Upgraded Eigen 3.2.7 -> 3.2.9

CMakeLists.txt

@@ -19,7 +19,7 @@ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 
 set(EXT_BOOST_ROOT ${CMAKE_CURRENT_SOURCE_DIR}/ext/boost_1_59_0)
-set(EXT_EIGEN_ROOT ${CMAKE_CURRENT_SOURCE_DIR}/ext/eigen-3.2.7)
+set(EXT_EIGEN_ROOT ${CMAKE_CURRENT_SOURCE_DIR}/ext/eigen-3.2.9)
 set(EXT_RAPIDJSON_ROOT ${CMAKE_CURRENT_SOURCE_DIR}/ext/rapidjson/include)
 set(EXT_TCLAP_ROOT ${CMAKE_CURRENT_SOURCE_DIR}/ext/tclap-1.2.1/include)
 

ext/eigen-3.2.9/.hg_archival.txt

@@ -1,4 +1,4 @@
 repo: 8a21fd850624c931e448cbcfb38168cb2717c790
-node: b30b87236a1b1552af32ac34075ee5696a9b5a33
+node: dc6cfdf9bcec5efc7b6593bddbbb3d675de53524
 branch: 3.2
-tag: 3.2.7
+tag: 3.2.9

ext/eigen-3.2.9/.hgtags

@@ -30,3 +30,5 @@ ffa86ffb557094721ca71dcea6aed2651b9fd610 3.2.0
 10219c95fe653d4962aa9db4946f6fbea96dd740 3.2.4
 bdd17ee3b1b3a166cd5ec36dcad4fc1f3faf774a 3.2.5
 c58038c56923e0fd86de3ded18e03df442e66dfb 3.2.6
+b30b87236a1b1552af32ac34075ee5696a9b5a33 3.2.7
+07105f7124f9aef00a68c85e0fc606e65d3d6c15 3.2.8

ext/eigen-3.2.9/CMakeLists.txt

@@ -1,6 +1,5 @@
 project(Eigen)
-
-cmake_minimum_required(VERSION 2.8.2)
+cmake_minimum_required(VERSION 2.8.5)
 
 # guard against in-source builds
 
@@ -55,6 +54,7 @@ endif(EIGEN_HG_CHANGESET)
 
 
 include(CheckCXXCompilerFlag)
+include(GNUInstallDirs)
 
 set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
 
@@ -288,25 +288,26 @@ option(EIGEN_TEST_C++0x "Enables all C++0x features." OFF)
 
 include_directories(${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR})
 
-# the user modifiable install path for header files
-set(EIGEN_INCLUDE_INSTALL_DIR ${EIGEN_INCLUDE_INSTALL_DIR} CACHE PATH "The directory where we install the header files (optional)")
-
-# set the internal install path for header files which depends on wether the user modifiable
-# EIGEN_INCLUDE_INSTALL_DIR has been set by the user or not.
-if(EIGEN_INCLUDE_INSTALL_DIR)
-  set(INCLUDE_INSTALL_DIR
-    ${EIGEN_INCLUDE_INSTALL_DIR}
-    CACHE INTERNAL
-    "The directory where we install the header files (internal)"
-  )
+# Backward compatibility support for EIGEN_INCLUDE_INSTALL_DIR
+if(EIGEN_INCLUDE_INSTALL_DIR AND NOT INCLUDE_INSTALL_DIR)
+  set(INCLUDE_INSTALL_DIR ${EIGEN_INCLUDE_INSTALL_DIR}
+      CACHE PATH "The directory relative to CMAKE_PREFIX_PATH where Eigen header files are installed")
 else()
   set(INCLUDE_INSTALL_DIR
-    "include/eigen3"
-    CACHE INTERNAL
-    "The directory where we install the header files (internal)"
-  )
+      "${CMAKE_INSTALL_INCLUDEDIR}/eigen3"
+      CACHE PATH "The directory relative to CMAKE_PREFIX_PATH where Eigen header files are installed"
+      )
 endif()
 
