Various documentation improvements.

* Add short documentation for Array class
* Put all classes explicitly in Core module (where applicable)
* Section on Modules in Quick Reference Guide
* Put Page 7 after Page 6 in Contents :)

Eigen/src/Core/Array.h

@@ -25,6 +25,20 @@
 #ifndef EIGEN_ARRAY_H
 #define EIGEN_ARRAY_H
 
+/** \class Array 
+  * \ingroup Core_Module
+  *
+  * \brief General-purpose arrays with easy API for coefficient-wise operations
+  *
+  * The %Array class is very similar to the Matrix class. It provides
+  * general-purpose one- and two-dimensional arrays. The difference between the
+  * %Array and the %Matrix class is primarily in the API: the API for the
+  * %Array class provides easy access to coefficient-wise operations, while the
+  * API for the %Matrix class provides easy access to linear-algebra
+  * operations.
+  *
+  * \sa \ref TutorialArrayClass
+  */
 template<typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols>
 struct ei_traits<Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols> > : ei_traits<Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols> >
 {
@@ -231,6 +245,7 @@ class Array
 };
 
 /** \defgroup arraytypedefs Global array typedefs
+  * \ingroup Core_Module
   *
   * Eigen defines several typedef shortcuts for most common 1D and 2D array types.
   *

Eigen/src/Core/ArrayBase.h

@@ -28,6 +28,7 @@
 template<typename ExpressionType> class MatrixWrapper;
 
 /** \class ArrayBase
+  * \ingroup Core_Module
   *
   * \brief Base class for all 1D and 2D array, and related expressions
   *

Eigen/src/Core/ArrayWrapper.h

@@ -26,6 +26,7 @@
 #define EIGEN_ARRAYWRAPPER_H
 
 /** \class ArrayWrapper
+  * \ingroup Core_Module
   *
   * \brief Expression of a mathematical vector or matrix as an array object
   *
@@ -110,6 +111,7 @@ class ArrayWrapper : public ArrayBase<ArrayWrapper<ExpressionType> >
 };
 
 /** \class MatrixWrapper
+  * \ingroup Core_Module
   *
   * \brief Expression of an array as a mathematical vector or matrix
   *

Eigen/src/Core/BandMatrix.h

@@ -27,6 +27,7 @@
 
 /**
   * \class BandMatrix
+  * \ingroup Core_Module
   *
   * \brief Represents a rectangular matrix with a banded storage
   *
@@ -205,6 +206,7 @@ class BandMatrix : public EigenBase<BandMatrix<_Scalar,Rows,Cols,Supers,Subs,Opt
 
 /**
   * \class TridiagonalMatrix
+  * \ingroup Core_Module
   *
   * \brief Represents a tridiagonal matrix
   *

Eigen/src/Core/Block.h

@@ -27,6 +27,7 @@
 #define EIGEN_BLOCK_H
 
 /** \class Block
+  * \ingroup Core_Module
   *
   * \brief Expression of a fixed-size or dynamic-size block
   *

Eigen/src/Core/CommaInitializer.h

@@ -27,6 +27,7 @@
 #define EIGEN_COMMAINITIALIZER_H
 
 /** \class CommaInitializer
+  * \ingroup Core_Module
   *
   * \brief Helper class used by the comma initializer operator
   *

Eigen/src/Core/CwiseBinaryOp.h

@@ -27,6 +27,7 @@
 #define EIGEN_CWISE_BINARY_OP_H
 
 /** \class CwiseBinaryOp
+  * \ingroup Core_Module
   *
   * \brief Generic expression where a coefficient-wise binary operator is applied to two expressions
   *

Eigen/src/Core/CwiseNullaryOp.h

@@ -26,6 +26,7 @@
 #define EIGEN_CWISE_NULLARY_OP_H
 
 /** \class CwiseNullaryOp
+  * \ingroup Core_Module
   *
   * \brief Generic expression of a matrix where all coefficients are defined by a functor
   *

Eigen/src/Core/CwiseUnaryOp.h

@@ -27,6 +27,7 @@
 #define EIGEN_CWISE_UNARY_OP_H
 
 /** \class CwiseUnaryOp
+  * \ingroup Core_Module
   *
   * \brief Generic expression where a coefficient-wise unary operator is applied to an expression
   *

