diff --git a/dox/doxygen/DoxygenFooter.html.in b/dox/doxygen/DoxygenFooter.html.in index eb8c3af84..fbb1be661 100644 --- a/dox/doxygen/DoxygenFooter.html.in +++ b/dox/doxygen/DoxygenFooter.html.in @@ -10,18 +10,6 @@ elastix logo - - - - - diff --git a/dox/doxygen/MainPage.dox.in b/dox/doxygen/MainPage.dox.in index 408a03391..18c117288 100644 --- a/dox/doxygen/MainPage.dox.in +++ b/dox/doxygen/MainPage.dox.in @@ -21,7 +21,7 @@ * Related Pages.

* *

A list of frequently asked questions can be found - * here.

+ * here.

* * \section manual Manual * diff --git a/dox/doxygen/doxyfile.in b/dox/doxygen/doxyfile.in index e0aba21ba..4f184cb3f 100644 --- a/dox/doxygen/doxyfile.in +++ b/dox/doxygen/doxyfile.in @@ -874,7 +874,7 @@ RECURSIVE = YES # Note that relative paths are relative to the directory from which doxygen is # run. -EXCLUDE = "@elastix_SOURCE_DIR@/Common/KNN/ann_1.1" \ +EXCLUDE = "@elastix_SOURCE_DIR@/Components/Metrics/KNNGraphAlphaMutualInformation/KNN/ann_1.1" \ "@elastix_SOURCE_DIR@/Components/Transforms/AffineDTITransform/itkAffineDTITransform.h" \ "@elastix_SOURCE_DIR@/Components/Transforms/EulerTransform/itkEulerTransform.h" \ "@elastix_SOURCE_DIR@/Components/Transforms/SimilarityTransform/itkSimilarityTransform.h" \ @@ -905,24 +905,41 @@ EXCLUDE_PATTERNS = */.svn/* # Note that the wildcards are matched against the file with absolute path, so to # exclude all test directories use the pattern */test/* -EXCLUDE_SYMBOLS = AdaptiveStochasticGradientDescent::SettingsType \ +EXCLUDE_SYMBOLS = AdaGrad::SettingsType \ + AdaptiveStochasticGradientDescent::SettingsType \ + Append \ Command \ DataObject \ *Dispatch \ *DispatchBase \ + DualVisit* \ ExceptionObject \ + EulerGroup* \ GetConstNumberOfWeightsHack* \ + GPUCast \ + GPUMath \ + GPUTraits \ + HasType \ + IndexOf \ KernelFunction \ + Length \ + LightObject \ + MakeTypeList \ MeshSource \ NDImageTemplate::ConvertTo*Array \ + NullType \ Object \ ObjectFactoryBase \ + PixelType \ ProcessObject \ ResamplerBase::ITKBaseType \ Sample \ Transform \ + TypeAt \ + TypeList \ vector \ VectorDataContainer::*Iterator \ + Visit \ xoutbase*::Send # The EXAMPLE_PATH tag can be used to specify one or more files or directories @@ -2173,36 +2190,36 @@ INCLUDE_FILE_PATTERNS = # This tag requires that the tag ENABLE_PREPROCESSING is set to YES. PREDEFINED = "itkNotUsed(x)=" \ - "itkSetMacro(name,type)= virtual void Set##name (type _arg);" \ - "itkGetMacro(name,type)= virtual type Get##name ();" \ - "itkGetConstMacro(name,type)= virtual type Get##name () const;" \ - "itkSetStringMacro(name)= virtual void Set##name (const char* _arg);" \ - "itkGetStringMacro(name)= virtual const char* Get##name () const;" \ - "itkSetClampMacro(name,type,min,max)= virtual void Set##name (type _arg);" \ - "itkSetObjectMacro(name,type)= virtual void Set##name (type* _arg);" \ - "itkGetObjectMacro(name,type)= virtual type* Get##name ();" \ - "itkSetConstObjectMacro(name,type)= virtual void Set##name ( const type* _arg);" \ - "itkGetConstObjectMacro(name,type)= virtual const type* Get##name ();" \ - "itkGetConstReferenceMacro(name,type)= virtual const type& Get##name ();" \ - "itkGetConstReferenceObjectMacro(name,type)= virtual const type::Pointer& Get##name () const;" \ - "itkBooleanMacro(name)= virtual void name##On (); virtual void name##Off ();" \ - "itkSetVector2Macro(name,type)= virtual void Set##name (type _arg1, type _arg2) virtual void Set##name (type _arg[2]);" \ - "itkGetVector2Macro(name,type)= virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2) const; virtual void Get##name (type _arg[2]) const;" \ - "itkSetVector3Macro(name,type)= virtual void Set##name (type _arg1, type _arg2, type _arg3) virtual void Set##name (type _arg[3]);" \ - "itkGetVector3Macro(name,type)= virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2, type& _arg3) const; virtual void Get##name (type _arg[3]) const;" \ - "itkSetVector4Macro(name,type)= virtual void Set##name (type _arg1, type _arg2, type _arg3, type _arg4) virtual void Set##name (type _arg[4]);" \ - "itkGetVector4Macro(name,type)= virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2, type& _arg3, type& _arg4) const; virtual void Get##name (type _arg[4]) const;" \ - "itkSetVector6Macro(name,type)= virtual void Set##name (type _arg1, type _arg2, type _arg3, type _arg4, type _arg5, type _arg6) virtual void Set##name (type _arg[6]);" \ - "itkGetVector6Macro(name,type)= virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2, type& _arg3, type& _arg4, type& _arg5, type& _arg6) const; virtual void Get##name (type _arg[6]) const;" \ - "itkSetVectorMacro(name,type,count)= virtual void Set##name(type data[]);" \ - "itkGetVectorMacro(name,type,count)= virtual type* Get##name () const;" \ - "itkNewMacro(type)= static Pointer New();" \ - "itkTypeMacro(thisClass,superclass)= virtual const char *GetClassName() const;" \ - "itkConceptMacro(name,concept)= enum { name = 0 };" \ - "vcl_numeric_limits= std::numeric_limits" \ - "ITK_TYPENAME= typename" \ - "FEM_ABSTRACT_CLASS(thisClass,parentClass)= public: /** Standard Self typedef.