+set(CMAKEPACKAGE_INSTALL_DIR
+    "${CMAKE_INSTALL_LIBDIR}/cmake/eigen3"
+    CACHE PATH "The directory relative to CMAKE_PREFIX_PATH where Eigen3Config.cmake is installed"
+    )
+set(PKGCONFIG_INSTALL_DIR
+    "${CMAKE_INSTALL_DATADIR}/pkgconfig"
+    CACHE PATH "The directory relative to CMAKE_PREFIX_PATH where eigen3.pc is installed"
+    )
+
 # similar to set_target_properties but append the property instead of overwriting it
 macro(ei_add_target_property target prop value)
 
@@ -324,21 +325,9 @@ install(FILES
   )
 
 if(EIGEN_BUILD_PKGCONFIG)
-    SET(path_separator ":")
-    STRING(REPLACE ${path_separator} ";" pkg_config_libdir_search "$ENV{PKG_CONFIG_LIBDIR}")
-    message(STATUS "searching for 'pkgconfig' directory in PKG_CONFIG_LIBDIR ( $ENV{PKG_CONFIG_LIBDIR} ), ${CMAKE_INSTALL_PREFIX}/share, and ${CMAKE_INSTALL_PREFIX}/lib")
-    FIND_PATH(pkg_config_libdir pkgconfig ${pkg_config_libdir_search} ${CMAKE_INSTALL_PREFIX}/share ${CMAKE_INSTALL_PREFIX}/lib ${pkg_config_libdir_search})
-    if(pkg_config_libdir)
-        SET(pkg_config_install_dir ${pkg_config_libdir})
-        message(STATUS "found ${pkg_config_libdir}/pkgconfig" )
-    else(pkg_config_libdir)
-        SET(pkg_config_install_dir ${CMAKE_INSTALL_PREFIX}/share)
-        message(STATUS "pkgconfig not found; installing in ${pkg_config_install_dir}" )
-    endif(pkg_config_libdir)
-
-    configure_file(eigen3.pc.in eigen3.pc)
+    configure_file(eigen3.pc.in eigen3.pc @ONLY)
     install(FILES ${CMAKE_CURRENT_BINARY_DIR}/eigen3.pc
-        DESTINATION ${pkg_config_install_dir}/pkgconfig
+        DESTINATION ${PKGCONFIG_INSTALL_DIR}
         )
 endif(EIGEN_BUILD_PKGCONFIG)
 
@@ -401,12 +390,15 @@ if(cmake_generator_tolower MATCHES "makefile")
   message(STATUS "--------------+--------------------------------------------------------------")
   message(STATUS "Command       |   Description")
   message(STATUS "--------------+--------------------------------------------------------------")
-  message(STATUS "make install  | Install to ${CMAKE_INSTALL_PREFIX}. To change that:")
-  message(STATUS "              |     cmake . -DCMAKE_INSTALL_PREFIX=yourpath")
-  message(STATUS "              |   Eigen headers will then be installed to:")
-  message(STATUS "              |     ${CMAKE_INSTALL_PREFIX}/${INCLUDE_INSTALL_DIR}")
-  message(STATUS "              |   To install Eigen headers to a separate location, do:")
-  message(STATUS "              |     cmake . -DEIGEN_INCLUDE_INSTALL_DIR=yourpath")
+  message(STATUS "make install  | Install Eigen. Headers will be installed to:")
+  message(STATUS "              |     <CMAKE_INSTALL_PREFIX>/<INCLUDE_INSTALL_DIR>")
+  message(STATUS "              |   Using the following values:")
+  message(STATUS "              |     CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX}")
+  message(STATUS "              |     INCLUDE_INSTALL_DIR:  ${INCLUDE_INSTALL_DIR}")
+  message(STATUS "              |   Change the install location of Eigen headers using:")
+  message(STATUS "              |     cmake . -DCMAKE_INSTALL_PREFIX=yourprefix")
+  message(STATUS "              |   Or:")
+  message(STATUS "              |     cmake . -DINCLUDE_INSTALL_DIR=yourdir")
   message(STATUS "make doc      | Generate the API documentation, requires Doxygen & LaTeX")
   message(STATUS "make check    | Build and run the unit-tests. Read this page:")
   message(STATUS "              |   http://eigen.tuxfamily.org/index.php?title=Tests")

