DOC: Use Doxygen automatic class links in module descriptions

Use Doxygen automatic class links in module descriptions: use qualified
class names, and take advantage of the commit to fix the spelling of
some class names.

Fix the `itk::QuadEdgeMeshFunctionBase` class name in its Doxygen class
documentation so that the
- class detailed description is displayed correctly in the ITK Doxygen
  documentation,
- links in the module descriptions point to the proper class

CMake/ITKGroups.cmake

@@ -16,8 +16,8 @@ set(group_list
 
 set(Core_documentation "This group of modules contain the toolkit framework used
 by other modules.  There are common base classes for data objects and process
-objects, basic data structures such as Image, Mesh, QuadEdgeMesh, and
-SpatialObjects, and common functionality for operations such as finite
+objects, basic data structures such as itk::Image, itk::Mesh, itk::QuadEdgeMesh, and
+ik::SpatialObject, and common functionality for operations such as finite
 differences, image adaptors, or image transforms.")
 
 set(Compatibility_documentation "This group contains modules that ease the transition to ITKv4 and Deprecated classes.")

Modules/Core/Common/itk-module.cmake

@@ -1,8 +1,9 @@
 set(DOCUMENTATION "This module contains the central classes of the ITK
-toolkit.  They include, basic data structures \(such as Points, Vectors,
-Images, Regions\) the core of the process objects \(such as base
-classes for image filters\) the pipeline infrastructure classes, the support
-for multi-threading, and a collection of classes that isolate ITK from
+toolkit. They include, basic data structures \(such as points, vectors,
+images, regions: itk::Point, itk::Vector, itk::Image, itk::Region)
+the core of the process objects \(such as base classes for image
+filters\) the pipeline infrastructure classes, the support for
+multi-threading, and a collection of classes that isolate ITK from
 platform specific features. It is anticipated that most other ITK modules will
 depend on this one.")
 

Modules/Core/QuadEdgeMesh/include/itkQuadEdgeMeshFunctionBase.h

@@ -24,11 +24,11 @@
 namespace itk
 {
 /**
- * \class MeshFunctionBase
+ * \class QuadEdgeMeshFunctionBase
  * \ingroup QEMeshModifierFunctions
  * \brief Base class for mesh function object modifiers.
  *
- * MeshFunctionBase is the base class for itkQE function objects specialised
+ * QuadEdgeMeshFunctionBase is the base class for itkQE function objects specialised
  * in Mesh "small" (reduced in range) modification.
  * Subclasses of itk::FunctionBase cannot modify their InputType since
  * the signature of their Evaluate( const InputType& ) method guarantees it.
@@ -39,8 +39,8 @@ namespace itk
  * But for small modifications (think of the Euler operators) that an
  * algorithm needs to apply many times, this systematic duplication can
  * be daunting.
- * MeshFunctionBase thus offers a lightweight alternative to itk Filter.
- * Subclasses of MeshFunctionBase, which should override Evaluate(), are
+ * QuadEdgeMeshFunctionBase thus offers a lightweight alternative to itk Filter.
+ * Subclasses of QuadEdgeMeshFunctionBase, which should override Evaluate(), are
  * function objects that apply reduced and localised modifications
  * (geometry, or connectivity) on the InputType mesh.
  *

Modules/Core/QuadEdgeMesh/itk-module.cmake

@@ -36,21 +36,22 @@ But itk::FunctionBase could not be inherited since its
 itk::FunctionBase::Evaluate method promises to leave its argument (the mesh we
 want to modify in our case) untouched.
 
-Hence the itk::MeshFunctionBase class was created whose main difference with
-itk::FunctionBase is that its itk::MeshFunctionBase::Evaluate method allows
-to modify the considered mesh.
+Hence the itk::QuadEdgeMeshFunctionBase class was created whose main
+difference with itk::FunctionBase is that its
+itk::QuadEdgeMeshFunctionBase::Evaluate method allows to modify the considered
+mesh.
 
 When considering a new QuadEdgeMesh method there are four possible \"slots\"
 to implement it:
-  - The QuadEdgeMesh method.
+  - The itk::QuadEdgeMesh class.
   - A derived class from itk::FunctionBase when the method leaves the mesh
   constant.
-  - A derived class from itk::MeshFunctionBase when the method modifies the
+  - A derived class from itk::QuadEdgeMeshFunctionBase when the method modifies the
   mesh (typically in the case of Euler operators).
   - As a classic ITKMesh filter.
 
 The choice of the slot is a mere matter of trade-off and in order to keep
-QuadEdgeMesh tiny and humanly readable key decision factors can be the
+itk::QuadEdgeMesh tiny and humanly readable key decision factors can be the
 occurrence of the calls and the human level complexity of the code.
 