Eigen/src/Core/CwiseUnaryView.h

@@ -26,6 +26,7 @@
 #define EIGEN_CWISE_UNARY_VIEW_H
 
 /** \class CwiseUnaryView
+  * \ingroup Core_Module
   *
   * \brief Generic lvalue expression of a coefficient-wise unary operator of a matrix or a vector
   *

Eigen/src/Core/DenseBase.h

@@ -27,6 +27,7 @@
 #define EIGEN_DENSEBASE_H
 
 /** \class DenseBase
+  * \ingroup Core_Module
   *
   * \brief Base class for all dense matrices, vectors, and arrays
   *

Eigen/src/Core/Diagonal.h

@@ -26,6 +26,7 @@
 #define EIGEN_DIAGONAL_H
 
 /** \class Diagonal
+  * \ingroup Core_Module
   *
   * \brief Expression of a diagonal/subdiagonal/superdiagonal in a matrix
   *

Eigen/src/Core/DiagonalMatrix.h

@@ -87,6 +87,7 @@ void DiagonalBase<Derived>::evalTo(MatrixBase<DenseDerived> &other) const
 #endif
 
 /** \class DiagonalMatrix
+  * \ingroup Core_Module
   *
   * \brief Represents a diagonal matrix with its storage
   *
@@ -188,6 +189,7 @@ class DiagonalMatrix
 };
 
 /** \class DiagonalWrapper
+  * \ingroup Core_Module
   *
   * \brief Expression of a diagonal matrix
   *

Eigen/src/Core/Flagged.h

@@ -26,6 +26,7 @@
 #define EIGEN_FLAGGED_H
 
 /** \class Flagged
+  * \ingroup Core_Module
   *
   * \brief Expression with modified flags
   *

Eigen/src/Core/ForceAlignedAccess.h

@@ -26,6 +26,7 @@
 #define EIGEN_FORCEALIGNEDACCESS_H
 
 /** \class ForceAlignedAccess
+  * \ingroup Core_Module
   *
   * \brief Enforce aligned packet loads and stores regardless of what is requested
   *

Eigen/src/Core/IO.h

@@ -31,6 +31,7 @@ enum { StreamPrecision = -1,
        FullPrecision = -2 };
 
 /** \class IOFormat
+  * \ingroup Core_Module
   *
   * \brief Stores a set of parameters controlling the way matrices are printed
   *
@@ -80,6 +81,7 @@ struct IOFormat
 };
 
 /** \class WithFormat
+  * \ingroup Core_Module
   *
   * \brief Pseudo expression providing matrix output with given format
   *

Eigen/src/Core/Map.h

@@ -27,6 +27,7 @@
 #define EIGEN_MAP_H
 
 /** \class Map
+  * \ingroup Core_Module
   *
   * \brief A matrix or vector expression mapping an existing array of data.
   *

Eigen/src/Core/MapBase.h

@@ -27,6 +27,7 @@
 #define EIGEN_MAPBASE_H
 
 /** \class MapBase
+  * \ingroup Core_Module
   *
   * \brief Base class for Map and Block expression with direct access
   *

Eigen/src/Core/Matrix.h

@@ -27,6 +27,7 @@
 #define EIGEN_MATRIX_H
 
 /** \class Matrix
+  * \ingroup Core_Module
   *
   * \brief The matrix class, also used for vectors and row-vectors
   *

Eigen/src/Core/MatrixBase.h

@@ -27,6 +27,7 @@
 #define EIGEN_MATRIXBASE_H
 
 /** \class MatrixBase
+  * \ingroup Core_Module
   *
   * \brief Base class for all dense matrices, vectors, and expressions
   *

Eigen/src/Core/MatrixStorage.h

@@ -79,6 +79,7 @@ struct ei_matrix_array<T, 0, MatrixOptions, Alignment>
 /** \internal
   *
   * \class ei_matrix_storage
+  * \ingroup Core_Module
   *
   * \brief Stores the data of a matrix
   *

Eigen/src/Core/NestByValue.h

@@ -27,6 +27,7 @@
 #define EIGEN_NESTBYVALUE_H
 
 /** \class NestByValue
+  * \ingroup Core_Module
   *
   * \brief Expression which must be nested by value
   *

Eigen/src/Core/NoAlias.h

@@ -26,6 +26,7 @@
 #define EIGEN_NOALIAS_H
 
 /** \class NoAlias
+  * \ingroup Core_Module
   *
   * \brief Pseudo expression providing an operator = assuming no aliasing
   *