ext/eigen-3.2.9/Eigen/CholmodSupport

@@ -12,7 +12,7 @@ extern "C" {
 /** \ingroup Support_modules
   * \defgroup CholmodSupport_Module CholmodSupport module
   *
-  * This module provides an interface to the Cholmod library which is part of the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">suitesparse</a> package.
+  * This module provides an interface to the Cholmod library which is part of the <a href="http://www.suitesparse.com">suitesparse</a> package.
   * It provides the two following main factorization classes:
   * - class CholmodSupernodalLLT: a supernodal LLT Cholesky factorization.
   * - class CholmodDecomposiiton: a general L(D)LT Cholesky factorization with automatic or explicit runtime selection of the underlying factorization method (supernodal or simplicial).

ext/eigen-3.2.9/Eigen/SPQRSupport

@@ -10,7 +10,7 @@
 /** \ingroup Support_modules
   * \defgroup SPQRSupport_Module SuiteSparseQR module
   * 
-  * This module provides an interface to the SPQR library, which is part of the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">suitesparse</a> package.
+  * This module provides an interface to the SPQR library, which is part of the <a href="http://www.suitesparse.com">suitesparse</a> package.
   *
   * \code
   * #include <Eigen/SPQRSupport>

ext/eigen-3.2.9/Eigen/UmfPackSupport

@@ -12,7 +12,7 @@ extern "C" {
 /** \ingroup Support_modules
   * \defgroup UmfPackSupport_Module UmfPackSupport module
   *
-  * This module provides an interface to the UmfPack library which is part of the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">suitesparse</a> package.
+  * This module provides an interface to the UmfPack library which is part of the <a href="http://www.suitesparse.com">suitesparse</a> package.
   * It provides the following factorization class:
   * - class UmfPackLU: a multifrontal sequential LU factorization.
   *

ext/eigen-3.2.9/Eigen/src/Core/CommaInitializer.h

@@ -76,8 +76,11 @@ struct CommaInitializer
   template<typename OtherDerived>
   CommaInitializer& operator,(const DenseBase<OtherDerived>& other)
   {
-    if(other.cols()==0 || other.rows()==0)
+    if(other.rows()==0)
+    {
+      m_col += other.cols();
       return *this;
+    }
     if (m_col==m_xpr.cols())
     {
       m_row+=m_currentBlockRows;
@@ -86,7 +89,7 @@ struct CommaInitializer
       eigen_assert(m_row+m_currentBlockRows<=m_xpr.rows()
         && "Too many rows passed to comma initializer (operator<<)");
     }
-    eigen_assert(m_col<m_xpr.cols()
+    eigen_assert((m_col<m_xpr.cols() || (m_xpr.cols()==0 && m_col==0))
       && "Too many coefficients passed to comma initializer (operator<<)");
     eigen_assert(m_currentBlockRows==other.rows());
     if (OtherDerived::SizeAtCompileTime != Dynamic)

