + /** @ITKEndGrouping */ /** Type of DataObjects to use for Size inputs */ using InputHistogramSizeObjectType = SimpleDataObjectDecorator; @@ -112,15 +113,17 @@ class ITK_TEMPLATE_EXPORT ImageToHistogramFilter : public ImageSink /** Methods for setting and getting the Minimum and Maximum values of the * histogram bins. */ + /** @ITKStartGrouping */ itkSetGetDecoratedInputMacro(HistogramBinMinimum, HistogramMeasurementVectorType); itkSetGetDecoratedInputMacro(HistogramBinMaximum, HistogramMeasurementVectorType); - + /** @ITKEndGrouping */ /** Methods for setting and getting the boolean flag that defines whether the * minimum and maximum of the histogram are going to be computed * automatically from the values of the sample */ + /** @ITKStartGrouping */ itkSetGetDecoratedInputMacro(AutoMinimumMaximum, bool); itkBooleanMacro(AutoMinimumMaximum); - + /** @ITKEndGrouping */ /** Method that facilitates the use of this filter in the internal * pipeline of another filter. */ virtual void diff --git a/Modules/Numerics/Statistics/include/itkImageToListSampleFilter.h b/Modules/Numerics/Statistics/include/itkImageToListSampleFilter.h index c6206127891..340d9f91b0c 100644 --- a/Modules/Numerics/Statistics/include/itkImageToListSampleFilter.h +++ b/Modules/Numerics/Statistics/include/itkImageToListSampleFilter.h @@ -115,9 +115,10 @@ class ITK_TEMPLATE_EXPORT ImageToListSampleFilter : public ProcessObject * specified, only pixels with this value will be added to the list sample, if * no mask has been specified all pixels will be added as measurement vectors * to the list sample. */ + /** @ITKStartGrouping */ itkSetMacro(MaskValue, MaskPixelType); itkGetConstMacro(MaskValue, MaskPixelType); - + /** @ITKEndGrouping */ protected: ImageToListSampleFilter(); ~ImageToListSampleFilter() override = default; diff --git a/Modules/Numerics/Statistics/include/itkImageToNeighborhoodSampleAdaptor.h b/Modules/Numerics/Statistics/include/itkImageToNeighborhoodSampleAdaptor.h index a2f436c3735..0ec21e481d8 100644 --- a/Modules/Numerics/Statistics/include/itkImageToNeighborhoodSampleAdaptor.h +++ b/Modules/Numerics/Statistics/include/itkImageToNeighborhoodSampleAdaptor.h @@ -85,6 +85,7 @@ class ITK_TEMPLATE_EXPORT ImageToNeighborhoodSampleAdaptor using OffsetTableType = typename RegionType::OffsetTableType; using SizeType = typename ImageType::SizeType; using ImageIteratorType = ImageRegionIteratorWithIndex; + /** Neighborhood Iterator type alias support */ using NeighborhoodIteratorType = ConstNeighborhoodIterator; using NonConstNeighborhoodIteratorType = NeighborhoodIterator; @@ -289,7 +290,6 @@ class ITK_TEMPLATE_EXPORT ImageToNeighborhoodSampleAdaptor return iter; } - /** returns an iterator that points to the beginning of the container */ ConstIterator Begin() const diff --git a/Modules/Numerics/Statistics/include/itkJointDomainImageToListSampleAdaptor.h b/Modules/Numerics/Statistics/include/itkJointDomainImageToListSampleAdaptor.h index 04736899994..5eefe604215 100644 --- a/Modules/Numerics/Statistics/include/itkJointDomainImageToListSampleAdaptor.h +++ b/Modules/Numerics/Statistics/include/itkJointDomainImageToListSampleAdaptor.h @@ -175,10 +175,11 @@ class ITK_TEMPLATE_EXPORT JointDomainImageToListSampleAdaptor GetMeasurementVector(InstanceIdentifier id) const override; /** Method to set UsePixelContainer flag */ + /** @ITKStartGrouping */ itkSetMacro(UsePixelContainer, bool); itkGetConstMacro(UsePixelContainer, bool); itkBooleanMacro(UsePixelContainer); - + /** @ITKEndGrouping */ // void PrintSelf(std::ostream& os, Indent indent) const override; /** \class ConstIterator diff --git a/Modules/Numerics/Statistics/include/itkKdTreeBasedKmeansEstimator.h b/Modules/Numerics/Statistics/include/itkKdTreeBasedKmeansEstimator.h index 8ea350a18fc..3527922c99d 100644 --- a/Modules/Numerics/Statistics/include/itkKdTreeBasedKmeansEstimator.h +++ b/Modules/Numerics/Statistics/include/itkKdTreeBasedKmeansEstimator.h @@ -121,17 +121,22 @@ class ITK_TEMPLATE_EXPORT KdTreeBasedKmeansEstimator : public Object GetOutput() const; /** Set the position to initialize the optimization. */ + /** @ITKStartGrouping */ itkSetMacro(Parameters, ParametersType); itkGetConstMacro(Parameters, ParametersType); + /** @ITKEndGrouping */ /** Set/Get maximum iteration limit. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumIteration, int); itkGetConstMacro(MaximumIteration, int); + /** @ITKEndGrouping */ /** Set/Get the termination threshold for the squared sum * of changes in centroid positions after one iteration */ itkSetMacro(CentroidPositionChangesThreshold, double); itkGetConstMacro(CentroidPositionChangesThreshold, double); + /** Set/Get the pointer to the KdTree */ void SetKdTree(TKdTree * tree); @@ -306,15 +311,20 @@ class ITK_TEMPLATE_EXPORT KdTreeBasedKmeansEstimator : public Object private: /** current number of iteration */ int m_CurrentIteration{ 0 }; + /** maximum number of iteration. termination criterion */ int m_MaximumIteration{ 100 }; + /** sum of squared centroid position changes at the current iteration */ double m_CentroidPositionChanges{ 0.0 }; + /** threshold for the sum of squared centroid position changes. * termination criterion */ double m_CentroidPositionChangesThreshold{ 0.0 }; + /** pointer to the k-d tree */ typename TKdTree::Pointer m_KdTree{}; + /** pointer to the euclidean distance function */ typename EuclideanDistanceMetric::Pointer m_DistanceMetric{}; diff --git a/Modules/Numerics/Statistics/include/itkKdTreeGenerator.h b/Modules/Numerics/Statistics/include/itkKdTreeGenerator.h index a8cbd51691f..4a224235004 100644 --- a/Modules/Numerics/Statistics/include/itkKdTreeGenerator.h +++ b/Modules/Numerics/Statistics/include/itkKdTreeGenerator.h @@ -111,16 +111,18 @@ class ITK_TEMPLATE_EXPORT KdTreeGenerator : public Object using SubsamplePointer = typename SubsampleType::Pointer; /** Set/Get the input sample that provides the measurement vectors. */ + /** @ITKStartGrouping */ void SetSample(TSample * sample); itkGetConstMacro(SourceSample, TSample *); - + /** @ITKEndGrouping */ /** Sets the number of measurement vectors that can be stored in a * terminal node. */ + /** @ITKStartGrouping */ void SetBucketSize(unsigned int size); itkGetConstMacro(BucketSize, unsigned int); - + /** @ITKEndGrouping */ /** Returns the pointer to the generated k-d tree. */ OutputPointer GetOutput() diff --git a/Modules/Numerics/Statistics/include/itkMahalanobisDistanceMembershipFunction.h b/Modules/Numerics/Statistics/include/itkMahalanobisDistanceMembershipFunction.h index 49d764763b0..9c61cfca8e2 100644 --- a/Modules/Numerics/Statistics/include/itkMahalanobisDistanceMembershipFunction.h +++ b/Modules/Numerics/Statistics/include/itkMahalanobisDistanceMembershipFunction.h @@ -70,9 +70,10 @@ class ITK_TEMPLATE_EXPORT MahalanobisDistanceMembershipFunction : public Members using ConstPointer = SmartPointer; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(MahalanobisDistanceMembershipFunction); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** SmartPointer class for superclass */ using MembershipFunctionPointer = typename Superclass::Pointer; diff --git a/Modules/Numerics/Statistics/include/itkMahalanobisDistanceMetric.h b/Modules/Numerics/Statistics/include/itkMahalanobisDistanceMetric.h index 4a997ec9bd2..dc932d2edbf 100644 --- a/Modules/Numerics/Statistics/include/itkMahalanobisDistanceMetric.h +++ b/Modules/Numerics/Statistics/include/itkMahalanobisDistanceMetric.h @@ -54,9 +54,10 @@ class ITK_TEMPLATE_EXPORT MahalanobisDistanceMetric : public DistanceMetric; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(MahalanobisDistanceMetric); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Typedef to represent the measurement vector type */ using typename Superclass::MeasurementVectorType; @@ -109,9 +110,10 @@ class ITK_TEMPLATE_EXPORT MahalanobisDistanceMetric : public DistanceMetric; using SampleType = TSample; - /**Standard Macros */ + /** Standard Macros */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(MeanSampleFilter); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Type of each measurement vector in sample */ using MeasurementVectorType = typename SampleType::MeasurementVectorType; diff --git a/Modules/Numerics/Statistics/include/itkMembershipSample.h b/Modules/Numerics/Statistics/include/itkMembershipSample.h index 828a5ec3124..3a87f443f89 100644 --- a/Modules/Numerics/Statistics/include/itkMembershipSample.h +++ b/Modules/Numerics/Statistics/include/itkMembershipSample.h @@ -66,9 +66,10 @@ class ITK_TEMPLATE_EXPORT MembershipSample : public DataObject using ConstPointer = SmartPointer; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(MembershipSample); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Typedefs for Measurement vector, measurement, Instance Identifier, * frequency, size, size element value from the template argument TSample */ using SampleType = TSample; @@ -96,9 +97,10 @@ class ITK_TEMPLATE_EXPORT MembershipSample : public DataObject using ClassSampleConstPointer = typename ClassSampleType::ConstPointer; /** Set/Get the actual sample data */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(Sample, SampleType); itkGetConstObjectMacro(Sample, SampleType); - + /** @ITKEndGrouping */ /** Sets the number of classes (class labels) */ void SetNumberOfClasses(unsigned int numberOfClasses); diff --git a/Modules/Numerics/Statistics/include/itkNeighborhoodSampler.h b/Modules/Numerics/Statistics/include/itkNeighborhoodSampler.h index a9789362122..b4fffc8a1de 100644 --- a/Modules/Numerics/Statistics/include/itkNeighborhoodSampler.h +++ b/Modules/Numerics/Statistics/include/itkNeighborhoodSampler.h @@ -53,9 +53,10 @@ class ITK_TEMPLATE_EXPORT NeighborhoodSampler : public SampleToSubsampleFilter; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(NeighborhoodSampler); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Typedefs for Measurement vector, measurement, Instance Identifier, * frequency, size, size element value from the template argument TSample */ using typename Superclass::SampleType; diff --git a/Modules/Numerics/Statistics/include/itkSampleClassifierFilter.h b/Modules/Numerics/Statistics/include/itkSampleClassifierFilter.h index 016967e3f1a..f003e020893 100644 --- a/Modules/Numerics/Statistics/include/itkSampleClassifierFilter.h +++ b/Modules/Numerics/Statistics/include/itkSampleClassifierFilter.h @@ -54,9 +54,10 @@ class ITK_TEMPLATE_EXPORT SampleClassifierFilter : public ProcessObject using ConstPointer = SmartPointer; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(SampleClassifierFilter); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Type of the input Sample */ using SampleType = TSample; @@ -105,13 +106,15 @@ class ITK_TEMPLATE_EXPORT SampleClassifierFilter : public ProcessObject /** Number of classes. This must match the number of labels and membership * functions provided by the user, otherwise an exception will be thrown at */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfClasses, unsigned int); itkGetConstMacro(NumberOfClasses, unsigned int); - + /** @ITKEndGrouping */ /** Set/Get the decision rule. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(DecisionRule, DecisionRuleType); itkGetConstObjectMacro(DecisionRule, DecisionRuleType); - + /** @ITKEndGrouping */ /** Sets input vector of class labels. The length of this vector must match * the number of classes, otherwise an exception will be thrown at run time. * */ @@ -144,11 +147,12 @@ class ITK_TEMPLATE_EXPORT SampleClassifierFilter : public ProcessObject * called. * \sa ProcessObject */ + /** @ITKStartGrouping */ using DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType; using Superclass::MakeOutput; DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx) override; - + /** @ITKEndGrouping */ private: unsigned int m_NumberOfClasses{}; diff --git a/Modules/Numerics/Statistics/include/itkSampleToHistogramFilter.h b/Modules/Numerics/Statistics/include/itkSampleToHistogramFilter.h index 614d7cfac48..984006cbf70 100644 --- a/Modules/Numerics/Statistics/include/itkSampleToHistogramFilter.h +++ b/Modules/Numerics/Statistics/include/itkSampleToHistogramFilter.h @@ -136,9 +136,10 @@ class ITK_TEMPLATE_EXPORT SampleToHistogramFilter : public ProcessObject /** Methods for setting and getting the Minimum and Maximum values of the * histogram bins. \warning To use those values you need to set the AutoMinimumMaximum flag to false.*/ + /** @ITKStartGrouping */ itkSetGetDecoratedInputMacro(HistogramBinMinimum, HistogramMeasurementVectorType); itkSetGetDecoratedInputMacro(HistogramBinMaximum, HistogramMeasurementVectorType); - + /** @ITKEndGrouping */ /** Methods for setting and getting the boolean flag that defines whether the * minimum and maximum of the histogram are going to be computed * automatically from the values of the sample. @@ -163,11 +164,12 @@ class ITK_TEMPLATE_EXPORT SampleToHistogramFilter : public ProcessObject * called. * \sa ProcessObject */ + /** @ITKStartGrouping */ using DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType; using Superclass::MakeOutput; DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx) override; - + /** @ITKEndGrouping */ // Where the histogram is actually computed void GenerateData() override; diff --git a/Modules/Numerics/Statistics/include/itkSampleToSubsampleFilter.h b/Modules/Numerics/Statistics/include/itkSampleToSubsampleFilter.h index 387b4bf1917..4ea23f14adb 100644 --- a/Modules/Numerics/Statistics/include/itkSampleToSubsampleFilter.h +++ b/Modules/Numerics/Statistics/include/itkSampleToSubsampleFilter.h @@ -92,11 +92,12 @@ class ITK_TEMPLATE_EXPORT SampleToSubsampleFilter : public ProcessObject * called. * \sa ProcessObject */ + /** @ITKStartGrouping */ using DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType; using Superclass::MakeOutput; DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx) override; - + /** @ITKEndGrouping */ }; // end of class } // end of namespace Statistics } // end of namespace itk diff --git a/Modules/Numerics/Statistics/include/itkScalarImageToCooccurrenceMatrixFilter.h b/Modules/Numerics/Statistics/include/itkScalarImageToCooccurrenceMatrixFilter.h index 03bfa8a6452..7e88facc042 100644 --- a/Modules/Numerics/Statistics/include/itkScalarImageToCooccurrenceMatrixFilter.h +++ b/Modules/Numerics/Statistics/include/itkScalarImageToCooccurrenceMatrixFilter.h @@ -133,16 +133,18 @@ class ITK_TEMPLATE_EXPORT ScalarImageToCooccurrenceMatrixFilter : public Process /** Get/Set the offset or offsets over which the co-occurrence pairs will be computed. Calling either of these methods clears the previous offsets. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(Offsets, OffsetVector); itkGetConstObjectMacro(Offsets, OffsetVector); - + /** @ITKEndGrouping */ void SetOffset(const OffsetType offset); /** Set number of histogram bins along each axis */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfBinsPerAxis, unsigned int); itkGetConstMacro(NumberOfBinsPerAxis, unsigned int); - + /** @ITKEndGrouping */ /** Set the min and max (inclusive) pixel value that will be placed in the histogram */ void @@ -153,10 +155,11 @@ class ITK_TEMPLATE_EXPORT ScalarImageToCooccurrenceMatrixFilter : public Process /** Set the calculator to normalize the histogram (divide all bins by the total frequency). Normalization is off by default. */ + /** @ITKStartGrouping */ itkSetMacro(Normalize, bool); itkGetConstMacro(Normalize, bool); itkBooleanMacro(Normalize); - + /** @ITKEndGrouping */ /** Method to set/get the image */ using Superclass::SetInput; void @@ -178,9 +181,10 @@ class ITK_TEMPLATE_EXPORT ScalarImageToCooccurrenceMatrixFilter : public Process /** Set the pixel value of the mask that should be considered "inside" the object. Defaults to one. */ + /** @ITKStartGrouping */ itkSetMacro(InsidePixelValue, MaskPixelType); itkGetConstMacro(InsidePixelValue, MaskPixelType); - + /** @ITKEndGrouping */ protected: ScalarImageToCooccurrenceMatrixFilter(); ~ScalarImageToCooccurrenceMatrixFilter() override = default; diff --git a/Modules/Numerics/Statistics/include/itkScalarImageToRunLengthFeaturesFilter.h b/Modules/Numerics/Statistics/include/itkScalarImageToRunLengthFeaturesFilter.h index 1093f378ed6..b339523a246 100644 --- a/Modules/Numerics/Statistics/include/itkScalarImageToRunLengthFeaturesFilter.h +++ b/Modules/Numerics/Statistics/include/itkScalarImageToRunLengthFeaturesFilter.h @@ -145,17 +145,23 @@ class ITK_TEMPLATE_EXPORT ScalarImageToRunLengthFeaturesFilter : public ProcessO GetInput() const; /** Return the feature means and deviations. */ + /** @ITKStartGrouping */ itkGetConstReferenceObjectMacro(FeatureMeans, FeatureValueVector); itkGetConstReferenceObjectMacro(FeatureStandardDeviations, FeatureValueVector); + /** @ITKEndGrouping */ /** Set the desired feature set. Optional, for default value see above. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(RequestedFeatures, FeatureNameVector); itkGetConstObjectMacro(RequestedFeatures, FeatureNameVector); + /** @ITKEndGrouping */ /** Set the offsets over which the co-occurrence pairs will be computed. Optional; for default value see above. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(Offsets, OffsetVector); itkGetConstObjectMacro(Offsets, OffsetVector); + /** @ITKEndGrouping */ /** Set number of histogram bins along each axis. Optional; for default value see above. */ diff --git a/Modules/Numerics/Statistics/include/itkScalarImageToRunLengthMatrixFilter.h b/Modules/Numerics/Statistics/include/itkScalarImageToRunLengthMatrixFilter.h index 1b844409299..349550efd61 100644 --- a/Modules/Numerics/Statistics/include/itkScalarImageToRunLengthMatrixFilter.h +++ b/Modules/Numerics/Statistics/include/itkScalarImageToRunLengthMatrixFilter.h @@ -223,9 +223,10 @@ class ITK_TEMPLATE_EXPORT ScalarImageToRunLengthMatrixFilter : public ProcessObj * Set the pixel value of the mask that should be considered "inside" the * object. Defaults to 1. */ + /** @ITKStartGrouping */ itkSetMacro(InsidePixelValue, PixelType); itkGetConstMacro(InsidePixelValue, PixelType); - + /** @ITKEndGrouping */ protected: ScalarImageToRunLengthMatrixFilter(); ~ScalarImageToRunLengthMatrixFilter() override = default; diff --git a/Modules/Numerics/Statistics/include/itkScalarImageToTextureFeaturesFilter.h b/Modules/Numerics/Statistics/include/itkScalarImageToTextureFeaturesFilter.h index 3a28afada64..2c352cb4fb5 100644 --- a/Modules/Numerics/Statistics/include/itkScalarImageToTextureFeaturesFilter.h +++ b/Modules/Numerics/Statistics/include/itkScalarImageToTextureFeaturesFilter.h @@ -162,17 +162,23 @@ class ITK_TEMPLATE_EXPORT ScalarImageToTextureFeaturesFilter : public ProcessObj GetInput() const; /** Return the feature means and deviations. */ + /** @ITKStartGrouping */ itkGetConstReferenceObjectMacro(FeatureMeans, FeatureValueVector); itkGetConstReferenceObjectMacro(FeatureStandardDeviations, FeatureValueVector); + /** @ITKEndGrouping */ /** Set the desired feature set. Optional, for default value see above. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(RequestedFeatures, FeatureNameVector); itkGetConstObjectMacro(RequestedFeatures, FeatureNameVector); + /** @ITKEndGrouping */ /** Set the offsets over which the co-occurrence pairs will be computed. Optional; for default value see above. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(Offsets, OffsetVector); itkGetConstObjectMacro(Offsets, OffsetVector); + /** @ITKEndGrouping */ /** Set number of histogram bins along each axis. Optional; for default value see above. */ diff --git a/Modules/Numerics/Statistics/include/itkSparseFrequencyContainer2.h b/Modules/Numerics/Statistics/include/itkSparseFrequencyContainer2.h index 0eb303fc61d..8b833ba5b17 100644 --- a/Modules/Numerics/Statistics/include/itkSparseFrequencyContainer2.h +++ b/Modules/Numerics/Statistics/include/itkSparseFrequencyContainer2.h @@ -51,9 +51,10 @@ class ITKStatistics_EXPORT SparseFrequencyContainer2 : public Object using ConstPointer = SmartPointer; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(SparseFrequencyContainer2); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** instance identifier alias */ using InstanceIdentifier = MeasurementVectorTraits::InstanceIdentifier; diff --git a/Modules/Numerics/Statistics/include/itkSpatialNeighborSubsampler.h b/Modules/Numerics/Statistics/include/itkSpatialNeighborSubsampler.h index d8d2749bd2f..c7e471e755c 100644 --- a/Modules/Numerics/Statistics/include/itkSpatialNeighborSubsampler.h +++ b/Modules/Numerics/Statistics/include/itkSpatialNeighborSubsampler.h @@ -89,11 +89,12 @@ class ITK_TEMPLATE_EXPORT SpatialNeighborSubsampler : public RegionConstrainedSu using ImageHelperType = ImageHelper; /** Method to set the radius */ + /** @ITKStartGrouping */ void SetRadius(const RadiusType & radius); void SetRadius(unsigned int radius); - + /** @ITKEndGrouping */ /** Method to get the radius */ itkGetConstReferenceMacro(Radius, RadiusType); diff --git a/Modules/Numerics/Statistics/include/itkStandardDeviationPerComponentSampleFilter.h b/Modules/Numerics/Statistics/include/itkStandardDeviationPerComponentSampleFilter.h index 54bb9f6e7b7..69e51c38416 100644 --- a/Modules/Numerics/Statistics/include/itkStandardDeviationPerComponentSampleFilter.h +++ b/Modules/Numerics/Statistics/include/itkStandardDeviationPerComponentSampleFilter.h @@ -60,9 +60,10 @@ class ITK_TEMPLATE_EXPORT StandardDeviationPerComponentSampleFilter : public Pro using SampleType = TSample; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(StandardDeviationPerComponentSampleFilter); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Length of a measurement vector */ using MeasurementVectorSizeType = typename TSample::MeasurementVectorSizeType; diff --git a/Modules/Numerics/Statistics/include/itkSubsamplerBase.h b/Modules/Numerics/Statistics/include/itkSubsamplerBase.h index 4a9e0afdfc8..77802173d1e 100644 --- a/Modules/Numerics/Statistics/include/itkSubsamplerBase.h +++ b/Modules/Numerics/Statistics/include/itkSubsamplerBase.h @@ -77,22 +77,27 @@ class ITK_TEMPLATE_EXPORT SubsamplerBase : public Object using SeedType = unsigned int; /** Plug in the actual sample data */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(Sample, SampleType); itkGetConstObjectMacro(Sample, SampleType); + /** @ITKEndGrouping */ /** Indicate whether the Search method can return the query point * as one element of the Subsample */ + /** @ITKStartGrouping */ itkSetMacro(CanSelectQuery, bool); itkGetConstReferenceMacro(CanSelectQuery, bool); itkBooleanMacro(CanSelectQuery); + /** @ITKEndGrouping */ /** Provide an interface to set the seed. * The seed value will be used by subclasses where appropriate. */ + /** @ITKStartGrouping */ itkSetMacro(Seed, SeedType); itkGetConstReferenceMacro(Seed, SeedType); - + /** @ITKEndGrouping */ /** Specify whether the subsampler should return all possible * matches. */ diff --git a/Modules/Numerics/Statistics/include/itkVectorContainerToListSampleAdaptor.h b/Modules/Numerics/Statistics/include/itkVectorContainerToListSampleAdaptor.h index dc44d8c34ed..ff3b4cdbe61 100644 --- a/Modules/Numerics/Statistics/include/itkVectorContainerToListSampleAdaptor.h +++ b/Modules/Numerics/Statistics/include/itkVectorContainerToListSampleAdaptor.h @@ -83,9 +83,10 @@ class ITK_TEMPLATE_EXPORT VectorContainerToListSampleAdaptor : public ListSample /** Get/Set method for the point set container which will be actually used * for storing measurement vectors. */ + /** @ITKStartGrouping */ itkSetObjectMacro(VectorContainer, VectorContainerType); itkGetConstObjectMacro(VectorContainer, VectorContainerType); - + /** @ITKEndGrouping */ /** Returns the number of measurement vectors in this container. */ InstanceIdentifier Size() const override; diff --git a/Modules/Numerics/Statistics/include/itkWeightedCovarianceSampleFilter.h b/Modules/Numerics/Statistics/include/itkWeightedCovarianceSampleFilter.h index b389412c7d0..4a19be3f19c 100644 --- a/Modules/Numerics/Statistics/include/itkWeightedCovarianceSampleFilter.h +++ b/Modules/Numerics/Statistics/include/itkWeightedCovarianceSampleFilter.h @@ -53,9 +53,10 @@ class ITK_TEMPLATE_EXPORT WeightedCovarianceSampleFilter : public CovarianceSamp using ConstPointer = SmartPointer; /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(WeightedCovarianceSampleFilter); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Types derived from the base class */ using typename Superclass::SampleType; using typename Superclass::MeasurementVectorType; diff --git a/Modules/Numerics/Statistics/include/itkWeightedMeanSampleFilter.h b/Modules/Numerics/Statistics/include/itkWeightedMeanSampleFilter.h index a8c67005971..39ccfac5c94 100644 --- a/Modules/Numerics/Statistics/include/itkWeightedMeanSampleFilter.h +++ b/Modules/Numerics/Statistics/include/itkWeightedMeanSampleFilter.h @@ -51,10 +51,11 @@ class ITK_TEMPLATE_EXPORT WeightedMeanSampleFilter : public MeanSampleFilter; using ConstPointer = SmartPointer; - /**Standard Macros */ + /** Standard Macros */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(WeightedMeanSampleFilter); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Types derived from the base class */ using typename Superclass::SampleType; using typename Superclass::MeasurementVectorType; diff --git a/Modules/Registration/Common/include/itkBlockMatchingImageFilter.h b/Modules/Registration/Common/include/itkBlockMatchingImageFilter.h index ca27824a54a..871748b7afa 100644 --- a/Modules/Registration/Common/include/itkBlockMatchingImageFilter.h +++ b/Modules/Registration/Common/include/itkBlockMatchingImageFilter.h @@ -127,25 +127,30 @@ class ITK_TEMPLATE_EXPORT BlockMatchingImageFilter : public MeshToMeshFilter m_ThreaderTransform; @@ -492,6 +503,7 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetric : public SingleValuedCostFunction * image derivatives are computed using central differencing. */ using BSplineInterpolatorType = BSplineInterpolateImageFunction; + /** Typedefs for using central difference calculator. */ using DerivativeFunctionType = CentralDifferenceImageFunction; using ImageDerivativesType = CovariantVector; @@ -643,6 +655,7 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetric : public SingleValuedCostFunction GetValueThread(ThreadIdType threadId) const; /** Get the match Measure. */ + /** @ITKStartGrouping */ virtual inline void GetValueThreadPreProcess(ThreadIdType itkNotUsed(threadId), bool itkNotUsed(withinSampleThread)) const {} @@ -657,7 +670,7 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetric : public SingleValuedCostFunction virtual inline void GetValueThreadPostProcess(ThreadIdType itkNotUsed(threadId), bool itkNotUsed(withinSampleThread)) const {} - + /** @ITKEndGrouping */ void GetValueAndDerivativeMultiThreadedInitiate() const; diff --git a/Modules/Registration/Common/include/itkImageToSpatialObjectMetric.h b/Modules/Registration/Common/include/itkImageToSpatialObjectMetric.h index abb9d0c80b3..1f0bc2933c4 100644 --- a/Modules/Registration/Common/include/itkImageToSpatialObjectMetric.h +++ b/Modules/Registration/Common/include/itkImageToSpatialObjectMetric.h @@ -125,13 +125,15 @@ class ITK_TEMPLATE_EXPORT ImageToSpatialObjectMetric : public SingleValuedCostFu itkOverrideGetNameOfClassMacro(ImageToSpatialObjectMetric); /** Get/Set the FixedImage. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(FixedImage, FixedImageType); itkGetConstObjectMacro(FixedImage, FixedImageType); - + /** @ITKEndGrouping */ /** Get/Set the MovingSpatialObject */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(MovingSpatialObject, MovingSpatialObjectType); itkGetConstObjectMacro(MovingSpatialObject, MovingSpatialObjectType); - + /** @ITKEndGrouping */ /** Connect the Interpolator. */ itkSetObjectMacro(Interpolator, InterpolatorType); diff --git a/Modules/Registration/Common/include/itkImageToSpatialObjectRegistrationMethod.h b/Modules/Registration/Common/include/itkImageToSpatialObjectRegistrationMethod.h index a6367c9687c..8cd4e198855 100644 --- a/Modules/Registration/Common/include/itkImageToSpatialObjectRegistrationMethod.h +++ b/Modules/Registration/Common/include/itkImageToSpatialObjectRegistrationMethod.h @@ -135,33 +135,40 @@ class ITK_TEMPLATE_EXPORT ImageToSpatialObjectRegistrationMethod : public Proces using DataObjectPointer = typename DataObject::Pointer; /** Set/Get the Fixed image. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(FixedImage, FixedImageType); itkGetConstObjectMacro(FixedImage, FixedImageType); - + /** @ITKEndGrouping */ /** Set/Get the Moving Spatial Object. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(MovingSpatialObject, MovingSpatialObjectType); itkGetConstObjectMacro(MovingSpatialObject, MovingSpatialObjectType); - + /** @ITKEndGrouping */ /** Set/Get the Optimizer. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Optimizer, OptimizerType); itkGetModifiableObjectMacro(Optimizer, OptimizerType); - + /** @ITKEndGrouping */ /** Set/Get the Metric. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Metric, MetricType); itkGetModifiableObjectMacro(Metric, MetricType); - + /** @ITKEndGrouping */ /** Set/Get the Transform. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Transform, TransformType); itkGetModifiableObjectMacro(Transform, TransformType); - + /** @ITKEndGrouping */ /** Set/Get the Interpolator. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Interpolator, InterpolatorType); itkGetModifiableObjectMacro(Interpolator, InterpolatorType); - + /** @ITKEndGrouping */ /** Set/Get the initial transformation parameters. */ + /** @ITKStartGrouping */ itkSetMacro(InitialTransformParameters, ParametersType); itkGetConstReferenceMacro(InitialTransformParameters, ParametersType); - + /** @ITKEndGrouping */ /** Get the last transformation parameters visited by * the optimizer. */ itkGetConstReferenceMacro(LastTransformParameters, ParametersType); diff --git a/Modules/Registration/Common/include/itkKappaStatisticImageToImageMetric.h b/Modules/Registration/Common/include/itkKappaStatisticImageToImageMetric.h index 46cf02cb188..7af829f6885 100644 --- a/Modules/Registration/Common/include/itkKappaStatisticImageToImageMetric.h +++ b/Modules/Registration/Common/include/itkKappaStatisticImageToImageMetric.h @@ -112,17 +112,19 @@ class ITK_TEMPLATE_EXPORT KappaStatisticImageToImageMetric : public ImageToImage /** This method allows the user to set the foreground value. The default * value is 255. */ + /** @ITKStartGrouping */ itkSetMacro(ForegroundValue, RealType); itkGetConstMacro(ForegroundValue, RealType); - + /** @ITKEndGrouping */ /** Set/Get whether this metric returns 2*|A&B|/(|A|+|B|) * (ComplementOff, the default) or 1.0 - 2*|A&B|/(|A|+|B|) * (ComplementOn). When using an optimizer that minimizes * metric values use ComplementOn(). */ + /** @ITKStartGrouping */ itkSetMacro(Complement, bool); itkBooleanMacro(Complement); itkGetConstMacro(Complement, bool); - + /** @ITKEndGrouping */ protected: KappaStatisticImageToImageMetric(); ~KappaStatisticImageToImageMetric() override = default; diff --git a/Modules/Registration/Common/include/itkKullbackLeiblerCompareHistogramImageToImageMetric.h b/Modules/Registration/Common/include/itkKullbackLeiblerCompareHistogramImageToImageMetric.h index 7f1edbca84c..691b033c059 100644 --- a/Modules/Registration/Common/include/itkKullbackLeiblerCompareHistogramImageToImageMetric.h +++ b/Modules/Registration/Common/include/itkKullbackLeiblerCompareHistogramImageToImageMetric.h @@ -121,6 +121,7 @@ class ITK_TEMPLATE_EXPORT KullbackLeiblerCompareHistogramImageToImageMetric } /** Forms the histogram of the training images to prepare to evaluate the */ + /** metric. Must set all parameters first */ void Initialize() override; @@ -128,11 +129,12 @@ class ITK_TEMPLATE_EXPORT KullbackLeiblerCompareHistogramImageToImageMetric protected: /** Constructor is protected to ensure that \c New() function is used to create instances. */ + /** @ITKStartGrouping */ KullbackLeiblerCompareHistogramImageToImageMetric(); ~KullbackLeiblerCompareHistogramImageToImageMetric() override = default; void PrintSelf(std::ostream & os, Indent indent) const override; - + /** @ITKEndGrouping */ /** Form the Histogram for the Training data */ void FormTrainingHistogram(); diff --git a/Modules/Registration/Common/include/itkMatchCardinalityImageToImageMetric.h b/Modules/Registration/Common/include/itkMatchCardinalityImageToImageMetric.h index 12a52c711c8..b72424b2cb4 100644 --- a/Modules/Registration/Common/include/itkMatchCardinalityImageToImageMetric.h +++ b/Modules/Registration/Common/include/itkMatchCardinalityImageToImageMetric.h @@ -120,9 +120,11 @@ class ITK_TEMPLATE_EXPORT MatchCardinalityImageToImageMetric : public ImageToIma * other words, the metric measures the percentage of pixel matches * or mismatches. The default is to measure matches * (MeasureMatchesOn). */ + /** @ITKStartGrouping */ itkSetMacro(MeasureMatches, bool); itkBooleanMacro(MeasureMatches); itkGetConstMacro(MeasureMatches, bool); + /** @ITKEndGrouping */ /** Return the multithreader used by this class. */ MultiThreaderBase * diff --git a/Modules/Registration/Common/include/itkMattesMutualInformationImageToImageMetric.h b/Modules/Registration/Common/include/itkMattesMutualInformationImageToImageMetric.h index 83cd6baf306..fc6813e62d2 100644 --- a/Modules/Registration/Common/include/itkMattesMutualInformationImageToImageMetric.h +++ b/Modules/Registration/Common/include/itkMattesMutualInformationImageToImageMetric.h @@ -176,8 +176,10 @@ class ITK_TEMPLATE_EXPORT MattesMutualInformationImageToImageMetric * windowing with a cubic-BSpline kernel. Note that even if the metric * is used on binary images, the number of bins should at least be * equal to five. */ + /** @ITKStartGrouping */ itkSetClampMacro(NumberOfHistogramBins, SizeValueType, 5, NumericTraits::max()); itkGetConstReferenceMacro(NumberOfHistogramBins, SizeValueType); + /** @ITKEndGrouping */ /** This variable selects the method to be used for computing the Metric * derivatives with respect to the Transform parameters. Two modes of @@ -203,9 +205,11 @@ class ITK_TEMPLATE_EXPORT MattesMutualInformationImageToImageMetric * the PDF bins. This is an array of floating point values with size equals to (number of * histogram bins)^2. This method is well suited for Transforms with a large * number of parameters, such as, BSplineTransforms. */ + /** @ITKStartGrouping */ itkSetMacro(UseExplicitPDFDerivatives, bool); itkGetConstReferenceMacro(UseExplicitPDFDerivatives, bool); itkBooleanMacro(UseExplicitPDFDerivatives); + /** @ITKEndGrouping */ /** The marginal PDFs are stored as std::vector. */ using PDFValueType = double; // NOTE: floating point precision is not as stable. Double precision proves faster and diff --git a/Modules/Registration/Common/include/itkMeanReciprocalSquareDifferenceImageToImageMetric.h b/Modules/Registration/Common/include/itkMeanReciprocalSquareDifferenceImageToImageMetric.h index b5cb1207f03..42cde125c1a 100644 --- a/Modules/Registration/Common/include/itkMeanReciprocalSquareDifferenceImageToImageMetric.h +++ b/Modules/Registration/Common/include/itkMeanReciprocalSquareDifferenceImageToImageMetric.h @@ -92,14 +92,16 @@ class ITK_TEMPLATE_EXPORT MeanReciprocalSquareDifferenceImageToImageMetric /** Set/Get Lambda value. This factor regulates the capture radius of this metric */ + /** @ITKStartGrouping */ itkGetConstMacro(Lambda, double); itkSetMacro(Lambda, double); - + /** @ITKEndGrouping */ /** Set/Get Delta value. This value is used as the differential in the * computation of the metric derivative using the finite differences method. */ + /** @ITKStartGrouping */ itkGetConstMacro(Delta, double); itkSetMacro(Delta, double); - + /** @ITKEndGrouping */ protected: MeanReciprocalSquareDifferenceImageToImageMetric(); ~MeanReciprocalSquareDifferenceImageToImageMetric() override = default; diff --git a/Modules/Registration/Common/include/itkMeanReciprocalSquareDifferencePointSetToImageMetric.h b/Modules/Registration/Common/include/itkMeanReciprocalSquareDifferencePointSetToImageMetric.h index ad41669f82d..286c8b8896d 100644 --- a/Modules/Registration/Common/include/itkMeanReciprocalSquareDifferencePointSetToImageMetric.h +++ b/Modules/Registration/Common/include/itkMeanReciprocalSquareDifferencePointSetToImageMetric.h @@ -97,9 +97,10 @@ class ITK_TEMPLATE_EXPORT MeanReciprocalSquareDifferencePointSetToImageMetric /** Set/Get the lambda distance. (controls the capture radius of the metric). */ + /** @ITKStartGrouping */ itkSetMacro(Lambda, double); itkGetConstMacro(Lambda, double); - + /** @ITKEndGrouping */ protected: MeanReciprocalSquareDifferencePointSetToImageMetric(); ~MeanReciprocalSquareDifferencePointSetToImageMetric() override = default; diff --git a/Modules/Registration/Common/include/itkMeanSquaresHistogramImageToImageMetric.h b/Modules/Registration/Common/include/itkMeanSquaresHistogramImageToImageMetric.h index 5e633a6a3af..240322810d1 100644 --- a/Modules/Registration/Common/include/itkMeanSquaresHistogramImageToImageMetric.h +++ b/Modules/Registration/Common/include/itkMeanSquaresHistogramImageToImageMetric.h @@ -77,9 +77,10 @@ class ITK_TEMPLATE_EXPORT MeanSquaresHistogramImageToImageMetric protected: /** Constructor is protected to ensure that \c New() function is used to create instances. */ + /** @ITKStartGrouping */ MeanSquaresHistogramImageToImageMetric() = default; ~MeanSquaresHistogramImageToImageMetric() override = default; - + /** @ITKEndGrouping */ /** Evaluates the sum of squared differences from the histogram. */ MeasureType EvaluateMeasure(HistogramType & histogram) const override; diff --git a/Modules/Registration/Common/include/itkMultiResolutionImageRegistrationMethod.h b/Modules/Registration/Common/include/itkMultiResolutionImageRegistrationMethod.h index f5397b42205..72c19ceaa34 100644 --- a/Modules/Registration/Common/include/itkMultiResolutionImageRegistrationMethod.h +++ b/Modules/Registration/Common/include/itkMultiResolutionImageRegistrationMethod.h @@ -139,41 +139,50 @@ class ITK_TEMPLATE_EXPORT MultiResolutionImageRegistrationMethod : public Proces StopRegistration(); /** Set/Get the Fixed image. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(FixedImage, FixedImageType); itkGetConstObjectMacro(FixedImage, FixedImageType); - + /** @ITKEndGrouping */ /** Set/Get the Moving image. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(MovingImage, MovingImageType); itkGetConstObjectMacro(MovingImage, MovingImageType); - + /** @ITKEndGrouping */ /** Set/Get the Optimizer. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Optimizer, OptimizerType); itkGetModifiableObjectMacro(Optimizer, OptimizerType); - + /** @ITKEndGrouping */ /** Set/Get the Metric. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Metric, MetricType); itkGetModifiableObjectMacro(Metric, MetricType); - + /** @ITKEndGrouping */ /** Set/Get the Metric. */ + /** @ITKStartGrouping */ itkSetMacro(FixedImageRegion, FixedImageRegionType); itkGetConstReferenceMacro(FixedImageRegion, FixedImageRegionType); - + /** @ITKEndGrouping */ /** Set/Get the Transform. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Transform, TransformType); itkGetModifiableObjectMacro(Transform, TransformType); - + /** @ITKEndGrouping */ /** Set/Get the Interpolator. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Interpolator, InterpolatorType); itkGetModifiableObjectMacro(Interpolator, InterpolatorType); - + /** @ITKEndGrouping */ /** Set/Get the Fixed image pyramid. */ + /** @ITKStartGrouping */ itkSetObjectMacro(FixedImagePyramid, FixedImagePyramidType); itkGetModifiableObjectMacro(FixedImagePyramid, FixedImagePyramidType); - + /** @ITKEndGrouping */ /** Set/Get the Moving image pyramid. */ + /** @ITKStartGrouping */ itkSetObjectMacro(MovingImagePyramid, MovingImagePyramidType); itkGetModifiableObjectMacro(MovingImagePyramid, MovingImagePyramidType); - + /** @ITKEndGrouping */ /** Set/Get the schedules for the fixed and moving image pyramid. */ void SetSchedules(const ScheduleType & fixedImagePyramidSchedule, const ScheduleType & movingImagePyramidSchedule); @@ -191,15 +200,17 @@ class ITK_TEMPLATE_EXPORT MultiResolutionImageRegistrationMethod : public Proces itkGetConstMacro(CurrentLevel, SizeValueType); /** Set/Get the initial transformation parameters. */ + /** @ITKStartGrouping */ itkSetMacro(InitialTransformParameters, ParametersType); itkGetConstReferenceMacro(InitialTransformParameters, ParametersType); - + /** @ITKEndGrouping */ /** Set/Get the initial transformation parameters of the next resolution level to be processed. The default is the last set of parameters of the last resolution level. */ + /** @ITKStartGrouping */ itkSetMacro(InitialTransformParametersOfNextLevel, ParametersType); itkGetConstReferenceMacro(InitialTransformParametersOfNextLevel, ParametersType); - + /** @ITKEndGrouping */ /** Get the last transformation parameters visited by * the optimizer. */ itkGetConstReferenceMacro(LastTransformParameters, ParametersType); diff --git a/Modules/Registration/Common/include/itkMutualInformationHistogramImageToImageMetric.h b/Modules/Registration/Common/include/itkMutualInformationHistogramImageToImageMetric.h index 21adbc007f5..00666f05479 100644 --- a/Modules/Registration/Common/include/itkMutualInformationHistogramImageToImageMetric.h +++ b/Modules/Registration/Common/include/itkMutualInformationHistogramImageToImageMetric.h @@ -76,9 +76,10 @@ class ITK_TEMPLATE_EXPORT MutualInformationHistogramImageToImageMetric protected: /** Constructor is protected to ensure that \c New() function is used to create instances. */ + /** @ITKStartGrouping */ MutualInformationHistogramImageToImageMetric() = default; ~MutualInformationHistogramImageToImageMetric() override = default; - + /** @ITKEndGrouping */ /** Evaluates the mutual information from the histogram. */ MeasureType EvaluateMeasure(HistogramType & histogram) const override; diff --git a/Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.h b/Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.h index 50f55b7549f..bd13166d9b2 100644 --- a/Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.h +++ b/Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.h @@ -159,28 +159,31 @@ class ITK_TEMPLATE_EXPORT MutualInformationImageToImageMetric : public ImageToIm * calculation. Default value is 0.4 which works well for image intensities * normalized to a mean of 0 and standard deviation of 1.0. * Value is clamped to be always greater than zero. */ + /** @ITKStartGrouping */ itkSetClampMacro(MovingImageStandardDeviation, double, NumericTraits::NonpositiveMin(), NumericTraits::max()); itkGetConstReferenceMacro(MovingImageStandardDeviation, double); - + /** @ITKEndGrouping */ /** Set/Get the fixed image intensity standard deviation. This defines * the kernel bandwidth used in the joint probability distribution * calculation. Default value is 0.4 which works well for image intensities * normalized to a mean of 0 and standard deviation of 1.0. * Value is clamped to be always greater than zero. */ + /** @ITKStartGrouping */ itkSetClampMacro(FixedImageStandardDeviation, double, NumericTraits::NonpositiveMin(), NumericTraits::max()); itkGetConstMacro(FixedImageStandardDeviation, double); - + /** @ITKEndGrouping */ /** Set/Get the kernel function. This is used to calculate the joint * probability distribution. Default is the GaussianKernelFunction. */ + /** @ITKStartGrouping */ itkSetObjectMacro(KernelFunction, KernelFunctionType); itkGetModifiableObjectMacro(KernelFunction, KernelFunctionType); - + /** @ITKEndGrouping */ protected: MutualInformationImageToImageMetric(); diff --git a/Modules/Registration/Common/include/itkNormalizedCorrelationImageToImageMetric.h b/Modules/Registration/Common/include/itkNormalizedCorrelationImageToImageMetric.h index 13979876fe3..11961d4b661 100644 --- a/Modules/Registration/Common/include/itkNormalizedCorrelationImageToImageMetric.h +++ b/Modules/Registration/Common/include/itkNormalizedCorrelationImageToImageMetric.h @@ -95,10 +95,11 @@ class ITK_TEMPLATE_EXPORT NormalizedCorrelationImageToImageMetric : public Image * from the sample values in the cross-correlation formula and * typically results in narrower valleys in the cost function. * Default value is false. */ + /** @ITKStartGrouping */ itkSetMacro(SubtractMean, bool); itkGetConstReferenceMacro(SubtractMean, bool); itkBooleanMacro(SubtractMean); - + /** @ITKEndGrouping */ protected: NormalizedCorrelationImageToImageMetric(); ~NormalizedCorrelationImageToImageMetric() override = default; diff --git a/Modules/Registration/Common/include/itkNormalizedCorrelationPointSetToImageMetric.h b/Modules/Registration/Common/include/itkNormalizedCorrelationPointSetToImageMetric.h index 1af7a34767d..e40224eb754 100644 --- a/Modules/Registration/Common/include/itkNormalizedCorrelationPointSetToImageMetric.h +++ b/Modules/Registration/Common/include/itkNormalizedCorrelationPointSetToImageMetric.h @@ -97,10 +97,11 @@ class ITK_TEMPLATE_EXPORT NormalizedCorrelationPointSetToImageMetric * from the sample values in the cross-correlation formula and * typically results in narrower valleys in the cost function. * Default value is false. */ + /** @ITKStartGrouping */ itkSetMacro(SubtractMean, bool); itkGetConstReferenceMacro(SubtractMean, bool); itkBooleanMacro(SubtractMean); - + /** @ITKEndGrouping */ protected: NormalizedCorrelationPointSetToImageMetric(); ~NormalizedCorrelationPointSetToImageMetric() override = default; diff --git a/Modules/Registration/Common/include/itkNormalizedMutualInformationHistogramImageToImageMetric.h b/Modules/Registration/Common/include/itkNormalizedMutualInformationHistogramImageToImageMetric.h index 8cb8e93b9b7..1b8ab2aab6d 100644 --- a/Modules/Registration/Common/include/itkNormalizedMutualInformationHistogramImageToImageMetric.h +++ b/Modules/Registration/Common/include/itkNormalizedMutualInformationHistogramImageToImageMetric.h @@ -90,9 +90,10 @@ class ITK_TEMPLATE_EXPORT NormalizedMutualInformationHistogramImageToImageMetric protected: /** Constructor is protected to ensure that \c New() function is used to create instances. */ + /** @ITKStartGrouping */ NormalizedMutualInformationHistogramImageToImageMetric() = default; ~NormalizedMutualInformationHistogramImageToImageMetric() override = default; - + /** @ITKEndGrouping */ /** Evaluates the normalized mutual information from the histogram. */ MeasureType EvaluateMeasure(HistogramType & histogram) const override; diff --git a/Modules/Registration/Common/include/itkPointSetToImageMetric.h b/Modules/Registration/Common/include/itkPointSetToImageMetric.h index 976e20367d4..bf56a84ce57 100644 --- a/Modules/Registration/Common/include/itkPointSetToImageMetric.h +++ b/Modules/Registration/Common/include/itkPointSetToImageMetric.h @@ -112,13 +112,15 @@ class ITK_TEMPLATE_EXPORT PointSetToImageMetric : public SingleValuedCostFunctio using ParametersType = Superclass::ParametersType; /** Get/Set the Fixed Image. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(FixedPointSet, FixedPointSetType); itkGetConstObjectMacro(FixedPointSet, FixedPointSetType); - + /** @ITKEndGrouping */ /** Get/Set the Moving Image. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(MovingImage, MovingImageType); itkGetConstObjectMacro(MovingImage, MovingImageType); - + /** @ITKEndGrouping */ /** Connect the Transform. */ itkSetObjectMacro(Transform, TransformType); @@ -148,9 +150,10 @@ class ITK_TEMPLATE_EXPORT PointSetToImageMetric : public SingleValuedCostFunctio * at the price of large memory footprint. Mode OFF results in small * memory footprint at the price of large computation time */ + /** @ITKStartGrouping */ itkSetMacro(ComputeGradient, bool); itkGetConstReferenceMacro(ComputeGradient, bool); - + /** @ITKEndGrouping */ /** Get the number of parameters required by the Transform. */ unsigned int GetNumberOfParameters() const override diff --git a/Modules/Registration/Common/include/itkPointSetToImageRegistrationMethod.h b/Modules/Registration/Common/include/itkPointSetToImageRegistrationMethod.h index ab72976c485..29b73578f32 100644 --- a/Modules/Registration/Common/include/itkPointSetToImageRegistrationMethod.h +++ b/Modules/Registration/Common/include/itkPointSetToImageRegistrationMethod.h @@ -118,29 +118,35 @@ class ITK_TEMPLATE_EXPORT PointSetToImageRegistrationMethod : public ProcessObje using DataObjectPointer = typename DataObject::Pointer; /** Set/Get the Fixed image. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(FixedPointSet, FixedPointSetType); itkGetConstObjectMacro(FixedPointSet, FixedPointSetType); - + /** @ITKEndGrouping */ /** Set/Get the Moving image. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(MovingImage, MovingImageType); itkGetConstObjectMacro(MovingImage, MovingImageType); - + /** @ITKEndGrouping */ /** Set/Get the Optimizer. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Optimizer, OptimizerType); itkGetModifiableObjectMacro(Optimizer, OptimizerType); - + /** @ITKEndGrouping */ /** Set/Get the Metric. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Metric, MetricType); itkGetModifiableObjectMacro(Metric, MetricType); - + /** @ITKEndGrouping */ /** Set/Get the Transform. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Transform, TransformType); itkGetModifiableObjectMacro(Transform, TransformType); - + /** @ITKEndGrouping */ /** Set/Get the Interpolator. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Interpolator, InterpolatorType); itkGetModifiableObjectMacro(Interpolator, InterpolatorType); - + /** @ITKEndGrouping */ /** Set/Get the initial transformation parameters. */ virtual void SetInitialTransformParameters(const ParametersType & param); diff --git a/Modules/Registration/Common/include/itkPointSetToPointSetMetric.h b/Modules/Registration/Common/include/itkPointSetToPointSetMetric.h index 2c8c0f856f2..6e16edc6654 100644 --- a/Modules/Registration/Common/include/itkPointSetToPointSetMetric.h +++ b/Modules/Registration/Common/include/itkPointSetToPointSetMetric.h @@ -98,13 +98,15 @@ class ITK_TEMPLATE_EXPORT PointSetToPointSetMetric : public MultipleValuedCostFu using ParametersType = Superclass::ParametersType; /** Get/Set the Fixed Pointset. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(FixedPointSet, FixedPointSetType); itkGetConstObjectMacro(FixedPointSet, FixedPointSetType); - + /** @ITKEndGrouping */ /** Get/Set the Moving Pointset. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(MovingPointSet, MovingPointSetType); itkGetConstObjectMacro(MovingPointSet, MovingPointSetType); - + /** @ITKEndGrouping */ /** Connect the Transform. */ itkSetObjectMacro(Transform, TransformType); diff --git a/Modules/Registration/Common/include/itkPointSetToPointSetRegistrationMethod.h b/Modules/Registration/Common/include/itkPointSetToPointSetRegistrationMethod.h index cf9e30c707b..c15ad5cb7b0 100644 --- a/Modules/Registration/Common/include/itkPointSetToPointSetRegistrationMethod.h +++ b/Modules/Registration/Common/include/itkPointSetToPointSetRegistrationMethod.h @@ -113,25 +113,30 @@ class ITK_TEMPLATE_EXPORT PointSetToPointSetRegistrationMethod : public ProcessO using DataObjectPointer = typename DataObject::Pointer; /** Set/Get the Fixed PointSet. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(FixedPointSet, FixedPointSetType); itkGetConstObjectMacro(FixedPointSet, FixedPointSetType); - + /** @ITKEndGrouping */ /** Set/Get the Moving PointSet. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(MovingPointSet, MovingPointSetType); itkGetConstObjectMacro(MovingPointSet, MovingPointSetType); - + /** @ITKEndGrouping */ /** Set/Get the Optimizer. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Optimizer, OptimizerType); itkGetModifiableObjectMacro(Optimizer, OptimizerType); - + /** @ITKEndGrouping */ /** Set/Get the Metric. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Metric, MetricType); itkGetModifiableObjectMacro(Metric, MetricType); - + /** @ITKEndGrouping */ /** Set/Get the Transform. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Transform, TransformType); itkGetModifiableObjectMacro(Transform, TransformType); - + /** @ITKEndGrouping */ /** Set/Get the initial transformation parameters. */ virtual void SetInitialTransformParameters(const ParametersType & param); diff --git a/Modules/Registration/Common/include/itkPointSetToSpatialObjectDemonsRegistration.h b/Modules/Registration/Common/include/itkPointSetToSpatialObjectDemonsRegistration.h index 4386c233ba0..e9619ce5e5b 100644 --- a/Modules/Registration/Common/include/itkPointSetToSpatialObjectDemonsRegistration.h +++ b/Modules/Registration/Common/include/itkPointSetToSpatialObjectDemonsRegistration.h @@ -73,13 +73,15 @@ class ITK_TEMPLATE_EXPORT PointSetToSpatialObjectDemonsRegistration : public Pro using MovingSpatialObjectConstPointer = typename MovingSpatialObjectType::ConstPointer; /** Set/Get the Fixed image. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(FixedPointSet, FixedPointSetType); itkGetConstObjectMacro(FixedPointSet, FixedPointSetType); - + /** @ITKEndGrouping */ /** Set/Get the Moving image. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(MovingSpatialObject, MovingSpatialObjectType); itkGetConstObjectMacro(MovingSpatialObject, MovingSpatialObjectType); - + /** @ITKEndGrouping */ protected: PointSetToSpatialObjectDemonsRegistration(); ~PointSetToSpatialObjectDemonsRegistration() override = default; diff --git a/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFilter.h b/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFilter.h index 0f59c1ecea2..fb4fce2974b 100644 --- a/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFilter.h +++ b/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFilter.h @@ -163,6 +163,7 @@ class GPUDemonsRegistrationFilterFactory : public itk::ObjectFactoryBase using ConstPointer = SmartPointer; /** Class methods used to interface with the registered factories. */ + /** @ITKStartGrouping */ const char * GetITKSourceVersion() const override { @@ -173,7 +174,7 @@ class GPUDemonsRegistrationFilterFactory : public itk::ObjectFactoryBase { return "A Factory for GPUDemonsRegistrationFilter"; } - + /** @ITKEndGrouping */ /** Method for class instantiation. */ itkFactorylessNewMacro(Self); diff --git a/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFunction.h b/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFunction.h index d23b24b55fb..7a39004bfb6 100644 --- a/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFunction.h +++ b/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFunction.h @@ -50,6 +50,7 @@ namespace itk * \ingroup FiniteDifferenceFunctions * \ingroup ITKGPUPDEDeformableRegistration */ + /** Create a helper GPU Kernel class for GPUDemonsRegistrationFunction */ itkGPUKernelClassMacro(GPUDemonsRegistrationFunctionKernel); @@ -213,6 +214,7 @@ class ITK_TEMPLATE_EXPORT GPUDemonsRegistrationFunction /** Select if the fixed image or moving image gradient is used for * computing the demon forces. The fixed image gradient is used * by default. */ + /** @ITKStartGrouping */ virtual void SetUseMovingImageGradient(bool flag) { @@ -223,7 +225,7 @@ class ITK_TEMPLATE_EXPORT GPUDemonsRegistrationFunction { return m_UseMovingImageGradient; } - + /** @ITKEndGrouping */ /** Set/Get the threshold below which the absolute difference of * intensity yields a match. When the intensities match between a * moving and fixed image pixel, the update vector (for that diff --git a/Modules/Registration/Metricsv4/include/itkDefaultImageToImageMetricTraitsv4.h b/Modules/Registration/Metricsv4/include/itkDefaultImageToImageMetricTraitsv4.h index c18f9785d34..053468f2315 100644 --- a/Modules/Registration/Metricsv4/include/itkDefaultImageToImageMetricTraitsv4.h +++ b/Modules/Registration/Metricsv4/include/itkDefaultImageToImageMetricTraitsv4.h @@ -109,8 +109,10 @@ class DefaultImageToImageMetricTraitsv4 /** Only floating-point images are currently supported. To support integer images, * several small changes must be made to use an internal floating-point type for * computations rather than the image pixel type itself. */ + /** @ITKStartGrouping */ itkConceptMacro(OnlyDefinedForFloatingPointTypes0, (itk::Concept::IsFloatingPoint)); itkConceptMacro(OnlyDefinedForFloatingPointTypes1, (itk::Concept::IsFloatingPoint)); + /** @ITKEndGrouping */ }; } // end namespace itk diff --git a/Modules/Registration/Metricsv4/include/itkDemonsImageToImageMetricv4.h b/Modules/Registration/Metricsv4/include/itkDemonsImageToImageMetricv4.h index 6e5c2e30dac..6d9568fc26c 100644 --- a/Modules/Registration/Metricsv4/include/itkDemonsImageToImageMetricv4.h +++ b/Modules/Registration/Metricsv4/include/itkDemonsImageToImageMetricv4.h @@ -111,9 +111,10 @@ class ITK_TEMPLATE_EXPORT DemonsImageToImageMetricv4 /** Accessors for the image intensity difference threshold use * in derivative calculation */ + /** @ITKStartGrouping */ itkGetConstMacro(IntensityDifferenceThreshold, TInternalComputationValueType); itkSetMacro(IntensityDifferenceThreshold, TInternalComputationValueType); - + /** @ITKEndGrouping */ /** Get the denominator threshold used in derivative calculation. */ itkGetConstMacro(DenominatorThreshold, TInternalComputationValueType); diff --git a/Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.h b/Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.h index 5219150ebc0..0a337df1fe8 100644 --- a/Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.h +++ b/Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.h @@ -193,6 +193,7 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetricv4 itkOverrideGetNameOfClassMacro(ImageToImageMetricv4); /** Type used internally for computations */ + /** It should be possible to derive the internal computation type from the class object. */ using InternalComputationValueType = TInternalComputationValueType; @@ -389,24 +390,31 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetricv4 } /* Get/Set the Fixed Image. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(FixedImage, FixedImageType); itkGetConstObjectMacro(FixedImage, FixedImageType); + /** @ITKEndGrouping */ /** Get/Set the Moving Image. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(MovingImage, MovingImageType); itkGetConstObjectMacro(MovingImage, MovingImageType); + /** @ITKEndGrouping */ /** Connect the fixed interpolator. */ itkSetObjectMacro(FixedInterpolator, FixedInterpolatorType); + /** Get a pointer to the fixed interpolator. */ itkGetModifiableObjectMacro(FixedInterpolator, FixedInterpolatorType); /** Connect the Moving interpolator. */ itkSetObjectMacro(MovingInterpolator, MovingInterpolatorType); + /** Get a pointer to the Moving interpolator. */ itkGetModifiableObjectMacro(MovingInterpolator, MovingInterpolatorType); /** Set/Get the moving image mask. */ + /** @ITKStartGrouping */ #ifndef ITK_FUTURE_LEGACY_REMOVE virtual void SetMovingImageMask(MovingImageMaskType * const arg) @@ -418,8 +426,9 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetricv4 #endif itkSetConstObjectMacro(MovingImageMask, MovingImageMaskType); itkGetConstObjectMacro(MovingImageMask, MovingImageMaskType); - + /** @ITKEndGrouping */ /** Set/Get the fixed image mask. */ + /** @ITKStartGrouping */ #ifndef ITK_FUTURE_LEGACY_REMOVE virtual void SetFixedImageMask(FixedImageMaskType * const arg) @@ -431,10 +440,11 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetricv4 #endif itkSetConstObjectMacro(FixedImageMask, FixedImageMaskType); itkGetConstObjectMacro(FixedImageMask, FixedImageMaskType); - + /** @ITKEndGrouping */ /** Set/Get the fixed image domain sampling point set * See main documentation regarding using fixed vs virtual domain * for the point set. */ + /** @ITKStartGrouping */ #ifndef ITK_FUTURE_LEGACY_REMOVE virtual void SetFixedSampledPointSet(FixedSampledPointSetType * const arg) @@ -446,25 +456,29 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetricv4 #endif itkSetConstObjectMacro(FixedSampledPointSet, FixedSampledPointSetType); itkGetConstObjectMacro(FixedSampledPointSet, FixedSampledPointSetType); - + /** @ITKEndGrouping */ /** Set/Get the virtual image domain sampling point set */ + /** @ITKStartGrouping */ itkSetObjectMacro(VirtualSampledPointSet, VirtualPointSetType); itkGetConstObjectMacro(VirtualSampledPointSet, VirtualPointSetType); - + /** @ITKEndGrouping */ /** Set/Get flag to use a domain sampling point set */ + /** @ITKStartGrouping */ itkSetMacro(UseSampledPointSet, bool); itkGetConstReferenceMacro(UseSampledPointSet, bool); itkBooleanMacro(UseSampledPointSet); - + /** @ITKEndGrouping */ /** Set/Get flag to indicate of the VirtualSampledPointSet is set * over the FixedSampledPointSet*/ + /** @ITKStartGrouping */ itkSetMacro(UseVirtualSampledPointSet, bool); itkGetConstReferenceMacro(UseVirtualSampledPointSet, bool); itkBooleanMacro(UseVirtualSampledPointSet); - + /** @ITKEndGrouping */ #if !defined(ITK_LEGACY_REMOVE) /** UseFixedSampledPointSet is deprecated and has been replaced * with UseSampledPointsSet. */ + /** @ITKStartGrouping */ itkLegacyMacro(virtual void SetUseFixedSampledPointSet(bool v)) { this->SetUseSampledPointSet(v); @@ -481,32 +495,36 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetricv4 { return this->UseSampledPointSetOff(); } + /** @ITKEndGrouping */ #endif - /** Set/Get the gradient filter */ + /** @ITKStartGrouping */ itkSetObjectMacro(FixedImageGradientFilter, FixedImageGradientFilterType); itkGetModifiableObjectMacro(FixedImageGradientFilter, FixedImageGradientFilterType); itkSetObjectMacro(MovingImageGradientFilter, MovingImageGradientFilterType); itkGetModifiableObjectMacro(MovingImageGradientFilter, MovingImageGradientFilterType); - + /** @ITKEndGrouping */ /** Set/Get gradient calculators */ + /** @ITKStartGrouping */ itkSetObjectMacro(FixedImageGradientCalculator, FixedImageGradientCalculatorType); itkGetModifiableObjectMacro(FixedImageGradientCalculator, FixedImageGradientCalculatorType); itkSetObjectMacro(MovingImageGradientCalculator, MovingImageGradientCalculatorType); itkGetModifiableObjectMacro(MovingImageGradientCalculator, MovingImageGradientCalculatorType); - + /** @ITKEndGrouping */ /** Set/Get gradient computation via an image filter, * for fixed image. */ + /** @ITKStartGrouping */ itkSetMacro(UseFixedImageGradientFilter, bool); itkGetConstReferenceMacro(UseFixedImageGradientFilter, bool); itkBooleanMacro(UseFixedImageGradientFilter); - + /** @ITKEndGrouping */ /** Set/Get gradient computation via an image filter. */ + /** @ITKStartGrouping */ itkSetMacro(UseMovingImageGradientFilter, bool); itkGetConstReferenceMacro(UseMovingImageGradientFilter, bool); itkBooleanMacro(UseMovingImageGradientFilter); - + /** @ITKEndGrouping */ /** Get number of work units to used in the most recent * evaluation. Only valid after GetValueAndDerivative() or * GetValue() has been called. */ @@ -516,11 +534,12 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetricv4 /** Set number of work units to use. This the maximum number of work units to use * when multithreaded. The actual number of work units used (may be less than * this value) can be obtained with \c GetNumberOfWorkUnitsUsed. */ + /** @ITKStartGrouping */ virtual void SetMaximumNumberOfWorkUnits(const ThreadIdType number); virtual ThreadIdType GetMaximumNumberOfWorkUnits() const; - + /** @ITKEndGrouping */ #if !defined(ITK_LEGACY_REMOVE) /** Get number of threads to used in the most recent * evaluation. Only valid after GetValueAndDerivative() or @@ -538,6 +557,7 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetricv4 * * NOTE: deprecated. Use SetMaximumNumberOfWorkUnits() and * GetMaximumNumberOfWorkUnits() */ + /** @ITKStartGrouping */ itkLegacyMacro(virtual void SetMaximumNumberOfThreads(const ThreadIdType count)) { this->SetMaximumNumberOfWorkUnits(count); @@ -546,9 +566,9 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetricv4 { return this->GetMaximumNumberOfWorkUnits(); } + /** @ITKEndGrouping */ #endif // !ITK_LEGACY_REMOVE - /** * Finalize the per-thread components for computing * metric. Some threads can accumulate their data @@ -587,17 +607,19 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetricv4 * of threads during registration. * \warning The metric does not perform any normalization so the results * of this truncation are highly dependent on the derivative magnitudes. */ + /** @ITKStartGrouping */ itkSetMacro(UseFloatingPointCorrection, bool); itkGetConstReferenceMacro(UseFloatingPointCorrection, bool); itkBooleanMacro(UseFloatingPointCorrection); - + /** @ITKEndGrouping */ /** Set/Get the floating point resolution used optionally by the derivatives. * If this is set, for example to 1e5, then the derivative will have precision up to 5 * points beyond the decimal point. And precision beyond that will be * truncated. */ + /** @ITKStartGrouping */ itkSetMacro(FloatingPointCorrectionResolution, DerivativeValueType); itkGetConstMacro(FloatingPointCorrectionResolution, DerivativeValueType); - + /** @ITKEndGrouping */ /* Initialize the metric before calling GetValue or GetDerivative. * Derived classes must call this Superclass version if they override * this to perform their own initialization. @@ -725,11 +747,12 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetricv4 /** Initialize the default image gradient filters. This must only * be called once the fixed and moving images have been set. */ + /** @ITKStartGrouping */ virtual void InitializeDefaultFixedImageGradientFilter(); virtual void InitializeDefaultMovingImageGradientFilter(); - + /** @ITKEndGrouping */ /** Get accessor for flag to calculate derivative. */ itkGetConstMacro(ComputeDerivative, bool); @@ -867,10 +890,12 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetricv4 /** Only floating-point images are currently supported. To support integer images, * several small changes must be made */ + /** @ITKStartGrouping */ using FixedImagePixelValueType = typename PixelTraits::ValueType; using MovingImagePixelValueType = typename PixelTraits::ValueType; itkConceptMacro(OnlyDefinedForFloatingPointTypes0, (itk::Concept::IsFloatingPoint)); itkConceptMacro(OnlyDefinedForFloatingPointTypes1, (itk::Concept::IsFloatingPoint)); + /** @ITKEndGrouping */ }; } // namespace itk diff --git a/Modules/Registration/Metricsv4/include/itkImageToImageMetricv4GetValueAndDerivativeThreader.h b/Modules/Registration/Metricsv4/include/itkImageToImageMetricv4GetValueAndDerivativeThreader.h index d12ea1c964e..11fbcbf65a4 100644 --- a/Modules/Registration/Metricsv4/include/itkImageToImageMetricv4GetValueAndDerivativeThreader.h +++ b/Modules/Registration/Metricsv4/include/itkImageToImageMetricv4GetValueAndDerivativeThreader.h @@ -110,6 +110,7 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetricv4GetValueAndDerivativeThreader< /** Get cached values for efficiency. Only valid once threading has started. * These methods should be used in tight loops (inlining helps measurably). * Put these methods here so derived threaders can access them directly. */ + /** @ITKStartGrouping */ inline NumberOfParametersType GetCachedNumberOfParameters() const { @@ -120,6 +121,7 @@ class ITK_TEMPLATE_EXPORT ImageToImageMetricv4GetValueAndDerivativeThreader< { return this->m_CachedNumberOfLocalParameters; } + /** @ITKEndGrouping */ }; /** \class ImageToImageMetricv4GetValueAndDerivativeThreader @@ -185,6 +187,7 @@ class ITK_TEMPLATE_EXPORT /** Get cached values for efficiency. Only valid once threading has started. * These methods should be used in tight loops (inlining helps measurably). * Put these methods here so derived threaders can access them directly. */ + /** @ITKStartGrouping */ inline NumberOfParametersType GetCachedNumberOfParameters() const { @@ -195,6 +198,7 @@ class ITK_TEMPLATE_EXPORT { return this->m_CachedNumberOfLocalParameters; } + /** @ITKEndGrouping */ }; } // end namespace itk diff --git a/Modules/Registration/Metricsv4/include/itkJointHistogramMutualInformationImageToImageMetricv4.h b/Modules/Registration/Metricsv4/include/itkJointHistogramMutualInformationImageToImageMetricv4.h index 2ccefacaa45..04e80cf1419 100644 --- a/Modules/Registration/Metricsv4/include/itkJointHistogramMutualInformationImageToImageMetricv4.h +++ b/Modules/Registration/Metricsv4/include/itkJointHistogramMutualInformationImageToImageMetricv4.h @@ -61,9 +61,12 @@ class ITK_TEMPLATE_EXPORT JointHistogramMutualInformationImageToImageMetricv4 /** Type used for representing parameter values */ using typename Superclass::CoordinateRepresentationType; + /** Type used internally for computations */ + /** It should be possible to derive the internal computation type from the class object. */ using InternalComputationValueType = TInternalComputationValueType; + /** Type of the parameters. */ using typename Superclass::ParametersType; using typename Superclass::ParametersValueType; @@ -129,13 +132,15 @@ class ITK_TEMPLATE_EXPORT JointHistogramMutualInformationImageToImageMetricv4 /** Get/Set the number of histogram bins */ + /** @ITKStartGrouping */ itkSetClampMacro(NumberOfHistogramBins, SizeValueType, 5, NumericTraits::max()); itkGetConstReferenceMacro(NumberOfHistogramBins, SizeValueType); - + /** @ITKEndGrouping */ /** Get/Set option to smooth the joint pdf after it's updated */ + /** @ITKStartGrouping */ itkSetMacro(VarianceForJointPDFSmoothing, TInternalComputationValueType); itkGetMacro(VarianceForJointPDFSmoothing, TInternalComputationValueType); - + /** @ITKEndGrouping */ /** Initialize the metric. Make sure all essential inputs are plugged in. */ void Initialize() override; diff --git a/Modules/Registration/Metricsv4/include/itkLabeledPointSetToPointSetMetricv4.h b/Modules/Registration/Metricsv4/include/itkLabeledPointSetToPointSetMetricv4.h index e44fb459376..21ab5ad9ae4 100644 --- a/Modules/Registration/Metricsv4/include/itkLabeledPointSetToPointSetMetricv4.h +++ b/Modules/Registration/Metricsv4/include/itkLabeledPointSetToPointSetMetricv4.h @@ -116,9 +116,10 @@ class ITK_TEMPLATE_EXPORT LabeledPointSetToPointSetMetricv4 * Set/get the specific unlabeled point set metric type. Default is * the \c EuclideanDistancePointSetToPointSetMetricv4. */ + /** @ITKStartGrouping */ itkSetObjectMacro(PointSetMetric, PointSetMetricType); itkGetModifiableObjectMacro(PointSetMetric, PointSetMetricType); - + /** @ITKEndGrouping */ /** * Ensure label type is an integer type */ diff --git a/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.h b/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.h index 5e99e4c8539..2f29fe22636 100644 --- a/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.h +++ b/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.h @@ -142,8 +142,10 @@ class ITK_TEMPLATE_EXPORT MattesMutualInformationImageToImageMetricv4 * windowing with a cubic-BSpline kernel. Note that even if the metric * is used on binary images, the number of bins should at least be * equal to five. */ + /** @ITKStartGrouping */ itkSetClampMacro(NumberOfHistogramBins, SizeValueType, 5, NumericTraits::max()); itkGetConstReferenceMacro(NumberOfHistogramBins, SizeValueType); + /** @ITKEndGrouping */ void Initialize() override; diff --git a/Modules/Registration/Metricsv4/include/itkPointSetToPointSetMetricWithIndexv4.h b/Modules/Registration/Metricsv4/include/itkPointSetToPointSetMetricWithIndexv4.h index ac807aa4c7b..50556c13825 100644 --- a/Modules/Registration/Metricsv4/include/itkPointSetToPointSetMetricWithIndexv4.h +++ b/Modules/Registration/Metricsv4/include/itkPointSetToPointSetMetricWithIndexv4.h @@ -216,15 +216,19 @@ class ITK_TEMPLATE_EXPORT PointSetToPointSetMetricWithIndexv4 } /** Get/Set the fixed pointset. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(FixedPointSet, FixedPointSetType); itkGetConstObjectMacro(FixedPointSet, FixedPointSetType); + /** @ITKEndGrouping */ /** Get the fixed transformed point set. */ itkGetModifiableObjectMacro(FixedTransformedPointSet, FixedTransformedPointSetType); /** Get/Set the moving point set. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(MovingPointSet, MovingPointSetType); itkGetConstObjectMacro(MovingPointSet, MovingPointSetType); + /** @ITKEndGrouping */ /** Get the moving transformed point set. */ itkGetModifiableObjectMacro(MovingTransformedPointSet, MovingTransformedPointSetType); @@ -307,16 +311,20 @@ class ITK_TEMPLATE_EXPORT PointSetToPointSetMetricWithIndexv4 * If this variable is set to false, then the derivative array will be of length * = PointDimension * m_FixedPointSet->GetNumberOfPoints(). */ + /** @ITKStartGrouping */ itkSetMacro(StoreDerivativeAsSparseFieldForLocalSupportTransforms, bool); itkGetConstMacro(StoreDerivativeAsSparseFieldForLocalSupportTransforms, bool); itkBooleanMacro(StoreDerivativeAsSparseFieldForLocalSupportTransforms); + /** @ITKEndGrouping */ /** * */ + /** @ITKStartGrouping */ itkSetMacro(CalculateValueAndDerivativeInTangentSpace, bool); itkGetConstMacro(CalculateValueAndDerivativeInTangentSpace, bool); itkBooleanMacro(CalculateValueAndDerivativeInTangentSpace); + /** @ITKEndGrouping */ protected: PointSetToPointSetMetricWithIndexv4(); @@ -437,6 +445,7 @@ class ITK_TEMPLATE_EXPORT PointSetToPointSetMetricWithIndexv4 */ virtual MeasureType GetLocalNeighborhoodValueWithIndex(const PointIdentifier &, const PointType &, const PixelType & pixel) const = 0; + /** * Function to be defined in the appropriate derived classes. Calculates * the local metric value for a single point. The \c PixelType may or diff --git a/Modules/Registration/PDEDeformable/include/itkDemonsRegistrationFilter.h b/Modules/Registration/PDEDeformable/include/itkDemonsRegistrationFilter.h index a53b37c80f5..0f5c218e9e7 100644 --- a/Modules/Registration/PDEDeformable/include/itkDemonsRegistrationFilter.h +++ b/Modules/Registration/PDEDeformable/include/itkDemonsRegistrationFilter.h @@ -110,10 +110,11 @@ class ITK_TEMPLATE_EXPORT DemonsRegistrationFilter /** Switch between using the fixed image and moving image gradient * for computing the displacement field updates. */ + /** @ITKStartGrouping */ itkSetMacro(UseMovingImageGradient, bool); itkGetConstMacro(UseMovingImageGradient, bool); itkBooleanMacro(UseMovingImageGradient); - + /** @ITKEndGrouping */ /** Set/Get the threshold below which the absolute difference of * intensity yields a match. When the intensities match between a * moving and fixed image pixel, the update vector (for that diff --git a/Modules/Registration/PDEDeformable/include/itkDemonsRegistrationFunction.h b/Modules/Registration/PDEDeformable/include/itkDemonsRegistrationFunction.h index ba431e53707..a4f74f3a880 100644 --- a/Modules/Registration/PDEDeformable/include/itkDemonsRegistrationFunction.h +++ b/Modules/Registration/PDEDeformable/include/itkDemonsRegistrationFunction.h @@ -187,6 +187,7 @@ class ITK_TEMPLATE_EXPORT DemonsRegistrationFunction /** Select if the fixed image or moving image gradient is used for * computing the demon forces. The fixed image gradient is used * by default. */ + /** @ITKStartGrouping */ virtual void SetUseMovingImageGradient(bool flag) { @@ -197,7 +198,7 @@ class ITK_TEMPLATE_EXPORT DemonsRegistrationFunction { return m_UseMovingImageGradient; } - + /** @ITKEndGrouping */ /** Set/Get the threshold below which the absolute difference of * intensity yields a match. When the intensities match between a * moving and fixed image pixel, the update vector (for that diff --git a/Modules/Registration/PDEDeformable/include/itkDiffeomorphicDemonsRegistrationFilter.h b/Modules/Registration/PDEDeformable/include/itkDiffeomorphicDemonsRegistrationFilter.h index 0914495c47f..c729dc79046 100644 --- a/Modules/Registration/PDEDeformable/include/itkDiffeomorphicDemonsRegistrationFilter.h +++ b/Modules/Registration/PDEDeformable/include/itkDiffeomorphicDemonsRegistrationFilter.h @@ -133,10 +133,11 @@ class ITK_TEMPLATE_EXPORT DiffeomorphicDemonsRegistrationFilter /** Use a first-order approximation of the exponential. * This amounts to using an update rule of the type * s <- s o (Id + u) instead of s <- s o exp(u) */ + /** @ITKStartGrouping */ itkSetMacro(UseFirstOrderExp, bool); itkGetConstMacro(UseFirstOrderExp, bool); itkBooleanMacro(UseFirstOrderExp); - + /** @ITKEndGrouping */ /** Set/Get the threshold below which the absolute difference of * intensity yields a match. When the intensities match between a * moving and fixed image pixel, the update vector (for that diff --git a/Modules/Registration/PDEDeformable/include/itkESMDemonsRegistrationFunction.h b/Modules/Registration/PDEDeformable/include/itkESMDemonsRegistrationFunction.h index 74654d3a32d..f28e255ba89 100644 --- a/Modules/Registration/PDEDeformable/include/itkESMDemonsRegistrationFunction.h +++ b/Modules/Registration/PDEDeformable/include/itkESMDemonsRegistrationFunction.h @@ -253,6 +253,7 @@ class ITK_TEMPLATE_EXPORT ESMDemonsRegistrationFunction #endif /** Set/Get the type of used image forces */ + /** @ITKStartGrouping */ virtual void SetUseGradientType(GradientEnum gtype) { @@ -263,6 +264,7 @@ class ITK_TEMPLATE_EXPORT ESMDemonsRegistrationFunction { return m_UseGradientType; } + /** @ITKEndGrouping */ protected: ESMDemonsRegistrationFunction(); diff --git a/Modules/Registration/PDEDeformable/include/itkMultiResolutionPDEDeformableRegistration.h b/Modules/Registration/PDEDeformable/include/itkMultiResolutionPDEDeformableRegistration.h index a4e1f63d2e5..5b4b9926df2 100644 --- a/Modules/Registration/PDEDeformable/include/itkMultiResolutionPDEDeformableRegistration.h +++ b/Modules/Registration/PDEDeformable/include/itkMultiResolutionPDEDeformableRegistration.h @@ -194,17 +194,20 @@ class ITK_TEMPLATE_EXPORT MultiResolutionPDEDeformableRegistration GetNumberOfValidRequiredInputs() const override; /** Get/Set the internal registrator. */ + /** @ITKStartGrouping */ itkSetObjectMacro(RegistrationFilter, RegistrationType); itkGetModifiableObjectMacro(RegistrationFilter, RegistrationType); - + /** @ITKEndGrouping */ /** Get/Set the fixed image pyramid. */ + /** @ITKStartGrouping */ itkSetObjectMacro(FixedImagePyramid, FixedImagePyramidType); itkGetModifiableObjectMacro(FixedImagePyramid, FixedImagePyramidType); - + /** @ITKEndGrouping */ /** Get/Set the moving image pyramid. */ + /** @ITKStartGrouping */ itkSetObjectMacro(MovingImagePyramid, MovingImagePyramidType); itkGetModifiableObjectMacro(MovingImagePyramid, MovingImagePyramidType); - + /** @ITKEndGrouping */ /** Set number of multi-resolution levels. */ virtual void SetNumberOfLevels(unsigned int num); @@ -216,14 +219,16 @@ class ITK_TEMPLATE_EXPORT MultiResolutionPDEDeformableRegistration itkGetConstReferenceMacro(CurrentLevel, unsigned int); /** Get/Set the moving image pyramid. */ + /** @ITKStartGrouping */ itkSetObjectMacro(FieldExpander, FieldExpanderType); itkGetModifiableObjectMacro(FieldExpander, FieldExpanderType); - + /** @ITKEndGrouping */ /** Set number of iterations per multi-resolution levels. */ + /** @ITKStartGrouping */ virtual void SetNumberOfIterations(NumberOfIterationsType numberOfIterations); itkSetVectorMacro(NumberOfIterations, unsigned int, m_NumberOfLevels); - + /** @ITKEndGrouping */ /** Get number of iterations per multi-resolution levels. */ itkGetConstReferenceMacro(NumberOfIterations, NumberOfIterationsType); diff --git a/Modules/Registration/PDEDeformable/include/itkPDEDeformableRegistrationFilter.h b/Modules/Registration/PDEDeformable/include/itkPDEDeformableRegistrationFilter.h index 759d6ee4ed3..cf24419b861 100644 --- a/Modules/Registration/PDEDeformable/include/itkPDEDeformableRegistrationFilter.h +++ b/Modules/Registration/PDEDeformable/include/itkPDEDeformableRegistrationFilter.h @@ -153,19 +153,21 @@ class ITK_TEMPLATE_EXPORT PDEDeformableRegistrationFilter * elastic in nature. If SmoothDisplacementField is on, then the * displacement field is smoothed with a Gaussian whose standard * deviations are specified with SetStandardDeviations() */ + /** @ITKStartGrouping */ itkSetMacro(SmoothDisplacementField, bool); itkGetConstMacro(SmoothDisplacementField, bool); itkBooleanMacro(SmoothDisplacementField); - + /** @ITKEndGrouping */ using StandardDeviationsType = FixedArray; /** Set the Gaussian smoothing standard deviations for the * displacement field. The values are set with respect to pixel * coordinates. */ + /** @ITKStartGrouping */ itkSetMacro(StandardDeviations, StandardDeviationsType); virtual void SetStandardDeviations(double value); - + /** @ITKEndGrouping */ /** Get the Gaussian smoothing standard deviations use for smoothing * the displacement field. */ itkGetConstReferenceMacro(StandardDeviations, StandardDeviationsType); @@ -175,16 +177,18 @@ class ITK_TEMPLATE_EXPORT PDEDeformableRegistrationFilter * viscous in nature. If SmoothUpdateField is on, then the * update field is smoothed with a Gaussian whose standard * deviations are specified with SetUpdateFieldStandardDeviations() */ + /** @ITKStartGrouping */ itkSetMacro(SmoothUpdateField, bool); itkGetConstMacro(SmoothUpdateField, bool); itkBooleanMacro(SmoothUpdateField); - + /** @ITKEndGrouping */ /** Set the Gaussian smoothing standard deviations for the update * field. The values are set with respect to pixel coordinates. */ + /** @ITKStartGrouping */ itkSetMacro(UpdateFieldStandardDeviations, StandardDeviationsType); virtual void SetUpdateFieldStandardDeviations(double value); - + /** @ITKEndGrouping */ /** Get the Gaussian smoothing standard deviations used for * smoothing the update field. */ itkGetConstReferenceMacro(UpdateFieldStandardDeviations, StandardDeviationsType); @@ -198,14 +202,16 @@ class ITK_TEMPLATE_EXPORT PDEDeformableRegistrationFilter /** Set/Get the desired maximum error of the Gaussian kernel approximate. * \sa GaussianOperator. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumError, double); itkGetConstMacro(MaximumError, double); - + /** @ITKEndGrouping */ /** Set/Get the desired limits of the Gaussian kernel width. * \sa GaussianOperator. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumKernelWidth, unsigned int); itkGetConstMacro(MaximumKernelWidth, unsigned int); - + /** @ITKEndGrouping */ protected: PDEDeformableRegistrationFilter(); ~PDEDeformableRegistrationFilter() override = default; diff --git a/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h b/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h index 70593ae9f58..09e2f8bd5dd 100644 --- a/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h +++ b/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h @@ -224,6 +224,7 @@ class ITK_TEMPLATE_EXPORT ImageRegistrationMethodv4 : public ProcessObject using MetricSamplePointSetType = typename ImageMetricType::FixedSampledPointSetType; /** Set/get the fixed images. */ + /** @ITKStartGrouping */ virtual void SetFixedImage(const FixedImageType * image) { @@ -237,8 +238,10 @@ class ITK_TEMPLATE_EXPORT ImageRegistrationMethodv4 : public ProcessObject virtual void SetFixedImage(SizeValueType, const FixedImageType *); virtual const FixedImageType * GetFixedImage(SizeValueType) const; + /** @ITKEndGrouping */ /** Set the moving images. */ + /** @ITKStartGrouping */ virtual void SetMovingImage(const MovingImageType * image) { @@ -252,8 +255,10 @@ class ITK_TEMPLATE_EXPORT ImageRegistrationMethodv4 : public ProcessObject virtual void SetMovingImage(SizeValueType, const MovingImageType *); virtual const MovingImageType * GetMovingImage(SizeValueType) const; + /** @ITKEndGrouping */ /** Set/get the fixed point sets. */ + /** @ITKStartGrouping */ virtual void SetFixedPointSet(const PointSetType * pointSet) { @@ -267,8 +272,10 @@ class ITK_TEMPLATE_EXPORT ImageRegistrationMethodv4 : public ProcessObject virtual void SetFixedPointSet(SizeValueType, const PointSetType *); virtual const PointSetType * GetFixedPointSet(SizeValueType) const; + /** @ITKEndGrouping */ /** Set the moving point sets. */ + /** @ITKStartGrouping */ virtual void SetMovingPointSet(const PointSetType * pointSet) { @@ -282,10 +289,13 @@ class ITK_TEMPLATE_EXPORT ImageRegistrationMethodv4 : public ProcessObject virtual void SetMovingPointSet(SizeValueType, const PointSetType *); virtual const PointSetType * GetMovingPointSet(SizeValueType) const; + /** @ITKEndGrouping */ /** Set/Get the optimizer. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Optimizer, OptimizerType); itkGetModifiableObjectMacro(Optimizer, OptimizerType); + /** @ITKEndGrouping */ /** * Set/Get the optimizer weights. Allows setting of a per-local-parameter @@ -295,17 +305,23 @@ class ITK_TEMPLATE_EXPORT ImageRegistrationMethodv4 : public ProcessObject * The size of the weights must be equal to the number of the local transformation * parameters. */ + /** @ITKStartGrouping */ void SetOptimizerWeights(OptimizerWeightsType &); itkGetConstMacro(OptimizerWeights, OptimizerWeightsType); + /** @ITKEndGrouping */ /** Set/Get the metric. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Metric, MetricType); itkGetModifiableObjectMacro(Metric, MetricType); + /** @ITKEndGrouping */ /** Set/Get the metric sampling strategy. */ + /** @ITKStartGrouping */ itkSetEnumMacro(MetricSamplingStrategy, MetricSamplingStrategyEnum); itkGetEnumMacro(MetricSamplingStrategy, MetricSamplingStrategyEnum); + /** @ITKEndGrouping */ /** Reinitialize the seed for the random number generators that * select the samples for some metric sampling strategies. @@ -318,19 +334,23 @@ class ITK_TEMPLATE_EXPORT ImageRegistrationMethodv4 : public ProcessObject * will indeed increase the non-deterministic behavior of the * metric. */ + /** @ITKStartGrouping */ void MetricSamplingReinitializeSeed(); void MetricSamplingReinitializeSeed(int seed); + /** @ITKEndGrouping */ /** Set the metric sampling percentage. Valid values are in (0.0, 1.0] */ void SetMetricSamplingPercentage(const RealType); /** Set the metric sampling percentage. Valid values are in (0.0,1.0]. */ + /** @ITKStartGrouping */ virtual void SetMetricSamplingPercentagePerLevel(const MetricSamplingPercentageArrayType & samplingPercentages); itkGetConstMacro(MetricSamplingPercentagePerLevel, MetricSamplingPercentageArrayType); + /** @ITKEndGrouping */ /** Set/Get the initial fixed transform. */ itkSetGetDecoratedObjectInputMacro(FixedInitialTransform, InitialTransformType); @@ -356,10 +376,12 @@ class ITK_TEMPLATE_EXPORT ImageRegistrationMethodv4 : public ProcessObject itkSetGetDecoratedObjectInputMacro(InitialTransform, InitialTransformType); /** Set/Get the transform adaptors. */ + /** @ITKStartGrouping */ void SetTransformParametersAdaptorsPerLevel(TransformParametersAdaptorsContainerType &); const TransformParametersAdaptorsContainerType & GetTransformParametersAdaptorsPerLevel() const; + /** @ITKEndGrouping */ /** * Set/Get the number of multi-resolution levels. In setting the number of @@ -368,9 +390,11 @@ class ITK_TEMPLATE_EXPORT ImageRegistrationMethodv4 : public ProcessObject * \li sigma smoothing parameter * \li transform adaptor with specific parameters for the specified level */ + /** @ITKStartGrouping */ void SetNumberOfLevels(const SizeValueType); itkGetConstMacro(NumberOfLevels, SizeValueType); + /** @ITKEndGrouping */ /** * Set the shrink factors for each level where each level has a constant @@ -421,16 +445,20 @@ class ITK_TEMPLATE_EXPORT ImageRegistrationMethodv4 : public ProcessObject * filter (specifically, the \c itkDiscreteGaussianImageFilter) is applied. Sigma values are * specified according to the option \c m_SmoothingSigmasAreSpecifiedInPhysicalUnits. */ + /** @ITKStartGrouping */ itkSetMacro(SmoothingSigmasPerLevel, SmoothingSigmasArrayType); itkGetConstMacro(SmoothingSigmasPerLevel, SmoothingSigmasArrayType); + /** @ITKEndGrouping */ /** * Set/Get whether to specify the smoothing sigmas for each level in physical units * (default) or in terms of voxels. */ + /** @ITKStartGrouping */ itkSetMacro(SmoothingSigmasAreSpecifiedInPhysicalUnits, bool); itkGetConstMacro(SmoothingSigmasAreSpecifiedInPhysicalUnits, bool); itkBooleanMacro(SmoothingSigmasAreSpecifiedInPhysicalUnits); + /** @ITKEndGrouping */ /** Make a DataObject of the correct type to be used as the specified output. */ using DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType; @@ -438,10 +466,12 @@ class ITK_TEMPLATE_EXPORT ImageRegistrationMethodv4 : public ProcessObject DataObjectPointer MakeOutput(DataObjectPointerArraySizeType) override; /** Return the transform resulting from the registration process. */ + /** @ITKStartGrouping */ virtual DecoratedOutputTransformType * GetOutput(); virtual const DecoratedOutputTransformType * GetOutput() const; + /** @ITKEndGrouping */ virtual DecoratedOutputTransformType * GetTransformOutput() @@ -477,18 +507,22 @@ class ITK_TEMPLATE_EXPORT ImageRegistrationMethodv4 : public ProcessObject /** Request that the InitialTransform be grafted onto the output, * there by not creating a copy. */ + /** @ITKStartGrouping */ itkSetMacro(InPlace, bool); itkGetConstMacro(InPlace, bool); itkBooleanMacro(InPlace); + /** @ITKEndGrouping */ /** * Initialize the current linear transform to be optimized with the center of the * previous transform in the queue. This provides a much better initialization than * the default origin. */ + /** @ITKStartGrouping */ itkBooleanMacro(InitializeCenterOfLinearOutputTransform); itkSetMacro(InitializeCenterOfLinearOutputTransform, bool); itkGetConstMacro(InitializeCenterOfLinearOutputTransform, bool); + /** @ITKEndGrouping */ /** * We try to initialize the center of a linear transform (specifically those diff --git a/Modules/Registration/RegistrationMethodsv4/include/itkSyNImageRegistrationMethod.h b/Modules/Registration/RegistrationMethodsv4/include/itkSyNImageRegistrationMethod.h index 59baa3d60e6..05546dc6e6d 100644 --- a/Modules/Registration/RegistrationMethodsv4/include/itkSyNImageRegistrationMethod.h +++ b/Modules/Registration/RegistrationMethodsv4/include/itkSyNImageRegistrationMethod.h @@ -135,54 +135,64 @@ class ITK_TEMPLATE_EXPORT SyNImageRegistrationMethod using NumberOfIterationsArrayType = Array; /** Set/Get the learning rate. */ + /** @ITKStartGrouping */ itkSetMacro(LearningRate, RealType); itkGetConstMacro(LearningRate, RealType); - + /** @ITKEndGrouping */ /** Set/Get the number of iterations per level. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfIterationsPerLevel, NumberOfIterationsArrayType); itkGetConstMacro(NumberOfIterationsPerLevel, NumberOfIterationsArrayType); - + /** @ITKEndGrouping */ /** Set/Get the convergence threshold */ + /** @ITKStartGrouping */ itkSetMacro(ConvergenceThreshold, RealType); itkGetConstMacro(ConvergenceThreshold, RealType); - + /** @ITKEndGrouping */ /** Set/Get the convergence window size */ + /** @ITKStartGrouping */ itkSetMacro(ConvergenceWindowSize, unsigned int); itkGetConstMacro(ConvergenceWindowSize, unsigned int); - + /** @ITKEndGrouping */ /** Let the user control whether we compute metric derivatives in the downsampled or full-res space. * The default is 'true' --- classic SyN --- but there may be advantages to the other approach. * Classic SyN did not have this possibility. This implementation will let us explore the question. */ + /** @ITKStartGrouping */ itkSetMacro(DownsampleImagesForMetricDerivatives, bool); itkGetConstMacro(DownsampleImagesForMetricDerivatives, bool); - + /** @ITKEndGrouping */ /** Allow the user to average the gradients in the mid-point domain. Default false. * One might choose to do this to further reduce bias. */ + /** @ITKStartGrouping */ itkSetMacro(AverageMidPointGradients, bool); itkGetConstMacro(AverageMidPointGradients, bool); - + /** @ITKEndGrouping */ /** * Get/Set the Gaussian smoothing variance for the update field. */ + /** @ITKStartGrouping */ itkSetMacro(GaussianSmoothingVarianceForTheUpdateField, RealType); itkGetConstReferenceMacro(GaussianSmoothingVarianceForTheUpdateField, RealType); - + /** @ITKEndGrouping */ /** * Get/Set the Gaussian smoothing variance for the total field. */ + /** @ITKStartGrouping */ itkSetMacro(GaussianSmoothingVarianceForTheTotalField, RealType); itkGetConstReferenceMacro(GaussianSmoothingVarianceForTheTotalField, RealType); - + /** @ITKEndGrouping */ /** Get modifiable FixedToMiddle and MovingToMiddle transforms to save the current state of the registration. */ + /** @ITKStartGrouping */ itkGetModifiableObjectMacro(FixedToMiddleTransform, OutputTransformType); itkGetModifiableObjectMacro(MovingToMiddleTransform, OutputTransformType); - + /** @ITKEndGrouping */ /** Set FixedToMiddle and MovingToMiddle transforms to restore the registration from a saved state. */ + /** @ITKStartGrouping */ itkSetObjectMacro(FixedToMiddleTransform, OutputTransformType); itkSetObjectMacro(MovingToMiddleTransform, OutputTransformType); - + /** @ITKEndGrouping */ protected: SyNImageRegistrationMethod(); ~SyNImageRegistrationMethod() override = default; diff --git a/Modules/Registration/RegistrationMethodsv4/include/itkTimeVaryingBSplineVelocityFieldImageRegistrationMethod.h b/Modules/Registration/RegistrationMethodsv4/include/itkTimeVaryingBSplineVelocityFieldImageRegistrationMethod.h index cba17904597..140345ac28e 100644 --- a/Modules/Registration/RegistrationMethodsv4/include/itkTimeVaryingBSplineVelocityFieldImageRegistrationMethod.h +++ b/Modules/Registration/RegistrationMethodsv4/include/itkTimeVaryingBSplineVelocityFieldImageRegistrationMethod.h @@ -186,25 +186,30 @@ class ITK_TEMPLATE_EXPORT TimeVaryingBSplineVelocityFieldImageRegistrationMethod using TimeVaryingWeightedMaskImageType = Image; /** Set/Get the learning rate. */ + /** @ITKStartGrouping */ itkSetMacro(LearningRate, RealType); itkGetConstMacro(LearningRate, RealType); - + /** @ITKEndGrouping */ /** Set/Get the number of iterations per level. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfIterationsPerLevel, NumberOfIterationsArrayType); itkGetConstMacro(NumberOfIterationsPerLevel, NumberOfIterationsArrayType); - + /** @ITKEndGrouping */ /** Set/Get the convergence threshold */ + /** @ITKStartGrouping */ itkSetMacro(ConvergenceThreshold, RealType); itkGetConstMacro(ConvergenceThreshold, RealType); - + /** @ITKEndGrouping */ /** Set/Get the convergence window size */ + /** @ITKStartGrouping */ itkSetMacro(ConvergenceWindowSize, unsigned int); itkGetConstMacro(ConvergenceWindowSize, unsigned int); - + /** @ITKEndGrouping */ /** Set/Get the number of time point samples. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfTimePointSamples, SizeValueType); itkGetConstMacro(NumberOfTimePointSamples, SizeValueType); - + /** @ITKEndGrouping */ protected: TimeVaryingBSplineVelocityFieldImageRegistrationMethod(); ~TimeVaryingBSplineVelocityFieldImageRegistrationMethod() override = default; diff --git a/Modules/Registration/RegistrationMethodsv4/include/itkTimeVaryingVelocityFieldImageRegistrationMethodv4.h b/Modules/Registration/RegistrationMethodsv4/include/itkTimeVaryingVelocityFieldImageRegistrationMethodv4.h index e7ed0053449..b9f27591574 100644 --- a/Modules/Registration/RegistrationMethodsv4/include/itkTimeVaryingVelocityFieldImageRegistrationMethodv4.h +++ b/Modules/Registration/RegistrationMethodsv4/include/itkTimeVaryingVelocityFieldImageRegistrationMethodv4.h @@ -141,21 +141,25 @@ class ITK_TEMPLATE_EXPORT TimeVaryingVelocityFieldImageRegistrationMethodv4 using NumberOfIterationsArrayType = Array; /** Set/Get the learning rate. */ + /** @ITKStartGrouping */ itkSetMacro(LearningRate, RealType); itkGetConstMacro(LearningRate, RealType); - + /** @ITKEndGrouping */ /** Set/Get the number of iterations per level. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfIterationsPerLevel, NumberOfIterationsArrayType); itkGetConstMacro(NumberOfIterationsPerLevel, NumberOfIterationsArrayType); - + /** @ITKEndGrouping */ /** Set/Get the convergence threshold */ + /** @ITKStartGrouping */ itkSetMacro(ConvergenceThreshold, RealType); itkGetConstMacro(ConvergenceThreshold, RealType); - + /** @ITKEndGrouping */ /** Set/Get the convergence window size */ + /** @ITKStartGrouping */ itkSetMacro(ConvergenceWindowSize, unsigned int); itkGetConstMacro(ConvergenceWindowSize, unsigned int); - + /** @ITKEndGrouping */ protected: TimeVaryingVelocityFieldImageRegistrationMethodv4(); ~TimeVaryingVelocityFieldImageRegistrationMethodv4() override = default; diff --git a/Modules/Segmentation/Classifiers/include/itkBayesianClassifierImageFilter.h b/Modules/Segmentation/Classifiers/include/itkBayesianClassifierImageFilter.h index 638d5486d4a..9733daa5ee2 100644 --- a/Modules/Segmentation/Classifiers/include/itkBayesianClassifierImageFilter.h +++ b/Modules/Segmentation/Classifiers/include/itkBayesianClassifierImageFilter.h @@ -161,18 +161,20 @@ class ITK_TEMPLATE_EXPORT BayesianClassifierImageFilter /** Set/Get the smoothing filter that may optionally be applied to the * posterior image. */ + /** @ITKStartGrouping */ void SetSmoothingFilter(SmoothingFilterType *); itkGetConstMacro(SmoothingFilter, SmoothingFilterPointer); - + /** @ITKEndGrouping */ /** Set the priors image. */ virtual void SetPriors(const PriorsImageType *); /** Number of iterations to apply the smoothing filter. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfSmoothingIterations, unsigned int); itkGetConstMacro(NumberOfSmoothingIterations, unsigned int); - + /** @ITKEndGrouping */ /** This is overloaded to create the Posteriors output image. */ using DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType; using Superclass::MakeOutput; diff --git a/Modules/Segmentation/Classifiers/include/itkBayesianClassifierInitializationImageFilter.h b/Modules/Segmentation/Classifiers/include/itkBayesianClassifierInitializationImageFilter.h index 11d767f57ca..90d58804aac 100644 --- a/Modules/Segmentation/Classifiers/include/itkBayesianClassifierInitializationImageFilter.h +++ b/Modules/Segmentation/Classifiers/include/itkBayesianClassifierInitializationImageFilter.h @@ -130,14 +130,16 @@ class ITK_TEMPLATE_EXPORT BayesianClassifierInitializationImageFilter * the filter will create ones for you. These default density functions * are Gaussian density functions centered around the K-means of the * input image. */ + /** @ITKStartGrouping */ virtual void SetMembershipFunctions(MembershipFunctionContainerType * membershipFunction); itkGetModifiableObjectMacro(MembershipFunctionContainer, MembershipFunctionContainerType); - + /** @ITKEndGrouping */ /** Set/Get methods for the number of classes. The user must supply this. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfClasses, unsigned int); itkGetConstMacro(NumberOfClasses, unsigned int); - + /** @ITKEndGrouping */ void GenerateOutputInformation() override; diff --git a/Modules/Segmentation/Classifiers/include/itkImageClassifierBase.h b/Modules/Segmentation/Classifiers/include/itkImageClassifierBase.h index 71ea80844df..181cb340c49 100644 --- a/Modules/Segmentation/Classifiers/include/itkImageClassifierBase.h +++ b/Modules/Segmentation/Classifiers/include/itkImageClassifierBase.h @@ -109,9 +109,10 @@ class ITK_TEMPLATE_EXPORT ImageClassifierBase : public ClassifierBase class ITK_TEMPLATE_EXPORT ConnectedComponentImageFilter : public ImageToImageFilter @@ -129,10 +128,11 @@ class ITK_TEMPLATE_EXPORT ConnectedComponentImageFilter * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ /** Type used as identifier of the different component labels. */ using LabelType = IdentifierType; @@ -149,9 +149,10 @@ class ITK_TEMPLATE_EXPORT ConnectedComponentImageFilter * regions of the image in the output. Note that this does NOT set * the background value to be used in the input image. */ + /** @ITKStartGrouping */ itkSetMacro(BackgroundValue, OutputImagePixelType); itkGetConstMacro(BackgroundValue, OutputImagePixelType); - + /** @ITKEndGrouping */ protected: ConnectedComponentImageFilter(); diff --git a/Modules/Segmentation/ConnectedComponents/include/itkRelabelComponentImageFilter.h b/Modules/Segmentation/ConnectedComponents/include/itkRelabelComponentImageFilter.h index eff13d37f25..45f3b1bcdf2 100644 --- a/Modules/Segmentation/ConnectedComponents/include/itkRelabelComponentImageFilter.h +++ b/Modules/Segmentation/ConnectedComponents/include/itkRelabelComponentImageFilter.h @@ -153,9 +153,10 @@ class ITK_TEMPLATE_EXPORT RelabelComponentImageFilter : public InPlaceImageFilte /** Get/Set the number of objects enumerated and described when the * filter is printed. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfObjectsToPrint, SizeValueType); itkGetConstReferenceMacro(NumberOfObjectsToPrint, SizeValueType); - + /** @ITKEndGrouping */ /** Set the minimum size in pixels for an object. All objects * smaller than this size will be discarded and will not appear * in the output label map. NumberOfObjects will count only the @@ -173,10 +174,11 @@ class ITK_TEMPLATE_EXPORT RelabelComponentImageFilter : public InPlaceImageFilte /** Controls whether the object labels are sorted by size. * If false, initial order of labels is kept. */ + /** @ITKStartGrouping */ itkSetMacro(SortByObjectSize, bool); itkGetConstMacro(SortByObjectSize, bool); itkBooleanMacro(SortByObjectSize); - + /** @ITKEndGrouping */ /** Get the size of each object in pixels. This information is only * valid after the filter has executed. Size of the background is * not calculated. Size of object #1 is diff --git a/Modules/Segmentation/ConnectedComponents/include/itkThresholdMaximumConnectedComponentsImageFilter.h b/Modules/Segmentation/ConnectedComponents/include/itkThresholdMaximumConnectedComponentsImageFilter.h index 187099f598b..3e5c758215e 100644 --- a/Modules/Segmentation/ConnectedComponents/include/itkThresholdMaximumConnectedComponentsImageFilter.h +++ b/Modules/Segmentation/ConnectedComponents/include/itkThresholdMaximumConnectedComponentsImageFilter.h @@ -97,9 +97,10 @@ class ITK_TEMPLATE_EXPORT ThresholdMaximumConnectedComponentsImageFilter * optimization portion of this filter. Essentially, it eliminates * noise from being counted as an object. The default value is * zero. */ + /** @ITKStartGrouping */ itkSetMacro(MinimumObjectSizeInPixels, unsigned int); itkGetConstMacro(MinimumObjectSizeInPixels, unsigned int); - + /** @ITKEndGrouping */ /** * The following Set/Get methods are for the binary threshold * function. This class automatically calculates the lower threshold @@ -113,13 +114,14 @@ class ITK_TEMPLATE_EXPORT ThresholdMaximumConnectedComponentsImageFilter * Upper threshold boundary is the * maximum pixel type intensity. */ + /** @ITKStartGrouping */ itkSetMacro(InsideValue, OutputPixelType); itkSetMacro(OutsideValue, OutputPixelType); itkSetMacro(UpperBoundary, PixelType); itkGetConstMacro(InsideValue, OutputPixelType); itkGetConstMacro(OutsideValue, OutputPixelType); itkGetConstMacro(UpperBoundary, PixelType); - + /** @ITKEndGrouping */ /** * Returns the number of objects in the image. This information is * only valid after the filter has executed. Useful if your counting diff --git a/Modules/Segmentation/DeformableMesh/include/itkDeformableSimplexMesh3DBalloonForceFilter.h b/Modules/Segmentation/DeformableMesh/include/itkDeformableSimplexMesh3DBalloonForceFilter.h index 44c4be915ca..4011af7b070 100644 --- a/Modules/Segmentation/DeformableMesh/include/itkDeformableSimplexMesh3DBalloonForceFilter.h +++ b/Modules/Segmentation/DeformableMesh/include/itkDeformableSimplexMesh3DBalloonForceFilter.h @@ -88,9 +88,10 @@ class ITK_TEMPLATE_EXPORT DeformableSimplexMesh3DBalloonForceFilter using GradientIntensityImagePointer = typename GradientIntensityImageType::Pointer; /** Set/Get the scalar for balloon force. */ + /** @ITKStartGrouping */ itkSetMacro(Kappa, double); itkGetConstMacro(Kappa, double); - + /** @ITKEndGrouping */ protected: DeformableSimplexMesh3DBalloonForceFilter(); ~DeformableSimplexMesh3DBalloonForceFilter() override = default; diff --git a/Modules/Segmentation/DeformableMesh/include/itkDeformableSimplexMesh3DFilter.h b/Modules/Segmentation/DeformableMesh/include/itkDeformableSimplexMesh3DFilter.h index 60669acc812..0929aba49ee 100644 --- a/Modules/Segmentation/DeformableMesh/include/itkDeformableSimplexMesh3DFilter.h +++ b/Modules/Segmentation/DeformableMesh/include/itkDeformableSimplexMesh3DFilter.h @@ -143,43 +143,51 @@ class ITK_TEMPLATE_EXPORT DeformableSimplexMesh3DFilter : public MeshToMeshFilte /** Set/Get the gradient image as an input. */ + /** @ITKStartGrouping */ void SetGradient(const GradientImageType * gradientImage); const GradientImageType * GetGradient() const; - + /** @ITKEndGrouping */ /** Set/Get the number of iterations for the deformation process. */ + /** @ITKStartGrouping */ itkSetMacro(Iterations, int); itkGetConstMacro(Iterations, int); - + /** @ITKEndGrouping */ /** Set/Get internal force scaling factor. */ + /** @ITKStartGrouping */ itkSetMacro(Alpha, double); itkGetConstMacro(Alpha, double); - + /** @ITKEndGrouping */ /** Set/Get external force scaling factor. */ + /** @ITKStartGrouping */ itkSetMacro(Beta, double); itkGetConstMacro(Beta, double); - + /** @ITKEndGrouping */ /** Set/Get reference metrics update scaling factor. */ + /** @ITKStartGrouping */ itkSetMacro(Gamma, double); itkGetConstMacro(Gamma, double); - + /** @ITKEndGrouping */ /** Set/Get reference metrics update scaling factor. */ + /** @ITKStartGrouping */ itkSetMacro(Damping, double); itkGetConstMacro(Damping, double); - + /** @ITKEndGrouping */ /** Set/Get the mesh smoothness value. */ + /** @ITKStartGrouping */ itkSetMacro(Rigidity, unsigned int); itkGetConstMacro(Rigidity, unsigned int); - + /** @ITKEndGrouping */ itkSetObjectMacro(Data, GeometryMapType); itkGetModifiableObjectMacro(Data, GeometryMapType); /** Get the width, height and depth of image. */ + /** @ITKStartGrouping */ itkGetConstMacro(ImageWidth, int); itkGetConstMacro(ImageHeight, int); itkGetConstMacro(ImageDepth, int); - + /** @ITKEndGrouping */ /** Get the current iteration number. */ itkGetConstMacro(Step, int); @@ -281,6 +289,7 @@ class ITK_TEMPLATE_EXPORT DeformableSimplexMesh3DFilter : public MeshToMeshFilte */ double m_Gamma{}; double m_Damping{}; + /** * This scalar determines the smoothness of the surface model. Values * should range from 0 to 10. It determines the radius of the neighborhood @@ -292,10 +301,13 @@ class ITK_TEMPLATE_EXPORT DeformableSimplexMesh3DFilter : public MeshToMeshFilte // definition of internal parameters /** Number of iterations */ int m_Step{}; + /** Image size */ int m_ImageWidth{}; + /** Image size */ int m_ImageHeight{}; + /** Image size */ int m_ImageDepth{}; diff --git a/Modules/Segmentation/DeformableMesh/include/itkDeformableSimplexMesh3DGradientConstraintForceFilter.h b/Modules/Segmentation/DeformableMesh/include/itkDeformableSimplexMesh3DGradientConstraintForceFilter.h index 0919b95a2b8..0094e1d74b1 100644 --- a/Modules/Segmentation/DeformableMesh/include/itkDeformableSimplexMesh3DGradientConstraintForceFilter.h +++ b/Modules/Segmentation/DeformableMesh/include/itkDeformableSimplexMesh3DGradientConstraintForceFilter.h @@ -132,6 +132,7 @@ class DeformableSimplexMesh3DGradientConstraintForceFilterEnums // Define how to print enumeration extern ITKDeformableMesh_EXPORT std::ostream & operator<<(std::ostream & out, const DeformableSimplexMesh3DGradientConstraintForceFilterEnums::SIDE value); + /** * \class DeformableSimplexMesh3DGradientConstraintForceFilter * \brief @@ -190,9 +191,10 @@ class ITK_TEMPLATE_EXPORT DeformableSimplexMesh3DGradientConstraintForceFilter using OriginalImagePointer = typename OriginalImageType::ConstPointer; /** control the range of search for Bresenham at normal line */ + /** @ITKStartGrouping */ itkSetMacro(Range, int); itkGetConstMacro(Range, int); - + /** @ITKEndGrouping */ using SIDEEnum = DeformableSimplexMesh3DGradientConstraintForceFilterEnums::SIDE; #if !defined(ITK_LEGACY_REMOVE) /**Exposes enums values for backwards compatibility*/ diff --git a/Modules/Segmentation/KLMRegionGrowing/include/itkKLMRegionGrowImageFilter.h b/Modules/Segmentation/KLMRegionGrowing/include/itkKLMRegionGrowImageFilter.h index 60b88d19141..064fd187677 100644 --- a/Modules/Segmentation/KLMRegionGrowing/include/itkKLMRegionGrowImageFilter.h +++ b/Modules/Segmentation/KLMRegionGrowing/include/itkKLMRegionGrowImageFilter.h @@ -158,7 +158,6 @@ namespace itk * \ingroup RegionGrowingSegmentation * \ingroup ITKKLMRegionGrowing */ - template class ITK_TEMPLATE_EXPORT KLMRegionGrowImageFilter : public RegionGrowImageFilter { @@ -263,13 +262,15 @@ class ITK_TEMPLATE_EXPORT KLMRegionGrowImageFilter : public RegionGrowImageFilte /** Set/Get the desired threshold parameter for lambda. See * itkSegmentationBorder documentation for details regarding this * parameter. */ + /** @ITKStartGrouping */ itkSetMacro(MaximumLambda, double); itkGetConstReferenceMacro(MaximumLambda, double); - + /** @ITKEndGrouping */ /** Set/Get the desired number of regions. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfRegions, unsigned int); itkGetConstReferenceMacro(NumberOfRegions, unsigned int); - + /** @ITKEndGrouping */ /** Generate labelled image. */ LabelImagePointer GetLabelledImage(); diff --git a/Modules/Segmentation/KLMRegionGrowing/include/itkKLMSegmentationBorder.h b/Modules/Segmentation/KLMRegionGrowing/include/itkKLMSegmentationBorder.h index eb3690da774..78ed4b69b4c 100644 --- a/Modules/Segmentation/KLMRegionGrowing/include/itkKLMSegmentationBorder.h +++ b/Modules/Segmentation/KLMRegionGrowing/include/itkKLMSegmentationBorder.h @@ -165,9 +165,10 @@ class ITKKLMRegionGrowing_EXPORT KLMSegmentationBorder : public SegmentationBord /** Set/Get the Lambda parameter associate with the borders * in the KLM algorithm */ + /** @ITKStartGrouping */ itkSetMacro(Lambda, double); itkGetConstReferenceMacro(Lambda, double); - + /** @ITKEndGrouping */ /** Evaluate the Lambda for a given border. */ void EvaluateLambda(); diff --git a/Modules/Segmentation/KLMRegionGrowing/include/itkKLMSegmentationRegion.h b/Modules/Segmentation/KLMRegionGrowing/include/itkKLMSegmentationRegion.h index b44c5428901..190405ef48a 100644 --- a/Modules/Segmentation/KLMRegionGrowing/include/itkKLMSegmentationRegion.h +++ b/Modules/Segmentation/KLMRegionGrowing/include/itkKLMSegmentationRegion.h @@ -147,8 +147,10 @@ class ITKKLMRegionGrowing_EXPORT KLMSegmentationRegion : public SegmentationRegi GetRegionBorderSize() const; /** Set/Get the mean pixel intensity in the region. */ + /** @ITKStartGrouping */ itkSetMacro(MeanRegionIntensity, MeanRegionIntensityType); itkGetConstReferenceMacro(MeanRegionIntensity, MeanRegionIntensityType); + /** @ITKEndGrouping */ /** Set the region with parameter values * defining the region. */ diff --git a/Modules/Segmentation/KLMRegionGrowing/include/itkRegionGrowImageFilter.h b/Modules/Segmentation/KLMRegionGrowing/include/itkRegionGrowImageFilter.h index e42a75ae2ee..b51e1d117f0 100644 --- a/Modules/Segmentation/KLMRegionGrowing/include/itkRegionGrowImageFilter.h +++ b/Modules/Segmentation/KLMRegionGrowing/include/itkRegionGrowImageFilter.h @@ -115,13 +115,15 @@ class ITK_TEMPLATE_EXPORT RegionGrowImageFilter : public ImageToImageFilterModified(); } itkGetConstMacro(MaximumNumberOfIterations, unsigned int); + /** @ITKEndGrouping */ /** True if the MaximumNumberOfIterations has been manually set. **/ itkGetConstMacro(HasMaximumNumberOfIterations, bool); @@ -182,8 +184,10 @@ class ITK_TEMPLATE_EXPORT MultiLabelSTAPLEImageFilter : public ImageToImageFilte /** Set termination threshold based on confusion matrix parameter updates. */ + /** @ITKStartGrouping */ itkSetMacro(TerminationUpdateThreshold, TWeights); itkGetConstMacro(TerminationUpdateThreshold, TWeights); + /** @ITKEndGrouping */ /** Set label value for undecided pixels. */ diff --git a/Modules/Segmentation/LabelVoting/include/itkVotingBinaryHoleFillingImageFilter.h b/Modules/Segmentation/LabelVoting/include/itkVotingBinaryHoleFillingImageFilter.h index e03410447ed..cb7ccbbac1c 100644 --- a/Modules/Segmentation/LabelVoting/include/itkVotingBinaryHoleFillingImageFilter.h +++ b/Modules/Segmentation/LabelVoting/include/itkVotingBinaryHoleFillingImageFilter.h @@ -80,9 +80,10 @@ class ITK_TEMPLATE_EXPORT VotingBinaryHoleFillingImageFilter : public VotingBina * 62, and if you set up a Majority threshold of 5, that means that the * filter will require 67 or more neighbor pixels to be ON in order to switch * the current OFF pixel to ON. The default value is 1. */ + /** @ITKStartGrouping */ itkGetConstReferenceMacro(MajorityThreshold, unsigned int); itkSetMacro(MajorityThreshold, unsigned int); - + /** @ITKEndGrouping */ /** Returns the number of pixels that changed when the filter was executed. */ itkGetConstReferenceMacro(NumberOfPixelsChanged, SizeValueType); @@ -98,6 +99,7 @@ class ITK_TEMPLATE_EXPORT VotingBinaryHoleFillingImageFilter : public VotingBina /** Make protected the methods SetBirthThreshold() and * SetSurvivalThreshold() so users of this filter do not have access to * them. */ + /** @ITKStartGrouping */ void SetBirthThreshold(const unsigned int value) override { @@ -108,7 +110,7 @@ class ITK_TEMPLATE_EXPORT VotingBinaryHoleFillingImageFilter : public VotingBina { this->Superclass::SetSurvivalThreshold(value); } - + /** @ITKEndGrouping */ /** VotingBinaryHoleFillingImageFilter can be implemented as a multithreaded filter. * Therefore, this implementation provides a ThreadedGenerateData() * routine which is called for each processing thread. The output diff --git a/Modules/Segmentation/LabelVoting/include/itkVotingBinaryImageFilter.h b/Modules/Segmentation/LabelVoting/include/itkVotingBinaryImageFilter.h index 71245529f81..14e6bf06793 100644 --- a/Modules/Segmentation/LabelVoting/include/itkVotingBinaryImageFilter.h +++ b/Modules/Segmentation/LabelVoting/include/itkVotingBinaryImageFilter.h @@ -79,24 +79,28 @@ class ITK_TEMPLATE_EXPORT VotingBinaryImageFilter : public ImageToImageFilterSetInput(feature); m_Canny->SetInput(m_Caster->GetOutput()); } + /** If FeatureImageType == ImageType, * assign directly to the Canny filter */ diff --git a/Modules/Segmentation/LevelSets/include/itkCannySegmentationLevelSetImageFilter.h b/Modules/Segmentation/LevelSets/include/itkCannySegmentationLevelSetImageFilter.h index cb72216dac3..faec77ca652 100644 --- a/Modules/Segmentation/LevelSets/include/itkCannySegmentationLevelSetImageFilter.h +++ b/Modules/Segmentation/LevelSets/include/itkCannySegmentationLevelSetImageFilter.h @@ -159,6 +159,7 @@ class ITK_TEMPLATE_EXPORT CannySegmentationLevelSetImageFilter /** Set the Threshold parameter of the CannyEdgeDetectionImageFilter * used by the underlying level set function. */ + /** @ITKStartGrouping */ void SetThreshold(ScalarValueType v) { @@ -169,9 +170,10 @@ class ITK_TEMPLATE_EXPORT CannySegmentationLevelSetImageFilter { return this->m_CannyFunction->GetThreshold(); } - + /** @ITKEndGrouping */ /** Set the Variance parameter of the CannyEdgeDetectionImageFilter * used by the underlying level set function. */ + /** @ITKStartGrouping */ void SetVariance(double v) { @@ -182,7 +184,7 @@ class ITK_TEMPLATE_EXPORT CannySegmentationLevelSetImageFilter { return this->m_CannyFunction->GetVariance(); } - + /** @ITKEndGrouping */ /** Get the Canny image that was used to create the speed and advection images */ OutputImageType * diff --git a/Modules/Segmentation/LevelSets/include/itkCurvesLevelSetFunction.h b/Modules/Segmentation/LevelSets/include/itkCurvesLevelSetFunction.h index 1d9deb9a358..c105e6160df 100644 --- a/Modules/Segmentation/LevelSets/include/itkCurvesLevelSetFunction.h +++ b/Modules/Segmentation/LevelSets/include/itkCurvesLevelSetFunction.h @@ -109,6 +109,7 @@ class ITK_TEMPLATE_EXPORT CurvesLevelSetFunction : public SegmentationLevelSetFu /** Set/Get the sigma for the Gaussian kernel used to compute the gradient * of the feature image needed for the advection term of the equation. */ + /** @ITKStartGrouping */ void SetDerivativeSigma(const double v) { @@ -119,7 +120,7 @@ class ITK_TEMPLATE_EXPORT CurvesLevelSetFunction : public SegmentationLevelSetFu { return m_DerivativeSigma; } - + /** @ITKEndGrouping */ void Initialize(const RadiusType & r) override; diff --git a/Modules/Segmentation/LevelSets/include/itkGeodesicActiveContourLevelSetFunction.h b/Modules/Segmentation/LevelSets/include/itkGeodesicActiveContourLevelSetFunction.h index 70f2cfe278d..70e96de3103 100644 --- a/Modules/Segmentation/LevelSets/include/itkGeodesicActiveContourLevelSetFunction.h +++ b/Modules/Segmentation/LevelSets/include/itkGeodesicActiveContourLevelSetFunction.h @@ -121,6 +121,7 @@ class ITK_TEMPLATE_EXPORT GeodesicActiveContourLevelSetFunction /** Set/Get the sigma for the Gaussian kernel used to compute the gradient * of the feature image needed for the advection term of the equation. */ + /** @ITKStartGrouping */ void SetDerivativeSigma(const double v) { @@ -131,7 +132,7 @@ class ITK_TEMPLATE_EXPORT GeodesicActiveContourLevelSetFunction { return m_DerivativeSigma; } - + /** @ITKEndGrouping */ void Initialize(const RadiusType & r) override { diff --git a/Modules/Segmentation/LevelSets/include/itkGeodesicActiveContourShapePriorLevelSetFunction.h b/Modules/Segmentation/LevelSets/include/itkGeodesicActiveContourShapePriorLevelSetFunction.h index ed6a3536cb9..d46bde044e9 100644 --- a/Modules/Segmentation/LevelSets/include/itkGeodesicActiveContourShapePriorLevelSetFunction.h +++ b/Modules/Segmentation/LevelSets/include/itkGeodesicActiveContourShapePriorLevelSetFunction.h @@ -137,6 +137,7 @@ class ITK_TEMPLATE_EXPORT GeodesicActiveContourShapePriorLevelSetFunction /** Set/Get the sigma for the Gaussian kernel used to compute the gradient * of the feature image needed for the advection term of the equation. */ + /** @ITKStartGrouping */ void SetDerivativeSigma(const double v) { @@ -147,7 +148,7 @@ class ITK_TEMPLATE_EXPORT GeodesicActiveContourShapePriorLevelSetFunction { return m_DerivativeSigma; } - + /** @ITKEndGrouping */ void Initialize(const RadiusType & r) override { diff --git a/Modules/Segmentation/LevelSets/include/itkLevelSetFunction.h b/Modules/Segmentation/LevelSets/include/itkLevelSetFunction.h index 8099987976e..c288a57b703 100644 --- a/Modules/Segmentation/LevelSets/include/itkLevelSetFunction.h +++ b/Modules/Segmentation/LevelSets/include/itkLevelSetFunction.h @@ -149,6 +149,7 @@ class ITK_TEMPLATE_EXPORT LevelSetFunction : public FiniteDifferenceFunction; /** Get/Set the input level set. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(InputLevelSet, LevelSetImageType); itkGetConstObjectMacro(InputLevelSet, LevelSetImageType); - + /** @ITKEndGrouping */ /** Set the value of the level set to be located. Default is 0. */ itkSetMacro(LevelSetValue, double); @@ -105,15 +106,17 @@ class ITK_TEMPLATE_EXPORT LevelSetNeighborhoodExtractor : public LightProcessObj itkSetMacro(NarrowBanding, bool); /** Get the narrowbanding flag. */ + /** @ITKStartGrouping */ itkGetConstMacro(NarrowBanding, bool); itkBooleanMacro(NarrowBanding); - + /** @ITKEndGrouping */ /** Set/Get the input narrowband. A narrowband is represented as * a VectorContainer of LevelSetNodes. */ + /** @ITKStartGrouping */ void SetInputNarrowBand(NodeContainer * ptr); itkGetModifiableObjectMacro(InputNarrowBand, NodeContainer); - + /** @ITKEndGrouping */ /** Get the container of inside points. The inside points are * stored in a VectorContainer of LevelSetNodes. */ NodeContainerPointer diff --git a/Modules/Segmentation/LevelSets/include/itkNarrowBandLevelSetImageFilter.h b/Modules/Segmentation/LevelSets/include/itkNarrowBandLevelSetImageFilter.h index 8ed1f12bbb0..a0fc2e0867e 100644 --- a/Modules/Segmentation/LevelSets/include/itkNarrowBandLevelSetImageFilter.h +++ b/Modules/Segmentation/LevelSets/include/itkNarrowBandLevelSetImageFilter.h @@ -176,6 +176,7 @@ class ITK_TEMPLATE_EXPORT NarrowBandLevelSetImageFilter : public NarrowBandImage /** Set/Get the feature image to be used for speed function of the level set * equation. Equivalent to calling Set/GetInput(1, ..) */ + /** @ITKStartGrouping */ virtual void SetFeatureImage(const FeatureImageType * f) { @@ -188,6 +189,7 @@ class ITK_TEMPLATE_EXPORT NarrowBandLevelSetImageFilter : public NarrowBandImage { return (static_cast(this->ProcessObject::GetInput(1))); } + /** @ITKEndGrouping */ /** Set/Get the initial level set model. Equivalent to calling SetInput(..) */ @@ -212,6 +214,7 @@ class ITK_TEMPLATE_EXPORT NarrowBandLevelSetImageFilter : public NarrowBandImage /** THIS METHOD IS DEPRECATED AND SHOULD NOT BE USED. This method reverses * the speed function direction, effectively changing inside feature values to * outside feature values and vice versa. */ + /** @ITKStartGrouping */ void SetUseNegativeFeaturesOn() { @@ -219,7 +222,6 @@ class ITK_TEMPLATE_EXPORT NarrowBandLevelSetImageFilter : public NarrowBandImage << "SetUseNegativeFeaturesOn has been deprecated. Please use ReverseExpansionDirectionOn() instead"); this->ReverseExpansionDirectionOn(); } - void SetUseNegativeFeaturesOff() { @@ -227,9 +229,11 @@ class ITK_TEMPLATE_EXPORT NarrowBandLevelSetImageFilter : public NarrowBandImage << "SetUseNegativeFeaturesOff has been deprecated. Please use ReverseExpansionDirectionOff() instead"); this->ReverseExpansionDirectionOff(); } + /** @ITKEndGrouping */ /** Set/Get the value of the UseNegativeFeatures flag. This method is * deprecated. Use Set/Get ReverseExpansionDirection instead. */ + /** @ITKStartGrouping */ void SetUseNegativeFeatures(bool u) { @@ -256,6 +260,7 @@ class ITK_TEMPLATE_EXPORT NarrowBandLevelSetImageFilter : public NarrowBandImage return false; } + /** @ITKEndGrouping */ /** Turn On/Off the flag which determines whether Positive or Negative speed * terms will cause surface expansion. If set to TRUE then negative speed @@ -265,9 +270,11 @@ class ITK_TEMPLATE_EXPORT NarrowBandLevelSetImageFilter : public NarrowBandImage * surface to contract. This method can be safely used to reverse the * expansion/contraction as appropriate to a particular application or data * set. */ + /** @ITKStartGrouping */ itkSetMacro(ReverseExpansionDirection, bool); itkGetConstMacro(ReverseExpansionDirection, bool); itkBooleanMacro(ReverseExpansionDirection); + /** @ITKEndGrouping */ /** Combined scaling of the propagation and advection speed terms. You should use either this -or- Get/SetPropagationScaling and @@ -288,6 +295,7 @@ class ITK_TEMPLATE_EXPORT NarrowBandLevelSetImageFilter : public NarrowBandImage /** Set/Get the scaling of the propagation speed. Setting the FeatureScaling parameter overrides any previous values set for PropagationScaling. */ + /** @ITKStartGrouping */ void SetPropagationScaling(ValueType v) { @@ -302,9 +310,11 @@ class ITK_TEMPLATE_EXPORT NarrowBandLevelSetImageFilter : public NarrowBandImage { return m_SegmentationFunction->GetPropagationWeight(); } + /** @ITKEndGrouping */ /** Set/Get the scaling of the advection field. Setting the FeatureScaling parameter will override any existing value for AdvectionScaling. */ + /** @ITKStartGrouping */ void SetAdvectionScaling(ValueType v) { @@ -319,11 +329,13 @@ class ITK_TEMPLATE_EXPORT NarrowBandLevelSetImageFilter : public NarrowBandImage { return m_SegmentationFunction->GetAdvectionWeight(); } + /** @ITKEndGrouping */ /** Set/Get the scaling of the curvature. Use this parameter to increase the * influence of curvature on the movement of the surface. Higher * values relative to Advection and Propagation values will give * smoother surfaces. */ + /** @ITKStartGrouping */ void SetCurvatureScaling(ValueType v) { @@ -338,6 +350,7 @@ class ITK_TEMPLATE_EXPORT NarrowBandLevelSetImageFilter : public NarrowBandImage { return m_SegmentationFunction->GetCurvatureWeight(); } + /** @ITKEndGrouping */ /** Set the segmentation function. In general, this should only be called by a subclass * of this object. It is made public to allow itk::Command objects access. */ @@ -352,6 +365,7 @@ class ITK_TEMPLATE_EXPORT NarrowBandLevelSetImageFilter : public NarrowBandImage /** Set/Get the maximum number of iterations allowed for the solver. This * prevents infinite loops if a solution "bounces". */ + /** @ITKStartGrouping */ void SetMaximumIterations(unsigned int i) { @@ -365,6 +379,7 @@ class ITK_TEMPLATE_EXPORT NarrowBandLevelSetImageFilter : public NarrowBandImage itkWarningMacro("GetMaximumIterations is deprecated. Please use GetNumberOfIterations instead."); return this->GetNumberOfIterations(); } + /** @ITKEndGrouping */ void SetMaximumRMSError(const double) override @@ -409,6 +424,7 @@ class ITK_TEMPLATE_EXPORT NarrowBandLevelSetImageFilter : public NarrowBandImage bool m_ReverseExpansionDirection{}; /** Reinitialization filters **/ + /** Internal filter types used for reinitialization */ using IsoFilterType = IsoContourDistanceImageFilter; using ChamferFilterType = FastChamferDistanceImageFilter; diff --git a/Modules/Segmentation/LevelSets/include/itkNarrowBandThresholdSegmentationLevelSetImageFilter.h b/Modules/Segmentation/LevelSets/include/itkNarrowBandThresholdSegmentationLevelSetImageFilter.h index c7c52926174..1524a4fc77b 100644 --- a/Modules/Segmentation/LevelSets/include/itkNarrowBandThresholdSegmentationLevelSetImageFilter.h +++ b/Modules/Segmentation/LevelSets/include/itkNarrowBandThresholdSegmentationLevelSetImageFilter.h @@ -114,6 +114,7 @@ class ITK_TEMPLATE_EXPORT NarrowBandThresholdSegmentationLevelSetImageFilter /** Get/Set the threshold values that will be used to calculate the speed function. */ + /** @ITKStartGrouping */ void SetUpperThreshold(ValueType v) { @@ -139,9 +140,11 @@ class ITK_TEMPLATE_EXPORT NarrowBandThresholdSegmentationLevelSetImageFilter { return m_ThresholdFunction->GetLowerThreshold(); } + /** @ITKEndGrouping */ /** Set/Get the weight applied to the edge (Laplacian) attractor in the speed * term function. Zero will turn this term off. */ + /** @ITKStartGrouping */ void SetEdgeWeight(ValueType v) { @@ -154,10 +157,12 @@ class ITK_TEMPLATE_EXPORT NarrowBandThresholdSegmentationLevelSetImageFilter { return m_ThresholdFunction->GetEdgeWeight(); } + /** @ITKEndGrouping */ /** Anisotropic diffusion is applied to the FeatureImage before calculating * the Laplacian (edge) term. This method sets/gets the number of diffusion * iterations. */ + /** @ITKStartGrouping */ void SetSmoothingIterations(int v) { @@ -170,10 +175,12 @@ class ITK_TEMPLATE_EXPORT NarrowBandThresholdSegmentationLevelSetImageFilter { return m_ThresholdFunction->GetSmoothingIterations(); } + /** @ITKEndGrouping */ /** Anisotropic diffusion is applied to the FeatureImage before calculating * the Laplacian (edge) term. This method sets/gets the diffusion time * step. */ + /** @ITKStartGrouping */ void SetSmoothingTimeStep(ValueType v) { @@ -186,10 +193,12 @@ class ITK_TEMPLATE_EXPORT NarrowBandThresholdSegmentationLevelSetImageFilter { return m_ThresholdFunction->GetSmoothingTimeStep(); } + /** @ITKEndGrouping */ /** Anisotropic diffusion is applied to the FeatureImage before calculating * the Laplacian (edge) term. This method sets/gets the smoothing * conductance. */ + /** @ITKStartGrouping */ void SetSmoothingConductance(ValueType v) { @@ -202,6 +211,7 @@ class ITK_TEMPLATE_EXPORT NarrowBandThresholdSegmentationLevelSetImageFilter { return m_ThresholdFunction->GetSmoothingConductance(); } + /** @ITKEndGrouping */ itkConceptMacro(OutputHasNumericTraitsCheck, (Concept::HasNumericTraits)); diff --git a/Modules/Segmentation/LevelSets/include/itkNormalVectorFunctionBase.h b/Modules/Segmentation/LevelSets/include/itkNormalVectorFunctionBase.h index 56c439cda92..fef985b9d8d 100644 --- a/Modules/Segmentation/LevelSets/include/itkNormalVectorFunctionBase.h +++ b/Modules/Segmentation/LevelSets/include/itkNormalVectorFunctionBase.h @@ -84,6 +84,7 @@ class ITK_TEMPLATE_EXPORT NormalVectorFunctionBase : public FiniteDifferenceSpar using NormalVectorType = typename NodeType::NodeDataType; /** GlobalData methods are not needed in this class. */ + /** @ITKStartGrouping */ void * GetGlobalDataPointer() const override { @@ -92,7 +93,7 @@ class ITK_TEMPLATE_EXPORT NormalVectorFunctionBase : public FiniteDifferenceSpar void ReleaseGlobalDataPointer(void *) const override {} - + /** @ITKEndGrouping */ /** For the global time step, we return the time step parameter. */ TimeStepType ComputeGlobalTimeStep(void *) const override diff --git a/Modules/Segmentation/LevelSets/include/itkParallelSparseFieldLevelSetImageFilter.h b/Modules/Segmentation/LevelSets/include/itkParallelSparseFieldLevelSetImageFilter.h index 53125c290fa..f035c63a7ad 100644 --- a/Modules/Segmentation/LevelSets/include/itkParallelSparseFieldLevelSetImageFilter.h +++ b/Modules/Segmentation/LevelSets/include/itkParallelSparseFieldLevelSetImageFilter.h @@ -313,13 +313,15 @@ class ITK_TEMPLATE_EXPORT ParallelSparseFieldLevelSetImageFilter /** Set/Get the number of layers to use in the sparse field. Argument is the * number of layers on ONE side of the active layer, so the total layers in * the sparse field is 2 * NumberOfLayers + 1 */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfLayers, StatusType); itkGetConstMacro(NumberOfLayers, StatusType); - + /** @ITKEndGrouping */ /** Set/Get the value of the isosurface to use in the input image. */ + /** @ITKStartGrouping */ itkSetMacro(IsoSurfaceValue, ValueType); itkGetConstMacro(IsoSurfaceValue, ValueType); - + /** @ITKEndGrouping */ LayerPointerType GetActiveListForIndex(const IndexType index) { @@ -683,11 +685,12 @@ class ITK_TEMPLATE_EXPORT ParallelSparseFieldLevelSetImageFilter /** Redistribute an load among the threads to obtain a more balanced load distribution. * This is performed in parallel by all the threads. */ + /** @ITKStartGrouping */ void ThreadedLoadBalance1(ThreadIdType ThreadId); void ThreadedLoadBalance2(ThreadIdType ThreadId); - + /** @ITKEndGrouping */ void SignalNeighborsAndWait(ThreadIdType ThreadId); diff --git a/Modules/Segmentation/LevelSets/include/itkReinitializeLevelSetImageFilter.h b/Modules/Segmentation/LevelSets/include/itkReinitializeLevelSetImageFilter.h index 74867b4e870..4b27c243459 100644 --- a/Modules/Segmentation/LevelSets/include/itkReinitializeLevelSetImageFilter.h +++ b/Modules/Segmentation/LevelSets/include/itkReinitializeLevelSetImageFilter.h @@ -82,22 +82,30 @@ class ITK_TEMPLATE_EXPORT ReinitializeLevelSetImageFilter : public ImageToImageF /** Set/Get the value of the level set to be located. The default value is * 0. */ + /** @ITKStartGrouping */ itkSetMacro(LevelSetValue, double); itkGetConstMacro(LevelSetValue, double); + /** @ITKEndGrouping */ /** Set/Get the narrowbanding flag. By default, narrowbanding is switched * off. */ + /** @ITKStartGrouping */ itkSetMacro(NarrowBanding, bool); itkGetConstMacro(NarrowBanding, bool); itkBooleanMacro(NarrowBanding); + /** @ITKEndGrouping */ /** Set/Get the input narrow bandwidth. The default value is 12. */ + /** @ITKStartGrouping */ itkSetClampMacro(InputNarrowBandwidth, double, 0.0, NumericTraits::max()); itkGetConstMacro(InputNarrowBandwidth, double); + /** @ITKEndGrouping */ /** Set/Get the output narrow bandwidth. The default value is 12. */ + /** @ITKStartGrouping */ itkSetClampMacro(OutputNarrowBandwidth, double, 0.0, NumericTraits::max()); itkGetConstMacro(OutputNarrowBandwidth, double); + /** @ITKEndGrouping */ /** Set the bandwidth for both the input and output narrowband, * By default, both the input and output are set to 12. */ @@ -109,6 +117,7 @@ class ITK_TEMPLATE_EXPORT ReinitializeLevelSetImageFilter : public ImageToImageF } /** Set/Get the input narrowband container. */ + /** @ITKStartGrouping */ void SetInputNarrowBand(NodeContainer * ptr); @@ -117,6 +126,7 @@ class ITK_TEMPLATE_EXPORT ReinitializeLevelSetImageFilter : public ImageToImageF { return m_InputNarrowBand; } + /** @ITKEndGrouping */ /** Get the output narrowband. */ NodeContainerPointer diff --git a/Modules/Segmentation/LevelSets/include/itkSegmentationLevelSetFunction.h b/Modules/Segmentation/LevelSets/include/itkSegmentationLevelSetFunction.h index f1769b9c95b..777a574597a 