Eigen/src/Core/NumTraits.h

@@ -26,6 +26,7 @@
 #define EIGEN_NUMTRAITS_H
 
 /** \class NumTraits
+  * \ingroup Core_Module
   *
   * \brief Holds information about the various numeric (i.e. scalar) types allowed by Eigen.
   *

Eigen/src/Core/PermutationMatrix.h

@@ -27,6 +27,7 @@
 #define EIGEN_PERMUTATIONMATRIX_H
 
 /** \class PermutationMatrix
+  * \ingroup Core_Module
   *
   * \brief Permutation matrix
   *

Eigen/src/Core/Product.h

@@ -27,6 +27,7 @@
 #define EIGEN_PRODUCT_H
 
 /** \class GeneralProduct
+  * \ingroup Core_Module
   *
   * \brief Expression of the product of two general matrices or vectors
   *
@@ -120,6 +121,7 @@ template<>              struct ei_product_type_selector<Small,Large,Small>  { en
 template<>              struct ei_product_type_selector<Large,Large,Small>  { enum { ret = GemmProduct }; };
 
 /** \class ProductReturnType
+  * \ingroup Core_Module
   *
   * \brief Helper class to get the correct and optimized returned type of operator*
   *

Eigen/src/Core/ProductBase.h

@@ -26,6 +26,7 @@
 #define EIGEN_PRODUCTBASE_H
 
 /** \class ProductBase
+  * \ingroup Core_Module
   *
   */
 template<typename Derived, typename _Lhs, typename _Rhs>

Eigen/src/Core/Replicate.h

@@ -27,6 +27,7 @@
 
 /**
   * \class Replicate
+  * \ingroup Core_Module
   *
   * \brief Expression of the multiple replication of a matrix or vector
   *

Eigen/src/Core/ReturnByValue.h

@@ -27,6 +27,7 @@
 #define EIGEN_RETURNBYVALUE_H
 
 /** \class ReturnByValue
+  * \ingroup Core_Module
   *
   */
 template<typename Derived>

Eigen/src/Core/Reverse.h

@@ -28,6 +28,7 @@
 #define EIGEN_REVERSE_H
 
 /** \class Reverse
+  * \ingroup Core_Module
   *
   * \brief Expression of the reverse of a vector or matrix
   *

Eigen/src/Core/Select.h

@@ -26,6 +26,7 @@
 #define EIGEN_SELECT_H
 
 /** \class Select
+  * \ingroup Core_Module
   *
   * \brief Expression of a coefficient wise version of the C++ ternary operator ?:
   *

Eigen/src/Core/SelfAdjointView.h

@@ -26,6 +26,7 @@
 #define EIGEN_SELFADJOINTMATRIX_H
 
 /** \class SelfAdjointView
+  * \ingroup Core_Module
   *
   *
   * \brief Expression of a selfadjoint matrix from a triangular part of a dense matrix

Eigen/src/Core/SelfCwiseBinaryOp.h

@@ -26,6 +26,7 @@
 #define EIGEN_SELFCWISEBINARYOP_H
 
 /** \class SelfCwiseBinaryOp
+  * \ingroup Core_Module
   *
   * \internal
   *

Eigen/src/Core/Stride.h

@@ -26,6 +26,7 @@
 #define EIGEN_STRIDE_H
 
 /** \class Stride
+  * \ingroup Core_Module
   *
   * \brief Holds strides information for Map
   *

Eigen/src/Core/Swap.h

@@ -26,6 +26,7 @@
 #define EIGEN_SWAP_H
 
 /** \class SwapWrapper
+  * \ingroup Core_Module
   *
   * \internal
   *

Eigen/src/Core/Transpose.h

@@ -27,6 +27,7 @@
 #define EIGEN_TRANSPOSE_H
 
 /** \class Transpose
+  * \ingroup Core_Module
   *
   * \brief Expression of the transpose of a matrix
   *

Eigen/src/Core/Transpositions.h

@@ -26,6 +26,7 @@
 #define EIGEN_TRANSPOSITIONS_H
 
 /** \class Transpositions
+  * \ingroup Core_Module
   *
   * \brief Represents a sequence of transpositions (row/column interchange)
   *

Eigen/src/Core/TriangularMatrix.h

@@ -29,6 +29,7 @@
 /** \internal
   *
   * \class TriangularBase
+  * \ingroup Core_Module
   *
   * \brief Base class for triangular part in a matrix
   */
@@ -112,6 +113,7 @@ template<typename Derived> class TriangularBase : public EigenBase<Derived>
 };
 