ext/eigen-3.2.9/Eigen/src/Core/CwiseUnaryView.h

@@ -38,7 +38,7 @@ struct traits<CwiseUnaryView<ViewOp, MatrixType> >
   typedef typename remove_all<MatrixTypeNested>::type _MatrixTypeNested;
   enum {
     Flags = (traits<_MatrixTypeNested>::Flags & (HereditaryBits | LvalueBit | LinearAccessBit | DirectAccessBit)),
-    CoeffReadCost = traits<_MatrixTypeNested>::CoeffReadCost + functor_traits<ViewOp>::Cost,
+    CoeffReadCost = EIGEN_ADD_COST(traits<_MatrixTypeNested>::CoeffReadCost, functor_traits<ViewOp>::Cost),
     MatrixTypeInnerStride =  inner_stride_at_compile_time<MatrixType>::ret,
     // need to cast the sizeof's from size_t to int explicitly, otherwise:
     // "error: no integral type can represent all of the enumerator values

ext/eigen-3.2.9/Eigen/src/Core/DiagonalMatrix.h

@@ -44,10 +44,10 @@ class DiagonalBase : public EigenBase<Derived>
     template<typename DenseDerived>
     void evalTo(MatrixBase<DenseDerived> &other) const;
     template<typename DenseDerived>
-    void addTo(MatrixBase<DenseDerived> &other) const
+    inline void addTo(MatrixBase<DenseDerived> &other) const
     { other.diagonal() += diagonal(); }
     template<typename DenseDerived>
-    void subTo(MatrixBase<DenseDerived> &other) const
+    inline void subTo(MatrixBase<DenseDerived> &other) const
     { other.diagonal() -= diagonal(); }
 
     inline const DiagonalVectorType& diagonal() const { return derived().diagonal(); }
@@ -98,7 +98,7 @@ class DiagonalBase : public EigenBase<Derived>
 
 template<typename Derived>
 template<typename DenseDerived>
-void DiagonalBase<Derived>::evalTo(MatrixBase<DenseDerived> &other) const
+inline void DiagonalBase<Derived>::evalTo(MatrixBase<DenseDerived> &other) const
 {
   other.setZero();
   other.diagonal() = diagonal();

ext/eigen-3.2.9/Eigen/src/Core/Dot.h

@@ -59,7 +59,7 @@ struct dot_nocheck<T, U, true>
   */
 template<typename Derived>
 template<typename OtherDerived>
-typename internal::scalar_product_traits<typename internal::traits<Derived>::Scalar,typename internal::traits<OtherDerived>::Scalar>::ReturnType
+inline typename internal::scalar_product_traits<typename internal::traits<Derived>::Scalar,typename internal::traits<OtherDerived>::Scalar>::ReturnType
 MatrixBase<Derived>::dot(const MatrixBase<OtherDerived>& other) const
 {
   EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)

ext/eigen-3.2.9/Eigen/src/Core/GeneralProduct.h

@@ -205,9 +205,6 @@ class GeneralProduct<Lhs, Rhs, InnerProduct>
   public:
     GeneralProduct(const Lhs& lhs, const Rhs& rhs)
     {
-      EIGEN_STATIC_ASSERT((internal::is_same<typename Lhs::RealScalar, typename Rhs::RealScalar>::value),
-        YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY)
-
       Base::coeffRef(0,0) = (lhs.transpose().cwiseProduct(rhs)).sum();
     }
 
@@ -264,8 +261,6 @@ class GeneralProduct<Lhs, Rhs, OuterProduct>
 
     GeneralProduct(const Lhs& lhs, const Rhs& rhs) : Base(lhs,rhs)
     {
-      EIGEN_STATIC_ASSERT((internal::is_same<typename Lhs::RealScalar, typename Rhs::RealScalar>::value),
-        YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY)
     }
     
     struct set  { template<typename Dst, typename Src> void operator()(const Dst& dst, const Src& src) const { dst.const_cast_derived()  = src; } };
@@ -425,15 +420,18 @@ template<> struct gemv_selector<OnTheRight,ColMajor,true>
     ResScalar actualAlpha = alpha * LhsBlasTraits::extractScalarFactor(prod.lhs())
                                   * RhsBlasTraits::extractScalarFactor(prod.rhs());
 