 With those criteria in mind the following choices were made:

Modules/Core/SpatialObjects/itk-module.cmake

@@ -1,6 +1,6 @@
 set(DOCUMENTATION "SpatialObjects are intended to represent regions in space.
-The basic functionality of a SpatialObject is to answer the question of
-whether a physical point is inside or outside of the SpatialObject. They are
+The basic functionality of an itk::SpatialObject is to answer the question of
+whether a physical point is inside or outside of the itk::SpatialObject. They are
 commonly used for representing masks in an analytical form, as well as
 approximations of shape by combining them into hierarchical structures similar
 to scene graphs.")

Modules/Filtering/FastMarching/itk-module.cmake

@@ -1,6 +1,6 @@
 set(DOCUMENTATION "This module contains implementations of generalized versions
 of the Fast Marching filter. These implementations cover the use of Fast
-Marching in both itk::Images and itk::QuadEdgeMeshes.")
+Marching in both itk::Image and itk::QuadEdgeMesh objects.")
 
 itk_module(ITKFastMarching
   ENABLE_SHARED

Modules/IO/ImageBase/itk-module.cmake

@@ -1,11 +1,11 @@
 set(DOCUMENTATION "This module contains base classes for IO, helper classes for
-IO, and classes that function as an ImageSource in an ITK pipeline.  Classes for
+IO, and classes that function as an ImageSource in an ITK pipeline. Classes for
 specific file formats, found in other modules in the IO group, should inherit
-from ImageIOBase or StreamingImageIOBase.  For an image source or sink in the ITK
+from itk::ImageIOBase or itk::StreamingImageIOBase. For an image source or sink in the ITK
 pipeline that handles all available file formats, see ImageFileReader,
-ImageFileWriter, ImageSeriesReader, or ImageSeriesWriter.  Convenience classes
-for reading series of files include ArchetypeSeriesFileNames,
-NumericSeriesFileNames, and RegularExpressionSeriesFileNames.")
+itk::ImageFileWriter, itk::ImageSeriesReader, or itk::ImageSeriesWriter. Convenience classes
+for reading series of files include itk::ArchetypeSeriesFileNames,
+itk::NumericSeriesFileNames, and itk::RegularExpressionSeriesFileNames.")
 
 itk_module(ITKIOImageBase
   ENABLE_SHARED

Modules/IO/MeshBase/itk-module.cmake

@@ -1,9 +1,9 @@
 set(DOCUMENTATION "This module contains base classes for IO, helper classes for
-IO, and classes that function as an MeshSource in an ITK pipeline.  Classes for
+IO, and classes that function as an itk::MeshSource in an ITK pipeline. Classes for
 specific file formats, found in other modules in the IO group, should inherit
-from MeshIOBase.  For a mesh source or sink in the ITK
-pipeline that handles all available file formats, see MeshFileReader,
-or MeshFileWriter.")
+from itk::MeshIOBase. For a mesh source or sink in the ITK
+pipeline that handles all available file formats, see itk::MeshFileReader,
+or itk::MeshFileWriter.")
 
 itk_module(ITKIOMeshBase
   ENABLE_SHARED

Modules/Numerics/Statistics/itk-module.cmake

@@ -3,7 +3,7 @@ statistical algorithms, and a classification for general statistical analysis
 and classification problems.  This includes, for examples, classes for
 calculating histograms, calculating sample statistics, creating decision rules,
 or for performing statistical pattern classification.  Statistics are calculated
-on a Sample, which contains MeasurementVector's.")
+on an itk::Sample, which contains measurement vectors.")
 
 itk_module(ITKStatistics
   ENABLE_SHARED

Modules/Video/Core/itk-module.cmake

@@ -2,7 +2,8 @@ set(DOCUMENTATION "This module contains base classes for processing data that
 possesses a temporal element. The classes contained in this module extend the
 traditional data object and process objects to handle time properly and also
 contain convenience classes for passing temporal regions and dealing with ITK
-images over time in the form of VideoStreams and VideoToVideoFilters.")
+images over time in the form of itk::VideoStream and itk::VideoToVideoFilter
+objects.")
 
 itk_module(ITKVideoCore
   ENABLE_SHARED

Modules/Video/IO/itk-module.cmake

@@ -1,5 +1,5 @@
 set(DOCUMENTATION "This module contains the basic framework for Video IO as
-well as the FileListIO mechanism that does not depend on any outside
+well as the itk::FileListVideoIO mechanism that does not depend on any outside
 libraries.")
 
 itk_module(ITKVideoIO