 /** \class TriangularView
+  * \ingroup Core_Module
   *
   * \brief Base class for triangular part in a matrix
   *

Eigen/src/Core/VectorBlock.h

@@ -27,6 +27,7 @@
 #define EIGEN_VECTORBLOCK_H
 
 /** \class VectorBlock
+  * \ingroup Core_Module
   *
   * \brief Expression of a fixed-size or dynamic-size sub-vector
   *

Eigen/src/Core/VectorwiseOp.h

@@ -27,6 +27,7 @@
 #define EIGEN_PARTIAL_REDUX_H
 
 /** \class PartialReduxExpr
+  * \ingroup Core_Module
   *
   * \brief Generic expression of a partially reduxed matrix
   *
@@ -154,6 +155,7 @@ struct ei_member_redux {
 };
 
 /** \class VectorwiseOp
+  * \ingroup Core_Module
   *
   * \brief Pseudo expression providing partial reduction operations
   *

Eigen/src/Core/util/Constants.h

@@ -38,7 +38,7 @@ const int Dynamic = -1;
   */
 const int Infinity = -1;
 
-/** \defgroup flags flags
+/** \defgroup flags Flags
   * \ingroup Core_Module
   *
   * These are the possible bits which can be OR'ed to constitute the flags of a matrix or

Eigen/src/Core/util/Memory.h

@@ -495,6 +495,7 @@ inline static Index ei_first_aligned(const Scalar* array, Index size)
 /****************************************************************************/
 
 /** \class aligned_allocator
+* \ingroup Core_Module
 *
 * \brief STL compatible allocator to use with with 16 byte aligned types
 *

doc/Overview.dox

@@ -23,8 +23,8 @@ For a first contact with Eigen, the best place is to have a look at the \ref Get
     - \ref TutorialArrayClass
     - \ref TutorialBlockOperations
     - \ref TutorialAdvancedInitialization
-    - Coming soon: "Reductions, visitors, and broadcasting"
     - \ref TutorialLinearAlgebra
+    - Coming soon: "Reductions, visitors, and broadcasting"
     - \ref TutorialGeometry
     - \ref TutorialSparse
   - \ref QuickRefPage

doc/QuickReference.dox

@@ -18,18 +18,21 @@ namespace Eigen {
 <a href="#" class="top">top</a>
 \section QuickRef_Headers Modules and Header files
 