+    // make sure Dest is a compile-time vector type (bug 1166)
+    typedef typename conditional<Dest::IsVectorAtCompileTime, Dest, typename Dest::ColXpr>::type ActualDest;
+
     enum {
       // FIXME find a way to allow an inner stride on the result if packet_traits<Scalar>::size==1
       // on, the other hand it is good for the cache to pack the vector anyways...
-      EvalToDestAtCompileTime = Dest::InnerStrideAtCompileTime==1,
+      EvalToDestAtCompileTime = (ActualDest::InnerStrideAtCompileTime==1),
       ComplexByReal = (NumTraits<LhsScalar>::IsComplex) && (!NumTraits<RhsScalar>::IsComplex),
-      MightCannotUseDest = (Dest::InnerStrideAtCompileTime!=1) || ComplexByReal
+      MightCannotUseDest = (ActualDest::InnerStrideAtCompileTime!=1) || ComplexByReal
     };
 
-    gemv_static_vector_if<ResScalar,Dest::SizeAtCompileTime,Dest::MaxSizeAtCompileTime,MightCannotUseDest> static_dest;
+    gemv_static_vector_if<ResScalar,ActualDest::SizeAtCompileTime,ActualDest::MaxSizeAtCompileTime,MightCannotUseDest> static_dest;
 
     bool alphaIsCompatible = (!ComplexByReal) || (numext::imag(actualAlpha)==RealScalar(0));
     bool evalToDest = EvalToDestAtCompileTime && alphaIsCompatible;
@@ -522,7 +520,7 @@ template<> struct gemv_selector<OnTheRight,RowMajor,true>
         actualLhs.rows(), actualLhs.cols(),
         actualLhs.data(), actualLhs.outerStride(),
         actualRhsPtr, 1,
-        dest.data(), dest.innerStride(),
+        dest.data(), dest.col(0).innerStride(), //NOTE  if dest is not a vector at compile-time, then dest.innerStride() might be wrong. (bug 1166)
         actualAlpha);
   }
 };

ext/eigen-3.2.9/Eigen/src/Core/MapBase.h

@@ -149,6 +149,10 @@ template<typename Derived> class MapBase<Derived, ReadOnlyAccessors>
       checkSanity();
     }
 
+    #ifdef EIGEN_MAPBASE_PLUGIN
+    #include EIGEN_MAPBASE_PLUGIN
+    #endif
+
   protected:
 
     void checkSanity() const

ext/eigen-3.2.9/Eigen/src/Core/MathFunctions.h

@@ -218,8 +218,8 @@ struct conj_retval
 * Implementation of abs2                                                 *
 ****************************************************************************/
 
-template<typename Scalar>
-struct abs2_impl
+template<typename Scalar,bool IsComplex>
+struct abs2_impl_default
 {
   typedef typename NumTraits<Scalar>::Real RealScalar;
   static inline RealScalar run(const Scalar& x)
@@ -228,15 +228,26 @@ struct abs2_impl
   }
 };
 
-template<typename RealScalar>
-struct abs2_impl<std::complex<RealScalar> >
+template<typename Scalar>
+struct abs2_impl_default<Scalar, true> // IsComplex
 {
-  static inline RealScalar run(const std::complex<RealScalar>& x)
+  typedef typename NumTraits<Scalar>::Real RealScalar;
+  static inline RealScalar run(const Scalar& x)
   {
     return real(x)*real(x) + imag(x)*imag(x);
   }
 };
 