100644 --- a/Modules/Segmentation/LevelSets/include/itkSegmentationLevelSetFunction.h +++ b/Modules/Segmentation/LevelSets/include/itkSegmentationLevelSetFunction.h @@ -87,6 +87,7 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetFunction : public LevelSetFunction using ContinuousIndexType = typename InterpolatorType::ContinuousIndexType; /** Set/Get the image which will be used to calculate the speed function. */ + /** @ITKStartGrouping */ virtual const FeatureImageType * GetFeatureImage() const { @@ -97,8 +98,9 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetFunction : public LevelSetFunction { m_FeatureImage = f; } - + /** @ITKEndGrouping */ /** Get/Set the image used as the speed function in the level set equation */ + /** @ITKStartGrouping */ virtual ImageType * GetSpeedImage() { @@ -106,8 +108,9 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetFunction : public LevelSetFunction } void SetSpeedImage(ImageType * s); - + /** @ITKEndGrouping */ /** Get/Set the image used as the advection field in the level set equation */ + /** @ITKStartGrouping */ virtual VectorImageType * GetAdvectionImage() const { @@ -115,7 +118,7 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetFunction : public LevelSetFunction } void SetAdvectionImage(VectorImageType * s); - + /** @ITKEndGrouping */ /** This method creates the appropriate member variable operators for the * level-set calculations. The argument to this function is a the radius * necessary for performing the level-set calculations. */ diff --git a/Modules/Segmentation/LevelSets/include/itkSegmentationLevelSetImageFilter.h b/Modules/Segmentation/LevelSets/include/itkSegmentationLevelSetImageFilter.h index aa186736b0b..24ecda6c380 100644 --- a/Modules/Segmentation/LevelSets/include/itkSegmentationLevelSetImageFilter.h +++ b/Modules/Segmentation/LevelSets/include/itkSegmentationLevelSetImageFilter.h @@ -181,6 +181,7 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetImageFilter /** Set/Get the maximum number of iterations allowed for the solver. This * prevents infinite loops if a solution "bounces". */ + /** @ITKStartGrouping */ void SetMaximumIterations(unsigned int i) { @@ -194,9 +195,11 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetImageFilter itkWarningMacro("GetMaximumIterations is deprecated. Please use GetNumberOfIterations instead."); return this->GetNumberOfIterations(); } + /** @ITKEndGrouping */ /** Set/Get the feature image to be used for speed function of the level set * equation. Equivalent to calling Set/GetInput(1, ..) */ + /** @ITKStartGrouping */ virtual void SetFeatureImage(const FeatureImageType * f) { @@ -209,11 +212,14 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetImageFilter } } itkGetInputMacro(FeatureImage, FeatureImageType); + /** @ITKEndGrouping */ /** Set/Get the initial level set model. Equivalent to calling SetInput(..) */ + /** @ITKStartGrouping */ itkSetInputMacro(InitialImage, InputImageType); itkGetInputMacro(InitialImage, InputImageType); + /** @ITKEndGrouping */ /** Set the feature image */ void @@ -259,6 +265,7 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetImageFilter /** THIS METHOD IS DEPRECATED AND SHOULD NOT BE USED. This method reverses * the speed function direction, effectively changing inside feature values to * outside feature values and vice versa. */ + /** @ITKStartGrouping */ void SetUseNegativeFeaturesOn() { @@ -274,9 +281,11 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetImageFilter << "SetUseNegativeFeaturesOff has been deprecated. Please use ReverseExpansionDirectionOff() instead"); this->ReverseExpansionDirectionOff(); } + /** @ITKEndGrouping */ /** THIS METHOD IS DEPRECATED AND SHOULD NOT BE USED. Set/Get the value of the UseNegativeFeatures flag. This method * is deprecated. Use Set/Get ReverseExpansionDirection instead. */ + /** @ITKStartGrouping */ void SetUseNegativeFeatures(bool u) { @@ -303,6 +312,7 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetImageFilter return false; } + /** @ITKEndGrouping */ /** Turn On/Off the flag which determines whether Positive or Negative speed * terms will cause surface expansion. If set to TRUE then negative speed @@ -312,18 +322,22 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetImageFilter * surface to contract. This method can be safely used to reverse the * expansion/contraction as appropriate to a particular application or data * set. */ + /** @ITKStartGrouping */ itkSetMacro(ReverseExpansionDirection, bool); itkGetConstMacro(ReverseExpansionDirection, bool); itkBooleanMacro(ReverseExpansionDirection); + /** @ITKEndGrouping */ /** Turn On/Off automatic generation of Speed and Advection terms when Update is called. If set to Off, the Speed and Advection images must be set explicitly using SetSpeedImage, SetAdvectionImage OR the methods GenerateSpeedImage() and GenerateAdvectionImage() should be called prior to updating the filter. */ + /** @ITKStartGrouping */ itkSetMacro(AutoGenerateSpeedAdvection, bool); itkGetConstMacro(AutoGenerateSpeedAdvection, bool); itkBooleanMacro(AutoGenerateSpeedAdvection); + /** @ITKEndGrouping */ /** Combined scaling of the propagation and advection speed terms. You should use either this -or- Get/SetPropagationScaling and @@ -344,6 +358,7 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetImageFilter /** Set/Get the scaling of the propagation speed. Setting the FeatureScaling parameter overrides any previous values set for PropagationScaling. */ + /** @ITKStartGrouping */ void SetPropagationScaling(ValueType v) { @@ -359,9 +374,11 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetImageFilter { return m_SegmentationFunction->GetPropagationWeight(); } + /** @ITKEndGrouping */ /** Set/Get the scaling of the advection field. Setting the FeatureScaling parameter will override any existing value for AdvectionScaling. */ + /** @ITKStartGrouping */ void SetAdvectionScaling(ValueType v) { @@ -377,11 +394,13 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetImageFilter { return m_SegmentationFunction->GetAdvectionWeight(); } + /** @ITKEndGrouping */ /** Set/Get the scaling of the curvature. Use this parameter to * increase the influence of curvature on the movement of the * surface. Higher values relative to Advection and Propagation * values will give smoother surfaces. */ + /** @ITKStartGrouping */ void SetCurvatureScaling(ValueType v) { @@ -397,8 +416,10 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetImageFilter { return m_SegmentationFunction->GetCurvatureWeight(); } + /** @ITKEndGrouping */ /** */ + /** @ITKStartGrouping */ void SetUseMinimalCurvature(bool b) { @@ -414,6 +435,7 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetImageFilter { return m_SegmentationFunction->GetUseMinimalCurvature(); } + /** @ITKEndGrouping */ void UseMinimalCurvatureOn() @@ -454,6 +476,7 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetImageFilter * calculation. Changing this value from the default is not recommended or * necessary but could be used to speed up the surface evolution at the risk * of creating an unstable solution. */ + /** @ITKStartGrouping */ void SetMaximumCurvatureTimeStep(double n) { @@ -469,11 +492,13 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetImageFilter { return m_SegmentationFunction->GetMaximumCurvatureTimeStep(); } + /** @ITKEndGrouping */ /** Set/Get the maximum constraint for the scalar/vector term factor of the time step * calculation. Changing this value from the default is not recommended or * necessary but could be used to speed up the surface evolution at the risk * of creating an unstable solution. */ + /** @ITKStartGrouping */ void SetMaximumPropagationTimeStep(double n) { @@ -483,12 +508,13 @@ class ITK_TEMPLATE_EXPORT SegmentationLevelSetImageFilter this->Modified(); } } - double + GetMaximumPropagationTimeStep() const { return m_SegmentationFunction->GetMaximumPropagationTimeStep(); } + /** @ITKEndGrouping */ /** Allocate and calculate the speed term image in the SegmentationFunction object. This method is called automatically on filter execution diff --git a/Modules/Segmentation/LevelSets/include/itkShapePriorMAPCostFunction.h b/Modules/Segmentation/LevelSets/include/itkShapePriorMAPCostFunction.h index dfdd9b64863..cfe899f3cbf 100644 --- a/Modules/Segmentation/LevelSets/include/itkShapePriorMAPCostFunction.h +++ b/Modules/Segmentation/LevelSets/include/itkShapePriorMAPCostFunction.h @@ -93,21 +93,24 @@ class ITK_TEMPLATE_EXPORT ShapePriorMAPCostFunction : public ShapePriorMAPCostFu using ArrayType = Array; /** Set/Get the array of shape parameters mean. */ + /** @ITKStartGrouping */ itkSetMacro(ShapeParameterMeans, ArrayType); itkGetConstMacro(ShapeParameterMeans, ArrayType); - + /** @ITKEndGrouping */ /** Set/Get the array of shape parameters standard deviation. */ + /** @ITKStartGrouping */ itkSetMacro(ShapeParameterStandardDeviations, ArrayType); itkGetConstMacro(ShapeParameterStandardDeviations, ArrayType); - + /** @ITKEndGrouping */ /** Set/Get the weights for each term. Default is a vector of all ones. * The weights are applied to terms in the following order: * LogInsideTerm, LogGradientTerm, LogShapePriorTerm and * LogPosePriorTerm. */ + /** @ITKStartGrouping */ using WeightsType = FixedArray; itkSetMacro(Weights, WeightsType); itkGetConstReferenceMacro(Weights, WeightsType); - + /** @ITKEndGrouping */ /** Compute the inside term component of the MAP cost function. * In particular, the method sums the number of pixels inside * the current contour (defined by nodes of the active region diff --git a/Modules/Segmentation/LevelSets/include/itkShapePriorMAPCostFunctionBase.h b/Modules/Segmentation/LevelSets/include/itkShapePriorMAPCostFunctionBase.h index 3217a5aba00..65d9f683821 100644 --- a/Modules/Segmentation/LevelSets/include/itkShapePriorMAPCostFunctionBase.h +++ b/Modules/Segmentation/LevelSets/include/itkShapePriorMAPCostFunctionBase.h @@ -89,17 +89,20 @@ class ITK_TEMPLATE_EXPORT ShapePriorMAPCostFunctionBase : public SingleValuedCos using ShapeFunctionPointer = typename ShapeFunctionType::Pointer; /** Set/Get the shape distance function. */ + /** @ITKStartGrouping */ itkSetObjectMacro(ShapeFunction, ShapeFunctionType); itkGetModifiableObjectMacro(ShapeFunction, ShapeFunctionType); - + /** @ITKEndGrouping */ /** Set/Get the active region. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(ActiveRegion, NodeContainerType); itkGetConstObjectMacro(ActiveRegion, NodeContainerType); - + /** @ITKEndGrouping */ /** Set/Get the feature image. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(FeatureImage, FeatureImageType); itkGetConstObjectMacro(FeatureImage, FeatureImageType); - + /** @ITKEndGrouping */ /** This method returns the value of the cost function corresponding * to the specified parameters. */ MeasureType diff --git a/Modules/Segmentation/LevelSets/include/itkShapePriorSegmentationLevelSetFunction.h b/Modules/Segmentation/LevelSets/include/itkShapePriorSegmentationLevelSetFunction.h index 8f7269db0a8..6ef41d8d5f5 100644 --- a/Modules/Segmentation/LevelSets/include/itkShapePriorSegmentationLevelSetFunction.h +++ b/Modules/Segmentation/LevelSets/include/itkShapePriorSegmentationLevelSetFunction.h @@ -88,6 +88,7 @@ class ITK_TEMPLATE_EXPORT ShapePriorSegmentationLevelSetFunction using ShapeFunctionPointer = typename ShapeFunctionType::ConstPointer; /** Zeta. The ShapePriorWeight scales the shape prior term values. */ + /** @ITKStartGrouping */ void SetShapePriorWeight(const ScalarValueType p) { @@ -98,9 +99,10 @@ class ITK_TEMPLATE_EXPORT ShapePriorSegmentationLevelSetFunction { return m_ShapePriorWeight; } - + /** @ITKEndGrouping */ /** The ShapeFunction encapsulates the signed distance to the shape used to * influence the evolution of the level set. */ + /** @ITKStartGrouping */ void SetShapeFunction(const ShapeFunctionType * ptr) { @@ -111,7 +113,7 @@ class ITK_TEMPLATE_EXPORT ShapePriorSegmentationLevelSetFunction { return m_ShapeFunction; } - + /** @ITKEndGrouping */ /** Compute the equation value with the additional shape prior term. */ PixelType ComputeUpdate(const NeighborhoodType & neighborhood, diff --git a/Modules/Segmentation/LevelSets/include/itkShapePriorSegmentationLevelSetImageFilter.h b/Modules/Segmentation/LevelSets/include/itkShapePriorSegmentationLevelSetImageFilter.h index 141d3ff6766..073a3bd3dc5 100644 --- a/Modules/Segmentation/LevelSets/include/itkShapePriorSegmentationLevelSetImageFilter.h +++ b/Modules/Segmentation/LevelSets/include/itkShapePriorSegmentationLevelSetImageFilter.h @@ -115,26 +115,35 @@ class ITK_TEMPLATE_EXPORT ShapePriorSegmentationLevelSetImageFilter using OptimizerPointer = typename OptimizerType::Pointer; /** Set/Get the shape signed distance function. */ + /** @ITKStartGrouping */ virtual void SetShapeFunction(ShapeFunctionType * s); itkGetModifiableObjectMacro(ShapeFunction, ShapeFunctionType); + /** @ITKEndGrouping */ /** Set/Get the shape prior MAP cost function. */ + /** @ITKStartGrouping */ itkSetObjectMacro(CostFunction, CostFunctionType); itkGetModifiableObjectMacro(CostFunction, CostFunctionType); + /** @ITKEndGrouping */ /** Set/Get the optimizer. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Optimizer, OptimizerType); itkGetModifiableObjectMacro(Optimizer, OptimizerType); + /** @ITKEndGrouping */ /** Set/Get the initial parameters. These are the initial parameters applied * to the ShapeFunction. The user should refer to the documentation of * the particular type of ShapeSignedDistanceFunction used to determine * the meaning of the parameters. */ + /** @ITKStartGrouping */ itkSetMacro(InitialParameters, ParametersType); itkGetConstMacro(InitialParameters, ParametersType); + /** @ITKEndGrouping */ /** Set/Get the scaling of the shape prior term. */ + /** @ITKStartGrouping */ void SetShapePriorScaling(ValueType v) { @@ -150,6 +159,7 @@ class ITK_TEMPLATE_EXPORT ShapePriorSegmentationLevelSetImageFilter { return m_ShapePriorSegmentationFunction->GetShapePriorWeight(); } + /** @ITKEndGrouping */ /** Set the shape prior segmentation function. In general, this should only be called * by a subclass of this object. It is made public to allow itk::Command objects access. */ diff --git a/Modules/Segmentation/LevelSets/include/itkSparseFieldLevelSetImageFilter.h b/Modules/Segmentation/LevelSets/include/itkSparseFieldLevelSetImageFilter.h index ddbdfe42c03..ce47e224401 100644 --- a/Modules/Segmentation/LevelSets/include/itkSparseFieldLevelSetImageFilter.h +++ b/Modules/Segmentation/LevelSets/include/itkSparseFieldLevelSetImageFilter.h @@ -295,13 +295,15 @@ class ITK_TEMPLATE_EXPORT SparseFieldLevelSetImageFilter : public FiniteDifferen /** Set/Get the number of layers to use in the sparse field. Argument is the * number of layers on ONE side of the active layer, so the total layers in * the sparse field is 2 * NumberOfLayers +1 */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfLayers, unsigned int); itkGetConstMacro(NumberOfLayers, unsigned int); - + /** @ITKEndGrouping */ /** Set/Get the value of the isosurface to use in the input image. */ + /** @ITKStartGrouping */ itkSetMacro(IsoSurfaceValue, ValueType); itkGetConstMacro(IsoSurfaceValue, ValueType); - + /** @ITKEndGrouping */ /** Get the RMS change calculated in the PREVIOUS iteration. This value is * the square root of the average square of the change value of all pixels * updated during the previous iteration. */ @@ -312,10 +314,12 @@ class ITK_TEMPLATE_EXPORT SparseFieldLevelSetImageFilter : public FiniteDifferen when calculating change at a voxel location. Turned on by default. Some applications may not use this value and can safely turn the flag off. */ + /** @ITKStartGrouping */ itkSetMacro(InterpolateSurfaceLocation, bool); itkGetConstMacro(InterpolateSurfaceLocation, bool); - + /** @ITKEndGrouping */ /** See Get/SetInterpolateSurfaceLocation */ + /** @ITKStartGrouping */ void InterpolateSurfaceLocationOn() { @@ -326,7 +330,7 @@ class ITK_TEMPLATE_EXPORT SparseFieldLevelSetImageFilter : public FiniteDifferen { this->SetInterpolateSurfaceLocation(false); } - + /** @ITKEndGrouping */ itkConceptMacro(OutputEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(DoubleConvertibleToOutputCheck, (Concept::Convertible)); itkConceptMacro(OutputOStreamWritableCheck, (Concept::OStreamWritable)); diff --git a/Modules/Segmentation/LevelSets/include/itkThresholdSegmentationLevelSetFunction.h b/Modules/Segmentation/LevelSets/include/itkThresholdSegmentationLevelSetFunction.h index 9d9773c30c2..cf4c90743d5 100644 --- a/Modules/Segmentation/LevelSets/include/itkThresholdSegmentationLevelSetFunction.h +++ b/Modules/Segmentation/LevelSets/include/itkThresholdSegmentationLevelSetFunction.h @@ -83,6 +83,7 @@ class ITK_TEMPLATE_EXPORT ThresholdSegmentationLevelSetFunction static constexpr unsigned int ImageDimension = Superclass::ImageDimension; /** Set/Get threshold values */ + /** @ITKStartGrouping */ void SetUpperThreshold(FeatureScalarType f) { @@ -103,7 +104,7 @@ class ITK_TEMPLATE_EXPORT ThresholdSegmentationLevelSetFunction { return m_LowerThreshold; } - + /** @ITKEndGrouping */ void CalculateSpeedImage() override; diff --git a/Modules/Segmentation/LevelSets/include/itkThresholdSegmentationLevelSetImageFilter.h b/Modules/Segmentation/LevelSets/include/itkThresholdSegmentationLevelSetImageFilter.h index edbb1673c49..d30a5f7e694 100644 --- a/Modules/Segmentation/LevelSets/include/itkThresholdSegmentationLevelSetImageFilter.h +++ b/Modules/Segmentation/LevelSets/include/itkThresholdSegmentationLevelSetImageFilter.h @@ -110,6 +110,7 @@ class ITK_TEMPLATE_EXPORT ThresholdSegmentationLevelSetImageFilter /** Get/Set the threshold values that will be used to calculate the speed function. */ + /** @ITKStartGrouping */ void SetUpperThreshold(ValueType v) { @@ -135,9 +136,11 @@ class ITK_TEMPLATE_EXPORT ThresholdSegmentationLevelSetImageFilter { return m_ThresholdFunction->GetLowerThreshold(); } + /** @ITKEndGrouping */ /** Set/Get the weight applied to the edge (Laplacian) attractor in the speed * term function. Zero will turn this term off. */ + /** @ITKStartGrouping */ void SetEdgeWeight(ValueType v) { @@ -150,10 +153,12 @@ class ITK_TEMPLATE_EXPORT ThresholdSegmentationLevelSetImageFilter { return m_ThresholdFunction->GetEdgeWeight(); } + /** @ITKEndGrouping */ /** Anisotropic diffusion is applied to the FeatureImage before calculating * the Laplacian (edge) term. This method sets/gets the number of diffusion * iterations. */ + /** @ITKStartGrouping */ void SetSmoothingIterations(int v) { @@ -166,10 +171,12 @@ class ITK_TEMPLATE_EXPORT ThresholdSegmentationLevelSetImageFilter { return m_ThresholdFunction->GetSmoothingIterations(); } + /** @ITKEndGrouping */ /** Anisotropic diffusion is applied to the FeatureImage before calculating * the Laplacian (edge) term. This method sets/gets the diffusion time * step. */ + /** @ITKStartGrouping */ void SetSmoothingTimeStep(ValueType v) { @@ -182,10 +189,12 @@ class ITK_TEMPLATE_EXPORT ThresholdSegmentationLevelSetImageFilter { return m_ThresholdFunction->GetSmoothingTimeStep(); } + /** @ITKEndGrouping */ /** Anisotropic diffusion is applied to the FeatureImage before calculating * the Laplacian (edge) term. This method sets/gets the smoothing * conductance. */ + /** @ITKStartGrouping */ void SetSmoothingConductance(ValueType v) { @@ -198,6 +207,7 @@ class ITK_TEMPLATE_EXPORT ThresholdSegmentationLevelSetImageFilter { return m_ThresholdFunction->GetSmoothingConductance(); } + /** @ITKEndGrouping */ protected: ~ThresholdSegmentationLevelSetImageFilter() override = default; diff --git a/Modules/Segmentation/LevelSets/include/itkVectorThresholdSegmentationLevelSetFunction.h b/Modules/Segmentation/LevelSets/include/itkVectorThresholdSegmentationLevelSetFunction.h index 2f25ae6c435..85222e48f42 100644 --- a/Modules/Segmentation/LevelSets/include/itkVectorThresholdSegmentationLevelSetFunction.h +++ b/Modules/Segmentation/LevelSets/include/itkVectorThresholdSegmentationLevelSetFunction.h @@ -93,6 +93,7 @@ class ITK_TEMPLATE_EXPORT VectorThresholdSegmentationLevelSetFunction using CovarianceMatrixType = typename MahalanobisFunctionType::CovarianceMatrixType; /** Set/Get mean and covariance */ + /** @ITKStartGrouping */ void SetMean(const MeanVectorType & mean) { @@ -103,7 +104,7 @@ class ITK_TEMPLATE_EXPORT VectorThresholdSegmentationLevelSetFunction { return m_Mahalanobis->GetMean(); } - + /** @ITKEndGrouping */ void SetCovariance(const CovarianceMatrixType & cov) { diff --git a/Modules/Segmentation/LevelSets/include/itkVectorThresholdSegmentationLevelSetImageFilter.h b/Modules/Segmentation/LevelSets/include/itkVectorThresholdSegmentationLevelSetImageFilter.h index c48d88c7555..1f51903b524 100644 --- a/Modules/Segmentation/LevelSets/include/itkVectorThresholdSegmentationLevelSetImageFilter.h +++ b/Modules/Segmentation/LevelSets/include/itkVectorThresholdSegmentationLevelSetImageFilter.h @@ -119,6 +119,7 @@ class ITK_TEMPLATE_EXPORT VectorThresholdSegmentationLevelSetImageFilter /** Set/Get mean and covariance that will be used to calculate the speed function */ + /** @ITKStartGrouping */ void SetMean(const MeanVectorType & mean) { @@ -131,6 +132,7 @@ class ITK_TEMPLATE_EXPORT VectorThresholdSegmentationLevelSetImageFilter { return m_ThresholdFunction->GetMean(); } + /** @ITKEndGrouping */ void SetCovariance(const CovarianceMatrixType & cov) @@ -146,6 +148,7 @@ class ITK_TEMPLATE_EXPORT VectorThresholdSegmentationLevelSetImageFilter } /** Set/Get the threshold for the Mahalanobis Distance */ + /** @ITKStartGrouping */ void SetThreshold(ScalarValueType thr) { @@ -158,6 +161,7 @@ class ITK_TEMPLATE_EXPORT VectorThresholdSegmentationLevelSetImageFilter { return m_ThresholdFunction->GetThreshold(); } + /** @ITKEndGrouping */ protected: ~VectorThresholdSegmentationLevelSetImageFilter() override = default; diff --git a/Modules/Segmentation/LevelSetsv4/include/itkBinaryImageToLevelSetImageAdaptor.h b/Modules/Segmentation/LevelSetsv4/include/itkBinaryImageToLevelSetImageAdaptor.h index ec0f49524c6..c18ef4099a6 100644 --- a/Modules/Segmentation/LevelSetsv4/include/itkBinaryImageToLevelSetImageAdaptor.h +++ b/Modules/Segmentation/LevelSetsv4/include/itkBinaryImageToLevelSetImageAdaptor.h @@ -90,8 +90,10 @@ class ITK_TEMPLATE_EXPORT BinaryImageToLevelSetImageAdaptorm_LevelSet = LevelSetType::New(); } diff --git a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetContainerBase.h b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetContainerBase.h index eefc5a39ff7..f88faadf13d 100644 --- a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetContainerBase.h +++ b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetContainerBase.h @@ -305,13 +305,15 @@ class ITK_TEMPLATE_EXPORT LevelSetContainerBase : public Object RemoveLevelSet(const LevelSetIdentifierType & iId); /** \todo add documentation */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(Heaviside, HeavisideType); itkGetConstObjectMacro(Heaviside, HeavisideType); - + /** @ITKEndGrouping */ /** Set/Get the domain map image filter. */ + /** @ITKStartGrouping */ itkSetObjectMacro(DomainMapFilter, DomainMapImageFilterType); itkGetModifiableObjectMacro(DomainMapFilter, DomainMapImageFilterType); - + /** @ITKEndGrouping */ /** Does the level set container have a domain map? */ bool HasDomainMap() const; diff --git a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDenseImage.h b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDenseImage.h index 2d0c413ad01..f0330729ba7 100644 --- a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDenseImage.h +++ b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDenseImage.h @@ -75,11 +75,12 @@ class ITK_TEMPLATE_EXPORT LevelSetDenseImage itkGetModifiableObjectMacro(Image, ImageType); /** Returns the value of the level set function at a given location inputIndex */ + /** @ITKStartGrouping */ OutputType Evaluate(const InputType & inputIndex) const override; void Evaluate(const InputType & inputIndex, LevelSetDataType & data) const override; - + /** @ITKEndGrouping */ protected: LevelSetDenseImage() = default; diff --git a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDomainPartitionBase.h b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDomainPartitionBase.h index 031e556fcae..481317b6fad 100644 --- a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDomainPartitionBase.h +++ b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDomainPartitionBase.h @@ -45,9 +45,10 @@ class ITK_TEMPLATE_EXPORT LevelSetDomainPartitionBase : public Object itkOverrideGetNameOfClassMacro(LevelSetDomainPartitionBase); /** Get/Set the number of level set functions */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfLevelSetFunctions, IdentifierType); itkGetMacro(NumberOfLevelSetFunctions, IdentifierType); - + /** @ITKEndGrouping */ virtual void PopulateListDomain() = 0; diff --git a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDomainPartitionImage.h b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDomainPartitionImage.h index ca51fd1e6bf..77b5633bb0c 100644 --- a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDomainPartitionImage.h +++ b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDomainPartitionImage.h @@ -77,9 +77,10 @@ class ITK_TEMPLATE_EXPORT LevelSetDomainPartitionImage : public LevelSetDomainPa /** Set the input image that will be used to compute an image with the list * of level sets domain overlaps. */ + /** @ITKStartGrouping */ itkSetConstObjectMacro(Image, ImageType); itkGetConstObjectMacro(Image, ImageType); - + /** @ITKEndGrouping */ /** Get the image with the list of level set domains. */ itkGetModifiableObjectMacro(ListDomain, ListImageType); diff --git a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDomainPartitionImageWithKdTree.h b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDomainPartitionImageWithKdTree.h index 71122ababa6..d4ada615dcd 100644 --- a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDomainPartitionImageWithKdTree.h +++ b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetDomainPartitionImageWithKdTree.h @@ -70,9 +70,10 @@ class ITK_TEMPLATE_EXPORT LevelSetDomainPartitionImageWithKdTree : public LevelS using NeighborsIdType = unsigned int; /** Get/Set number of neighbors in the kd-tree leaf node */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfNeighbors, NeighborsIdType); itkGetMacro(NumberOfNeighbors, NeighborsIdType); - + /** @ITKEndGrouping */ /** Populate a list image with each pixel being a list of overlapping * level set support at that pixel */ void diff --git a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationAdvectionTerm.h b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationAdvectionTerm.h index 51d28c759c8..0da607817b1 100644 --- a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationAdvectionTerm.h +++ b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationAdvectionTerm.h @@ -142,11 +142,12 @@ class ITK_TEMPLATE_EXPORT LevelSetEquationAdvectionTerm : public LevelSetEquatio /** Returns the term contribution for a given location iP, i.e. * \f$ \omega_i( p ) \f$. */ + /** @ITKStartGrouping */ LevelSetOutputRealType Value(const LevelSetInputIndexType & iP) override; LevelSetOutputRealType Value(const LevelSetInputIndexType & iP, const LevelSetDataType & iData) override; - + /** @ITKEndGrouping */ LevelSetOutputRealType m_NeighborhoodScales[ImageDimension]{}; private: diff --git a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationContainer.h b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationContainer.h index c0fc33eb320..450e1455082 100644 --- a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationContainer.h +++ b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationContainer.h @@ -112,9 +112,10 @@ class ITK_TEMPLATE_EXPORT LevelSetEquationContainer : public Object ComputeCFLContribution() const; /** Set/Get the input speed or feature image */ + /** @ITKStartGrouping */ itkSetObjectMacro(Input, InputImageType); itkGetModifiableObjectMacro(Input, InputImageType); - + /** @ITKEndGrouping */ itkSetObjectMacro(LevelSetContainer, LevelSetContainerType); itkGetModifiableObjectMacro(LevelSetContainer, LevelSetContainerType); diff --git a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationCurvatureTerm.h b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationCurvatureTerm.h index 52dd4336b43..8ae59a26c0b 100644 --- a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationCurvatureTerm.h +++ b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationCurvatureTerm.h @@ -91,10 +91,11 @@ class ITK_TEMPLATE_EXPORT LevelSetEquationCurvatureTerm : public LevelSetEquatio /** Set/Get the propagation image. By default, if no PropagationImage has been set, it casts the input image and uses it in the term contribution calculation. */ + /** @ITKStartGrouping */ void SetCurvatureImage(CurvatureImageType * iImage); itkGetModifiableObjectMacro(CurvatureImage, CurvatureImageType); - + /** @ITKEndGrouping */ itkSetMacro(UseCurvatureImage, bool); itkGetMacro(UseCurvatureImage, bool); itkBooleanMacro(UseCurvatureImage); diff --git a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationPropagationTerm.h b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationPropagationTerm.h index f9120f00c40..5db5b7c955d 100644 --- a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationPropagationTerm.h +++ b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationPropagationTerm.h @@ -97,9 +97,10 @@ class ITK_TEMPLATE_EXPORT LevelSetEquationPropagationTerm : public LevelSetEquat /** Set/Get the propagation image. By default, if no PropagationImage has been set, it casts the input image and uses it in the term contribution calculation. */ + /** @ITKStartGrouping */ itkSetObjectMacro(PropagationImage, PropagationImageType); itkGetModifiableObjectMacro(PropagationImage, PropagationImageType); - + /** @ITKEndGrouping */ /** \todo to be documented. */ void Update() override @@ -135,10 +136,12 @@ class ITK_TEMPLATE_EXPORT LevelSetEquationPropagationTerm : public LevelSetEquat /** Returns the term contribution for a given location iP, i.e. * \f$ \omega_i( p ) \f$. */ + /** @ITKStartGrouping */ LevelSetOutputRealType Value(const LevelSetInputIndexType & iP) override; LevelSetOutputRealType Value(const LevelSetInputIndexType & iP, const LevelSetDataType & iData) override; + /** @ITKEndGrouping */ }; } // namespace itk diff --git a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationTermBase.h b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationTermBase.h index 83e6481f5c5..7acb00a6ccc 100644 --- a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationTermBase.h +++ b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationTermBase.h @@ -85,9 +85,10 @@ class ITK_TEMPLATE_EXPORT LevelSetEquationTermBase : public Object using HeavisideConstPointer = typename HeavisideType::ConstPointer; /** Set/Get the image to be segmented */ + /** @ITKStartGrouping */ itkSetObjectMacro(Input, InputImageType); itkGetModifiableObjectMacro(Input, InputImageType); - + /** @ITKEndGrouping */ itkSetMacro(Coefficient, LevelSetOutputRealType); itkGetMacro(Coefficient, LevelSetOutputRealType); @@ -127,9 +128,10 @@ class ITK_TEMPLATE_EXPORT LevelSetEquationTermBase : public Object itkGetConstMacro(CFLContribution, LevelSetOutputRealType); /** Set/Get the term name */ + /** @ITKStartGrouping */ itkSetStringMacro(TermName); itkGetStringMacro(TermName); - + /** @ITKEndGrouping */ /** Update the term parameter values at end of iteration */ virtual void Update() = 0; diff --git a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationTermContainer.h b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationTermContainer.h index 77a87cd6486..e1819a00c4b 100644 --- a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationTermContainer.h +++ b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEquationTermContainer.h @@ -78,9 +78,10 @@ class ITK_TEMPLATE_EXPORT LevelSetEquationTermContainer : public Object using TermPointer = typename TermType::Pointer; /** Set/Get the input image to be segmented. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Input, InputImageType); itkGetModifiableObjectMacro(Input, InputImageType); - + /** @ITKEndGrouping */ itkSetMacro(CurrentLevelSetId, LevelSetIdentifierType); itkGetMacro(CurrentLevelSetId, LevelSetIdentifierType); diff --git a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEvolutionBase.h b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEvolutionBase.h index 66f303be02a..06764bd0db8 100644 --- a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEvolutionBase.h +++ b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetEvolutionBase.h @@ -94,21 +94,24 @@ class ITK_TEMPLATE_EXPORT LevelSetEvolutionBase : public Object itkGetModifiableObjectMacro(LevelSetContainer, LevelSetContainerType); /** Set/Get the value of alpha for computing the time-step using CFL conditions */ + /** @ITKStartGrouping */ itkSetMacro(Alpha, LevelSetOutputRealType); itkGetMacro(Alpha, LevelSetOutputRealType); - + /** @ITKEndGrouping */ /** Set a user-specified value of the time-step */ void SetTimeStep(const LevelSetOutputRealType & iDt); /** Set/Get the equation container for updating all the level sets */ + /** @ITKStartGrouping */ itkSetObjectMacro(EquationContainer, EquationContainerType); itkGetModifiableObjectMacro(EquationContainer, EquationContainerType); - + /** @ITKEndGrouping */ /** Set/Get the Stopping Criterion */ + /** @ITKStartGrouping */ itkSetObjectMacro(StoppingCriterion, StoppingCriterionType); itkGetModifiableObjectMacro(StoppingCriterion, StoppingCriterionType); - + /** @ITKEndGrouping */ /** Get the number of iterations that have occurred. */ itkGetConstMacro(NumberOfIterations, IdentifierType); diff --git a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetSparseImage.h b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetSparseImage.h index be670c98cf6..bf6b4aead11 100644 --- a/Modules/Segmentation/LevelSetsv4/include/itkLevelSetSparseImage.h +++ b/Modules/Segmentation/LevelSetsv4/include/itkLevelSetSparseImage.h @@ -99,10 +99,11 @@ class ITK_TEMPLATE_EXPORT LevelSetSparseImage : public DiscreteLevelSetImage; @@ -237,12 +245,16 @@ class ITK_TEMPLATE_EXPORT RGBGibbsPriorFilter : public MRFImageFilter m_LabelStatus{ nullptr }; @@ -266,26 +283,34 @@ class ITK_TEMPLATE_EXPORT RGBGibbsPriorFilter : public MRFImageFilter m_Region{ nullptr }; + /** Used for erasing regions. */ std::unique_ptr m_RegionCount{ nullptr }; @@ -293,14 +318,19 @@ class ITK_TEMPLATE_EXPORT RGBGibbsPriorFilter : public MRFImageFilter; /** Set Upper and Lower Threshold inputs as values */ + /** @ITKStartGrouping */ virtual void SetUpper(InputImagePixelType); virtual void SetLower(InputImagePixelType); - + /** @ITKEndGrouping */ /** Set Threshold inputs that are connected to the pipeline */ + /** @ITKStartGrouping */ virtual void SetUpperInput(const InputPixelObjectType *); virtual void SetLowerInput(const InputPixelObjectType *); - + /** @ITKEndGrouping */ /** Get Upper and Lower Threshold inputs as values. */ + /** @ITKStartGrouping */ virtual InputImagePixelType GetUpper() const; virtual InputImagePixelType GetLower() const; - + /** @ITKEndGrouping */ /** Get Threshold inputs that are connected to the pipeline. */ + /** @ITKStartGrouping */ virtual InputPixelObjectType * GetUpperInput(); virtual InputPixelObjectType * GetLowerInput(); - + /** @ITKEndGrouping */ /** Image dimension constants. */ static constexpr unsigned int InputImageDimension = TInputImage::ImageDimension; static constexpr unsigned int OutputImageDimension = TOutputImage::ImageDimension; @@ -168,9 +173,10 @@ class ITK_TEMPLATE_EXPORT ConnectedThresholdImageFilter : public ImageToImageFil /** Type of connectivity to use (fully connected OR 4(2D), 6(3D), * 2*N(ND) connectivity). */ + /** @ITKStartGrouping */ itkSetEnumMacro(Connectivity, ConnectedThresholdImageFilterEnums::Connectivity); itkGetEnumMacro(Connectivity, ConnectedThresholdImageFilterEnums::Connectivity); - + /** @ITKEndGrouping */ protected: ConnectedThresholdImageFilter(); ~ConnectedThresholdImageFilter() override = default; diff --git a/Modules/Segmentation/RegionGrowing/include/itkIsolatedConnectedImageFilter.h b/Modules/Segmentation/RegionGrowing/include/itkIsolatedConnectedImageFilter.h index 72737ac745f..6d563f0e7de 100644 --- a/Modules/Segmentation/RegionGrowing/include/itkIsolatedConnectedImageFilter.h +++ b/Modules/Segmentation/RegionGrowing/include/itkIsolatedConnectedImageFilter.h @@ -84,6 +84,7 @@ class ITK_TEMPLATE_EXPORT IsolatedConnectedImageFilter : public ImageToImageFilt itkNewMacro(Self); /** \see LightObject::GetNameOfClass() */ + /** @ITKStartGrouping */ itkOverrideGetNameOfClassMacro(IsolatedConnectedImageFilter); using InputImageType = TInputImage; using InputImagePointer = typename InputImageType::Pointer; @@ -92,7 +93,7 @@ class ITK_TEMPLATE_EXPORT IsolatedConnectedImageFilter : public ImageToImageFilt using InputImagePixelType = typename InputImageType::PixelType; using IndexType = typename InputImageType::IndexType; using SizeType = typename InputImageType::SizeType; - + /** @ITKEndGrouping */ using OutputImageType = TOutputImage; using OutputImagePointer = typename OutputImageType::Pointer; using OutputImageRegionType = typename OutputImageType::RegionType; @@ -142,21 +143,24 @@ class ITK_TEMPLATE_EXPORT IsolatedConnectedImageFilter : public ImageToImageFilt ClearSeeds2(); /** Method to access seed container */ + /** @ITKStartGrouping */ virtual const SeedsContainerType & GetSeeds1() const; virtual const SeedsContainerType & GetSeeds2() const; - + /** @ITKEndGrouping */ /** Set/Get the limit on the lower threshold value. The default is * the NonpositiveMin() for the InputPixelType. */ + /** @ITKStartGrouping */ itkSetMacro(Lower, InputImagePixelType); itkGetConstReferenceMacro(Lower, InputImagePixelType); - + /** @ITKEndGrouping */ /** Set/Get the limit on the upper threshold value. The default is * the max() for the InputPixelType. */ + /** @ITKStartGrouping */ itkSetMacro(Upper, InputImagePixelType); itkGetConstReferenceMacro(Upper, InputImagePixelType); - + /** @ITKEndGrouping */ #if !defined(ITK_LEGACY_REMOVE) /** \deprecated * Set/Get the limit on the upper threshold value. The default is @@ -177,24 +181,27 @@ class ITK_TEMPLATE_EXPORT IsolatedConnectedImageFilter : public ImageToImageFilt /** Set/Get the precision required for the intensity threshold * value. The default is 1. */ + /** @ITKStartGrouping */ itkSetMacro(IsolatedValueTolerance, InputImagePixelType); itkGetConstReferenceMacro(IsolatedValueTolerance, InputImagePixelType); - + /** @ITKEndGrouping */ /** Set/Get value to replace thresholded pixels. Pixels that lie * within the thresholds will be replaced with this value. The * default is 1. */ + /** @ITKStartGrouping */ itkSetMacro(ReplaceValue, OutputImagePixelType); itkGetConstReferenceMacro(ReplaceValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** Get value that isolates the two seeds. */ itkGetConstReferenceMacro(IsolatedValue, InputImagePixelType); /** Set/Get whether to find an upper threshold (separating two dark * regions) or a lower threshold (separating two bright regions). */ + /** @ITKStartGrouping */ itkSetMacro(FindUpperThreshold, bool); itkBooleanMacro(FindUpperThreshold); itkGetConstReferenceMacro(FindUpperThreshold, bool); - + /** @ITKEndGrouping */ /** Get the flag that tells whether the algorithm failed to find a * threshold. */ itkGetConstReferenceMacro(ThresholdingFailed, bool); diff --git a/Modules/Segmentation/RegionGrowing/include/itkNeighborhoodConnectedImageFilter.h b/Modules/Segmentation/RegionGrowing/include/itkNeighborhoodConnectedImageFilter.h index f1765bcc7bb..4049de080cd 100644 --- a/Modules/Segmentation/RegionGrowing/include/itkNeighborhoodConnectedImageFilter.h +++ b/Modules/Segmentation/RegionGrowing/include/itkNeighborhoodConnectedImageFilter.h @@ -79,20 +79,23 @@ class ITK_TEMPLATE_EXPORT NeighborhoodConnectedImageFilter : public ImageToImage AddSeed(const IndexType & seed); /** Set/Get the lower threshold. The default is 0. */ + /** @ITKStartGrouping */ itkSetMacro(Lower, InputImagePixelType); itkGetConstMacro(Lower, InputImagePixelType); - + /** @ITKEndGrouping */ /** Set/Get the upper threshold. The default is the largest possible * value for the InputPixelType. */ + /** @ITKStartGrouping */ itkSetMacro(Upper, InputImagePixelType); itkGetConstMacro(Upper, InputImagePixelType); - + /** @ITKEndGrouping */ /** Set/Get value to replace thresholded pixels. Pixels that lie * * within Lower and Upper (inclusive) will be replaced with this * value. The default is 1. */ + /** @ITKStartGrouping */ itkSetMacro(ReplaceValue, OutputImagePixelType); itkGetConstMacro(ReplaceValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** Set the radius of the neighborhood used for a mask. */ itkSetMacro(Radius, InputImageSizeType); diff --git a/Modules/Segmentation/RegionGrowing/include/itkVectorConfidenceConnectedImageFilter.h b/Modules/Segmentation/RegionGrowing/include/itkVectorConfidenceConnectedImageFilter.h index 41da92563de..ce9a5e0d485 100644 --- a/Modules/Segmentation/RegionGrowing/include/itkVectorConfidenceConnectedImageFilter.h +++ b/Modules/Segmentation/RegionGrowing/include/itkVectorConfidenceConnectedImageFilter.h @@ -112,22 +112,26 @@ class ITK_TEMPLATE_EXPORT VectorConfidenceConnectedImageFilter : public ImageToI /** Set/Get the multiplier to define the confidence interval. Multiplier * can be anything greater than zero. A typical value is 2.5 */ + /** @ITKStartGrouping */ itkSetMacro(Multiplier, double); itkGetConstMacro(Multiplier, double); - + /** @ITKEndGrouping */ /** Set/Get the number of iterations */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfIterations, unsigned int); itkGetConstMacro(NumberOfIterations, unsigned int); - + /** @ITKEndGrouping */ /** Set/Get value to replace thresholded pixels */ + /** @ITKStartGrouping */ itkSetMacro(ReplaceValue, OutputImagePixelType); itkGetConstMacro(ReplaceValue, OutputImagePixelType); - + /** @ITKEndGrouping */ /** Get/Set the radius of the neighborhood over which the statistics are evaluated */ + /** @ITKStartGrouping */ itkSetMacro(InitialNeighborhoodRadius, unsigned int); itkGetConstReferenceMacro(InitialNeighborhoodRadius, unsigned int); - + /** @ITKEndGrouping */ /** Get the Mean Vector computed during the segmentation */ const MeanVectorType & GetMean() const; diff --git a/Modules/Segmentation/SignedDistanceFunction/include/itkPCAShapeSignedDistanceFunction.h b/Modules/Segmentation/SignedDistanceFunction/include/itkPCAShapeSignedDistanceFunction.h index feabd367c43..56a86e87b45 100644 --- a/Modules/Segmentation/SignedDistanceFunction/include/itkPCAShapeSignedDistanceFunction.h +++ b/Modules/Segmentation/SignedDistanceFunction/include/itkPCAShapeSignedDistanceFunction.h @@ -132,8 +132,10 @@ class ITK_TEMPLATE_EXPORT PCAShapeSignedDistanceFunction itkGetConstMacro(NumberOfPrincipalComponents, unsigned int); /** Set/Get the mean image. */ + /** @ITKStartGrouping */ itkSetObjectMacro(MeanImage, ImageType); itkGetModifiableObjectMacro(MeanImage, ImageType); + /** @ITKEndGrouping */ /** Set/Get the principal component images. */ void @@ -146,12 +148,16 @@ class ITK_TEMPLATE_EXPORT PCAShapeSignedDistanceFunction /** Set/Get the principal component standard deviations. These values corresponds * to the square root of the eigenvalues of the principal components. */ + /** @ITKStartGrouping */ itkSetMacro(PrincipalComponentStandardDeviations, ParametersType); itkGetConstMacro(PrincipalComponentStandardDeviations, ParametersType); + /** @ITKEndGrouping */ /** Set/Get transform. */ + /** @ITKStartGrouping */ itkSetObjectMacro(Transform, TransformType); itkGetModifiableObjectMacro(Transform, TransformType); + /** @ITKEndGrouping */ /** A PCAShape is defined by a set of shape and pose parameters. */ void diff --git a/Modules/Segmentation/Voronoi/include/itkVoronoiPartitioningImageFilter.h b/Modules/Segmentation/Voronoi/include/itkVoronoiPartitioningImageFilter.h index 9aee52dfc50..50804a788a5 100644 --- a/Modules/Segmentation/Voronoi/include/itkVoronoiPartitioningImageFilter.h +++ b/Modules/Segmentation/Voronoi/include/itkVoronoiPartitioningImageFilter.h @@ -75,9 +75,10 @@ class ITK_TEMPLATE_EXPORT VoronoiPartitioningImageFilter * homogeneous. If the standard deviation of the intensities in the * Voronoi region is below this threshold, then the region is * considered homogeneous. */ + /** @ITKStartGrouping */ itkSetMacro(SigmaThreshold, double); itkGetConstMacro(SigmaThreshold, double); - + /** @ITKEndGrouping */ /** ImageDimension enumeration */ static constexpr unsigned int InputImageDimension = TInputImage::ImageDimension; static constexpr unsigned int OutputImageDimension = TOutputImage::ImageDimension; diff --git a/Modules/Segmentation/Voronoi/include/itkVoronoiSegmentationImageFilter.h b/Modules/Segmentation/Voronoi/include/itkVoronoiSegmentationImageFilter.h index 851754bb749..f1d5907662e 100644 --- a/Modules/Segmentation/Voronoi/include/itkVoronoiSegmentationImageFilter.h +++ b/Modules/Segmentation/Voronoi/include/itkVoronoiSegmentationImageFilter.h @@ -73,18 +73,21 @@ class ITK_TEMPLATE_EXPORT VoronoiSegmentationImageFilter using typename Superclass::InputImageType; /** Set/Get the Estimation of the mean pixel value for the object. */ + /** @ITKStartGrouping */ itkSetMacro(Mean, double); itkGetConstMacro(Mean, double); - + /** @ITKEndGrouping */ /** Set/Get the estimation of the STD of the pixel value for the * object. */ + /** @ITKStartGrouping */ itkSetMacro(STD, double); itkGetConstMacro(STD, double); - + /** @ITKEndGrouping */ /** Set/Get the Tolerance of Mean for classifying the regions. */ + /** @ITKStartGrouping */ itkSetMacro(MeanTolerance, double); itkGetConstMacro(MeanTolerance, double); - + /** @ITKEndGrouping */ /** Set the Tolerance of STD for classifying the regions. */ itkSetMacro(STDTolerance, double); @@ -98,10 +101,11 @@ class ITK_TEMPLATE_EXPORT VoronoiSegmentationImageFilter itkGetConstMacro(MeanPercentError, double); /** Set/Get the STD percent error. */ + /** @ITKStartGrouping */ itkGetConstMacro(STDPercentError, double); void SetSTDPercentError(double x); - + /** @ITKEndGrouping */ /** Take a prior from other segmentation node, should be an * binary object. */ void diff --git a/Modules/Segmentation/Voronoi/include/itkVoronoiSegmentationImageFilterBase.h b/Modules/Segmentation/Voronoi/include/itkVoronoiSegmentationImageFilterBase.h index 65d4b0701e6..fc01316d360 100644 --- a/Modules/Segmentation/Voronoi/include/itkVoronoiSegmentationImageFilterBase.h +++ b/Modules/Segmentation/Voronoi/include/itkVoronoiSegmentationImageFilterBase.h @@ -108,17 +108,23 @@ class ITK_TEMPLATE_EXPORT VoronoiSegmentationImageFilterBase : public ImageToIma using VDImagePointer = typename VDImage::Pointer; /** Set/Get the initial number of seeds for VD. */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfSeeds, int); itkGetConstMacro(NumberOfSeeds, int); + /** @ITKEndGrouping */ /** Set/Get the smallest region to be divided. */ + /** @ITKStartGrouping */ itkSetMacro(MinRegion, SizeValueType); itkGetConstMacro(MinRegion, SizeValueType); + /** @ITKEndGrouping */ /** Set/Get the number of iterations to run (if set to 0: the classification * run process runs until no more cells can be divided). */ + /** @ITKStartGrouping */ itkSetMacro(Steps, int); itkGetConstMacro(Steps, int); + /** @ITKEndGrouping */ /** Get the number of seeds before adding new ones. */ itkGetConstMacro(LastStepSeeds, int); @@ -127,26 +133,36 @@ class ITK_TEMPLATE_EXPORT VoronoiSegmentationImageFilterBase : public ImageToIma itkGetConstMacro(NumberOfSeedsToAdded, int); /** */ + /** @ITKStartGrouping */ itkSetMacro(UseBackgroundInAPrior, bool); itkGetConstMacro(UseBackgroundInAPrior, bool); + /** @ITKEndGrouping */ /** Enable the generation of the output boundary. */ + /** @ITKStartGrouping */ itkSetMacro(OutputBoundary, bool); itkGetConstMacro(OutputBoundary, bool); + /** @ITKEndGrouping */ /** Output the segmentation on every iteration. Useful for interactive sessions. The setting of OutputBoundary determines the type of output. */ + /** @ITKStartGrouping */ itkSetMacro(InteractiveSegmentation, bool); itkGetConstMacro(InteractiveSegmentation, bool); itkBooleanMacro(InteractiveSegmentation); + /** @ITKEndGrouping */ /** Set/Get the mean deviation. */ + /** @ITKStartGrouping */ itkSetMacro(MeanDeviation, double); itkGetConstMacro(MeanDeviation, double); + /** @ITKEndGrouping */ /** Set/Get the region size. */ + /** @ITKStartGrouping */ itkSetMacro(Size, SizeType); itkGetConstMacro(Size, SizeType); + /** @ITKEndGrouping */ /** Take a prior from other segmentation node. This should be a * binary object. */ @@ -187,7 +203,6 @@ class ITK_TEMPLATE_EXPORT VoronoiSegmentationImageFilterBase : public ImageToIma m_NumberOfSeeds = num; m_WorkingVD->SetSeeds(num, begin); } - #endif /** Seeds positions are randomly set. diff --git a/Modules/Segmentation/Voronoi/include/itkVoronoiSegmentationRGBImageFilter.h b/Modules/Segmentation/Voronoi/include/itkVoronoiSegmentationRGBImageFilter.h index 76c4351624d..ea8555f5e35 100644 --- a/Modules/Segmentation/Voronoi/include/itkVoronoiSegmentationRGBImageFilter.h +++ b/Modules/Segmentation/Voronoi/include/itkVoronoiSegmentationRGBImageFilter.h @@ -77,6 +77,7 @@ class ITK_TEMPLATE_EXPORT VoronoiSegmentationRGBImageFilter using RGBHCVImage = Image; /** \todo Document. */ + /** @ITKStartGrouping */ void SetMeanPercentError(const double x[6]); void @@ -145,13 +146,14 @@ class ITK_TEMPLATE_EXPORT VoronoiSegmentationRGBImageFilter x[i] = m_STDTolerance[i]; } } - + /** @ITKEndGrouping */ /** Maximum value of the RGB, needed for color space conversions. * default as 8 bit per channel, if it is different, need to be * set before doing anything. */ + /** @ITKStartGrouping */ itkSetMacro(MaxValueOfRGB, double); itkGetConstMacro(MaxValueOfRGB, double); - + /** @ITKEndGrouping */ /** Set the three channels to test the mean and STD respectively * 0:red, 1:green, 2:blue, 3:hue, 4:chroma, 5:value. */ void diff --git a/Modules/Segmentation/Watersheds/include/itkIsolatedWatershedImageFilter.h b/Modules/Segmentation/Watersheds/include/itkIsolatedWatershedImageFilter.h index 82bc1180be9..e7a15d19ffc 100644 --- a/Modules/Segmentation/Watersheds/include/itkIsolatedWatershedImageFilter.h +++ b/Modules/Segmentation/Watersheds/include/itkIsolatedWatershedImageFilter.h @@ -80,37 +80,43 @@ class ITK_TEMPLATE_EXPORT IsolatedWatershedImageFilter : public ImageToImageFilt /** Set seed point 1. This seed will be isolated from Seed2 (if * possible). All pixels connected to this seed will be replaced * with ReplaceValue1. */ + /** @ITKStartGrouping */ itkSetMacro(Seed1, IndexType); itkGetConstMacro(Seed1, IndexType); - + /** @ITKEndGrouping */ /** Set seed point 2. This seed will be isolated from Seed1 (if * possible). All pixels connected to this seed will be replaced * with ReplaceValue2. */ + /** @ITKStartGrouping */ itkSetMacro(Seed2, IndexType); itkGetConstMacro(Seed2, IndexType); - + /** @ITKEndGrouping */ /** Set/Get the Watershed threshold. The default is 0. */ + /** @ITKStartGrouping */ itkSetMacro(Threshold, double); itkGetConstMacro(Threshold, double); - + /** @ITKEndGrouping */ /** Set/Get the precision required for the intensity threshold * value. The default is .001. */ + /** @ITKStartGrouping */ itkSetMacro(IsolatedValueTolerance, double); itkGetConstMacro(IsolatedValueTolerance, double); - + /** @ITKEndGrouping */ /** Set/Get the limit on the upper waterlevel value. The default is * 1.0. */ + /** @ITKStartGrouping */ itkSetMacro(UpperValueLimit, double); itkGetConstMacro(UpperValueLimit, double); - + /** @ITKEndGrouping */ /** Set/Get value to replace Seed1(Seed2) pixels, pixels that are * within the basin that contains Seed1(Seed2) this value. The * default is 1(0). */ + /** @ITKStartGrouping */ itkSetMacro(ReplaceValue1, OutputImagePixelType); itkGetConstMacro(ReplaceValue1, OutputImagePixelType); itkSetMacro(ReplaceValue2, OutputImagePixelType); itkGetConstMacro(ReplaceValue2, OutputImagePixelType); - + /** @ITKEndGrouping */ /** Get value that isolates the two seeds. */ itkGetConstMacro(IsolatedValue, double); diff --git a/Modules/Segmentation/Watersheds/include/itkMorphologicalWatershedFromMarkersImageFilter.h b/Modules/Segmentation/Watersheds/include/itkMorphologicalWatershedFromMarkersImageFilter.h index 6e1a976f3f4..4170b724e7e 100644 --- a/Modules/Segmentation/Watersheds/include/itkMorphologicalWatershedFromMarkersImageFilter.h +++ b/Modules/Segmentation/Watersheds/include/itkMorphologicalWatershedFromMarkersImageFilter.h @@ -147,19 +147,21 @@ class ITK_TEMPLATE_EXPORT MorphologicalWatershedFromMarkersImageFilter * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ /** * Set/Get whether the watershed pixel must be marked or not. Default * is true. Set it to false do not only avoid writing watershed pixels, * it also decrease algorithm complexity. */ + /** @ITKStartGrouping */ itkSetMacro(MarkWatershedLine, bool); itkGetConstReferenceMacro(MarkWatershedLine, bool); itkBooleanMacro(MarkWatershedLine); - + /** @ITKEndGrouping */ protected: MorphologicalWatershedFromMarkersImageFilter(); ~MorphologicalWatershedFromMarkersImageFilter() override = default; diff --git a/Modules/Segmentation/Watersheds/include/itkMorphologicalWatershedImageFilter.h b/Modules/Segmentation/Watersheds/include/itkMorphologicalWatershedImageFilter.h index 4b05438a8df..7990143cf93 100644 --- a/Modules/Segmentation/Watersheds/include/itkMorphologicalWatershedImageFilter.h +++ b/Modules/Segmentation/Watersheds/include/itkMorphologicalWatershedImageFilter.h @@ -89,24 +89,27 @@ class ITK_TEMPLATE_EXPORT MorphologicalWatershedImageFilter : public ImageToImag * FullyConnectedOff. For objects that are 1 pixel wide, use * FullyConnectedOn. */ + /** @ITKStartGrouping */ itkSetMacro(FullyConnected, bool); itkGetConstReferenceMacro(FullyConnected, bool); itkBooleanMacro(FullyConnected); - + /** @ITKEndGrouping */ /** * Set/Get whether the watershed pixel must be marked or not. Default * is true. Set it to false do not only avoid writing watershed pixels, * it also decrease algorithm complexity. */ + /** @ITKStartGrouping */ itkSetMacro(MarkWatershedLine, bool); itkGetConstReferenceMacro(MarkWatershedLine, bool); itkBooleanMacro(MarkWatershedLine); - + /** @ITKEndGrouping */ /** */ + /** @ITKStartGrouping */ itkSetMacro(Level, InputImagePixelType); itkGetConstMacro(Level, InputImagePixelType); - + /** @ITKEndGrouping */ protected: MorphologicalWatershedImageFilter(); ~MorphologicalWatershedImageFilter() override = default; diff --git a/Modules/Segmentation/Watersheds/include/itkOneWayEquivalencyTable.h b/Modules/Segmentation/Watersheds/include/itkOneWayEquivalencyTable.h index 8b5dda6cf59..8b61ef92955 100644 --- a/Modules/Segmentation/Watersheds/include/itkOneWayEquivalencyTable.h +++ b/Modules/Segmentation/Watersheds/include/itkOneWayEquivalencyTable.h @@ -50,13 +50,14 @@ class ITKWatersheds_EXPORT OneWayEquivalencyTable : public DataObject ITK_DISALLOW_COPY_AND_MOVE(OneWayEquivalencyTable); /** Standard type alias and smart pointer declarations. */ + /** @ITKStartGrouping */ using Self = OneWayEquivalencyTable; using Superclass = DataObject; using Pointer = SmartPointer; using ConstPointer = SmartPointer; itkNewMacro(Self); itkOverrideGetNameOfClassMacro(OneWayEquivalencyTable); - + /** @ITKEndGrouping */ /** Define the container type for this table */ using HashTableType = std::unordered_map; diff --git a/Modules/Segmentation/Watersheds/include/itkWatershedBoundary.h b/Modules/Segmentation/Watersheds/include/itkWatershedBoundary.h index 9eae38490a6..be74e274d4c 100644 --- a/Modules/Segmentation/Watersheds/include/itkWatershedBoundary.h +++ b/Modules/Segmentation/Watersheds/include/itkWatershedBoundary.h @@ -74,6 +74,7 @@ class ITK_TEMPLATE_EXPORT Boundary : public DataObject /** Data type stored at each pixel in a face. */ struct face_pixel_t { + /**Index of the direction of watershed flow through this pixel. * A negative value indicates that the flow does not move out * of the region. A positive value is the index into the @@ -97,6 +98,7 @@ class ITK_TEMPLATE_EXPORT Boundary : public DataObject /** */ struct flat_region_t { + /** Indices into the associated Face containing boundary pixels. These * give access to spatial information, label and flow associated with * this boundary pixel connection. */ @@ -124,13 +126,14 @@ class ITK_TEMPLATE_EXPORT Boundary : public DataObject /** Itk type alias and macros defining smart pointer and type identification. */ + /** @ITKStartGrouping */ using Self = Boundary; using Superclass = DataObject; using Pointer = SmartPointer; using ConstPointer = SmartPointer; itkNewMacro(Self); itkOverrideGetNameOfClassMacro(Boundary); - + /** @ITKEndGrouping */ /** The following averts an internal compiler error on microsoft compilers */ using FacePointer = typename face_t::Pointer; @@ -176,6 +179,7 @@ class ITK_TEMPLATE_EXPORT Boundary : public DataObject } /** Get/Set the table of flat region connections specified by the index. */ + /** @ITKStartGrouping */ flat_hash_t * GetFlatHash(const IndexType & idx) { @@ -210,11 +214,13 @@ class ITK_TEMPLATE_EXPORT Boundary : public DataObject } this->Modified(); } + /** @ITKEndGrouping */ /** Marks a face in the boundary object as either valid (true) or * invalid (false). A valid face is assumed to be initialized * and contain information. No assumptions are made about an * invalid face. */ + /** @ITKStartGrouping */ void SetValid(bool & l, const IndexType & idx) { @@ -249,6 +255,7 @@ class ITK_TEMPLATE_EXPORT Boundary : public DataObject return m_Valid[dimension].second; } + /** @ITKEndGrouping */ protected: Boundary(); diff --git a/Modules/Segmentation/Watersheds/include/itkWatershedBoundaryResolver.h b/Modules/Segmentation/Watersheds/include/itkWatershedBoundaryResolver.h index a8106600fa1..76d77186c09 100644 --- a/Modules/Segmentation/Watersheds/include/itkWatershedBoundaryResolver.h +++ b/Modules/Segmentation/Watersheds/include/itkWatershedBoundaryResolver.h @@ -68,13 +68,14 @@ class ITK_TEMPLATE_EXPORT BoundaryResolver : public ProcessObject ITK_DISALLOW_COPY_AND_MOVE(BoundaryResolver); /** Set up smart pointer and object factory definitions. */ + /** @ITKStartGrouping */ using Self = BoundaryResolver; using Superclass = ProcessObject; using Pointer = SmartPointer; using ConstPointer = SmartPointer; itkNewMacro(Self); itkOverrideGetNameOfClassMacro(BoundaryResolver); - + /** @ITKEndGrouping */ /** Expose the image dimension at run time. */ static constexpr unsigned int ImageDimension = TDimension; @@ -86,6 +87,7 @@ class ITK_TEMPLATE_EXPORT BoundaryResolver : public ProcessObject using DataObjectPointer = DataObject::Pointer; /** Set/Get the first of two boundaries that are to be resolved. */ + /** @ITKStartGrouping */ void SetBoundaryA(BoundaryType * bd) { @@ -96,8 +98,9 @@ class ITK_TEMPLATE_EXPORT BoundaryResolver : public ProcessObject { return static_cast(this->GetInput(0)); } - + /** @ITKEndGrouping */ /** Set/Get the second of two boundaries that are to be resolved. */ + /** @ITKStartGrouping */ void SetBoundaryB(BoundaryType * bd) { @@ -108,15 +111,17 @@ class ITK_TEMPLATE_EXPORT BoundaryResolver : public ProcessObject { return static_cast(this->GetInput(1)); } - + /** @ITKEndGrouping */ /** Set/Get the face of the boundary object that we are going to * resolve. */ + /** @ITKStartGrouping */ itkSetMacro(Face, unsigned short); itkGetConstMacro(Face, unsigned short); - + /** @ITKEndGrouping */ /** This method sets/gets the equivalency table used to store equivalencies * among segments that are generated from the boundary resolution * algorithm. */ + /** @ITKStartGrouping */ void SetEquivalencyTable(EquivalencyTableType::Pointer a) { @@ -127,7 +132,7 @@ class ITK_TEMPLATE_EXPORT BoundaryResolver : public ProcessObject { return static_cast(this->ProcessObject::GetOutput(0)); } - + /** @ITKEndGrouping */ /** Standard non-threaded pipeline method */ void GenerateData() override; diff --git a/Modules/Segmentation/Watersheds/include/itkWatershedEquivalenceRelabeler.h b/Modules/Segmentation/Watersheds/include/itkWatershedEquivalenceRelabeler.h index 7791797322d..8885d437438 100644 --- a/Modules/Segmentation/Watersheds/include/itkWatershedEquivalenceRelabeler.h +++ b/Modules/Segmentation/Watersheds/include/itkWatershedEquivalenceRelabeler.h @@ -69,12 +69,14 @@ class ITK_TEMPLATE_EXPORT EquivalenceRelabeler : public ProcessObject using DataObjectPointer = DataObject::Pointer; /** Define smart pointers for this object. */ + /** @ITKStartGrouping */ using Pointer = SmartPointer; using ConstPointer = SmartPointer; itkNewMacro(Self); itkOverrideGetNameOfClassMacro(EquivalenceRelabeler); - + /** @ITKEndGrouping */ /** Set/Get the image to relabel. */ + /** @ITKStartGrouping */ void SetInputImage(ImageType * img) { @@ -85,7 +87,7 @@ class ITK_TEMPLATE_EXPORT EquivalenceRelabeler : public ProcessObject { return static_cast(this->ProcessObject::GetInput(0)); } - + /** @ITKEndGrouping */ /** Set/Get the output image */ void SetOutputImage(ImageType * img) diff --git a/Modules/Segmentation/Watersheds/include/itkWatershedMiniPipelineProgressCommand.h b/Modules/Segmentation/Watersheds/include/itkWatershedMiniPipelineProgressCommand.h index edf6b6eef87..bb137d0d1c8 100644 --- a/Modules/Segmentation/Watersheds/include/itkWatershedMiniPipelineProgressCommand.h +++ b/Modules/Segmentation/Watersheds/include/itkWatershedMiniPipelineProgressCommand.h @@ -35,13 +35,14 @@ class ITKWatersheds_EXPORT WatershedMiniPipelineProgressCommand : public Command { public: /** Smart pointer declaration methods */ + /** @ITKStartGrouping */ using Self = WatershedMiniPipelineProgressCommand; using Superclass = Command; using Pointer = itk::SmartPointer; using ConstPointer = itk::SmartPointer; itkOverrideGetNameOfClassMacro(WatershedMiniPipelineProgressCommand); itkNewMacro(Self); - + /** @ITKEndGrouping */ /** Standard Command virtual methods */ void Execute(Object * caller, const EventObject & event) override; @@ -51,6 +52,7 @@ class ITKWatersheds_EXPORT WatershedMiniPipelineProgressCommand : public Command /** Set/Get the filter whose UpdateProgress will be set by this * command object */ + /** @ITKStartGrouping */ void SetFilter(ProcessObject * p) { @@ -61,16 +63,18 @@ class ITKWatersheds_EXPORT WatershedMiniPipelineProgressCommand : public Command { return m_Filter; } - + /** @ITKEndGrouping */ /** Set/Get the base count for stepping through filter progress values */ + /** @ITKStartGrouping */ itkSetMacro(Count, double); itkGetConstMacro(Count, double); - + /** @ITKEndGrouping */ /** Set/Get the number of filters that this command will expect to be * observing */ + /** @ITKStartGrouping */ itkSetMacro(NumberOfFilters, unsigned int); itkGetConstMacro(NumberOfFilters, unsigned int); - + /** @ITKEndGrouping */ protected: WatershedMiniPipelineProgressCommand() = default; ~WatershedMiniPipelineProgressCommand() override = default; diff --git a/Modules/Segmentation/Watersheds/include/itkWatershedRelabeler.h b/Modules/Segmentation/Watersheds/include/itkWatershedRelabeler.h index d933ac4e74c..e2441251483 100644 --- a/Modules/Segmentation/Watersheds/include/itkWatershedRelabeler.h +++ b/Modules/Segmentation/Watersheds/include/itkWatershedRelabeler.h @@ -72,9 +72,10 @@ class ITK_TEMPLATE_EXPORT Relabeler : public ProcessObject using ConstPointer = SmartPointer; /** Method for creation through the object factory. */ + /** @ITKStartGrouping */ itkNewMacro(Self); itkOverrideGetNameOfClassMacro(Relabeler); - + /** @ITKEndGrouping */ /** Expose the ImageDimension template parameter at run time */ static constexpr unsigned int ImageDimension = TImageDimension; @@ -136,9 +137,10 @@ class ITK_TEMPLATE_EXPORT Relabeler : public ProcessObject /** Set/Get the percentage of the maximum saliency level * to merge to. */ + /** @ITKStartGrouping */ itkSetClampMacro(FloodLevel, double, 0.0, 1.0); itkGetConstMacro(FloodLevel, double); - + /** @ITKEndGrouping */ /** Standard ProcessObject method used in implementing mini-pipelines */ void GraftOutput(ImageType * graft); diff --git a/Modules/Segmentation/Watersheds/include/itkWatershedSegmentTable.h b/Modules/Segmentation/Watersheds/include/itkWatershedSegmentTable.h index 36aadbd9089..2bf39c72ea2 100644 --- a/Modules/Segmentation/Watersheds/include/itkWatershedSegmentTable.h +++ b/Modules/Segmentation/Watersheds/include/itkWatershedSegmentTable.h @@ -236,6 +236,7 @@ class ITK_TEMPLATE_EXPORT SegmentTable : public DataObject /** Set/Get the maximum depth of image on which this segment table is based. * (Should set really be calling modified? jc 11/16/01) */ + /** @ITKStartGrouping */ void SetMaximumDepth(ScalarType s) { @@ -248,6 +249,7 @@ class ITK_TEMPLATE_EXPORT SegmentTable : public DataObject { return m_MaximumDepth; } + /** @ITKEndGrouping */ /** Copies the contents of another segment table into this segment table. This is really operator= in disguise, although superclass information is diff --git a/Modules/Segmentation/Watersheds/include/itkWatershedSegmentTree.h b/Modules/Segmentation/Watersheds/include/itkWatershedSegmentTree.h index cd46c04b246..6ede5f0dfdb 100644 --- a/Modules/Segmentation/Watersheds/include/itkWatershedSegmentTree.h +++ b/Modules/Segmentation/Watersheds/include/itkWatershedSegmentTree.h @@ -51,6 +51,7 @@ class ITK_TEMPLATE_EXPORT SegmentTree : public DataObject ITK_DISALLOW_COPY_AND_MOVE(SegmentTree); /** Define itk Smart Pointers for this object */ + /** @ITKStartGrouping */ using Self = SegmentTree; using Superclass = DataObject; using Pointer = SmartPointer; @@ -59,6 +60,7 @@ class ITK_TEMPLATE_EXPORT SegmentTree : public DataObject itkOverrideGetNameOfClassMacro(SegmentTree); using ScalarType = TScalar; + /** @ITKEndGrouping */ /** Elements of the list (nodes of the tree). A record of a merge * between two segments (IdentifierType labels) at a particular * saliency. */ diff --git a/Modules/Segmentation/Watersheds/include/itkWatershedSegmentTreeGenerator.h b/Modules/Segmentation/Watersheds/include/itkWatershedSegmentTreeGenerator.h index 5def73e8915..e9c26e6be73 100644 --- a/Modules/Segmentation/Watersheds/include/itkWatershedSegmentTreeGenerator.h +++ b/Modules/Segmentation/Watersheds/include/itkWatershedSegmentTreeGenerator.h @@ -87,9 +87,10 @@ class ITK_TEMPLATE_EXPORT SegmentTreeGenerator : public ProcessObject using ConstPointer = SmartPointer; /** Method for creation through the object factory. */ + /** @ITKStartGrouping */ itkNewMacro(Self); itkOverrideGetNameOfClassMacro(SegmentTreeGenerator); - + /** @ITKEndGrouping */ /** Convenient type definitions */ using ScalarType = TScalar; using SegmentTableType = SegmentTable; @@ -152,9 +153,10 @@ class ITK_TEMPLATE_EXPORT SegmentTreeGenerator : public ProcessObject segments marked as equivalent in the EquivalencyTable. This is only useful for streaming applications and is turned off by default. (TRUE == merge, FALSE == do not merge). */ + /** @ITKStartGrouping */ itkSetMacro(Merge, bool); itkGetConstMacro(Merge, bool); - + /** @ITKEndGrouping */ /** Get/Set FloodLevel. FloodLevel is specified as a percentage (0.0 - 1.0) of the maximum possible saliency value in the initial image from which the segment table was derived. A value of 0.0 calculates no merges. A value of @@ -168,17 +170,19 @@ class ITK_TEMPLATE_EXPORT SegmentTreeGenerator : public ProcessObject /** Get/Set HighestCalculatedFloodLevel. HighestCalculatedFloodLevel keeps * track of the highest level this filter has computed. It is * used to prevent unnecessary re-execution of the filter. */ + /** @ITKStartGrouping */ itkSetMacro(HighestCalculatedFloodLevel, double); itkGetConstMacro(HighestCalculatedFloodLevel, double); - + /** @ITKEndGrouping */ /** Get/Set a flag that prevents the filter from copying its input * segment table before executing. This can be enabled to conserve * memory, especially in streaming applications where memory is a * concern. If enabled, the input to this filter must always be * re-executed on updates. Default is false. */ + /** @ITKStartGrouping */ itkSetMacro(ConsumeInput, bool); itkGetConstMacro(ConsumeInput, bool); - + /** @ITKEndGrouping */ /** Performs a merge of two segments in a SegmentTable according * to criteria specific to this algorithm. */ static void diff --git a/Modules/Segmentation/Watersheds/include/itkWatershedSegmenter.h b/Modules/Segmentation/Watersheds/include/itkWatershedSegmenter.h index 6e5e814e60f..0aec958be32 100644 --- a/Modules/Segmentation/Watersheds/include/itkWatershedSegmenter.h +++ b/Modules/Segmentation/Watersheds/include/itkWatershedSegmenter.h @@ -107,11 +107,13 @@ class ITK_TEMPLATE_EXPORT Segmenter : public ProcessObject /** Methods to implement smart pointers and work with the itk object factory */ + /** @ITKStartGrouping */ using Superclass = ProcessObject; using Pointer = SmartPointer; using ConstPointer = SmartPointer; itkNewMacro(Self); itkOverrideGetNameOfClassMacro(Segmenter); + /** @ITKEndGrouping */ /** Typedefs necessary on microsoft VC++ to avoid internal compiler errors */ using InputImageTypePointer = typename InputImageType::Pointer; @@ -190,6 +192,7 @@ class ITK_TEMPLATE_EXPORT Segmenter : public ProcessObject * complete volume being streamed. The member variables controlled by * this method will not be modified by the Itk pipeline and are necessary * for analysis of boundaries. */ + /** @ITKStartGrouping */ void SetLargestPossibleRegion(ImageRegionType reg) { @@ -206,6 +209,7 @@ class ITK_TEMPLATE_EXPORT Segmenter : public ProcessObject { return m_LargestPossibleRegion; } + /** @ITKEndGrouping */ /** Helper function. Other classes may have occasion to use this. Relabels an image according to a table of equivalencies. */ @@ -219,8 +223,10 @@ class ITK_TEMPLATE_EXPORT Segmenter : public ProcessObject /** Gets/Sets the initial label (IdentifierType integer value) used * by the labeling algorithm. Only necessary for streaming applications. */ + /** @ITKStartGrouping */ itkSetMacro(CurrentLabel, IdentifierType); itkGetConstMacro(CurrentLabel, IdentifierType); + /** @ITKEndGrouping */ /** Gets/Sets the input threshold. Threshold is specified as a percentage * (0.0 - 1.0) of the maximum height of the image. This filter thresholds the @@ -232,22 +238,27 @@ class ITK_TEMPLATE_EXPORT Segmenter : public ProcessObject * segmentation with fewer segments. The assumption is that the "shallow" * regions that this thresholding eliminates are generally not of * interest. */ + /** @ITKStartGrouping */ itkSetClampMacro(Threshold, double, 0.0, 1.0); itkGetConstMacro(Threshold, double); + /** @ITKEndGrouping */ /** Turns on special labeling of the boundaries for streaming applications. * The default value is FALSE, meaning that boundary analysis is turned * off. */ + /** @ITKStartGrouping */ itkSetMacro(DoBoundaryAnalysis, bool); itkGetConstMacro(DoBoundaryAnalysis, bool); + /** @ITKEndGrouping */ /** Determines whether the algorithm will sort the adjacencies in its * SegmentTable before returning. Default is true. This is an option only * useful for streaming applications where the sorting only needs to be done * after all iterations have taken place. */ + /** @ITKStartGrouping */ itkGetConstMacro(SortEdgeLists, bool); itkSetMacro(SortEdgeLists, bool); - + /** @ITKEndGrouping */ protected: /** Structure storing information about image flat regions. * Flat regions are connected pixels of the same value. */ diff --git a/Modules/Video/Core/include/itkImageToVideoFilter.h b/Modules/Video/Core/include/itkImageToVideoFilter.h index cd0eaacf615..e0e5de91d6c 100644 --- a/Modules/Video/Core/include/itkImageToVideoFilter.h +++ b/Modules/Video/Core/include/itkImageToVideoFilter.h @@ -99,9 +99,10 @@ class ITK_TEMPLATE_EXPORT ImageToVideoFilter : public VideoSource(m_DataObjectBuffer.GetPointer()); } - + /** @ITKEndGrouping */ /** Set the internal pixel buffer */ void SetFrameBuffer(BufferType * buffer); /** Provide access to the internal caches for the meta data */ + /** @ITKStartGrouping */ const SpatialRegionMapType & GetLargestPossibleSpatialRegionCache() const { @@ -125,7 +127,7 @@ class ITK_TEMPLATE_EXPORT VideoStream : public TemporalDataObject { m_LargestPossibleSpatialRegionCache = map; } - + /** @ITKEndGrouping */ const SpatialRegionMapType & GetRequestedSpatialRegionCache() const { @@ -200,11 +202,12 @@ class ITK_TEMPLATE_EXPORT VideoStream : public TemporalDataObject * Head of the ring buffer in place and just use the frame number as an * offset. This allows all references to frames to be processed by an * explicit frame number rather than a potentially confusing offset. */ + /** @ITKStartGrouping */ FrameType * GetFrame(SizeValueType frameNumber); const FrameType * GetFrame(SizeValueType frameNumber) const; - + /** @ITKEndGrouping */ /** Get/Set the LargestPossibleRegion of a frame */ void SetFrameLargestPossibleSpatialRegion(SizeValueType frameNumber, SpatialRegionType region); diff --git a/Modules/Video/Filtering/include/itkDecimateFramesVideoFilter.h b/Modules/Video/Filtering/include/itkDecimateFramesVideoFilter.h index f32e60c90c8..4ca6e7037ae 100644 --- a/Modules/Video/Filtering/include/itkDecimateFramesVideoFilter.h +++ b/Modules/Video/Filtering/include/itkDecimateFramesVideoFilter.h @@ -57,16 +57,18 @@ class ITK_TEMPLATE_EXPORT DecimateFramesVideoFilter : public VideoToVideoFilter< itkOverrideGetNameOfClassMacro(DecimateFramesVideoFilter); /** Get/Set the spacing of the preserved frames */ + /** @ITKStartGrouping */ void SetPreservedFrameSpacing(SizeValueType numFrames); SizeValueType GetPreservedFrameSpacing(); - + /** @ITKEndGrouping */ protected: /** Constructor and Destructor */ + /** @ITKStartGrouping */ DecimateFramesVideoFilter(); ~DecimateFramesVideoFilter() override = default; - + /** @ITKEndGrouping */ /** PrintSelf */ void PrintSelf(std::ostream & os, Indent indent) const override; diff --git a/Modules/Video/Filtering/include/itkFrameAverageVideoFilter.h b/Modules/Video/Filtering/include/itkFrameAverageVideoFilter.h index 1b51d7eebed..add6cc64268 100644 --- a/Modules/Video/Filtering/include/itkFrameAverageVideoFilter.h +++ b/Modules/Video/Filtering/include/itkFrameAverageVideoFilter.h @@ -59,16 +59,18 @@ class ITK_TEMPLATE_EXPORT FrameAverageVideoFilter : public VideoToVideoFilter); /** Override SetFileName to do parsing. */ + /** @ITKStartGrouping */ void SetFileName(const std::string & fileList) override; void SetFileName(const char * fileList) override; - + /** @ITKEndGrouping */ /** Close the reader and writer and reset members. */ void FinishReadingOrWriting() override; @@ -107,6 +108,7 @@ class ITKVideoIO_EXPORT FileListVideoIO : public VideoIOBase SetNextFrameToRead(FrameOffsetType frameNumber) override; /** Accessor functions for video specific information. */ + /** @ITKStartGrouping */ TemporalOffsetType GetPositionInMSec() const override { @@ -138,7 +140,7 @@ class ITKVideoIO_EXPORT FileListVideoIO : public VideoIOBase { return this->m_LastIFrame; } - + /** @ITKEndGrouping */ /** Override accessors to pass through to internal image reader. */ double GetSpacing(unsigned int i) const override; diff --git a/Modules/Video/IO/include/itkVideoFileReader.h b/Modules/Video/IO/include/itkVideoFileReader.h index 03b0008fb57..876aa48a647 100644 --- a/Modules/Video/IO/include/itkVideoFileReader.h +++ b/Modules/Video/IO/include/itkVideoFileReader.h @@ -77,15 +77,17 @@ class ITK_TEMPLATE_EXPORT VideoFileReader : public VideoSourceAll ITK Sphinx Examples ^^" "sphinxexample{2}=\\li \\2 ^^" - "endsphinx=^^ ^^ ^^") + "endsphinx=^^ ^^ ^^" + "ITKStartGrouping=@{" + "ITKEndGrouping=@}") set(DOXYGEN_TOC_INCLUDE_HEADINGS "0") set(DOXYGEN_BUILTIN_STL_SUPPORT "YES") set(DOXYGEN_DISTRIBUTE_GROUP_DOC "YES") @@ -52,9 +54,6 @@ set(DOXYGEN_EXAMPLE_PATH "${DOXYGEN_TEST_DIRS}") set(DOXYGEN_EXAMPLE_PATTERNS "*.cxx") set(DOXYGEN_EXAMPLE_RECURSIVE "YES") set(DOXYGEN_IMAGE_PATH "${ITK_SOURCE_DIR}/Documentation/Art" "${ITK_BINARY_DIR}/Utilities/Doxygen/Modules") -set(DOXYGEN_FILTER_PATTERNS - "*.h=${ITK_DOXYGEN_INPUT_FILTER}" - "*.cxx=${ITK_DOXYGEN_INPUT_FILTER}") set(DOXYGEN_FILTER_SOURCE_FILES "YES") set(DOXYGEN_SOURCE_BROWSER "YES") set(DOXYGEN_REFERENCED_BY_RELATION "YES") diff --git a/Utilities/Doxygen/itkgroup.py b/Utilities/Doxygen/itkgroup.py deleted file mode 100755 index 2ef1cd6aa66..00000000000 --- a/Utilities/Doxygen/itkgroup.py +++ /dev/null @@ -1,89 +0,0 @@ -#!/usr/bin/env python -# -# Copyright NumFOCUS -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# https://www.apache.org/licenses/LICENSE-2.0.txt -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -""" -Usage: itkgroup.py " - -Processes the input filename and prints to stdout. - -The file has additional Doxygen grouping markers to doxygen comment blocks, where the block does not contain an empty - line. This groups multiple functions or variables not separated by a newline, into a single doxygen group allowing - the same doxyen comment to apply to all of them. - -""" - - -import re -import sys - -ingroup = False -semicount = 0 -endbracecount = 0 -endparencount = 0 -leading_space = " " -savebuffer = "" - - -def process_line(line: str): - global ingroup, semicount, endbracecount, endparencount, leading_space, savebuffer - - line = line.rstrip() - if re.search(r"\S+", line): - match = re.search(r"/\*\*(.*)", line) - if match: - if ingroup: - print(f"{leading_space}/**{savebuffer}") - if re.search(r"(\\class|\\brief)", line): - print(line) - else: - savebuffer = f"{match.group(1)}\n" - ingroup = True - semicount = 0 - endbracecount = 0 - endparencount = 0 - leading_space = re.match(r"(^\s*)", line).group(1) - else: - if ingroup: - savebuffer += f"{line}\n" - else: - print(line) - if re.search(r";", line): - semicount += 1 - if re.search(r"\}", line): - endbracecount += 1 - if re.search(r"\)", line): - endparencount += 1 - else: - if ingroup: - if endparencount > 1 and (semicount > 1 or endbracecount > 1): - print(f"{leading_space}/**@{{{savebuffer}{leading_space}/**@}}*/\n") - else: - print(f"{leading_space}/**{savebuffer}") - savebuffer = "" - ingroup = False - else: - print(line) - - -if __name__ == "__main__": - if len(sys.argv) != 2: - print("Usage: python itkgroup.py ") - sys.exit(1) - - filename = sys.argv[1] - with open(filename) as file: - for line in file: - process_line(line) diff --git a/Wrapping/DoxygenConfig.cmake b/Wrapping/DoxygenConfig.cmake index 9b2514512f1..c3ef74f49e9 100644 --- a/Wrapping/DoxygenConfig.cmake +++ b/Wrapping/DoxygenConfig.cmake @@ -52,7 +52,6 @@ set(DOXYGEN_EXAMPLE_PATH "${DOXYGEN_TEST_DIRS}") set(DOXYGEN_EXAMPLE_PATTERNS "*.cxx") set(DOXYGEN_EXAMPLE_RECURSIVE "YES") set(DOXYGEN_IMAGE_PATH "${ITK_SOURCE_DIR}/Documentation/Art" "${ITK_BINARY_DIR}/Utilities/Doxygen/Modules") -set(DOXYGEN_INPUT_FILTER "${ITK_DOXYGEN_INPUT_FILTER}") set(DOXYGEN_FILTER_SOURCE_FILES "YES") set(DOXYGEN_SOURCE_BROWSER "YES") set(DOXYGEN_REFERENCED_BY_RELATION "YES")