+The Eigen library is divided in a Core module and several additional modules. Each module has a corresponding header file which has to be included in order to use the module. The \c %Dense and \c Eigen header files are provided to conveniently gain access to several modules at once.
+
 <table class="tutorial_code">
 <tr><td>Module</td><td>Header file</td><td>Contents</td></tr>
-<tr><td>Core</td><td>\code#include <Eigen/Core>\endcode</td><td>Matrix and Array classes, basic linear algebra (including triangular and selfadjoint products), array manipulation</td></tr>
+<tr><td>\link Core_Module Core \endlink</td><td>\code#include <Eigen/Core>\endcode</td><td>Matrix and Array classes, basic linear algebra (including triangular and selfadjoint products), array manipulation</td></tr>
-<tr><td>Geometry</td><td>\code#include <Eigen/Geometry>\endcode</td><td>Transformation, Translation, Scaling, 2D and 3D rotations (Quaternion, AngleAxis)</td></tr>
+<tr><td>\link Geometry_Module Geometry \endlink</td><td>\code#include <Eigen/Geometry>\endcode</td><td>Transform, Translation, Scaling, Rotation2D and 3D rotations (Quaternion, AngleAxis)</td></tr>
-<tr><td>LU</td><td>\code#include <Eigen/LU>\endcode</td><td>Inverse, determinant, LU decompositions (FullPivLU, PartialPivLU) with solver</td></tr>
+<tr><td>\link LU_Module LU \endlink</td><td>\code#include <Eigen/LU>\endcode</td><td>Inverse, determinant, LU decompositions with solver (FullPivLU, PartialPivLU)</td></tr>
-<tr><td>Cholesky</td><td>\code#include <Eigen/Cholesky>\endcode</td><td>LLT and LDLT Cholesky factorization with solver</td></tr>
+<tr><td>\link Cholesky_Module Cholesky \endlink</td><td>\code#include <Eigen/Cholesky>\endcode</td><td>LLT and LDLT Cholesky factorization with solver</td></tr>
-<tr><td>SVD</td><td>\code#include <Eigen/SVD>\endcode</td><td>SVD decomposition with solver (HouseholderSVD, JacobiSVD)</td></tr>
+<tr><td>\link Householder_Module Householder \endlink</td><td>\code#include <Eigen/Householder>\endcode</td><td>Householder transformations; this module is used by several linear algebra modules</td></tr>
-<tr><td>QR</td><td>\code#include <Eigen/QR>\endcode</td><td>QR decomposition with solver (HouseholderQR, ColPivHouseholerQR, FullPivHouseholderQR)</td></tr>
+<tr><td>\link SVD_Module SVD \endlink</td><td>\code#include <Eigen/SVD>\endcode</td><td>%SVD decomposition with solver (SVD, JacobiSVD)</td></tr>
-<tr><td>Eigenvalues</td><td>\code#include <Eigen/Eigenvalues>\endcode</td><td>Eigenvalue, eigenvector decompositions for selfadjoint and non selfadjoint real or complex matrices.</td></tr>
+<tr><td>\link QR_Module QR \endlink</td><td>\code#include <Eigen/QR>\endcode</td><td>QR decomposition with solver (HouseholderQR, ColPivHouseholderQR, FullPivHouseholderQR)</td></tr>
-<tr><td>Sparse</td><td>\code#include <Eigen/Sparse>\endcode</td><td>Sparse matrix storage and related basic linear algebra.</td></tr>
+<tr><td>\link Eigenvalues_Module Eigenvalues \endlink</td><td>\code#include <Eigen/Eigenvalues>\endcode</td><td>Eigenvalue, eigenvector decompositions (EigenSolver, SelfAdjointEigenSolver, ComplexEigenSolver)</td></tr>
-<tr><td></td><td>\code#include <Eigen/Dense>\endcode</td><td>Includes Core, Geometry, LU, Cholesky, SVD, QR, and Eigenvalues</td></tr>
+<tr><td>\link Sparse_Module Sparse \endlink</td><td>\code#include <Eigen/Sparse>\endcode</td><td>%Sparse matrix storage and related basic linear algebra (SparseMatrix, DynamicSparseMatrix, SparseVector)</td></tr>
-<tr><td></td><td>\code#include <Eigen/Eigen>\endcode</td><td>Includes Dense and Sparse</td></tr>
+<tr><td></td><td>\code#include <Eigen/Dense>\endcode</td><td>Includes Core, Geometry, LU, Cholesky, %SVD, QR, and Eigenvalues header files</td></tr>
+<tr><td></td><td>\code#include <Eigen/Eigen>\endcode</td><td>Includes %Dense and %Sparse header files (the whole Eigen library)</td></tr>
 </table>
 
 <a href="#" class="top">top</a>
@@ -486,7 +489,7 @@ Read-write access to sub-vectors:
 <tr><td>\code vec1.head(n)\endcode</td><td>\code vec1.head<n>()\endcode</td><td>the first \c n coeffs </td></tr>
 <tr><td>\code vec1.tail(n)\endcode</td><td>\code vec1.tail<n>()\endcode</td><td>the last \c n coeffs </td></tr>
 <tr><td>\code vec1.segment(pos,n)\endcode</td><td>\code vec1.segment<n>(pos)\endcode</td>
-    <td>the \c size coeffs in \n the range [\c pos : \c pos + \c n [</td></tr>
+    <td>the \c n coeffs in \n the range [\c pos : \c pos + \c n [</td></tr>
 <tr style="border-style: dashed none dashed none;"><td>
 
 Read-write access to sub-matrices:</td><td></td><td></td></tr>

unsupported/Eigen/NumericalDiff

@@ -30,7 +30,7 @@
 namespace Eigen {
 
 /** \ingroup Unsupported_modules
-  * \defgroup NumericalDiff_Module Numerical differenciation module
+  * \defgroup NumericalDiff_Module Numerical differentiation module
   *
   * \code
   * #include <unsupported/Eigen/NumericalDiff>
@@ -51,7 +51,7 @@ namespace Eigen {
   * want to achieve with Eigen.
   *
   * This is why we will not provide wrappers for every great numerical
-  * differenciation software that exist, but should rather stick with those
+  * differentiation software that exist, but should rather stick with those
   * basic ones, that still are useful for testing.
   *
   * Also, the \ref NonLinearOptimization_Module needs this in order to