+template<typename Scalar>
+struct abs2_impl
+{
+  typedef typename NumTraits<Scalar>::Real RealScalar;
+  static inline RealScalar run(const Scalar& x)
+  {
+    return abs2_impl_default<Scalar,NumTraits<Scalar>::IsComplex>::run(x);
+  }
+};
+
 template<typename Scalar>
 struct abs2_retval
 {
@@ -707,21 +718,21 @@ struct scalar_fuzzy_impl : scalar_fuzzy_default_impl<Scalar, NumTraits<Scalar>::
 
 template<typename Scalar, typename OtherScalar>
 inline bool isMuchSmallerThan(const Scalar& x, const OtherScalar& y,
-                                   typename NumTraits<Scalar>::Real precision = NumTraits<Scalar>::dummy_precision())
+                              const typename NumTraits<Scalar>::Real &precision = NumTraits<Scalar>::dummy_precision())
 {
   return scalar_fuzzy_impl<Scalar>::template isMuchSmallerThan<OtherScalar>(x, y, precision);
 }
 
 template<typename Scalar>
 inline bool isApprox(const Scalar& x, const Scalar& y,
-                          typename NumTraits<Scalar>::Real precision = NumTraits<Scalar>::dummy_precision())
+                     const typename NumTraits<Scalar>::Real &precision = NumTraits<Scalar>::dummy_precision())
 {
   return scalar_fuzzy_impl<Scalar>::isApprox(x, y, precision);
 }
 
 template<typename Scalar>
 inline bool isApproxOrLessThan(const Scalar& x, const Scalar& y,
-                                    typename NumTraits<Scalar>::Real precision = NumTraits<Scalar>::dummy_precision())
+                               const typename NumTraits<Scalar>::Real &precision = NumTraits<Scalar>::dummy_precision())
 {
   return scalar_fuzzy_impl<Scalar>::isApproxOrLessThan(x, y, precision);
 }

ext/eigen-3.2.9/Eigen/src/Core/PermutationMatrix.h

@@ -584,10 +584,11 @@ struct permut_matrix_product_retval
       const Index n = Side==OnTheLeft ? rows() : cols();
       // FIXME we need an is_same for expression that is not sensitive to constness. For instance
       // is_same_xpr<Block<const Matrix>, Block<Matrix> >::value should be true.
+      const typename Dest::Scalar *dst_data = internal::extract_data(dst);
       if(    is_same<MatrixTypeNestedCleaned,Dest>::value
           && blas_traits<MatrixTypeNestedCleaned>::HasUsableDirectAccess
           && blas_traits<Dest>::HasUsableDirectAccess
-          && extract_data(dst) == extract_data(m_matrix))
+          && dst_data!=0 && dst_data == extract_data(m_matrix))
       {
         // apply the permutation inplace
         Matrix<bool,PermutationType::RowsAtCompileTime,1,0,PermutationType::MaxRowsAtCompileTime> mask(m_permutation.size());

ext/eigen-3.2.9/Eigen/src/Core/PlainObjectBase.h

@@ -315,8 +315,8 @@ class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
     EIGEN_STRONG_INLINE void resizeLike(const EigenBase<OtherDerived>& _other)
     {
       const OtherDerived& other = _other.derived();
-      internal::check_rows_cols_for_overflow<MaxSizeAtCompileTime>::run(other.rows(), other.cols());
-      const Index othersize = other.rows()*other.cols();
+      internal::check_rows_cols_for_overflow<MaxSizeAtCompileTime>::run(Index(other.rows()), Index(other.cols()));
+      const Index othersize = Index(other.rows())*Index(other.cols());
       if(RowsAtCompileTime == 1)
       {
         eigen_assert(other.rows() == 1 || other.cols() == 1);
@@ -487,7 +487,7 @@ class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
     /** \sa MatrixBase::operator=(const EigenBase<OtherDerived>&) */
     template<typename OtherDerived>
     EIGEN_STRONG_INLINE PlainObjectBase(const EigenBase<OtherDerived> &other)
-      : m_storage(other.derived().rows() * other.derived().cols(), other.derived().rows(), other.derived().cols())
+      : m_storage(Index(other.derived().rows()) * Index(other.derived().cols()), other.derived().rows(), other.derived().cols())
     {
       _check_template_params();
       internal::check_rows_cols_for_overflow<MaxSizeAtCompileTime>::run(other.derived().rows(), other.derived().cols());