*/ typedef thisClass Self; /** Standard Superclass typedef. */ typedef parentClass Superclass; /** Pointer or SmartPointer to an object. */ typedef Self* Pointer; /** Const pointer or SmartPointer to an object. */ typedef const Self* ConstPointer; private:" \ - "FEM_CLASS(thisClass,parentClass)= FEM_ABSTRACT_CLASS(thisClass,parentClass) public: /** Create a new object from the existing one */ virtual Baseclass::Pointer Clone() const; /** Class ID for FEM object factory */ static const int CLID; /** Virtual function to access the class ID */ virtual int ClassID() const { return CLID; } /** Object creation in an itk compatible way */ static Self::Pointer New() { return new Self(); } private:" \ + "itkSetMacro(name,type)= virtual void Set##name (type _arg);" \ + "itkGetMacro(name,type)= virtual type Get##name ();" \ + "itkGetConstMacro(name,type)= virtual type Get##name () const;" \ + "itkSetStringMacro(name)= virtual void Set##name (const char* _arg);" \ + "itkGetStringMacro(name)= virtual const char* Get##name () const;" \ + "itkSetClampMacro(name,type,min,max)= virtual void Set##name (type _arg);" \ + "itkSetObjectMacro(name,type)= virtual void Set##name (type* _arg);" \ + "itkGetObjectMacro(name,type)= virtual type* Get##name ();" \ + "itkSetConstObjectMacro(name,type)= virtual void Set##name ( const type* _arg);" \ + "itkGetConstObjectMacro(name,type)= virtual const type* Get##name ();" \ + "itkGetConstReferenceMacro(name,type)= virtual const type& Get##name ();" \ + "itkGetConstReferenceObjectMacro(name,type)= virtual const type::Pointer& Get##name () const;" \ + "itkBooleanMacro(name)= virtual void name##On (); virtual void name##Off ();" \ + "itkSetVector2Macro(name,type)= virtual void Set##name (type _arg1, type _arg2) virtual void Set##name (type _arg[2]);" \ + "itkGetVector2Macro(name,type)= virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2) const; virtual void Get##name (type _arg[2]) const;" \ + "itkSetVector3Macro(name,type)= virtual void Set##name (type _arg1, type _arg2, type _arg3) virtual void Set##name (type _arg[3]);" \ + "itkGetVector3Macro(name,type)= virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2, type& _arg3) const; virtual void Get##name (type _arg[3]) const;" \ + "itkSetVector4Macro(name,type)= virtual void Set##name (type _arg1, type _arg2, type _arg3, type _arg4) virtual void Set##name (type _arg[4]);" \ + "itkGetVector4Macro(name,type)= virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2, type& _arg3, type& _arg4) const; virtual void Get##name (type _arg[4]) const;" \ + "itkSetVector6Macro(name,type)= virtual void Set##name (type _arg1, type _arg2, type _arg3, type _arg4, type _arg5, type _arg6) virtual void Set##name (type _arg[6]);" \ + "itkGetVector6Macro(name,type)= virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2, type& _arg3, type& _arg4, type& _arg5, type& _arg6) const; virtual void Get##name (type _arg[6]) const;" \ + "itkSetVectorMacro(name,type,count)= virtual void Set##name(type data[]);" \ + "itkGetVectorMacro(name,type,count)= virtual type* Get##name () const;" \ + "itkNewMacro(type)= static Pointer New();" \ + "itkTypeMacro(thisClass,superclass)= virtual const char *GetClassName() const;" \ + "itkConceptMacro(name,concept)= enum { name = 0 };" \ + "vcl_numeric_limits= std::numeric_limits" \ + "ITK_TYPENAME= typename" \ + "FEM_ABSTRACT_CLASS(thisClass,parentClass)= public: /** Standard Self typedef.*/ typedef thisClass Self; /** Standard Superclass typedef. */ typedef parentClass Superclass; /** Pointer or SmartPointer to an object. */ typedef Self* Pointer; /** Const pointer or SmartPointer to an object. */ typedef const Self* ConstPointer; private:" \ + "FEM_CLASS(thisClass,parentClass)= FEM_ABSTRACT_CLASS(thisClass,parentClass) public: /** Create a new object from the existing one */ virtual Baseclass::Pointer Clone() const; /** Class ID for FEM object factory */ static const int CLID; /** Virtual function to access the class ID */ virtual int ClassID() const { return CLID; } /** Object creation in an itk compatible way */ static Self::Pointer New() { return new Self(); } private:" \ "FREEVERSION" \ "ERROR_CHECKING" \ "HAS_TIFF" \ diff --git a/dox/doxygen/doxygenlayout.xml b/dox/doxygen/doxygenlayout.xml index 4a6312536..b6c675560 100644 --- a/dox/doxygen/doxygenlayout.xml +++ b/dox/doxygen/doxygenlayout.xml @@ -11,7 +11,7 @@ - + @@ -19,7 +19,7 @@ - +